Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 701 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 397 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 53 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 393 SARS 114 Fig 83 figure 64 RNA 58 ACE2 50 CoV-2 43 cell 42 RBD 30 protein 23 COVID-19 20 dna 14 PCR 13 covid-19 13 Supplementary 11 sequence 10 virus 9 gene 9 TMPRSS2 9 HLA 8 structure 8 mutation 8 drug 8 Spike 8 MERS 8 IFN 7 antibody 7 Data 6 Vero 6 CD8 5 mouse 5 d614 5 CD4 4 variant 4 vaccine 4 site 4 sample 4 TMS 4 ELISA 4 EEG 4 Coronavirus 4 CRISPR 3 time 3 spike 3 selection 3 receptor 3 read 3 pro 3 model 3 membrane 3 lung Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 18313 cell 12315 protein 8270 virus 7022 % 6559 sequence 5707 analysis 5553 infection 5378 gene 5120 datum 5084 study 5043 figure 4512 sample 4490 structure 4363 model 4104 antibody 3863 expression 3734 coronavirus 3671 mutation 3665 response 3658 genome 3607 receptor 3435 time 3306 result 3199 disease 3045 patient 3006 mouse 2967 type 2967 number 2957 level 2868 effect 2846 spike 2835 interaction 2799 site 2729 method 2715 host 2566 c 2488 drug 2440 assay 2370 lung 2348 value 2311 activity 2309 region 2303 residue 2274 system 2239 control 2192 group 2137 domain 2112 acid 2096 t 1953 vaccine Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 18593 SARS 13859 CoV-2 7103 al 6354 . 5809 et 5785 Fig 4507 RNA 4199 ACE2 3201 COVID-19 2728 T 2639 S 2449 RBD 2423 CoV 2062 C 1522 Table 1400 S1 1381 Figure 1284 PCR 1252 Coronavirus 931 S2 903 Supplementary 889 N 876 MERS 874 M 842 China 838 RT 836 G 820 TMPRSS2 771 Human 712 Spike 695 DOI 689 Vero 662 sha 658 A 644 B 635 Protein 632 IFN 622 Data 570 Wuhan 544 PBS 542 CD8 537 F 500 K 488 II 467 Virus 462 ± 459 HLA 457 pH 457 CD4 456 L Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 15991 we 4758 it 1528 they 1355 i 705 them 408 us 165 itself 159 one 76 themselves 50 he 48 you 27 his 15 she 9 me 9 imagej 7 em 6 ourselves 5 hao 4 si3n4 4 s 4 igg1 4 cbae-1 3 u 3 rrbd-15 3 ours 3 nlrp12 3 mine 3 iosns 3 directms1 2 ıt 2 y-27632 2 usa_wa1/2020 2 nsp7 2 mrnas 2 l452 2 l270 2 ippa17-a04 2 il-1β 2 igfbp2 2 https://github.com/ababaian/serratus 2 hace2 2 fncas9 2 dorfs 2 desb 2 atn-161 1 Δtotal 1 zar1-sub 1 z"ikv 1 yourself 1 y505a Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 81138 be 13896 use 10959 have 5897 show 4596 bind 4121 base 3453 identify 3089 include 3040 find 2749 perform 2657 compare 2644 do 2516 suggest 2445 observe 2417 follow 2326 indicate 2296 provide 2209 increase 2149 contain 2147 associate 1905 reveal 1877 induce 1829 report 1824 express 1799 predict 1799 detect 1761 determine 1723 generate 1722 describe 1630 see 1562 test 1531 infect 1483 obtain 1473 reduce 1450 cause 1411 result 1407 give 1387 know 1346 represent 1287 develop 1286 target 1286 allow 1270 demonstrate 1269 relate 1259 make 1256 require 1207 mediate 1192 lead 1157 analyze 1146 consider Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 6621 not 6605 - 5832 viral 5564 high 5152 human 5054 also 3766 other 3479 more 3234 different 2877 low 2720 well 2699 only 2625 specific 2570 such 2403 single 2387 first 2382 however 2364 immune 2216 then 2123 respiratory 2090 further 2068 severe 2056 non 1996 most 1980 large 1780 same 1776 positive 1726 similar 1712 clinical 1681 new 1570 molecular 1562 structural 1562 as 1545 multiple 1498 acute 1464 novel 1449 respectively 1438 highly 1424 small 1424 potential 1414 significant 1387 thus 1375 here 1344 available 1326 therefore 1267 antiviral 1265 anti 1248 several 1248 previously 1216 many Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 709 most 500 high 375 least 341 good 162 large 150 low 140 Most 85 close 68 near 54 great 51 strong 42 late 36 short 32 early 26 bad 24 small 21 long 19 simple 13 young 13 steep 12 fast 12 big 11 Least 10 old 7 scRNA 5 easy 3 ~20 3 weak 3 safe 3 postt 3 outermost 3 leftmost 3 few 3 broad 3 bright 3 -I 3 -8 2 ~15 2 wide 2 tremeGENE 2 topmost 2 ssRNA 2 slow 2 rv 2 lmert 2 farth 2 dense 2 dark 2 S4A 2 -which Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 1287 most 346 least 53 well 6 worst 5 highest 4 lowest 2 fast 2 8his 1 topmost 1 rrna 1 mir-1273d 1 long 1 hard 1 furthest 1 early 1 clustalw 1 bnab 1 0.5μl 1 -melanocyte 1 -j Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 122 github.com 72 doi.org 21 www.ncbi.nlm.nih.gov 21 www.gisaid.org 12 www.who.int 11 www.ebi.ac.uk 8 www.proteinatlas.org 7 www.cbs.dtu.dk 7 serratus.io 7 osf.io 7 artic.network 6 crossbar.kansil.org 6 app.swaggerhub.com 5 www.kegg.jp 5 tools.iedb.org 5 postera.ai 5 nextstrain.org 4 www.genomedetective.com 4 www.bio8.cs.hku.hk 4 webs.iiitd.edu.in 4 idseq.net 4 help.idseq.net 4 gtexportal.org 4 gisaid.org 4 cran.r-project.org 4 covid19.who.int 4 coronavirus.jhu.edu 3 zhanglab.ccmb.med.umich.edu 3 www.uniprot.org 3 www.rcsb.org 3 www.cdc.gov 3 www.bioinformatics.babraham.ac.uk 3 virological.org 3 tisigner.com 3 satijalab.org 3 pymol.org 3 metatryp.whoi.edu 3 gitlab.com 3 db.cngb.org 3 clinicaltrials.gov 3 ccg.epfl.ch 2 zenodo.org 2 www.worldometers.info 2 www.softberry.com 2 www.megasoftware.net 2 www.isrctn.com 2 www.gtexportal.org 2 www.endmemo.com 2 www.ddg-pharmfac.net 2 www.biorxiv.org Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 24 http://doi.org/10.1101/752592 12 http://doi.org/10.1101/2020.06.23.167544 11 http://www.gisaid.org/ 9 http://doi.org/10.1101/2020.08.29.272864 7 http://www.gisaid.org 7 http://doi.org/10.1101/2020.01.26.919985 6 http://doi.org/10.1101/2020.06.05.136861 4 http://help.idseq.net 4 http://github.com/ml-jku/DeepRC 4 http://gisaid.org 4 http://doi.org/10.1101/2020.07.22.215962 3 http://www.who.int/emergencies/diseases/novel-coronavirus-2019 3 http://www.proteinatlas.org/ 3 http://www.cbs.dtu.dk/services/TMHMM/ 3 http://tisigner.com/sodope 3 http://serratus.io/access 3 http://serratus.io 3 http://postera.ai/covid 3 http://gtexportal.org/home/ 3 http://github.com/hCoV-2019/pangolin 3 http://github.com/chanzuckerberg/idseq-dag 3 http://github.com/ahmedmagds/GNUVID 3 http://github.com/BIMIB-DISCo/VERSO 3 http://doi.org/10.1101/2020.07.18.210211 3 http://crossbar.kansil.org/covid_main.php 3 http://covid19.who.int/ 3 http://artic.network/ncov-2019 2 http://zhanglab.ccmb.med.umich.edu/I-TASSER/ 2 http://www.worldometers.info/coronavirus/ 2 http://www.uniprot.org/ 2 http://www.softberry.com 2 http://www.rcsb.org 2 http://www.proteinatlas.org/ENSG00000130234-ACE2/tissue 2 http://www.proteinatlas.org 2 http://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/ 2 http://www.ncbi.nlm.nih.gov/ 2 http://www.megasoftware.net 2 http://www.isrctn.com/ISRCTN66726260 2 http://www.gtexportal.org/home/datasets 2 http://www.genomedetective.com/app/typingtool/virus/ 2 http://www.genomedetective.com/app/typingtool/cov/ 2 http://www.cbs.dtu.dk/services/BepiPred/ 2 http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ 2 http://www.bio8.cs.hku.hk/sarscov2 2 http://www.R-project.org 2 http://www 2 http://web.expasy.org/protparam/ 2 http://w3id.org/EVI 2 http://swissmodel.expasy.org/ 2 http://seaborn.pydata.org/ Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 3 consortiumcontact@cogconsortium.uk 1 zkontos@ioi-investment.com 1 xiangruz@andrew.cmu.edu 1 wenqiangyu@fudan.edu.cn 1 weixiaofeng@cngb.org 1 vishwa.dixit@yale.edu 1 vincent.pasque@kuleuven.be 1 ttle@pennmedicine.upenn.edu 1 thato@iu.edu 1 teresa.lambe@ndm.ox.ac.uk 1 suweis@pd.infn.it 1 sureshm@vetmed.wisc.edu 1 slpeng@hnu.edu.cn 1 siyuan.ding@wustl.edu 1 simon.graham@pirbright.ac.uk 1 simon.dellicour@ulb.ac.be 1 sergey.n.knyazev@gmail.com 1 renia_laurent@immunol.a-star.edu.sg 1 rbluo@cs.hku.hk 1 qinlab313@163.com 1 qincf@bmi.ac.cn 1 priyamvada.acharya@duke.edu 1 pitta-cus@gmail.com 1 olivier.gascuel@pasteur.fr 1 nicholas.guydosh@nih.gov 1 nax3@cdc.gov 1 lawrence.moon@kcl.ac.uk 1 hoelzer.martin@gmail.com 1 gavoth@uchicago.edu 1 frederic.lemoine@pasteur.fr 1 dyz1@rice.edu 1 cec9@psu.edu 1 btk@lanl.gov 1 alexz@gsu.edu 1 xiaof@mailbox.sc.ecu 1 thin.nguyen@deakin.edu.au 1 nitschea@rki.de 1 janine.lamb@manchester.ac.uk 1 gcai@mailbox.sc.edu 1 bernhard.renard@hpi.de Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 131 receptor binding domain 50 cells were then 31 receptor binding domains 25 coronavirus indicating person 25 study are available 17 samples were then 15 cells were also 15 data are available 15 receptor binding site 14 data are consistent 14 receptor binding motif 13 cells did not 11 studies have also 10 cells were pre 10 rna was reverse 10 virus was not 9 cells was significantly 9 cells were co 9 cov-2 is not 9 infection did not 8 analysis are available 8 cells were further 8 cells were more 8 cov-2 does not 8 data did not 8 model is able 8 studies did not 8 study did not 7 cells do not 7 data are not 7 protein binding regions 7 protein is highly 7 sample was then 7 virus is also 6 ace2 is also 6 analysis was then 6 cells was also 6 cells were not 6 cells were significantly 6 cov-2 is critical 6 cov-2 is highly 6 expression was significantly 6 genes were also 6 protein did not 6 proteins are highly 6 receptor binding affinity 6 rna was also 6 samples were also 6 samples were not 6 sequences using tempest Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 5 sequences have no mutation 4 data are not available 3 samples is not possible 2 cells are not permissive 2 cov-2 has not yet 2 cov-2 is not due 2 infection is not yet 2 mutation had no effect 2 structure is not yet 1 . had no role 1 ace2 is not only 1 ace2 was not able 1 analysis are not short 1 analysis is not conclusive 1 analysis is not possible 1 analysis were not degs 1 antibodies are not cross 1 antibodies are not functional 1 antibodies had no mutation 1 antibodies is not very 1 antibodies were not detectable 1 antibody is no more 1 antibody is not specific 1 cells are not immunoregulatory 1 cells did not significantly 1 cells do not only 1 cells does not appreciably 1 cells has not previously 1 cells is not complete 1 cells is not completely 1 cells is not trivial 1 cells showed no correlation 1 cells was not detectable 1 cells were not active 1 cells were not detectable 1 cov-2 does not directly 1 cov-2 does not efficiently 1 cov-2 is not as 1 cov-2 is not clear 1 cov-2 is not closer 1 cov-2 is not consistent 1 cov-2 was not due 1 data are not entirely 1 data are not mutually 1 data suggest no risk 1 data were not correctly 1 data were not different 1 expression does not always 1 expression has not yet 1 expression is not responsive A rudimentary bibliography -------------------------- id = cord-347714-vxxhglx7 author = Abitogun, Folagbade title = COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding date = 2020-10-14 keywords = HLA; SARS; epitope; protein summary = (10, 11) The structure of the spike glycoprotein of the virus is also an extended similarity with SARS-CoV, (4) which together with COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding other proteins of the virus are candidates for vaccine development and are being explored in different settings due to the active roles of the proteins in the infectivity of the virus. (18) However studies have shown that full length spike protein vaccines for SARS-CoV may lead to antibody mediated disease enhancement causing inflammatory and liver damage in animal models (19, 20) which is why in this manuscript, we applied immuno-informatics "in silico" approaches to identify potential CD8+ cytotoxic T Cell epitopes from proteins of SARS-CoV-2, SARS-CoV and MERS-CoV. Multi-epitope Based Peptide Vaccine Design Using Three Structural Proteins (S, E, and M) of SARS-CoV-2: An In Silico Approach doi = 10.1101/2020.10.14.339689 id = cord-315982-iuez41zj author = Achdout, Hagit title = COVID Moonshot: Open Science Discovery of SARS-CoV-2 Main Protease Inhibitors by Combining Crowdsourcing, High-Throughput Experiments, Computational Simulations, and Machine Learning date = 2020-10-30 keywords = DMSO; SARS; assay; cell; plate summary = title: COVID Moonshot: Open Science Discovery of SARS-CoV-2 Main Protease Inhibitors by Combining Crowdsourcing, High-Throughput Experiments, Computational Simulations, and Machine Learning Herein we provide a living summary of the data generated during the COVID Moonshot project focused on the development of SARS-CoV-2 main protease (Mpro) inhibitors. The COVID Moonshot project has focused on progressing early fragment-screening results into potent compounds with activity against both the main protease and the virus. The rationales for each design include docking-based approaches, by-eye structure-based designs, machine learning approaches, crawling of the past literature on SARS and MERS compounds, and other general medicinal-chemistry insights that can be visualised at https://postera.ai/covid. At 24 h post-seeding, cell culture medium was discarded, cells were washed twice with PBS and infected with SARS-CoV-2 at an MOI of 0.01 in the presence of six concentrations of the inhibitors (25 M -0.06 M). doi = 10.1101/2020.10.29.339317 id = cord-103448-xa5zgkd3 author = Adachi, Hiroaki title = Jurassic NLR: conserved and dynamic evolutionary features of the atypically ancient immune receptor ZAR1 date = 2020-10-12 keywords = NLR; ZAR1; ZAR1-CIN; ZAR1-SUB; figure summary = The phylogenetic tree was generated in MEGA7 by the neighbour-joining method using NB-ARC domain sequences of ZAR1-like proteins identified from the prior BLAST searches and 1019 NLRs identified from 6 representative plant species, taro, stout camphor, columbine, tomato, sugar beet and Arabidopsis. The overall conservation of the 120 ZAR1 orthologs enabled us to perform phylogenetic analyses using the full-length protein sequence and not just the NB-ARC domain as generally done with NLRs ( ZAR1 phylogenetic tree with well-supported branches that generally mirrored established phylogenetic relationships between the examined plant species (Smith and Brown, 2018; Chaw et al., 2019) . Taken together, based on the conserved motifs depicted in Figure 3A , we propose that angiosperm ZAR1 orthologs share the main functional features of Arabidopsis ZAR1: 1) effector recognition via RLCK binding, 2) remodelling of intramolecular interactions via ADP/ATP switch, 3) oligomerisation via the NBD-NBD interface and 4) α1 helix/MADA motifmediated activation of hypersensitive cell death. doi = 10.1101/2020.10.12.333484 id = cord-102595-3lbrfsrh author = Adam, Kirsten C.S. title = Steady-state visually evoked potentials and feature-based attention: Pre-registered null results and a focused review of methodological considerations date = 2020-10-13 keywords = SSVEP; attention; effect; feature summary = doi = 10.1101/2020.08.31.275602 id = cord-103396-jiuqk6kg author = Adler, Paul N. title = Short distance non-autonomy and intercellular transfer of chitin synthase in Drosophila date = 2020-05-26 keywords = Drosophila; Fig; cuticle summary = In experiments where we imaged Kkv::NG in living pupae we noticed fluorescent puncta in the 219 extracellular space between the pupal cuticle and the epidermal cells that were in the process of 220 synthesizing the adult cuticle (Fig. 6BC ). No fluorescence was observed in the region 227 between the pupal cuticle and the apical surface of the epithelial cells in Ore-R pupae (Fig. 6EF) . We also observed puncta in very young pupae (20 237 hr awp) prior to the detachment of the epithelial cells from the pupal cuticle (Fig. S6B) . These animals showed a large 253 number of fluorescent puncta present in the space between the pupal cuticle and the apical surface of 254 the epithelial cells ( Fig 6GHI) . However, in carrying out these in vivo imaging experiments we observed that the autofluorescence of 259 the thoracic and abdominal pupal cuticles was quite distinct (Fig S8) . doi = 10.1101/2020.05.24.113803 id = cord-336343-qbcb9qi3 author = Agarwal, Ajay title = in-silica Analysis of SARS-CoV-2 viral strain using Reverse Vaccinology Approach: A Case Study for USA date = 2020-06-16 keywords = Class; MHC summary = Using in-silica analysis and reverse vaccinology, two leader proteins were identified to be potential vaccine candidates for development of a multi-epitope drug. This study aims to utilize a reverse-vaccinology approach in order to identify potential vaccine candidates for COVID19 for the country USA. For MHC Class-I T-cell epitope prediction for ORF1ab leader proteins, NetMHCpan EL 4.0 method was used. The T-cell epitopes of the MHC Class-I for both the leader protein were determined using the NetMHCpan EL 4.0 prediction method of the IEDB server keeping the sequence length at 9. For MHC class-II, T-cell epitopes (HLA DRB1*04-01 allele) of the proteins were also determined using the IEDB Analysis tools. The potential T-cell epitopes, whose topology, antigenicity, allergenicity, toxicity and conservancy was analysed, for ORF1ab leader proteins MT326102 and MT326175 are depicted in the following tables. Out of the two MHC Class-I epitopes selected for leader proteins ORF1ab MT326102 and MT326175, the global energy was lowest for LSLPVLQVR. doi = 10.1101/2020.06.16.154559 id = cord-102720-ka95resa author = Aguilar, César title = Convergent evolution of Streptomyces protease inhibitors involving a tRNA-mediated condensation-minus NRPS date = 2020-10-27 keywords = BGC; Streptomyces; figure summary = doi = 10.1101/2020.10.26.356543 id = cord-333089-ufyzqgqk author = Aguilar-Pineda, Jorge Alberto title = Structural and functional analysis of female sex hormones against SARS-Cov2 cell entry date = 2020-07-29 keywords = ACE2; RBD; SARS; figure; protein summary = Based on the structural complementarity and steric impediments between the S protein and human ACE2 (hACE2) protein membranes, we mapped the glycosylation sites of both models [21] [22] [23] [24] and performed molecular dynamics simulations (MDS) by 250 ns to stabilize the glycosylated SARS-CoV2 spike (S) and hACE2 complex (suppl. Given the possibility that occupancy at glycosylated residues or S-RBD binding sites by estrogens could modify the affinity of the SARS-CoV2 virus and alter entry into the cell thereby reducing infectivity, we sought to further examine these interactions using a range of complementary experimental approaches (see Table S1 ). In an effort to explore the potential protective effects of female sex hormones against SARS-CoV-2 infection, we examined the impact of estradiol (17β-diol) and a dietary-derived phytoestrogen (S-equol) on hACE2 structure and protein expression by a combination of in silico modeling, in vitro, and in vivo analysis. doi = 10.1101/2020.07.29.227249 id = cord-103528-3tib5o1m author = Ahmed, Asad title = DEELIG: A Deep Learning-based approach to predict protein-ligand binding affinity date = 2020-09-28 keywords = affinity; ligand; protein summary = title: DEELIG: A Deep Learning-based approach to predict protein-ligand binding affinity Here, we have incorporated Convolutional Neural Networks that find spatial relationships among data to help us predict affinity of binding of proteins in whole superfamilies towards a diverse set of ligands. Initial raw data database created contained protein structures in PDB format, protein sequences in FASTA format, ligand in SDF format and binding affinity values of corresponding protein-ligand pairs for 5464 complexes. We propose a deep-learning based approach to predict ligand (eg., drug)-target binding affinity using only structures of target protein (PDB format) and ligand (SDF format) as inputs. We have trained two models to predict the binding affinity between protein and ligand in a given complex. We have constructed a novel dataset that represents a diverse set of ligands and using a novel deep learning based approach we have achieved significant improvement in prediction of binding affinity of protein-ligand complexes. doi = 10.1101/2020.09.28.316224 id = cord-290445-vb53bih9 author = Ahmed, Shiek SSJ title = Interplay of host regulatory network on SARS-CoV-2 binding and replication machinery date = 2020-04-23 keywords = Fig; SARS; protein summary = Secondly, the viral replication machinery network from SET-B with 332 seed proteins extended to 1486 neighboring proteins with 11438 interacting edges which representing the mechanism attributed to evasion of the SARS-CoV2 genome into the host. Similarly, the viral replication machinery network was acquired with 1522 proteins with 9747 interacting edges showing the complex SARS-CoV-2 mechanism in the human lungs. These common molecules represent the inter-connecting mechanism involved in the transcription machinery, immune response, cell growth and/or maintenance, transport, metabolism, protein metabolism, cell communication and signal transduction that activated upon virus binding and has been subsequently utilized for viral replication process (S5 Table) Also mapping with other viral infection dataset, 50 hub proteins of the replication machinery network have noticed in influenza virus infection (S4 Table) , which suggests SARS-CoV2 and influenza may have a similar mode of host infection machinery [17] . The molecular pathways of interconnecting protein hubs could be the intermediate phase that connects the receptor activation mechanism and viral replication process (Fig 10) . doi = 10.1101/2020.04.20.050138 id = cord-297754-d4xnj551 author = Aktas, Emre title = Bioinformatic Analysis Reveals That Some Mutations May Affect On Both Spike Structure Damage and Ligand Binding Site date = 2020-09-03 keywords = d614; mutation summary = It might be thought like case of influenza(where mutations slowly accumulate in the hemagglutinin protein during a flu season),and there is a complex interplay between mutations that can confer immune resistance to the virus, and the fitness landscape of the particular variant in which they arise [5] .The SARS-CoV-2 ,which mutation rate rate remarkable high and many variation have already characterized, has shown to have gone through certain mutations both in its structural and non structural proteins within several months while spreading throughout the world [8, 10] I focused my study on both determining some mutations that occurred based on the regions and evaluating whether this new mutation had an effect on the shapes of spike proteins.Besides I tried to predict that how mutations affect on ligand site. doi = 10.1101/2020.08.10.244632 id = cord-330384-yujbcwg5 author = Al-Mulla, Fahd title = A comprehensive germline variant and expression analyses of ACE2, TMPRSS2 and SARS-CoV-2 activator FURIN genes from the Middle East: Combating SARS-CoV-2 with precision medicine date = 2020-05-16 keywords = ACE2; Fig; SARS; TMPRSS2 summary = The increased cleavage activity of this protease was suggested to diminish viral recognition by neutralizing antibodies and by activating SARS spike (S) protein for virus-cell fusion 11 and facilitates the active binding of SARS-CoV-2 through ACE2 receptor, which is a risk factor for a more serious COVID-19 presentation [8] [9] [10] . Recent studies, assessed the genetic variations and eQTL (expression quantitative trait locus) expression profiles in the candidate genes ACE2, TMPRSS2, and FURIN to demonstrate the sex and population-wise differences that may influence the pathogenicity of SARS-CoV-2 9, [15] [16] [17] [18] [19] . Therefore, we screened the genetic variations and eQTL expression of the SARS-CoV-2 candidate genes, ACE2, TMPRSS2 and FURIN in three Middle Eastern populations: Kuwaiti, Iranian, and Qatari and compared them to available MAF data in the gnomAD database 41 . doi = 10.1101/2020.05.16.099176 id = cord-102766-n6mpdhyu author = Alam, Md. Nafis Ul title = Short k-mer Abundance Profiles Yield Robust Machine Learning Features and Accurate Classifiers for RNA Viruses date = 2020-06-25 keywords = RNA; feature; sequence summary = doi = 10.1101/2020.06.25.170779 id = cord-353877-wzndpcq3 author = Albagi, Sahar Obi Abd title = A Multiple Peptides Vaccine against nCOVID-19 Designed from the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics Approach date = 2020-05-20 keywords = HLA; MHC; Spike summary = Due to the current COVID-19 pandemic, the rapid discovery of a safe and effective vaccine is an essential issue, consequently, this study aims to predict potential COVID-19 peptide-based vaccine utilizing the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics approach. Consistent with global efforts, this study aims to predict potential COVID-19 Peptide-based vaccine utilizing the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics approach. The molecular docking results showed that the Spike peptide FTISVTTEI has the lowest docking energy score with the MHC I HLA-B1503 allele, hence it is predicted to have the highest binding affinity. Regarding the interaction with the MHC II molecule, the Spike peptide EVFNATRFASVYAWN showed the lowest docking energy score with the three MHC II alleles HLA-DPA1*01:03/DPB1*02:01, HLA-DQA1*01:02/DQB1*06:02, and HLA-DRB1, hence it is predicted to have the highest binding affinity to the three alleles. doi = 10.1101/2020.05.20.106351 id = cord-103735-nil1vv6h author = Alfano, Niccolo title = Non-invasive surveys of mammalian viruses using environmental DNA date = 2020-03-29 keywords = PCR; RNA; Suppl; dna; sample summary = Using a curated set of RNA oligonucleotides based on the ViroChip microarray assay [7] as baits in a hybridization capture system, multiple mammalian RNA and DNA viruses were detected from both eDNA and iDNA samples. Highlights Environmental DNA (water and blood-sucking leeches) provided a non-invasive method of screening wildlife for viruses A comprehensive viral RNA oligonucleotide bait set was developed to capture known and unknown mammalian virus diversity Leech blood meal host determination and viruses identified were congruent Viruses determined from water correlated with known and observed species visiting the water sources In brief Alfano, Dayaram, et al. In filtered water and sediment samples collected from the same waterhole, only one virus per sample was generally identified and in one location (WM20 and SM20) contigs from different viral families were isolated based on sample type. We provide evidence that environmental and invertebrate-derived DNA samples including waterhole water, sediment and wild haematophagous terrestrial leeches can be used to survey known and unknown viruses. doi = 10.1101/2020.03.26.009993 id = cord-344236-qp3ianzf author = Ali, Fedaa title = ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity date = 2020-05-08 keywords = ACE2; SARS summary = Classical electrostatic calculations based on solving Poisson-Boltzmann (PB) equation is used to investigate the interaction energies between SARS-CoV-2 and ACE2 for different mutated ACE2 structures. In an attempt to better understand the susceptibility of different populations to infection by SARS-CoV-2, we gathered data on ACE2 missense variants from different projects and databases that aggregate allele frequencies (AF). These projects and databases included Single Nucleotide Polymorphism Database (dbSNP) 12, 13 , 1000 genomes project phase 3 (1KGP3) 14 , Allele Frequency Aggregator (ALFA project) a , Exome Aggregation Consortium (ExAC) 15 SARS-CoV-2 was reported to bind to human ACE2 via different ACE2 residues; Q24, D30, H34, Y41, Q42, M82, K353 and R357 5 . The electrostatic and the van der Waal contribution to the interaction energies of SARS-CoV-2/ACE2 were compared between single mutated and WT protein at pH =7 (Table 1 ). doi = 10.1101/2020.05.08.084384 id = cord-102481-obig3mu1 author = Alić, Ivan title = “Patient-specific Alzheimer-like pathology in trisomy 21 cerebral organoids reveals BACE2 as a gene-dose-sensitive AD-suppressor in human brain” date = 2020-01-31 keywords = Fig; Supplementary; T21; bace2 summary = doi = 10.1101/2020.01.29.918037 id = cord-102257-da4zn49x author = Almodaresi, Fatemeh title = Puffaligner: An Efficient and Accurate Aligner Based on the Pufferfish Index date = 2020-08-12 keywords = Bowtie2; CPM; STAR; alignment; read; reference summary = doi = 10.1101/2020.08.11.246892 id = cord-104031-vodwptdo author = Altshuler, Anna title = Capturing limbal epithelial stem cell population dynamics, signature, and their niche date = 2020-07-01 keywords = Fig; LSC; cell; epithelial; limbal; limbus; outer summary = Tremendous efforts have been made by many research groups to discover markers for the identification of LSCs. Keratin 15 (Krt15) 33 41 , C/EBPdelta and BMI1 42 , ABCB5 43 , ABCG2 44 and P63 45 represent a partial list of genes proposed to identify LSCs. Recently, we have shown that the Krt15-GFP transgene (green fluorescent protein coding gene under the promoter of Krt15) labeled a discrete population of murine LSCs. Krt15-GFP + basal limbal epithelial cells were located at close proximity to the site of corneal regeneration origin, as evident by lineage tracing of Krt14 + cells 33 . In silico analysis revealed discrete cell states in the corneal epithelial lineage Cell filtering and unbiased clustering were performed with R package Seurat 46 revealing 11 cell populations displaying a markedly distinct signature of gene expression (Fig. 1b, S1b) . doi = 10.1101/2020.06.30.179754 id = cord-103990-qvuv289g author = Amster, Guy title = Changes in life history and population size can explain relative neutral diversity levels on X and autosomes in extant human populations date = 2019-09-09 keywords = population; ratio summary = We revisit this question in light of our new theory about the effects of life history and given pedigree-based estimates of the dependence of human mutation rates on sex and age. We demonstrate that life history effects, particularly higher generation times in males than females, likely had multiple effects on human X-to-autosomes (X:A) polymorphism ratios, through the extent of male mutation bias, the equilibrium X:A ratios of effective population sizes, and differential responses to changes in population size. Our results suggest that ancestral human populations were highly polygynous; that non-African populations experienced a substantial reduction in polygyny and/or increase in male-biased generation times around the out of Africa bottleneck; and that extant diversity levels were affected by fairly recent changes in sex-specific life history. Indeed, we show that the ratios observed across human populations can be explained by demographic history, assuming plausible, sex-specific mutation rates, generation times and reproductive variances. doi = 10.1101/763524 id = cord-348635-1pb2ag9j author = Anand, Praveen title = SARS-CoV-2 selectively mimics a cleavable peptide of human ENaC in a strategic hijack of host proteolytic machinery date = 2020-04-30 keywords = ACE2; SARS summary = We report that SARS-CoV-2 has evolved a unique S1/S2 cleavage site (RRARSVAS), absent in any previous coronavirus sequenced, that results in mimicry of an identical FURIN-cleavable peptide on the human epithelial sodium channel α-subunit (ENaC-α). We extrapolate that the evolution of SARS-CoV-2 into a global coronavirus pandemic may be in part due to its targeted mimicry of human ENaC and hijack of the associated host proteolytic network. The overlap of the cell-types expressing ACE2 and ENaC-ɑ, and similar spatial distributions at the apical surfaces, suggest that SARS-CoV-2 may be leveraging the protease network responsible for ENaC cleavage. In order to extrapolate the tissue tropism of SARS-CoV-2 from the lens of the host proteolytic network, we assessed the co-expression of these proteases concomitant with the viral receptor ACE2 and ENaC-ɑ (Figure 2) . doi = 10.1101/2020.04.29.069476 id = cord-259084-lwh3rww4 author = Anderson, Cole title = Pooling nasopharyngeal swab specimens to increase testing capacity for SARS-CoV-2 date = 2020-05-22 keywords = SARS summary = title: Pooling nasopharyngeal swab specimens to increase testing capacity for SARS-CoV-2 Current diagnosis of COVID-19 relies on the detection of SARS-CoV-2 RNA by RT-PCR in upper and lower respiratory specimens. Implementing a pooling strategy can significantly increase laboratory testing capacity while simultaneously reducing turnaround times for rapid identification and isolation of positive COVID-19 cases in high risk populations. This protocol allows for 35 the rapid detection of SARS-CoV-2 RNA from clinical specimens such as, nasopharyngeal and 36 oropharyngeal swabs, sputum, bronchoalveolar lavage, and tracheal aspirates. 43 In this study, we examined the feasibility of pooling nasopharyngeal swab specimens submitted 44 for COVID-19 testing using the CDC 2019-nCoV RT-PCR diagnostic panel without compromising 45 Specimens were submitted to 54 the Virology laboratory at Landstuhl Regional Medical Center for routine SARS-CoV-2 testing 55 using the CDC 2019-nCoV RT-PCR assay. Pooling nasopharyngeal/throat swab specimens to increase testing 176 capacity for influenza viruses by PCR doi = 10.1101/2020.05.22.110932 id = cord-321027-64y43o0y author = Andreano, Emanuele title = Identification of neutralizing human monoclonal antibodies from Italian Covid-19 convalescent patients date = 2020-05-09 keywords = SARS summary = The SARS-CoV-2 spike glycoprotein (S-protein) has a pivotal role in viral pathogenesis and it is 63 considered the main target to elicit potent neutralizing antibodies and the focus for the development 64 of therapeutic and prophylactic tools against this virus (3, 4) . Results shown in Table 1 and Figure 1 show that, among the seven donors 97 included in this study, six were able to produce high titers of SARS-CoV-2 S-protein specific 98 antibodies and in particular donors R-042, R-122 and R-188 showed the highest virus neutralizing 99 titers. In the case of SARS-CoV-2, where so far we do not have any effective therapeutic nor prophylactic 154 interventions, mAbs have the possibility to become one of the first drugs that can be used for 155 immediate therapy of any patient testing positive for the virus, and even to provide immediate 156 protection from infection in high risk populations. doi = 10.1101/2020.05.05.078154 id = cord-321369-xzu2faol author = Andreano, Emanuele title = Extremely potent human monoclonal antibodies from convalescent Covid-19 patients date = 2020-10-07 keywords = Fig; SARS; antibody summary = By single cell sorting 4277 SARS-CoV-2 spike protein specific memory B cells from 14 Covid-19 survivors, 453 neutralizing antibodies were identified and 220 of them were expressed as IgG. The three most potent monoclonal antibodies identified were able to neutralize the wild type and D614G mutant viruses with less than 10 ng/mL and are good candidates for the development of prophylactic and therapeutic tools against SARS-CoV-2. As for the authentic virus neutralization assay, supernatants containing naturally produced IgG or IgA were tested for their ability to protect the layer of Vero E6 cells from the cytopathic effect triggered by SARS-CoV-2 infection (Fig. S2) . This work describes a systematic screening of memory B cells from convalescent people to identify extremely potent human monoclonal antibodies against the spike protein of the SARS-CoV-2 virus, to be used for prevention and therapy of Covid-19. doi = 10.1101/2020.10.07.328302 id = cord-261662-d0tg9i90 author = Andres, Cristina title = Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients date = 2020-06-08 keywords = SARS summary = title: Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients Here, we deep-sequenced the complete SARS-CoV-2 S gene from 18 patients (10 with mild and 8 with severe COVID-19), and found that the virus accumulates deletions upstream and very close to the S1/S2 cleavage site, generating a frameshift with appearance of a stop codon. Because of the importance of the S protein, we carried out a deep-sequencing study of the S gene in upper respiratory tract samples from 18 patients with mild or severe SARS-CoV-2 disease. The fact that the truncated S protein was present in only a low percentage of the entire viral quasispecies suggests that natural selection may have designed a favorable equilibrium in which a limited number of deleted virions are generated to balance virus production with infection of new cells during disease progression. doi = 10.1101/2020.06.03.129585 id = cord-102555-vnmc9ii8 author = Araki, Takuma title = Sphingobium sp. SYK-6 syringate O-demethylase gene is regulated by DesX, unlike other vanillate and syringate catabolic genes regulated by DesR date = 2020-07-28 keywords = SYK-6 summary = doi = 10.1101/2020.07.27.224295 id = cord-356264-q0yqnlyl author = Armijos-Jaramillo, Vinicio title = SARS-CoV-2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability date = 2020-03-23 keywords = RBD; SARS; selection; site summary = With this analysis, we determine a region inside the receptor-binding domain with putative sites under positive selection interspersed among highly conserved sites, which are implicated in structural stability of the viral spike protein and its union with human receptor hACE2. We employ a multidisciplinary approach to look for evidence of diversifying selection on the S-protein gene, and model the interactions between human ACE2 (hACE2) and the RBD of selected coronavirus strains, which ultimately afforded us novel insights detailing virus and host cell interactions. All these experiments were performed again using the S-protein genes of a shorter list of accessions and more distantly related (broad dataset) to SARS-COV-2 (AY304488, AY395003, DQ412043, FJ882957, KY417144, MG772933, MG772934, MN908947, NC_004718) to test the reproducibility of the predicted branches and sites under positive selection. Modeling results suggest that interference with the hot spot 353 could be and effective strategy for inhibiting the recognition of the RBD of the SARS-COV-2 spike protein by its human host receptor ACE2 and hence prevent infections. doi = 10.1101/2020.03.21.001933 id = cord-103580-6rf1xs0d author = Arokiaraj, Mark Christopher title = A Novel Method of Immunomodulation of Endothelial cells Using Streptococcus Pyogenes and its Lysate date = 2020-05-15 keywords = cell; factor; immune; streptococcus summary = In this study, a novel method of immune-modulation to modify the endothelial function was studied to modulate the features of the endothelial cells, and thereby to reduce coronary artery disease and other disorders modulated by endothelium. Conclusion There is potential for a novel method of immunomodulation of the endothelial cells, which have pleiotropic functions, using streptococcus pyogenes and its lysates. The study was performed in search of novel applications of streptococcus pyogenes in regulating immune functions, and its related effects on cardiovascular and its pleiotropic functions. When the cells were treated with streptococcus pyogenes'' lysate, the levels of BLC -the B lymphocyte chemoattractant protein (CXCL13) was increased. 72 The heat map analysis shows a significant change in more proteins, and thereby it is possible to infer that streptococcus has a role in immune regulation. 78 Our study also reflects the immune regulation changes due to streptococcus pyogenes as well as by its lysate. doi = 10.1101/2020.05.13.082180 id = cord-104133-d01joq23 author = Arthur, Ronan F. title = Adaptive social contact rates induce complex dynamics during epidemics date = 2020-07-14 keywords = model; time summary = We develop a model for adaptive optimal control of the effective social contact rate within a Susceptible-Infectious-Susceptible (SIS) epidemic model using a dynamic utility function with delayed information. To represent endogenous behavior-change, we start with the classical discrete-time 112 susceptible-infected-susceptible (SIS) model [28] , which, when incidence is relatively 113 small compared to the total population [29, 30] , can be written in terms of the recursions 114 In order to introduce human behavior, we 121 substitute for b a time-dependent b t , which is a function of both b 0 , the probability that 122 disease transmission takes place on contact, and a dynamic social rate of contact c t 123 whose optimal value, c * t , is determined at each time t as in economic epidemiological 124 models [31] , namely doi = 10.1101/2020.04.14.028407 id = cord-283109-ka3n9pft author = Arumugam, Arunkumar title = The Potential Use of Unprocessed Sample for RT-qPCR Detection of COVID-19 without an RNA Extraction Step date = 2020-04-08 keywords = SARS summary = Using flu and RSV clinical specimens, we have collected evidence that the RT-qPCR assay can be performed directly on patient sample material from a nasal swab immersed in virus transport medium (VTM) without an RNA extraction step. Using Inf and RSV clinical specimens, we successfully performed RT-qPCR reactions by simply adding a few microliters of the unprocessed sample in viral transport medium (VTM) directly into the RT-qPCR assay master mix. We next tested whether the RNA from SARS-CoV-2 can be detected by directly spiking samples of the non-replicative recombinant virus particles (SeraCare AccuPlex SARS-CoV-2 reference material) in VTM to master mix without an extraction step. As shown in Fig. 3 , the SARS-CoV-2 RNA from directly spiked samples was successfully detected by the RT-qPCR reaction without a nucleic acid extraction step (N1 target shown). doi = 10.1101/2020.04.06.028811 id = cord-354725-lqio7l8k author = Arumugam, Arunkumar title = A Rapid COVID-19 RT-PCR Detection Assay for Low Resource Settings date = 2020-04-30 keywords = PCR summary = Using COVID-19 positive clinical specimens, we demonstrated that RT-PCR assays can be performed in as little as 12 minutes using untreated samples, heat-inactivated samples, or extracted RNA templates. 5 Despite its established performance in sensitivity and specificity, RT-qPCR requires expensive equipment such as RNA isolation instruments and real-time PCR thermal cyclers, which are not available in many resource limiting settings. Two water baths (one for denaturation and one for the reverse transcription and then the annealing/extension steps) were made using food storage plastic containers heated by sous vide immersion heaters. We tested this rapid water bath RT-PCR approach using untreated or heat-inactivated samples directly added to one-step RT-PCR master mixes without an RNA extraction step. Extracted templates from COVID-19 positive clinical specimens and contrived negative samples were tested using water bath-based RT-PCR. With a 3-minute RNA extraction protocol, we were able to get positive RT-PCR results with all ten COVID-19 positive clinical samples. doi = 10.1101/2020.04.29.069591 id = cord-353742-k4gxww2c author = Arévalo, AP title = Ivermectin reduces coronavirus infection in vivo: a mouse experimental model date = 2020-11-02 keywords = SARS summary = SARS-CoV2 is a single strand RNA virus member of the type 2 coronavirus family, responsible for causing COVID-19 disease in humans. The objective of this study was to test the ivermectin drug in a murine model of coronavirus infection using a type 2 family RNA coronavirus similar to SARS-CoV2, the mouse hepatitis virus (MHV). Overall results demonstrated that viral infection induces the typical MHV disease in infected animals, with livers showing severe hepatocellular necrosis surrounded by a severe lymphoplasmacytic inflammatory infiltration associated with a high hepatic viral load (52,158 AU), while ivermectin administration showed a better health status with lower viral load (23,192 AU; p<0.05) and few livers with histopathological damage (p<0.05), not showing statistical differences with control mice (P=NS). In conclusion, ivermectin seems to be effective to diminish MHV viral load and disease in mice, being a useful model for further understanding new therapies against coronavirus diseases. doi = 10.1101/2020.11.02.363242 id = cord-268034-7id7sfsu author = Auerswald, Heidi title = Assessment of Inactivation Procedures for SARS-CoV-2 date = 2020-05-28 keywords = CoV-2; SARS summary = This data demonstrates that all chemical (AVL, inactivating sample buffer and formaldehyde) and heat treatment (56°C and 98°C) methods tested completely inactivated viral loads of up to 5 log10. The buffers used in this lysis step yield varying results [11, 13, 15, 16] ; however, unlike 224 previous studies [11] , this study found that AVL buffer alone was successfully able to fully 225 inactivate up to 5 log10 of virus from three different primary isolates of SARS-CoV-2. Previous 234 studies have shown that GITC-lysis buffers are able to inactivate SARS-CoV-2 samples [11, 12] ; 235 however, the addition of Triton-X may be necessary for complete inactivation [11] . Therefore, formaldehyde treatment does not appear to be a 247 solution for increased molecular SARS-CoV-2 testing; however, it does remain a viable alternative 248 for sample inactivation or disinfection. doi = 10.1101/2020.05.28.120444 id = cord-102270-rfhtlodc author = Azhar, Mohd. title = Rapid, field-deployable nucleobase detection and identification using FnCas9 date = 2020-04-21 keywords = CRISPR; FELUDA; dna; figure summary = We then fixed the position of this mutation with respect to PAM and changed every other base in the sgRNA sequence to identify which combination led to complete loss of cleavage of a wild type substrate in an in vitro cleavage (IVC) assay with FnCas9 ( Figure 1B, Supplementary Figure 1A ). Taken together, these experiments suggest that FELUDA design can be universally used for detection of SNVs and and would not require extensive optimization or validation steps for new SNVs. To aid users for quick design and implementation of FELUDA for a target SNV, we have developed a webtool JATAYU (Junction for Analysis and Target Design for Your FELUDA assay) that incorporates the above features and generates primer sequences for amplicon and sgRNA synthesis (https:// jatayu.igib.res.in, Supplementary Figure 2 ). doi = 10.1101/2020.04.07.028167 id = cord-104142-0nfprn2a author = Azmi, Maryam A. title = A laboratory module that explores RNA interference and codon optimization through fluorescence microscopy using Caenorhabditis elegans date = 2020-10-19 keywords = GFPNCO; figure; student summary = In this laboratory module, students learn about RNA interference (RNAi) and codon optimization using the research organism Caenorhabditis elegans (C. elegans Understand the process of RNA interference and importance of codon optimization Learn basic microscopy techniques and image analysis Learn how to properly use the scientific method Enhance critical thinking skills Learning Objectives Students will be able to: Lab 1 and 2: Identify specific larval stages of C. elegans larvae using alkaline hypochlorite treatment Understand codon usage Formulate hypotheses and design a controlled experiment Lab 3 and 4: Acquire images using an epifluorescence microscope Effectively communicate results and formulate conclusions from data Describe what RNAi is and how it affects gene expression/activity Calculate mean fluorescent intensity from acquired fluorescence micrographs Perform statistical tests to determine the significance of results Generate publication quality figures and figure legends doi = 10.1101/2020.10.17.344069 id = cord-103592-lkngp2u6 author = Bachmaier, Kurt title = Selective Nanotherapeutic Targeting of the Neutrophil Subset Mediating Inflammatory Injury date = 2020-07-02 keywords = ANP; LPS; PANP; PMN; figure summary = Using cecal ligation and puncture (CLP), a reproducible and clinically relevant mouse model of polymicrobial infection that causes ALI, we found that in naïve control mice after 2 sequential i.v. injections of ANP only ~4% of lung PMN endocytosed ANP as evidenced by ANP-specific fluorescence ( Figure 1B) . Importantly, we found that CCR1 receptor cell surface expression, consistent with the mRNA data, was significantly greater on lung ANP high PMN than in ANP low PMN before and 3h, 6h, and 12h after LPS stimulation ( Figure 3B ). We observed that nitrotyrosine-specific staining in inflammatory and parenchymal cells was significantly reduced in lungs and livers of mice treated with PANP when compared to ANP-treated controls ( Figure 6D ,E). Measuring a markers of overall cell damage, lactic dehydrogenase (LDH) (34) , revealed that the polymicrobial sepsis-induced increased serum activity of LDH was significantly reduced by PANP treatment when compared to ANP treated controls ( Figure 6G ). doi = 10.1101/2020.06.30.180927 id = cord-309512-d8n9711b author = Bacus, Michael G. title = Global genetic patterns reveal host tropism versus cross-taxon transmission of bat Betacoronaviruses date = 2020-05-05 keywords = bat summary = Emerging infectious diseases due to coronavirus (CoV) infections have received significant global attention in the past decade and have been linked to bats as the original source. As such, deviant patterns were observed such as for 2D-IV, wherein cross-taxon transmission due to overlap in bat habitats and geographic range among genetically divergent African bat hosts could have played a strong role on their shared CoV lineages. In fact, a few bat taxa especially the subfamily Pteropodinae were shown to host diverse groups of BetaCoVs. Therefore, ecological imbalances that disturb bat distribution may lead to loss of host specificity through cross-taxon transmission and multi-CoV infection. Importance Bat Betacoronaviruses (BetaCoVs) pose a significant threat to global public health and have been implicated in several epidemics such as the recent pandemic by severe acute respiratory syndrome coronavirus 2. Although bat BetaCoVs are host taxon-specific, their evolutionary pathways are different from evolution with its host. doi = 10.1101/2020.05.04.076281 id = cord-300423-q2i328sz author = Bai, Lei title = Co-infection of influenza A virus enhances SARS-CoV-2 infectivity date = 2020-10-14 keywords = IAV; SARS summary = Remarkably, increased SARS-CoV-2 viral load and more severe lung damage were observed in mice co-infected with IAV in vivo. The results demonstrate that the pre-infection of 57 IAV strongly enhances the infectivity of SARS-CoV-2 by boosting viral entry in the cells 58 and by elevating viral load plus more severe lung damage in infected mice. We 75 further tested more cell lines to show that the enhancement of the pSARS-CoV-2 infectivity 76 by IAV was a general effect although the increased folds were different (lower basal level 77 of infectivity, higher enhancement fold) (Fig.1D ). We found that the pre-infection of IAV 80 strongly increased the copy numbers of the SARS-CoV-2 genome (E and N genes) in both 81 cell lysates and supernatants of A549 (~15 folds) (Fig.1F) . The histological data in Fig. 2D further illustrated that IAV and 98 SARS-CoV-2 co-infection induced more severe lung pathologic changes with massive 99 infiltrating cells and obvious alveolar necrosis as compared to SARS-CoV-2 single 100 infection or mock infection. doi = 10.1101/2020.10.14.335893 id = cord-270550-if748w2n author = Bailey, Adam L. title = SARS-CoV-2 Infects Human Engineered Heart Tissues and Models COVID-19 Myocarditis date = 2020-11-05 keywords = ACE2; CoV-2; Fig; RNA; SARS summary = To ascertain whether human pluripotent stem cell-derived cardiomyocytes (hPSC-derived 150 CMs) can serve as an appropriate model to study cardiac SARS-CoV-2 infection, we measured 151 ACE2 mRNA expression in hPSC-derived CMs. Quantitative RT-PCR revealed that hPSC-152 derived CMs abundantly expressed ACE2 mRNA. We identified numerous host genes that were differentially 226 regulated upon SARS-CoV-2 infection in each of the examined cell types and two-dimensional 227 tissues (Fig. 3c) . 236 GO pathway analysis revealed that infected hPSC-derived CMs and two-dimensional co-237 culture tissues showed upregulation of genes associated with immune cell activation, stress-238 induced transcription, and responses to pathogens including viruses. Consistent with the 343 possibility that disrupted sarcomere gene expression might contribute to reduced EHT 344 contractility, immunostaining of hPSC-derived CMs infected with SARS-CoV-2 revealed evidence 345 of sarcomere loss 3 days following infection (Fig. 6c) , a time point that preceded cell death. doi = 10.1101/2020.11.04.364315 id = cord-332271-slouuryl author = Baker, Jeremy D. title = A drug repurposing screen identifies hepatitis C antivirals as inhibitors of the SARS-CoV-2 main protease date = 2020-08-27 keywords = Mpro; SARS; drug summary = title: A drug repurposing screen identifies hepatitis C antivirals as inhibitors of the SARS-CoV-2 main protease Here we show the existing pharmacopeia contains many drugs with potential for therapeutic repurposing 27 as selective and potent inhibitors of SARS-CoV-2 Mpro. Taken together this work suggests previous large-scale commercial 35 drug development initiatives targeting hepatitis C NS3/4A viral protease should be revisited because some 36 previous lead compounds may be more potent against SARS-CoV-2 Mpro than Boceprevir and suitable for 37 rapid repurposing. Taken together this work suggests previous large-scale commercial 35 drug development initiatives targeting hepatitis C NS3/4A viral protease should be revisited because some 36 previous lead compounds may be more potent against SARS-CoV-2 Mpro than Boceprevir and suitable for 37 rapid repurposing. Before screening the Broad library, 100 we piloted our assay conditions against the NIH Clinical collections library (~650 compounds) and 101 calculated our Z''-factor for each plate at 0.780 and 0.784 (Fig 1C and D) . doi = 10.1101/2020.07.10.197889 id = cord-284627-qvz63m93 author = Banerjee, Shuvam title = Decoding the lethal effect of SARS-CoV-2 (novel coronavirus) strains from global perspective: molecular pathogenesis and evolutionary divergence date = 2020-04-09 keywords = SARS summary = The fatality rates in different countries were matched against the mutation number, rarity of the nucleotide alterations and functional impact of the Non Synonymous changes at protein level, separately and in combination. 20 Non Synonymous mutations are located in viral genome spanning Orf1ab polyprotein, Surface glycoprotein, Nucleocapsid protein etc. Interpretation The fatality outcome depends on three important factors (a) number of mutation (b) rarity of the allelic variation and (c) functional consequence of the mutation at protein level. 12, 14 In this study, we comprehensively analyzed the whole genome sequence homology from the available patient data uploaded by affected countries in NCBI Virus database, identified the mutations developed by different strains from the ancestor strain and studied the impact of those mutations at functional level. In summary, the present study reveals that the fatality rate increases with not only the number of mutations but also depending on its allelic rarity as well as functional alteration of protein. doi = 10.1101/2020.04.06.027854 id = cord-335075-6wo2o5pp author = Bangaru, Sandhya title = Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate date = 2020-08-06 keywords = SARS; figure; spike summary = Here, we performed cryo-EM and site-specific glycan analysis of one of the leading subunit vaccine candidates from Novavax based on a full-length spike protein formulated in polysorbate 80 (PS 80) detergent. Site-specific glycosylation of the SARS-CoV-2 prefusion spike protein produced in SF9 insect cells was analyzed using our recently described mass spectrometry proteomics-based method, involving treatment with proteases followed by sequential treatment with the endoglycosidases (Endo H and PNGase F) to introduce mass signatures in peptides with N-linked sequons (Asn-X-Thr/Ser) to assess the extent of glycosylation and the degree of glycan processing from high mannose/hybrid type to complex type (24) . In this study, we performed structural analysis of the Novavax SARS-CoV We also observed two non-spike densities within the spike trimer that corresponded with linoleic acid and polysorbate 80 detergent. doi = 10.1101/2020.08.06.234674 id = cord-311445-b6bc6vwd author = Bansal, Kanika title = Codon pattern reveals SARS-CoV-2 to be a monomorphic strain that emerged through recombination of replicase and envelope alleles of bat and pangolin origin date = 2020-10-12 keywords = SARS; cup summary = Systematic analysis of CUP of replicase (rdrp), spike, envelope (E), membrane glycoprotein (M), and nucleocapsid (N) encoding genes of SARS-CoV-2 from reported diverse lineages to suggest one-time host jump of a SARS-CoV-2 isolate into the human host. In contrast to human isolates, a high degree of variation in CUP of these genes suggests that bats, pangolins, and dogs are natural reservoirs of diverse strains. In the present study, we have focused on codon usage pattern (CUP) of SARS coronavirus from different hosts under debate (bat, pangolin, and dog) as a probable origin for SARS-CoV-2. However, another study comparing the codon usage pattern of SARS-CoV-2 with other betacoronaviruses suggested that current pandemic coronavirus is subjected to different evolutionary pressures (Gu et al., 2020) . The above analysis reveals single patterns for all five genes in different lineages of SARS-CoV-2 affirms a single event of host jump of codon-optimized SARS strain from its animal reservoir. doi = 10.1101/2020.10.12.335521 id = cord-311843-un6urdb1 author = Baray, Juwel Chandra title = BANCOVID, the first D614G variant mRNA-based vaccine candidate against SARS-CoV-2 elicits neutralizing antibody and balanced cellular immune response date = 2020-09-30 keywords = CD4; CD45; SARS summary = title: BANCOVID, the first D614G variant mRNA-based vaccine candidate against SARS-CoV-2 elicits neutralizing antibody and balanced cellular immune response The anti-sera and purified IgGs from immunized mice on day 7 and 14 neutralized SARS-CoV-2 pseudovirus in ACE2-expressing HEK293 cells in a dose dependent manner. The reactivity of the sera from each 221 group of mice immunized with BANCOVID was measured against SARS-CoV-2 S antigen 222 (SinoBiologicals, China). Analysis revealed IgG binding against SARS-CoV-2 S protein 223 antigens in the sera of the immunized mice. Flow cytometric analysis of total T cell (CD4 + ) populations producing TFN alpha on mouse splenocyte upon SARS-CoV-2 S protein stimulation. Flow cytometric analysis of total T cell (CD4 + ) populations producing IL-6 on mouse splenocyte upon SARS-CoV-2 S protein stimulation. Flow cytometric analysis of total T cell (CD4 + ) populations producing IL-6 on mouse splenocyte upon SARS-CoV-2 S protein stimulation. doi = 10.1101/2020.09.29.319061 id = cord-103208-krann2ir author = Barber-Axthelm, Isaac M title = Coformulation with tattoo ink for immunological assessment of vaccine immunogenicity in the draining lymph node date = 2020-08-29 keywords = Fig summary = In order to improve the accurate isolation of antigen-exposed lymph nodes during biopsies and necropsies, we developed and validated a method for co-formulating candidate vaccines with tattoo ink, which allows for direct visual identification of vaccine-draining lymph nodes and evaluation of relevant antigen-specific B and T cell responses by flow cytometry. We tested if sampling accuracy, and the characterisation of vaccine-elicited immune responses ex vivo, could be improved using tattoo ink to label vaccine-draining LNs in NHPs. Pigtail macaques (Macaca nemastrina) were immunised in the right quadriceps with SARS-CoV-2 spike (100μg) formulated with monophosphoryl lipid A (MPLA) liposomal adjuvant ( 2 9 ) , and were boosted IM in the right and left quadriceps with SARS-CoV-2 spike (100μg) formulated with MPLA and tattoo ink (1.0%). . Animals were additionally immunised in the right and left deltoids with human immunodeficiency virus-1 (HIV-1) fixed trimeric envelope protein (SOSIP) vaccines (100μg) formulated with MPLA and 1.0% tattoo ink (ink in the right deltoid only), with expected drainage to the axillary LNs (Fig 3A) ( doi = 10.1101/2020.08.27.270975 id = cord-347982-omxcdiwt author = Basso, Fernanda Gisele title = Cooperative efforts on developing vaccines and therapies for COVID-19 Cooperative efforts for COVID-19 date = 2020-09-06 keywords = COVID-19; cooperation summary = The present research analyzes how the cooperation networks were set off considering the clinical trials on therapies and vaccines that were developed specifically to treat or prevent COVID-19. For the construction of cooperation networks, it was assumed that organizations signed agreements and/or treaties to develop specific studies, establishing joint ownership of the results and the new drug or vaccine, with the purpose of forming an alliance for innovation [20] . Regarding the distribution of the types of organizations that cooperate by category (Fig 3) , a greater diversity of partnerships was observed in antibodies, followed by vaccines and proteins, because these categories address complex therapies and require complementarity among several disciplines (e.g., adjuvants in Because clinical adoption and commercial success are due to the incorporation degree of existing practices in innovation processes [23] , the diffusion of disruptive technologies in this field may encounter greater challenges. doi = 10.1101/2020.09.06.282145 id = cord-330337-d41imvo7 author = Basu, Souradip title = Impact of clade specific mutations on structural fidelity of SARS-CoV-2 proteins date = 2020-10-20 keywords = SARS; mutation; protein summary = Our observations and analysis direct us to identify that all the major mutations have a negative impact in context of stability of the viral proteins under study and the mutant proteins suffer both structural and functional alterations as a result of the mutations. The secondary structure of the wild type and the mutant proteins along with their degree of disordered residues and accessible surface area was predicted using the primary sequence of the protein. Each of the seven proteins were assigned a score of either ''-1'' or ''0'', for each of the four computational tools used for epitope prediction, where ''-1'' corresponds to any change in number or binding efficacy of antigenic determinants, that may have surfaced because of mutation and ''0'' corresponds to no changes between wild type and mutant forms. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure doi = 10.1101/2020.10.20.347021 id = cord-103715-53v1qoyc author = Bauman, Neda title = Computational image analysis reveals the structural complexity of Toxoplasma gondii tissue cysts date = 2020-05-21 keywords = cyst summary = title: Computational image analysis reveals the structural complexity of Toxoplasma gondii tissue cysts A novel approach to analyze the structure of in vivo-derived tissue cysts may be the increasingly used computational image analysis. gondii cysts by morphological, particle, and fractal analysis, as well as to determine if and how it is impacted by parasite strain, cyst age, and host factors. The parameters of interest included diameter, circularity, relative particle count (RPC), fractal dimension (FD), lacunarity, and packing density (PD). Cysts were transferred to black background images for subsequent particle analysis. In that manner, all of the cyst cross-section images were subjected to an 148 automated processing and the obtained particle numbers, N p , were expected to be proportional to the Fig 2C. Novel approaches reveal that Toxoplasma 357 gondii bradyzoites within tissue cysts are dynamic and replicating entities in vivo Vet S2 Data -Fractal dimension and lacunarity of tissue cysts (n=31) doi = 10.1101/2020.05.21.108118 id = cord-348727-o38uplxe author = Beaudoin-Bussières, Guillaume title = Decline of humoral responses against SARS-CoV-2 Spike in convalescent individuals date = 2020-07-09 keywords = SARS summary = Similarly, we observed a significant decrease in the capacity of convalescent plasma to neutralize pseudoparticles bearing SARS-CoV-2 S wild-type or its D614G variant. Neutralizing activity against pseudoparticles bearing the SARS-CoV S 120 glycoprotein was detected in only 25% of convalescent plasma and exhibited low potency, as 121 previously reported (Figure 2) (14) . Of note, while we observed enhanced infectivity for the 122 D614G variant compared to its WT SARS-CoV-2 S counterpart ( Figure S3A ), no major 123 differences in neutralization with convalescent plasma were detected at both time-points ( Figure 124 S3B), thus suggesting that the D614G change does not affect the overall conformation of the 125 Spike, in agreement with recent findings (18) . 126 127 The capacity to neutralize SARS-CoV-2 S WT or D614G-pseudotyped particles 128 significantly correlated with the presence of RBD-specific IgG, IgM and anti-S antibodies 129 ( Figure S4 ). Interestingly, we observed a pronounced decrease (20-30%) in the percentage of 130 patients able to neutralize pseudoparticles bearing SARS-CoV-2 S glycoprotein between 6 and 131 10 weeks after symptoms onset. doi = 10.1101/2020.07.09.194639 id = cord-318499-uihof6k6 author = Beddingfield, Brandon title = The Integrin Binding Peptide, ATN-161, as a Novel Therapy for SARS-CoV-2 Infection date = 2020-06-16 keywords = ATN-161; SARS summary = Many efforts to design and screen therapeutics for the current severe acute respiratory syndrome coronavirus (SARS-CoV-2) pandemic have focused on inhibiting viral host cell entry by disrupting ACE2 binding with the SARS-CoV-2 spike protein. This work focuses on the potential to inhibit SARS-CoV-2 entry through a hypothesized α5β1integrin-based mechanism, and indicates that inhibiting α5β1 integrin interaction with ACE2 and the spike protein using a novel molecule ATN-161 represents a promising approach to treat COVID-19. In order to assess disruption of binding of α5β1 to SARS-CoV-2 Spike protein, 96-well plates were coated as before, but incubation with ATN-161 was performed in conjunction with 1µg/mL spike (produced under HHSN272201400008C and obtained through BEI Resources, NIAID, NIH: Spike Glycoprotein Receptor Binding Domain (RBD) from SARS-Related Coronavirus 2, Wuhan-Hu-1, Recombinant from HEK293 Cells, NR-52306) in the presence of 1mM MnCl2, followed by detection with an anti-spike antibody. Inhibition of SARS-CoV-2 spike protein binding to human ACE2 by ATN-161. doi = 10.1101/2020.06.15.153387 id = cord-262573-wdgbno9p author = Begum, Feroza title = Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India date = 2020-05-03 keywords = Bengal; West summary = We report one unique mutation at position 723 and the other at 1124 in the S2 domain of spike protein of the isolates from West Bengal only and one mutation downstream of the receptor binding domain at position 614 in S1 domain which was common with the sequence from Gujarat (a state of western part of India). We downloaded the five new SARS-CoV2 sequences from West Bengal (EPI_ISL_430468; EPI_ISL_430467; EPI_ISL_430465; EPI_ISL_430464; EPI_ISL_430466) from GISAID database and the spike protein sequences corresponding to Kerala isolates [2] and Gujarat isolate [3] from the NCBI virus database. Since, currently we have sequences against SARS-CoV2 only from three states in India i.e. Kerala, Gujarat and now West Bengal, we compared all the sequences to detect possible changes ( Figure 2) . This is the first report of mutations of such types in the isolates of the state of West Bengal and further sequencing followed by sequence analyses would help expanding the knowledge about variations of spike protein in human SARS-CoV. doi = 10.1101/2020.04.28.066985 id = cord-281565-v8s2ski3 author = Belmonte-Reche, Efres title = Exploring G and C-quadruplex structures as potential targets against the severe acute respiratory syndrome coronavirus 2 date = 2020-08-20 keywords = RNA; dna summary = These PQS and PiMS have been assessed according to their potential to form, uniqueness, frequency of appearance, conservation rates between 3297 different 2019-nCoV clinical cases, confirmed quadruplex-forming sequence presence and localization within the genome. Then, these PQS and PiMS were evaluated by their frequency of appearance in the corresponding genome, the presence of known-to-form quadruplex structures sequences within and their probability of quadruplex-formation score (as the mean of G4Hunter (52) and the adaptation of the PQSfinder algorithm (53) ). A flexible configuration of quadruplex definitions will detect larger amounts of candidates at the expense of requiring more computing power and accepting sequences that are more ambiguous in forming quadruplex structures in vitro (as determined by their score; with longer loops, smaller runs, more bulges and more complementary G/C %, Figure 1 , B). Expanding the search for common candidates to the entire virus realm, we matched one PQS and PiMS from the 2019-nCoV with the potential quadruplexes found in four viruses from doi = 10.1101/2020.08.19.257493 id = cord-291156-zxg3dsm3 author = Bernasconi, Anna title = Empowering Virus Sequences Research through Conceptual Modeling date = 2020-05-01 keywords = SARS; VCM; sequence; virus summary = We hereby present the Viral Conceptual Model (VCM), centered on the virus sequence and described from four perspectives: biological (virus type and hosts/sample), analytical (annotations and variants), organizational (sequencing project) and technical (experimental technology). -We propose a new Viral Conceptual Model (VCM), a general conceptual model for describing viral sequences, organized along specific dimensions that highlight a conceptual schema similar to GCM [6] ; -Focusing on SARS-CoV2, we show how VCM can be profitably linked to a phenotype database with information on COVID-19 infected patients; -We provide a list of interesting queries replicating newly released literature on infectious diseases; these can be easily performed on VCM. Some interesting portals have become interfaces to GISAID data with particular focuses: NextStrain [18] overviews emergent viral outbreaks based on the visualization of sequence data integrated with geographic information, serology, and host species; CoV-GLUE, 9 part of the GLUE suite [38] , contains a database of replacements, insertions and deletions observed in sequences sampled from the pandemic. doi = 10.1101/2020.04.29.067637 id = cord-355758-tk7eturq author = Berrio, Alejandro title = Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function date = 2020-09-22 keywords = Coronavirus; RNA; SARS summary = Background The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. In Importantly, we also detected signals of positive selection in two additional regions of the 414 SARS-CoV-2 genome, specifically within the genes encoding Nsp4 and Nsp16 (Fig 1A) . Comparative analysis of coronavirus genomic RNA structure reveals 718 conservation in SARS-like coronaviruses. doi = 10.1101/2020.09.16.300038 id = cord-284191-05djnz4p author = Bert, Nina Le title = Different pattern of pre-existing SARS-COV-2 specific T cell immunity in SARS-recovered and uninfected individuals date = 2020-05-27 keywords = SARS summary = To study SARS-CoV-2 specific T cells associated with viral clearance, we collected peripheral blood of 24 individuals who recovered from mild to severe COVID-19 (demographic, clinical and virological information are summarized in Extended Data Table 1 ) and studied the T cell response against selected structural (nucleocapsid protein-NP) and non-structural proteins (NSP7 and NSP13 of ORF1) of the large SARS-CoV-2 proteome ( Figure 1A) . To confirm and further delineate the multispecificity of the NP-specific T cell response detected ex vivo in COVID-19 recovered patients, we defined in nine individuals, the distinctive sections of NP targeted by T cells. This is consistent with the findings of Grifoni et al 11 : using selected peptides, they detected ORF-1 specific T preferentially in some SARS-CoV-2 unexposed donors while T cells of COVID-19 recovered donors preferentially recognized structural proteins. Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals doi = 10.1101/2020.05.26.115832 id = cord-102866-40s64455 author = Bhadra, Sanchita title = One enzyme reverse transcription qPCR using Taq DNA polymerase date = 2020-05-30 keywords = RNA; dna summary = doi = 10.1101/2020.05.27.120238 id = cord-103320-2rpr7aph author = Bhandari, Bikash K. title = Solubility-Weighted Index: fast and accurate prediction of protein solubility date = 2020-03-26 keywords = Fig; Protein; SWI; Solubility; biology summary = Results We have discovered that global structural flexibility, which can be modeled by normalised B-factors, accurately predicts the solubility of 12,216 recombinant proteins expressed in Escherichia coli. Protein solubility, at least in part, depends upon extrinsic factors such as ionic strength, temperature and pH, as well as intrinsic factors-the physicochemical properties of the protein sequence and structure, including molecular weight, amino acid composition, hydrophobicity, aromaticity, isoelectric point, structural propensities and the polarity of surface residues (Wilkinson and Harrison 1991; Chiti et al. 2003 ) Among these sets of B-factors, sequence composition scoring using the most recently published set of normalised B-factors produced the highest AUC score ( To improve the prediction accuracy of solubility, we iteratively refined the weights of amino acid residues using the Nelder-Mead optimisation algorithm (Nelder and Mead 1965) . To understand the properties of soluble and insoluble proteins, we determined the enrichment of amino acid residues in the PSI:Biology targets relative to the eSOL sequences (see Methods). doi = 10.1101/2020.02.15.951012 id = cord-259261-fmuozy3w author = Bickler, Stephen W. title = AGE IS ASSOCIATED WITH INCREASED EXPRESSION OF PATTERN RECOGNITION RECEPTOR GENES AND ACE2, THE RECEPTOR FOR SARS-COV-2: IMPLICATIONS FOR THE EPIDEMIOLOGY OF COVID-19 DISEASE date = 2020-06-16 keywords = PRR; SARS summary = title: AGE IS ASSOCIATED WITH INCREASED EXPRESSION OF PATTERN RECOGNITION RECEPTOR GENES AND ACE2, THE RECEPTOR FOR SARS-COV-2: IMPLICATIONS FOR THE EPIDEMIOLOGY OF COVID-19 DISEASE Using a large dataset of genome-wide RNA-seq profiles derived from human dermal fibroblasts (GSE113957) we investigated whether age affects the expression of pattern recognition receptor (PRR) genes and ACE2, the receptor for SARS-CoV-2. We also asked the question if the differentially expressed genes between the oldest and youngest age groups encode proteins that interact with SARS-CoV-2 (see "Methods" section). Our analysis revealed eleven differentially expressed genes between the oldest and youngest age groups that encode proteins known to interact with SARS-CoV-2 (Fig. 3d) . Using a large dataset of genome-wide RNA-seq profiles derived from human dermal fibroblasts we show that expression of PRR genes and ACE2, the receptor for SARS-CoV-2 vary with age. doi = 10.1101/2020.06.15.134403 id = cord-265453-z6aux01t author = Bierig, Tobias title = Design, expression, purification and characterization of a YFP-tagged 2019-nCoV spike receptor-binding domain construct date = 2020-09-29 keywords = NTA; YFP summary = The receptor-binding domain (RBD) of the 2019-nCoV spike (S) protein contains disulfide bonds and N-linked glycosylations, therefore, it is typically produced by secretion. Here, we describe a construct and protocol for the expression and purification of yellow fluorescent protein (YFP) labeled 2019-nCoV spike RBD. The fusion protein, in the vector pcDNA 4/TO, comprises an N-terminal interferon alpha 2 (IFNα2) signal peptide, an eYFP, a FLAG-tag, a human rhinovirus 3C protease cleavage site, the RBD of the 2019-nCoV spike protein and a C-terminal 8x His-tag. Our experiments confirmed that the fusion protein (also after proteolytic removal of YFP) binds the human ACE2 peptidase domain. Ni-NTA IMAC After removal of detached cells by centrifugation, the expression medium containing the secreted fusion protein was supplemented with 1/4 tablet of protease inhibitor (complete EDTA-free protease inhibitor cocktail tablets, Roche Diagnostic GmbH, 45148300) and transferred to a 15 ml Falcon tube containing 200 l of washed, pre-equilibrated Ni-NTA agarose (Qiagen Cat. No. doi = 10.1101/2020.09.29.318196 id = cord-272513-umuiovrd author = Bindayna, Khalid Mubarak title = Variant analysis of SARS-CoV-2 genomes in the Middle East date = 2020-10-09 keywords = East; Middle; variant summary = We also aim to analyse the variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) to characterise the common genome variants and provide useful data in the global effort to prevent further spread of COVID-19. Methods The approach uses bioinformatics approaches including multiple sequence alignment, variant calling and annotation and phylogenetic analysis to identify the genomic variants found in the region. The approach uses 122 samples from the 13 countries of the Middle East sourced from the Global Initiative on Sharing All Influenza Data (GISAID). Variant alignment and phylogenetic tree generation indicates that samples from Iran likely introduced COVID-19 to the rest of the Middle East. • Our hypothesis is that variants found in SARS-CoV-2 genomes from Middle Eastern samples will indicate delivery from Iran. • The aim is to explore the structure of Middle Eastern genome strains using multiple sequence alignment, tree generation and variant prediction (and others). doi = 10.1101/2020.10.09.332692 id = cord-103301-v4l9sovt author = Bloom, David C. title = Immunization by replication-competent controlled herpesvirus vectors date = 2018-04-11 keywords = HSV; replication summary = We found that localized activation in 8 mice of efficient but limited replication of a replication-competent controlled herpesvirus 9 vector resulted in a greatly enhanced immune response to the virus or an expressed 10 heterologous antigen. We found that localized activation in 8 mice of efficient but limited replication of a replication-competent controlled herpesvirus 9 vector resulted in a greatly enhanced immune response to the virus or an expressed 10 heterologous antigen. HSV-GS7 replication was also tightly controlled in vivo, two of three groups of mice 8 were administered HSV-GS7 virus (50,000 pfu per mouse) to the footpad, and the mice 9 of one of the latter groups were given ulipristal intraperitoneally (i,p.) as well as, 3 h 10 later, were subjected to a heat treatment to the footpads at 45 0 C for 10 min. doi = 10.1101/299230 id = cord-313910-bwe2f7xf author = Bojadzic, Damir title = Small-Molecule In Vitro Inhibitors of the Coronavirus Spike – ACE2 Protein-Protein Interaction as Blockers of Viral Attachment and Entry for SARS-CoV-2 date = 2020-10-22 keywords = DRI; PPI; SARS summary = Among promising candidates identified, several dyes (Congo red, direct violet 1, Evans blue) and novel drug-like compounds (DRI-C23041, DRI-C91005) inhibited the interaction of hACE2 with the spike proteins of SARS-CoV-2 as well as SARS-CoV with low micromolar activity in our cell-free ELISA-type assays (IC50s of 0.2-3.0 μM); whereas, control compounds, such as sunset yellow FCF, chloroquine, and suramin, showed no activity. We were able to set up a cell-free ELISA-type assay to quantify the binding of SARS-CoV-2 S protein (as well as its SARS-CoV analog) to their cognate receptors (human ACE2) and used this to screen our existing in-house compound library containing a large variety of organic dyes and a set of colorless analogs prepared as potential SMIs for costimulatory PPIs. These maintain the main molecular framework of dyes but lack the aromatic azo chromophores responsible for the color as they are replaced with amide linkers (58, 59). doi = 10.1101/2020.10.22.351056 id = cord-102321-csdezu6y author = Booeshaghi, A. Sina title = Normalization of single-cell RNA-seq counts by log(x+1)* or log(1+x)* date = 2020-10-14 keywords = ACE2 summary = log(1+x) count normalization introduces errors for lowly expressed genes The average log(1+x) expression differs considerably from log(x) when x is small An alternative approach is to use the fraction of cells with non-zero expression As is common in single-cell RNA-seq, the expression estimates of ACE2 are derived from counts that are filtered and normalized. While single-cell RNA-seq expression data has been modeled with many different distributions [4, 5] , for simplicity in illustrating our points we model this count data with a simple Poisson random variable X with parameter λ in order to demonstrate the implications of this restriction. Since f is approximately equal to this expression when f is small, this provides an interpretation of the fraction of cells with at least one copy of a low-abundance gene as an estimate of the rate parameter λ in a Poisson distribution. doi = 10.1101/2020.05.19.100214 id = cord-102551-8igfuaw2 author = Boonyaratanakornkit, Jim title = Protective Antibodies Against Human Parainfluenza Virus Type 3 (HPIV3) Infection date = 2020-10-30 keywords = Fig; HPIV3; RSV; Thermo; pi3-e12 summary = HPIV3, like respiratory syncytial virus (RSV), infects early in life and frequently causes severe bronchiolitis and pneumonia in infants under six months of age who are unable to mount a robust antibody response 2,3 . HPIV3 F was recently stabilized in the preF conformation and induced higher serum neutralizing titers than the HPIV3 postF To focus upon B cells producing neutralizing antibodies, we modified our assay to sort individual B cells onto irradiated 3T3 feeder cells expressing CD40L, IL-2, and IL-21 to allow for higher throughput screening of culture supernatants for neutralization prior to antibody cloning, as described 27 . Using this approach, we found that 14% of IgD -HPIV3 preF-binding B cells sorted from tonsils produced HPIV3 neutralizing antibodies, as compared to 5% from the spleen and 2% from peripheral blood (Fig. 3b) . doi = 10.1101/2020.06.15.153478 id = cord-271970-i35pic5o author = Boris, Bonaventure title = A genome-wide CRISPR/Cas9 knock-out screen identifies the DEAD box RNA helicase DDX42 as a broad antiviral inhibitor date = 2020-10-28 keywords = HIV-1; IFN; cell; ddx42; figure summary = Depletion of endogenous DDX42 using siRNA or CRISPR/Cas9 knock-out increased HIV-1 infection, both in model cell lines and in physiological targets of HIV-1, primary CD4+ T cells and monocyte-derived macrophages (MDMs), and irrespectively of the IFN treatment. Deep sequencing analysis of the GeCKO cell populations showed more than 94% coverage for both libraries (≥ 10 reads for 61,598 and 54,609 sgRNA-coding sequences out of GeCKO populations were subjected to type 1 IFN treatment in order to induce the antiviral state and, 24h later, incubated with VSV-G-pseudotyped, HIV-1 based LVs coding for an antibiotic resistance cassette. In order to validate the effect of DDX42 KO on HIV-1 infection in another model cell line, two additional sgRNAs were designed (sgRNA-2 and -3) and used in parallel to the one identified in the GeCKO screen (sgDDX42-1) (Figure 2A ). doi = 10.1101/2020.10.28.359356 id = cord-326736-jd6fvaop author = Bosco-Lauth, Angela M. title = Pathogenesis, transmission and response to re-exposure of SARS-CoV-2 in domestic cats date = 2020-05-29 keywords = SARS summary = title: Pathogenesis, transmission and response to re-exposure of SARS-CoV-2 in domestic cats Due to concern for human-pet transmission, we investigated the susceptibility of domestic cats and dogs to infection and potential for infected cats to transmit to naïve cats. These studies confirm that cats are susceptible to productive SARS-CoV-2 infection, but are unlikely to develop clinical disease. There is currently no evidence that cats or dogs play a significant role in human exposure; however, reverse zoonosis is possible if infected owners expose their domestic pets during acute infection. The first report of reverse zoonosis, or transmission from human to animal, was reported 46 from Hong Kong, where a COVID patient''s dog tested PCR positive for SARS2 multiple times 47 (Sit et al. Absence of SARS-CoV-2 infection in cats and dogs in close contact with a cluster of 414 COVID-19 patients in a veterinary campus Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2 Transmission of 422 SARS-CoV-2 in Domestic Cats doi = 10.1101/2020.05.28.120998 id = cord-102449-6foh1uvn author = Bosker, Hans Rutger title = Beat gestures influence which speech sounds you hear date = 2020-07-13 keywords = Experiment; gesture; syllable summary = doi = 10.1101/2020.07.13.200543 id = cord-336560-m5u6ryy9 author = Boudewijns, Robbert title = STAT2 signaling as double-edged sword restricting viral dissemination but driving severe pneumonia in SARS-CoV-2 infected hamsters date = 2020-07-02 keywords = Fig; RNA; SARS; STAT2; lung summary = Our results reveal the importance of STAT2-dependent interferon responses in the pathogenesis and virus control during SARS-CoV-2 infection and may help rationalizing new strategies for the treatment of COVID-19 patients. The lack of readily accessible serum markers or the absence of overt disease symptoms in hamsters prompted us to establish a non-invasive means to score for lung infection and SARS-CoV-2 induced lung disease by computed tomography (CT) as used in standard patient care to aid COVID-19 diagnosis with high sensitivity and monitor progression/recovery 7, 33, 35, 36 . Similar as in humans 37 , semiquantitative lung pathology scores were obtained from high-resolution chest micro-CT scans of freebreathing animals 38 The increase in replication of SARS-CoV-2 seen in IL28R-a -/hamsters, on one hand, combined with a tempered inflammatory response and lung injury as compared to WT hamsters, on the other hand, is in line with the role of type III IFN plays during respiratory virus infections, including SARS-CoV-1 53 . doi = 10.1101/2020.04.23.056838 id = cord-300707-k9uk14b3 author = Bouwman, Kim M. title = Multimerization- and glycosylation-dependent receptor binding of SARS-CoV-2 spike proteins date = 2020-09-04 keywords = RBD; SARS summary = Here we created monomeric and trimeric fluorescent RBD proteins, derived from adherent HEK293T, as well as in GnTI mutant cells, to analyze the effect of complex vs high mannose glycosylation on receptor binding. Our results show that fully glycosylated trimeric RBD proteins are attractive to analyze receptor binding and explore ACE2 expression profiles in tissues. The results demonstrate 104 that fully glycosylated trimeric SARS-CoV-2 RBD proteins reveal the 105 differences in ACE2 expression between cell cultures and tissue sections. A similar trend of binding intensities was observed for 214 monomeric, trimeric, and different N-glycosylated SARS-CoV-RBD proteins 215 fused to mOrange2 ( Fig S3A) . 226 227 To confirm our observations of different binding on tissues, we quantified the 228 intensities of the ACE2 antibody and SARS-CoV-1 and -2 RBD proteins, except 229 for the monomeric GnTI derived proteins as these were almost at the 230 background ( Fig 4D) . doi = 10.1101/2020.09.04.282558 id = cord-279474-c5y2lygj author = Bozzo, Caterina Prelli title = IFITM proteins promote SARS-CoV-2 infection of human lung cells date = 2020-08-18 keywords = IFITM; SARS summary = Interferon-induced transmembrane proteins (IFITMs 1, 2 and 3) restrict numerous viral pathogens and are thought to prevent infection by severe acute respiratory syndrome coronaviruses (SARS-CoVs). In striking contrast, however, endogenous IFITM expression promoted genuine SARS-CoV-2 infection in human lung cells both in the presence and absence of interferon. Taken together, our results show that all three IFITMs prevent SARS-CoV-2 S/ACE2-mediated attachment and membrane fusion in single round pseudotype infection assays. Notably, titration experiments showed that IFITMs do not promote genuine SARS-CoV-2 247 infection in HEK239T cells over a broad range of expression levels ( Figure S4E ). (F) Quantification of the entry of VSV(luc)ΔG*-SARS-CoV-2-S by luciferase activity in HEK293T cells transiently expressing indicated proteins (IFITM mutants) and infected 24 h post-transfection with the VSVpp (MOI 0.025) for 16 h. (G) Quantification of the entry of HIV(Fluc)Δenv*-SARS-CoV-2-S by luciferase activity in HEK293T cells stably expressing indicated proteins (IFITM mutants) and ACE2 doi = 10.1101/2020.08.18.255935 id = cord-102530-wetqqt2i author = Brandell, Ellen E. title = The rise of disease ecology date = 2020-07-17 keywords = disease; ecology; topic summary = The steady increase in topics such as climate change, and emerging infectious diseases, superspreaders indicate that disease ecology as a field of research will continue advancing our understanding of complex host-pathogen interactions and forms a critical and adaptable component of the global response to emergent health and environmental threats. In addition 164 to topics that emerged from the literature, we also generated and assessed our own topic lists based on key research areas, such as climate change, dilution effect, superspreaders, network 166 analysis, EIDs, bovine tuberculosis, infectious diseases in bats and rodents, and chytrid fungus 167 ( Fig. 4) . Using key term searches, we next explored select topic trends: climate change, emerging 293 infectious diseases (EIDs), the dilution effect, superspreaders, network analysis, pathogens in 294 rodents and bats, bovine tuberculosis, and chytrid fungus in amphibians (Fig. 4B) . doi = 10.1101/2020.07.16.207100 id = cord-260793-bb4h255w author = Brann, David H. title = Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia date = 2020-05-18 keywords = ACE2; SARS; TMPRSS2; cell; figure; gene; olfactory; type summary = doi = 10.1101/2020.03.25.009084 id = cord-290694-jmav8xi4 author = Bridgland, Victoria M. E. title = Why the COVID-19 pandemic is a traumatic stressor date = 2020-09-22 keywords = covid-19 summary = The COVID-19 pandemic does not fit into prevailing Post-traumatic Stress Disorder (PTSD) models, or diagnostic criteria, yet emerging research shows traumatic stress symptoms as a result of this ongoing global stressor. Nevertheless, among a sample of online participants (N = 1,040) in five western countries, we found participants had PTSD-like symptoms for events that had not happened and when participants had been directly (e.g., contact with virus) or indirectly exposed to COVID-19 (e.g., via media). Posttraumatic Stress Disorder Checklist-5 (PCL-5 (22)), adapted to measure pre/peri/post-145 traumatic reactions, and measures of general emotional reactions, well-being, psychosocial 146 functioning, and depression, anxiety, and stress symptoms. We then re-presented the 209 same list of events, but asked participants to select events they were concerned about 210 happening in the future ("other" events led to three additional categories [seven responses The PTSD Checklist (PCL-5 (22)). doi = 10.1101/2020.09.22.307637 id = cord-328189-jpkxjn6e author = Brielle, Esther S. title = The SARS-CoV-2 exerts a distinctive strategy for interacting with the ACE2 human receptor date = 2020-03-12 keywords = ACE2; RBD summary = We compare the interaction between the human ACE2 receptor and the SARS-CoV-2 spike protein with that of other pathogenic coronaviruses using molecular dynamics simulations. Herein, we analyze the binding of several CoV RBDs to ACE2 with molecular dynamics (MD) simulations and compare the stability, relative interaction strength, and dynamics of the interaction between the viral spike protein and the human ACE2 receptor. While the sequence identity between the RBDs of COVID-19 and SARS-2002 is 73% (Table 1) , we observe a significantly higher residue substitution rate at the interaction interface with the ACE2 receptor. Our MD simulation analysis reveals that the SARS-des has a substantially lower interaction scores with ACE2 (median of -2199.2, Fig. S2) , as expected for an optimized human ACE2-binding RBD design. We relied on the crystal structure of the spike protein receptor-binding domain from a SARS coronavirus designed human strain complexed with the human receptor ACE2 (PDB 3SCI, resolution 2.9Å) as a template for comparative modeling. doi = 10.1101/2020.03.10.986398 id = cord-103511-31njndob author = Broggi, Achille title = Type III interferons disrupt the lung epithelial barrier upon viral recognition date = 2020-05-05 keywords = Fig; IFN; RNA summary = Accordingly, sorted lung resident dendritic cells express 192 high levels of IFN-λ transcript after 5 days of poly (I:C) treatment, in contrast to epithelial cells, 193 alveolar macrophages and monocytes (Fig. 4A) , which, instead, express inflammatory cytokines (Fig. S8A, B) . Moreover, diphtheria toxin (DT)-mediated depletion of 195 CD11c + cells in CD11c-DT receptor (DTR) mice was sufficient to completely abolish IFN-λ 9 transcript and protein upregulation upon 6 days of poly (I:C) treatment (Fig. 4B, C) , while production remained unaltered (Fig. S8C with the response measured in vivo, TLR7 stimulation did not induce IFN production while it 207 induced upregulation of pro-inflammatory cytokines, and intracellular delivery of poly (I:C) induced 208 high levels of IFN-I but not IFN-λ (Fig.4D, Fig. S9A , B). Dendritic cells sorted from Ticam1 -/mice treated with poly (I:C) for six 222 days did not express appreciable levels of IFN-λ transcripts while still produced type I interferons 223 ( Fig. 4E, F) . doi = 10.1101/2020.05.05.077867 id = cord-312038-g76cpjp7 author = Brunaugh, Ashlee D. title = Broad-Spectrum, Patient-Adaptable Inhaled Niclosamide-Lysozyme Particles are Efficacious Against Coronaviruses in Lethal Murine Infection Models date = 2020-10-07 keywords = COVID-19; DPI; Fig; MERS; NIC; SARS; hlys summary = Utilizing repurposed NIC, and with the goal of developing a therapeutically effective, rapidly scalable and globally distributable antiviral therapy to reduce the spread of SARS-CoV-2, we describe an inhalable NIC formulation that can be administered using three major models or respiratory tract delivery systems: DPI, nasal spray and nebulizer. At the highest dose tested (0.125 µg/mL NIC), Vero cells with an established MERS-CoV infection exhibited an 82.2% ± 0.8% decrease in viral load compared to untreated controls after 24-hours of exposure to NIC-hLYS particles ( Fig 1D) . While brain viral titres did not exhibit further reduction from levels noted in the preliminary efficacy study, the inoculation of Vero E6 cells with viral particles obtained from lung and brain homogenates of surviving animals resulted in no observation of CPE at any of the inoculum concentrations tested, which indicates that remaining viral particles were not active. doi = 10.1101/2020.09.24.310490 id = cord-298716-pubhq564 author = Bryche, Bertrand title = Massive transient damage of the olfactory epithelium associated with infection of sustentacular cells by SARS-CoV-2 in golden Syrian hamsters date = 2020-06-16 keywords = Fig; SARS summary = title: Massive transient damage of the olfactory epithelium associated with infection of sustentacular cells by SARS-CoV-2 in golden Syrian hamsters Anosmia observed in COVID-19 patient is therefore likely to be linked to a massive and fast desquamation of the OE following sustentacular cells infection with SARS-CoV-2 and subsequent recruitment of immune cells in the OE and lamina propria. We measured the OE thickness, the OSN cilia quality (based on Golf staining) and the immune cell infiltration of the olfactory mucosa (based on the Iba1 staining) on 6 images per animal taken from 3 different slides spread along the nasal cavity. Two recent reports indicate that olfactory neurons in hamster (Sia et al., 2020) and respiratory cells in ferret (Ryan et al., 2020) may be the target of SARS-CoV-2 but these studies did not focus on the nasal cavity and they did not use double staining to clearly identify the infected cells in the OE. doi = 10.1101/2020.06.16.151704 id = cord-325432-geb4esu5 author = Bukreyeva, Natalya title = The IMPDH inhibitor merimepodib suppresses SARS-CoV-2 replication in vitro date = 2020-04-09 keywords = MMPD summary = Drugs with history of being tested in human patients or used for treatment of other conditions offer the most expedient option, and several such drugs are currently being tested for efficacy against SARS-CoV-2, including many broad-spectrum antivirals. One such antiviral, merimepodib (MMPD), has already being tested against hepatitis C in patients as well as against many emerging RNA viruses in cell culture, including Zika, Ebola, Lassa, Junin, and chikungunya viruses (1) . Early work suggests that IMPDH may directly interact with SARS-CoV-2 nsp13, perhaps indicating that drugs targeting IMPDH such as MMPD might have an impact on viral replication (5) . Our results show that MMPD can inhibit SARS-CoV-2 replication at low concentrations. Further work is needed to characterize the full mechanism behind MMPD inhibition of SARS-CoV-2 as well as its efficacy in animal models of corona virus infections. Merimepodib, an IMPDH inhibitor, suppresses replication of Zika virus and other emerging viral pathogens doi = 10.1101/2020.04.07.028589 id = cord-102918-bkyk7or9 author = Burns, C. Sean title = Methodological Issues with Search in MEDLINE: A Longitudinal Query Analysis date = 2020-05-22 keywords = MEDLINE; search summary = This study compares the results of data collected from a longitudinal query analysis of the MEDLINE database hosted on multiple platforms that include PubMed, EBSCOHost, Ovid, ProQuest, and Web of Science in order to identify variations among the search results on the platforms after controlling for search query syntax. The variation is due to trends in scholarly publication that include publishing online first versus publishing in journal issues, which leads to metadata differences in the bibliographic record; to differences in the level of specificity among search fields provided by the platforms; to database integrity issues that lead to large fluctuations in monthly search results based on the same query; and to database currency issues that arise due to when each platform updates its MEDLINE file. Specific bibliographic databases, like PubMed and MEDLINE, are used to inform clinical decision-making, create systematic reviews, and construct knowledge bases for clinical decision support systems. Comparing the coverage, recall, and precision of searches for 120 systematic reviews in Embase, MEDLINE, and Google Scholar: a prospective study doi = 10.1101/2020.05.22.110403 id = cord-287372-ya5uvoki author = Böszörményi, Kinga P. title = Comparison of SARS-CoV-2 infection in two non-human primate species: rhesus and cynomolgus macaques date = 2020-11-05 keywords = RNA; SARS; macaque summary = This study provides a detailed description of the pathogenesis of a low-passage SARS-CoV-2 isolate in two macaque models and suggests that both species represent an equally good model in research for both COVID-19 prophylactic and therapeutic treatments. Rhesus macaques have also been applied 116 in COVID-19 pathogenesis studies [22, 24, 32, 33] , and to test the efficacy of remdesivir in the 117 treatment of SARS-CoV-2 infection [34] . we compared SARS-CoV-2 replication in rhesus and cynomolgus macaque species and 129 monitored signs of COVID-19-like disease symptoms for three weeks after infection. The animals from this study were not 342 euthanized to be able to perform re-infection studies or to monitor them for late clinical signs, 343 or co-morbidities related to We conclude that the course of SARS-CoV-2 infection of both macaque species is highly 345 similar, indicating that they are equally suitable models to test vaccines and antivirals in a 346 preclinical setting for safety and efficacy. doi = 10.1101/2020.11.05.369413 id = cord-102916-t2lcd300 author = Cai, Guoshuai title = SCANNER: A Web Resource for Annotation, Visualization and Sharing of Single Cell RNA-seq Data date = 2020-07-14 keywords = SCANNER; cell summary = title: SCANNER: A Web Resource for Annotation, Visualization and Sharing of Single Cell RNA-seq Data Also, it is equipped with multiple data interfaces for easy data sharing and currently provide a database for studying the smoking effect on single cell gene expression in lung. Contact GCAI@mailbox.sc.edu or XIAOF@mailbox.sc.ecu Key Points SCANNER provides a new web server resource for promoting scRNA-seq data analysis SCANNER enables comprehensive and dynamic analysis and visualization, novel functional annotation and activeness inference, online databases and easy data sharing. In this study, we developed the Single Cell Transcriptomics Annotated Viewer (SCANNER), as a public web resource for scRNA-seq data management, analysis and interpretation in a comprehensive, flexible and collaborative manner. Exploring our database of smoking lung, we found that the gene of the SARS-CoV-2 receptor, ACE2, is mainly expressed in pneumocytes, secretory cells and ciliated cells (Fig. S6) , which is consistent with the recent study of Ziegler et al. doi = 10.1101/2020.01.25.919712 id = cord-295257-iguhy1z8 author = Calcagnile, Matteo title = ACE2 polymorphisms and individual susceptibility to SARS-CoV-2 infection: insights from an in silico study date = 2020-04-24 keywords = ACE2; Fig; SARS; Spike summary = SARS-CoV-2 and respiratory syndrome corona virus (SARS-CoV) Spike proteins share very high phylogenetic similarities (99%), and, indeed, both viruses exploit the same human cell receptor namely angiotensin-converting enzyme 2 (ACE2), a transmembrane enzyme whose expression dominates on lung alveolar epithelial cells 6, 15, 16 . In this study we have used a combination of in silico tools to analyze the possible impact of ACE2 single-nucleotide polymorphisms (SNPs) on the interaction with SARS-CoV-2 Spike glycoprotein. Results indicate that some residues of the ACE2 interface, which are involved in the interaction with SARS-CoV-2 Spike glycoprotein can actually fluctuate (Fig. 5cd ). Indeed, in the rodent blockade of the renin-angiotensin-aldosterone system limits the acute lung injury induced by the SARS-CoV-1 spike protein 49 , suggesting that if ACE2 function is preserved (because of increased baseline expression, as especially seen in pre-menopausal women), clinical course of infection might be less severe. doi = 10.1101/2020.04.23.057042 id = cord-270049-54t3w94z author = Campione, Elena title = Pleiotropic effect of Lactoferrin in the prevention and treatment of COVID-19 infection: randomized clinical trial, in vitro and in silico preliminary evidences date = 2020-08-17 keywords = MOI; SARS summary = We performed a randomized, prospective, interventional study assessing the role of oral and intra-nasal lactoferrin to treat mild-to-moderate and asymptomatic COVID-19 patients to prevent disease evolution. The antiviral activity of lactoferrin related to its binding to SARS-CoV-2 and cells and protein-protein docking methods, provided the direct recognition between lactoferrin and spike S, thus hindering the spike S attachment to the human ACE2 receptor and consequently virus entering into the cells. 222 We performed the same analysis over the evaluated human lactoferrin (hLF)-Spike complex, 223 obtaining a binding pose superimposable to that observed for the bovine protein (Fig. 5B) . Clinical trial 397 We performed a randomized, prospective, interventional study to assess the efficacy of a liposomal Blood parameters obtained at T0 in COVID-19 group and control group were compared using t-test. doi = 10.1101/2020.08.11.244996 id = cord-273613-cpiveo7j author = Cao, Xia title = Discovery and Development of Human SARS-CoV-2 Neutralizing Antibodies using an Unbiased Phage Display Library Approach date = 2020-09-29 keywords = SARS; STI-1499; STI-2020; Spike summary = Following functional profiling in vitro against an early pandemic isolate as well as a recently emerged isolate bearing the D614G Spike mutation, the clinical candidate antibody, STI-1499, and the affinity-engineered variant, STI-2020, were evaluated for in vivo efficacy in the Syrian golden hamster model of COVID-19. Affinity maturation of STI-1499 resulted in identification of STI-2020, an antibody with a 35-fold increased affinity for the SARS-CoV-2 Spike receptor-binding domain (RBD) leading to a greater than 50-fold increase in virus neutralization potency against live WA-1/2020 and 2020001 viruses in vitro. In this study, we detail the initial discovery and profiling of a SARS-CoV-2 nAb isolated from a phage display antibody library derived from the B-cell repertoire of over 600 healthy normal individuals. Candidate nAbs were characterized for binding of Spike S1 subunit and neutralization of related clinical SARS-CoV-2 isolates. doi = 10.1101/2020.09.27.316174 id = cord-272986-ebgusf3o author = Cao, Yipeng title = Computational Study of Ions and Water Permeation and Transportation Mechanisms of the SARS-CoV-2 Pentameric E Protein Channel date = 2020-05-17 keywords = SARS; ion; protein summary = title: Computational Study of Ions and Water Permeation and Transportation Mechanisms of the SARS-CoV-2 Pentameric E Protein Channel (SARS-CoV) In this study, we provide insights into the function of the SARS-CoV-2 E protein channel and the ion and water permeation mechanisms on the basis of combined in silico methods. Overall, these results provide structural-basis insights and molecular-dynamic information that are needed to understand the regulatory mechanisms of ion permeability in the pentameric SARS-CoV-2 E protein channel. We tried to use potential mean force (PMF) to reveal the permeability of different physiological ions and water molecules in the pores of the E protein pentamer. Figure 3A shows the PMF of ions and water molecules permeating through the SARS-CoV-2 E protein pentamer pore. The free energy calculation of the ions permeating through the SARS-CoV-2 pentameric E protein channel strongly suggests that the pore has selection permeability for monovalent ions. doi = 10.1101/2020.05.17.099143 id = cord-102178-ju826pao author = Carey, Clayton M. title = Conflicts with diarrheal pathogens trigger rapid evolution of an intestinal signaling axis date = 2020-03-30 keywords = buffer; figure summary = Under normal conditions, GC-C interacts with endogenous guanylin peptides to promote water secretion in the intestine, but signaling can be hijacked by bacterially-encoded heat-stable enterotoxins (STa) during infection, which leads to overstimulation of GC-C and diarrhea. Phylogenetic analysis in mammals revealed evidence of recurrent positive selection in the GC-C ligand-binding domain in primates and bats, consistent with selective pressures to evade interactions with STa. Using in vitro assays and transgenic intestinal organoids to model STa-mediated diarrhea, we show that GC-C diversification in these lineages results in substantial variation in toxin susceptibility. Under normal conditions, GC-C activity is stimulated by interactions with the endogenous peptides guanylin and uroguanylin, leading to an increase in intracellular cGMP levels in enterocytes lining the small intestine and colon 3 ( Figure 1A ). To test if rapid evolution of GC-C ligand-binding domains result in functional differences in STa susceptibility, we generated cell lines stably expressing GC-C from seven primate and five bat species. doi = 10.1101/2020.03.29.014761 id = cord-103460-5thh6syt author = Carlson, Colin J. title = Climate change will drive novel cross-species viral transmission date = 2020-07-14 keywords = bat; viral summary = In addition, changing climate and land use are already driving geographic range shifts in wildlife, producing novel species assemblages and opportunities for viral sharing between previously isolated species4,5. Here, we map potential hotspots of viral sharing, using a phylogeographic model of the mammal-virus network, and projections of geographic range shifts for 3,870 mammal species under climate change and land use scenarios for the year 2070. Range-shifting mammal species are predicted to aggregate at high elevations, in biodiversity hotspots, and in areas of high human population density in Asia and Africa, driving the cross-species transmission of novel viruses at least 4,000 times. Even with dispersal limits, these first encounters are predicted to produce al-207 most one hundred new viral sharing events (RCP 2.6: 96 ± 2.3; RCP 8.5: 86 ± 3.9) that might 208 include ZEBOV, and which cover a much broader part of Africa than the current zoonotic niche 209 of Ebola 68 . doi = 10.1101/2020.01.24.918755 id = cord-324892-mg2dziuw author = Carneiro, João title = CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2 date = 2020-06-12 keywords = SARS summary = The first SARS-CoV-2 genomic sequences already showed novel mutations, which may affect the efficiency of available screening tests leading to false-negative diagnosis or inefficient therapeutics. Here we describe the CoV2ID (http://covid.portugene.com/), a free database built to facilitate the evaluation of molecular methods for detection of SARS-CoV-2 and treatment of COVID-19. The database evaluates the available oligonucleotide sequences (PCR primers, RT-qPCR probes, etc.) considering the genetic diversity of the virus. Evaluation of a quantitative RT-PCR assay for the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay Development of a Novel, Genome Subtraction-Derived, SARS-CoV-2-Specific COVID-19-nsp2 Real-Time RT-PCR Assay and Its Evaluation Using Clinical Specimens doi = 10.1101/2020.04.19.048991 id = cord-103271-l9n27ocf author = Carozza, Jacqueline A title = Structure-aided development of small molecule inhibitors of ENPP1, the extracellular phosphodiesterase of the immunotransmitter cGAMP date = 2020-05-31 keywords = ENPP1; Fig; compound; inhibitor summary = Cancer cells initiate an innate immune response by synthesizing and exporting the small molecule immunotransmitter cGAMP, which activates the anti-cancer Stimulator of Interferon Genes (STING) pathway in the host. Inspired by the molecular scaffold of a previous inhibitor, QS1, 26, 28 which lacks potency at physiological conditions, we build structure-activity relationships (SAR) around the three sections of the molecule -the zinc-binding head, the core, and the tail -and develop several inhibitors with nanomolar Ki values. Assays used to assess the potency of previously attempted ENPP1 inhibitors are inconsistent 26-34 ; however, developing an appropriate assay is key to determining the utility of the molecules in inhibiting cGAMP degradation under physiological conditions. Since our crystal structure suggests that the zinc-binding phosphonate head and quinazoline tail form the most important interactions with ENPP1, we next sought to explore the core region to achieve optimal geometry between these two functional groups ( Fig. 4a-b) . doi = 10.1101/2020.05.30.125534 id = cord-355397-y69bk5jc author = Caruso, Ícaro P. title = Dynamics of the N-terminal domain of SARS-CoV-2 nucleocapsid protein drives dsRNA melting in a counterintuitive tweezer-like mechanism date = 2020-09-06 keywords = NTD; RNA; figure summary = Here, we used molecular dynamics (MD) simulations to study the binding of SARS-CoV-2 N-NTD to non-specific (NS) and TRS dsRNAs. We probed dsRNAs'' Watson and Crick (WC) base-pairing over 25 replicas of 100 ns MD simulations, showing that only one N-NTD of dimeric N is enough to destabilize dsRNAs, initiating melting. We calculated the structural model of the N-NTD:dsTRS complex based on the experimental data for the N-NTD interaction with a non-specific dsRNA (5''-CACUGAC-3'') (dsNS) (16) using the HADDOCK 2.2 server (20) . In contrast to the decrease in the number of intramolecular hydrogen bonds between the sense and anti-sense strands of dsRNAs (WC base-pairing) due to N-NTD binding, we observed an increase in the average number of intermolecular hydrogen bonds formed between the nitrogenous bases of dsTRS and N-NTD (protein-RNA interaction) along the 100 ns MD simulation, whereas for dsNS, this average value was constant ( Figure 3B top). doi = 10.1101/2020.08.24.264465 id = cord-260054-iihgc5nr author = Cavallo, Luigi title = D936Y and Other Mutations in the Fusion Core of the SARS-Cov-2 Spike Protein Heptad Repeat 1 Undermine the Post-Fusion Assembly date = 2020-06-08 keywords = HR1; SARS; fusion summary = 3D structures are now available from the Protein Data Bank (PDB) (21) for the SARS-CoV-2 S protein in the pre-fusion conformation, also bound to the ACE2 receptor (22) (23) (24) (25) (26) (27) (28) , and for the post-fusion core of its S2 subunit in the postfusion conformation (29) . We downloaded all the SARS-CoV-2 genomic sequences from the GISAID resource on April 21 st 2020, extracted from them 7,692 complete S protein sequences and identified all the point mutations occurring in at least two identical sequences (see Methods). When looking at the post-fusion conformation of the SARS-CoV-2 spike protein S2 subunit, these mutations appear more revealing. Based on a thorough analysis of the S protein sequences, that we extracted from the genomic sequences of SARS-CoV-2 reported in GISAID on April 21 st , we identified the fusion core of the HR1 as a mutational hotspot. doi = 10.1101/2020.06.08.140152 id = cord-332178-0xyrmk5a author = Chadchan, Sangappa B. title = The SARS-CoV-2 receptor, Angiotensin converting enzyme 2 (ACE2) is required for human endometrial stromal cell decidualization date = 2020-06-24 keywords = ACE2; Fig; SARS summary = title: The SARS-CoV-2 receptor, Angiotensin converting enzyme 2 (ACE2) is required for human endometrial stromal cell decidualization STUDY QUESTION Is SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE 2) expressed in the human endometrium during the menstrual cycle, and does it participate in endometrial decidualization? The ACE2 mRNA (P < 0.0001) and protein abundance increased during primary human endometrial stromal cell (HESC) decidualization. WIDER IMPLICATIONS OF THE FINDINGS Expression of ACE2 in the endometrium allow SARS-CoV-2 to enter endometrial epithelial and stromal cells, which could impair in vivo decidualization, embryo implantation, and placentation. Given the important function of the uterine stroma and the possibility that SARS-CoV-2 could infect the uterus, our goal here was to 101 determine whether ACE2 is expressed in endometrial stromal cells, is regulated by progesterone, 102 and is required for decidualization. Given the high ACE2 expression in the human 143 endometrium, SARS-CoV-2 may be able to enter endometrial stromal cells and elicit pathological 144 manifestations in women with COVID-19. doi = 10.1101/2020.06.23.168252 id = cord-326337-s0fp5z1q author = Chan, Kui K. title = An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants date = 2020-10-19 keywords = ACE2; RBD; SARS; figure summary = Deep mutagenesis of the isolated receptor-binding domain (RBD) by yeast surface display 44 has easily identified mutations in S that retain high expression and ACE2 affinity, yet are no longer bound 45 by monoclonal antibodies and confer resistance (19) . An alternative protein-based antiviral to monoclonal antibodies is to use soluble ACE2 (sACE2) as a 56 decoy to compete for receptor-binding sites on the viral spike (6, (22) (23) (24) (25) of diverse SARS-associated betacoronaviruses that use ACE2 for entry. The sequence 162 diversity observed among natural betacoronaviruses, which display high diversity at the ACE2 binding 163 site, is therefore replicated in the deep mutational scan, which predicts the SARS-CoV-2 spike tolerates 164 substantial genetic diversity at the receptor-binding site for function. From this accessible sequence 165 diversity SARS-CoV-2 might feasibly mutate to acquire resistance to monoclonal antibodies or 166 engineered decoy receptors targeting the ACE2-binding site. doi = 10.1101/2020.10.18.344622 id = cord-301535-eui41zyg author = Chandler-Brown, Devon title = A Highly Scalable and Rapidly Deployable RNA Extraction-Free COVID-19 Assay by Quantitative Sanger Sequencing date = 2020-04-10 keywords = GCE; RNA; SARS summary = This assay uses the addition of a frame-shifted spike-in, a modified PCR master mix, and custom Sanger sequencing data analysis to detect and quantify SARS-CoV-2 RNA at a limit of detection comparable to existing qPCR-based assays, at 10-20 genome copy equivalents. Crucially, our assay was able to detect SARS-CoV-2 RNA from viral particles suspended in transport media that was directly added to the PCR master mix, suggesting that RNA extraction can be skipped entirely without any degradation of test performance. Quantitative analysis of the Sanger sequence chromatogram gives qSanger an extremely high sensitivity and specificity for all positive results with a limit of detection of 10-20 genome copy equivalents (GCE), equivalent to gold-standard qPCR methods. To further evaluate the feasibility of a direct VTM, extraction-free method for Sars-CoV-2 detection, we also examined the ability of qSanger to quantify the amount of viral particles in the Seracare positive control specimens (Fig. 3B ). doi = 10.1101/2020.04.07.029199 id = cord-102366-2alcsd1p author = Cheek, Martin title = Taxonomic revision of the threatened African genus Pseudohydrosme Engl. (Araceae), with P. ebo, a new, Critically Endangered species from Ebo, Cameroon date = 2020-10-07 keywords = Cameroon; Cheek; Ebo; Gabon; Libreville; Pseudohydrosme summary = doi = 10.1101/2020.10.05.326850 id = cord-104025-ysxc7rpl author = Cheek, Martin title = Deinbollia onanae (Sapindaceae), a new, Endangered, montane tree species from the Cameroon Highlands date = 2020-10-26 keywords = Cameroon; Cheek; Deinbollia; Highlands summary = title: Deinbollia onanae (Sapindaceae), a new, Endangered, montane tree species from the Cameroon Highlands Deinbollia onanae is an infrequent tree species known from five locations in surviving islands of montane (or upper submontane) forest along the line of the Cameroon Highlands. As part of the project to designate Important Plant Areas (IPAs) in Cameroon (also known as Tropical Important Plant Areas or TIPAs), we are striving to name, assess the conservation status and include in IPAs (Darbyshire et al., 2017) rare and threatened plant species in the surviving, threatened natural habitat of the Cross-Sanaga interval (Cheek et al., 2001) . Apart from Deinbollia onanae, the only other montane tree species endemic to the Cameroon Highland chain are the nearly extinct Ternstroemia cameroonensis Cheek (Cheek et al., 2017) and the more common and widespread Schleffera mannii (Hook.f.)Harms (Keay, 1958) . doi = 10.1101/2020.10.24.353680 id = cord-276017-2375ipkk author = Chen, Dongsheng title = Single-cell screening of SARS-CoV-2 target cells in pets, livestock, poultry and wildlife date = 2020-06-14 keywords = ACE2; SARS summary = Notably, the proportion of SARS-CoV-2 target cells in cat was found considerably higher than other species we investigated and SARS-CoV-2 target cells were detected in multiple cell types of domestic pig, implying the necessity to carefully evaluate the risk of cats during the current COVID-19 pandemic and keep pigs under surveillance for the possibility of becoming intermediate hosts in future coronavirus outbreak. Previous studies have proposed that animal tissues show high heterogeneity in terms of cellular composition and gene expression profiles 15 , and ACE2 is only expressed in a small proportion of specific cell populations 16 , making single cell analysis of SARS-CoV-2 target cells an attracting field to investigate. Here, we constructed the single cell atlas for livestock, poultry, pets and wildlife, then screened putative SARS-CoV-2 target cells (indicated by the co-expression patterns of SARS-CoV-2 entry receptor ACE2 and SARS-CoV-2 entry activator TMPRSS2) and systematically evaluated their susceptibility, with the aim to understand the virus transmission routes and provide clues to fight against COVID-19. doi = 10.1101/2020.06.13.149690 id = cord-314321-klb8oe9q author = Chen, Serena H. title = Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets date = 2020-04-18 keywords = SARS; protein; structure summary = Recent experimental structures of the SARS-CoV-2 S protein receptor binding domain (RBD) in complex with ACE2 provide detailed interface information [4] , [6] ; targeting this interface represents an active area of research for therapeutic development [11] . By first comparing the S protein protomer structure of SARS-CoV-2 to those from previous human coronaviruses, we identified distinct clusters for each virus in the 3-D latent space, where representative structures from these clusters highlight their differences in domain flexibility. To further understand the molecular structures of different human coronavirus S proteins and the oligomeric state of SARS-CoV-2 S protein, we deployed a custom-built deep learning architecture, a convolutional variational autoencoder (CVAE), to encode the high dimensional protein structures from the MD simulations into lower dimensional latent spaces. The size of each resulting matrix was also 191 ⇥ 191, and we merged a total of 10,000 distance matrices of the protomer and trimer of SARS-CoV-2 S protein. doi = 10.1101/2020.04.17.047548 id = cord-102226-aioqogaw author = Chiu, Elliott S. title = Presence of endogenous viral elements negatively correlates with FeLV susceptibility in puma and domestic cat cells date = 2020-06-24 keywords = LTR; cat; domestic summary = doi = 10.1101/2020.06.23.168351 id = cord-334891-4jgtxg07 author = Choudhury, Abhigyan title = In silico analyses on the comparative sensing of SARS-CoV-2 mRNA by intracellular TLRs of human date = 2020-11-11 keywords = RNA; SARS; figure summary = This study is hoped to rationalize the comparative binding and sensing of SARS-CoV-2 mRNA towards the intracellular TLRs, considering the solvent-based force-fields operational in the cytosolic aqueous microenvironment that predominantly drive these reactions. Our in-silico study on the binding of all mRNAs with the intracellular TLRs shown that the mRNA of NSP10, S2, and E proteins of SARS-CoV-2 are potent enough to bind with TLR3, TLR9, and TLR7 and trigger downstream cascade reactions, and may be used as an option for validation of therapeutic option and immunomodulation against COVID-19. The binding of Spike protein with the human ACE2 receptor triggers the pathogenesis 3 of the SARS-CoV-2, leading to the activation of TLRs to activate the proliferation and 4 production of pro-inflammatory cytokines causing cytokine storm, those results in 5 inflammations. doi = 10.1101/2020.11.11.377713 id = cord-309556-xv3413k1 author = Chow, Ryan D. title = The aging transcriptome and cellular landscape of the human lung in relation to SARS-CoV-2 date = 2020-04-15 keywords = SARS; age; cluster; figure; gene summary = In aggregate, these analyses showed that the age-associated genes with functional roles in SARS-CoV are expressed in specific cell types of the human lung. Of note, the overlap between lung ageassociated genes and SARS-CoV-2 regulated genes was statistically significant across all 3 cell lines (Figure 6d-f) , suggesting a degree of similarity between the transcriptional changes associated with aging and with SARS-CoV-2 infection. Among the age-associated genes that were induced by SARS-CoV-2 infection, the majority of these genes increase in expression with age (Cluster 1) (Figure 6g-i) . To identify a consensus set of age-associated genes that are regulated by SARS-CoV-2 infection, we integrated the analyses from all 3 cell lines. By integrating these data with single cell transcriptomes of human lung tissue, we further pinpointed the specific cell types that normally express the age-associated genes. doi = 10.1101/2020.04.07.030684 id = cord-328644-odtue60a author = Comandatore, Francesco title = Insurgence and worldwide diffusion of genomic variants in SARS-CoV-2 genomes date = 2020-05-28 keywords = Coronavirus; SARS; sequence; variant summary = These variants might arise during the spread of the epidemic, as viruses are known for their high frequency of mutation, particularly in single stranded RNA viruses -as in the case of SARS-CoV-2 (Sanjuán and Domingo-Calap 2016) , which has a single, positive-strand RNA genome. To have a better insight on the history and spread of the COVID-19 pandemic in Italy and thanks to the sequences deposited in the Gisaid database, we identified 7 non synonymous mutations that are differentially frequent in Italian SARS-CoV-2 strains respect to strains circulating globally. Our analysis allowed us to identify 7 positions in four proteins that present drastic changes in amino acid frequencies when comparing Italian sequences with worldwide sequences available on Gisaid.org on April, 10, 2020 ( Figure 1 ). doi = 10.1101/2020.04.30.071027 id = cord-103430-x6zzuu7v author = Contu, Lara title = Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay date = 2020-10-12 keywords = NMD; RNA; figure; protein; sfv summary = Among the many identified cellular interactors of SFV proteins, the enrichment of factors involved in translation and nonsense-mediated mRNA decay (NMD) was striking, reflecting the virus'' hijacking of the translation machinery and indicating viral countermeasures for escaping NMD by inhibiting NMD at later time points during the infectious cycle. Gene ontology (GO) enrichment analyses of protein complexes that could 10 form between the identified host interactors revealed highly significant GO terms related to 11 translation and Nonsense-mediated mRNA Decay (NMD). In addition to ribosomal proteins, many other RNA binding proteins were also 37 identified as having a potential role in SFV replication (Figure 3a (nsP1, nsP2, nsP3-Z, nsP4, capsid and Env) as well as for the merged list (All baits) was also applied. doi = 10.1101/2020.10.12.335497 id = cord-270919-0hldozml author = Cortey, Martí title = SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins date = 2020-05-17 keywords = SARS summary = title: SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic offers a unique opportunity to study the introduction and evolution of a pathogen into a completely naïve human population. At the moment of writing this paper, these mutations present a varied success in the SARS-CoV-2 virus population; ranging from a change in the spike protein that becomes absolutely prevalent, two mutations in the nucleocapsid protein showing frequencies around 25%, to a mutation in the matrix protein that nearly fades out after reaching a frequency of 20%. 54 The aim of the present study was to determine the amino acid substitutions in viral 55 proteins that were widely present in available sequences of SARS-CoV-2, relating them 56 to the known chronology of the pandemic. doi = 10.1101/2020.05.16.099499 id = cord-102158-5xg40s4o author = Coulibali, Zonlehoua title = Site-specific machine learning predictive fertilization models for potato crops in Eastern Canada date = 2020-03-12 keywords = nitrogen summary = doi = 10.1101/2020.03.12.988626 id = cord-311066-62edsbfc author = Cox, Brian J. title = Integration of viral transcriptome sequencing with structure and sequence motifs predicts novel regulatory elements in SARS-CoV-2 date = 2020-06-24 keywords = SARS; TRS summary = Analysis of SARS-CoV-2 RNA sequencing data from whole RNA transcriptomes identified TRS dependent and independent transcripts. Integration of transcripts and 5''-UTR sequence motifs identified that the pentaloop and the stem-loop 3 were also located upstream of spliced genes. Some RNAs, especially non-coding RNAs, generally lack a poly-A tail, which could explain poor detection of TRS independent sgmRNAs. Using published sequencing data of ribosome depleted total RNA from SARS-CoV-2 infected cells and animals (Blanco-Melo et al., 2020) , I aligned these against the viral genome (Figure 2) . Using the aligned reads, I generated transcript models using stringtie, which identified multiple spliced species that aligned with the TRS-L templated events (Figure 2) . Split reads also identified TRS-independent sgmRNAs. In support of my observations on SARS-CoV-2, I also assessed SARS-CoV and MERs transcriptional data, two other human pathogenic CoV. I also identified the TIR motif, a novel sequence element (ATTGGC) flanking the spliced regions of TRS independent sgmRNAs in both SARS-CoV-2 and SARS-CoV. doi = 10.1101/2020.06.24.169144 id = cord-102151-26lumewy author = Cox, Robert M. title = Therapeutic Targeting of Measles Virus Polymerase with ERDRP-0519 Suppresses All RNA Synthesis Activity date = 2020-09-24 keywords = ERDRP-0519 summary = Results demonstrate that unlike all other mononegavirus small molecule inhibitors identified to date, ERDRP-0519 inhibits all phosphodiester bond formation in both de novo initiation of RNA synthesis at the promoter and RNA elongation by a committed polymerase complex. Photocrosslinking and resistance profiling-informed ligand docking revealed that this unprecedented mechanism of action of ERDRP-0519 is due to simultaneous engagement of the L protein polyribonucleotidyl transferase (PRNTase)-like domain and the flexible intrusion loop by the compound, pharmacologically locking the polymerase in pre-initiation conformation. Photocrosslinking-based target site 27 mapping demonstrated that this class-defining prototype inhibitor stabilizes a pre-initiation conformation 28 of the viral polymerase complex that sterically cannot accommodate template RNA. Photocrosslinking-based target site 27 mapping demonstrated that this class-defining prototype inhibitor stabilizes a pre-initiation conformation 28 of the viral polymerase complex that sterically cannot accommodate template RNA. doi = 10.1101/2020.09.23.311043 id = cord-329504-91te3nu8 author = Croll, Tristan title = Making the invisible enemy visible date = 2020-10-07 keywords = PDB; RNA; SARS; structure summary = A general indication of how well the atomic model fits the measurement data can be obtained by comparing the deposited R-factors to results from PDB-REDO (10) (including Whatcheck (11)) to determine the overall density fit as well as many other diagnostics. Our remodelled structure is offering a valuable structural basis for future studies, such as in-silico docking and drug design targeting at SARS-CoV-2 RdRp (34), as well as for computational modelling or simulations to investigate the molecular mechanism of viral replication (31, 35, 36) . This has included a number of posts on our homepage aimed at non-scientists and live streaming the reprocessing of data on Twitch, as well as the design, production, and public release of an accurate 3D printed model of SARS-CoV-2 based on deposited structures for use as a prop for outreach activities. doi = 10.1101/2020.10.07.307546 id = cord-265277-ymvrserl author = Crooke, Stephen N. title = Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome date = 2020-05-14 keywords = HLA; SARS summary = A final round of selection on the basis of HLA 197 promiscuity (i.e., predicted binding to > 3 HLA molecules) and predicted antigenicity scoring using the 198 VaxiJen 2.0 server produced a subset of five candidate peptides (four ORF1ab, one S protein) as potential 199 targets for vaccine development (Table 1) with the hypothesis that increased HLA binding promiscuity 200 meant broader population base coverage by those peptides. As selective pressures are known to introduce viral mutations that promote fitness and can lead 266 to evasion of immune responses (59, 60), we first sought to investigate the genetic similarity of all 267 reported SARS-CoV-2 clinical isolates and identify a consensus sequence for use in our epitope 268 prediction studies. An increasing number of studies have employed predictive algorithms to identify potential HLA 285 class I epitopes for SARS-CoV-2, although relatively few have comprehensively analyzed the entire viral 286 proteome. doi = 10.1101/2020.05.14.093757 id = cord-344909-0o55l4iy author = Cross, Robert W. title = Use of convalescent serum reduces severity of COVID-19 in nonhuman primates date = 2020-10-14 keywords = COVID-19; SARS summary = However, and importantly, lower levels of SARS-CoV-2 in respiratory compartments, reduced gross and histopathological lesion severity in the lungs, and reductions in several parameters associated with coagulation and inflammatory processes were observed in monkeys that received convalescent sera versus untreated controls. Differences in clinical parameters of the LD-treated group with untreated control animals from this study or historical control animals were minimal; however, the lack of infectious SARS-CoV-2 in the BAL samples from all of the LD-treated animals and reduced lung pathology suggest that an antiviral effect was present despite the lower concentration of neutralizing antibodies in the dose of convalescent sera administered. PRNT50 assays were performed on pooled convalescent sera from AGMs challenged with the homologous isolate of SARS-CoV-2 in previous studies (Cross et al., 2020; Woolsey et al., 2020) compared with control animals on day 2 post infection (d) and doi = 10.1101/2020.10.14.340091 id = cord-302146-51hof7it author = Cross, Thomas J. title = Sequence characterization and molecular modeling of clinically relevant variants of the SARS-CoV-2 main protease date = 2020-05-15 keywords = SARS; pro summary = Here we report sequence analysis, structure predictions, and molecular modeling for seventy-nine Mpro variants, constituting all clinically observed mutations in this protein as of April 29, 2020. Modeling and protein structure network analysis suggest differences in cohesion and active site flexibility, revealing patterns in viral evolution that have relevance for drug discovery. Molecular modeling is an important tool for guiding inhibitor discovery, making it possible to evaluate large numbers of candidate drugs in silico to select experimental targets; however, standard approaches screen against only one version of the protein, typically the reference or wild-type (WT) sequence. Here we characterize all 79 known variants of M pro as of 29 April, 2020, and analyze trends in amino acid substitutions and the resulting structural changes using network analysis and molecular modeling. Analysis of active site networks (ASN) from M pro variants suggests differences in active site flexibility and cohesion that may serve to guide the design of robust, mutation-resistant inhibitors. doi = 10.1101/2020.05.15.097493 id = cord-317628-1inxq7t5 author = Cuccarese, Michael F. title = Functional immune mapping with deep-learning enabled phenomics applied to immunomodulatory and COVID-19 drug discovery date = 2020-08-14 keywords = COVID-19; Fig; SARS; TGF; TNF; Thermo; cell; compound summary = We deploy the platform to develop phenotypic models of active SARS-CoV-2 infection and of COVID-19-associated cytokine storm, surfacing compounds with demonstrated clinical benefit and identifying several new candidates for drug repurposing. We used these capabilities to rapidly develop high-throughput-ready disease models for both SARS-CoV-2 viral infection and the resulting cytokine storm, and immediately launched large-scale drug screens that recapitulated known effective and ineffective therapies and, more importantly, identified several new potential treatments for both SARS-CoV-2 infection and COVID-19-associated cytokine storm. To define the model, we evaluated the effect of SARS-CoV-2 infection in multiple cell types, of which three resulted in robust phenoprints as compared to either mock infected or inactivated virus control populations: Calu3 (a lung adenocarcinoma line), Vero (an immortalized interferondeficient African green monkey kidney line 55 ), and primary Human Renal Cortical Epithelium (HRCE) (Fig. 5C, Fig. S6D ). doi = 10.1101/2020.08.02.233064 id = cord-303832-1kcqhgjw author = Dai, Manman title = Long-term survival of salmon-attached SARS-CoV-2 at 4°C as a potential source of transmission in seafood markets date = 2020-09-06 keywords = SARS summary = Several outbreaks of COVID-19 were associated with seafood markets, raising concerns that fish-attached SARS-CoV-2 may exhibit prolonged survival in low-temperature environments. ABSTRACT 21 Several outbreaks of COVID-19 were associated with seafood markets, raising concerns that 22 fish-attached SARS-CoV-2 may exhibit prolonged survival in low-temperature environments. In this study, we detected the titer (50% tissue culture infectious dose/mL, TCID 50 /mL) of 35 viable SARS-CoV-2 attached on salmon or untreated SARS-CoV-2 in culture medium stored at 36 4°C, the temperature in refrigerators or cold rooms for the temporary storage of fish, or 25°C, the 37 regular room temperature, respectively, using end-point titration assay on Vero E6 cells as 38 described previously (8). As shown in Figure A and B, salmon-attached SARS-CoV-2 remained 39 viable at 4°C and 25°C for 8 and 2 days, respectively, while the untreated SARS-CoV-2 in 40 culture medium remained infectious at 4°C and 25°C for more than 8 days. doi = 10.1101/2020.09.06.284695 id = cord-102613-hly07ne3 author = Danko, David title = Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance date = 2020-05-04 keywords = AMR; Supp; city; figure; sample summary = doi = 10.1101/724526 id = cord-259340-1ir19s25 author = Das, Rohit Pritam title = Identification of peptide candidate against COVID-19 through reverse vaccinology: An immunoinformatics approach date = 2020-07-01 keywords = SARS summary = Here the authors have attempted to design epitope based potential peptide as a vaccine candidate using immunoinformatics approach. As of evidence from literatures, SARS-CoV-2 Spike protein is a key protein to initiate the viral infection within a host cell thus used here as a reasonable vaccine target. To its support, strong molecular interaction of the predicted peptide was also observed with MHC molecules and Toll Like receptors. The B-cell epitopic regions present in SARS-CoV-2 S protein were identified using BcePred prediction server (https://webs.iiitd.edu.in/cgibin/bcepred/) [17] . Molecular docking was performed between the predicted peptides and MHC representative structures using PatchDock web server [22, 23, 24] . Interaction of both TLR2 and TLR4 structures with the predicted peptides were performed using PatchDock web server [22, 23, 24] . This study is focused on the prediction of effective epitopes from Spike protein of SARS-CoV-2. doi = 10.1101/2020.07.01.150805 id = cord-262485-sx2q5ol4 author = Davda, Jayeshkumar Narsibhai title = An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance date = 2020-06-08 keywords = PCR; SARS summary = The method employs real time quantitative reverse transcription polymerase chain reaction (RT-qPCR) of RNA extracted from nasopharyngeal (NP) swab samples, to measure amplification of a short segment of a viral gene in the course of a PCR reaction following reverse transcription of viral RNA. We developed and tested a RT-nPCR protocol comprising a multiplex primary RT-PCR for amplification of four SARS-CoV-2 amplicons and a control human RPP30 amplicon followed by a secondary nested PCR for individual amplicons 4 and visualization by agarose gel electrophoresis. Based on the experimentally measured false negative rate by RT-nPCR tests from this study we estimated that as many as 50% of positive samples may escape detection in single pass testing by RT-qPCR in an actual testing scenario. To detect the presence of SARS-CoV-2 in RNA isolated from NP swabs we performed a multiplex one-step RT-PCR on RNA from positive and negative samples using pooled primers for the four viral amplicons together with human RPP30 control. doi = 10.1101/2020.06.08.139477 id = cord-103554-11avjsqu author = Davies, Jennifer L title = Using transcranial magnetic stimulation to map the cortical representation of lower-limb muscles date = 2019-10-17 keywords = EMG; MEP; TMS summary = The aim of this study was to evaluate the extent to which transcranial magnetic stimulation (TMS) can identify discrete cortical representation of lower-limb muscles in healthy individuals. The results of this study indicate that TMS delivered with a 110-mm double-cone coil could not reliably identify discrete cortical representations of resting lower-limb muscles when responses were measured using bipolar surface electromyography. Cortical representation was 4 mapped for seven resting lower-limb muscles involved in control of the knee joint (rectus femoris, vastus lateralis, vastus medialis, medial hamstring, lateral hamstring, medial gastrocnemius, and lateral gastrocnemius) and was quantified using size, CoG, hotspot and number of discrete peaks. The current results indicate bipolar surface EMG used with TMS delivered through a doublecone coil cannot reliably identify discrete cortical representation of lower-limb muscles in young, healthy individuals. The results of this study indicate that TMS delivered with a 110-mm double-cone coil cannot reliably identify discrete cortical representations of resting lower-limb muscles when MEPs are measured using bipolar surface EMG. doi = 10.1101/807339 id = cord-102336-ex3zlq38 author = De Wijngaert, Brent title = Cryo-EM structures reveal transcription initiation steps by yeast mitochondrial RNA polymerase date = 2020-04-14 keywords = RNA; dna summary = Cryo-EM structures of transcription pre-initiation complex (PIC) and initiation complex (IC) of yeast mitochondrial RNA polymerase show fully resolved transcription bubbles and explain promoter melting, template alignment, DNA scrunching, transition into elongation, and abortive synthesis. Hence, the structural basis for promoter melting, DNA scrunching, and transcription initiation remains largely unknown for the mtRNAPs. RPO41 (∆N100) and MTF1 were assembled on a pre-melted promoter (-21 to +12, 15S yeast mtDNA promoter; Fig. 1A ) to generate the yeast mitochondrial transcription preinitiation complex (y-mtPIC) (Fig. S1 ). The 3.7 Å density map of IC locates many previously uncharacterized structural elements, including the C-tail of MTF1 and the scrunched DNA ( Fig. 2B-C) , and reveals the mechanism of template alignment and RNA synthesis during initiation. During the transition, the upstream DNA from position -1 onward is locked in the MTF1 NT-groove while the template strand undergoes a large conformational switching to align with the 2-mer RNA and the incoming UTPaS at the active site ( Fig. 2C; Movie S2). doi = 10.1101/2020.04.13.038620 id = cord-302733-rfuyd041 author = Dellicour, Simon title = A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages date = 2020-10-21 keywords = Belgium; SARS; belgian summary = At the country scale, our spatially-explicit phylogeographic analyses highlight that the national lockdown had a relatively low impact on both the lineage dispersal velocity and the long-distance dispersal events within Belgium. At the country scale, our spatially-explicit phylogeographic analyses highlight that the national lockdown had a relatively low impact on both the lineage dispersal velocity and the long-distance dispersal events within Belgium. We generated a time-scaled phylogenetic tree using a rapid maximum likelihood approach 16 and subsequently ran a preliminary discrete phylogeographic analysis along this tree to identify internal nodes and descending clades that likely correspond to distinct introductions into the Belgian territory ( Fig. 1, S2 ). We used the continuous diffusion model 13 available in BEAST 1.10 14 to perform a spatially-explicit (or "continuous") phylogeographic reconstruction of the dispersal history of SARS-CoV-2 lineages in Belgium. doi = 10.1101/2020.05.05.078758 id = cord-102968-mhawyect author = Desirò, Daniel title = SilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structural RNAs date = 2018-09-23 keywords = RNA; SIM summary = Results Here, we developed SilentMutations (SIM), an easy-to-use tool to analyze the effect of multiple point mutations on the secondary structures of two interacting viral RNAs. The tool can simulate destructive and compensatory mutants of two interacting single-stranded RNAs. This will facilitate a fast and accurate assessment of key regions, possibly involved in functional long-range RNA-RNA interactions and finally help virologists to design appropriate experiments. In this study, we present a tool called SilentMutations (SIM) that effectively simulates synonymous (silent) compensatory mutations in two single-stranded viral RNAs and is therefore appropriate for the in vitro assessment of predicted LRIs. Here, we present a command-line tool, called SilentMutations (SIM), that can simulate synonymous structure-destroying and structurepreserving mutation pairs within coding regions for long-range RNA-RNA interaction experiments. Figure 1 : Overall workflow of the SilentMutations tool, exemplary shown for two sequences from a negative single-stranded RNA virus genome (ssRNA-) (a) The first step will extract the defined range in each sequence and possibly increase the range to preserve codons in the given reading frame. doi = 10.1101/424002 id = cord-268224-5tbb8df1 author = Di Gioacchino, Andrea title = The heterogeneous landscape and early evolution of pathogen-associated CpG dinucleotides in SARS-CoV-2 date = 2020-08-27 keywords = Fig; ORF; SARS summary = Using a model of the viral gene evolution under human host pressure, we find that synonymous mutations seem driven, in the N protein coding region, both by the viral codon bias and by the high value of the CpG content, leading to a loss in CpG. Finally we use a model of the viral gene evolution under human host pressure, characterized by the CpG force, to study synonymous mutations, and in particular those which change CpG content, observed since the SARS-CoV-2 entered the human population (Sec. 2.3). We first compute the global force on CpG dinucleotides for SARS-Cov-2 and a variety of other viruses from the Coronaviridae family affecting humans or other mammals (bat, pangolin), see Fig. 1a , using as null model the nucleotide usage calculated from human genome [22] (see Methods Sec. 4.2) 1 . doi = 10.1101/2020.05.06.074039 id = cord-262726-lfuxhlki author = Diallo, Aïssatou Bailo title = Daytime variation in SARS-CoV-2 infection and cytokine production date = 2020-09-11 keywords = SARS summary = doi = 10.1101/2020.09.09.290718 id = cord-331786-wgt7kg6f author = Diego-Martin, Borja title = Pilot production of SARS-CoV-2 related proteins in plants: a proof of concept for rapid repurposing of indoors farms into biomanufacturing facilities date = 2020-10-13 keywords = Fig; RBD; SARS; antibody summary = For this purpose, we tested our ability to produce, in the framework of an academic lab and in a matter of weeks, milligram amounts of six different recombinant monoclonal antibodies against SARS-CoV-2 in Nicotiana benthamiana. In parallel, we also produced the recombinant SARS-CoV-2 N protein and its Receptor Binding Domain (RBD) in planta and used them to test the binding specificity of the recombinant mAbs. Finally, for two of the antibodies we assayed a simple scale-up production protocol based on the extraction of apoplastic fluid. Finally, we performed sandwich ELISA tests of sybody17 and nanobody72 ( Fig 5E and Fig 5F, respectively) using the total and concentrated apoplastic fluid as detection reagent against serial dilutions of crude plant extracts from RBD-producing plants, showing that this simple antibody preparation can be directly employed in detection procedures without the need of additional purification steps. doi = 10.1101/2020.10.13.331306 id = cord-281717-kzd9vvci author = Digard, Paul title = Intra-genome variability in the dinucleotide composition of SARS-CoV-2 date = 2020-05-08 keywords = Fig; ORF; RNA; SARS summary = CpG dinucleotides are under-represented in the genomes of single stranded RNA viruses, and coronaviruses, including SARS-CoV-2, are no exception to this. CpG suppression amongst coronaviruses does not significantly differ according to genera of virus, but does vary according to host species and primary replication site (a proxy for tissue tropism), supporting the hypothesis that viral CpG content may influence cross-species transmission. 79 SARS-CoV-2 was recently reported to have a CpG composition lower than other members of the 80 betacoronavirus genus, comparable to certain canine alphacoronaviruses; an observation used to draw 81 inferences over its origin and/or epizootic potential (Xia 2020 in GC content (from ~ 0.32 -0.47) was seen across the Coronaviridae, and as expected, all viruses 97 exhibited some degree of CpG suppression, with CpG O:E ratios ranging from 0.37 to 0.74 (Fig 2A) . doi = 10.1101/2020.05.08.083816 id = cord-334584-xh41koro author = Dilucca, Maddalena title = Temporal evolution and adaptation of SARS-COV 2 codon usage date = 2020-05-29 keywords = CAI; SARS; codon summary = Thus, we compared the codon usage patterns, every two weeks, of 13 of SARS-CoV-2 genes encoding for the membrane protein (M), envelope (E), spike surface glycoprotein (S), nucleoprotein (N), non-structural 3C-like proteinase (3CLpro), ssRNA-binding protein (RBP), 2''-O-ribose methyltransferase (OMT), endoRNase (RNase), helicase, RNA-dependent RNA polymerase (RdRp), Nsp7, Nsp8, and exonuclease ExoN. An EN C plot analysis was performed to estimate the relative contributions of mutational bias and natural selection in shaping CUB of 13 genes encoding proteins that are crucial for SARS-CoV-2. For the funtionally important genes in each genome, we calculated the average values of CAI and ENC over time, as compared to the reference SARS-CoV-2 sequence (WSM). Based on the SiD combined with the CAI results ( Figure 5 ), we suggest that SARS-CoV-2, over time, has preferentially accumulated mutations in its genome which correspond to codons that adapt better to the human host. doi = 10.1101/2020.05.29.123976 id = cord-267613-hsc2x36j author = Dittmar, Mark title = Drug repurposing screens reveal FDA approved drugs active against SARS-Cov-2 date = 2020-06-19 keywords = Calu-3; Fig; Huh7.5; SARS; Vero; cell summary = Moreover, we found 9 drugs are antiviral in lung cells, 7 of which have been tested in humans, and 3 are FDA approved including Cyclosporine which we found is targeting Cyclophilin rather than Calcineurin for its antiviral activity. Previous studies found that the antiviral drug remdesivir, which was developed against the RNA-dependent RNA polymerase of Ebola virus, was also active against SARS-CoV-2 in vitro, with promising results in clinical trials (5) (6) (7) . Both cepharanthine and tetrandrine were previously shown to have antiviral activity against the human coronavirus OC43 and in recent studies on SARS-CoV-2 in Vero cell screens (13, 62, 63) . Strikingly, the activities of all of these drugs is similar in the two cell lines suggesting the same target and mechanism-of-action and that Cyclosporine would block SARS-CoV-2 in diverse infected tissues in vivo. doi = 10.1101/2020.06.19.161042 id = cord-297684-9q3oopaz author = Dobaño, Carlota title = Highly sensitive and specific multiplex antibody assays to quantify immunoglobulins M, A and G against SARS-CoV-2 antigens date = 2020-06-12 keywords = ELISA; SARS; antibody; figure summary = The Receptor-Binding Domain (RBD) of the spike (S) glycoprotein of SARS-CoV-2, the leading vaccine candidate target, was selected as the primary antigen to develop the initial qSAT assay because (i) S is one of the most immunogenic surface proteins together with the nucleocapsid protein (N) (20) (ii) RBD is the fragment of the virus that mediates binding to the host receptor ACE2 in the lung cells (21) (iii) antibodies to RBD correlate with neutralizing antibodies (20)(22) that could be associated with protection based on studies of other coronaviruses and animal models (23) (24) (25) (26) , and (iv) an ELISA based on this same protein has received FDA approval for COVID-19 serology (11) . We developed three novel multiplex immunoassays for quantifying IgM, IgA and IgG to eight SARS-CoV-2 protein constructs and evaluated by machine learning classification algorithms the performance of several isotype/antigen combinations to detect any positive antibody response to infection, obtaining specificities of 100% and sensitivities of 94.94% (≥14 days since symptoms onset) or 96.08% (≥21 days since symptoms onset), and very high predictability (AUC ≥0.99). doi = 10.1101/2020.06.11.147363 id = cord-103417-2uinislh author = Doi, Hideyuki title = On-site eDNA detection of species using ultra-rapid mobile PCR date = 2020-10-01 keywords = PCR; dna summary = Our method reduced the measurement time to 30 min and provided high detectability of aquatic organisms compared to the national observation surveys using multiple fishing nets and laboratory extraction/detection using a benchtop qPCR platform. Ultra-rapid methods from DNA collection to detection are still not well developed (1), especially for environmental DNA (eDNA) analysis, which uses water or soil samples to track the presence of target species (2, 3) . Here, we developed a new innovative method for the field processing of eDNA samples and measurements using an ultra-rapid mobile PCR platform (hereafter, mobile PCR) to reduce the measurement time to 30 min and maintain high detectability of aquatic organisms. We compared the on-site eDNA measurement to the laboratory extraction and detection using a benchtop qPCR platform and the national survey to confirm the performance. Our ultra-rapid on-site eDNA extraction and measurement method using mobile PCR successfully detected the eDNA of H. doi = 10.1101/2020.09.28.314625 id = cord-266444-rw94yls8 author = Dominguez Andres, Ana title = SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells date = 2020-08-19 keywords = CoV-2; Fig; ORF9c; SARS; protein summary = The interactome and proteome studies identified cellular processes affected by SARS-CoV-2 infection or specific viral proteins, notably innate immune signaling (19, 20, 23, (28) (29) (30) , ubiquitin ligase activities (19, 20, 23, (28) (29) (30) , p38 mitogenactivated protein kinase (MAPK) signaling (19, 20, 23, (28) (29) (30) . To assess if there were notable differences in the intensity of the changes in protein abundance in response to proteasome inhibition, we calculated relative changes in protein abundance between control and ORF9c-expressing cells from both the DMSO and MG132 conditions for proteins associated with IFN signaling or the ubiquitin proteasome (UBP) system and antigen presentation (Fig. 2D ). In contrast to the proteomic results that revealed predominant downregulation of proteins following ORF9c expression, RNA-seq analysis showed a similar number of transcripts were increased or decreased in the presence or absence of MG132 (Fig. 3A, table S2 ). doi = 10.1101/2020.08.18.256776 id = cord-346546-yffwd0dc author = Douangamath, Alice title = Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease date = 2020-05-27 keywords = SARS; figure; fragment; structure summary = To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease. For 113 another series of hit compounds, containing a N-chloroacetyl piperidinyl-4-carboxamide 114 motif (Table S2 ) which displays lower reactivity and were not frequent hitters in previous 115 screens, we attempted crystallization despite their absence of labelling in the stringent 116 The bound fragments comprehensively sample all subsites of the active 287 site revealing diverse expansion vectors, and the electrophiles provide extensive, systematic 288 as well as serendipitous, data for designing covalent compounds. Crystal structure of SARS-CoV-2 main protease 763 provides a basis for design of improved alpha-ketoamide inhibitors doi = 10.1101/2020.05.27.118117 id = cord-350935-p6euuop3 author = Doğan, Tunca title = CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations date = 2020-09-15 keywords = COVID-19; SARS; protein summary = We aimed to address this issue by constructing a new biological and biomedical data resource, CROssBAR, a comprehensive system that integrates large-scale biomedical data from various resources and store them in a new NoSQL database, enrich these data with deep-learning-based prediction of relations between numerous biomedical entities, rigorously analyse the enriched data to obtain biologically meaningful modules and display them to users via easy-to-interpret, interactive and heterogenous knowledge graph (KG) representations within an open access, user-friendly and online web-service at https://crossbar.kansil.org. In this project, we aimed to address the current shortcomings by developing a comprehensive open access biomedical system entitled CROssBAR via integrating various biological databases to each other, inferring the missing relations between existing data points, and constructing informative knowledge graphs based on specific biomedical components/terms such as a disease/phenotype, biological process, gene/protein and drug/compound, or specific combinations of them. doi = 10.1101/2020.09.14.296889 id = cord-343317-97n1j0jj author = Duan, Xiaohua title = Identification of Drugs Blocking SARS-CoV-2 Infection using Human Pluripotent Stem Cell-derived Colonic Organoids date = 2020-05-02 keywords = CoV-2; Fig; SARS; cell summary = Multiple cell types in the COs can be infected by a SARS-CoV-2 pseudo-entry virus, which was further validated in vivo using a humanized mouse model. Multiple cell types in the COs can be infected by a SARS-CoV-2 pseudo-entry virus, which was further validated in vivo using a humanized mouse model. The organoids infected with SARS-CoV-2 pseudo-entry virus at MOI=0.01 showed a strong signal at 24 hpi (Fig. 2a) . The mRNAs of SARS-CoV-2 pseudo-entry virus, including VSV-NS, VSV-N, and VSV-M, were detected in all five cell populations (Fig. 2f) , but not in the uninfected COs (Extended Data Fig. 2f) . Immunohistochemistry detected luciferase in ACE2 + and Villin + cells, suggesting these are permissive to SARS-CoV-2 pseudo-entry virus infection in vivo (Fig. 2k) . Next, we adapted hPSC-COs to a high throughput screening platform and probed the Prestwick FDA-approved drug library to identify drug candidates capable of blocking SARS-CoV-2 pseudo-virus infection. doi = 10.1101/2020.05.02.073320 id = cord-322885-ob5euspo author = Durdagi, Serdar title = Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing date = 2020-09-09 keywords = 7CWB; 7cwc; Fig; Mpro; SARS; drug; structure summary = One Sentence Summary Radiation-damage-free high-resolution SARS-CoV-2 main protease SFX structures obtained at near-physiological-temperature offer invaluable information for immediate drug-repurposing studies for the treatment of COVID19. Radiation-damage-free SFX method which enables obtaining the novel high-resolution ambient-temperature structures of the binding pocket of Mpro provides an unprecedented opportunity for identification of highly effective inhibitors for drug repurposing by using a hybrid approach that combines structural and in silico methods. We determined two radiation-damage-free SFX crystal structures of SARS-CoV-2 Mpro in two crystal forms at 1.9 Å and 2.1 Å resolutions with the following PDB IDs: 7CWB and 7CWC, respectively (Fig. 1A, B) (Supplementary Table 1&2 The diffraction data collected remotely at the MFX instrument of the LCLS at SLAC National Laboratory, Menlo Park, CA (Sierra et al., They reveal novel active site residue conformations and dynamics at atomic level, revealing several differences compared to the prior ambient-temperature structure of SARS-CoV-2 Mpro that was obtained at a home X-ray source (Fig. 1A, B ). doi = 10.1101/2020.09.09.287987 id = cord-103915-rzy7mejb author = Duricki, Denise A. title = Corticospinal neuroplasticity and sensorimotor recovery in rats treated by infusion of neurotrophin-3 into disabled forelimb muscles started 24 h after stroke date = 2018-07-11 keywords = CST; Fig; NT3; Supplementary; rat; spinal; stroke summary = We have previously shown that gene therapy delivery of human NT3 into the affected triceps brachii forelimb muscle improves sensorimotor recovery after ischemic stroke in adult and elderly rats. We also recently showed that injection of an adeno-associated viral vector (AAV) encoding full-length human NT3 (preproNT3, 30kDa) into forelimb muscles 24 hours after stroke in adult or elderly rats improved sensorimotor recovery 19 . We examined anatomical neuroplasticity in the C7 cervical spinal cord because we knew from experiments using adult and elderly rats that the less-affected corticospinal tract sprouts at this level (as well as other levels) after injection of AAV-NT3 into muscles including triceps brachii 19 . fMRI performed one week after stroke confirmed that somatosensory cortex was not active when the affected paw was stimulated in either vehicle or NT3 treated rats (p>0.05, Supplementary Fig. 6b ). Treatment of disabled arm muscles with NT3 protein, initiated 24 hours after stroke, caused changes in multiple locomotor circuits, and promoted a progressive recovery of sensory and motor function in rats. doi = 10.1101/367573 id = cord-296237-i9cti2ok author = Díez, José-María title = Cross-neutralization activity against SARS-CoV-2 is present in currently available intravenous immunoglobulins date = 2020-06-19 keywords = CoV-2; IVIG; MERS; SARS summary = Recently, ELISA binding cross-reactivity against components of human epidemic coronaviruses with currently available intravenous immunoglobulins (IVIG) Gamunex-C and Flebogamma DIF (5% and 10%) have been reported. Conclusion In cell culture neutralization assays, the tested IVIG products contain antibodies with significant cross-neutralization capacity against SARS-CoV-2 and SARS-CoV. Recently, cross-reactivity in ELISA binding assays against antigens of SARS-CoV, SARS-CoV-2, and MERS-CoV has been reported with currently available intravenous immunoglobulins (IVIG) such as Gamunex-C and Flebogamma DIF 19 . In this study, the neutralization capacity of the IVIG products Gamunex-C and Flebogamma DIF against these epidemic human coronaviruses -SARS-CoV, SARS-CoV-2, and MERS-CoV-was evaluated. Six different lots of Flebogamma DIF and Gamunex-C were tested at several dilutions for cross-reactivity against SARS-CoV, SARS-CoV-2, and MERS-CoV by: i) ELISA techniques; and ii) well-stablished neutralization assays in cell cultures. For SARS-CoV-2 MAD6 isolate, all IVIG lots, except F1 (inconclusive results) showed a significant neutralizing activity and reached PRNT50 titers ranging from 4.5 to >5 (Figure 2 ). doi = 10.1101/2020.06.19.160879 id = cord-331701-izkz1hz4 author = Eden, John-Sebastian title = An emergent clade of SARS-CoV-2 linked to returned travellers from Iran date = 2020-03-17 keywords = Iran; SARS summary = Phylogenetic analyses of whole genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases. Herein, we show that the genomic analyses of SARS-CoV-2 strains from Australian returned travellers with COVID-19 disease may provide important insights into viral diversity present in regions currently lacking genomic data. However, while we cannot completely discount that the cases in Australia and New Zealand came from other sources including China, our phylogenetic analyses, as well as epidemiological (recent travel to Iran) and clinical data (date of symptom onset), provide evidence that this clade of SARS-CoV-2 is linked to the Iranian epidemic, from where genomic data is currently lacking. doi = 10.1101/2020.03.15.992818 id = cord-334394-qgyzk7th author = Edgar, Robert C. title = Petabase-scale sequence alignment catalyses viral discovery date = 2020-08-10 keywords = Extended; Figure; RNA; SRA; Serratus; genome; sequence summary = To address the ongoing pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 and expand the known sequence diversity of viruses, we aligned pangenomes for coronaviruses (CoV) and other viral families to 5.6 petabases of public sequencing data from 3.8 million biologically diverse samples. To expand the known repertoire of viruses and catalyse global virus discovery, in particular for Coronaviridae (CoV) family, we developed the Serratus cloud computing architecture for ultra-high throughput sequence alignment. We aligned 3,837,755 public RNA-seq, meta-genome, meta-virome and meta-transcriptome datasets (termed a sequencing run [5] ) against a collection of viral family pangenomes comprising all GenBank CoV records clustered at 99% identity plus all non-retroviral RefSeq records for vertebrate viruses (see Methods and Extended Table 1 ). We performed de novo assembly on 52,772 runs potentially containing CoV sequencing reads by combining 37,131 SRA accessions identified by the Serratus search with 18,584 identified by an ongoing cataloguing initiative of the SRA called STAT [5] . doi = 10.1101/2020.08.07.241729 id = cord-102377-n57hoty4 author = Egli, Adrian title = High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters date = 2020-04-04 keywords = quarter; urban summary = doi = 10.1101/2020.04.03.023135 id = cord-102463-d440jsek author = Eguchi, Raphael R. title = IG-VAE: Generative Modeling of Immunoglobulin Proteins by Direct 3D Coordinate Generation date = 2020-08-10 keywords = VAE; figure; structure summary = doi = 10.1101/2020.08.07.242347 id = cord-304544-tqtdjh2m author = Enes, Ak title = Transcriptional response of signalling pathways to SARS-CoV-2 infection in normal human bronchial epithelial cells date = 2020-06-20 keywords = H1N1; NHBE; SARS summary = Comparison of transcriptome of NHBE cells 24 hours after mock-infection and SARS-CoV-2 infection demonstrated that most genes that respond to infection were upregulated (320 genes) rather than being downregulated (115 genes).While upregulated genes were enriched in signalling pathways related to virus response, downregulated genes are related to kidney development. Although virus entry protein ACE2 has low expression in NHBE cells, pathogen response pathways are strongly activated within 24 hours of infection. Upregulated MMPs and chemokines demonstrate the response generated by NHBE cells to trigger the immune system, these two subgroups of genes are further discussed below comparatively in SARS-CoV-2 and H1N1 infection. Interestingly, none of the IL-17 ligands were expressed in detectable amounts in NHBE cells, and none of the ligands or receptors were upregulated in response to virus infection, therefore the positive feedback loop is likely to be initiated by activation of NFκB via other signalling pathways. doi = 10.1101/2020.06.20.163006 id = cord-281699-pxof67pl author = Eskier, Doğa title = Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load date = 2020-08-13 keywords = SARS; mutation summary = In our previous study, we examined the top 10 most frequent mutations in the SARS-CoV-2 nsp12, and identified that four of them are associated with an increase in mutation density in two genes, the membrane glycoprotein (M) and the envelope glycoprotein (E) (the combination of which is hereafter referred to as MoE, as we previously described), which are not under selective pressure, and mutations in these genes are potential markers of reduced replication fidelity (Eskier et al., 2020) . To identify the trends in SARS-CoV-2 mutation load over time, we calculated the average mutation density per day for all isolates for whole genome, S gene, and MoE regions, capping outliers at the 95th and 5th percentile values to minimize the potential effects of sequencing errors ( Fig. 1) . doi = 10.1101/2020.08.12.248732 id = cord-285159-gytebbua author = Eydoux, Cecilia title = A Fluorescence-based High Throughput-Screening assay for the SARS-CoV RNA synthesis complex date = 2020-07-07 keywords = RNA; SARS summary = Here, we report the use of a purified and highly active SARS-CoV replication/transcription complex (RTC) to set-up a high-throughput screening of Coronavirus RNA synthesis inhibitors. Principle of SARS-CoV RNA synthesis detection by a fluorescence-based high throughput screening assay Highlights A new SARS-CoV non radioactive RNA polymerase assay is described The robotized assay is suitable to identify RdRp inhibitors based on HTS -A new SARS-CoV non radioactive RNA polymerase assay is described -The robotized assay is suitable to identify RdRp inhibitors based on HTS the RdRp core nsp12 and shown to confer full activity and processivity to nsp12 (Subissi et al., 2014) . Picogreen kinetic assay was based on polymerase activity of SARS nsp12 in complex with nsp7L8, which catalyzed the reaction using a poly (A) template and uridine triphosphate (UTP). doi = 10.1101/2020.07.07.192005 id = cord-281684-m3m4mhye author = Fagre, Anna C. title = A potent SARS-CoV-2 neutralizing human monoclonal antibody that reduces viral burden and disease severity in Syrian hamsters date = 2020-09-28 keywords = ACE2; CoV-2; SARS summary = title: A potent SARS-CoV-2 neutralizing human monoclonal antibody that reduces viral burden and disease severity in Syrian hamsters We identified a panel of human monoclonal antibody clones from a yeast display library with specificity to the SARS-CoV-2 spike protein receptor binding domain that neutralized the virus in vitro. However, to date, there has been only a gross histological analysis of the lung pathological changes following infection and the impact of SARS-CoV-2 neutralizing antibody clones on lung immune infiltrates has yet to be fully assessed. Those antibody clones that blocked the interaction of the RBD with ACE2 and bound to native spike protein were then tested for neutralization of SARS-CoV-2 in a cytopathic effect (CPE) assay with Vero E6 cells. Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association Emergence of SARS-CoV-2 spike RBD mutants that enhance viral infectivity through increased human ACE2 receptor binding affinity doi = 10.1101/2020.09.25.313601 id = cord-279576-wt4crton author = Fajardo, Álvaro title = Evaluation Of SYBR Green Real Time PCR For Detecting SARS-CoV-2 From Clinical Samples date = 2020-05-13 keywords = Green; PCR; SARS; SYBR summary = Several methods based on real time reverse transcription polymerase chain reaction (RT-qPCR) for the detection of SARS-CoV-2 genomic RNA have been developed. The aim of the study was to set up an alternative molecular protocol to detect SARS-CoV-2 from clinical samples, without the need of TaqMan probes or post-PCR steps (i.e. gel electrophoresis), which can be implemented in case of difficulties to get specific reagents or kits because of the current pandemic situation. In order to select an appropriate amount of control vector to use in the comparison between the two real time qPCR methods, we prepared plasmids dilutions (107, 106, 105 and 104 copies/μL) and assayed them following both protocols: the probe-based One Step RT-qPCR developed by the University of Hong Kong Poon et al. The amplification data for the SYBR Green-based qPCR protocol showed that the ORF1b-nsp14 region was correctly amplified for all SARS-CoV-2 positive samples (1 to 7) (Fig. 3) . doi = 10.1101/2020.05.13.093609 id = cord-353129-ivbf4kuq author = Faryami, Ahmad title = Open source 3D printed Ventilation Device date = 2020-05-22 keywords = pressure summary = The following is intended to review the development and testing of a 3D printed and open-source mechanical ventilation device that is capable of adjusting breathing rate, volume, and pressure simultaneously and was designed according to the latest clinical observations of the current pandemic. This open-source positive pressure ventilation device (OSPPVD) is a response to the shortages in the hospitals'' ventilation capacity, which has been reported to be essential to many COVID-19 patients throughout the world. According to the initial reports published by healthcare providers, the loss of compliance due to the onset of fibrosis in the lungs is observed in patients diagnosed with severe cases of COVID-19 infection 9 . An advantage of OSPPVD presented here is its capability to perform hyperventilation with high flow rates under relatively wide pressure range from 5 2 that would allow the delivery of oxygen without the over-expansion of the lungs while being able to supply pressurized air as high as 40 or 50 2 even though the current setup is designed to only reach 30 2 . doi = 10.1101/2020.05.21.108043 id = cord-329240-atisrhas author = Fedorenko, Aliza title = Virus survival in evaporated saliva microdroplets deposited on inanimate surfaces date = 2020-06-16 keywords = Phi6; SARS summary = Here we combine microscopy imaging with virus viability assays to study survival of three bacteriophages suggested as good models for human respiratory pathogens: the enveloped Phi6 (a surrogate for SARS-CoV-2), and the non-enveloped PhiX174 and MS2. The observed high virus survival in dry saliva deposited on surfaces, under a wide range of RH levels, can have profound implications for human public health, specifically the COVID-19 pandemic. To study virus survival in microdroplets deposited on a smooth inanimate surface, we sprayed Phi6, MS2, and PhiX174 viruses suspended in three media -human saliva, water, and SM bufferon glass-bottom 12-well plates (Fig. 1, Methods) . The observation that at a given RH, the microscopic hydration conditions of deposited droplets of various media can differ so widely (see along the rows of Fig. 3 ) suggests that RH does not directly affect virus stability and infectivity in drying microdroplets deposited on surfaces, but rather RH indirectly affects survival through its effect on physicochemical conditions at the scale that matters for viruses (~ µm). doi = 10.1101/2020.06.15.152983 id = cord-307536-qeo5dfxg author = Feng, Ye title = Multi-epitope vaccine design using an immunoinformatics approach for 2019 novel coronavirus (SARS-CoV-2) date = 2020-06-30 keywords = SARS summary = title: Multi-epitope vaccine design using an immunoinformatics approach for 2019 novel coronavirus (SARS-CoV-2) When four vaccine peptide candidates from the spike protein of SARS-CoV-2 were selected to immunize mice, a significantly larger amount of IgG in serum as well as an increase of CD19+ cells in ILNs was observed in peptide-immunized mice compared to the control mice. This study screened antigenic B-cell and T-cell epitopes in all encoded proteins of SARS-CoV-2, and further designed multi-epitope based peptide vaccine against viral structural proteins. In this study, we performed an in silico approach to identify the antigenic B-cell epitopes and human-leukocyte-antigen (HLA) restricted T-cell epitopes, and designed a panel of multi-epitope peptide vaccines. The resulting SARS-CoV-2 multi-epitope peptide vaccine could elicit specific humoral and cellular immune responses in mice efficiently, displaying its great potential in our fight of COVID-19. Based on both the epitope counts and HLA score, we 250 eventually selected 13 T-cell epitopes-only vaccine peptides. doi = 10.1101/2020.03.03.962332 id = cord-102570-lpwwlrqm author = Fenn, Gareth D. title = Crystallization and structure of ebselen bound to cysteine 141 of human inositol monophosphatase (IMPase) date = 2020-08-18 keywords = PDB; cys141 summary = In the human-IMPase-complex ebselen, in a ring opened conformation, is covalently attached to Cys141, a residue located away from the active site. In the crystal structure presented in this publication, the active site in the tetramer is still accessible, suggesting that ebselen may function as an allosteric inhibitor, or may block the binding of partner proteins. Synopsis Here we present a 1.47Å crystal structure of human inositol monophosphatase (IMPase) bound to the inhibitor ebselen (PDB entry 6ZK0). In this paper, we present a 1.47Å structure of ebselen covalently bound to cysteine residue 141 of human IMPase (PDB entry 6ZK0). Each monomer of IMPase in this structure has a single ebselen molecule bound to Cys141 (PDB entry 6ZK0). The IMPase crystal structure that is presented (PDB entry 6ZK0) has ebselen covalently attached to Cys141, however it is not clear to what extent this binding brings about ebselen''s inhibitory effects on IMPase. doi = 10.1101/2020.07.08.193284 id = cord-102964-zh737cjk author = Ferraro, Francesco title = Modulation of endothelial organelle size as an antithrombotic strategy date = 2020-05-17 keywords = Ferraro; Golgi; VWF; WPB summary = Out of 1280 human licensed drugs we found 58 compounds fitting our criteria, with a variety of mechanisms of action consistent suggesting a number of pathways that influence biogenesis of WPBs. A quantitative high-throughput microscopy-based workflow, dubbed highthroughput morphometry (HTM), allows rapid quantification of the size of tens to hundreds of thousands of WPBs within thousands of endothelial cells (Ferraro et al., 2014) . We have previously shown that treatment of endothelial cells with two statins, simvastatin and fluvastatin, induces WPB size shortening, resulting in reduced adhesive properties of the VWF released by activated endothelial cells (HUVEC), measured by the reduced size of platelet-decorated VWF strings and by the recruitment of VWF from a flowing plasma pool (Ferraro et al., 2016) . Further to the potential toxicity associated with administration of drugs at high concentrations, we note that in vitro combination of WPB-size reducing treatments, acting through different mechanisms, can display synergy in the abatement of plasma VWF recruitment to the endothelial surface (Supplemental Figure 1) . doi = 10.1101/2020.05.16.099580 id = cord-103606-5gbk6t6y author = Fettrow, Tyler title = Walking cadence affects the recruitment of the medial-lateral balance mechanisms date = 2019-06-03 keywords = balance; foot; low; mechanism summary = We limited our analysis to the time interval from the heel-strike triggering the stimulus to the end of the second double stance post-stimulus, which encompasses the three previously identified balance mechanisms of lateral ankle roll, foot placement shift and push-off modulation. We had expected the foot placement shift to be smaller in the Low condition, due to an increased and prolonged lateral ankle mechanism response, based on modeling results (Reimann et al., 2017) . The results indicate that all three previously identified balance mechanisms are used to respond to the perceived fall, but the majority of the balance response is shifted to the lateral ankle mechanism when walking with a low cadence. We also know that people with Parkinson''s disease take shorter faster steps (Knutsson, 1972) , and although their overall gait speed is diminished, an increase in cadence may shift the majority of the balance response to the foot placement compared to age matched controls. doi = 10.1101/658070 id = cord-282878-8qgsq2km author = Fignani, Daniela title = SARS-CoV-2 receptor Angiotensin I-Converting Enzyme type 2 (ACE2) is expressed in human pancreatic β-cells and in the human pancreas microvasculature date = 2020-10-23 keywords = ACE2; SARS; cell; figure; human; pancreatic summary = Finally, using RT-qPCR, RNA-seq and High-Content imaging screening analysis, we demonstrated that pro-inflammatory cytokines, but not palmitate, increases ACE2 expression in the β-cell line EndoC-βH1 and in primary human pancreatic islets. To address this question, we screened the ACE2 expression pattern in human pancreata obtained from adult non-diabetic multiorgan donors and in the insulin-producing human β-cell line EndoC-βH1, using different methodologies, multiple reagents, and publicly available or in-house generated RNA sequencing datasets. Here, we adopted multiple technologies and reagents to thoroughly analyse presence of ACE2, both at mRNA and protein level, in order to evaluate its expression and localization in pancreatic tissue samples obtained from adult non-diabetic multiorgan donors from the INNODIA EUnPOD biobank collection, in enzymatic-and LCM-isolated primary adult human pancreatic islets and in human β-cell line EndoC-βH1. Importantly, a recent report showed that human pancreatic islets can be infected in vitro by SARS-CoV-2 (23), supporting our observations of a specific tropism of the virus due to ACE2 expression. doi = 10.1101/2020.07.23.208041 id = cord-312702-fruzsn26 author = Finch, Courtney L. title = Characteristic and quantifiable COVID-19-like abnormalities in CT- and PET/CT-imaged lungs of SARS-CoV-2-infected crab-eating macaques (Macaca fascicularis) date = 2020-05-14 keywords = COVID-19; SARS summary = title: Characteristic and quantifiable COVID-19-like abnormalities in CTand PET/CT-imaged lungs of SARS-CoV-2-infected crab-eating macaques (Macaca fascicularis) Based on the rather limited X-97 ray findings in the lungs of reported NHP models of SARS-CoV-2 infection with either 98 mild or no clinical signs (11, 25, 27-29), we turned to high-resolution chest CT and 99 Increases in PCLH or PCLH/LV 169 were not seen in the mock-exposed macaques over the entire study (Figure 8a A key advantage of quantifiable CT chest imaging readout over serial euthanasia 212 studies, in addition to potentially reduced experimental animal numbers, is the ability not 213 only to evaluate between-group differences, but also to compare severity and duration of 214 disease at higher resolution in single animals and even in isolated parenchymal areas 215 sequentially. follow-up confirmation of these pilot results in this model of mild-moderate COVID-19 233 is needed to further establish quantifiable lung CT as a reliable disease readout and to 234 forge imaging-pathologic correlates in macaques euthanized at peak radiographic 235 abnormality. doi = 10.1101/2020.05.14.096727 id = cord-255888-znfgh78m author = Fisher, Dale title = Seeding of outbreaks of COVID-19 by contaminated fresh and frozen food date = 2020-08-18 keywords = SARS summary = SARS-CoV-2 was detected on workers and environmental samples, including a cutting board used to slice imported salmon. We have assessed the survival of SARS-CoV-2 on refrigerated and frozen meat and salmon over 3 weeks to assess the potential of outbreaks being seeded by imported contaminated food. The clusters of infection of COVID-19 among workers in slaughterhouses and meat processing facilities in many countries can be attributed to factors that promote transmission of virus directly between workers, such as crowding, poor ventilation, and shouting in close proximity due to high ambient noise levels. With a significant burden of virus present in infected workers and the environment then contamination of meat with SARS-CoV-2 is possible during butchering and processing. Our laboratory work has shown that SARS-CoV-2 can survive the time and temperatures associated with transportation and storage conditions associated with international food trade. We believe it is possible that contaminated imported food can transfer virus to workers as well as the environment. doi = 10.1101/2020.08.17.255166 id = cord-103135-nly9vojr author = Fletcher, Nicola F. title = A novel antiviral formulation inhibits a range of enveloped viruses date = 2020-03-30 keywords = ViroSAL; cell; figure; virus summary = ViroSAL had no effect on the infectivity of a non-enveloped virus, norovirus, which is in agreement with previous studies demonstrating that free fatty acids are ineffective against nonenveloped viruses (Thormar et al., 1987 , Kohn et al., 1980 . In this study, ViroSAL at the indicated concentrations was mixed with an equal volume of viral inoculum (MeV:original TCID50 = 4.48 7 /mL, HSV-1: 100 PFU/mL, EBV: MOI=10, Zika: MOI=10, Orf: 4 PFU/mL) or pseudoviruses bearing VSV, Ebola, Lassa or SARS-CoV-1 envelope glycoproteins, and incubated at room temperature for 2 minutes. Virus/ViroSAL or control treated virus was inoculated onto appropriate target cells and incubated for 48h at 37°C, then fixed and infection enumerated, or, for pseudovirus assays, lysed and luciferase activity quantified as previously described (Fletcher et al., 2015) . Milk-based free fatty acids, as well as fatty acid emulsions, have been shown to inhibit infection of Vero cells with VSV and HSV-1, with no antiviral effect on poliovirus, a non-enveloped virus (Thormar et al., 1987) . doi = 10.1101/2020.03.29.009464 id = cord-326866-nbd4arhx author = Fox, Charles W. title = The representation of women as authors of submissions to ecology journals during the COVID-19 pandemic date = 2020-05-29 keywords = covid summary = At these six ecology journals there is no evidence of a decline in the proportion of submissions that are authored by women (as either first or submitting author) since the start of the COVID-19 disruptions; the proportion of papers authored by women in the post-COVID period of 2020 has increased relative to the same period in 2019, and is higher than in the period pre-COVID in 2020. At these six ecology journals there is no evidence of a decline in the proportion of submissions that are authored by women (as either first or submitting author) since the start of the COVID-19 disruptions; the proportion of papers authored by women in the post-COVID period of 2020 has increased relative to the same period in 2019, and is higher than in the period pre-COVID in 2020. doi = 10.1101/2020.05.29.123455 id = cord-343027-ks3fn9pq author = Fraser, Nicholas title = Preprinting the COVID-19 pandemic date = 2020-09-18 keywords = Fig; Supplemental; covid-19; preprint summary = When the data was broken down by server, it 132 was evident that whilst posting of COVID-19 preprints to bioRxiv had remained relatively steady, 133 preprints posted to medRxiv increased with time (Supplemental Fig. 2A) . Server usage differences were more pronounced 237 for COVID-19 preprints; multiple post-hoc comparisons confirmed that bioRxiv and medRxiv received 238 significantly higher usage per COVID-19 preprint than all other servers for which data was available 239 (Tukey HSD; all p values < 0.001). However, for non COVID-19 preprints, the only observed pairwise 240 differences between servers indicated greater bioRxiv usage than SSRN or Research Square (Tukey 241 HSD; all p values < 0.001). We also compared rates of PDF downloads for bioRxiv and medRxiv preprints 506 with a number of other preprint servers (Preprints.org, SSRN, and Research Square) (Supplemental Counts of multiple altmetric indicators (mentions in tweets, blogs, and news articles) were retrieved 510 via Altmetric (https://www.altmetric.com), a service that monitors and aggregates mentions to 511 scientific articles on various online platforms. doi = 10.1101/2020.05.22.111294 id = cord-103964-k6jnv87v author = Friedl, Jana title = More than just a ticket canceller: The mitochondrial processing peptidase matures complex precursor proteins at internal cleavage sites date = 2020-07-03 keywords = MPP; arg5,6 summary = title: More than just a ticket canceller: The mitochondrial processing peptidase matures complex precursor proteins at internal cleavage sites After import into mitochondria, these targeting signals are cleaved off by the mitochondrial processing peptidase MPP, giving rise to shorter mature proteins. Arg5,6 is synthesized as a polyprotein precursor that is imported into the mitochondrial matrix and subsequently separated into two distinct enzymes that function in arginine biogenesis. Our data suggest that, in addition to its role as "ticket canceller" for the removal of presequences, MPP exhibits a second, widely conserved activity as internal processing peptidase for complex mitochondrial precursor proteins. We conclude that Arg5,6 is imported into the mitochondrial matrix 104 via the presequence pathway and cleaved into separate polypeptides inside mitochondria. Incubation of radiolabeled Arg5,6 precursor protein with MPP resulted in the formation of smaller 124 fragments whose size perfectly matched those that were generated after import into isolated 125 mitochondria (Fig. 1E ). doi = 10.1101/2020.07.02.183996 id = cord-297787-t9neub6d author = Fu, Ziyang title = Structural basis for the inhibition of the papain-like protease of SARS-CoV-2 by small molecules date = 2020-07-18 keywords = GRL0617; SARS summary = The co-crystal structure of SARS-CoV-2 PLpro-C111S in complex with GRL0617 suggests that GRL0617 is a non-covalent inhibitor. The antiviral activity of GRL0617 reveal that PLpro is a promising drug target for therapeutically treating COVID-19. The in-vitro 85 IC50 of GRL0617 against SARS-COV-2 PLpro was 2.1 ± 0.2 μM, suggesting a promising lead 86 compound and therefore it was subjected to further structural and mechanistic studies ( Fig. 2A) . Taken together, our NMR and X-ray analysis indicates that GRL0617 162 is a potent PPI (protein-protein interaction) inhibitor for PLpro blocking the binding of ISG15. Our co-crystal structure of PLpro C111S in complex with the potent 175 inhibitor GRL0617 validated that SARS-COV-2 PLpro is a druggable target. Based on the structure, GRL0617 resides in the S3/S4 site of PLpro, naturally it will also 179 inhibit the processing of viral polyproteins of SARS-CoV-2 since these viral polyproteins share the 180 same substrate cleavage sequence with Ub and ISG15. The SARS-coronavirus papain-like 257 protease: structure, function and inhibition by designed antiviral compounds doi = 10.1101/2020.07.17.208959 id = cord-311333-shvtfxog author = Fukumoto, Tatsuya title = Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification date = 2020-05-28 keywords = SARS summary = title: Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification The virus was detected in 53/71 fresh samples by the direct method and 55/71 corresponding frozen samples by the nCoV-DK. Concordance rates were 95.2% (95% CI, 83.8-99.4), 95.5% (95% CI, 77.2-99.9), 85.7% (95% CI, 42.1-99.6) in nasopharyngeal swab, saliva, and sputum samples, respectively. These results indicate that the nCoV-DK effectively detects SARS-CoV-2 in all types of the samples including saliva, while reducing time required for detection, labor, and risk of human error. Nasopharyngeal swab, sputum and saliva samples were collected from 9 patients who 69 were admitted to our hospital after a diagnosis of COVID-19. Saliva as a 187 non-invasive specimen for detection of SARS-CoV-2 Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva Detection of noroviruses in fecal specimens by direct RT-PCR 195 without RNA purification doi = 10.1101/2020.05.27.120410 id = cord-103180-5hkoeca7 author = Furstenau, Tara N. title = Sample pooling methods for efficient pathogen screening: Practical implications date = 2020-07-16 keywords = number; sample summary = Sample pooling methods improve the efficiency of large-scale pathogen screening campaigns by reducing the number of tests and reagents required to accurately categorize positive and negative individuals. Here we use computational simulations to determine how several theoretical approaches compare in terms of (a) the number of tests, to minimize costs and save reagents, (b) the number of sequential steps, to reduce the time it takes to complete the assay, (c) the number of samples per pool, to avoid the limits of detection, (d) simplicity, to reduce the risk of human error, and (e) robustness, to poor estimates of the number of positive samples. 25 Due to practical concerns, Dorfman''s group testing approach was never applied to 26 syphilis screening because the large number of negative samples had a tendency to 27 dilute the antigen in positive samples below the level of detection [6] . doi = 10.1101/2020.07.16.206060 id = cord-103654-k02z72gb author = Gamboa Arana, Olga Lucia title = Dose-dependent enhancement of motion direction discrimination with transcranial magnetic stimulation of visual cortex date = 2020-06-15 keywords = EEG; TMS; motion; stimulation summary = Studies of motion perception are particularly well-suited for exploring mechanisms of TMS due to the superficial location of motion sensitive cortex and its well-characterized spatiotemporal progression of electroencephalographic (EEG) activation described by the P1/N2/P3 Visual Evoked Potential (VEP) complex. For this purpose, we used a three-visit study design consisting of an initial dose-finding session to derive individualized motion coherence thresholds and stimulation parameters based on the onset of the N2 VEP component ("N2-Onset"), followed by two dose-testing sessions during which spTMS was delivered according to the spatial, temporal, and intensity parameters derived from the first session. The overall goal was to map the behavioral and evoked EEG dose-response functions within the constructs of individualized spatiotemporal targeting with the expectation that spTMS delivered at the onset of the N2 component would disrupt motion processes in the brain and lead to monotonic effects across different stimulation intensities. doi = 10.1101/2020.06.14.151118 id = cord-103497-1ls2dvzy author = Ganier, C title = CD147 (BSG) but not ACE2 expression is detectable in vascular endothelial cells within single cell RNA sequencing datasets derived from multiple tissues in healthy individuals date = 2020-05-29 keywords = ACE2; SARS summary = title: CD147 (BSG) but not ACE2 expression is detectable in vascular endothelial cells within single cell RNA sequencing datasets derived from multiple tissues in healthy individuals To define the endothelial cell populations that are susceptible to infection with SARS-CoV-2, we investigated the expression of ACE2 as well as other genes implicated in the cellular entry of SARS-Cov-2 in the vascular endothelium through the analysis of single cell sequencing data derived from multiple human tissues (skin, liver, kidney, lung and intestine). The ACE2 receptor has been shown to mediate uptake of the virus responsible for COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in human cells (Hoffmann, Kleine-Weber, Schroeder, et al. In order to define the endothelial cell populations that are susceptible to infection with SARS-CoV-2, we investigated the expression of ACE2 in the vascular endothelium through the analysis of single cell sequencing data derived from multiple human tissues (skin, liver, kidney, lung and intestine). doi = 10.1101/2020.05.29.123513 id = cord-255552-k1retwa4 author = Gassen, Nils C. title = Analysis of SARS-CoV-2-controlled autophagy reveals spermidine, MK-2206, and niclosamide as putative antiviral therapeutics date = 2020-04-15 keywords = CoV-2; SARS summary = Pharmacological modulation of metabolism-dependent cellular pathways such as autophagy reduced propagation of highly pathogenic Middle East respiratory syndrome (MERS)-CoV. In-depth analyses of autophagy signaling and metabolomics indicate that SARS-CoV-2 reduces glycolysis and protein translation by limiting activation of AMP-protein activated kinase (AMPK) and mammalian target of rapamycin complex 1 (mTORC1). Targeting of these pathways by exogenous administration of spermidine, AKT inhibitor MK-2206, and the Beclin-1 stabilizing, antihelminthic drug niclosamide inhibited SARS-CoV-2 propagation by 85, 88, and >99%, respectively. In the case of highly pathogenic Middle East respiratory syndrome 57 (MERS)-CoV, we recently showed that autophagy is limited by a virus-induced AKT1-dependent 58 activation of the E3-ligase S-phase kinase-associated protein 2 (SKP2), which targets the key autophagy 59 initiating protein Beclin-1 (BECN1) for proteasomal degradation (10). Direct blocking of the negative BECN1 regulator SPK2 by previously 175 described inhibitors SMIP004, SMIP004-7, valinomycin, and niclosamide (10) showed SARS-CoV-2 176 growth inhibition from 50 (SMIP004, SMIP004-7) to over 99% in case of valinomycin and niclosamide 177 (Figure 4a, lower panel, Figure S3d,e) . doi = 10.1101/2020.04.15.997254 id = cord-302920-jkr438p9 author = Gasser, Romain title = Major role of IgM in the neutralizing activity of convalescent plasma against SARS-CoV-2 date = 2020-10-09 keywords = SARS summary = key: cord-302920-jkr438p9 title: Major role of IgM in the neutralizing activity of convalescent plasma against SARS-CoV-2 cord_uid: jkr438p9 Characterization of the humoral response to SARS-CoV-2, the etiological agent of Covid-19, is essential to help control the infection. In this regard, we and others recently reported that the neutralization activity of plasma from COVID-19 patients decreases rapidly during the first weeks after recovery. In this study, we selected plasma from a cohort of Covid-19 convalescent patients and selectively depleted immunoglobulin A, M or G before testing the remaining neutralizing capacity of the depleted plasma. This observation may help design efficient antibody-based COVID-19 therapies and may also explain the increased susceptibility to SARS-CoV-2 of autoimmune patients receiving therapies that impair the production of IgM. Decline of humoral 409 responses against SARS-CoV-2 Spike in convalescent individuals Potent neutralizing 413 antibodies from COVID-19 patients define multiple targets of vulnerability doi = 10.1101/2020.10.09.333278 id = cord-307701-fujejfwb author = Gaurav, Shubham title = Identification of unique mutations in SARS-CoV-2 strains isolated from India suggests its attenuated pathotype date = 2020-06-07 keywords = CoV-2; SARS summary = Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which was first reported in Wuhan, China in November 2019 has developed into a pandemic since March 2020, causing substantial human casualties and economic losses. In this study, we sequenced and analyzed the genomic information of the SARS-CoV-2 isolates from two infected Indian patients and explored the possible implications of point mutations in its biology. Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the cause of the novel human Corona Virus Disease COVID-19, first reported on November 17 th , 2019 in Wuhan, China [12] . In addition to structural and NSPs, SARS-CoV-2 genome also codes for at least two other viroporin candidates (other than the E protein), namely ORF3a and ORF8 [3] . Moreover, the 29-nucleotide deleted SARS CoV-1 strain had a 23-fold less viral replication as compared to its wild type, suggesting that this mutation effectively attenuated the virus. doi = 10.1101/2020.06.06.137604 id = cord-280979-0vaarrji author = Gauttier, V. title = Tissue-resident memory CD8 T-cell responses elicited by a single injection of a multi-target COVID-19 vaccine date = 2020-08-14 keywords = CD8; HLA; SARS summary = These data provide insights for further development of a second generation of COVID-19 vaccine focused on inducing lasting Th1-biased memory CD8 T cell sentinels protection using immunodominant epitopes naturally observed after SARS-CoV-2 infection resolution. These data provide insights for further development of a second generation of COVID-19 vaccine focused on inducing lasting Th1biased memory CD8 T cell sentinels protection using immunodominant epitopes naturally observed after SARS-CoV-2 infection resolution. Altogether, these data showed that optimized peptide vaccination against selected SARS-CoV-2 epitopes elicits robust and broad Th1-biased immunogenicity against several structural (S, M, N) and non-structural proteins in HLA-A2 expressing mice and that several peptides induce viral-specific memory CD8 T cells displaying all characteristics of T lymphocyte sentinels in barrier tissues. Using sequence design through reverse vaccinology selection approach based on previous CoVs knowledge on immunodominant epitopes and computational immunology optimization, we developed a combination of 12 CD8 T cell synthetic peptides originating from 11 SARS-CoV-2 structural and non-structural proteins capable to cover HLA polymorphism with high coverage globally and to induce immunogenicity to different proteins independently of HLA alleles expression. doi = 10.1101/2020.08.14.240093 id = cord-325473-hrdanbn1 author = Ghahremanpour, Mohammad M. title = Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2 date = 2020-08-28 keywords = SARS; drug summary = 2000 approved drugs to seek inhibitors of the main protease (Mpro) of SARS-CoV-2, the virus responsible for COVID-19. 5 Thus, M pro is viewed as a promising target for anti SARS-CoV-2 drug design; it has been the focus of several studies since the pandemic has emerged. For instance, a molecular docking study suggested remdesivir as a potential therapeutic that could be used against SARS-CoV-2, 10 which was supported experimentally by an EC50 value of 23 μM in an infected-cell assay. Structural Basis for the Inhibition of SARS-CoV-2 Main Protease by Antineoplastic Drug Carmofur Crystal Structure of SARS-CoV-2 Main Protease Provides a Basis for Design of Improved α-Ketoamide Inhibitors Prediction of Novel Inhibitors of the Main Protease (M-pro) of SARS-CoV-2 through Consensus Docking and Drug Reposition Structure-based Design of Antiviral Drug Candidates Targeting the SARS-CoV-2 Main Protease Targeting the SARS-CoV-2 Main Protease to Repurpose Drugs for doi = 10.1101/2020.08.28.271957 id = cord-287172-h8zoplkm author = Ghobrial, Moheb title = The human brain vasculature shows a distinct expression pattern of SARS-CoV-2 entry factors date = 2020-10-21 keywords = SARS summary = To understand the potential mechanisms underlying SARS-CoV-2 tropism for brain vasculature, we constructed a molecular atlas of the expression patterns of SARS-CoV-2 viral entry-associated genes (receptors and proteases) and SARS-CoV-2 interaction partners in human (and mouse) adult and fetal brain as well as in multiple non-CNS tissues in single-cell RNA-sequencing data across various datasets. Notably, the top regulated pathways included inflammation, angiogenesis, coagulation, cell-extracellular matrix interaction, viral-host interaction, vascular metabolism, blood-brain-barrier permeability, and reactive oxygen species (ROS) in both the adult and the fetal brain endothelium ( Together, these data reveal that CTSB is highly expressed in various endothelial cell clusters of the fetal and adult human brain and that pathways downstream of CTSB might provide a suggestive explanation of some of the neurovascular symptoms observed in COVID-19 doi = 10.1101/2020.10.10.334664 id = cord-310230-9wfb43gt author = Ghorbani, Mahdi title = Critical Sequence Hot-spots for Binding of nCOV-2019 to ACE2 as Evaluated by Molecular Simulations date = 2020-06-27 keywords = ACE2; RBD; SARS summary = Our goal is to provide a detailed structural mechanism of how nCOV-2019 recognizes and establishes contacts with ACE2 and its difference with an earlier coronavirus SARS-COV in 2002 via extensive molecular dynamics (MD) simulations. 7 Based on the sequence similarity between RBD of nCOV-2019 and SARS-COV and also the tight binding between RBD of nCOV-2019 and ACE2, it is most probable that nCOV-2019 uses this receptor on human cells to gain entry into the body. The focus of this article is to elucidate the differences between the interface of SARS-COV and nCOV-2019 with ACE2 to understand with atomic resolution the interaction mechanism and hotspot residues at the RBD/ACE2 interface using long-timescale molecular dynamics (MD) simulation. The binding energetics between ACE2 and the RBD of SARS-COV, nCOV-2019 and all its mutant complexes were investigated by the MMPBSA method. Computational Simulations Reveal the Binding Dynamics between Human ACE2 and the Receptor Binding Domain of SARS-CoV-2 Spike Protein doi = 10.1101/2020.06.27.175448 id = cord-296981-tded20ih author = Gilmore, Kerry title = In vitro efficacy of Artemisinin-based treatments against SARS-CoV-2 date = 2020-10-05 keywords = SARS; figure summary = We report in vitro efficacy of Artemisia annua extracts as well as artemisinin, artesunate, and artemether against SARS-CoV-2. Subsequent concentration-response studies using a high-throughput antiviral assay, based on immunostaining of SARS-CoV-2 spike glycoprotein, revealed that pretreatment and treatment with extracts, artemisinin, and artesunate inhibited SARS-CoV-2 infection of VeroE6 cells. The selectivity index (SI), calculated based on treatment and cell viability assays, was highest for artemisinin (54), and roughly equal for the extracts (5-10), artesunate (6) and artemether (<7). annua extracts, as well as pure artemisinin, artesunate, and artemether are active against SARS-CoV-2 in vitro. To initially screen whether extracts and pure artemisinin were active against SARS-CoV-2, their antiviral activity was tested by pretreating VeroE6 cells at different time points during 120 minutes with selected concentrations of the extracts or compounds prior to infection with the first European SARS-CoV-2 isolated in München (SARS-CoV-2/human/Germany/BavPat 1/2020). doi = 10.1101/2020.10.05.326637 id = cord-267115-6jqdi417 author = Giobbe, Giovanni Giuseppe title = SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids date = 2020-06-24 keywords = CoV-2; Fig; PCW; RNA; SARS; infection summary = Collectively, we established the first expandable human gastric organoid culture across fetal developmental stages, and we support the hypothesis that fetal tissue seems to be less susceptible to SARS-CoV-2 infection, especially in early stages of development. Principal component analysis (PCA) showed smaller heterogeneity in the organoid groups derived at different stages of fetal and pediatric development with respect to the primary tissues analyzed at the same stages, which may also include some heterogeneity from the surrounding cells as a result of the isolation procedure (Fig. 3a) . In order to validate both fetal and pediatric gastric organoids as functional in vitro models of SARS-CoV-2 infection and replication, we optimized the culture condition for viral infection in a 3D system (Fig. 4a) . doi = 10.1101/2020.06.24.167049 id = cord-350286-n7ylgqfu author = Giri, Rajanish title = When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses date = 2020-04-03 keywords = Bat; Human; RNA; SARS; Supplementary; Table; figure; protein summary = The results of this analysis are summarized in Table 2 , which clearly shows that most of the SARS-CoV-2 proteins contain at least one MoRF, indicating that disorder does play an important role in the functionality of these viral proteins. As it follows from Figure 3 , these cleavage sites are located within the IDPRs. In Human SARS CoV S protein, fusion peptide (residues 770-788) is located within a flexible region, is characterized by the mean disorder score of 0.232±0.053. Global analysis of intrinsic disorder in the replicase polyprotein 1ab Table 3 represents the PPID mean scores of 15 non-structural proteins (Nsps) derived from the Replicase polyprotein 1ab in SARS-CoV-2, Human SARS CoV, and Bat CoV. Similar to many other non-structural proteins of coronaviruses, Nsp15s from SARS-CoV-2, Human SARS, and Bat CoV are predicted to possess multiple flexible regions but contain virtually no IDPRs (see Figures 32A, 32B, and 32C) . doi = 10.1101/2020.03.13.990598 id = cord-103358-1hbw3yo3 author = Gisbert-Muñoz, Sandra title = MULTIMAP: Multilingual picture naming test for mapping eloquent areas during awake surgeries date = 2020-06-08 keywords = MULTIMAP; language; object; verb summary = Although the use of object naming tasks is widespread across surgical teams in many different geographical locations, heterogeneity in the stimuli selection criteria of previous batteries (i.e., differences in picture size, color, image quality, name agreement), in addition to the use of morphologically and typologically different languages across different studies (see supplementary material for a table review), has greatly hindered the comparison and generalization of results. Notably, direct cortical stimulation studies also show this double dissociation when object and action naming tasks are used, and allow for the identification of distinct territories in frontal and temporal brain areas in which stimulation selectively impairs verb or noun production (Corina et al., 2005; Crepaldi, Berlingeri, Paulesu, & Luzzatti, 2011; Lubrano et al., 2014; J. To address this need, we developed the MULTIMAP test, a multilingual picture naming task including both objects and actions for mapping eloquent areas during awake brain surgery. doi = 10.1101/2020.02.20.957282 id = cord-346670-34wfy52f author = Gobeil, Sophie M-C. title = D614G mutation alters SARS-CoV-2 spike conformational dynamics and protease cleavage susceptibility at the S1/S2 junction date = 2020-10-12 keywords = RBD; SARS; d614 summary = Most structures of the SARS-CoV-2 S ectodomain currently available include two mutations, one to disrupt the furin cleavage site (RRAR to GSAS = S-GSAS), and a double proline mutation (PP) of residues 986-987, designed to prevent conformational change to the post-fusion state (Wrapp et al., 2020) . While the SARS-CoV-2 S ectodomain construct that includes mutations of residues K986 and V987, between the HR1 and CH subdomains (S2 domain), to prolines (PP) (named S-GSAS/PP in this study) (Figure 1 ) is widely used in the field, the origin of this PP construct was based upon the stabilization of the pre-fusion conformation of other coronavirus spikes (Pallesen et al., 2017; Walls et al., 2020; Wrapp et al., 2020) . Similar to observations made with the S-GSAS/D614G S ectodomain structure, the RBD up/down motion in the furin-cleaved G614 S ectodomain was associated with a movement in the SD1 domain and in the region of the RBD-to-NTD linker that joined the SD1 b sheet ( Figure 7C, S8B) . doi = 10.1101/2020.10.11.335299 id = cord-332539-v1bfm57x author = Gohl, Daryl M. title = A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2 date = 2020-05-11 keywords = ARTIC; PCR; SARS summary = Several variants of the ARTIC protocol exist in which the pooled SARS-CoV-2 amplicons from a sample are taken through a NGS library preparation protocol (using either ligation or tagmentation-based approaches) in which sample-specific barcodes are added, and are then sequenced using either short-read (Illumina) or long-read (Oxford Nanopore, PacBio) technologies. We sequenced these samples using Illumina''s Nextera DNA Flex Enrichment protocol using a respiratory virus oligo panel containing probes for SARS-CoV-2, the ARTIC v3 tiled primers, and a novel tailed amplicon method designed to reduce cost and streamline the preparation of SARS-CoV-2 sequencing libraries. For the Illumina DNA Flex Enrichment protocol, SARS-CoV-2 genome coverage was more complete for samples with lower N1 and N2 Cts (ranging from ~20-30) at comparable read depths and coverage thresholds than with amplicon approaches, similar to the BEI WA isolate data ( Figure 3C , Supplemental Figure S2 -S3). doi = 10.1101/2020.05.11.088724 id = cord-351011-v4zmksio author = Golden, Joseph W. title = Human angiotensin-converting enzyme 2 transgenic mice infected with SARS-CoV-2 develop severe and fatal respiratory disease date = 2020-07-09 keywords = CoV-2; Fig; SARS; mouse summary = In contrast to non-transgenic mice, intranasal exposure of K18-hACE2 animals to two different doses of SARS-CoV-2 resulted in acute disease including weight loss, lung injury, brain infection and lethality. In comparison with the normal lung architecture in uninfected control animals, infected mice necropsied on day 3, and those succumbing to disease on days 5-11, had varying levels of lung injury including area of lung consolidation characterized by inflammation/expansion of 145 alveolar septa with fibrin, edema and mononuclear leukocytes and infiltration of vessel walls by numerous mononuclear leukocytes (Fig 3A, Fig S4, and Table S1 ). Importantly, in our study some animals at the lower dose survived infection despite significant Infection of K18-hACE2 mice by SARS-CoV-2 produces a disease similar to that observed in acute human cases, with development of an acute lung injury associated with edema, production 285 of inflammatory cytokines and the accumulation of mononuclear cells in the lung. doi = 10.1101/2020.07.09.195230 id = cord-255325-tl5fm2yu author = Goletic, Teufik title = Phylogenetic pattern of SARS-CoV-2 from COVID-19 patients from Bosnia and Herzegovina: lessons learned to optimize future molecular and epidemiological approaches date = 2020-06-19 keywords = SARS summary = Objectives of this research were: To share obtained sequences of the complete genome of SARS-CoV-2 strains from clinical samples of BiH patients diagnosed with COVID-19, and To contribute to the understanding of the interaction of molecular and classical epidemiology findings of COVID 19 in BH and the whole region and give recommendations for the improvement of prevention and future measures. Livno and Banja Luka samples WGS was performed according to the ARTIC amplicon sequencing protocol for MinION for nCoV-2019, which uses two primer pools to generate the sequence, as described elsewhere [7] . The constructed phylogenetic tree in Figure 2 indicates probable multiple independent introduction events as reflected by clustering of each single BiH sequence in a separate cluster, highlighted with red (Livno, EPI_ISL_462753), green (Banja Luka, EPI_ISL_462990), blue (Sarajevo, EPI_ISL_467300) and purple (Tuzla, EPI_ISL_463893). doi = 10.1101/2020.06.19.160606 id = cord-102886-oo7q05ml author = Gomes, Fabio M. title = “Proliferation of DBLOX Peroxidase-Expressing Oenocytes Maintains Innate Immune Memory in Primed Mosquitoes” date = 2020-09-10 keywords = DBLOX; Fig summary = title: "Proliferation of DBLOX Peroxidase-Expressing Oenocytes Maintains Innate Immune Memory in Primed Mosquitoes" Immune priming in Anopheles gambiae mosquitoes following infection with Plasmodium parasites is mediated by the systemic release of a hemocyte differentiation factor (HDF), a complex of lipoxin A4 bound to Evokin, a lipid carrier. We provide direct evidence that modifications mediated by the histone acetyltransferase AgTip60 (AGAP01539) are essential for sustained oenocyte proliferation, HDF synthesis and immune priming. We propose that oenocytes function as a population of "memory" cells that continuously release lipoxin to orchestrate and maintain a broad, systemic and long-lasting state of enhanced immune surveillance. We recently showed that two heme peroxidases, HPX7 and HPX8, are necessary for midgut PGE 2 synthesis and are essential to establish immune priming in response to Plasmodium infection (8) . These cells express high levels of DBLOX and their proliferation is essential for HDF synthesis and to maintain the priming response. doi = 10.1101/2020.09.09.290312 id = cord-102406-9gnbe3n1 author = González-Arias, Fabio title = Scalable Analysis of Authentic Viral Envelopes on FRONTERA date = 2020-07-06 keywords = Frontera; VMD summary = doi = 10.1101/2020.07.05.188367 id = cord-356090-oj3d9ail author = Gorgun, D. title = Binding Mode of SARS-CoV2 Fusion Peptide to Human Cellular Membrane date = 2020-10-27 keywords = Fig; SARS; membrane summary = Here, we use an array of molecular dynamics (MD) simulations taking advantage of the Highly Mobile Membrane Mimetic (HMMM) model, to investigate the interaction of the SARS-CoV2 FP with a lipid bilayer representing mammalian cellular membranes at an atomic level, and to characterize the membrane-bound form of the peptide. Taken into account the sequence conservation among the viral FPs and the results of mutagenesis studies establishing the role of specific residues in the helical portion of the FP in membrane association, we propose that the helix-binding mode represents more closely the biologically relevant form. In this study, using molecular dynamics simulations, we describe how the fusion peptide from the SARS-CoV2 virus binds human cellular membranes and characterize, at an atomic level, lipid-protein interactions important for the stability of the bound state. In this study, using a large set of simulations, we describe how the SARS-CoV2 FP binds mammalian cellular membranes and characterize, at atomic details, lipid-protein interactions important for the stability of the bound state. doi = 10.1101/2020.10.27.357350 id = cord-331680-qlzhtxs0 author = Goryachev, A.N. title = Potential Opportunity of Antisense Therapy of COVID-19 on an in Vitro Model date = 2020-11-03 keywords = RNA; SARS; Vero summary = In accordance with the purpose of the study, the following tasks were set: -to select the nucleotide sequence of the virus that is supposed to be inhibited, -to carry out the synthesis of oligonucleotide, -to determine cytotoxicity and antiviral activity in an in vitro experiment on cell culture. The assessment of antiviral activity of the drug in addition to cytopathic action was also taken into account by reducing the infectious titer of the virus in the culture of Vero cells E6 according to PCR RNA SARS-CoV-2, determined by the threshold of the number of reaction cycles (cycle treshold, Ct) in various dilutions of the study drug. Determination of the antiviral efficacy of the antisense oligonucleotide according to the treatment scheme (administration of the drug 24 hours after infection) was taken into account by the decrease in the infectious titer of the virus in the culture of Vero E6 cells by the cytopathic effect. doi = 10.1101/2020.11.02.363598 id = cord-351321-6d2mn5ok author = Gouveia, Duarte title = Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window date = 2020-06-19 keywords = ADETQALPQR; SARS; peptide; swab summary = Simili nasopharyngeal swabs spiked with different quantities of purified SARS-CoV-2 viral material were used to develop a nanoLC-MS/MS acquisition method, which was then successfully applied on COVID-19 clinical samples. By using a short LC gradient focusing on the region of interest identified in our previous study, we tested the detection of the virus in samples containing different quantities of viral peptides, as well as COVID-19 clinical samples, paving the way for the development of time-efficient viral diagnostic tests based on an alternative platform. To assess the performance of shotgun MS-based proteomics in detecting SARS-CoV-2 peptides in a background matrix consisting of nasopharyngeal swab protein material, we experimentally created tryptic peptidomes from i) a purified virus solution obtained from Vero E6 cells infected with a SARS-CoV-2 reference strain, and ii) nasopharyngeal swabs obtained from two healthy volunteers (Figure 1) . Simili swabs containing specific quantities of SARS-CoV-2 virus and the equivalent of 8.4% of the nasal matrix protein material collected during sampling were analysed by MS/MS with a short gradient. doi = 10.1101/2020.06.19.161000 id = cord-277487-jgbjxgh1 author = Graham, Simon P. title = Evaluation of the immunogenicity of prime-boost vaccination with the replication-deficient viral vectored COVID-19 vaccine candidate ChAdOx1 nCoV-19 date = 2020-06-20 keywords = CoV-2; IFN; SARS; pig summary = Clinical development of the COVID-19 vaccine candidate ChAdOx1 nCoV-19, a replication-deficient simian adenoviral vector expressing the full-length SARS-CoV-2 spike (S) protein was initiated in April 2020 following non-human primate studies using a single immunisation. Whilst a single dose induced antigen-specific antibody and T cells responses, a booster immunisation enhanced antibody responses, particularly in pigs, with a significant increase in SARS-CoV-2 neutralising titres. Analysis of SARS-CoV-2 S protein-specific murine splenocyte responses by IFNγ ELISpot assay showed no statistically significant difference between the prime-only and primeboost vaccination regimens, in either strain of mouse ( Figure 1A ). IFN-γ ELISpot analysis of porcine peripheral blood mononuclear cells (PBMC) showed responses on 42 dpv (2 weeks after boost) that were significantly greater in the prime-boost pigs compared to prime-only animals (p < 0.05; Figure 1C ). : SARS-CoV-2 S protein-specific antibody responses following ChAdOx1 nCoV-19 primeonly and prime-boost vaccination regimens in mice and pigs. doi = 10.1101/2020.06.20.159715 id = cord-299737-r34d0rx7 author = Grant, Paul R title = Extraction-free COVID-19 (SARS-CoV-2) diagnosis by RT-PCR to increase capacity for national testing programmes during a pandemic date = 2020-04-08 keywords = PCR summary = The standard molecular diagnostic test is a multistep process involving viral RNA extraction and real-time quantitative reverse transcriptase PCR (qRT-PCR). We have developed a simplified qRT-PCR assay that removes the need for an RNA extraction process and can be run on a real-time thermal cycler. The standard molecular diagnostic test for this virus is a multistep process involving viral RNA extraction and real-time quantitative reverse transcriptase PCR (qRT-PCR). Using the same primers and probes, we have now developed a qRT-PCR that can be run on a real-time thermal cycler without the need for an RNA extraction process. Direct addition of samples to the qRT-PCR without extraction with a diagnostic sensitivity of 98.0%, specificity of 100% and accuracy of 98.8% compared to the method on the Panther Fusion. Many laboratories use real-time thermal cyclers, so this method can be used to increase national screening capacity without the need for other specialized equipment or RNA extraction reagents. doi = 10.1101/2020.04.06.028316 id = cord-304356-jyp9gjh9 author = Grant, Rogan A. title = Alveolitis in severe SARS-CoV-2 pneumonia is driven by self-sustaining circuits between infected alveolar macrophages and T cells date = 2020-08-05 keywords = COVID-19; RNA; SARS; cell; figure; pneumonia summary = We performed single cell RNA-Seq in 5 bronchoalveolar lavage fluid samples collected from patients with severe COVID-19 within 48 hours of intubation. b. Sankey diagram illustrating relationship between number of BAL samples from participants with COVID-19, other viral pneumonia, non-viral pneumonia (other pneumonia) and non-pneumonia controls 1) enrolled in the SCRIPT study (534 samples), 2) analyzed via flow cytometry (344 samples), 3) bulk RNA-seq on flow-sorted alveolar macrophages (243 samples) and 4) single-cell RNA-seq (6 samples). To define the immune cell profile over the course of severe SARS-CoV-2-induced pneumonia, we analyzed 116 samples from 61 patients with confirmed COVID-19 in our cohort. As our analysis of transcriptomic data from alveolar macrophages suggested that SARS-CoV-2 pneumonia is uniquely associated with the activation of pathways induced by interferons, we looked for the expression of type I interferons in our single cell dataset. doi = 10.1101/2020.08.05.238188 id = cord-255515-7se14455 author = Graudenzi, Alex title = Mutational Signatures and Heterogeneous Host Response Revealed Via Large-Scale Characterization of SARS-COV-2 Genomic Diversity date = 2020-07-06 keywords = SARS summary = To dissect the mechanisms underlying the observed inflation of variants in SARS-CoV-2 genome, we present the largest up-to-date analysis of intra-host genomic diversity, which reveals that the majority of samples present a complex sublineage architecture, due to the interplay between host-related mutational processes and transmission dynamics. Strikingly, our analysis allowed to identify three non-overlapping mutational signatures, i.e., specific distributions of nucleotide substitutions, which are observed in distinct clusters of samples in a mutually exclusive fashion, suggesting the presence of host-related mutational processes. Finally, the analysis of homoplasies, i.e., (low-frequency) variants shared across distinct viral lineages and unlikely due to infection events, demonstrate that a high number of mutations can independently emerge in multiple samples, due to mutational hotspots often related to signatures or, possibly, to positive (functional) selection. doi = 10.1101/2020.07.06.189944 id = cord-326380-9ecsp66y author = Griesemer, Sara B title = Assessment of sample pooling for clinical SARS-CoV-2 testing date = 2020-05-27 keywords = pool; sample summary = The greatest concern with this approach in a clinical setting is the potential for reduced sensitivity, particularly the risk of false negative results when weak positive samples are pooled. To investigate this possibility, detection rates in pooled samples were evaluated, with extensive assessment of pools containing weak positive specimens. Additionally, the percentage of positive samples at different viral loads, as assessed by Ct value, was reviewed across nine weeks of the pandemic, to determine if these weak positive specimens comprise a significant component of total tested specimens and whether the proportion has changed over the course of the pandemic. In contrast, for weak positive specimens in VTM transport media, nine-sample pools caused multiple replicates to return negative results. We then sought to assess what component of the total specimens tested are comprised of these weak positive specimens, to evaluate how much of an impact pooling might have overall on testing sensitivity across positive patient detection in the pandemic. doi = 10.1101/2020.05.26.118133 id = cord-294120-8fxrqorg author = Guebre-Xabier, Mimi title = NVX-CoV2373 vaccine protects cynomolgus macaque upper and lower airways against SARS-CoV-2 challenge date = 2020-08-19 keywords = SARS summary = title: NVX-CoV2373 vaccine protects cynomolgus macaque upper and lower airways against SARS-CoV-2 challenge Cynomolgus macaques (Macaca fascicularis) immunized with NVX-CoV2373 and the saponin-based Matrix-M adjuvant induced anti-S antibody that was neutralizing and blocked binding to the human angiotensin-converting enzyme 2 (hACE2) receptor. And, hACE2 receptor 158 inhibition titers of 649, 1,410, and 1,320 in 2.5, 5, and 25 µg NVX-CoV2373 dose groups 159 respectively were 5.2 -11.2-fold higher than in convalescent sera ( Figure 1C) . Finally, 160 SARS-CoV-2 GMT neutralization antibody titers of 17,920 -23,040 CPE 100 in 161 immunized macaques, were 7.9 -10.1-fold higher than in convalescent sera ( Figure 162 1D) . To evaluate the potential efficacy of NVX-CoV2373 vaccine, macaques were 165 challenged with SARS-CoV-2 virus in upper and lower airways. SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 214 elicits immunogenicity in baboons and protection in mice These interests do not alter the authors adherence to policies on 209 sharing data and materials. doi = 10.1101/2020.08.18.256578 id = cord-264204-4ablrwuo author = Guintivano, Jerry title = Psychiatric Genomics Research During the COVID-19 Pandemic: A Survey of Psychiatric Genomics Consortium Researchers date = 2020-10-08 keywords = COVID-19; PGC; research summary = We provide recommendations for institutions, organizations such as the PGC, as well as individual senior investigators to ensure that the futures of early career investigators, especially those underrepresented in academic medicine such as women and underrepresented minorities, are not disproportionately disadvantaged by the COVID-19 pandemic. Four main themes characterized the comments: maintain team dynamics (e.g., utilizing videoconferencing for regular team meetings, being flexible with deadlines, use clear communication) (32.8% of responses); maintain good personal habits (e.g., keeping in mind productivity may be reduced, practicing self-care, keeping work and personal areas separate) (27.2%); reprioritize research goals (e.g., spending more effort on dry-lab projects rather than wet-lab, using available time to complete analyses or manuscripts, utilizing existing data for new projects) (20.8%); and shift recruitment to online approaches (e.g., phone interviews rather than face-to-face, development of online recruitment and consent protocols) (8.0%). doi = 10.1101/2020.10.08.331421 id = cord-280392-ij5gtesw author = Gultom, Mitra title = Susceptibility of well-differentiated airway epithelial cell cultures from domestic and wildlife animals to SARS-CoV-2 date = 2020-11-10 keywords = AEC; SARS summary = In this study, we inoculated well-differentiated animal AEC cultures of monkey, cat, ferret, dog, rabbit, pig, cattle, goat, llama, camel, and two neotropical bat species with SARS-CoV-2. The AEC 131 cultures from 12 different species (rhesus macaque, cat, ferret, dog, rabbit, pig, cattle, goat, llama, 132 camel, and two neotropical bats) were inoculated with 10.000 TCID50 of either IAV or IDV and incubated 133 at 33°C and 37°C. For IDV we observed 137 antigen-positive cells in all AEC model, except for rhesus macaque and one of the neotropical bat 138 species, indicating that the AEC cultures were all well-differentiated and susceptible to virus infection. In the viral sequences in the 96 hpi samples from virus-infected 156 rhesus macaque and cat AEC cultures, we observed no obvious signs of nucleotide transitions that lead 157 to nonsynonymous mutations compared to the respective inoculums ( Fig. 3) , irrespective of 158 temperature and animal species. doi = 10.1101/2020.11.10.374587 id = cord-270698-9w3ap3gz author = Guo, Hua title = Evolutionary arms race between virus and host drives genetic diversity in bat SARS related coronavirus spike genes date = 2020-05-13 keywords = ACE2; SARS summary = title: Evolutionary arms race between virus and host drives genetic diversity in bat SARS related coronavirus spike genes The Chinese horseshoe bat (Rhinolophus sinicus), reservoir host of severe acute respiratory syndrome coronavirus (SARS-CoV), carries many bat SARS-related CoVs (SARSr-CoVs) with high genetic diversity, particularly in the spike gene. Despite these variations, some bat SARSr-CoVs can utilize the orthologs of human SARS-CoV receptor, angiotensin-converting enzyme 2 (ACE2), for entry. Consistent results were observed by binding affinity assays between SARSand SARSr-CoV spike proteins and receptor molecules from bats and humans. In a host-virus arms race situation, the genes involved tend to display dN/dS ratios Codon-based analysis of molecular evolution 536 Bat ACE2 and SARSr-CoV spike sequences were analyzed for positive selection. Identification of key amino acid 671 residues required for horseshoe bat angiotensin-I converting enzyme 2 to function as a 672 receptor for severe acute respiratory syndrome coronavirus doi = 10.1101/2020.05.13.093658 id = cord-320165-1b6sycgv author = Guo, Qirui title = Small molecules inhibit SARS-COV-2 induced aberrant inflammation and viral replication in mice by targeting S100A8/A9-TLR4 axis date = 2020-09-09 keywords = MHV; Paquinimod; S100A8; SARS; figure summary = S100A8/A9 specific inhibitor, Paquinimod, significantly reduced the number of neutrophils activated by the coronavirus, inhibited viral replication and rescued lung damage a result of SARS-CoV-2 infection. The whole genome wide RNA-seq analysis of the lungs from infected rhesus macaques showed that a number of transcripts were induced or inhibited at day 3 and day 5 after SARS-CoV-2 infection (Supplementary Figure 1A) . Similar to the data from rhesus macaque experiments, compared to other alarmins, S100A8 was robustly induced by SARS-CoV-2 but not by IAV infection in mice ( Figure 2E ). The expression of these B cell related genes was rescued or induced by Paquinimod during MHV infection, which was confirmed by qRT-PCR analysis ( Figure 3M ). Moreover, both Paquinimod and Resatorvid suppressed the activation of coronavirus related neutrophils in lung during SARS-CoV-2 infection ( Figure 4D ). doi = 10.1101/2020.09.09.288704 id = cord-298172-iyxyennq author = Guo, Youjia title = Potent mouse monoclonal antibodies that block SARS-CoV-2 infection date = 2020-10-02 keywords = Fig; S1D7; S3D8; SARS summary = Various recombinant monoclonal antibodies of human origin that neutralize SARS-CoV-2 infection have been isolated from convalescent patients and will be applied as therapies and prophylaxis. Here, we produced mouse anti-SARS-CoV-2 spike monoclonal antibodies that exhibit not only robust performance in immunoassays including western blotting, ELISA, immunofluorescence, and immunoprecipitation, but also neutralizing activity against SARS-CoV-2 infection in vitro. Among them, two antibodies were shown to attenuate the interaction of spike proteins with ACE2 and neutralized infection of VeroE6/TMPRSS2 cells by SARS-CoV-2. Mice were immunized with these recombinant spike proteins to generate antibodies against the SARS-CoV-2 virus, followed by cell fusion to generate a hybridoma-producing antibody. The performance of our antibodies in IP experiments prompted us to examine whether they were capable of inhibiting spike-ACE2 binding or even neutralizing SARS-CoV-2 infection. Our antibodies, S1D7 and S3D8, have been shown to attenuate the interaction of spike proteins with ACE2 and neutralize infection of VeroE6/TM2 cells by SARS-CoV-2. doi = 10.1101/2020.10.01.323220 id = cord-102705-mcit0luk author = Gupta, Chitrak title = Mind reading of the proteins: Deep-learning to forecast molecular dynamics date = 2020-07-29 keywords = ADK; Fig; time summary = doi = 10.1101/2020.07.28.225490 id = cord-300078-svu06v9c author = Haghani, Milad title = Covid-19 pandemic and the unprecedented mobilisation of scholarly efforts prompted by a health crisis: Scientometric comparisons across SARS, MERS and 2019-nCov literature date = 2020-06-01 keywords = Covid-19; MERS; SARS; study summary = To compare the scientometric aspects of the studies on SARS, MERS and Covid-19, three separate datasets of publications on these three topics were retrieved from Scopus through three separate search strategies. Figures A1 and A2 in the Appendix illustrate the map associated with the SARS literature overlaid respectively with the average year of publication and average number of citations associated with the studies where these keywords have occurred. Maps of term occurrences based on the analysis of the title and abstract of studies on SARS, MERS and Covid-19 have also been presented in Figures 7, 8 and 9 respectively. An inspection of the maps overlaid with the average year of publications for SARS and MERS in Figures A1 and A3 in the Appendix suggests that, on average, this cohort of studies are generally the last to emerge in the published domain compared to the two other major clusters, but they receive relatively high citations on average (according to Figures A2, A4 and A6). doi = 10.1101/2020.05.31.126813 id = cord-102958-q8jamg07 author = Hahka, Taija M. title = Resiniferatoxin (RTX) ameliorates acute respiratory distress syndrome (ARDS) in a rodent model of lung injury date = 2020-09-14 keywords = ALI; RTX; TRPV1; lung summary = We ablated cardiopulmonary spinal afferents through either epidural T1-T4 dorsal root ganglia (DRG) application or intra-stellate ganglia delivery of a selective afferent neurotoxin, resiniferatoxin (RTX) in rats 3 days post bleomycin-induced lung injury. Our data showed that both epidural and intra-stellate ganglia injection of RTX significantly reduced plasma extravasation and reduced the level of lung pro-inflammatory cytokines providing proof of principle that cardiopulmonary spinal afferents are involved in lung pathology post ALI. Therefore, in the current study we hypothesized that ablation of lung afferent innervation (thoracic spinal) by application of an ultrapotent, selective afferent neurotoxin, resiniferatoxin (RTX) will modify the course of the pathology including lung edema and local pulmonary inflammation associated with progressive ALI. 2 1 Our data suggest that pulmonary spinal afferent ablation by intra-stellate injection of RTX reduces plasma extravasation and local pulmonary inflammation post bleomycininduced lung injury which results in improved blood gas exchange. doi = 10.1101/2020.09.14.296731 id = cord-255895-6at9gelt author = Han, Namshik title = Identification of SARS-CoV-2 induced pathways reveal drug repurposing strategies date = 2020-08-25 keywords = Proguanil; SARS; Sulfasalazine; drug; figure summary = We constructed a SARS-CoV-2-induced protein (SIP) network, based on disease signatures defined by COVID-19 multi-omic datasets(Bojkova et al., 2020; Gordon et al., 2020), and cross-examined these pathways against approved drugs. This analysis identified 200 drugs predicted to target SARS-CoV-2-induced pathways, 40 of which are already in COVID-19 clinical trials(Clinicaltrials.gov, 2020) testifying to the validity of the approach. Importantly, treatment of Calu-3 and Vero E6 cell lines with Proguanil and Sulfasalazine led to a significant downregulation of the mRNA of key cytokines (Figures 4G-J and S8), which are dictated by the p38/MAPK signalling pathway and shown to become elevated during SARS-CoV-2 infection and replication (CXCL3, IFNB1 and TNF-A). Here we have used a series of computational approaches, including bespoke methods for data integration, network analysis, computer simulation and machine learning, to identify novel SARS-CoV-2 induced pathways that could be targeted therapeutically by repurposing existing and approved drugs ( Figure S9 ). doi = 10.1101/2020.08.24.265496 id = cord-103524-1w9tdhdd author = Hao, Siyuan title = Establishment of a Replicon System for Bourbon Virus and Identification of Small Molecules that Efficiently Inhibit Virus Replication date = 2020-04-25 keywords = BRBV; Fig summary = By using the luciferase reporter, we screened a few small molecule compounds of anti-endonuclease that inhibited the nicking activity by parvovirus B19 (B19V) NS1, as well as FDA-approved drugs targeting the RdRP of influenza virus. Our results demonstrated that myricetin, and an anti-B19V NS1 nicking inhibitor, efficiently inhibited the RdRP activity of BRBV and virus replication. We then used the replicon reporter to examine anti-influenza drugs that target viral RNA-dependent RNA polymerase (RdRP) and endonuclease inhibitors of human parvovirus B19 (B19V) for inhibition of BRBV RdRP activity and BRBV replication in HEK293T and Vero cells. BRBV GFP reporter assay: pHW-ΔCMV-GP-GFP was co-transfected with the four pcDNA-PA, PB1, PB2, and NP plasmids into HEK293T cells confluent in six-well plates. BRBV luciferase reporter assay: pHW-ΔCMV-GP-gLuc and the four pcDNA-based plasmids were co-transfected into HEK293T cells in 96-well plate. doi = 10.1101/2020.04.24.058693 id = cord-337973-djqzgc1k author = Hao, Siyuan title = Long Period Modeling SARS-CoV-2 Infection of in Vitro Cultured Polarized Human Airway Epithelium date = 2020-08-28 keywords = ALI; HAE; SARS summary = title: Long Period Modeling SARS-CoV-2 Infection of in Vitro Cultured Polarized Human Airway Epithelium We also identified that SARS-CoV-2 does not infect HAE from the basolateral side, and the dominant SARS-CoV-2 permissive epithelial cells are ciliated cells and goblet cells, whereas virus replication in basal cells and club cells was not detectable. Our observation that SARS-CoV-2 was unable to infect epithelial cells from the 299 basolateral side supports that the viral entry receptor ACE2 is polarly expressed at the apical 300 side 30, 31 . We 332 determined that 1 pfu of SARS-CoV-2 in Vero-E6 cells has a particle (viral genome copy) 333 number of 820, suggesting that a load of 2.46 x 10 5 particles is required to productively infect 1 334 cm 2 of the airway epithelium, which is much higher than the small DNA virus parvovirus human 335 bocavirus 1 (HBoV1) we studied 55 . doi = 10.1101/2020.08.27.271130 id = cord-307811-6e3j0pn7 author = Hao, Wei title = Binding of the SARS-CoV-2 Spike Protein to Glycans date = 2020-07-02 keywords = MERS; SARS; protein summary = Infection normally starts with the attachment of the virus to cell-surface glycans like heparan sulfate (HS) and sialic acid-containing oligosaccharides. Previous studies of many other viruses suggested that SARS-CoV-2 S protein may use other molecules on host cell surface as attachment factors to facilitate binding to the high-affinity receptor ACE2. 36 A recent study suggested that HS may bind to the receptor binding domain (RBD, the C-terminal region of the S1 subunit, Fig. 2 ) of the SARS-CoV-2 spike protein and change its conformation. 38 In this study, we systematically examined and compared the binding of the SARS-CoV-2 S protein subunits, full-length molecule and its trimer to different HS using microarray experiments (Fig. 2) . In addition to binding protein-based receptors, many viruses can interact with cell surface glycans, including GAGs and sialic acid-containing oligosaccharides. doi = 10.1101/2020.05.17.100537 id = cord-102156-v98vrely author = Harda, Zofia title = Loss of mu and delta opioid receptors on neurons expressing dopamine receptor D1 has no effect on reward sensitivity date = 2020-03-20 keywords = Fig; neuron; opioid; receptor summary = doi = 10.1101/2020.03.18.996454 id = cord-336012-8klkojpo author = Harilal, Divinlal title = SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission date = 2020-06-18 keywords = RNA; SARS; USA summary = Unlike RT-qPCR, SARS-CoV-2 Whole Genome Sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. Methods We performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 full genome amplification and sequencing with respect to virus detection, scalability, and cost-effectiveness. Conclusions SARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic. Here we show that cWGS is cost-effective and is highly scalable when using a target enrichment sequencing method, and we also demonstrate its utility in tracking the origin of SARS-CoV-2 transmission. doi = 10.1101/2020.06.06.138339 id = cord-103868-iwpiti2h author = Harrison, Angela R. title = The Ebola virus interferon antagonist VP24 undergoes active nucleocytoplasmic trafficking date = 2020-08-11 keywords = GFP; VP24 summary = Functions of the Ebola virus (EBOV) IFN antagonist VP24 include nucleocapsid assembly during cytoplasmic replication and inhibition of IFN-activated signalling by STAT1. Proteins of many viruses with cytoplasmic replication cycles similar to EBOV interact with the nuclear trafficking machinery, resulting in active nucleocytoplasmic shuttling important to immune evasion and other intranuclear functions. Thus, it appears that active In this study we have shown that EBOV VP24 undergoes active trafficking between the nucleus 275 and cytoplasm involving CRM1-dependent nuclear export via a NES at the VP24 C-terminus. Notably, the EBOV 287 matrix protein VP40 has also been reported to localise to the nucleus in infected and transfected 288 cells (16, 50); however, a direct role for active trafficking pathways to regulate localisation, 289 distinct from mechanisms such as diffusion or interaction with other host factors, has not been 290 defined. doi = 10.1101/2020.08.10.245563 id = cord-297786-jz1d1m2e author = Hasan, Md. Mahbub title = Global and Local Mutations in Bangladeshi SARS-CoV-2 Genomes date = 2020-08-26 keywords = Bangladesh; CoV-2; SARS summary = Corona Virus Disease-2019 (COVID-19) warrants comprehensive investigations of publicly available Severe Acute Respiratory Syndrome-CoronaVirus-2 (SARS-CoV-2) genomes to gain new insight about their epidemiology, mutations and pathogenesis. In this study, we compared 207 of SARS-CoV-2 genomes reported from different parts of Bangladesh and their comparison with 467 globally reported sequences to understand the origin of viruses, possible patterns of mutations, availability of unique mutations, and their apparent impact on pathogenicity of the virus in victims of Bangladeshi population. Then, we studied the variants present in different isolates of Bangladesh to investigate the pattern of mutations, identify UMs, and discuss the pseudo-effect of these mutations on the structure and function of encoded proteins, with their role in pathogenicity. To understand the SARS-CoV-2 viral transmission in Bangladesh, we performed phylogenetic analysis on the selected 207 viral genomes reported from different districts of Bangladesh along with selected 467 globally submitted sequences as reported from 42 countries and 6 continents ( Figure 1 ). doi = 10.1101/2020.08.25.267658 id = cord-102504-d840uu3e author = Hass, Kenneth N. title = Integrated Micropillar Polydimethylsiloxane Accurate CRISPR Detection (IMPACT) System for Rapid Viral DNA Sensing date = 2020-03-20 keywords = CRISPR; detection; dna; impact summary = doi = 10.1101/2020.03.17.994137 id = cord-312999-3erodkv9 author = Hassan, Sk. Sarif title = Notable sequence homology of the ORF10 protein introspects the architecture of SARS-COV-2 date = 2020-09-06 keywords = ORF10; Pangolin; SARS summary = SARS-CoV-2 has been reported to be uniquely characterized by the accessory protein ORF10, which contains eleven cytotoxic T lymphocyte (CTL) epitopes of nine amino acids length each, across various human leukocyte antigen (HLA) subtypes. In this study, all missense mutations found in sequence databases were examined across twnety-two unique SARS-CoV-2 ORF10 variants that could possibly alter viral pathogenicity. The high degree of physicochemical and structural similarity of ORF10 proteins of SARS-CoV-2 and Pangolin-CoV open questions about the architecture of SARS-CoV-2 due to the disagreement of these two ORF10 proteins over their sub-structure (loop/coil region), solubility, antigenicity and change from the strand to coil at amino acid position 26, where tyrosine is present. Based on the mutations, conserved and non-conserved residues in ORF10 proteins are identified and marked in different colors in (Figure There are altogether 22 distinct missense mutations which were examined across 22 unique ORF10 variants of SARS-CoV-2. doi = 10.1101/2020.09.06.284976 id = cord-338055-2d6n4cve author = Hassan, Sk. Sarif title = A unique view of SARS-CoV-2 through the lens of ORF8 protein date = 2020-08-26 keywords = Bat; ORF8; Pangolin; SARS summary = In this present study, we identified the distinct mutations present across unique variants of the SARS-CoV-2 ORF8 and classified them according to their predicted effect on the host, i.e disease or neutral and the consequences on protein structural stability. The ORF8 sequences of SARS-CoV-2, Bat-CoV RaTG13 and Pangolin-CoV have almost the same positive and negative charged amino acids, therefore we can say that probably they have similar kind of electrostatic and hydrophobic interactions, 135 which also contribute to the functionality of the proteins. • QKV07730.1: The T11A mutation occurred as the second mutation in this sequence, which was predicted to be of disease-increasing type and the polarity was changed from hydrophilic to hydrophobic, hence the structure and 305 function of the protein are expected to differ. doi = 10.1101/2020.08.25.267328 id = cord-102935-cx3elpb8 author = Hassani-Pak, Keywan title = KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species date = 2020-04-24 keywords = gene; node summary = Here we report the main design principles behind KnetMiner and provide use cases for mining public datasets to identify unknown links between traits such grain colour and pre-harvest sprouting in Triticum aestivum, as well as, an evidence-based approach to identify candidate genes under an Arabidopsis thaliana petal size QTL. KnetMiner is the first open-source gene discovery platform that can leverage genome-scale knowledge graphs, generate evidence-based biological networks and be deployed for any species with a sequenced genome. Even when 38 the task of gathering information is complete, it is demanding to assemble a coherent view of how 39 each piece of evidence might come together to "tell a story" about the biology that can explain how 40 multiple genes might be implicated in a complex trait or disease. doi = 10.1101/2020.04.02.017004 id = cord-329840-f3dsu36p author = Hati, Sanchita title = Impact of Thiol-Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin Converting Enzyme 2 Receptor date = 2020-05-11 keywords = ACE2; SARS; protein summary = In this study, the role of thiol-disulfide balance on the interactions between SARS-CoV/CoV-2 spike proteins and ACE2 was investigated using molecular dynamic simulations. The study revealed that the binding affinity was significantly impaired when all the disulfide bonds of both ACE2 and SARS-CoV/CoV-2 spike proteins were reduced to thiol groups. In the backdrop of significant mortality rate for SARS-CoV-2 (hereinafter referred to as CoV-2) infection, it is important to know if the thiol-disulfide balance plays any role on the binding of the spike glycoprotein on to the host cell receptor protein ACE2. Using these reported structures, molecular dynamics simulations and electrostatic field calculations were performed to explore the impact of thioldisulfide balance on CoV/CoV-2 and ACE2 binding affinities. The structural and dynamical changes due to the change in the redox states of cysteines in the interacting proteins were analyzed and their effects on binding free energies were studied. doi = 10.1101/2020.05.07.083147 id = cord-334624-chnibsa1 author = Hayn, Manuel title = Imperfect innate immune antagonism renders SARS-CoV-2 vulnerable towards IFN-γ and -λ date = 2020-10-30 keywords = Fig; IFN; Nsp15; SARS summary = Here, we systematically assessed the impact of 29 SARS-CoV-2 proteins on viral sensing, type I, II and III interferon (IFN) signaling, autophagy and inflammasome formation. Our results identify ineffective type I and II antagonism as weakness of SARS-CoV-2 that may allow to devise safe and effective anti-viral therapies based on targeted innate immune activation. SARS-CoV-1 ORF6 is about 4-fold less potent in antagonizing type I IFN signaling (Fig. 243 4b) but induces higher levels of autophagy (Fig. 4c) . Examination of the functional conservation showed that SARS-CoV-2 Nsp15 was less 319 efficient in blocking innate immune activation, both type I IFN induction and signaling, than SARS-320 Hepatitis C virus viruses to block anti-viral autophagic turnover 50 and thus may represent a common studies will see more mechanistic data to explain the molecular details of the impact of SARS-CoV-2 343 proteins on innate immune activation. doi = 10.1101/2020.10.15.340612 id = cord-254855-gmy9zyad author = He, Sijia title = PSGL-1 inhibits the virion incorporation of SARS-CoV and SARS-CoV-2 spike glycoproteins and impairs virus attachment and infectivity date = 2020-07-06 keywords = PSGL-1; SARS summary = Here we report that the expression of PSGL-1 in virus-producing cells impairs the incorporation of SARS-CoV and SARS-CoV-2 spike (S) glycoproteins into pseudovirions and blocks virus attachment and infection of target cells. Together, these results demonstrate that PSGL-1 expression in the virus-producer cells severely diminishes the infectivity of virions bearing SARS coronavirus S proteins. We and other previously reported that PSGL-1-mediated inhibition of virion infectivity is through steric hindrance of particle attachment to target cells, which does not depend on the presence of viral envelope glycoproteins (1, 5) . We performed a virion attachment assay and observed that the lentiviral particles pseudotyped with SARS-CoV or SARS-CoV-2 S protein produced from PSGL-1-expressing cells were impaired in their ability to attach to target cells (Fig. 2D) . These results demonstrate that the presence of PSGL-1 on virus particles can structurally hinder virion interaction with the target cells even in the presence of remaining S proteins, consistent with previous studies of PSGL-1 and HIV-1 infection (1, 5) . doi = 10.1101/2020.05.01.073387 id = cord-323908-8dgngwmw author = He, Zhesheng title = Molecules inhibit the enzyme activity of 3-chymotrypsin-like cysteine protease of SARS-CoV-2 virus: the experimental and theory studies date = 2020-05-31 keywords = SARS summary = title: Molecules inhibit the enzyme activity of 3-chymotrypsin-like cysteine protease of SARS-CoV-2 virus: the experimental and theory studies Herein, we report that the clinical approved auranofin could perfectly inhibit the activity of 3-chymotrypsin-like cysteine protease (Mpro or 3CLpro) of SARS-CoV-2. As Au(I) ion is active metabolism specie derived from gold compounds or gold clusters in vivo, further computational studies revealed Au ion could tightly bind thiol group of Cys145 residue of 3CLpro thus inhibit enzyme activity. Also, phenyl isothiocyanate and Vitamin K3 may interact with thiol group of Cys145 via Michael addition reaction, molecular dynamic (MD) theory studied are applied to confirmed these small molecules are stable in the pocket and inhibit Mpro activity. These compounds could serve as potential anti-SARS-CoV-2 lead molecules for further drug studies to combat COVID-19. The interactions between the gold atom with the binding pockets of proteins were studied by density functional theory (DFT) calculations. doi = 10.1101/2020.05.28.120642 id = cord-353731-7xn7m662 author = Heaton, Brook E. title = SRSF protein kinases 1 and 2 are essential host factors for human coronaviruses including SARS-CoV-2 date = 2020-08-18 keywords = SARS; SRPK1 summary = sgRNA sequencing data indicated that the host gene with the highest probability of being 125 required for SARS-CoV-2 infection was the serine/arginine-rich protein kinase, SRPK1 126 ( Figure 1B) . We next wanted to define the degree to which inhibition of SRPK1 mediated N 141 phosphorylation would affect viral replication, especially since other non-SRPK1 kinases 142 have been predicted to be responsible for SARS-CoV-2 protein phosphorylation 12,13 . SRPIN340 treatment of cells infected with the 183 alphacoronavirus 229E (which is only distantly related to betacoronavirus SARS-CoV-2) 184 inhibited the virus by more than 1,000-fold at non-toxic concentrations of the drug ( Figure 185 2G-H). Human papillomavirus type 1 E1^E4 protein is a potent 533 inhibitor of the serine-arginine (SR) protein kinase SRPK1 and inhibits 534 phosphorylation of host SR proteins and of the viral transcription and replication 535 regulator E2 doi = 10.1101/2020.08.14.251207 id = cord-295545-ruxz77i8 author = Hennighausen, Lothar title = Activation of the SARS-CoV-2 receptor Ace2 by cytokines through pan JAK-STAT enhancers date = 2020-05-11 keywords = SARS; stat summary = The ACE2 gene is expressed in SARS-CoV-2 target cells, including Type II Pneumocytes (Ziegler, 2020), and is activated by interferons. The presence of pan JAK-STAT components in mammary alveolar cells and in Type II Pneumocytes combined with the autoregulation of both STAT1 and STAT5 suggests a prominent role of cytokine signaling pathways in cells targeted by SARS-CoV-2. A study in pneumocytes demonstrated that ACE2 expression is induced by interferons (Ziegler, 2020) , possibly through the transcription factors Signal Transducer and Activator of Transcription (STAT) 1 and 2, as the authors suggest. Ace2 mRNA levels vary widely between cell types, with high expression detected in lactating mammary and intestinal tissues ( Figure 1A -B) and Type II Pneumocytes (Ziegler, 2020) . To explore the possibility that Ace2 gene expression in SARS-CoV-2 target cells is regulated not only by interferons but also by a range of cytokines through the family of STAT transcription factors, we mined available scRNA-seq data (Ziegler, 2020) (Table 1) . doi = 10.1101/2020.05.11.089045 id = cord-103502-asphso2s author = Herrgårdh, Tilda title = An organ-based multi-level model for glucose homeostasis: organ distributions, timing, and impact of blood flow date = 2020-10-21 keywords = Fig; glucose; model summary = Due to the involvement of numerous organs and sub-systems, each with their own intra-cellular control, we have developed a multi-level mathematical model, for glucose homeostasis, which integrates a variety of data. The final multi-level model describes >300 data points in >40 time-series and dose-response curves, resulting from a large variety of perturbations, describing both intra-cellular processes, organ fluxes, and whole-body meal responses. However, neither this model, nor any of the previously mentioned multi-level models, have subdivided the glucose uptake into the individual contributions of all of the main insulin-responding and glucose-utilizing organs: adipose tissue, muscle, and liver. The final combined model (Q4) can fit to all of the new data for glucose uptake in all organs (Fig 6) , as well as to all previous data, such as the postprandial glucose and insulin fluxes and concentrations in (Dalla Man et al. doi = 10.1101/2020.10.21.344499 id = cord-296657-mymndjvd author = Higuchi, Yusuke title = High affinity modified ACE2 receptors prevent SARS-CoV-2 infection date = 2020-09-16 keywords = ACE2; RBD; SARS summary = The extracellular domain of modified ACE2 fused to the Fc region of the human immunoglobulin IgG1 had stable structure and neutralized SARS-CoV-2 pseudotyped lentivirus and authentic virus with more than 100-fold lower concentration than wild-type. Engineering ACE2 decoy receptors with directed evolution is a promising approach to develop a SARS-CoV-2 neutralizing drug that has affinity comparable to monoclonal antibodies yet displaying resistance to escape mutations of virus. Three cycles of screening resulted in an identification of mutant ACE2 clones with more than 100-fold higher binding affinity to the RBD and lower half-maximal inhibitory concentration (IC50) for SARS-CoV-2 pseudotyped lentivirus as well as authentic virus. We engineered ACE2 to bind the RBD of the SARS-CoV-2 spike protein with the combination of surface display of mutagenized library and fluorescence-activated cell sorting (FACS) to perform the evolution in 293T human cells. doi = 10.1101/2020.09.16.299891 id = cord-103925-i73ymrov author = Hill, Chris H. title = Structural and molecular basis for protein-stimulated ribosomal frameshifting in Theiler’s murine encephalomyelitis virus date = 2020-08-11 keywords = EMCV; PRF; RNA; TMEV; figure summary = Finally, we use metabolic labelling and ribosome profiling to study 2A-mediated frameshifting and translation of the TMEV genome at sub-codon resolution in infected cells. A meta-analysis of the inferred P site positions of ribosomes relative to host mRNA start and stop codons reveals that RPFs map to coding sequences with a triplet periodicity reflective of the length of a codon ( Figure S3D ). Moving on to look specifically at the frameshift site, a single-nucleotide resolution plot of reads mapping to this region reveals a peak on the SS mutant genome corresponding to a ribosome paused with the GUU codon of the slippery sequence in the P site ( Figure 5G , Figure S4C ). These read lengths were selected for analysis as potential "disome-protected fragments", and their density plotted on the viral genome at the inferred P site position of the upstream, colliding ribosome ( Figure 6C and D). doi = 10.1101/2020.08.11.245068 id = cord-328960-46zui1sl author = Hillen, Hauke S. title = Structure of replicating SARS-CoV-2 polymerase date = 2020-04-27 keywords = RNA; SARS summary = Particle classification yielded a 3D reconstruction at a nominal resolution of 2.9 Å and led to a refined structure of the RdRp-RNA complex (Extended Data Figures 1 and 2) . The structure resembles that of the free enzyme 16 , but also reveals large additional protein regions in nsp8 that became ordered upon RNA binding and interact with RNA far outside the core enzyme (Extended Data Figure 3a ). The supernatant containing nsp12 was filtered using a 5-μm syringe filter, followed by filtration with a 0.8-µm syringe filter (Millipore) and applied onto a HisTrap HP 5 mL (GE Healthcare), preequilibrated in lysis buffer (300 mM NaCl, 50 mM Na-HEPES pH 7.4, 10 % (v/v) glycerol, 30 mM imidazole pH 8.0, 3 mM MgCl2, 5 mM β-mercaptoethanol, 0.284 µg ml-1 leupeptin, 1.37 µg ml-1 pepstatin, 0.17 mg ml-1 PMSF, and 0.33 mg ml-1 benzamidine). doi = 10.1101/2020.04.27.063180 id = cord-342456-5gp3cry0 author = Hoagland, Daisy A. title = Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds date = 2020-07-13 keywords = ACE2; RNA; SARS; figure summary = Utilizing expression patterns of SARS-CoV-2-infected cells, we identified a region in gene expression space that was unique to virus infection and inversely proportional to the transcriptional footprint of known compounds characterized in the Library of Integrated Network-based Cellular Signatures. These signatures were then used as queries against the LINCS L1000 dataset, a collection of gene expression profiles generated following the administration of >20,000 bioactive compounds including >1,000 FDA-approved drugs to human cell lines at a variety of different times and concentrations (Subramanian et al., 2017) With L1000FWD , we could identify reciprocal transcriptional signatures generated between SARS-CoV-2 infection and a given compound. Overall, based on the L1000 data, these seven compounds influence the same pharmacological high-dimensional gene expression signature space and are predicted to disrupt key cellular processes that are modulated in response to SARS-CoV-2 infection. doi = 10.1101/2020.07.12.199687 id = cord-350817-tmszrtju author = Hoepel, Willianne title = Anti-SARS-CoV-2 IgG from severely ill COVID-19 patients promotes macrophage hyper-inflammatory responses date = 2020-07-13 keywords = SARS; anti; covid-19; figure; spike summary = Here, we show that anti-Spike IgG from serum of severely ill COVID-19 patients induces a hyper-inflammatory response by human macrophages, which subsequently breaks pulmonary endothelial barrier integrity and induces microvascular thrombosis. Taken together, these data demonstrate that anti-Spike IgG immune complexes generated from serum of severely ill COVID-19 patients induce a strong pro-inflammatory response by (otherwise immunosuppressive) human M2 macrophages, which is characterized by high production of classical cytokine storm mediators such as IL-1β, IL-6, IL-8, and TNF. As shown in Figure 4A , the used human macrophage model highly expressed all FcγRs. To determine whether FcγRs are involved in activation by anti-Spike immune complexes, we blocked the different FcγRs with specific antibodies during stimulation, and analyzed cytokine production. In conclusion, our data show that anti-Spike IgG from serum of severely ill COVID-19 patients strongly amplifies pro-inflammatory responses by human macrophages, and can contribute to subsequent endothelial barrier disruption and thrombosis. doi = 10.1101/2020.07.13.190140 id = cord-327431-dnppshnv author = Hognon, Cécilia title = Role of RNA Guanine Quadruplexes in Favoring the Dimerization of SARS Unique Domain in Coronaviruses date = 2020-05-27 keywords = SARS; SUD summary = In the present contribution we study, by all-atom equilibrium and enhanced sampling molecular dynamics simulations, the interaction between the SARS Unique Domain and RNA guanine quadruplexes, a process involved in eluding the defensive response of the host thus favoring viral infection of human cells. 28, 37 In this letter, we report an extended all-atom molecular dynamics (MD) study of the interactions produced between a dimeric SUD domain and a short RNA G4 sequence. To further examine the conformational space spanned by the G4/SUD complex, and in particular the role of the RNA in favoring the dimerization and the structure of the interface, we resorted to enhanced sampling MD simulations to obtain the 2D free energy profile along two relevant collective variables: first, the distance between G4 and SUD, and second, the separation between the two SUD subdomains. doi = 10.1101/2020.04.07.029447 id = cord-264919-0jlg2gkc author = Hopp, Marie-Thérèse title = Unravelling the debate on heme effects in COVID-19 infections date = 2020-06-12 keywords = ACE2; COVID-19; SARS; TMPRSS2 summary = On the one hand, we examine the possibility of a direct interaction of heme with select SARS-CoV-2 proteins and specific host cell proteins by applying our webserver HeMoQuest (Paul that is based on experimental data. One of the most promising findings was the prediction of heme-binding motifs (HBMs) in the host cell proteins ACE2 and TMPRSS2. We leveraged this multimodal information to hypothesize the pathways that connect key molecules associated with SARS-CoV-2 and heme to phenotypes observed in COVID-19 patients. Here, we have investigated the possibility of a direct interaction of heme with SARS-CoV-2 surface proteins and their human counterparts ACE2 and TMPRSS2. Apart from investigating the direct impact of heme on proteins at the interface of the virus-host cell interaction, we also explored similarities between relevant pathways characterizing the respective pathologies, i.e. labile heme occurrence in hemolytic conditions and COVID-19 disease progression ( Figure 4) . doi = 10.1101/2020.06.09.142125 id = cord-297775-ug4ovsws author = Hosie, Margaret J title = Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK date = 2020-09-23 keywords = SARS summary = High throughput sequencing of the virus from cat 2 revealed that the feline viral genome contained five single nucleotide polymorphisms (SNPs) compared to the nearest UK human SARS-CoV-2 sequence. Recent reports from Dutch mink farms of both mink-to-cat and mink-tohuman transmission of the virus provide support for this scenario (5, 9) We used a range of laboratory techniques to show that two domestic cats from households with suspected cases of COVID-19, and which displayed either mild or severe respiratory disease, were infected with SARS-CoV-2. As we do not have the owner''s virus sequence, we cannot determine whether the observed mutations in cat 2''s viral genome arose in a human prior to transmission. Table 1 details the SNPs observed in the cat 2 viral genome, and their frequency in the existing UK human population and among existing feline SARS-CoV-2 sequences. doi = 10.1101/2020.09.23.309948 id = cord-339012-4juhmjaj author = Hou, Wei title = Rapid host response to an infection with Coronavirus. Study of transcriptional responses with Porcine Epidemic Diarrhea Virus date = 2020-07-28 keywords = MRV; PEDV; SARS; Vero; cell; gene summary = Instead, PEDV down-regulated the expression of a set of zinc finger proteins with putative antiviral activity and enhanced the expression of the transmembrane serine protease gene TMPRSS13 (alias MSPL) to support its own infection by virus-cell membrane fusion (Shi et al, 2017, Viruses, 9(5):114). Furthermore, by comprehensive datamining in biological and chemical databases and consulting related literature we identified sets of PEDV-response genes with potential to influence i) the metabolism of biogenic amines (e.g. histamine), ii) the formation of cilia and "synaptic clefts" between cells, iii) epithelial mucus production, iv) platelets activation, and v) physiological processes in the body regulated by androgenic hormones (like blood pressure, salt/water balance and energy homeostasis). The detected sets of differential expressed genes (DEGs) for PEDV and MRV were analyzed by gene set enrichment analysis (GSEA) using functional bioinformatic programs to retrieve biological processes (pathways and Gene Ontology terms [GO-term]) and associations with chemical compounds, including drugs. doi = 10.1101/2020.07.28.224576 id = cord-302608-fw4pmaoc author = Huang, Jiao-Mei title = Evidence of the Recombinant Origin and Ongoing Mutations in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date = 2020-03-19 keywords = CoV-2; SARS summary = However, RBD and key amino acid residues supposed to be crucial for human-to-human and cross-species transmission are homologues between SARS-CoV-2 and pangolin CoVs. These results from our analysis suggest that SARS-CoV-2 is a recombinant virus of bat and pangolin CoVs. Moreover, this study also reports mutations in coding regions of 125 SARS-CoV-2 genomes signifying its aptitude for evolution. The host specificity of virus particle is determined by amino acid sequence of RBD and is usually dissimilar among different CoVs. Therefore, RBD is a core determinant for tissue tropism and host range of CoVs. This article presents SARS-CoV-2 phylogenetic trees, comparison and analysis of genome, spike protein, and RBD amino acid sequences of different CoVs, deducing source and etiology of COVID-19 and evolutionary relationship among SARS-CoV-2 in human. The S-protein amino acid sequence identity between SARS-CoV-2 and related beta-CoVs showed that bat/Yunnan/RaTG13 shares highest similarity of 97.43%. doi = 10.1101/2020.03.16.993816 id = cord-262145-i29e3fge author = Huang, Kuan-Ying A. title = Breadth and function of antibody response to acute SARS-CoV-2 infection in humans date = 2020-10-19 keywords = RBD; SARS summary = A subset of anti-spike (10 of 32) and over half of anti-nucleocapsid (19 of 35) antibodies cross-reacted with other betacoronaviruses tested and harboured extensive somatic mutations, indicative of an expansion of memory B cells upon SARS-CoV-2 infection. The MAbs with 161 strong anti-RBD binding have a relatively long heavy chain CDR3 length (50% 162 binding concentration <0.5 µg/ml versus >0.5 µg/ml, p=0.03, two-tailed Mann-163 Whitney test; Supplemental Figure 3 The 32 anti-spike glycoprotein MAbs were systematically examined by plaque 173 reduction neutralisation (PRNT) assay for neutralisation of wild type SARS-CoV-2 174 virus (see methods; summarised in Table 1 ). Potent neutralising antibodies to the RBD of SARS-CoV-2 spike glycoprotein were 188 identified and we thus analyse the blockade of the ACE2-RBD interaction by anti-189 RBD antibodies in two assays ( Figure 3 , Table 1 The structure of VHH72-Fc bound to RBD is known (17) and its footprint on the 198 RBD does not overlap that of ACE2, so inhibition is thought to occur by steric 199 hindrance. doi = 10.1101/2020.08.28.267526 id = cord-256572-sqz8yc7b author = Huo, Jiandong title = Neutralization of SARS-CoV-2 by destruction of the prefusion Spike date = 2020-05-06 keywords = ACE2; RBD; SARS; cr3022 summary = doi = 10.1101/2020.05.05.079202 id = cord-103204-gt6upfri author = Hölzer, Martin title = PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection date = 2020-05-20 keywords = selection summary = Summary PoSeiDon is an easy-to-use pipeline that helps researchers to find recombination events and sites under positive selection in protein-coding sequences. A comprehensive evolutionary analysis of significantly positively selected sites consist of several complicated steps, including (1) in-frame alignment; (2) Indel correction; (3) phylogenetic tree calculation; (4) selection of a best-fitting nucleotide substitution * To whom correspondence should be addressed. model; (5) detection of topological incongruence and breakpoint selection to describe putative recombination events; (6) calculation of positively selected sites (ω > 1) under varying models; (7) and their impact on the selective pressure acting on the whole alignment. PoSeiDon comprises an assembly of different scripts and tools ( Fig. 1) that allow for the detection of recombination and positive selection in protein-coding sequences. Here we present PoSeiDon, an easy-to-use Nextflow pipeline for the accurate detection of site-specific positive selection and recombination events in protein-coding sequences. doi = 10.1101/2020.05.18.102731 id = cord-103568-zesg4atp author = Iacullo, Carly title = Non-selective inhibition of the motor system following unexpected and expected infrequent events date = 2020-03-26 keywords = CSE; Wessel; unexpected summary = Consequently, in line with the proposal that unexpected sensory events lead to an automatic recruitment of the brain''s reactive inhibition circuity even when stopping is not explicitly required (i.e., in the absence of proactive control), such events do indeed also produce non-selective suppression of CSE (Wessel & Aron, 2013) . Therefore, the goal of the current study was to investigate whether expected infrequent events can produce reactive motor inhibition, as indexed by non-selective CSE suppression. Using single-pulse TMS combined with EMG of task-unrelated hand muscles while participants performed forced-choice reaction time tasks with their feet, we found that infrequent expected sounds are indeed followed by a non-selective suppression of task-unrelated motor effectors. The latter finding replicates our previous report of non-selective CSE suppression in a verbal reaction time task when unexpected sounds were presented prior to the imperative stimulus (Wessel & Aron, 2013) . doi = 10.1101/2020.03.25.008789 id = cord-320490-3jmo35jc author = Ismail, Saba title = Immuno-informatics Characterization SARS-CoV-2 Spike Glycoprotein for Prioritization of Epitope based Multivalent Peptide Vaccine date = 2020-04-12 keywords = HLA; MEPVC; SARS; TLR3; energy; mol summary = In this study, we characterized the SARS-CoV-2 spike glycoprotein by immune-informatics techniques to put forward potential B and T cell epitopes, followed by the use of epitopes in construction of a multi-epitope peptide vaccine construct (MEPVC). Stable conformation of the MEPVC with a representative innate immune TLR3 receptor was observed involving strong hydrophobic and hydrophilic chemical interactions, along with enhanced contribution from salt-bridges towards inter-molecular stability. The study presented, herein, is an attempt to get insights about antigenic determinants of SARS-CoV-2 spike glycoprotein and highlight all antigenic epitopes [31] of the spike that can be used specifically for the design of a multi-epitope peptide vaccine construct (MEPVC) [32] to counter COVID-19 infections. The epitopes predicted by immunoinformatics techniques were fused together as well as to β-defensin adjuvant [33, 34] to boost the antibody production and longThe MEPVC affinity for an appropriate immune receptor as an agonist was checked in the step of molecular docking [60] . doi = 10.1101/2020.04.05.026005 id = cord-332374-cbiw6yvb author = Israeli, Ofir title = Evaluating the efficacy of RT-qPCR SARS-CoV-2 direct approaches in comparison to RNA extraction date = 2020-06-10 keywords = SARS summary = Very recently, two studies [6] [7] used a direct no-buffer RT-qPCR approach which identified > 90% of the tested clinical samples. In this study, we tested the diagnostic efficiency following thermal inactivation (65°C for 30min and 95°C for 10min) without addition of lysis buffers ("no buffer") or following lysis by three buffers (Virotype, QuickExtract and 2% Triton-X-100) and compared it to diagnosis after standard RNA extraction. Samples included buffers spiked with SARS-CoV-2, at concentrations 0.1-100,000 PFU/ml and 30 clinical samples, previously diagnosed as positive (20) and negative (10). The limit of detection was 1 PFU/ml: In this concentration samples in the no buffer mode and Virotype at 95°C were not detected, while the RNA extraction mode averaged the lowest critical threshold ( Ct=29.8) followed by QuickExtract and Triton. SARS-CoV-2 detection by direct rRT-PCR without RNA extraction. Direct RT-qPCR detection of SARS-CoV-2 RNA from patient nasopharyngeal swabs without an RNA extraction step doi = 10.1101/2020.06.10.144196 id = cord-256607-wpywh8c9 author = Itokawa, Kentaro title = Disentangling primer interactions improves SARS-CoV-2 genome sequencing by the ARTIC Network’s multiplex PCR date = 2020-06-01 keywords = primer summary = The resulting primer set, version N1 (NIID-1), exhibits improved overall coverage compared to the ARTIC Network''s original (V1) and modified (V3) primer set. Alongside with this modification, the ARTIC Network itself released another 108 modified version of primer set known as V3 in 24 th March 2020 (Loman and Quick 2020) after replacement for the same clinical sample (previously deposited to GISAID with ID EPI_ISL_416596, Ct=28.5, 1/25 input per reaction). Fig 3 Abundance of 98 amplicons at 8 different annealing/extension temperatures with the three different primer sets on a same clinical sample (previously deposited to GISAID with ID EPI_ISL_416584, Ct=16, 1/300 input per reaction). The orange lines and points indicate the abundances of amplicons whose primers were not modified but predicted to be eliminated the adverse primer interactions in the N1 primer set. doi = 10.1101/2020.03.10.985150 id = cord-104035-ykyr2gvl author = Ivanov, Mark V. title = Boosting the MS1-only proteomics with machine learning allows 2000 protein identifications in 5-minute proteome analysis date = 2020-10-29 keywords = Mass summary = A number of methods and approaches to MS/MS-free proteome analysis have been proposed and widely explored starting from the early Accurate Mass and Tag (Time) method [21] [22] [23] [24] [25] to a recent truly (e.g., without employing tandem mass spectrometry at any step in the workflow) MS/MS-free realizations 26, 27 . 27 Because the method does not employ isolation and fragmentation steps, the time for peptide separation can be reduced significantly to few minutes and the number of MS1 spectra available for processing will only be limited by the acquisition rate of the mass analyzer operating at high mass resolution. Also, the method was upgraded and tested for processing MS1-only data obtained using high resolution mass spectrometry and the high-field asymmetric waveform ion mobility, FAIMS 35 , which was found increasingly applicable in proteomic research 36, 37 as it provides additional separation dimension for peptides at the front end of a mass spectrometer. doi = 10.1101/2020.10.29.359075 id = cord-350821-0qfoc553 author = Jahromi, Reza title = Synergistic effects of anionic surfactants on coronavirus (SARS-CoV-2) virucidal efficiency of sanitizing fluids to fight COVID-19 date = 2020-06-01 keywords = COVID-19; SARS summary = title: Synergistic effects of anionic surfactants on coronavirus (SARS-CoV-2) virucidal efficiency of sanitizing fluids to fight COVID-19 In this study, we present the effect of surfactants on coronavirus (SARS-CoV-2) virucidal efficiency in sanitizing fluids. Sodium dodecylbenzenesulfonate (SDBS), sodium laureth sulfate (SLS), and two commercial dish soap and liquid hand soap were studied with the goal of evaporation rate reduction in sanitizing liquids to maximize surface contact time. Twelve fluids with different recipes composed of ethanol, isopropanol, SDBS, SLS, glycerin, and water of standardized hardness (WSH) were tested for their evaporation time and virucidal efficiency. Twelve sanitizing fluids with different recipes, as shown in Table 1 , were prepared to examine the effect of individual components and mixtures on evaporation rate and SARS-CoV-2 virucidal efficiency of the solutions. Furthermore, the addition of 3% dish soap to the ethanol solution (S1) increased the evaporation time by about 63% from 24 to 39 s (of fluid S9), as shown in Figure 2 . doi = 10.1101/2020.05.29.124107 id = cord-303069-ss6g3jkg author = Jakhar, Renu title = An Immunoinformatics Study to Predict Epitopes in the Envelope Protein of SARS-COV-2 date = 2020-05-26 keywords = MHC; SARS summary = A total of available 370 sequences of SARS-CoV-2 were retrieved from NCBI for bioinformatics analysis using Immune Epitope Data Base (IEDB) to predict B and T cells epitopes. CTL cell epitopes namely interacted with MHC class I alleles and we suggested them to become universal peptides based vaccine against COVID-19. The aim of this study is to analyze envelope protein strains using in silico approaches looking for the conservancy, which is further studied to predict all potential epitopes that can be used after in vitro and in vivo confirmation as a therapeutic peptide vaccine [22, 23, 24] . Envelope protein from the SARS-CoV-2 was analyzed using the IEDB MHC-1 binding prediction tool to predict the T cell epitope suggested interacting with different types of MHC Class I alleles. Analysis of the genome sequence and prediction of B-cell epitopes of the envelope protein of Middle East respiratory syndrome-coronavirus doi = 10.1101/2020.05.26.115790 id = cord-103081-k7ev5qkn author = Janosevic, Danielle title = The orchestrated cellular and molecular responses of the kidney to endotoxin define the sepsis timeline date = 2020-05-30 keywords = Fig; Supplementary; cell; sepsis summary = Note that the expression of cluster-defining markers varied significantly during the injury and 63 recovery phases of sepsis ( Fig. S1b; Supplementary Table 1 ). One of the subclusters showed 112 increased expression of alternatively activated macrophages (M2) markers such as Arg1 113 (Arginase 1) and Mrc1 (Cd206) 27 at later time points (36 hours, Supplementary Fig. 4b) . Such 181 communication patterns among these four cell types may also explain macrophage clustering 182 around S1 tubules at later time points in sepsis as we previously reported 13 . To this end, we selected the differentially expressed genes from all cells combined (pseudo 203 bulk) for each time point across the mouse sepsis timeline (Supplementary Table 4) . Our data 215 cover nearly all renal cell types and are time-anchored, thus providing a detailed and precise 216 view of the evolution of sepsis in the kidney at the cellular and molecular level. doi = 10.1101/2020.05.27.118620 id = cord-307242-e20gtx0z author = Jegouic, Sophie M. title = Recombinant SARS-CoV-2 spike proteins for sero-surveillance and epitope mapping date = 2020-05-22 keywords = SARS; figure summary = Similar western blot analysis of total protein extracts following induction of logarithmic phase E.coli cultures with IPTG confirmed the expression of His-tagged S antigen of the predicted molecular weight in all cases ( Figure 3 , upper panel). Nevertheless, we found that S protein fragments prepared for gel electrophoresis using non-reducing loading buffer could be used successfully for epitope mapping of 2 S reactive monoclonal antibodies, 3G9, an unpublished mouse mAb generated to SARS S, and CR3022, a human mAb also isolated originally to SARS [19] but shown to cross-react with SARS-CoV-2. To provide an additional level of validation and to add epitope specificity to the data, 2 of the sera scoring positive by S1 ELISA were used as probes on western blots using full length S expressed in insect cells (cf. Optimization of the Production Process and Characterization of the Yeast-Expressed SARS-CoV Recombinant Receptor-Binding Domain ( RBD219-N1 ), a SARS Vaccine Candidate doi = 10.1101/2020.05.21.109298 id = cord-270257-5f95gve3 author = Jeon, Sangeun title = Identification of antiviral drug candidates against SARS-CoV-2 from FDA-approved drugs date = 2020-03-28 keywords = SARS summary = Drug repositioning represents the only feasible option to address this global challenge and a panel of 48 FDA-approved drugs that have been pre-selected by an assay of SARS-CoV was screened to identify potential antiviral drug candidates against SARS-CoV-2 infection. In near future, these already FDA-approved drugs could be further developed following clinical trials in order to provide additional therapeutic options for patients with COVID-19. We screened approximately 3,000 FDA-and IND-approved drug library against SARS-CoV to identify antiviral drug candidates (manuscript in preparation). Among the 48 drugs that were evaluated in our study, 24 drugs showed potential antiviral activities against SARS-CoV-2 with IC 50 values in Second, ciclesonide is another interesting drug candidate for further development although its antiviral potency was much lower (IC 50 = 4.33 µM) than niclosamide. Prior to our evaluation of 48 drugs against SARS-CoV-2 infection, we also tested antiviral activity of several other drugs based on the cytopathic effect of the virus in the presence of each drug ( Figure 2 ). doi = 10.1101/2020.03.20.999730 id = cord-353777-t8q99tlq author = Jia, Yong title = Analysis of the mutation dynamics of SARS-CoV-2 reveals the spread history and emergence of RBD mutant with lower ACE2 binding affinity date = 2020-04-11 keywords = CoV-2; SARS summary = The discrepant phylogenies for the spike protein and its receptor binding domain proved a previously reported structural rearrangement prior to the emergence of SARS-CoV-2. Despite that we found the spike glycoprotein of SARS-CoV-2 is particularly more conserved, we identified a mutation that leads to weaker receptor binding capability, which concerns a SARS-CoV-2 sample collected on 27th January 2020 from India. We provided first evidence that a mutated SARS-COV-2 with reduced human ACE2 receptor binding affinity have emerged in India based on a sample collected on 27th January 2020. The discrepant phylogenies for the spike protein and its 23 receptor binding domain proved a previously reported structural rearrangement prior to the emergence of SARSDespite that we found the spike glycoprotein of SARS-CoV-2 is particularly more conserved, we identified a mutation that 25 leads to weaker receptor binding capability, which concerns a SARS-CoV-2 sample collected on 27 th January 2020 from 26 doi = 10.1101/2020.04.09.034942 id = cord-297044-tpp40j0g author = Jin, Zhenming title = Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug Carmofur date = 2020-04-28 keywords = Carmofur summary = title: Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug Carmofur The antineoplastic drug Carmofur was shown to inhibit SARS-CoV-2 main protease (Mpro). The antineoplastic drug Carmofur was shown to inhibit SARS-CoV-2 main protease 24 (M pro ). Here the X-ray crystal structure of M pro in complex with Carmofur reveals that 25 the carbonyl reactive group of Carmofur is covalently bound to catalytic Cys145, 26 whereas its fatty acid tail occupies the hydrophobic S2 subsite. Here, we present the 1.6 Å X-ray crystal structure of SARS-CoV-2 M pro in complex 49 with Carmofur (Fig. 1b, domain II feature the catalytic dyad residues Cys145 and His41 (Fig. 1c, d) . Here we determined the inhibitory 94 effect of Carmofur against SARS-CoV-2 infection on Vero E6 cells, as previously 95 described 20 (Fig. 2) . doi = 10.1101/2020.04.09.033233 id = cord-103249-k35o3gxe author = Johannsen, Leif title = Robotic light touch assists human balance control during maximum forward reaching date = 2019-11-20 keywords = IPT summary = We speculated, therefore, that minimization of the interaction 106 forces and their variability at the contact location during IPT acts as an implicit task constraint and shared goal In the present study, we intended to contrast the effects of human IPT (hIPT) on CR''s postural performance 112 against the effects of two different modes of robotic IPT (rIPT) and expected specific costs and benefits on body 113 sway and postural performance due to the robotic response modes. As the coupling 116 between two humans with IPT in terms of the interaction forces is intrinsically more noisy due to each 117 individual''s motion dynamics and response delays, we expected that a predictive mode of the robotic system 118 would result in a less noisy haptic coupling and therefore enhance performance in the MFR task, such as greater 119 reaching distance with less body sway. doi = 10.1101/848432 id = cord-258650-aeyf0yu1 author = Joshi, Bhrugesh title = deepMINE - Natural Language Processing based Automatic Literature Mining and Research Summarization for Early-Stage Comprehension in Pandemic Situations specifically for COVID-19 date = 2020-04-02 keywords = article; research summary = title: deepMINE Natural Language Processing based Automatic Literature Mining and Research Summarization for Early-Stage Comprehension in Pandemic Situations specifically for COVID-19 In the demanding situation of COVID-19, we applied the literature mining with user entered keyword(s) and automatic generation of brief summary of research articles, that user searches for. The deepMINE is primarily performing two major functions namely mining of articles from available open data sources using user-entered keywords and generate brief technical summary in natural language for a quick review of articles that user interested with. The system has used the deep natural language processing-based text summarization for generating detailed technical summary given the research article as an input. Our system deepMINE is providing mining from 29,315 research articles with keywords by scanning nearly 1,46,115,136 English words available in literature dataset in not greater than 1.5 seconds. doi = 10.1101/2020.03.30.014555 id = cord-324251-wgtatr8v author = Joshi, Madhvi title = Genomic variations in SARS-CoV-2 genomes from Gujarat: Underlying role of variants in disease epidemiology date = 2020-07-13 keywords = SARS summary = title: Genomic variations in SARS-CoV-2 genomes from Gujarat: Underlying role of variants in disease epidemiology Latest edition to this pandemic list is COVID-19, caused by the novel coronavirus, SARS-CoV-2. Here, 361 SARS-CoV-2 genomes from across Gujarat have been sequenced and analyzed in order to understand its phylogenetic distribution and variants against global and national sequences. Further, variants were analyzed from diseased and recovered patients from Gujarat and the World to understand its role in pathogenesis. From missense mutations, found from Gujarat SARS-CoV-2 genomes, C28854T, deleterious mutation in nucleocapsid (N) gene was found to be significantly associated with mortality in patients. SARS-CoV-2 genomes from Gujarat are forming distinct cluster under GH clade of GISAID. Positive selection of ORF3a and 477 ORF8 genes drives the evolution of SARS-CoV-2 during the 2020 COVID-19 pandemic Full-genome sequences of the first two SARS-CoV-2 485 viruses from India doi = 10.1101/2020.07.10.197095 id = cord-103213-oinumv1z author = Kalantar, Katrina L. title = IDseq – An Open Source Cloud-based Pipeline and Analysis Service for Metagenomic Pathogen Detection and Monitoring date = 2020-04-18 keywords = IDseq; Kraken2; NCBI; figure; read summary = The IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes an assembly-based alignment pipeline which results in the assignment of reads and contigs to taxonomic categories. First, relevant QC metrics and pipeline run information, including the number of reads remaining at each step of the host and quality filtering steps as well as estimates of internal control abundances are provided for each sample (Figure 2AB, Methods) . The idseq-bench tool was used to generate 17 simulated NGS samples from Rhinovirus C genomes at varying levels of divergence (after in-silico forward evolution from a reference sequence obtained from the NCBI database), ranging from 100% identical to the reference sequence to 25% similar (at the nucleotide level) (Methods, Figure 4A , Table S3 ). doi = 10.1101/2020.04.07.030551 id = cord-103674-pmbpx162 author = Kalaycı, Salih title = The Linkage among Sea Transportation, Trade Liberalization and Industrial Development in the context of Carbon Dioxide Emissions: An Empirical Investigation from China date = 2020-07-13 keywords = ARDL; China; emission summary = According to results of FMOLS, DOLS and CCR models there is a long-term stable relationship between sea transportation, trade liberalization, industrial development and carbon dioxide emissions which is proved empirically. In this study, empirical results proved the impact of sea transportation, trade liberalization and industrial development on carbon dioxide emissions for China from 1980 to 2013. The long-run relationship between carbon dioxide emissions 2 sea transportation trade liberalization and industrial development is investigated through f bounds test which is considered the zero hypothesis. Findings from FMOLS, DOLS and CCR models indicate that maritime transport, trade liberalization and industrial development are the determinants of long-term carbon emissions, just as in the results of the ARDL model. Findings from FMOLS, DOLS and CCR models indicate that maritime transport, trade liberalization and industrial development are the determinants of long-term carbon emissions, just as in the results of the ARDL model. doi = 10.1101/2020.07.13.200386 id = cord-329855-pr7g6ivu author = Kalfaoglu, Bahire title = T-cell hyperactivation and paralysis in severe COVID-19 infection revealed by single-cell analysis date = 2020-05-30 keywords = CD4; Fig; covid-19 summary = By in silico sorting CD4+ T-cells from a single cell RNA-seq dataset, we found that CD4+ T-cells were highly activated and showed unique differentiation pathways in the lung of severe COVID-19 patients. Notably, those T-cells in severe COVID-19 patients highly expressed immunoregulatory receptors and CD25, whilst repressing the expression of the transcription factor FOXP3 and interestingly, both the differentiation of regulatory T-cells (Tregs) and Th17 was inhibited. Collectively, CD4+ T-cells from severe COVID-19 patients are hyperactivated and FOXP3-mediated negative feedback mechanisms are impaired in the lung, while activated CD4+ T-cells continue to promote further viral infection through the production of Furin. These CD25 + activated T-cells are likely to be short-lived and do not initiate FOXP3 transcription in severe COVID-19 patients, while they can differentiate into Tregs in moderate infections. These collectively support that FURIN expression is induced in highly activated non-regulatory CD25 + CD4 + T-cells in severe COVIDOur study has shown that CD4 + T-cells in severe COVID-19 patients have dysregulated activation and differentiation mechanisms. doi = 10.1101/2020.05.26.115923 id = cord-263594-jd9ako6c author = Kang, Sisi title = A COVID-19 antibody curbs SARS-CoV-2 nucleocapsid protein-induced complement hyper-activation date = 2020-09-11 keywords = Fig; SARS summary = Although human antibodies elicited by severe acute respiratory distress syndrome coronavirus-2 (SARS-CoV-2) nucleocapsid (N) protein are profoundly boosted upon infection, little is known about the function of N-directed antibodies. Severe acute 57 respiratory distress syndrome-associated coronavirus-2 (SARS-CoV-2) nucleocapsid (N) protein 58 is a highly immunopathogenic and multifunctional viral protein (14) (15) (16) (17) (18) (19) , which elicited high titers 59 of binding antibodies in humoral immune responses (20) (21) (22) . Herein, 66 we report a human mAb derived from COVID-19 convalescent, with specific targeting to SARS-67 CoV-2 N protein and functionally compromising complement hyper-activation ex vivo. Isolation of N protein-directed mAbs 69 To profile antibody response to SARS-CoV-2 N protein in early recovered patients, we collected 70 six convalescent blood samples at seven to 25 days after the onset of the disease symptoms. doi = 10.1101/2020.09.10.292318 id = cord-267831-uu883ofc author = Kang, Yuan-Lin title = Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2 date = 2020-06-15 keywords = SARS; virus summary = We describe here potent inhibitory effects on content release and infection by chimeric VSV containing the envelope proteins of Zaire ebolavirus (VSV-ZEBOV) or SARS-CoV-2 (VSV-SARS-CoV-2) elicited by Apilimod and Vacuolin-1, small molecule inhibitors of the main endosomal Phosphatidylinositol-3-Phosphate/Phosphatidylinositol 5-Kinase, PIKfyve. 143 All of these viruses require low pH to trigger viral membrane fusion with the endosomal 144 membranes, and as expected, infection was fully blocked by Bafilomycin A1, which 145 inhibits the vacuolar type H + -ATPase (V-ATPase) acidification activity (Fig. 1C) . Mammalian cell morphology and 671 endocytic membrane homeostasis require enzymatically active phosphoinositide 672 5-kinase PIKfyve The phosphatidylinositol-3-phosphate 5-kinase inhibitor 710 apilimod blocks filoviral entry and infection A transmembrane serine protease is linked to the severe 735 acute respiratory syndrome coronavirus receptor and activates virus entry Characterization of severe acute respiratory syndrome-744 associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry doi = 10.1101/2020.04.21.053058 id = cord-268339-jxm69ndw author = Karamitros, Timokratis title = SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies date = 2020-03-28 keywords = SARS summary = We analyzed NGS data derived from clinical samples of three Chinese patients infected with SARS-CoV-2, in order to identify smalland large-scale intra-host variations in the viral genome. The isolated SNVs and genomic rearrangements, reflect the intra-patient capacity of the polymorphic quasispecies, which may arise rapidly during the outbreak, allowing immunological escape of the virus, offering resistance to anti-viral drugs and affecting the sensitivity of the molecular diagnostics assays. Here, we explore intra-host genomic variants and low-frequency polymorphic quasispecies in Next Generation Sequencing (NGS) data derived from patients infected by SARS-CoV-2. The S1 subunit consists of a signal peptide and the NT and receptor binding (RB) domains, with the latter sharing only 40% amino acid identity with other SARS-related CoVs. Our analysis revealed that similarly to other genomic regions, the S1 subunit hosts many low-frequency SNVs, characterized by higher density compared to the rest of the S gene sequence (Figure 1-E) . doi = 10.1101/2020.03.27.009480 id = cord-103377-j1mmx7k7 author = Karasik, Agnes title = Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences date = 2020-09-11 keywords = AUG; ORF; RNA; figure summary = Since it was reported that RNase L activation increased translation of 3''UTR regions downstream of stop codons by interfering with factors that promote translation termination (eRF3) or ribosome recycling (ABCE1) (Le Roy et al., 2005) , we assessed the level of ribosome footprints in 3''UTRs. This level was assayed by computing the ratio of footprints in every 3''UTR relative to its respective main ORF within the coding sequence (density ratio, 3''UTR:ORF) for each transcript . The similarity in the effects suggests that translation of non-canonical regions occurs when RNase L is activated via naturally produced 2-5A from broad activation of the antiviral response by double-stranded RNAs. It should be noted that poly I:C treatment did result in slightly elevated 3''UTR ribosome footprints on some genes in a RNase L KO cell line (Supplemental Figure 4A ). doi = 10.1101/2020.09.10.291690 id = cord-322955-7dw32xby author = Kathwate, Gunderao H title = In Silico design and characterization of multi-epitopes vaccine for SARS-CoV2 from its spike proteins date = 2020-06-12 keywords = SARS; cell; epitope; protein; vaccine summary = title: In Silico design and characterization of multi-epitopes vaccine for SARS-CoV2 from its spike proteins Designed vaccine was rich in effective BCR and TCR epitopes screened from the sequence of S-protein of SARS-CoV2. Those properties are calculated by different methods at IEDB server (http://tools.iedb.org/bcell/ )like Kolaskar-Tongaonkar antigenicity scale provide physiology of the amino acid residues(45), Emini Surface accessible score for accessible surface of the epitope(46), Secondary structure of epitopes also has role in antigenicity. High scored and common peptides predicted by various tools were selected for deriving sequence of potential vaccine candidate. We designed a multi-epitopes vaccine construct from S-protein of SARS-CoV2. From various epitopes predicted by the online server based on common sequence and high score three TCR and two BCR epitopes were selected as part of COVID19 vaccine. This vaccine codes epitopes form S protein of SARS-CoV2 virus for T and B cell receptors. doi = 10.1101/2020.06.03.131755 id = cord-252097-4kslllaq author = Kaur, S. title = Local computational methods to improve the interpretability and analysis of cryo-EM maps date = 2020-06-19 keywords = map summary = In this work, we propose 1) approaches to enhance high-resolution features of cryo-EM maps, while preventing map distortions and 2) methods to obtain local B-factors and electron density occupancy maps. Secondly, we also propose approaches to determine local B-factors and density occupancy maps to improve the analysis of cryo-EM reconstructions. The link between the different proposed approaches is the use of the spiral phase transform to estimate a modulation or amplitude map of the cryo-EM reconstruction at different resolutions. In the second row of Figure 2 , we show maps with improved contrast at high-resolution obtained after processing EMD-8441 by the LocSpiral method and by Relion (Fernandez, Luque et al. The common link between all these approaches is the use of the spiral phase transform, which is used to factorize cryo-EM maps into amplitude and phase terms in real space for different resolutions. doi = 10.1101/2020.05.11.088013 id = cord-304792-8sdxqmkb author = Khan, Md. Abdullah-Al-Kamran title = SARS-CoV-2 proteins exploit host’s genetic and epigenetic mediators for the annexation of key host signaling pathways that confers its immune evasion and disease pathophysiology date = 2020-05-08 keywords = CoV-2; SARS; figure summary = title: SARS-CoV-2 proteins exploit host''s genetic and epigenetic mediators for the annexation of key host signaling pathways that confers its immune evasion and disease pathophysiology In this study we aimed to correlate how SARS-CoV-2 utilizes its proteins for tackling the host immune response; parallelly, how host epigenetic factors might play a role in this pathogenesis was also investigated. Also, enrichment analyses suggest that deregulated genes in SARS-CoV-2 infection are involved in heart development, kidney development, AGE-RAGE signaling pathway in diabetic complications etc. Our results suggest that SARS-CoV-2 integrates its proteins in different immune signaling pathway and other cellular signaling pathways for developing efficient immune evasion mechanisms, while leading the host to more complicated disease condition. We have utilized KEGG mapper tool (Kanehisa and Sato, 2020) for the mapping of 197 deregulated genes SARS-CoV-2 interacting host proteins in different cellular pathways. doi = 10.1101/2020.05.06.050260 id = cord-102511-7zgd45fl author = Khodakov, Dmitriy title = Donut PCR: a rapid, portable, multiplexed, and quantitative DNA detection platform with single-nucleotide specificity date = 2020-05-05 keywords = Donut; Fig; PCR; dna summary = doi = 10.1101/2020.04.24.058453 id = cord-266869-fs8dn7ir author = Kim, So Young title = Glycosaminoglycan binding motif at S1/S2 proteolytic cleavage site on spike glycoprotein may facilitate novel coronavirus (SARS-CoV-2) host cell entry date = 2020-04-15 keywords = Fig; SARS; SGP summary = title: Glycosaminoglycan binding motif at S1/S2 proteolytic cleavage site on spike glycoprotein may facilitate novel coronavirus (SARS-CoV-2) host cell entry Our discovery of a novel insertion of glycosaminoglycan (GAG)-binding motif at S1/S2 proteolytic cleavage site (681-686 (PRRARS)) and two other GAG-binding-like motifs within SARS-CoV-2 spike glycoprotein (SGP) led us to hypothesize that host cell surface GAGs might be involved in host cell entry of SARS-CoV-2. Finally, unbiased computational ligand docking indicates that heparan sulfate interacts with the GAG-binding motif at the S1/S2 site on each monomer interface in the trimeric SARS-CoV-2 SGP, and at another site (453-459 (YRLFRKS)) when the receptor-binding domain is in an open conformation. Using a modified version of Autodock Vina tuned for use with carbohydrates (Vina-Carb) [20, 21] , we performed blind docking on the trimeric SARS-CoV-2 SGP model to discover objectively the preferred binding GAG-binding sites on the SGP protein surface. doi = 10.1101/2020.04.14.041459 id = cord-335443-iv2gs3kg author = Kim, Youngchang title = Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2 date = 2020-06-28 keywords = Nsp15; RNA; SARS; Tipiracil summary = Here, we combine crystallography, biochemical and whole cell assays, and show that this compound inhibits SARS-CoV-2 Nsp15 and interacts with the uridine binding pocket of the enzyme''s active site, providing basis for the uracil scaffold-based drug development. For SARS-CoV it was reported that Nsp15 cleaves highly conserved non-translated RNA on (+) sense strand showing that both RNA sequence and structure are important for cleavage 6, 7 . The enzyme cleaves efficiently eicosamer 5''GAACU¯CAU¯GGACCU¯U¯GGCAG3'' at all four uridine sites (Fig. 1) , as well as synthetic EndoU substrate ( 5′-6-FAM-dArU¯dAdA -6-TAMRA-3′ ) 8 in the presence of Mn 2+ and the reaction rate increases with metal ion concentration. SARS-CoV-2 Nsp15 protein was crystallized with 5''UMP, 3''UMP, 5''GpU and Tipiracil using methods described previously 8 and the structures were determined at 1.82 Å, 1.85 Å, 1.97 Å and 1.85 Å, respectively. In the crystal structure of Nsp15/5''GpU, the dinucleoside monophosphate binds to the active site with uracil interacting with Tyr343 and Ser294 (Fig. 4B ), as seen in the Nsp15/5''UMP complex. doi = 10.1101/2020.06.26.173872 id = cord-102498-km03fnc4 author = Kinaneh, Safa title = Identification, Localization and Expression of NHE Isoforms in the Alveolar Epithelial Cells date = 2020-09-03 keywords = AEC; NHE8 summary = doi = 10.1101/2020.09.03.280677 id = cord-273891-7w334xgt author = Kirchdoerfer, Robert N. title = Receptor binding and proteolysis do not induce large conformational changes in the SARS-CoV spike date = 2018-03-31 keywords = RBD; SARS summary = The viral spike glycoprotein (S) utilizes angiotensin-converting enzyme 2 (ACE2) as a host protein receptor and mediates fusion of the viral and host membranes, making S essential to viral entry into host cells and host species tropism. Subsequent studies of the highly pathogenic human coronavirus S proteins of SARS-64 CoV 15,22 and MERS-CoV 17,22 showed that these viral S1 RBD do indeed sample an ''up'' 65 conformation where the receptor-binding site is accessible. 70 To examine the hypothesized conformational transitions induced by proteolysis and 71 receptor binding, we used single-particle cryo-EM to determine structures of S in uncleaved, 72 S1/S2 cleaved and ACE2-bound states. Three-dimensional classification of the S1 RBD 73 positions and corresponding atomic protein models revealed that neither ACE2-binding nor 74 trypsin cleavage at the S1/S2 boundary induced substantial conformational changes in the CoV may use a distinct mechanism of FP2 membrane insertion. Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein 381 reveal a prerequisite conformational state for receptor binding doi = 10.1101/292672 id = cord-319100-3gdawhfn author = Kirkland, P.D. title = The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses date = 2020-06-10 keywords = RNA; SARS; VTM summary = authors: Kirkland, P.D.; Frost, M.J. title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses Also of concern are recommendations (3, 4) to include foetal bovine serum (fbs) as a source of protein to enhance the stabilising properties of VTMs. This report documents observations of the adverse impact of certain VTMs on real time reverse transcription PCR (qRT-PCR) assays for the detection of SARS-CoV-2 virus as well as on a Type A influenza virus and a herpesvirus and discuss the broader implications of the inclusion of foetal bovine serum as a protein supplement to VTMs. During the initial investigation, purified RNA from an Australian isolate (WMD DC1) of SARS-CoV-2 was supplied to the Elizabeth Macarthur Agriculture Institute (EMAI) by the Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, New South Wales (NSW). doi = 10.1101/2020.06.09.142323 id = cord-102691-pij32hbi author = Klein, Steffen title = Post-correlation on-lamella cryo-CLEM reveals the membrane architecture of lamellar bodies date = 2020-08-14 keywords = Fig; a549; cryo; tem summary = doi = 10.1101/2020.02.27.966739 id = cord-342657-od48cntc author = Klemm, Theresa title = Mechanism and inhibition of SARS-CoV-2 PLpro date = 2020-06-19 keywords = Data; Fig summary = More variability is seen in MERS PLpro, which binds to ubiquitin and 138 ISG15 CTD similarly through its ability to ''close'' the Fingers subdomain 26 (see 139 discussion in Extended Data Fig. 4) . A 1536-well low-volume high-throughput assay previously used to identify inhibitors Together, our data suggests that a repurposing strategy using 3727 unique known 199 drugs towards SARS2 PLpro is unlikely to yield drug candidates, and highlights the 200 importance of a counterscreen in assessing the validity of hits coming from a screen 201 of known drugs before any conclusions on their therapeutic potential can be drawn. Since it had previously 237 been shown that these inhibitors are specific for PLpro over human DUBs 1 (also see 238 Figure 3b ) and since treatment with rac5c did not affect Lys48-linked polyubiquitin in 239 the absence of nsp3 expression (Extended Data Fig 8f) , the effect of rac5c on 240 Lys48-polyubiquitin is likely due to inhibition of nsp3/PLpro. doi = 10.1101/2020.06.18.160614 id = cord-102356-knvfbuzv author = Knyazev, Sergey title = Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction date = 2020-10-08 keywords = SNV; haplotype summary = doi = 10.1101/264242 id = cord-102612-xx5l8r9e author = Kodani, Andrew title = Zika virus alters centrosome organization to suppress the innate immune response date = 2020-09-15 keywords = CEP63; TBK1; ZIKV; ns3 summary = doi = 10.1101/2020.09.15.298083 id = cord-340291-bah2ege0 author = Kohmer, Niko title = Clinical performance of SARS-CoV-2 IgG antibody tests and potential protective immunity date = 2020-05-10 keywords = SARS summary = With exception of one sample, all positive tested samples in the analysed cohort, using the commercially available assays examined (including the in-house developed IFA), demonstrated neutralizing (protective) properties in the PRNT, indicating a potential protective immunity to SARS-CoV-2. With exception of one sample, all positive tested samples in the analysed cohort, using the 37 commercially available assays examined (including the in-house developed IFA), demonstrated 38 neutralizing (protective) properties in the PRNT, indicating a potential protective immunity to SARS-39 there is an increasing demand in the detection of antibodies -especially of IgG antibodies. Currently there are many S 57 protein based commercially or in-house developed assays available, but there is limited data on how 58 these tests perform with clinical samples and if the detected IgG antibodies provide protective 59 doi = 10.1101/2020.05.08.085506 id = cord-280025-4hmecfi0 author = Korber, B title = Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2 date = 2020-05-05 keywords = Fig; G614; GISAID; SARS; Spike; d614 summary = We have developed an analysis pipeline to facilitate real-time mutation tracking in SARS-CoV-2, focusing initially on the Spike (S) protein because it mediates infection of human cells and is the target of most vaccine strategies and antibody-based therapeutics. Over the past two months, the HIV database team at Los Alamos National Laboratory has turned to developing an analysis pipeline to track in real time the evolution of the SARS-CoV-2 Spike (S) protein in the COVID-19 pandemic, using the Global Initiative for Sharing All Influenza Data GISAID SARS-CoV-2 sequence database as our baseline (Sup. Item 1 is the GISAID acknowledgments table, listing all the groups who contribute sequences to this global effort) (Elbe and Buckland-Merrett, 2017; Shu and McCauley, 2017) . GISAID is the primary SARS-CoV-2 sequence database resource, and our intent is to complement what they provide with visualizations and summary data specifically intended to support the immunology and vaccine communities, and to alert the broader community to changes in frequency of mutations that might signal positive selection and a change in either viral phenotype or antigenicity. doi = 10.1101/2020.04.29.069054 id = cord-330031-c1n994j6 author = Kratzel, Annika title = Efficient inactivation of SARS-CoV-2 by WHO-recommended hand rub formulations and alcohols date = 2020-03-17 keywords = SARS summary = title: Efficient inactivation of SARS-CoV-2 by WHO-recommended hand rub formulations and alcohols We therefore determined the virucidal activity of two alcohol-based hand rub solutions for hand disinfection recommended by the World Health Organization (WHO), as well as commercially available alcohols. We show the inactivation of the novel coronavirus for the first time and endorse the importance of disinfectant-based hand hygiene to reduce SARS-CoV-2 transmission. The recent emergence of Severe acute respiratory syndrome coronavirus 2 (SARS-2 CoV-2) causing COVID-19 is a major burden for health care systems worldwide. The recent emergence of Severe acute respiratory syndrome coronavirus 2 (SARS-2 CoV-2) causing COVID-19 is a major burden for health care systems worldwide. We therefore determined the virucidal activity of two 5 alcohol-based hand rub solutions for hand disinfection recommended by the World 6 Hand Hygiene in Health Care'' suggests two alcohol-based formulations for hand 9 sanitization to reduce pathogen infectivity and spreading. doi = 10.1101/2020.03.10.986711 id = cord-333703-1ku3jc9s author = Kraus, Aurora title = A zebrafish model for COVID-19 recapitulates olfactory and cardiovascular pathophysiologies caused by SARS-CoV-2 date = 2020-11-08 keywords = ACE2; COVID-19; CoV-2; RBD; SARS; figure; zebrafish summary = Exposure of larvae to SARS-CoV-2 Spike (S) receptor binding domain (RBD) recombinant protein was sufficient to elevate larval heart rate and treatment with captopril, an ACE inhibitor, reverted this effect. In mice and humans, ace2 expression is detected in 121 sustentacular cells, olfactory stem cells known as horizontal and globose basal cells in the 122 olfactory epithelium, and vascular cells (pericytes) in the olfactory bulb (Brann et al., 2020 The present study reports for the first time that zebrafish larvae exposed to SARS-CoV-2 appear 134 to mount innate immune responses that resemble cytokine responses of mild COVID-19 patients. There are copious amounts of immune cells in the teleost olfactory organ ( Intranasal delivery of SARS-CoV-2 S RBD induces inflammatory responses and 318 widespread loss of olfactory receptor expression in adult zebrafish olfactory organ 319 320 doi = 10.1101/2020.11.06.368191 id = cord-265418-yqe9vdj1 author = Kumar, Nilesh title = Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis date = 2020-04-11 keywords = CSI; Fig; SARS; Supplementary summary = Integrated interactome-transcriptome analysis to generate Calu-3-specific humanIt is likely that the outcome of SARS-CoV-2 infection can largely be determined by the interaction patterns of host proteins and viral factors. By integrating this Calu-3 co-expression network with SIPs-derived PPI subnetwork, we generated Calu-3-specific human-SARS-CoV-2 Interactome (CSI) that contains 214 SIPs interacting with their first and second neighbors make a network of 4,123 nodes and 14,650 edges (Fig. 1c, Supplementary Data 1) . We showed that CSI follows a power law degree distribution with a few nodes harboring increased connectivity, and thus exhibits properties of a scale-free network (r 2 = 0.91; (Fig. 1d , Supplementary Data 1), similar to the previously generated other human-viral interactomes 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28 . In conclusion, we generated a human-SARS-CoV-2 interactome, integrated virusrelated transcriptome to interactome, discover COVID-19 pertinent structural and functional modules, identify high-value viral targets, and perform dynamic transcriptional modeling. doi = 10.1101/2020.04.09.033910 id = cord-311214-eqwxkwqa author = Kumar, Roshan title = Comparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Viruses Reveal Mosaic Pattern of Phylogeographical Distribution date = 2020-04-16 keywords = CoV-2; SARS; USA summary = Through the construction of SARS-CoV-2-human interactome, we further revealed that multiple host proteins (PHB, PPP1CA, TGF-β, SOCS3, STAT3, JAK1/2, SMAD3, BCL2, CAV1 & SPECC1) are manipulated by the viral proteins (nsp2, PL-PRO, N-protein, ORF7a, M-S-ORF3a complex, nsp7-nsp8-nsp9-RdRp complex) for mediating host immune evasion. A manually annotated reference database was generated using the Genbank 128 file of Severe acute respiratory syndrome coronavirus 2 isolate-SARS-CoV-129 2/SH01/human/2020/CHN (Accession number: MT121215) and open reading frames (ORFs) 130 were predicted against the formatted database using prokka (-gcode 1) [22] . All these isolates 189 were found to harbor 9 open reading frames coding for ORF1a (13218 bp) and ORF1b (7788 190 bp) polyproteins, surface glycoprotein or S-protein (3822 bp), ORF3a protein (828 bp Our analysis revealed that strains of human infecting SARS-CoV-2 are novel and highly 201 identical (>99.9%). In this study, the analysis was 358 performed on the genomes of the novel SARS-CoV-2 isolates recently reported from different 359 countries to understand viral pathogenesis. doi = 10.1101/2020.03.25.006213 id = cord-340240-dk48pdqa author = Kuo, Tsun-Yung title = Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19 date = 2020-08-11 keywords = S-2P; SARS summary = title: Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19 S-2P was combined with various adjuvants, including CpG 1018, and administered to mice to test its effectiveness in eliciting anti-SARS-CoV-2 neutralizing antibodies. S-2P in combination with CpG 1018 and aluminum hydroxide (alum) was found to be the most potent immunogen and induced high titer of spike-specific antibodies in sera of immunized mice. In this study, we present data from preclinical studies aimed at developing a COVID-19 candidate subunit 84 vaccine using CHO cell-expressed SARS-CoV-2 S-2P antigen combined with various adjuvants. We have 85 shown that S-2P, when mixed with CpG 1018 and aluminum hydroxide adjuvants, was most effective in 86 inducing antibodies that neutralized pseudovirus and wild-type live virus while minimizing Th2-biased 87 responses with no vaccine-related adverse effects. Previous studies showed that the lung-infiltrating eosinophils were a common 308 indication of Th2-biased immune responses seen in animal models testing SARS-CoV vaccine candidates [22] . doi = 10.1101/2020.08.11.245704 id = cord-103773-1b961lfz author = Kurokawa, Shunji title = In vivo recellularization of xenogeneic vascular grafts decellularized with high hydrostatic pressure method in a porcine carotid arterial interpose model date = 2020-05-29 keywords = Fig; HHP; phase summary = title: In vivo recellularization of xenogeneic vascular grafts decellularized with high hydrostatic pressure method in a porcine carotid arterial interpose model In the present study, we conducted xenogeneic implantation of HHP-decellularized bovine vascular grafts from dorsalis pedis arteries to porcine carotid arteries then evaluated graft patency, ECM preservation and recellularization. Scanning electron microscopy on luminal surface of implanted grafts exhibited cobblestone-like endothelial cell layer which is similar to native vascular endothelium. Elastica van Gieson staining and Sirius red staining exhibited a fair preservation of elastin layer (internal elastic lamina), tunica media consisted of collagen fibers and stratified elastin layers in HHP-decellularized grafts, and recellularization at 4 weeks after implantation, respectively (Fig. 4B) . The luminal surface of decellularized bovine graft implanted at porcine carotid artery for 4 weeks showed endothelium with cobblestone-like appearance by fair recellularization similar with those in bovine and porcine native arteries (recipient animal) (Fig. 5A , C, D). doi = 10.1101/2020.05.29.123018 id = cord-103517-1itisiup author = Kwesi-Maliepaard, Eliza Mari title = The histone methyltransferase DOT1L prevents antigen-independent differentiation and safeguards epigenetic identity of CD8+ T cells date = 2019-11-18 keywords = CD8; Fig; TCR; dot1l summary = T-cell specific ablation of Dot1L resulted in loss of naïve CD8+ T cells and premature differentiation towards a memory-like state, independent of antigen exposure and in a cell-intrinsic manner. Mechanistically, DOT1L controlled T-cell differentiation and function by ensuring normal T-cell receptor density and signaling, and by maintaining epigenetic identity, in part by indirectly supporting the repression of developmentally-regulated genes. Analysis of CD8 + T cell subsets in the spleen revealed that Dot1L-KO mice showed a severe loss of naïve (CD44 -CD62L + ) CD8 + T (T N ) cells which was linked to a massive gain of the CD44 + CD62L + phenotype, a feature of central memory T cells (T CM ; Fig. 1A -B). To determine whether peripheral T AIM cells observed in the Dot1L-KO setting originate intrathymically, as reported previously for IL-4 dependent innate memory T cells 3 , we compared RNA-Seq data from SP CD8 + thymocytes from KO and WT mice. doi = 10.1101/826255 id = cord-298321-8871aifz author = Laamarti, Meriem title = Genetic analysis of SARS-CoV-2 strains collected from North Africa: viral origins and mutational spectrum date = 2020-07-01 keywords = SARS; Tunisia summary = The comparison of genetic variants of fourty North African strains revealed that two non-synonymous mutations D614G (in spike) and Q57H (in ORF3a) were common in four countries (Morocco, Tunisia, Algeria and Egypt), with a prevalence of 92.5% (n = 37) and 42.5% (n = 17), respectively, of the total genomes. Our recent study (13) based on the analysis of 30,983 genomes of SARS-CoV-2 variants belonging to 80 countries, revealed 5.67% of total mutations with a frequency greater than 1% of all the sequences analyzed suggesting that this virus is not yet adapted to its host. In all Moroccan SARS-CoV-2 genomes, the analysis of genetic variants revealed 61 mutations compared to the reference sequence (Fig 1) , including 29 non-syn(Fig 2A) . doi = 10.1101/2020.06.30.181123 id = cord-288824-sygnmiun author = Lam, SD title = SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals date = 2020-08-19 keywords = ACE2; SARS; Supplementary; TMPRSS2 summary = To predict infection risks, we modelled S-protein:ACE2 complexes from 215 vertebrate species, calculated changes in the energy of the complex caused by mutations in each species, relative to human ACE2, and correlated these changes with COVID-19 infection data. We correlated changes in the energy of the complex with changes in the structure of ACE2, chemical properties of residues in the binding interface, and experimental COVID-19 infection phenotypes from in vivo and in vitro animal studies. We used multiple methods to assess the relative change in binding energy (ΔΔG) of the SARS-CoV-2 S-protein:ACE2 complex following mutations in DC residues and DCEX residues that are likely to influence binding. Irrespective of host, the SARS-CoV-2 spike receptor binding domain is conserved (Fig. 4b) across tested human and animal associated SARS-CoV-2, suggesting mutations in the RBD are not required for infections observed in non-human species to date. doi = 10.1101/2020.05.01.072371 id = cord-329102-2y49kcwu author = Lan, Tammy C. T. title = Structure of the full SARS-CoV-2 RNA genome in infected cells date = 2020-06-30 keywords = FSE; RNA; SARS; figure; structure summary = We evaluated the robustness of our in-cell data derived genome-wide model by varying two critical RNA folding parameters used by RNAstructure: 1) the maximum allowed distance for base pairing and 2) the threshold for DMS signal normalization. Previous studies that computationally predicted genome-wide SARS-Cov-2 RNA structures used 1) RNAz, a thermodynamic-based model that additionally takes sequence alignment and considers base pairing conservation (Gruber et al., 2010; Rangan, Zheludev and Das, 2020) , and 2) Contrafold, which predicts RNA secondary structures without physics-based models and instead uses learned parameters based on known structures (Do, Woods and Batzoglou, 2006) . Interestingly, in silico predictions of the RNA structure of the SARS-CoV-2 genome using RNAz (Rangan, Zheludev and Das, 2020) and ScanFold (Andrews et al., 2020) do not find the 3-stem pseudoknot but instead support our in-cell model of Alternative Stem 1. doi = 10.1101/2020.06.29.178343 id = cord-323041-wf0hlhim author = Larsen, Mads Delbo title = Afucosylated immunoglobulin G responses are a hallmark of enveloped virus infections and show an exacerbated phenotype in COVID-19 date = 2020-05-18 keywords = Fig summary = Here, we report that afucosylated IgG which are of minor abundance in humans (∼6% of total IgG) are specifically formed against surface epitopes of enveloped viruses after natural infections or immunization with attenuated viruses, while protein subunit immunization does not elicit this low fucose response. Moreover, we have reported the lowered IgG-Fc fucosylation to be one of the factors 58 determining disease severity in pregnancy associated alloimmunizations, resulting in 59 excessive thrombocytopenia''s and blood cell destruction when targeted by afucosylated 60 antibodies (11-13). 109 Analogous to the platelet and Red Blood cell alloantigens (10-12, 18), the response to these 110 enveloped viruses also showed significant afucosylation of the antigen-specific IgG (Fig.2B) , 111 while the afucosylation was absent against the non-enveloped virus Parvo B19 (Fig.2C ). Regulated glycosylation patterns of IgG during alloimmune 405 responses against human platelet antigens doi = 10.1101/2020.05.18.099507 id = cord-274409-4ugdxbmy author = Laskar, Rezwanuzzaman title = Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India date = 2020-10-19 keywords = Disease; SARS; site summary = title: Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India Further, constitution of ''Disease'' mutations in genomes from asymptomatic people was mere 11% but those from deceased patients was over three folds higher at 38% indicating contribution of these mutations to the pathophysiology of the SARS-CoV-2. With a definitive possibility of India becoming the most affected country by SARS-CoV-2 in near future and the demographic burden involved, its pertinent to be analyze the accumulating variations in the genome accounting for possible changes in protein and their potential to alter the virus in any manner. Herein we extend our study using the same congregation of sequences to analyze the nature and composition of the observed mutations and their impact on proteins of SARS-CoV-2. The distribution of Disease and Neutral variants across the different genes of SARS-CoV-2 has been shown in Table 4 and Supplementary file 5. doi = 10.1101/2020.10.19.345066 id = cord-102324-tu804znm author = Le Sage, Valerie title = Pre-existing immunity provides a barrier to airborne transmission of influenza viruses date = 2020-06-15 keywords = Fig; H1N1; H3N2 summary = doi = 10.1101/2020.06.15.103747 id = cord-349794-mhviub6e author = Le, Brian L. title = Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19 date = 2020-10-23 keywords = COVID-19; SARS; drug; signature summary = We applied a computational drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available data. By infecting human adenocarcinomic alveolar basal epithelial cells with SARS-CoV-2 and comparing to controls, the authors generated a list of 120 differentially expressed genes. Here, we applied our existing computational drug repositioning pipeline to identify drug profiles with significantly reversed differential gene expression compared to predicted inhibitors (including one tested in Calu-3) were incubated with SARS-CoV-2 infected human embryonic kidney 293T cells overexpressing ACE2 (293T-ACE2) with viral replication determined using an immunofluorescence-based assay. In this study, we applied our drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available RNA-seq data ( Figure 1 ). Here, we used a transcriptomics-based drug repositioning pipeline to predict therapeutic drug hits for three different input SARS-CoV-2 signatures, each of which came from distinct human cell or tissue origins. doi = 10.1101/2020.10.23.352666 id = cord-102588-vpu5w9wh author = Le, Trang T. title = treeheatr: an R package for interpretable decision tree visualizations date = 2020-07-10 keywords = node; tree summary = doi = 10.1101/2020.07.10.196352 id = cord-255069-9xueqdri author = Leary, Shay title = Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence date = 2020-04-11 keywords = HLA; SARS summary = The findings suggest that homologous recombination may have occurred since its introduction into humans and be a mechanism for increased viral fitness and adaptation of SARS-CoV-2 to human populations. Evidence of viral adaptation to selective pressures as it spreads among diverse human populations has implications for the ongoing potential for changes in viral fitness over time, which in turn may impact transmissibility, disease pathogenesis and immunogenicity. Here we describe a new emerging strain of SARS-CoV-2 within the LGG clade that appears to be the result of a homologous recombination event that introduced three adjacent nucleotide changes spanning two residues of the nucleocapsid protein. Evidence for such adaptations with closely linked compensatory mutations are known to occur under host immune pressure as is well established for other adaptable RNA viruses such as HIV 1,2 and Hepatitis C virus (HCV) 3 . doi = 10.1101/2020.04.10.029454 id = cord-293826-2p7dqacd author = Lee, Cheryl Yi-Pin title = Neutralizing antibodies from early cases of SARS-CoV-2 infection offer cross-protection against the SARS-CoV-2 D614G variant date = 2020-10-09 keywords = SARS summary = Given that a majority of the developing antibody-mediated therapies 68 and serological assays are based on the S antigen of the original Wuhan reference 69 sequence, it is crucial to determine if humoral immunity acquired from the original 70 SARS-CoV-2 isolate is able to induce cross-detection and cross-protection against 71 the novel prevailing D614G variant. Given that a majority of the developing antibody-mediated therapies 68 and serological assays are based on the S antigen of the original Wuhan reference 69 sequence, it is crucial to determine if humoral immunity acquired from the original 70 SARS-CoV-2 isolate is able to induce cross-detection and cross-protection against 71 the novel prevailing D614G variant. Overall, our study shows that the D614G mutation on the S protein does not 150 impact SARS-CoV-2 neutralization by the host antibody response, nor confer viral 151 resistance against the humoral immunity. doi = 10.1101/2020.10.08.332544 id = cord-258360-fqrn02lr author = Lee, Jimmy title = No evidence of coronaviruses or other potentially zoonotic viruses in Sunda pangolins (Manis javanica) entering the wildlife trade via Malaysia date = 2020-06-19 keywords = SARS summary = doi = 10.1101/2020.06.19.158717 id = cord-341502-jlzufa28 author = Lee, Sungyul title = The SARS-CoV-2 RNA interactome date = 2020-11-02 keywords = OC43; Probe; RNA; RNP; SARS; figure summary = The second pool of 275 oligos ("Probe II") covers the remaining region (21563:29872, NC_045512.2) which is shared by both the gRNA and sgRNAs. To first check whether our method specifically captures the viral RNP complexes, we compared the resulting purification from Vero cells infected with SARS-CoV-2 (BetaCoV/Korea/KCDC03/2020) at MOI 0.1 for 24 hours (Kim et al., 2020b ) by either Probe I or Probe II. In combination, we define these 109 proteins as the "SARS-CoV-2 RNA interactome." 37 host proteins such as CSDE1 (Unr), EIF4H, FUBP3, G3BP2, PABPC1, ZC3HAV1 were enriched in both the Probe I and Probe II RNP capture experiments on infected cells ( Figure 1F ), thus identifying a robust set of the "core SARS-CoV-2 RNA interactome." Gene ontology (GO) term enrichment analysis revealed that these host factors are involved in RNA stability control, mRNA function, and viral process ( Figure S1F ). To measure the impact of these host proteins on coronavirus RNAs, we conducted knockdown experiments and infected Calu-3 cells with SARS-CoV-2 ( Figure 5A and 5B). doi = 10.1101/2020.11.02.364497 id = cord-102905-rlee32x7 author = Leis, Jonathan title = Ilaprazole and other novel prazole-based compounds that bind Tsg101 inhibit viral budding of HSV-1/2 and HIV from cells date = 2020-05-04 keywords = ESCRT; HIV-1; tsg101; virus summary = In this report we show that tenatoprazole and a related prazole drug, ilaprazole, effectively block infectious Herpes Simplex Virus (HSV)-1/2 release from Vero cells in culture. Our results indicate that prazole-based compounds may represent a class of drugs with potential to be broad-spectrum antiviral agents against multiple enveloped viruses, by interrupting cellular Tsg101 interaction with maturing virus, thus blocking the budding process that releases particles from the cell. Tenatoprazole and esomeprazole were shown to quantitatively inhibit the release of infectious HIV-1 from 293T cells in culture, and it was suggested that these effects may be mediated via changes in viral interaction with Tsg101, a key component of the cellular ESCRT complex (5, 33) . Given multiple reports suggesting that herpes viruses also use cellular ESCRT proteins in their replication process (20) (21) (22) (23) we tested if the Tsg101-binding prazole drugs, which blocked budding of HIV-1, would also block the release of herpes viruses from cells. doi = 10.1101/2020.05.04.075036 id = cord-285592-0in22wzv author = Lemoine, Frédéric title = COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM date = 2020-05-25 keywords = GISAID; MSA summary = Moreover, COVID-Align provides summary statistics, which can be used to determine the sequencing quality and evolutionary novelty of input genomes (e.g. number of new mutations and indels). Unique mutations and indels are possibly due to errors (sequencing, assembly etc.), while new ones (seen at least twice in submitted genomes, for the first time) likely correspond to evolutionary novelties (see Sup. Info. Right: Statistics summary, displaying the number of High and Low Quality genomes, and the number of evolutionary events (mutations, gaps, gap openings, insertions, insertion openings). For each of the input genomes, COVID-Align computes a series of summary statistics to help users analyze their data, remove problematic sequences, and detect those containing evolutionary novelties. When new sequences with confirmed insertions and deletions will be available from emerging genomes, they will be incorporated in the profile and the resulting MSA will closely account for these indels. doi = 10.1101/2020.05.25.114884 id = cord-324888-oak27okj author = Leng, Ling title = Potential microenvironment of SARS-CoV-2 infection in airway epithelial cells revealed by Human Protein Atlas database analysis date = 2020-04-18 keywords = ACE2; SARS; figure summary = title: Potential microenvironment of SARS-CoV-2 infection in airway epithelial cells revealed by Human Protein Atlas database analysis Based on the analysis of the Human Protein Atlas database, we compared the virus-related receptors of epithelial-derived cells from different organs and found potential key molecules in the local microenvironment for SARS-CoV-2 entering airway epithelial cells. Therefore, we wonder whether there are some key local microenvironment proteins specifically expressed on the surface of airway EpC that makes the virus prefer airway EpCs. In some cases, additional cell surface molecules or co-receptors are required for sufficient viral entry into host cells. We used the human protein atlas (HPA) database [16] to extract the protein expression level of 65 receptors involved in "virus receptor activity" (GO:0001618) of EpCs and epithelial or epithelial-derived cells from 14 organs (16 cell types) ( Figure 1A and Supplementary Materials and Methods). doi = 10.1101/2020.04.16.045799 id = cord-103733-blam1f4c author = Levade, Inès title = Predicting Vibrio cholerae infection and disease severity using metagenomics in a prospective cohort study date = 2020-06-24 keywords = figure; table summary = title: Predicting Vibrio cholerae infection and disease severity using metagenomics in a prospective cohort study cholerae susceptibility and identify predictors of symptomatic disease, we applied deep shotgun metagenomic sequencing to a cohort of household contacts of patients with cholera. Conclusion Our results highlight the power of metagenomics to predict disease outcomes and suggest specific species and genes for experimental testing to investigate mechanisms of microbiome-related protection from cholera. SUMMARY Cholera infection and disease severity can be predicted using metagenomic sequencing of the gut microbiome pre-infection in a prospective cohort, and suggests potentially protective bacterial species and genes. Our metagenomic analysis yielded improved 85 outcome predictions compared to 16S rRNA sequencing, and identified bacterial genes 86 associated with remaining uninfected after exposure to V. Applied to the Midani 230 2018 cohort, this model predicted outcomes significantly better than random (shuffled labels) 231 using species, strains or pathway data, but not gene families ( Table 1 ; see Table S3 for p-232 values). doi = 10.1101/2020.02.25.960930 id = cord-104008-luqvw0y8 author = Levinson, Julia title = Investigating the effectiveness of school health services delivered by a health provider: a systematic review of systematic reviews date = 2019-02-07 keywords = health; intervention; school summary = Systematic reviews of intervention studies that evaluated school-based or school-linked 31 health services delivered by a health provider were included. Systematic reviews of intervention studies that evaluated school-based or school-linked 31 health services delivered by a health provider were included. Through a comprehensive literature search, the 71 overview aimed to identify health areas and specific school health service interventions that 72 have at least some evidence of effectiveness. Finally, 74 the overview aimed to identify the health areas and specific school health services 75 interventions for which no SRs were found, whether because the primary literature does not 76 exist or where there are primary studies but no SR has been conducted. It is difficult to determine overall effectiveness of school health services from this overview because the included SRs do not sufficiently cover the health areas most relevant for children and adolescents. doi = 10.1101/543868 id = cord-102835-71ome9h8 author = Levinson, Maxwell Adam title = FAIRSCAPE: A Framework for FAIR and Reproducible Biomedical Analytics date = 2020-08-15 keywords = Data; FAIRSCAPE; Service; evidence summary = All results are annotated with FAIR metadata using the evidence graph model for access, validation, reproducibility, and re-use of archived data and software. We set out to construct a provenance-aware computational data lake, as described above, by significantly extending and refactoring the identifier and metadata services framework we and our colleagues developed in the NIH Data Commons Pilot Project Consortium (Timothy Clark et al. We extended and re-engineered this framework over time to track and visualize computations and their evidence, to manage the computational objects (such as data and software) as well as their metadata, to analyze very large datasets with horizontal scale-out, to support neuroimaging workflows, and to make it generally more easy for scientists and computational analysts to use, by providing Binder and Notebook services (Jupyter et al. It supports transparent disclosure of the Evidence Graphs of computed results, with access to the persistent identifiers of the cited data or software, and to their stored metadata. doi = 10.1101/2020.08.10.244947 id = cord-325124-0hxan9rw author = Li, Chenyu title = Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing date = 2020-05-18 keywords = Fig; PCR; SARS summary = However, it has been reported that only 47-59% of the positive cases were identified by some RT-PCR methods, probably due to low viral load, timing of sampling, degradation of virus RNA in the sampling process, or possible mutations spanning the primer binding sites. With the goal of improving sensitivity and accommodating various application settings, we developed a multiplex-PCR-based method comprised of 343 pairs of specific primers, and demonstrated its efficiency to detect SARS-CoV-2 at low copy numbers. We further amplified the entire SARS-CoV-2 genome from 8 to half a million viral copies purified from 13 COVID-19 positive specimens, and detected mutations through next generation sequencing. Finally, we developed a multiplex-PCR-based metagenomic method in parallel, that required modest sequencing depth for uncovering SARS-CoV-2 mutational diversity and potentially novel or emerging isolates. To overcome this constraint, we developed a multiplex-PCR-based metagenomic method that achieved >96% coverage of the S and N genes of SARS-CoV-2 in the contest of human gDNA, while only required ~0.6M of total reads per library. doi = 10.1101/2020.03.12.988246 id = cord-274528-mr81o9cu author = Li, Fei title = Distinct mechanisms for TMPRSS2 expression explain organ-specific inhibition of SARS-CoV-2 infection by enzalutamide date = 2020-09-12 keywords = Data; Fig; SARS; TMPRSS2 summary = Among these drugs, a relatively new antiandrogen agent, enzalutamide, was proposed because it reduces the expression of transmembrane serine protease 2 (TMPRSS2), a key component mediating SARS-CoV-2-driven entry into host cells, in prostate cancer cells. Here, we evaluated the antiviral efficacy of enzalutamide in prostate cancer cells, lung cancer cells, human lung organoids and SARS-CoV-2-infected Ad-ACE2-transduced Tmprss2 knockout (Tmprss2-KO) and wild-type (WT) mice. Although Tmprss2 knockout effectively blocked SARS-CoV-2 infection in ACE2-transduced mice, enzalutamide showed no antiviral activity due to the AR independence of TMPRSS2 expression in mouse and human lung epithelial cells. Notably, in addition to prostate, other essential 40 organs, including lung, kidney and liver, which are permissive for SARS-CoV-2 infection in human, were 41 characterized with Tmprss2-postive epithelial cells ( Fig. 1b and Extended Data Fig. 1c ). Consistently, 25 enzalutamide significantly decreased TMPRSS2 expression and inhibited SARS-CoV-2 infection in human 26 prostate cancer cells (Fig. 2) . doi = 10.1101/2020.09.11.293035 id = cord-294275-pp0vlaye author = Li, Jingjing title = Rapid detection of SARS-CoV-2 and other respiratory viruses by using LAMP method with Nanopore Flongle workflow date = 2020-06-03 keywords = Flongle; SARS summary = Here, we propose a method to detect SARC-Cov-2 infection within two hours combined with Loop-mediated Isothermal Amplification (LAMP) reaction and nanopore Flongle workflow. Here, we use nanopore Flongle workflow combined with LAMP reaction to propose a faster and more convenient method to detect SARS-CoV-2 and other respiratory viruses in two hours. This study presents a LAMP based method combined with nanopore Flongle rapid realtime sequencing workflow to detect COVID-19 as low as 3.25×10^2 copies/mL of SARS-CoV-2 in both laboratory and wild-caught environment. To test the limit of detection, the amplification products of dilution gradient 3.25×10^4, 3.25 × 10^3, 1.1 × 10^3, 6.5 × 10^2, 3.25 × 10^2 copies/mL and negative control total 12 samples were constructed another barcoding library (Oxford Nanopore, SQK-RBK004) as described above and sequenced using a PromethION flowcell to achieve more data. The study design ( Figure 2 ) for SARS-CoV-2 detection is based on LAMP rapid amplification of specific genes and sequenced by nanopore Flongle workflow. doi = 10.1101/2020.06.03.131474 id = cord-102184-8u73adnk author = Li, Jinzhi title = Visual input into the Drosophila melanogaster mushroom body date = 2020-05-02 keywords = GFP; Kenyon; figure; neuron summary = doi = 10.1101/2020.02.07.935924 id = cord-103946-c5i8btp7 author = Li, Maohua title = Next generation of anti-PD-L1 Atezolizumab with better anti-tumor efficacy in vivo date = 2020-07-01 keywords = ADCC; Atezolizumab; Maxatezo summary = Our data shown that insertion of GGGS, without altering the anti-PD-L1 antibody affinity and inhibitory activity, completely abolished the ADCC activity, as same as Atezolizumab. Based on the structural information acquired from different antibodies in Protein data bank (e.g., PDB ID: 1IGT), we hypothesized that an insertion of a short but very flexible sequence in the hinge region or somewhere upstream of the glycosylation site of N297 may cut off the stress transmission signal between the Fv and Fc domain. Clearly, the insertion of GGGS between G237 and G238 of human IgG1 heavy chain showed no significant negative impact on antibody''s affinity and inhibitory activity. Our data demonstrated that the insertion of GGGS in the hinge regions of human IgG1 could abolish their ADCC activities completely without concering negative impact on antibody affinities, inhibitory activities, expression levels, stabilities or immunogenicity. For those well-known antibody drugs, such as Genentech''s aglycosylated anti-PD-L1 Atezolizumab, we demonstrated that inserting GGGS in the hinge regions of human IgG1 Fc could remove the ADCC activities completely. doi = 10.1101/2020.06.30.166207 id = cord-326882-bbn1tfq5 author = Li, Quan title = Genetic Variability of Human Angiotensin-Converting Enzyme 2 (hACE2) Among Various Ethnic Populations date = 2020-04-14 keywords = ACE2; SARS summary = We set out to examine genetic differences in the human angiotensin-converting enzyme 2 (hACE2) gene, as its receptor serves as a cellular entry for SARSCoV-2. To explore the variability in genetic polymorphisms and expression in human ACE2 (hACE2), we set out to determine if there were any differences between the Asian and Caucasian populations for ACE2 polymorphisms and compare the variability of hACE2 expression in peripheral blood among eight different populations. In order to investigate whether differences in genetic variations exist between Caucasians and Asians and if these variants can influence the efficiency of cell entry of SARS-CoV-2, we retrieved the variants in the hACE2 from gnomAD v2.1 exomes13. Asians and Other Races Express Similar Levels of and Share the Same Genetic Polymorphisms of the SARS-CoV-2 Cell-Entry Receptor doi = 10.1101/2020.04.14.041434 id = cord-332134-88wfcc3y author = Li, Tingting title = A potent synthetic nanobody targets RBD and protects mice from SARS-CoV-2 infection date = 2020-09-24 keywords = Fig; RBD; SARS summary = title: A potent synthetic nanobody targets RBD and protects mice from SARS-CoV-2 infection Molecular mechanism for neutralization 157 Structure alignment of SR4-, MR17-and ACE2-RBD 4 showed that both sybodies 158 engage with RBD at the receptor-binding motif (RBM) ( Fig. 2A, 2B) . Taken together, SR4 169 and MR17, and probably MR3, neutralize SARS-CoV-2 by competitively blocking the For biparatopic fusion, we first identified two sybodies, namely LR1 and LR5 (Fig. 208 3A, 3B), that could bind RBD in addition to MR3 using the BLI assay. As LR5 showed 209 higher affinity and neutralization activity than LR1 (Fig. 1A) , we fused this non-210 competing sybody to the N-terminal of MR3 with various length of GS linkers ranging 211 from 13 to 34 amino acids (Extended Data Table S1 ). Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with 803 doi = 10.1101/2020.06.09.143438 id = cord-264051-ps0x2es1 author = Li, Wei title = Human Identical Sequences of SARS-CoV-2 Promote Clinical Progression of COVID-19 by Upregulating Hyaluronan via NamiRNA-Enhancer Network date = 2020-11-05 keywords = HEK293; RNA; SARS; covid-19 summary = Mechanically, HIS-SARS-CoV-2, behaving as virus-derived miRNAs, directly target to the human genomic loci and further interact with host enhancers to activate the expression of adjacent and distant genes, including cytokines gene and angiotensin converting enzyme II (ACE2), a well-known cell entry receptor of SARS-CoV-2, and hyaluronan synthase 2 (HAS2), which further increases hyaluronan formation. Besides, these virus fragments containing HIS can increase the H3K27 acetylation (H3K27ac) enrichment at their corresponding regions of the human genome in different mammalian cells and activate the expression of adjacent and distant genes associated with inflammation. Collectively, we identified HIS in SARS-CoV-2 genome, and the targeted human genome loci enriched with cytokines genes suggested that HIS may underly the clinical characteristics of COVID-19 patients and serve as a vital player in the pathological progression. doi = 10.1101/2020.11.04.361576 id = cord-300847-ycuiso0g author = Li, Wei title = Rapid selection of a human monoclonal antibody that potently neutralizes SARS-CoV-2 in two animal models date = 2020-06-02 keywords = Fig; RBD; SARS summary = We identified panels of fully human monoclonal antibodies (mAbs) from eight large phage-displayed Fab, scFv and VH libraries by panning against the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) glycoprotein. By using phage display we have previously identified a number of potent fully human mAbs (m396, m336, m102.4) against emerging viruses including severe acute respiratory syndrome coronavirus (SARS-CoV) (4) , Middle East respiratory syndrome coronavirus (MERS-CoV) (5) and henipaviruses (6, 7) , respectively, which are also highly effective in animal models of infection (8) (9) (10) (11) ; one of them was administered on a compassionate basis to humans exposed to henipaviruses and successfully evaluated in a clinical trial (12) . Thus, to generate high affinity and safe mAbs we used eight very large (size ~ 10 11 clones each) naive human antibody libraries in Fab, scFv or VH format using PBMCs from 490 individuals total obtained before the SARS-CoV-2 outbreak. doi = 10.1101/2020.05.13.093088 id = cord-252910-7qvnj6c8 author = Li, Xin title = The discovery of a recombinant SARS2-like CoV strain provides insights into SARS and COVID-19 pandemics date = 2020-09-21 keywords = ORF8; SARS; figure summary = In the present study, we identified key recombination regions and mutation sites cross the SARS-CoV-2, SARS-CoV and SARS-like CoV clusters of betacoronavirus subgroup B. Different from these studies, we previously reported several other findings on SARS-CoV-2 for the first time, including the following in particular: (1) the alternative translation of Nankai coding sequence (CDS) that characterize the rapid mutation rate of betacoronavirus at the nucleotide level [2] ; (2) a furin cleavage site (FCS) "RRAR" in the junction region between S1 and S2 subunits (junction FCS) of SARS-CoV-2 that may increase the efficiency of viral entry into cells [3] ; and (3) the use of 5'' untranslated-region (UTR) barcoding for the detection, identification, classification and phylogenetic analysis of-though not limited to-CoVs [4] . Using the insertions and deletions (InDels) at six sites, we identified two recently detected betacoronavirus strains RmYN01 and RmYN02 from a bat [6] and discovered that RmYN02 was a recombinant SARS2-like CoV strain. doi = 10.1101/2020.07.22.213926 id = cord-103802-mygo3qx0 author = Li, Yanpeng title = Multiple known and a novel parvovirus associated with an outbreak of feline diarrhea and vomiting date = 2020-03-25 keywords = Shelter; cat summary = title: Multiple known and a novel parvovirus associated with an outbreak of feline diarrhea and vomiting An unexplained outbreak of feline diarrhea and vomiting, negative for common enteric viral and bacterial pathogens, was subjected to viral metagenomics and PCR. We characterized from fecal samples the genome of a novel chapparvovirus we named fechavirus that was shed by 8/17 affected cats and different feline bocaviruses shed by 9/17 cats. Epidemiological investigation of disease signs, time of onset, and transfers of affected cats between three facilities support a possible role for this new chapparvovirus in a highly contagious feline diarrhea and vomiting disease. Shelter 2 a total of 5 individual cats and a sample pool (mixed feces from 3 cats) were Using metagenomics, we found FeBoV1, 2, and 3 and a novel chaphamaparvovirus we named 311 fechavirus in a large fraction of fecal samples and fechavirus in all vomit samples from sick cats 312 in a multi-facility outbreak. Feline Virome-A Review of 409 Novel Enteric Viruses Detected in Cats Feline fecal virome reveals novel and prevalent enteric viruses doi = 10.1101/2020.03.24.005876 id = cord-102454-fqwks0rb author = Liao, Yan Shin J. title = Acid exposure impairs mucus secretion and disrupts mucus transport in neonatal piglet airways date = 2019-06-13 keywords = MUC5B; airway; figure summary = doi = 10.1101/669879 id = cord-104036-790vk1cf author = Liekkinen, Juho title = Understanding the Functional Properties of Lipid Heterogeneity in Pulmonary Surfactant Monolayers at the Atomistic Level date = 2020-07-08 keywords = APL; Fig; Surfactant; monolayer summary = In this work, we combined all-atom molecular dynamics simulations, Langmuir trough measurements, and AFM imaging to study synthetic four-component lipid monolayers designed to model protein-free pulmonary surfactant. 22 It has been shown that the pulmonary surfactant monolayers and membranes exhibit phase behaviour that is believed to play roles in lung mechanics; tight packing of lipids with saturated lipid chains promotes its ability to lower surface tension, whereas lipids with unsaturated chains increase pulmonary surfactant fluidity and thus allow for its rapid adsorption to the air-water interface. By using our recently developed protocol for performing simulations of lipid monolayers at the air-water interface, 33, 46 we were able to reach quantitative agreement with experimental surface pressure-area isotherms. Plateau Surface pressure-area isotherm is a key quantity representing monolayer behavior at the water-air interface, and it is readily extracted from both Langmuir trough measurements and computer simulations. doi = 10.1101/2020.07.07.191569 id = cord-264012-q2quyijg author = Lim, Su Bin title = ACE2-expressing endothelial cells in aging mouse brain date = 2020-07-11 keywords = ACE2; SARS summary = Further, scRNA-seq dataset specifically derived from brain vasculature in young adult and aged mice (T3) confirms the elevated ACE2 expression in subsets of the three identified cell types, which consist of 32.8% of the cell populations ( Fig. 1 C) . While our study provides a foundation for a more refined level of analysis of EC and vascular PC, a cell type that remains poorly understood despite its key roles in immune response and microvascular stability [17] , our analyses are limited only to the normal aging mouse and human brains, lacking the context of COVID-19 neuropathology. Despite the works that failed to identify direct signs of SARS-CoV-2 infection in the brains of COVID-19 patients [12, 13] , other lines of evidence support the neurotropism of the virus, as evidenced by experimental platforms leveraging human induced pluripotent stem cell (iPSC)derived dopaminergic neurons [22] and an organotypic brain model [23] . doi = 10.1101/2020.07.11.198770 id = cord-338734-laeocs3j author = Lima, Amorce title = Validation and Comparison of a Modified CDC Assay with two Commercially Available Assays for the Detection of SARS-CoV-2 in Respiratory Specimen date = 2020-06-30 keywords = CDC; SARS summary = In silico analysis and clinical sample testing showed that the primesr/probes designed by the CDC were specific to the SARS-CoV-2 as they accurately detected all reactive samples with an assay LoD of 200 copies/ml. A 149 series of two-fold dilutions of SARS-CoV-2 strain USA_WA1/2020 RNA were spiked in pooled 150 sputum at concentrations of 800 copies/ml to 0.05 copy/ml in order to determine the limit of 151 detection (LoD) of the assay. On the other hand, the average Ct values difference between 235 samples run within 2 days between DiaSorin Simplexa Covid 19 Direct assay and the modified 236 CDC SARS-CoV-2 assay was -2.42, and -6.0 between samples run within 5 days. In this study, we validated a modified CDC SARS-CoV-2 assay and compared its 263 performance to two commercial automated sample-to-answer assays for the detection of SARS-264 The difference is even greater 286 in samples that were run 5 days after the routine testing on the modified CDC SARS-CoV-2 287 assay. doi = 10.1101/2020.06.29.179192 id = cord-328073-bqeffvzl author = Limonta, Daniel title = Nodosome inhibition as a novel broad-spectrum antiviral strategy against arboviruses and SARS-CoV-2 date = 2020-11-06 keywords = NOD2; SARS summary = The studies were prompted by the observation that infection of human fetal brain cells with Zika virus (ZIKV) induces expression of nucleotide-binding oligomerization domain-containing protein 2 (NOD2), a host factor that was found to promote ZIKV replication and spread. A drug that targets NOD2 was shown to have potent broad-spectrum antiviral activity against other flaviviruses, alphaviruses and SARS-CoV-2, the causative agent of COVID-19. Next, we demonstrated that the NOD2 inhibitor GSK717 blocks infection by and 205 spread of ZIKV in human fetal brain and cell lines. Similarly, the work here which demonstrated the antiviral activity of NOD2 and RIPK2 inhibitors using tissue explants, 216 primary cells and cell lines, support the potential clinical use of these compounds in mono or co-217 infections by arboviruses as well as coronavirus infections at early and/or advanced stages. Calu-3 and Huh7 cells infected with SARS-CoV-2 (MOI=0.1) were also treated with GSK583 for 24 hours before collecting the cell supernatants for viral titer determination. doi = 10.1101/2020.11.05.370767 id = cord-102608-1ilforzm author = Litviňuková, Monika title = Cells and gene expression programs in the adult human heart date = 2020-04-10 keywords = cardiac; cell; figure; heart summary = doi = 10.1101/2020.04.03.024075 id = cord-102977-yci9kq6x author = Liu, Haiming title = GHSR-1a is not Required for Ghrelin’s Anti-inflammatory and Fat-sparing Effects in Cancer Cachexia date = 2019-12-06 keywords = WAT; bat summary = This study characterizes the pathways involved in AT atrophy in the Lewis Lung Carcinoma (LLC)-induced cachexia model and those mediating the effects of ghrelin in Ghsr+/+ and Ghsr−/− mice. GHSR-1a is not expressed in adipocytes (Sun, Garcia et 243 al., 2007) but is present in macrophages (Ma, Lin et al., 2013) and our findings are consistent with a 244 previous report showing that old, non-tumor-bearing Ghsr -/mice have reduced macrophage 245 infiltration, a shift on macrophage differentiation towards a more anti-inflammatory phenotype, and 246 decreased inflammation in adipose tissue (Lin, Lee et al., 2016) . In this study, we did 278 not see a significant effect of ghrelin on preventing LLC-induced fat browning, BAT thermogenesis, 279 increased REE or decreased physical activity in the setting of CACS despite the fact that ghrelin 280 prevented fat and weight loss and anorexia. doi = 10.1101/866376 id = cord-277253-vy0mvzeb author = Liu, Hongbo title = Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro date = 2020-04-11 keywords = CoV-2; SARS summary = title: Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro We further identified four baicalein analogue compounds from other herbs that inhibit SARS-CoV-2 3CLpro activity at microM concentration. baicalensis has effective anti-SARS-CoV-2 activity and baicalein and analogue compounds are strong SARS-CoV-2 3CLpro inhibitors. Inspired by the previous studies, several covalent inhibitors were experimentally identified to inhibit the 3CL pro activity and viral replication of SARS-CoV-2, and some of the complex crystal structures were solved [14, 15] . baicalensis inhibits SARS-CoV-2 3CL pro activity and the most active ingredient baicalein exhibits an IC50 of 0.39 M. We also identified four baicalein analogue compounds from other herbs that inhibit SARS-CoV-2 3CL pro activity at microM concentration. baicalensis and tested its inhibitory activity against SARS-CoV-2 3CL pro . baicalensis extract at different concentrations on SARS-CoV-2 3CL pro activity were 6 shown in Figure 1A . doi = 10.1101/2020.04.10.035824 id = cord-258630-mvz2l3yj author = Liu, Tiantian title = A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples date = 2020-11-10 keywords = Fig; SARS; SNV summary = We compared seven different library construction protocols and specifically evaluated the cross-protocol performance in sequencing read mappability, viral genome coverage percentage and uniformity, effect of sequence depth, SNV calling concordance (reproducibility), precision (positive predictive value), and sensitivity (proportion of consensus variants identified at different sequencing depths and viral copy number inputs) across protocols. Here, we compared seven WGS protocols for SARS-CoV-2 using clinical samples from infected patients, benchmarking the performances of these protocols in several aspects including the sequencing read mappability, genome coverage (percentage and uniformity, minimum sequences required); sample storage condition; effects of viral input, sequencing depth, length and platform; sensitivity, reproducibility and precision of SNV calling and related assay factors (e.g., amount of viral input, sequencing depth and bioinformatics pipeline). doi = 10.1101/2020.11.10.375022 id = cord-273416-332stbjl author = Liu, Tianyuan title = Transcriptional differences for COVID-19 Disease Map genes between males and females indicate a different basal immunophenotype relevant to the disease date = 2020-10-01 keywords = COVID-19; Disease summary = We created DeCovid, an R shiny app that combines gene expression data of different human tissue from the Genotype-Tissue Expression (GTEx) project and the COVID-19 Disease Map gene collection to explore basal gene expression differences across healthy demographic groups. In this paper, we present the DeCovid app, a Shiny app, to explore basal expression level differences in COVID-19 disease map genes between men and women and different age groups. The DeCovid shiny app combines a selection of human tissue specific GTEx data with the COVID-19 Disease Map database to allow quick exploration of basal gene expression values and differences in the healthy human population for genes described to be important for COVID-19. Here we present the DeCovid app as a resource to explore sex and age differential expression patterns in the healthy population for genes described to be involved in COVID-19 disease pathways. doi = 10.1101/2020.09.30.321059 id = cord-348729-kejlm425 author = Liu, Xiaoyu title = Neutralizing Antibodies Isolated by a site-directed Screening have Potent Protection on SARS-CoV-2 Infection date = 2020-05-04 keywords = ACE2; SARS; figure summary = SARS-CoV-2 infects host cells by interacting with angiotensin converting enzyme-2 (ACE2) via the S1 receptor-binding domain (RBD) of its surface spike glycoprotein. Among them, 4A3 and three domain antibodies (4A12, 4D5, and 4A10) were identified to act as neutralizing antibodies due to their capabilities to block the interaction between SARS-CoV-2-RBD and ACE2-positive cells. These determined infection mechanisms indicated that blocking the interaction of SARS-CoV-2-RBD and ACE2 would cause a direct neutralizing effect against virus. This information suggests that the ACE2 interface of SARS-CoV-2-RBD might have high immunogenicity, which would be a suitable targeting epitope to develop SARS-CoV-2-specific antibodies with potent neutralizing function by in vitro screening. We performed site-directed antibody screening by phage display and finally obtained one IgG antibody and three single domain antibodies with potent neutralizing activities for SARS-CoV-2. Notably, the eluted phage exhibited a stronger binding signal on SARS-CoV-2-RBD compared to that on SARS-CoV-2-RBD mut, especially those from the domain antibody library ( Figure 2C ), indicating an expected precleaning effect during selection. doi = 10.1101/2020.05.03.074914 id = cord-305054-4d84b2g6 author = Liu, Yuan title = The selection of reference genome and the search for the origin of SARS-CoV-2 date = 2020-08-11 keywords = SARS; Wuhan summary = The assembly obtained using RaTG13 as reference showed better statistics in total length and N50 than the assembly guided by SARS-CoV-2, indicating that RaTG13 maybe a better reference for assembling CoV in pangolin or other potential intermediate hosts. Zhang, Wu, and Zhang [13] re-analyzed the RNA-Seq reads from two pangolins carrying coronavirus using reference-guided de novo assembly method, with Wuhan-Hu-1 as the reference genome. They also performed RNA sequencing in five archived pangolins samples from Guangdong, and assembled the genomes using WIV04, another SARS-CoV-2 genome from human, as reference genome. Using de novo assembly method, they obtained viral genome that showed 90.32% and 90.24% of whole genome identify to Wuhan-Hu-1and Bat-CoV RaTG13, respectively. RaTG13, which is a bat CoV, had 1,287 reads mapped to it, and the resulting assembly has total length of 21,925 and N50 of 1,428. doi = 10.1101/2020.08.10.245290 id = cord-349015-5oisrm5s author = Liu, Zhe title = Identification of a common deletion in the spike protein of SARS-CoV-2 date = 2020-04-02 keywords = SARS summary = In this study, we identified two variants from the first Guangdong SARS-CoV-2 cell strain, with deletion mutations on polybasic cleavage site (PRRAR) and its flank sites. These data indicate (1) the deletion of QTQTN, at the flank of polybasic cleavage site, is likely benefit the SARS-CoV-2 replication or infection in vitro but under strong purification selection in vivo since it is rarely identified in clinical samples; (2) there could be a very efficient mechanism for deleting this region from viral genome as the variants losing 23585-23599 is commonly detected after two rounds of cell passage. By sequencing the whole genome of SARS-CoV-2, we identified two variants having deletion mutations on polybasic cleavage site (PRRAR) and its flank sites. To investigate whether these deletions described above are random mutations occasionally identified in a strain or would commonly occur after cell passages, we performed whole genome sequencing on the other 21 SARS-CoV-2 viral strains collected after 2 rounds of cell passage in Vero-E6 or Vero cells (Supplemental Table) . doi = 10.1101/2020.03.31.015941 id = cord-103872-yzqic5vt author = Liu, Zhijin title = Global view on virus infection in non-human primates and implication for public health and wildlife conservation date = 2020-05-13 keywords = NHP; SARS summary = Research has revealed that SARS-CoV-2 and other coronaviruses have been transmitted from animals to humans and vice versa, and across animal species, and hence, attracted public attention concerning host-virus interactions and transmission ways. We suggest epidemiological investigations in NHPs, specifically in Old World monkeys with close contact to humans, and other effective measures to prevent this potential circular transmission. First, we generated a summary statistics of worldwide reported VI-NHPs. We then 61 identified and predicted NHP species with a high risk of virus transmission from humans and 62 predicted geographic locations where disease outbreaks are likely to occur. Since centrality in primate-virus networks could assess the potential for the 72 circulation of viruses among NHPs and humans, we estimated the centrality using four metrics: 73 strength degree centrality, eigenvector centrality, betweenness centrality, and closeness centrality 74 implemented in the R package "igraph" and UCINET 6. Centrality in primate-parasite networks 225 reveals the potential for the transmission of emerging infectious diseases to humans doi = 10.1101/2020.05.12.089961 id = cord-314072-av3r7it7 author = Liu, Zhuoming title = Landscape analysis of escape variants identifies SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization date = 2020-11-08 keywords = SARS summary = title: Landscape analysis of escape variants identifies SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization To define the immune-mediated mutational landscape in S protein, we used a VSV-eGFP-SARS-CoV-2-S chimeric virus and 19 neutralizing monoclonal antibodies (mAbs) against the receptor binding domain (RBD) to generate 48 escape mutants. Although each mAb had unique resistance profiles, many shared residues within an epitope, as several variants were resistant to multiple mAbs. Remarkably, we identified mutants that escaped neutralization by convalescent human sera, suggesting that some humans induce a narrow repertoire of neutralizing antibodies. By comparing the antibody-mediated mutational landscape in S protein with sequence variation in circulating SARS-CoV-2 strains, we identified single amino acid substitutions that could attenuate neutralizing immune responses in some humans. To select for SARS-CoV-2 S variants that escape neutralization, we used VSV-SARSas we isolated this mutation alone, and acquisition of the L517R substitution appeared to 141 increase viral fitness as judged by plaque morphology (Fig S2) . doi = 10.1101/2020.11.06.372037 id = cord-102632-yazl9usb author = Lobet, Guillaume title = QuoVidi: a open-source web application for the organisation of large scale biological treasure hunts date = 2020-07-01 keywords = activity; picture; student summary = doi = 10.1101/2020.06.30.177006 id = cord-343517-vf32wxkx author = Lokman, Syed Mohammad title = Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: a computational biology approach date = 2020-04-11 keywords = CoV-2; SARS; spike summary = However, SARS-CoV-2 has emerged with remarkable properties like glutamine-rich 42 aa long exclusive molecular signature (DSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIE) in position 983-1024 of polyprotein 1ab (pp1ab) [16] , diversified receptor-binding domain (RBD), unique furin cleavage site (PRRAR↓SV) at S1/S2 boundary in S glycoprotein which could play roles in viral pathogenesis, diagnosis and treatment [17] . There is growing evidence that spike protein, a 1273 amino acid long glycoprotein having multiple domains, possibly plays a major role in SARS-CoV-2 pathogenesis. In this study, we have analyzed 320 genomic sequences of SARS-CoV-2 to identify mutations between the available genomes followed by the amino acid variations in the glycoprotein S to foresee their impact on the viral entry to host cell from structural biology viewpoint. The evolutionary distances showed that all the SARS-CoV-2 spike proteins cluster in the same node of the phylogenetic tree confirming the sequences are similar to Refseq YP_009724390 (Fig. 2) . doi = 10.1101/2020.04.07.030924 id = cord-102279-ena1usqv author = Long, Rory K. M. title = Super Resolution Microscopy and Deep Learning Identify Zika Virus Reorganization of the Endoplasmic Reticulum date = 2020-06-23 keywords = ZIKV; cer summary = projections of 3D STED image stacks show high intensity ERmoxGFP and Sec61β-GFP labeling in a 89 CER region and low intensity labeling in PER tubules in mock-infected cells ( Figure 1A ), as reported 90 previously by diffraction limited confocal microscopy (3). Density-based segmentation of the ERmoxGFP-96 and Sec61β-GFP-labelled ER of ZIKV-infected cells showed that the higher density crescent-shaped 97 CER region exhibited significant overlap with dsRNA-positive ER structures relative to the rest of 98 the ER ( Figure 1B ). Morphological comparison of the dsRNA-positive and -negative CER of 133 ZIKV-infected cells with the CER of mock-infected cells showed that the CER was composed of a 134 convoluted network of tubules for both the ERmoxGFP-and Sec61β-labeled ER ( Figure 3B ). 3D STED analysis showed a predominant distribution of both NS2B and 149 NS4B to the CER and more particularly to the dense ZIKV-induced crescent-shaped tubular matrix 150 in ERmoxGFP transfected U87 cells ( Figure 5A ). doi = 10.1101/2020.05.12.091611 id = cord-334313-v2syspu6 author = Long, S. Wesley title = Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston, Texas date = 2020-05-03 keywords = CoV-2; Houston; SARS; covid-19 summary = We sequenced the genomes of 320 SARS-CoV-2 strains from COVID-19 patients in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. We sequenced the genomes of 320 SARS-CoV-2 strains from COVID-19 patients in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. To better understand the first phase of virus spread in metropolitan Houston, Texas, we sequenced the genomes of 320 SARS-CoV-2 strains recovered from COVID-19 patients early in the Houston viral arc. To better understand the first phase of virus spread in metropolitan Houston, Texas, we sequenced the genomes of 320 SARS-CoV-2 strains recovered from COVID-19 patients early in the Houston viral arc. Because in vitro resistance of SARS-CoV to remdesivir has been reported to be caused by either of two amino acid replacements in RdRp (Phe476Leu and Val553Leu), we interrogated our data for polymorphisms in the nsp12 gene. doi = 10.1101/2020.05.01.072652 id = cord-287658-c2lljdi7 author = Lopez-Rincon, Alejandro title = Classification and Specific Primer Design for Accurate Detection of SARS-CoV-2 Using Deep Learning date = 2020-09-10 keywords = CoV-2; RNA; SARS; sequence summary = The discovered sequences are first validated on samples from other repositories, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. The discovered sequences are validated on samples from NCBI and GISAID, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. For example, we can use this sequencing data with cDNA, resulting from the PCR of the original viral RNA; e,g, Real-Time PCR amplicons to identify the SARS-CoV-2 16 . The global impact of SARS-CoV-2 prompted researchers to apply effective alignment-free methods to the classification of the virus: For example, in 26 the authors propose the use of Machine Learning Digital Signal Processing for separating the virus from similar strains, with remarkable accuracy. We calculated the frequency of appearance of different primer sets'' sequences used in SARS-CoV-2 RT-PCR tests developed by WHO referral laboratories and compared it to our primer design in the dataset from the GISAID ( Table 2) repository. doi = 10.1101/2020.03.13.990242 id = cord-102868-wnsgjdcp author = Love, R. Rebecca title = Inversion Genotyping in the Anopheles gambiae Complex Using High-Throughput Array and Sequencing Platforms date = 2020-05-28 keywords = Anopheles summary = doi = 10.1101/2020.05.25.114793 id = cord-326282-uxn64olw author = Lu, Maolin title = Real-time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles date = 2020-09-13 keywords = RBD; SARS summary = To measure conformational dynamics of the SARS-CoV-2 S trimer on the surface of virus particles, we established two types of particles, lentiviral pseudoparticles carrying S, as well as coronaviruslike particles generated by expression of S, membrane (M), envelope (E) and nucleocapsid (N) 15 protein (S-MEN)(24, 25) (Fig. 1, A and B ). Analyses of smFRET data from ligand-free S protein on lentiviral particles revealed that the SARS-CoV-2 S protein is dynamic, sampling at least four distinct conformational states To identify the receptor-bound conformation of the SARS-CoV-2 S protein by smFRET, we measured the conformational consequences of soluble, monomeric hACE2 binding. Addition of 5 the monomeric hACE2 receptor to surface-immobilized virus particles lead to increased occupancy of the low-(~0.1) FRET S protein conformation (Fig. 2E) , which was observed at both the single-molecule and population level (Fig. 2F ). Relative state-occupancy and fitting parameters in each of four FRET-defined conformational states of SARS-CoV-2 spike protein on the surface of virus particles. doi = 10.1101/2020.09.10.286948 id = cord-103077-sh4w2mye author = Lu, Shuai title = Leveraging Sequential and Spatial Neighbors Information by Using CNNs Linked With GCNs for Paratope Prediction date = 2020-10-16 keywords = AUC; antibody; residue summary = In this article, we propose a method to identify which amino acid residues of an antibody directly interact with its associated antigen based on the features from sequence and structure. Our algorithm uses convolution neural networks (CNNs) linked with graph convolution networks (GCNs) to make use of information from both sequential and spatial neighbors to understand more about the local environment of the target amino acid residue. According to the type of selecting neighbors of target residue for representing and predicting, the machine learning-based methods can be divided into two categories, leveraging sequential neighbors or spatial neighbors. And the stateof-art method [19] represented an antibody as a graph where each amino acid residue was a node and K nearest spatial neighbors were used in the convolution operator. In this work, we utilize the sequential and spatial neighbors of the target antibody residue by using Convolutional Neural Networks (CNNs) linked with Graph Neural Networks (GCNs) for paratope prediction. doi = 10.1101/2020.10.15.339168 id = cord-328585-1rkrrx8a author = Lu, Shuai title = The immunodominant and neutralization linear epitopes for SARS-CoV-2 date = 2020-08-27 keywords = SARS summary = To investigate the spectrum of antibodies in COVID-19 patients, we detected the binding of the 155 early convalescent sera of 8 imported (Europe) cases which infected SARS-CoV-2 in early April, 156 2020 and 12 domestic (China) cases in early February, 2020 to various epitopes ( Table 1) K203R204/G189R203G204/R203G204/R203G204S344 in N protein, respectively (Table 1) , 172 resulting in different immunodominant epitopes of different virus sub-strains which provide the 173 bases for the differential diagnosis. The predicted epitopes induce neutralization antibody production 175 SARS-CoV-2 pseudo-virus neutralization assay is a well-accepted method to detect the ability of 176 vaccine to inhibit SARS-CoV-2 infection . To assess 8 neutralization antibodies induced by S protein epitopes, we incubated the immunization sera with 178 D614 or G614 SARS-CoV-2 pseudo-viruses and then the mixture was added to ACE2-293FT 179 cells which stably expressed ACE2. doi = 10.1101/2020.08.27.267716 id = cord-273645-czh3zfb3 author = Lu, Shuaiyao title = Comparison of SARS-CoV-2 infections among 3 species of non-human primates date = 2020-07-17 keywords = SARS summary = In this study, two families of non-human primates, Old world monkeys (12 Macaca mulatta, 6 Macaca fascicularis) and New world monkeys (6 Callithrix jacchus), were experimentally inoculated with SARS-CoV-2. Here, to establish the COVID-19 model, two families including 3 species of non-human primates, which are widely used for animal models with their own advantages and disadvantages, were experimentally infected with SARS-CoV-2, followed by comparisons of clinical symptoms, hematology, biochemical indexes, immunology and histopathology among 3 species. Given that host factors may be involved in viral pathogenesis, we designed an experiment in the present study to investigate whether host genetics, age and gender affect SARS-CoV-2 infection in non-human primates ( Figure 1 ). To know dynamics of viral replication and virus shedding, samples of nasal swabs, throat swabs, anal swabs, feces, blood and tissues were collected at the indicated time points, and SARS-CoV-2 genomes were quantitated by RT-qPCR. doi = 10.1101/2020.04.08.031807 id = cord-344949-9zyz4hll author = Luban, Jeremy title = The DHODH Inhibitor PTC299 Arrests SARS-CoV-2 Replication and Suppresses Induction of Inflammatory Cytokines date = 2020-08-05 keywords = COVID-19; DHODH; PTC299; SARS summary = a Selectivity index is the ratio of CC50 to EC50 b values are mean ± standard deviation (SD) Abbreviations: CC50, compound concentration at which cell number is reduced by 50%; EC50, compound concentration at which viral replication on a linear scale is inhibited by 50%; GFP, green fluorescent protein; HCV, hepatitis C virus replicon genotype 1b; PIV-3, Parainfluenza type 3; RSV, respiratory syncytial virus; RT-qPCR, quantitative reverse transcription PCR; SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2; TCID50, tissue culture infectious dose 50%. In the BT co-cell culture system, which models chronic inflammatory conditions driven by B cell activation and antibody production, incubation of cells with 10 nM PTC299 resulted in a significant reduction in the levels of soluble (s)IgG, sIL-17A, sIL-17F, sIL-6, and sTNFα released from the cells after 72 hours of stimulation (range, 49% to 68%) (all p values <0.01) ( Figure 4 and Table 2 ). doi = 10.1101/2020.08.05.238394 id = cord-313215-diqfmitr author = Luo, Lei title = Air and surface contamination in non-health care settings among 641 environmental specimens of 39 COVID-19 cases date = 2020-07-09 keywords = SARS; covid-19 summary = title: Air and surface contamination in non-health care settings among 641 environmental specimens of 39 COVID-19 cases Background Little is known about the SARS-CoV-2 contamination of environmental surfaces and air in non-health care settings among COVID-19 cases. To address this question, in this study, we sampled total of 641 surfaces 63 environmental and air specimens among 39 cases in Guangzhou, China, to explore the 64 surrounding environmental surfaces and air contamination by SARS-CoV-2 in non-65 health care settings. A total of 641 157 environmental surfaces and air specimens were collected among 39 COVID-19 cases, 158 and 20 specimens (20/641, 3.1%) were positive by RT-PCR testing from 9 COVID-19 159 cases (9/39, 23.1%), with 5 (5/101, 5.0%) positive specimens from 3 asymptomatic 160 cases, 5 (5/220, 2.3%) from 3 mild cases, and 10 (10/374, 2.7%) from 3 moderate cases 161 ( of SARS-CoV-2 (Table 2) . doi = 10.1101/2020.07.09.195008 id = cord-347804-kxhasabe author = Luo, Ruibang title = Tracking cytosine depletion in SARS-CoV-2 date = 2020-10-26 keywords = SARS summary = Results We built a website to track the composition change of mono-, di-, and tri-nucleotide of SARS-CoV-2 over time. Using 137,315 SARS-CoV-2 strains collected in ten months, we observed cytosine depletion at a rate of about one cytosine loss per month from the whole genome. We built an interactive website at http://www.bio8.cs.hku.hk/sarscov2 to show the mono-, di-, and tri-nucleotide composition trends of the whole genome and single genes. In Table 1 , we first compared the composition of nucleotides in multiple coronaviruses, including SARS-CoV-2 (an average of 76 strands collected from Dec 20, 2019 to Feb 15, 2020), SARS, MERS, and four that causes a common cold. Compared to SARS-CoV-2, which we assumed a relative mortality level of 3, the percentage of cytosine is lower in almost all of the eleven genes in the four common cold coronaviruses with a lower mortality level 1. The results are available on an interactive website at http://www.bio8.cs.hku.hk/sarscov2. doi = 10.1101/2020.10.26.354787 id = cord-297747-kifqgskc author = Lupala, Cecylia S. title = Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein date = 2020-03-27 keywords = ACE2; RBD; SARS summary = Using homology modeling and molecular dynamics (MD) simulation methods, we report here the detailed structure of the ACE2 in complex with the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. The simulation data further revealed critical residues at the complex interface and provided more details about the interactions between the SARS-CoV-2 RBD and human ACE2. When this study was started, neither the crystal structure of the SARS-CoV-2 spike protein nor the RBD segment were determined, so the homology modeling approach was applied to construct the model of the SARS-CoV-2 spike RBD in complex with the human ACE2 binding domain (denoted as CoV2-RBD/ACE2 in the following). Although the crystal structure and the predicted model of the CoV2-RBD/ACE2 complex provide important information about the binding interactions at the molecular interfaces, MD simulations can extend the knowledge to a dynamics regime in a fully solvated environment. doi = 10.1101/2020.03.24.005561 id = cord-104055-47ren7ie author = Lutkenhoff, Evan S. title = EEG power spectra and subcortical pathology in chronic disorders of consciousness date = 2020-09-01 keywords = EEG; brain; patient summary = Objective To determine (i) the association between long-term impairment of consciousness after severe brain injury, spontaneous brain oscillations, and underlying subcortical damage, and (ii) whether such data can be used to aid patient diagnosis, a process known to be susceptible to high error rates. Conclusions These results ground, for the first time, electroencephalographic presentation detected with routine clinical techniques in the underlying brain pathology of disorders of consciousness and demonstrate how multimodal combination of clinical, electroencephalographic, and imaging data can be employed in potentially mitigating the high rates of misdiagnosis typical of this patient cohort. Sex, 19 age, time-post-injury, etiology (i.e., TBI vs non-TBI), were included as covariates, 20 along with NBV (to ensure that observed tissue displacement reflect local subcortical 21 shape changes independent of overall brain atrophy ( In this analysis, we related the patients'' behavioral presentation, as captured by the 7 CRS-R subscales, with subcortical atrophy. doi = 10.1101/695288 id = cord-322654-6nccarjn author = Luzes, Rafael title = Angiotensin-(3–4) modulates angiotensin converting enzyme 2 (ACE2) downregulation in proximal tubule cells due to overweight and undernutrition: implications regarding the severity of renal lesions in Covid-19 infection date = 2020-06-29 keywords = ACE2 summary = title: Angiotensin-(3–4) modulates angiotensin converting enzyme 2 (ACE2) downregulation in proximal tubule cells due to overweight and undernutrition: implications regarding the severity of renal lesions in Covid-19 infection Since the renin-angiotensin-aldosterone system (RAAS) has been implicated in the progress of kidney failure during Covid-19, we also investigated the influence of Angiotensin-(3–4) (Ang-(3–4)) the shortest angiotensin-derived peptide, which is considered the physiological antagonist of several angiotensin II effects. That Ang-(3-4)-mediated upregulation of renal ACE2 126 occurred in overweight rats, but not in the CTR group, is indicative that a "pro-127 hypertensive tissular microenvironment" (high Ang II) develops in animals fed with a 128 diet rich in lipids, causing downregulation of ACE2 (Figure 2A The influence of chronic undernutrition on renal ACE2 levels present some 132 similarity, but also a huge difference, compared with overweight rats (Figure 3) . doi = 10.1101/2020.06.29.178293 id = cord-102367-l1u094bp author = López, María S. title = Dengue arbovirus affecting temperate Argentina province for more than a decade 2009-2020 date = 2020-08-11 keywords = Santa summary = doi = 10.1101/2020.08.11.246272 id = cord-104037-39kk37fb author = Ma, Jiahao title = Cryo-EM structure of S-Trimer, a subunit vaccine candidate for COVID-19 date = 2020-09-21 keywords = Trimer summary = Cryo-EM structures of the WT and MT S-Trimers, determined at 3.2 Å and 2.6 Å respectively, revealed that both antigens adopt a tightly closed conformation and their structures are essentially identical to that of the previously solved full-length WT S protein in detergent. The newly-formed structural motif makes 152 direct contact with the previously identified pH switch 1 of the adjacent protomer, 153 accounting for the enhanced stability of the WT S-Trimer at lower pH (Fig. 3A) . When revisiting the electron density map for full-163 length wild-type S protein (EMDB: 22292), we spotted unassigned density at the become predominant over the ancestral form worldwide and has been shown to interaction with K854 at the conformational switch region (Fig. 4C ). Purified MT S-trimer protein diluted to 0.2 and 0.5 mg/ml in PBS buffer were applied to glow-discharged gold holey carbon 1.2/1.3 300-mesh grids with and without graphene oxide, respectively. doi = 10.1101/2020.09.21.306357 id = cord-343476-0chuwvg6 author = MacLean, Oscar A. title = Evidence of significant natural selection in the evolution of SARS-CoV-2 in bats, not humans date = 2020-05-29 keywords = SARS summary = Here we contrast the role of positive selection and recombination in the Sarbecoviruses in horseshoe bats to SARS-CoV-2 evolution in humans. While methods can detect some evidence for positive selection in SARS-CoV-2, we demonstrate these are mostly due to recombination and sequencing artefacts. For all but two of the ten positive selected codons, this signal was being driven by apparent convergent evolution (or homoplasy) in the tree, with the same mutation occurring in parallel across the phylogeny. To investigate whether this observation was truly due to independent events or because of recombination signatures in the SARS-CoV-2 outbreak tree, we firstly determined if the samples with these convergent mutations were geographically correlated. The Spike V367F signal was driven by apparent convergent evolution between four french samples sequenced in January and a Hong Kong sample 412028, which shows shared variation either side of the homoplasy suggesting it is not a recombinant (Supplementary figure 3C) . doi = 10.1101/2020.05.28.122366 id = cord-103341-q7yqnvm2 author = MacPherson, Ailene title = A General Birth-Death-Sampling Model for Epidemiology and Macroevolution date = 2020-10-11 keywords = birth summary = As an illustration of the utility of our mathematical approach, we use our approach to derive a yet unstudied variant of the birth-death process in which the key rates emerge deterministically from a classic susceptible infected recovered (SIR) epidemiological model. Similarly, in the case of past CSAs we must 99 include the probability, r l , that sampled hosts are removed from the infectious pool during the CSA at time 100 ary case to explicitly model the collection of samples from the fossil record (e.g., the fossilized birth-death 102 process [19]). Step 6: Conditioning the likelihood -Finally, we condition the likelihood on observing at least one lineage 285 given the TMRCA, Here we derive a phylogenetic birth-death-sampling model in a more general form than previously attempted, 294 making as few assumptions about the processes that generated the data as possible. doi = 10.1101/2020.10.10.334383 id = cord-104138-qagyaegp author = Magee, Michelle title = Effects of face masks on acoustic analysis and speech perception: Implications for peri-pandemic protocols date = 2020-10-08 keywords = N95; mask summary = Here we investigated how three face mask types (N95, surgical and cloth) affect acoustic analysis of speech and perceived intelligibility in healthy subjects. We compared speech produced with and without the different masks on acoustic measures of timing, frequency, perturbation and power spectral density. Our data show that face masks change the speech signal, but some specific acoustic features remain largely unaffected (e.g., measures of voice quality) irrespective of mask type. Where the interaction was significant, planned comparisons were made for each 1Khz frequency band to determine differences between masks types compared to no mask. For recordings produced with the tabletop microphone, there was a significant effect of mask type for percentage of pauses (F3,7.87=8.17, p=0.008), and spectral tilt (F3,8.39=15.43, p=0.001) ( Table 1) . We observed significant differences in acoustic power distribution across relevant frequency bands for speech in all three mask conditions compared to no mask. doi = 10.1101/2020.10.06.327452 id = cord-102967-dx0tg077 author = Mahajan, Lakshmi S. title = Mapping RNA dependent RNA polymerase activity and immune gene expression using PRO-seq date = 2020-06-16 keywords = RNA; pro summary = Coupled to PRO-seq in human blood samples, we propose to use PRO-seq as a single package method to detect (+)ssRNA virus RdRp activity and its interaction with host immune response through transcriptome-wide profiling of leukocyte gene expressions at once. This is different from Drosophila RNA Polymerase II, which appears to have comparable substrate specificity for all 4 biotin-NTPs. The ORF-proximal accumulation coincides with quadruplet rich regions of the template-strand of the DAV genome ( Figure 1D ). From this data, we did not detect significant PRO-seq sequences from (+)ssRNA viral genomes, indicating that none of the individuals had direct viral infections in the blood immune cells. Our PRO-seq data show expression levels of immune-response related genes from human peripheral blood leukocytes. PRO-seq density on DAV genome and base-quadruplet counts.The read count is indicated along the left side of each graph. Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq) doi = 10.1101/2020.06.15.151738 id = cord-281141-ouno4jpl author = Mahajan, Swapnil title = Immunodominant T-cell epitopes from the SARS-CoV-2 spike antigen reveal robust pre-existing T-cell immunity in unexposed individuals date = 2020-11-05 keywords = CD8; HLA; SARS summary = A selected pool of 11 predicted epitopes induced robust T-cell activation in unexposed donors demonstrating pre-existing CD4 and CD8 T-cell immunity to SARS-CoV-2 antigen. A key finding of our study is that pre-existing T-cell immunity to SARS-CoV-2 is contributed by TCRs that recognize common viral antigens such as Influenza and CMV, even though the viral epitopes lack sequence identity to the SARS-CoV-2 epitopes. We performed T-cell activation assay using the selected 11 epitopes from the SARS-CoV-2 spike antigen in unexposed donors. As shown in Figure Multiple studies have reported pre-existing T-cell immunity in unexposed donors using spike peptide pools and attributed the response to T-cells recognizing epitopes from common coldcausing coronaviruses to which a large section of the global population is exposed (7, 8, 10) . A recent large-scale study mapped a few immunogenic regions in the SARS-CoV-2 proteome responsible for expanding many unique TCRs in a large number of convalescent COVID-19 patients and unexposed healthy donors (21) . doi = 10.1101/2020.11.03.367375 id = cord-103363-efd80dgn author = Mahan, Margaret title = tbiExtractor: A framework for extracting traumatic brain injury common data elements from radiology reports date = 2019-03-21 keywords = radiology; report summary = title: tbiExtractor: A framework for extracting traumatic brain injury common data elements from radiology reports Here, we set out to develop and validate a framework to extract pertinent clinical conditions for traumatic brain injury (TBI) from computed tomography (CT) reports. Materials and Methods We developed tbiExtractor, which extends pyConTextNLP, a regular expression algorithm using negation detection and contextual features, to create a framework for extracting TBI common data elements from radiology reports. The algorithm inputs radiology reports and outputs a structured summary containing 27 clinical findings with their respective annotations. Discussion and Conclusion tbiExtractor is a validated algorithm for extraction of TBI common data elements from radiology reports. At this stage of processing, each sentence in the radiology report will be marked with lexical 245 targets and linked lexical modifiers. With the nature of TBIs, some visible pathologies are only seen on follow-up CTs developed to automate the extraction of TBI common data elements from 438 radiology reports doi = 10.1101/585331 id = cord-338296-2hk7h132 author = Malla, Tek Narsingh title = Ebselen Reacts with SARS Coronavirus-2 Main Protease Crystals date = 2020-08-23 keywords = Ebselen summary = title: Ebselen Reacts with SARS Coronavirus-2 Main Protease Crystals The SARS coronavirus 2 main protease 3CLpro tailor cuts various essential virus proteins out of long poly-protein translated from the virus RNA. Any compound that inhibits the 3CLpro is therefore a potential drug to end the pandemic. Here we show that the diffraction power of 3CLpro crystals is effectively destroyed by Ebselen. Apart from the fragments, the most promising compounds are the α-ketoamides (Fig. 1) 24 which bind tightly to the 3CLpro 1-3 . SARS CoV-2 3CLpro in its functional, dimeric form 1 . expensive, but also less known compound that binds to the 3CLpro is Ebselen 4 . Ebselen has been shown 29 to bind strongly to the CoV-2 3CLpro 4 , but the structure of the complex is unknown. show what happens when Ebselen is added to 3CLpro crystals. Accordingly, the structure of only the untreated 3CLpro can be solved. doi = 10.1101/2020.08.10.244525 id = cord-297021-fzfl08qa author = Manomaipiboon, Anan title = The new silicone N99 half-piece respirator, VJR-NMU N99: A novel and effective tool to prevent COVID-19 date = 2020-07-23 keywords = N95; N99; filter summary = To meet the need for FFRs during a pandemic, Navamindradhiraj University has invented a new model of silicone N99 facepiece respirator by using the silicone mask and the HEPA filter normally used in the operating room (CareStar or SafeStar, Draeger, Germany) (Fig 1) . As required by Occupational Safety and Health Administration OSHA) [7] , the half piece respirators need to pass the fit test to identify those individuals who do not achieve a sufficiently good fit necessary for adequate protection. The study was conducted to achieve two specific research objectives: (1) to investigate the fit characteristics of the novel silicone mask and whether the strap adjustment can help reduce the face-seal leakage; and (2) to determine the level of performance by measuring the inward leakage of the generated aerosols with a new filter and a used filter (for up to 24 h). doi = 10.1101/2020.07.23.217372 id = cord-102931-vxkbctiz author = Mao, Kai title = Induction of RNA interference by C. elegans mitochondrial dysfunction via the DRH-1/RIG-I homologue RNA helicase and the EOL-1/RNA decapping enzyme date = 2020-06-06 keywords = Caenorhabditis; EOL-1; RNA; figure summary = Here, we report that mitochondrial dysfunction in Caenorhabditis elegans activates RNAi-directed silencing via induction of a pathway homologous to the mammalian RIG-I helicase viral response pathway. elegans compared to most animals, and surprisingly, loss of function mutations in some of those genes cause an increase in the response to siRNAs: mutations in the RdRp RRF-3, the specialized Argonaute ERGO-1, the RNA helicase ERI-6/7, or the exoribonuclease ERI-1 enhance silencing by siRNAs (Fischer et al., 2008; Kennedy et al., 2004) . We find that reduction of function mutations in a wide range of mitochondrial components robustly enhanced RNA interference-mediated silencing of endogenous genes as well as a variety of reporters of RNAi. These antiviral responses to mitochondrial dysfunction are homologous to the RIG-I-based mitochondrial response in mammals because they depend on the RIG-I homologue, the DRH-1 RNA helicase. Our analysis of the eol-1 and drh-1 pathway from mitochondrial dysfunction to enhanced RNA interference and antiviral activity is a key output from mitochondria for anti-aging. doi = 10.1101/2020.06.05.136978 id = cord-102370-5uy8dq18 author = Marano, Jeffrey M. title = Rolling Circle Amplification is a high fidelity and efficient alternative to plasmid preparation for the rescue of infectious clones date = 2020-06-23 keywords = RCA; dna; plasmid summary = doi = 10.1101/2020.06.22.165241 id = cord-103105-iqjksoim author = Marinaik, Chandranaik B. title = Programming Multifaceted Pulmonary T-Cell Immunity by Combination Adjuvants date = 2020-07-10 keywords = CD4; CD8; Fig summary = An acrylic acid-based adjuvant (ADJ), in combination with TLR agonists glucopyranosyl lipid adjuvant (GLA) or CpG promoted mucosal imprinting but engaged distinct transcription programs to drive different degrees of terminal differentiation and disparate polarization of TH1/TC1/TH17/TC17 effector/memory T cells. Further, these studies provided the first glimpse of the evolution of T-cell responses to adjuvanted vaccines in the lungs to define the quantitative, phenotypic and functional attributes of mucosal effector/memory CD8 and CD4 T cells that are associated with effective viral control in the lungs, and protection against H1N1 and H5N1 influenza infections. Studies to determine the transcriptional basis for the disparate differentiation of effector CD8 T cells in different adjuvant groups showed that the expressions of T-bet, IRF-4 and BATF were substantially greater in ADJ and ADJ+CpG groups, compared to GLA and ADJ+GLA groups ( Fig. 1D) . doi = 10.1101/2020.07.10.197459 id = cord-263970-9w6ciglv author = Marquez-Miranda, Valeria title = Analysis of SARS-CoV-2 ORF3a structure reveals chloride binding sites date = 2020-10-22 keywords = SARS; cavity; ion summary = SARS-CoV-2 ORF3a is believed to form ion channels, which may be involved in the modulation of virus release, and has been implicated in various cellular processes like the up-regulation of fibrinogen expression in lung epithelial cells, downregulation of type 1 interferon receptor, caspase-dependent apoptosis, and increasing IFNAR1 ubiquitination. Here we used this dimeric structure to perform full atom molecular dynamic simulations and electrostatic potential calculations to ask questions concerning the dimers'' stability and whether ions could be populating specific regions of the channel. To assess the impact of the ion occupancies described above, we obtained the electrostatic potential maps for the ORF3a channel for the initial configuration, and the last frame, at the end of a trajectory of 500 ns of the molecular dynamics simulations, by employing the Poison-Boltzmann approach implemented in the APBS package [12] . This analysis shows that the entry of Cl-ions through the inter-subunit tunnel into the central polar cavity and the accumulation of K+ ions at the cytosolic domain''s surface changed the channel''s electrostatic profile. doi = 10.1101/2020.10.22.349522 id = cord-102231-cquxqbc2 author = Martinez, Xavier title = FAIR sharing of molecular visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments date = 2020-08-28 keywords = experience; figure summary = doi = 10.1101/2020.08.27.270140 id = cord-313571-umcbulcw author = Martínez-Murcia, Antonio title = In silico design and validation of commercial kit GPS™ CoVID-19 dtec-RT-qPCR Test under criteria of UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012 date = 2020-05-05 keywords = SARS summary = title: In silico design and validation of commercial kit GPS™ CoVID-19 dtec-RT-qPCR Test under criteria of UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012 Background The Corona Virus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has become a serious infectious disease affecting human health worldwide and rapidly declared a pandemic by WHO. Objectives A few days later, when additional SARS-CoV-2 genome were retrieved, the kit GPS™ CoVID-19 dtec-RT-qPCR Test was designed to provide a highly specific detection method and commercially available worldwide. Results The GPS™ RT-qPCR primers and probe showed the highest number of mismatches with the closet related non-SARS-CoV-2 coronavirus, including some indels. As the number of genomes available rapidly expanded during last January, the GPS™ CoVID-19 230 dtec-RT-qPCR Test was based on a more specific target for SARS-CoV-2 detection, being this 231 company one of the pioneers marketing a PCR-kit for the CoVID-19 worldwide. doi = 10.1101/2020.04.27.065383 id = cord-102189-wo9gg7nx author = Mathew, Nimitha R. title = Single cell BCR and transcriptome analysis after respiratory virus infection reveals spatiotemporal dynamics of antigen-specific B cell responses date = 2020-08-24 keywords = BCR; Bmem; Fig; cell summary = doi = 10.1101/2020.08.24.264069 id = cord-336793-9bbyu1qx author = Matsuyama, Shutoku title = The inhaled steroid ciclesonide blocks SARS-CoV-2 RNA replication by targeting viral replication-transcription complex in culture cells date = 2020-08-24 keywords = SARS summary = title: The inhaled steroid ciclesonide blocks SARS-CoV-2 RNA replication by targeting viral replication-transcription complex in culture cells We screened steroid compounds to obtain a drug expected to block host inflammatory responses and MERS-CoV replication. Ciclesonide, an inhaled corticosteroid, suppressed replication of MERS-CoV and other coronaviruses, including SARS-CoV-2, the cause of COVID-19, in cultured cells. Eight consecutive passages of 43 SARS-CoV-2 isolates in the presence of ciclesonide generated 15 resistant mutants harboring single amino acid substitutions in non-structural protein 3 (nsp3) or nsp4. These observations indicate that the suppressive effect of ciclesonide on viral replication is specific to coronaviruses, highlighting it as a candidate drug for the treatment of COVID-19 patients. In the present study, we found that an inhaled corticosteroid, ciclesonide suppresses replication of coronaviruses, including beta-coronaviruses (MHV-2, MERS-CoV, SARS-CoV, and SARS-CoV-2) and an alpha-coronavirus (HCoV-229E) in cultured cells. The inhaled corticosteroid ciclesonide blocks coronavirus RNA replication by targeting viral doi = 10.1101/2020.08.22.258459 id = cord-103914-ppgx7mci author = Maughan, Elizabeth F. title = Cell-intrinsic differences between human airway epithelial cells from children and adults date = 2020-04-20 keywords = RNA; SARS; basal; cell; figure summary = Here, we perform bulk RNA sequencing studies in laser-capture microdissected whole epithelium, FACS-sorted basal cells and cultured basal cells, as well as in vitro cell proliferation experiments, to address the intrinsic molecular differences between paediatric and adult airway basal cells. We found no significant differences in the proportion of cells in these three cellular compartments in paediatric and adult biopsies either by immunohistochemistry ( Figure 1A /1B), or by assessing basal, mucosecretory or ciliated cellassociated gene expression (Table S2 ) in bulk RNA sequencing in which we had laser-capture microdissected the whole epithelium ( Figure 1C ; Figure S1 ). Analysing this laser-capture microdissected whole epithelium RNA sequencing dataset using DESeq2 (Love et al., 2014) with a false discovery rate (FDR) of 1% and log2 fold change threshold of 1.2, we identified 37 genes with significant differential expression between paediatric and adult donors of which 17 were upregulated in adults and 20 were expressed at higher levels in children ( Figure 2A ; Table S3 ). doi = 10.1101/2020.04.20.027144 id = cord-103542-mf721oa9 author = Mazhari, Ramin title = A comparison of non-magnetic and magnetic beads for measuring IgG antibodies against P. vivax antigens in a multiplexed bead-based assay using Luminex® technology (Bio-Plex® 200 or MAGPIX®) date = 2020-08-10 keywords = bead; magnetic summary = Multiplexed bead-based assays that use Luminex xMAP® technology have become popular for measuring antibodies against proteins of interest in many fields, including malaria and more recently SARS-CoV-2/COVID-19. Our external validation indicated that results generated in different laboratories using the same coupled beads are also highly comparable, particularly if a reference standard curve is used. To be able to measure all plasma 123 samples at the same dilution, we optimized all protein concentrations by generating a log-linear 124 standard curve with a positive control plasma pool from immune PNG donors (high responders to 125 Plasmodium antigens). Optimization of 374 a magnetic bead-based assay (MAGPIX((R))-Luminex) for immune surveillance of exposure to 375 malaria using multiple Plasmodium antigens and sera from different endemic settings Comparison of non-404 magnetic and magnetic beads multiplex assay for assessment of Plasmodium falciparum 405 antibodies doi = 10.1101/2020.08.10.243980 id = cord-313795-jr3n3uo9 author = McAuley, Julie L. title = Liquid chalk is an antiseptic against SARS-CoV-2 and influenza A respiratory viruses date = 2020-11-02 keywords = SARS; chalk summary = We investigated whether liquid chalk is an antiseptic against highly pathogenic human viruses including, SARS-CoV-2, influenza virus and noroviruses. We observed that addition of chalk before or after virus contact lead to a significant reduction on recovery of infectious SARS-CoV-2 and influenza but had little impact on norovirus. To further our study, we also tested the antiviral effect of Liquid Chalk against another 155 highly infectious and pathogenic respiratory viral pathogen IAV. 157 As can be observed in Figure 2 , all four Liquid Chalk products were effective in restricting the 158 recovery of IAV compared to SARS-CoV-2. transmission of SARS-CoV-2 (the 52 causative agent of the COVID-19 pandemic), influenza A virus (H1N1) (IAV) and norovirus, 53 using the surrogate model of mouse norovirus As a comparator, we also investigated the ability of Liquid Chalk to inactivate another 178 highly infectious viral pathogen, norovirus. doi = 10.1101/2020.11.02.364661 id = cord-102770-t4zgph9k author = McComb, Scott title = Fine Molecular Tuning of Chimeric Antigen Receptors through Hinge Length Optimization date = 2020-10-30 keywords = EGFR; Fig; car; cell summary = doi = 10.1101/2020.10.30.360925 id = cord-314445-4cb4a9r5 author = McNamara, Ryan P. title = High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States date = 2020-06-19 keywords = CoV-2; SARS; U.S. summary = This study contributes to the understanding of COVID-19 by providing an extensive set of genomes from a non-urban setting and further informs vaccine design by defining D614G as a dominant and emergent SARS-CoV-2 isolate in the U.S. The current COVID-19 pandemic is an urgent public health emergency with over 112,000 deaths in the United States (U.S.) alone. At a CP ≥35 most positive samples still yielded reads that mapped to the target genome 227 and thus allowed detection of SARS-CoV-2 sequences; however, the results were less consistent, 228 and coverage was more variable. In sum, this study generated exhaustive SNV information representing the introduction and 325 spread of SARS-CoV-2 across a suburban low-density area in the Southern U.S. All samples were 326 from symptomatic cases and the majority of genomes clustered with variants that predominate the 327 outbreak in the U.S., rather than Europe or China. doi = 10.1101/2020.06.19.161141 id = cord-103757-fed21fhu author = McPherson, Malinda J. title = Time-dependent discrimination advantages for harmonic sounds suggest efficient coding for memory date = 2020-10-15 keywords = Harmonic; Interleaved; delay; experiment; figure summary = The similarity in performance between harmonic and inharmonic tones without a delay provides circumstantial evidence that listeners are computing changes in the same way for both types of stimuli, presumably using a representation of the spectrum in both cases. We examined the relationship between pitch perception and memory by measuring the discrimination of harmonic and inharmonic sounds with and without a time delay between stimuli. The results provide evidence for two distinct mechanisms for pitch discrimination, reveal the constraints that determine when they are used, and demonstrate a form of abstraction within the auditory system whereby the representations of memory differ in format from those used for rapid on-line judgments about sounds. We found consistent overall pitch discrimination advantages for musicians compared to non-musicians ( Supplementary Figures 1-3 ), but found no evidence that this benefit was specific to f0 representations: musicianship did not interact with the effects of inharmonicity or inter-stimulus delay. doi = 10.1101/2020.05.07.082511 id = cord-104140-o46kvd0b author = McPherson, Malinda J. title = Harmonicity aids hearing in noise date = 2020-09-30 keywords = SNR; experiment; harmonic; noise; tone summary = To explore whether harmonic frequency relations aid hearing of sounds in noise, we compared detection and discrimination of harmonic and inharmonic tones and spoken vowels embedded in noise. However, detection thresholds were substantially better for harmonic than inharmonic complex tones even though they each had 10 frequency components (significant differences in both sine and random phase conditions, Wilcoxon signed-rank test: sine phase: Z=6.97, p<.001; random phase: Z=6.83, p<.001). Specifically, it seemed plausible that being better able to separate tones from noise might help listeners discriminate successive tones at low SNRs. Using an adaptive procedure, we measured traditional up-down discrimination thresholds for Harmonic, Inharmonic, and Pure Tone conditions (Fig. 3a) at a range of SNRs. Participants. We replotted the pitch discrimination curves in terms of the SNR relative to the detection thresholds measured in Experiment 1 (-21.00 dB SNR, -19.77 dB SNR, -17.39 dB SNR, for Harmonic, Inharmonic and Pure Tone conditions, respectively, Fig. 2b, inset) . doi = 10.1101/2020.09.30.321000 id = cord-103071-6cgih8o9 author = Mead, Benjamin E. title = High-throughput organoid screening enables engineering of intestinal epithelial composition date = 2020-04-28 keywords = Fig; KPT-330; LYZ; Paneth; Xpo1; cell; iii summary = Strikingly, in our screen we identify inhibitors of the nuclear exporter Xpo1 modulate stem cell fate commitment by inducing a pan-epithelial stress response combined with an interruption of mitogen signaling in cycling intestinal progenitors, thereby significantly increasing the abundance of Paneth cells independent of known WNT and Notch differentiation cues. Administration of KPT-330 below 160 nM for 6 days (NB higher concentrations proved toxic in primary screening) showed LYZ secretion increasing in a dose-dependent manner, with 160 nM of KPT-330 as the most effective dose among tested concentrations KPT-330 is a selective inhibitor of nuclear export (SINE); these molecules act by suppressing the Xpo1-regulated nuclear export of multiple proteins and mRNAs from the nucleus to the cytoplasm -including genes involved in stem cell maintenance and differentiation as well as inflammatory stress response (Sendino et al., 2018) . doi = 10.1101/2020.04.27.063727 id = cord-281679-xmbnpawj author = Meekins, David A. title = Susceptibility of swine cells and domestic pigs to SARS-CoV-2 date = 2020-08-16 keywords = CoV-2; SARS; pig summary = In the current study, we determined the ability of SARS-CoV-2 to (i) replicate in porcine cell lines, (ii) establish infection in domestic pigs via experimental oral/intranasal/intratracheal inoculation, and (iii) transmit to co-housed naive sentinel pigs. These data indicate that although different porcine cell lines are permissive to SARS-CoV-2, five-week old pigs are not susceptible to infection via oral/intranasal/intratracheal challenge. Cats, hamsters, and ferrets are highly susceptible to SARS-CoV-2 infection, demonstrate varying clinical and pathological disease manifestations, readily transmit the virus to naïve animals, and mount a virusspecific immune response [22] [23] [24] [25] [26] [27] [28] . Pigs are therefore unlikely to play an important role in the COVID-19 pandemic as a virus reservoir or as a pre-clinical animal model to study SARS-CoV-2 pathogenesis or develop novel countermeasures. doi = 10.1101/2020.08.15.252395 id = cord-102502-hroxg2u1 author = Megremis, Spyridon title = Microbial and autoantibody immunogenic repertoires in TIF1γ autoantibody positive dermatomyositis date = 2020-03-26 keywords = NGS; P20; figure; trim summary = doi = 10.1101/2020.03.25.007534 id = cord-354315-yfn9vaan author = Meirson, Tomer title = Structural basis of SARS-CoV-2 spike protein induced by ACE2 date = 2020-05-24 keywords = ACE2; SARS summary = This conformational changes lead to an alternating pattern in conserved disulfide bond configurations positioned at the hinge, indicating a possible disulfide exchange, an important allosteric switch implicated in viral entry of various viruses, including HIV and murine coronavirus. The critical step in SARS-CoV-2 infection which involves the transition between a metastable prefusion state to a stable post-fusion state is triggered by binding to ACE2 which induces conformational changes in the RBD and the hinge region (Gui, et al., 2017; Pallesen, et al., 2017; Song, et al., 2018; Walls, et al., 2020) . To gain insights into the effects of ACE2 interaction on the S protein of SARS-COV-2, we analyzed the intramolecular structural variations in the bound versus the unbound-closed Numerous structures of the prefusion human CoV S proteins were determined at different states, and the key regions responsible for the interaction with the receptor were previously reported (Lan, et al., 2020; Shang, et al., 2020; Walls, et al., 2020; Wan, et al., 2020; Wrapp, et al., 2020; Yan, et al., 2020) . doi = 10.1101/2020.05.24.113175 id = cord-296268-kb7fgfaq author = Mendonça, Luiza title = SARS-CoV-2 Assembly and Egress Pathway Revealed by Correlative Multi-modal Multi-scale Cryo-imaging date = 2020-11-05 keywords = CoV-2; SARS; SEM summary = Here, we investigated SARS-CoV-2 replication in Vero cells under the near-native frozen-hydrated condition using a unique correlative multi-modal, multi-scale cryo-imaging approach combining soft X-ray cryo-tomography and serial cryoFIB/SEM volume imaging of the entire SARS-CoV-2 infected cell with cryo-electron tomography (cryoET) of cellular lamellae and cell periphery, as well as structure determination of viral components by subtomogram averaging. Understanding the genome 27 replication, assembly and egress of SARS-CoV-2, a multistage process that involves different 28 cellular compartments and the activity of many viral and cellular proteins, is critically Krios to identify each individual infected cell (39.2 % for MOI of 0.1 and 45.4% for MOI 124 0.5) where cryoET tilt series were collected at the cell periphery. The grids were then 125 transferred to a FIB/SEM dualbeam instrument and the same infected cells were subjected to 126 either serial cryoFIB/SEM volume imaging (Zhu et al., 2021) or cryoFIB milling of cellular 127 lamellae where additional cryoET tilt series were collected (Sutton et al., 2020) . doi = 10.1101/2020.11.05.370239 id = cord-102908-sr7j8z9c author = Mersmann, Sophia F. title = Learning to count: determining the stoichiometry of bio-molecular complexes using fluorescence microscopy and statistical modelling date = 2020-07-24 keywords = antibody; figure; particle; virus summary = We used differential binary labelling and statistical modelling to extract estimates of stoichiometry, our strategy is outlined in Figure 1 ; note that this approach can be generalised to apply to many other multi-component systems (i.e. how many protein x are found in assembly y?). As described above, our experimental design utilizes antibody labelled with spectrally distinct dyes allowing binary scoring of individual virus particles as positive if they interact with at least one Ab B molecule ( Figure 1 ). We have demonstrated quantitative analysis of 9C12 interaction with individual Adv particles ( Figure 3) ; we have confirmed that differential labelling of antibody does not bias binding ( Figure 4A & B) ; and that we could detect single molecules of 9C12 Biotin allowing discrimination of positive and negative AdV-9C12 complexes ( Figure 4C & D). However, using stoichiometric estimates to calibrate fluorescent data revealed population heterogeneity with a small proportion of virus particles binding ∼200 antibody molecules. doi = 10.1101/2020.07.23.217745 id = cord-334220-sqvfr31q author = Messina, Francesco title = Looking for pathways related to COVID-19 phenotypes: Confirmation of pathogenic mechanisms by SARS-CoV-2 - Host interactome date = 2020-11-03 keywords = COVID-19; CoV-2; SARS; protein summary = The functional analysis for all proteins, linked to many aspects of COVID-19 pathogenesis, allows to identify the subcellular districts, where SARS-CoV-2 proteins seem to be distributed, while in each interactome built around one single viral protein, a different response was described, underlining as ORF8 and ORF3a modulated cardiovascular diseases and pro-inflammatory pathways, respectively. We identified possible host responses induced by specific proteins of SARS-CoV-2, underlining the important role of specific viral accessory proteins in pathogenic phenotypes of severe COVID-19 patients. In SFigure For KEGG database the gene enrichment analysis on interactomes of NS7b, ORF1a, ORF3a and ORF8 showed pathway clusters highly significant and consistent with possible pathogenic mechanisms, such as the activation of the complement and of the coagulative cascade, (29) and the TGF-β-dominated immune response (30) . We identified different host response induced by specific proteins of SARS-CoV-2, underlining the important role of ORF3a and ORF8 in phenotypes of severe COVID-19 patients. doi = 10.1101/2020.11.03.366666 id = cord-271849-wxmr8eki author = Meysman, Pieter title = Tracking SARS-CoV-2 T cells with epitope-T-cell receptor recognition models date = 2020-09-09 keywords = SARS summary = In this paper, we demonstrate the use of machine learning to classify SARS-CoV-2 epitope specific T-cell clonotypes in T-cell receptor (TCR) sequencing data. We apply these models to public TCR data and show how they can be used to study T-cell longitudinal profiles in COVID-19 patients to characterize how the adaptive immune system reacts to the SARS-CoV-2 virus. No other epitopes present in TCRex (including the 49 non-SARS-CoV-2 models) were predicted to have a single TCR target within this data set. Once established, these models can be applied to any TCR repertoire data and thus can be used to study putative SARS-CoV-2 reactive T cells in the currently available COVID-19 data. In addition, using such models on longitudinal data reveals a potential difference in temporal dynamics between T cells predicted to react against epitopes that are unique to SARS-CoV-2 and those that are shared among other coronaviruses. doi = 10.1101/2020.09.09.289355 id = cord-102704-wfuzk2dp author = Meza, Diana K. title = Predicting the presence and titer of rabies virus neutralizing antibodies from low-volume serum samples in low-containment facilities date = 2020-04-30 keywords = Rabies; antibody; test; virus summary = Despite small conflicts, titer predictions were correlated across tests repeated on different dates both for dog samples (r = 0.93), and for a second dataset of sera from wild common vampire bats (r = 0.72, N = 41), indicating repeatability. The pmRFFIT enables high-throughput detection of rabies virus neutralizing antibodies in low-biocontainment settings and is suited to studies in wild or captive animals where large serum volumes cannot be obtained. The binomial and log-normal models fit to 193 this data subset included only the fixed effect of the virus-infected N2A cell counts, but the random 194 effects were identical to those explained above (i.e. test date and field). A final distinction is that 316 instead of scoring microscope field or wells as virus positive or negative, the pmRFFIT predicts 317 serological status and RVNA titer from infected cell counts in a single serum dilution using statistical 318 doi = 10.1101/2020.04.24.060095 id = cord-103864-4kec8re4 author = Miao, Zhen title = Single cell resolution regulatory landscape of the mouse kidney highlights cellular differentiation programs and renal disease targets date = 2020-06-04 keywords = cell; single summary = Here, we profiled open chromatin and gene expression in developing and adult mouse kidneys at single cell resolution. Mapping single nucleotide variants associated with human kidney disease identified critical cell types, developmental stages, genes, and regulatory mechanisms. Here, we reasoned that 474 single cell accessible chromatin information could be extremely useful to identify the cell type-475 specific enhancer regions and thereby the target cell type for the GWAS hits, however, such maps 476 have not been generated for the human kidney. 539 540 By performing massively parallel single cell profiling of chromatin state, we were able to define 541 the key regulatory logic for each kidney cell type by investigating cis-regulatory elements and TF-542 target gene interaction. 548 549 We also observed that the single cell open chromatin atlas was able to define more distinct cell 550 types even in the developing kidney compared to scRNA-seq analysis. doi = 10.1101/2020.05.24.113910 id = cord-102729-b1q7gbd6 author = Mickael, Alexandra title = Asip (Agouti-signaling protein) aggression gene regulate auditory processing genes in mice date = 2020-06-12 keywords = Asip; aggression; gene; hearing; receptor summary = ASIP (nonagouti) gene plays a vital role in regulating the melanocortin GPCRs family function, and it is responsible for regulating aggression in mice. We found that ASIP KO in mice upregulates several genes controlling auditory function, including Phox2b, Mpk13, Fat2, Neurod2, Slc18a3, Gon4l Gbx2, Slc6a3(Dat1) Aldh1a7 Tyrp1 and Lbx1. In order to confirm that our mice model study would be representative of aggression hearing link, we conducted an evolutionary study that revealed that ASIP is negatively selected between mice and humans. When we analyzed RNA-seq for Asip ko mouse model we found that several genes controlling hearing were upregulated in the KO samples. We found these results reflected in the molecular pathway of melanocortin receptors 1 and 4, where their knocking out their negative agonist; Asip resulted in upregulating various hearing associated genes such as Fat2 among others. doi = 10.1101/2020.06.10.141325 id = cord-323967-2mo915u1 author = Miersch, Shane title = Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations date = 2020-11-01 keywords = Fig; RBD; SARS summary = Moreover, structural studies reveal that the best nAb targets the host receptor binding site of the virus spike protein, and thus, its tetravalent version can block virus infection with a potency that exceeds that of the bivalent IgG by an order of magnitude. Moreover, the use of a highly stable framework 77 enabled facile and modular design of ultra-high affinity nAbs in tetravalent formats that retained 78 favorable drug-like properties and exhibited neutralization potencies that greatly exceeded those 79 of the bivalent IgG format. Fab-phage were screened by ELISA and those that exhibited >50% loss in binding 92 to RBD in the presence of 200 nM ACE2 were sequenced, revealing 34 unique clones (Fig. 1A) , 93 deemed to be potential nAbs and converted into the full-length human IgG1 format for 94 purification and functional characterization. doi = 10.1101/2020.10.31.362848 id = cord-330213-reb9vo7x author = Miladi, Milad title = The landscape of SARS-CoV-2 RNA modifications date = 2020-07-18 keywords = RNA; SARS; TRS summary = From sequencing three isolates, we derive a robust identification of SARS-CoV-2 modification sites within a physiologically relevant host cell type. A comparison of our data with the DRS data from a previous SARS-CoV-2 isolate, both raised in monkey renal cells, reveals consistent RNA modifications across the viral genome. The long RNA sequencing reads generated for this study cover the entire SARS-CoV-2 genomic RNA as well as the different ORFs (Fig 1b,c, Fig. S1b ). Two sets of Galaxy workflows based on Tombo (16) and Nanocompore (17) tools were designed to compute the modification scores from the DRS data (Table S3) . Figure 5 : Direct RNA sequencing raw electrical signals of downsampled reads obtained from unmodified RNA (IVT, black), from samples generated for this study and from isolate from a published korean data set (Fr1-3 and Kr, red). doi = 10.1101/2020.07.18.204362 id = cord-102458-7sssm3zk author = Milanez-Almeida, Pedro title = Blood gene expression-based prediction of lethality after respiratory infection by influenza A virus in mice date = 2020-10-27 keywords = IAV; LD50; PR8 summary = During training (i.e., model selection via cross-validation), the algorithm learned that 11 genes had expression values in blood that could be linearly combined to generate a scoring system of infected animals as a function of the day of death ( In both the multinomial and the lethal Cox models, high levels of expression of genes associated with monocytes and neutrophils, together with low levels of transcripts associated with lymphocytes, indicated high risk of death (Fig. S3 ), consistent with previously described analyses of the immune response to IAV infection (10, 12, 13) and also recent data from COVID-19 patients (29). While the lack of accuracy later in the course of infection (i.e., days seven and eight) was likely due to the fact that the model was trained for early detection of lethality, before adaptive immune cells fully developed and reached the circulation, these data suggest that PAMPs and DAMPs eventually reach different levels in the lungs of different mice, impacting their blood cell composition and lethal score, which can be used for prediction of lethality of individual animals even in the challenging scenario of experimental infection with an 1 LD50 IAV dose. doi = 10.1101/2020.10.27.357053 id = cord-103714-06hhlma3 author = Miller, Mariël title = Examination of a first-in-class bis-dialkylnorspermidine-terphenyl antibiotic in topical formulation against mono and polymicrobial biofilms date = 2020-06-04 keywords = CFU; MRSA summary = In this study, an in vitro assessment was performed to determine the potential efficacy of a unique first-in-class series of antibiofilm antibiotics and compare outcomes to current clinical standards of care. The agent, CZ-01179, was formulated into a hydrogel and tested against mature biofilms of a clinical isolate of methicillin-resistant Staphylococcus aureus and Pseudomonas aeruginosa ATCC 27853 using two separate methods. Confocal imaging and staining indicated that CZ-01179 was 357 highly effective against well-established biofilms that were exposed to the formulated gel, 358 whereas clinical products had limited efficacy (Fig 5) . Outcomes indicated that of the clinical standards of care, gentamicin was most effective 366 against both monomicrobial and polymicrobial biofilms of MRSA and of P. CZ-01179 gels were more efficacious at 415 eradicating biofilms in all other cases when compared to the standard of care topicals in the 416 collagen tests (Fig. 6) . doi = 10.1101/2020.06.04.133934 id = cord-274114-fglyfz8p author = Minervina, Anastasia A. title = Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection date = 2020-10-01 keywords = CD4; CD8; SARS summary = In this study we use longitudinal TCRalpha and TCRbeta repertoire sequencing to quantitatively track T cell clones that significantly expand and contract after recovery from a mild COVID-19 infection, and determine their phenotype. We reveal the dynamics and the phenotype of the memory cells formed after infection, identify pre-existing T cell memory clones participating in the response, and describe public TCR sequence motifs of SARS-CoV-2-reactive clones, suggesting a response to immunodominant epitopes. At the time of writing, no data on TCR sequences specific to MHC-II class epitopes exist to map specificities of CD4+ T-cells in a similar way as we did with MIRA-specific TCRs. However, a recently published database of 1414 bulk TCRbeta repertoires from COVID-19 patients allowed us to confirm the SARS-CoV-2 specificity of contracting clones indirectly. Public TCRbeta sequences that can recognize SARS-CoV-2 epitopes are expected to be clonally expanded and thus sampled more frequently in the repertoires of COVID-19 patients than in control donors. doi = 10.1101/2020.05.18.100545 id = cord-272869-381qupdn author = Mirvakili, Seyed M title = Reverse Pneumatic Artificial Muscles for Application in Low-Cost Artificial Respirators date = 2020-05-21 keywords = device; figure; peep; pressure summary = In this work, we propose a low-cost, portable, yet high-performance design for a volume-controlled mechanical ventilator. With the current design, mechanical ventilation for respiration rate ranging from 10 b/min to 30 b/min with a tidal volume range of 150 mL to 1000 mL and I:E ratio of 1:1 to 1:5 can be performed. The state-of-the-art mechanical ventilators address the need for all range of respiratory failures; however, their time-to-manufacture, design sophistication, cost, and scalability for deployment in mass emergencies such as pandemics, make them not a viable solution in many situations. The user interface lets the operator set parameters, stop/start the device, and monitor the pressure and flow rate on the LCD ( Figure 1C ). As depicted in Figure 7 , when pressure drops below -2 cmH2O, the device starts the ventilation and delivers the set tidal volume. doi = 10.1101/2020.05.20.107342 id = cord-328659-miujzgtd author = Mishra, Akhilesh title = Mutation landscape of SARS-CoV-2 reveals five mutually exclusive clusters of leading and trailing single nucleotide substitutions date = 2020-07-27 keywords = RNA; SARS summary = title: Mutation landscape of SARS-CoV-2 reveals five mutually exclusive clusters of leading and trailing single nucleotide substitutions Furthermore, clustering analysis revealed unique geographical distribution of SARS-CoV-2 variants defined by their mutation profile. The rapid global spread of SARS-CoV-2 in a short period of time and the availability of a large number of fully sequenced genomes provide us with a unique opportunity of understanding the short-term temporal evolution of this virus in humans in a near real-time scale. By this approach we propose the classification of the SARS-CoV-2 virus genomes into 5 mutually exclusive lineages with unique set of co-occurring mutations and geographic distribution. Our analysis revealed a total of 40 nucleotide substitutions which occurred at > 1% in the SARS-CoV-2 genomes (Table 1 and Figure 1A ). We consider a specific mutation or a set of cooccurring mutations as "lineage-defining" for SARS-CoV-2, only when they are present in at least 2% (n=30) of the sequences analysed. doi = 10.1101/2020.05.07.082768 id = cord-103408-vhrlrd2c author = Mishra, Preet title = Decision Support Systems based on Scientific Evidence: Bibliometric Networks of Invasive Lantana camara date = 2020-08-10 keywords = DSS; Lantana; figure summary = Network approach to decipher large data sets has long been known as one of the best analytical strategies, and this applies equally well for bibliographic information (Shiffrin and Börner, 2004) , with the added benefits of being able to explore, model and restructure literature metadata to draw insights from both static and dynamic representations of individuals, organizations or themes of research (Newman, 2004) . High dimensional literature metadata, when visualized efficiently through networks can reveal communities sharing common node or edge attributes in both coarse-grained and fine-grained routines (Babu et al., 2016) Availability of metadata can often overcome constraints of limited access to full-text and enable one to focus on a lower ease-of-access threshold, i.e. critical information within the title, abstract and citation. Here we present case studies from invasive plant species bibliographic metadata and share how emerging co-authorship networks can improve and inform decisions, and how diverse network visualizations can be integrated as modules in a DSS. doi = 10.1101/2020.08.10.240879 id = cord-103150-e9q8e62v author = Mishra, Shreya title = Improving gene-network inference with graph-wavelets and making insights about ageing associated regulatory changes in lungs date = 2020-11-04 keywords = at2; cell; expression; gene; network summary = Just like gene-expression profile, inferred gene network could also be used to find differences in two groups of cells(sample) [13] to reveal changes in the regulatory pattern caused due to disease, environmental exposure or ageing. In order to test the hypothesis that graph-based denoising could improve gene-network inference, we first evaluated the performance of our method on bulk expression data-set. Our approach of graph-wavelet based pre-processing of mESC scRNA-seq data-set improved the performance of gene-network inference methods by 8-10 percentage (Fig. 2B) . Similarly in comparison to graph-wavelet based denoising, the other 7 methods did not provided substantial improvement in AUC for overlap among gene-network inferred by two data-sets of mESC (Fig. 2C , supplementary Figure S1B ). However, graph wavelet-based filtering improved the overlap between networks inferred from different batches of scRNA-seq profile of mESC even if they were denoised separately (Fig. 2C , supplementary Figure S1B ). doi = 10.1101/2020.07.24.219196 id = cord-267536-rvhwl4ea author = Miyashita, L title = Traffic-derived particulate matter and angiotensin-converting enzyme 2 expression in human airway epithelial cells date = 2020-05-27 keywords = ACE2 summary = title: Traffic-derived particulate matter and angiotensin-converting enzyme 2 expression in human airway epithelial cells Objective To assess the effect of traffic-derived PM10 on human airway epithelial cell ACE2 expression in vitro. Conclusion Traffic-related PM10 increases the expression of the receptor for SARS-CoV-2 in human respiratory epithelial cells. Culture of A549 cells with 5% CSE, a putative positive control, increased ACE2 expression (MFI, n=4, 0 (0 to 28) vs. We also found that traffic-derived PM 10 upregulates ACE2 expression in human primary nasal epithelial cells, suggesting that this response occurs throughout the respiratory tract. First, we did not determine whether increased In conclusion, this study provides the first mechanistic evidence that traffic-derived air pollution increases ACE2 expression in human airway cells and therefore 1 3 vulnerability to SARS-CoV-2 infection. doi = 10.1101/2020.05.15.097501 id = cord-296007-1gsgd22t author = Mohseni, Amir Hossein title = Inferring MHC interacting SARS-CoV-2 epitopes recognized by TCRs towards designing T cell-based vaccines date = 2020-09-12 keywords = HLA; SARS summary = Our TCR-pMHC models predicted that position 2 of the homologous peptide antigens ( Figure 1A ) related 2 2 0 to TCR-pMHC complex of SARS-CoV-2 as well as SARS-CoV and bat-CoV N proteins prefers the 2 2 1 hydrophobic amino acid residues (e.g. Ile, Leu, Met, and Phe), and the second position of these hit peptides 2 2 2 is an hydrophobic amino acid residue Pro forming five strong VDW forces with residues Y99, V67, M45, 2 2 3 Y7, and F9 and two H-bonds with residues K66 and E63 on MHC molecule ( Figure S2A , left). Visualization of interactions in the atomic level structure of a TCR-pMHC complex in the hit peptide of 2 4 9 SARS-CoV-2 N protein for HLA-E ( Figure S3C ) within 20 and 8 Å was generated on-the-fly using of the homologous peptide antigens of all queries has no detectable binding to both MHC and TCR. doi = 10.1101/2020.09.12.294413 id = cord-284068-sbon3aes author = Mok, Chee Keng title = Calcitriol, the active form of vitamin D, is a promising candidate for COVID-19 prophylaxis date = 2020-06-22 keywords = CoV-2; SARS summary = Validation assays to determine changes in infectious virus titres upon treatment was carried out by testing selected hit compounds in dose-dependent assays in Vero E6 to confirm the primary screen observation and also in the human hepatocarcinoma HuH7 cell line as the latter cell line expresses high levels of the ACE2 receptor (10) and supports replication of coronaviruses (11) . While recent data has shown that vitamin D levels are negatively associated with morbidity and mortality of COVID-19 cases (13, 14) , this is the first report of a direct inhibitory effect of calcitriol on SARS-CoV-2. The authors speculated that vitamin D supplementation could protect against SARS-CoV-2 infection and improve patient disease outcomes (16) , and our finding certainly provides credence to this hypothesis. Given the high transmissibility of SARS-CoV-2 globally (23), if these findings can be replicated in clinical trials, calcitriol may certainly prove to be an effective tool in the effort to control the pandemic while waiting for an effective vaccine to be rolled out globally. doi = 10.1101/2020.06.21.162396 id = cord-340516-9dfaqsv7 author = Moore, Anne C. title = Pre-clinical studies of a recombinant adenoviral mucosal vaccine to prevent SARS-CoV-2 infection date = 2020-09-06 keywords = CoV-2; SARS; vaccine summary = We demonstrate that, compared to expression of the S1 domain or a stabilized spike antigen, the full length, wild-type spike antigen induces significantly higher neutralizing antibodies in the periphery and in the lungs, when the vaccine is administered mucosally. Here, we report the induction of neutralizing antibody (Nab), IgG and IgA antibody responses, and T cell responses in mice following immunization of rAd vectors expressing one or more SARS-CoV-2 antigens. We have previously demonstrated that an oral, tableted rAd-based vaccine can induce protection against respiratory infection and shedding following influenza virus challenge 15 as well as intestinal immunity to norovirus antigens in humans 12 . In summary, these studies in mice represent our first step in creating a vaccine candidate, demonstrating the immunogenicity of the construct at even low vaccine doses and the elucidation of the full-length spike protein as a leading candidate antigen to induce T cell responses and superior systemic and mucosal neutralizing antibody. doi = 10.1101/2020.09.04.283853 id = cord-104030-eb29t38n author = Morales-Nebreda, Luisa title = Aging imparts cell-autonomous dysfunction to regulatory T cells during recovery from influenza pneumonia date = 2020-06-05 keywords = Treg; cell; dna; figure summary = Using heterochronic (age-mismatched) adoptive Treg cell transfer experiments and molecular profiling in mice, we sought to determine whether the age-related impairment in repair following influenza-induced lung injury is intrinsic to Treg cells. Our data support a paradigm in which aged Treg cells fail to upregulate youthful reparative programs, activate maladaptive responses and consequently exhibit a cell-autonomous impairment in pro-recovery function, which delays resolution from viralinduced lung injury in aged hosts. Gene set enrichment analysis of these genes demonstrated that this methylation-regulated gene expression program was associated with pro-recovery processes and was significantly skewed toward young Treg cells ( Figure 6C) . Combined, these results show that age-related DNA methylation regulates the pro-reparative transcriptional regulatory network during recovery from influenza-induced lung injury. What are the molecular mechanisms underpinning the age-associated Treg cell gain or loss-of pro-reparative function in the lung following influenza infection? doi = 10.1101/2020.06.05.135194 id = cord-104128-0gyk9cwx author = Morand, Serge title = The accelerated infectious disease risk in the Anthropocene: more outbreaks and wider global spread date = 2020-04-20 keywords = Anthropocene; disease; global; outbreak summary = Countries which are more centrally located within these disease networks tend to be also the more developed and emerging countries with significantly higher GDPs. Therefore, one cost of increased global mobility (which is currently tightly linked to economic growth and globalization, see Discussion below) is the increased risk of disease outbreaks and their faster and wider spread (although we note that the risk per capita may be decreasing, Smith et al., 2014) . Similarly, increasing levels of (1) isolation of infectious hosts, household quarantine and related behavioral changes which reduce transmission rates and (2) air traffic reduction increasingly slowed the global spread of influenza, although the latter control strategy required the almost complete halt of global air traffic (Cooper et al., 2006; Ferguson et al., 2006; Flahault et al., 2006; Hollingsworth et al., 2006; Epstein et al., 2007; Bajardi 11 et al., 2011) . doi = 10.1101/2020.04.20.049866 id = cord-311240-o0zyt2vb author = Motayo, Babatunde Olarenwaju title = Evolution and Genetic Diversity of SARSCoV-2 in Africa Using Whole Genome Sequences date = 2020-07-27 keywords = Africa; SARS; sequence summary = Our study has revealed a rapidly diversifying viral population with the G614 spike protein variant dominating, we advocate for up scaling NGS sequencing platforms across Africa to enhance surveillance and aid control effort of SARSCoV-2 in Africa. The pathogen was later identified to be a novel coronavirus closely related to the severe acute respiratory syndrome virus (SARS), with a possible bat origin (Zhou et al, 2020) . This study was designed to determine to the genetic diversity and evolutionary history of genome sequences of SARSCoV-2 isolated in Africa. Results of recombination analysis of the African SARSCoV-2 (AfrSARSCoV-2) sequences against references whole genome sequences of SARS, Recombination signals were observed between the African SARSCoV-2 sequences and reference sequence (Major recombinant hCoV-19 Pangolin/Guangu P4L/2017; Minor parent hCoV-19 B batYunan/RaTG13) between the RdRP and S gene regions (Figure 2 ). doi = 10.1101/2020.07.27.222901 id = cord-312524-ee5xw1r8 author = Moustafa, Ahmed M. title = Rapid whole genome sequence typing reveals multiple waves of SARS-CoV-2 spread date = 2020-06-08 keywords = SARS; figure summary = Here we present a rapid, whole genome, allele-based method (GNUVID) for assigning sequence types to sequenced isolates of SARS-CoV-2 sequences. Rapid sequencing of the SARS-CoV-2 pandemic virus has presented an 40 unprecedented opportunity to track the evolution of the virus and to understand the 41 emergence of a new pathogen in near-real time. Our panallelome approach to developing a whole genome (wgMLST) scheme for 58 SARS-CoV-2 uses a modified version of our recently developed tool, WhatsGNU [10], 59 to rapidly assign an allele number to each gene nucleotide sequence in the virus''s 60 genome creating a sequence type (ST). We developed the GNU-based Virus IDentification (GNUVID) system as a tool 71 that automatically assigns a number to each unique allele of the 10 open reading 72 frames (ORFs) of SARS-CoV-2 ( Figure 1A) information. When the global region of origin for each genome sequence was mapped to 102 each CC there was a strong association of some CCs with certain geographical 103 locations. doi = 10.1101/2020.06.08.139055 id = cord-280454-etf32afd author = Moustaqil, Mehdi title = SARS-CoV-2 proteases cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): implications for disease presentation across species and the search for reservoir hosts date = 2020-06-05 keywords = Fig; GFP; IRF3; NLRP12; SARS; TAB1; cleavage summary = title: SARS-CoV-2 proteases cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): implications for disease presentation across species and the search for reservoir hosts Direct cleavage of IRF3 by NSP3 could explain the blunted TypeI IFN response seen during SARS-CoV-2 infections while NSP5 mediated cleavage of NLRP12 and TAB1 point to a molecular mechanism for enhanced production of IL-6 and inflammatory response observed in COVID-19 patients. In this report, we show that the viral proteases PLpro and 3CLpro of SARS-CoV2 lead to the in-vitro proteolytic cleavage of three important proteins of the host immune response: IRF3, TAB1 and NLRP12 (Fig. 1B) . The presence of the five human-like cleavage sites for IRF3, TAB1 and NLRP12 in a single species shows that it is possible that the SARS viruses could have gained the new functionality of cleaving these Human Innate Immune Proteins in a single reservoir host, potentially in Myotis Davidii. doi = 10.1101/2020.06.05.135699 id = cord-296187-nnv2e7gr author = Mulgaonkar, Nirmitee title = Bcr-Abl tyrosine kinase inhibitor imatinib as a potential drug for COVID-19 date = 2020-08-18 keywords = ACE2; RBD; SARS; VSV summary = The SARS-CoV-2 spike glycoprotein, due to its primary interaction with the human angiotensin-converting enzyme 2 (ACE2) cell-surface receptor, is considered as a potential target for drug development. Based on in silico screening followed by in vitro studies, here we report that the existing FDA-approved Bcr-Abl tyrosine kinase inhibitor, imatinib, inhibits SARS-CoV-2 with an IC50 of 130 nM. We provide evidence that although imatinib binds to the receptor-binding domain (RBD) of SARS-CoV-2 spike protein with an affinity at micromolar, i.e., 2.32 ± 0.9 μM levels, imatinib does not directly inhibit the spike RBD:ACE2 interaction – suggesting a Bcr-Abl kinase-mediated fusion inhibition mechanism is responsible for the inhibitory action. This study utilizes in silico methodology followed by in vitro experimental validation to screen existing FDA-approved small molecule drugs specific to the RBD of the spike protein of SARS-CoV-2 to identify repurposable drugs targeting further clinical validation. doi = 10.1101/2020.06.18.158196 id = cord-103597-mt0h06y3 author = Muller, Alana title = Neurophysiological Correlates of the Dunning-Kruger Effect date = 2020-05-20 keywords = Addante; DKE; Dunning; ERP; Kruger; Yonelinas; memory summary = Between-group EEG differences were evident between over-estimators and under-estimators during Dunning-Kruger responses, which revealed FN400-like effects of familiarity supporting differences for over-estimators from 400-600 ms, whereas ''old-new'' memory ERP effects revealed a late parietal component (LPC) associated with recollection-based processing from 600-900 ms for under-estimators that was not evident for over-estimators. Results Between-group EEG differences were evident between over-estimators and underestimators during Dunning-Kruger responses, which revealed FN400-like effects of familiarity supporting differences for over-estimators from 400-600 ms, whereas ''oldnew'' memory ERP effects revealed a late parietal component (LPC) associated with recollection-based processing from 600-900 ms for under-estimators that was not evident for over-estimators. One suggestion from these results is that the frontal effect at 400-600 ms may be characteristic of the FN400 ERP effect related to familiarity-based processing, in that over-estimators may be relying on the less-specific memory process of familiarity or intuitions of increased fluency to guide making their metacognitive judgments, instead of relying upon the more distinct recollection-related processes (Yonelinas et al., 2010 ) that evidently appears to be supporting the people who were under-estimating their performance relative to the group (Figure 7 ). doi = 10.1101/2019.12.26.888511 id = cord-262602-on0w55x0 author = Muruato, Antonio E. title = A high-throughput neutralizing antibody assay for COVID-19 diagnosis and vaccine evaluation date = 2020-05-22 keywords = PRNT summary = Therefore, a high-throughput assay to measure SARS-CoV-2 neutralizing antibodies is urgently needed for COVID-19 serodiagnosis, convalescent plasma therapy, and vaccine development. Here we report on a fluorescence-based SARS-CoV-2 neutralization assay that detects SARS-CoV-2 neutralizing antibodies in COVID-19 patient specimens and yields comparable results to plaque reduction neutralizing assay, the gold standard of serological testing. To validate the reporter virus neutralization results, we performed the conventional 6 4 PRNT on the same set of patient specimens. The results demonstrate that when diagnosing 6 8 patient specimens, the reporter virus assay delivers neutralization results comparable to the 6 9 PRNT assay, the gold standard of serological testing. Next, we evaluated the specificity of reporter neutralization assay using potentially cross-7 1 reactive sera and interfering substances (Table 1) . Nevertheless, the 1 0 3 mNeonGreen reporter assay offers a rapid, high-throughput platform to test COVID-19 patient 1 0 4 sera not previously available. doi = 10.1101/2020.05.21.109546 id = cord-262470-nkql7h9x author = Muus, Christoph title = Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells date = 2020-04-20 keywords = ACE2; COVID-19; CTSL; Data; Extended; Fig; SARS; Supplementary; TMPRSS2; at2; cell; expression summary = title: Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells Here, we assess the cell type-specific RNA expression of ACE2, TMPRSS2, and CTSL through an integrated analysis of 107 single-cell and single-nucleus RNA-Seq studies, including 22 lung and airways datasets (16 unpublished), and 85 datasets from other diverse organs. Performing the first meta-analyses of scRNA-seq studies, we analyzed 1,176,683 cells from 282 nasal, airway, and lung parenchyma samples from 164 donors spanning fetal, childhood, adult, and elderly age groups, associate increased levels of ACE2, TMPRSS2, and CTSL in specific cell types with increasing age, male gender, and smoking, all of which are epidemiologically linked to COVID-19 susceptibility and outcomes. To assess the association of age, sex, and smoking status with the expression of ACE2, TMPRSS2, and CTSL, we aggregated 22 scRNA-seq datasets of healthy human nasal and lung cells, as well as fetal samples. doi = 10.1101/2020.04.19.049254 id = cord-292862-ezrkg0dc author = Myerson, Jacob W. title = Supramolecular Organization Predicts Protein Nanoparticle Delivery to Neutrophils for Acute Lung Inflammation Diagnosis and Treatment date = 2020-04-18 keywords = ARDS; DBCO; LPS; PBS; Supplementary; figure; lung summary = We show that polystyrene nanoparticles and five liposome formulations do not accumulate in injured lungs, indicating that nanostructures that are not based on protein are not intrinsically drawn to marginated neutrophils in acute inflammation. 6, 10, 14, 18 Single cell suspensions prepared from mouse lungs were probed by flow cytometry to further characterize pulmonary neutrophils in naïve mice and in mice following LPS-induced inflammation. The protein component of each particle was labeled with 125 I for tracing in biodistributions, and assessed 30 minutes after IV administration of NPs. Both absolute LDNG lung uptake and ratio of lung uptake to liver uptake registered a ~25-fold increase between naïve control and LPS-injured animals (Figure 2A , Supplementary Table 1) . As with LDNGs and albumin NPs in Figure 2C -H, single cell suspensions were prepared from LPS-inflamed and naïve control lungs after circulation of fluorescent DBCO-IgG liposomes. doi = 10.1101/2020.04.15.037564 id = cord-349364-vert186n author = Márquez-López, Cristina title = SARS-CoV-2 protein Nsp1 alters actomyosin cytoskeleton and phenocopies arrhythmogenic cardiomyopathy-related PKP2 mutant date = 2020-09-14 keywords = Myh10; Nsp1; PKP2; R735X; figure summary = The fact that Nsp1 and PKP2 mutant R735X share similar phenotypes also suggests that direct SARS-CoV-2 heart infection could induce a transient ACM-like disease in COVID-19 patients, which may contribute to right ventricle dysfunction, observed in patients with poor survival prognosis. Using atomic force microscopy together with fluorescence imaging, we show that expression of PKP2 (c.2203C>T), encoding the R735X mutant found in ACM patients from different families (Alcalde et al., 2014; Gerull et al, 2004) alters cell mechanical stiffness, and alike Nsp1, modifies actomyosin cytoskeleton. All together, these results suggest that cytoplasmic localization of PKP2 either by a mutant involved in ACM development, or by Nsp1 hijack by SARS-CoV-2 infection can alter the integrity and assembly of the actin cytoskeleton by modulating the cortical distribution of Myh9 and Myh10. doi = 10.1101/2020.09.14.296178 id = cord-103892-v6gkubd4 author = Mäkinen, Janne J. title = The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases date = 2020-07-01 keywords = Fig; RNAP; Supplementary; dna summary = Overall, these data demonstrated that the enhanced or diminished capabilities of the variant RNAPs to utilize 2''dGTP in the SNA assays reflected, in qualitative terms, their capabilities to utilize all four 2''dNTPs. The role of the β''Arg425 in selectively promoting the binding of NTPs was easy to explain because the β''Arg425 interacts with the 2''OH of the NTP analogues in several RNAP structures (Supplementary Table 5 , Fig. 1c, 4a, b) . We further hypothesized and demonstrated by in silico docking experiments that the 3''OH could move to within the hydrogen bond distance of the β''Arg425 if the deoxyribose moiety adopted a 2''-endo conformation (Supplementary Fig. 8 To test this hypothesis in crystallo, we solved the X-ray crystal structure of the initially transcribing complexes containing T. Overall, the comparative analysis of RNAP structures with CMPCPP, 2''dCTP and 3''dCTP suggested that the β''Arg425 inhibited the incorporation of 2''dNTPs by interacting with their 3''OH group and favoring the 2''-endo conformation of the deoxyribose moiety. doi = 10.1101/2020.06.30.179606 id = cord-103781-bycskjtr author = Mönke, Gregor title = Optimal time frequency analysis for biological data - pyBOAT date = 2020-06-04 keywords = analysis; figure; frequency; signal; time; wavelet summary = With this challenge in mind, we have developed pyBOAT, a Python-based fully automatic stand-alone software that integrates multiple steps of non-stationary oscillatory time series analysis into an easy-to-use graphical user interface. Our approach integrates data-visualization, optimized sinc-filter detrending, amplitude envelope removal and a subsequent continuous-wavelet based time-frequency analysis. Computational methods that enable analysis of periods, amplitudes and phases of rhythmic time series data have been essential to unravel function and design principles of biological clocks (Lauschke et al. This allows to use a straightforward numerical method to estimate a lter response | w(ω)| 2 , i.e. applying the smoothing operation to simulated white noise and time averaging the Wavelet spectra. Continuous wavelet analysis allows to reveal non-stationary period, amplitude and phase dynamics and to identify multiple frequency components across dierent scales within a single oscillatory signal (Leise [2013] , Leise et al. doi = 10.1101/2020.04.29.067744 id = cord-352943-ztonp62x author = Nagpal, Sunil title = What if we perceive SARS-CoV-2 genomes as documents? Topic modelling using Latent Dirichlet Allocation to identify mutation signatures and classify SARS-CoV-2 genomes date = 2020-08-20 keywords = LDA; SARS; mutation summary = Here we describe how SARS-CoV-2 genomic mutation profiles can be structured into a ''Bag of Words'' to enable identification of signatures (topics) and their probabilistic distribution across various genomes using LDA. Use of the non-phylogenetic albeit classical approaches like topic modeling and other data centric pattern mining algorithms is therefore proposed for supplementing the efforts towards understanding the genomic diversity of the evolving SARS-CoV-2 genomes (and other pathogens/microbes). In fact, Latent Dirichlet Allocation (LDA), an unsupervised machine learning approach, is particularly known for identifying latent topics in large document collections and deciphering the words that define the inferred topics using a generative statistical model. Classical LDA was employed to generate topic models leading to identification of 16 amino acid mutation signatures and 18 nucleotide mutation signatures (equivalent to topics) in the corpus of chosen genomes through rigorous hyper-parameter tuning for coherence optimization (Figure 2) . doi = 10.1101/2020.08.20.258772 id = cord-103343-k4v5ksvq author = Naim, Nikki title = NHR-49 Acts in Distinct Tissues to Promote Longevity versus Innate Immunity date = 2020-09-11 keywords = NHR-49 summary = title: NHR-49 Acts in Distinct Tissues to Promote Longevity versus Innate Immunity Aging and immunity are inextricably linked and many genes that extend lifespan also enhance immunoresistance. Here, we demonstrate that the Caenorhabditis elegans pro-longevity factor, NHR-49, also promotes resistance against Pseudomonas aeruginosa, but modulates immunity and longevity by spatially and mechanistically distinct mechanisms. NHR-49 expression is increased by germline ablation, an intervention that extends lifespan, but lowered by pathogen exposure. NHR-49 acted in multiple somatic tissues to promote longevity, whereas, it''s pro-immunity function was mediated by neuronal expression. Thus, NHR-49 targets share the largest overlap with genes whose 182 In this study, we demonstrate that NHR-49 is a pro-longevity factor that modulates 368 lifespan and immunity through distinct mechanisms. In fertile, nhr-49 single 393 mutants, immunity was restored by presence in neurons or intestine, but lifespan 394 could be rescued from other tissues as well. elegans lifespan in a NHR-49/PPARalpha-dependent manner doi = 10.1101/2020.09.11.290452 id = cord-301233-nenw0f81 author = Naydenova, Katerina title = Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP date = 2020-10-21 keywords = Fig; RNA; RTP; SARS summary = Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure reveals an unusual, non-productive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp which explains its low rate of incorporation into the RNA primer strand. Here we report the structure of the SARS-CoV-2 RdRp, comprising subunits nsp7, nsp8 and nsp12, in complex with template:primer double-stranded RNA and favipiravir ribonucleoside triphosphate (favipiravir-RTP), determined by cryoEM at 2.5Å resolution. In this study, we determined the cryoEM structure of favipiravir-RTP at the catalytic site of the SARS-CoV-2 RdRp, in complex with template:primer dsRNA, and investigated the influence of this nucleotide analogue inhibitor on RNA synthesis in vitro. doi = 10.1101/2020.10.21.347690 id = cord-279629-t1xjy12y author = Nazneen Akhand, Mst Rubaiat title = Genome based Evolutionary study of SARS-CoV-2 towards the Prediction of Epitope Based Chimeric Vaccine date = 2020-04-15 keywords = COVID-19; SARS; protein; vaccine summary = The present in silico study aimed to predict a novel chimeric vaccines by simultaneously targeting four major structural proteins via the establishment of ancestral relationship among different strains of coronaviruses. Hence, the study was designed to develop a chimeric recombinant vaccine against COVID-19 by targeting four major structural proteins of the pathogen, while revealing the evolutionary history of different species of coronavirus based on whole genome and protein domain-based phylogeny. Apart from the human coronaviruses, we introduced other coronaviruses which choose different species of bats, whale, turkey, rat, mink, ferret, swine, camel, rabbit, cow and others as host (Supplementary TableDomain analysis of spike protein of coronaviruses reveals that they contain mainly one signature domains namely, coronavirus S2 glycoprotein (IPR002552), which is present in all the candidates. Design of an epitope-based peptide vaccine against spike protein of human coronavirus: an in silico approach. doi = 10.1101/2020.04.15.036285 id = cord-291420-40xsypzt author = Nelson-Sathi, Shijulal title = Mutational landscape and in silico structure models of SARS-CoV-2 Spike Receptor Binding Domain reveal key molecular determinants for virus-host interaction date = 2020-10-01 keywords = RBD; SARS summary = title: Mutational landscape and in silico structure models of SARS-CoV-2 Spike Receptor Binding Domain reveal key molecular determinants for virus-host interaction Formation of a stable binding interface between the Spike (S) protein Receptor Binding Domain (RBD) of SARS-CoV-2 and Angiotensin-Converting Enzyme 2 (ACE2) of host actuates viral entry. In silico structure modelling of interfaces induced by mutations on residues which directly engage ACE2 or lie in the near vicinity revealed molecular rearrangements and binding energies unique to each RBD mutant. The structural analysis of the mutated spike glycoprotein of SARS-CoV-2 RBD domain was done to assess the impact of interface amino acid residue mutations on binding affinity towards the human ACE2 (hACE2) receptor. Comparative analysis of structures showed key differences in all three binding clusters of SARS-CoV-2 RBD wild type and mutant interfaces with human or mouse ACE2 (Figure 2C, 2D and Table S1 ). doi = 10.1101/2020.05.02.071811 id = cord-336628-0evl3wnd author = Neufeldt, Christopher J. title = SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB date = 2020-07-21 keywords = RNA; SARS; cell; sting summary = Consistently, secreted cytokine profiles from both severe COVID-19 patients and SARS-CoV-2 infected lung epithelial cells, were enriched for pro-inflammatory cytokines and lacked type I/III IFNs. We also demonstrate that SARS-CoV-2 infection leads specifically to NF-κB but not IRF3 nuclear localization and that poly(I:C)-induced pathway activation is attenuated in infected cells. To confirm that the lack of IFN response in Calu-3 or A549-ACE2 cells infected with SARS-CoV-2 was not due to defects in the activation of innate immune pathways, we To test if IFNs could limit virus replication even after establishment of infection, A549-ACE2 cells were treated with high levels of various IFNs at the time point of infection or 6 h thereafter. these results indicate that SARS-CoV2-infection triggers the cGAS-STING pathway, leading to NF-κB-mediated induction of pro-inflammatory cytokines, and that this response can be controlled with STING inhibitors. doi = 10.1101/2020.07.21.212639 id = cord-103638-n5kpvsvg author = Nguyen, Long T. title = Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection date = 2020-04-14 keywords = CRISPR; Fig; RNA; Supplementary summary = By extending the 3''or 5''-ends of the crRNA with different lengths of ssDNA, ssRNA, and phosphorothioate ssDNA, we discovered a new self-catalytic behavior and an augmented rate of LbCas12a-mediated collateral cleavage activity as high as 3.5-fold compared to the wild-type crRNA. With isothermal amplification of SARS-CoV-2 RNA using RT-LAMP, the modified crRNAs were incorporated in a paper-based lateral flow assay that could detect the target with up to 23-fold higher sensitivity within 40-60 minutes. However, the ENHANCE showed 5.4-fold and 3.4-fold and higher trans-cleavage activity compared to the wild-type crRNA for targeting the methylated dsDNA and ssDNA, respectively (Fig. 3e, Supplementary Fig. 20a) . While no clinical samples were tested, the results indicated the 3''DNA7-modified crRNA consistently demonstrated higher sensitivity for detecting CoV-2 dsDNA within 30 minutes as compared to the wild-type crCoV-2 ( Supplementary Figs. doi = 10.1101/2020.04.13.036079 id = cord-255371-o9oxchq6 author = Nguyen, Thanh Thi title = Genomic Mutations and Changes in Protein Secondary Structure and Solvent Accessibility of SARS-CoV-2 (COVID-19 Virus) date = 2020-07-10 keywords = SARS; mutation; protein; sequence summary = title: Genomic Mutations and Changes in Protein Secondary Structure and Solvent Accessibility of SARS-CoV-2 (COVID-19 Virus) This paper reports and analyses genomic mutations in the coding regions of SARS-CoV-2 and their probable protein secondary structure and solvent accessibility changes, which are predicted using deep learning models. We use 6,324 SARS-CoV-2 genome sequences collected in 45 countries and deposited to the NCBI GenBank so far and create a spreadsheet dataset of all mutations occurred across different genes. In this paper, to evaluate the possible impacts of genomic mutations on the virus functions, we propose the use of the SSpro/ACCpro 5 methods to predict protein secondary structure and relative solvent accessibility [13] . By comparing the prediction results obtained on the reference genome and mutated genomes, we are able to assess whether the detected mutations have the potential to change the protein structure and solvent accessibility, and thus lead to possible changes of the virus characteristics. doi = 10.1101/2020.07.10.171769 id = cord-291523-4dtk1kyh author = Nguyen, Thanh Thi title = Origin of Novel Coronavirus (COVID-19): A Computational Biology Study using Artificial Intelligence date = 2020-07-01 keywords = CoV-2; Fig; SARS summary = Outcomes of a phylogenetic analysis suggest that the virus belongs to the genus Betacoronavirus, sub-genus Sarbecovirus, which includes many bat SARS-like CoVs and SARS CoVs. Another study in [5] confirms this finding by analysing genomes obtained from three adult patients admitted to a hospital in Wuhan on December 27, 2019. With the cut-off parameter C is set equal to 0.7, the hierarchical clustering algorithm separates the reference sequences into 6 clusters in which cluster "5" comprises all examined viruses of the Sarbecovirus sub-genus, including many SARS CoVs, bat SARS-like CoVs and pangolin CoVs (Fig. 7A) . With the results obtained in Fig. 7D (and also in the experiments with the DBSCAN method presented next), we support a hypothesis that bats or pangolins are the probable origin of SARS-CoV-2. In this Appendix, we first present results of the hierarchical clustering method applied to the dataset that combines Set 1 of reference sequences (Table 1 ) with all 334 SARS-CoV-2 sequences (see Fig. 9 ). doi = 10.1101/2020.05.12.091397 id = cord-102823-zult69f2 author = Nguyen, Thin title = GraphDTA: Predicting drug–target binding affinity with graph neural networks date = 2020-10-02 keywords = GAT; GCN; drug summary = doi = 10.1101/684662 id = cord-268894-amfv3z2y author = Nguyen-Contant, Phuong title = S protein-reactive IgG and memory B cell production after human SARS-CoV-2 infection includes broad reactivity to the S2 subunit date = 2020-07-21 keywords = RBD; SARS summary = Serum IgG levels specific for SARS-CoV-2 proteins (S, including the RBD 31 and S2 subunit, and nucleocapsid [N] ) and non-SARS-CoV-2 proteins were related to 32 measurements of circulating IgG MBCs. Anti-RBD IgG was absent in unexposed subjects. Serum IgG levels specific for SARS-CoV-2 proteins (S, including the RBD 31 and S2 subunit, and nucleocapsid [N] ) and non-SARS-CoV-2 proteins were related to 32 measurements of circulating IgG MBCs. Anti-RBD IgG was absent in unexposed subjects. Approximately one-third of non-SARS-CoV-140 2-exposed subjects in the healthy donor cohort had low levels of serum IgG against the S and N 141 proteins of SARS-CoV-2, likely reflecting cross-reactivity with seasonal HCoVs ( Figure 1A ). In contrast, IgG MBCs reactive to the S proteins of the HCoVs OC43 and 229E 192 and the control proteins H1 and TTd were detected in nearly 50% or more of non-SARS-CoV-2-193 exposed subjects, consistent with the higher levels of serum IgG against these antigens ( Figure 2E -194 2H) . doi = 10.1101/2020.07.20.213298 id = cord-103703-t03r6ny8 author = Nguyen-Tu, Marie-Sophie title = Reduced expression of TCF7L2 in adipocyte impairs glucose tolerance associated with decreased insulin secretion, incretins levels and lipid metabolism dysregulation in male mice date = 2020-05-20 keywords = TCF7L2; glucose; insulin; mouse summary = title: Reduced expression of TCF7L2 in adipocyte impairs glucose tolerance associated with decreased insulin secretion, incretins levels and lipid metabolism dysregulation in male mice Mice with biallelic Tcf7l2 deletion exposed to high fat diet for 9 weeks exhibited impaired glucose tolerance (p=0.003 at 15 min after glucose injection) which was associated with reduced in vivo glucose-stimulated insulin secretion (decreased 0.51 ± 0.03-fold, p=0.02). Therefore, alterations in pancreatic beta cell function observed ex vivo in the absence of TCF7L2 in adipocyte have no impact on whole body glucose-stimulated insulin secretion. A striking finding in the present study is that TCF7L2 is required in adipose tissue for normal incretin production and insulin secretion: we reveal that decreased Tcf7l2 expression in mature adipocytes leads to lowered circulating levels of GLP-1 and GIP ( Fig.4a and b) . doi = 10.1101/2020.05.18.102384 id = cord-323828-ug2duzw1 author = Ni, Dongchun title = Structural investigation of ACE2 dependent disassembly of the trimeric SARS-CoV-2 Spike glycoprotein date = 2020-10-12 keywords = SARS; Spike summary = Here we report a single particle cryo-electron microscopy analysis of SARS-CoV-2 trimeric Spike in presence of the human ACE2 ectodomain. The binding of purified hACE2 ectodomain to Spike induces the disassembly of the trimeric form of Spike and a structural rearrangement of its S1 domain to form a stable, monomeric complex with hACE2. The clinical-grade soluble form of hACE2 has been reported to be a 74 potential novel therapeutic approach for reducing the infection of SARS-CoV-2 (Monteil et al., 2020) by preventing the viral Spike from interacting with other hACE2 present on human cells. The final 3D 115 reconstruction from 72''446 particles at 5.1Å overall resolution showed a density map corresponding to a single, 116 monomeric Spike protein in complex with hACE2 (Fig. 1a) . Figure 1 Cryo-EM maps of SARS-CoV-2 Spike-hACE2 complexes and fitted models. Cryo-EM structure of the SARS coronavirus spike glycoprotein in 352 complex with its host cell receptor ACE2 doi = 10.1101/2020.10.12.336016 id = cord-298326-f5q7j3iu author = Nick, Benjamin C. title = Identification of a critical horseshoe-shaped region in the nsp5 (Mpro, 3CLpro) protease interdomain loop (IDL) of coronavirus mouse hepatitis virus (MHV) date = 2020-06-19 keywords = MHV summary = In this study, we describe the identification of an essential, conserved horseshoe-shaped region in the nsp5 interdomain loop (IDL) of mouse hepatitis virus (MHV), a common coronavirus replication model. Structural modeling and sequence analysis of these sites in other coronaviruses, including all 7 human coronaviruses, suggests that the identified structure and sequence of this horseshoe regions is highly conserved and may represent a new, non-active-site regulatory region of the nsp5 (3CLpro) protease to target with coronavirus inhibitors. To evaluate whether any of 207 the recovered MHV nsp5 IDL mutants may exhibit a temperature-sensitive phenotype, we 208 performed an efficiency of plating (EOP) analysis by comparing the titers of each IDL virus by 209 plaque assay determined at a physiologic (37°C) and elevated temperature (40°C) (Fig. 3A) . doi = 10.1101/2020.06.18.160671 id = cord-282604-xp71rkxc author = Nikolaev, EN title = Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein date = 2020-05-25 keywords = SARS; protein summary = title: Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein We have developed a mass-spectrometry based method for the detection of the SARS CoV-2 virus in nasopharynx epithelial swabs, based on the detection of the viral nucleocapsid N protein. The N protein of the SARS-COV-2 virus, the most abundant protein in the virion, is the best candidate for mass-spectrometric detection of the infection, and MS-based detection of several peptides from the SARS-COoV-2 nucleoprotein has been reported earlier by the Sinz group [4]. We have performed a pilot study on nasopharynx epithelial swabs already collected from patients with CODIV-19 for RT-qPCR and showed confident identification of the N protein of the SARS CoV-2 virus by mass-spectrometry with the use of a very basic sample preparation procedure. Mass Spectrometric Identification of SARS-CoV-2 Proteins from Gargle Solution Samples of COVID-19 Patients doi = 10.1101/2020.05.24.113043 id = cord-104157-rivaoo73 author = Noreika, Valdas title = Alertness fluctuations during task performance modulate cortical evoked responses to transcranial magnetic stimulation date = 2019-06-28 keywords = Alertness; EEG; Level; MEP; TEP; TMS summary = We observed rapid, non-linear changes in TMS-evoked neural responses – specifically, motor evoked potentials and TMS-evoked cortical potentials – as EEG activity indicated decreasing levels of alertness, even while participants remained awake and responsive in the behavioural task. Here we combined single-pulse TMS with concurrent EEG recording and a simple behavioural task to quantify changes in motor and cortical reactivity with fluctuating levels of alertness defined objectively on the basis of ongoing brain activity. To assess the instantaneous level of alertness, a two-fold EEG analysis was applied over the time window immediately preceding each TMS pulse: (1) a binary definition of awake and drowsy states following EEG spectral power signatures (θ/α) averaged across all EEG electrodes (Bareham et al., 2014) , and (2) a dynamical definition of alertness levels following a detailed sub-staging system for scoring the transition to N1 sleep (Hori et al., 1994) (Fig. 1C ). doi = 10.1101/155754 id = cord-103812-ls6zgipi author = Norris, Rachael P. title = Gap junction internalization and processing in vivo: a 3D immuno-electron microscopy study date = 2020-06-30 keywords = cx43; gap; junction; membrane summary = Less is understood about their internalization, which forms double membrane vesicles containing cytosol and membranes from another cell, called connexosomes or annular gap junctions. Gap junction internalization can also be considered to be a form of trogocytosis (Joly and Hudriser, 2003) in which a portion of the plasma membrane and cytosol of the neighboring cell is transferred to the engulfing cell (See Fig. 1A ). Serial sections were then imaged to obtain threedimensional information; this distinguished between internalized connexosomes and gap junctions in the process of invagination. In 7 of the 56 modified connexosomes, a patch of unlabeled outer membrane bulged outward from a labeled inner membrane ( suggesting that different types of vesicles were involved. Five serial sections through a modified connexosome containing several internal vesicles labeled with Cx43. doi = 10.1101/2020.06.29.178475 id = cord-103294-1lrfna4v author = Northrop, Amanda C. title = Clockwise and counterclockwise hysteresis characterize state changes in the same aquatic ecosystem date = 2020-05-02 keywords = enrichment summary = A model system for understanding ecosystem recovery is the aquatic microecosystem that inhabits the cup-shaped leaves of the pitcher plant Sarracenia purpurea. At low enrichment rates, ecosystems showed a substantial lag in the recovery of [O2] (clockwise hysteresis). At high enrichment rates, we observed a novel response: changes in [O2] were proportionally larger during the recovery phase than during the enrichment phase (counter-clockwise hysteresis). With counter-clockwise hysteresis, rapid reduction of a driver variable following high enrichment rates may be a viable restoration strategy. In ecosystems where hysteresis is counter-clockwise, rapid reduction in a driver variable from high to low levels may be 111 a successful restoration strategy. In contrast, systems that have experienced chronic low-levels of enrichment may exhibit 112 clockwise hysteresis that requires more extreme reductions of the driver variable, or alternative restoration strategies 36 , to 113 restore. doi = 10.1101/2020.05.01.073239 id = cord-102725-k0xhbssu author = Norwood, Jordan N. title = Intranasal Administration of Functionalized Soot Particles Disrupts Olfactory Sensory Neuron Progenitor Cells in the Neuroepithelium date = 2020-08-19 keywords = CSF; olfactory; soot summary = doi = 10.1101/2020.08.19.256297 id = cord-103888-ggm29vrz author = Nova, Nicole title = Susceptible host availability modulates climate effects on dengue dynamics date = 2020-10-19 keywords = dengue; figure summary = By analyzing incidence data, estimated susceptible population size, and climate data with methods based on nonlinear time series analysis (collectively referred to as empirical dynamic modeling), we identified drivers and their interactive effects on dengue dynamics in San Juan, Puerto Rico. By capturing mechanistic, nonlinear, and context-dependent effects of population susceptibility, temperature, and rainfall on dengue transmission empirically, our model improves forecast skill over recent, state-of-the-art models for dengue incidence. Scenario exploration with multivariate EDM allowed us to assess the effect of a 270 small change in temperature or rainfall on dengue incidence, across different states 271 of the system. Compared to 298 the other drivers, the converging cross-mapping skill of the temperature null 299 models were relatively high (Figures 3 and S8 As expected, EDM tests for putative causality in the nonsensical directions-304 incidence driving temperature or rainfall-were not significant (i.e., no convergence; Figure S7 , black lines). doi = 10.1101/2019.12.20.883363 id = cord-103563-7a3wdduq author = Nunez-Bajo, Estefania title = Ultra-Low-Cost Integrated Silicon-based Transducer for On-Site, Genetic Detection of Pathogens date = 2020-03-25 keywords = PCR; dna; figure summary = Unlike other silicon-based technologies, TriSilix can be produced at wafer-scale in a standard laboratory; we have developed a series of methodologies based on metal-assisted chemical (wet) etching, electroplating, thermal bonding and laser-cutting to enable a cleanroom-free low-cost fabrication that does not require processing in an advanced semiconductor foundry. To create an ultra-low-cost device, the architecture proposed exploits the intrinsic properties of silicon and integrates three modes of operation in a single chip: i) electrical (Joule) heater, ii) temperature sensor (i.e. thermistor) with a negative temperature coefficient that can provide the precise temperature of the sample solution during reaction and iii) electrochemical sensor for detecting target NA. Using TriSilix, the sample solution can be maintained at a single, specific temperature (needed for isothermal amplification of NA such as Recombinase Polymerase Amplification (RPA) or cycled between different temperatures (with a precision of ±1.3°C) for Polymerase Chain Reaction (PCR) while the exact concentration of amplicons is measured quantitatively and in real-time electrochemically. doi = 10.1101/2020.03.23.002931 id = cord-291590-24psoaer author = Ogando, Natacha S. title = The enzymatic activity of the nsp14 exoribonuclease is critical for replication of Middle East respiratory syndrome-coronavirus date = 2020-06-20 keywords = Fig; MERS; RNA; SARS summary = In line with such a role, ExoN-knockout mutants of mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus (SARS-CoV) were previously found to have a crippled but viable hypermutation phenotype. Remarkably, using an identical reverse genetics approach, an extensive mutagenesis study revealed the corresponding ExoN-knockout mutants of another betacoronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV), to be non-viable. Our study thus reveals an additional function for MERS-CoV nsp14 ExoN, which apparently is critical for primary viral RNA synthesis, thus differentiating it from the proofreading activity thought to boost long-term replication fidelity in MHV and SARS-CoV. Strikingly, we now established that the equivalent knockout mutants of MERS-CoV ExoN are non-viable and completely deficient in RNA synthesis, thus revealing an additional and more critical function of ExoN in coronavirus replication. doi = 10.1101/2020.06.19.162529 id = cord-103770-4svaq0at author = Ogrodzinski, Martin P. title = Metabolomic profiling of mouse mammary tumor derived cell lines reveals targeted therapy options for cancer subtypes date = 2019-10-07 keywords = EMT summary = title: Metabolomic profiling of mouse mammary tumor derived cell lines reveals targeted therapy options for cancer subtypes Here, we used tumor-derived cell lines derived from the MMTV-Myc mouse model to investigate metabolic pathways that are differentially utilized between two subtypes of breast cancer. To determine metabolic profiles of histologically distinct mouse mammary tumor subtypes, 84 polar metabolites were extracted from tumor-derived cell lines and quantitated using LC-MS/MS. We found metabolites involved in several central carbon metabolic pathways to be differentially 86 abundant between EMT and papillary tumor-derived cell lines (Figure 2 ). In the EMT subtype, both oxidized and reduced forms of glutathione, a key metabolite in 88 redox homeostasis, are elevated ( Figure 2B ). Metabolites 92 increased in the papillary subtype include fructose bisphosphate (FBP; glycolysis); acetyl-CoA indicating relative metabolite differences between EMT and papillary tumor derived cell lines. (B) Representative bar graphs of metabolites with statistically significant differences between EMT and papillary subtypes. doi = 10.1101/796573 id = cord-103174-4m3ajc8a author = Okada, Megan title = Doxycycline has Distinct Apicoplast-Specific Mechanisms of Antimalarial Activity date = 2020-10-16 keywords = DOX; cycle summary = Doxycycline (DOX) is a key antimalarial drug thought to kill Plasmodium parasites by blocking protein translation in the essential apicoplast organelle. Exogenous iron rescues parasites and apicoplast biogenesis from first-but not second-cycle effects of 10 μM DOX, revealing that first-cycle activity involves a metal-dependent mechanism distinct from the delayed-death mechanism. We observed that IPP shifted the 48-hour EC50 value of DOX from 5 ± 1 to 12 ± 2 µM 100 (average ± SD of 5 independent assays, P = 0.001 by unpaired t-test) ( Figure 2C and Figure 2 -101 figure supplement 1), suggesting that first-cycle growth defects from 5-10 µM DOX reflect an 102 apicoplast-specific mechanism but that DOX concentrations >10 µM cause off-target defects 103 outside this organelle. doi = 10.1101/2020.06.11.146407 id = cord-322942-y4zd2oui author = Olagnier, David title = Identification of SARS-CoV2-mediated suppression of NRF2 signaling reveals a potent antiviral and anti-inflammatory activity of 4-octyl-itaconate and dimethyl fumarate date = 2020-07-17 keywords = Fig; NRF2; SARS summary = Further, we uncover that NRF2 agonists 4-octyl-itaconate (4-OI) and the clinically approved dimethyl fumarate (DMF) induce a cellular anti-viral program, which potently inhibits replication of SARS-CoV2 across cell lines. In conclusion, NRF2 agonists 4-OI and DMF induce a distinct IFN-independent antiviral program that is broadly effective in limiting virus replication and suppressing the pro-inflammatory responses of human pathogenic viruses, including SARS-CoV2. Here we demonstrate that expression of NRF2-dependent genes is suppressed in biopsies from 104 COVID-19 patients and that treatment of cells with NRF2 agonists 4-OI and DMF induces a 105 strong anti-viral program that limits SARS-CoV2 replication. Interestingly, when 176 treating Calu3 cells with DMF, another known NRF2 inducer and a clinically approved drug in 177 the first-line-of treatment of multiple sclerosis, we could also observe an anti-viral effect toward 178 SARS-CoV2 replication similar in magnitude as what we had observed with 4-OI (Fig 2p-q) as 179 well as a reduced but significant effect when using Vero cells (Fig. 2r) . doi = 10.1101/2020.07.16.206458 id = cord-280198-bhjw6xc5 author = Olaleye, Omonike A. title = Discovery of Clioquinol and Analogues as Novel Inhibitors of Severe Acute Respiratory Syndrome Coronavirus 2 Infection, ACE2 and ACE2 - Spike Protein Interaction In Vitro date = 2020-08-14 keywords = ACE2; SARS summary = title: Discovery of Clioquinol and Analogues as Novel Inhibitors of Severe Acute Respiratory Syndrome Coronavirus 2 Infection, ACE2 and ACE2 Spike Protein Interaction In Vitro Here in, we discovered Clioquinol (5-chloro-7-iodo-8-quinolinol (CLQ)), a FDA approved drug and two of its analogues (7-bromo-5-chloro-8-hydroxyquinoline (CLBQ14); and 5, 7-Dichloro-8-hydroxyquinoline (CLCQ)) as potent inhibitors of SARS-CoV-2 infection induced cytopathic effect in vitro. In addition, all three compounds showed potent anti-exopeptidase activity against recombinant human angiotensin converting enzyme 2 (rhACE2) and inhibited the binding of rhACE2 with SARS-CoV-2 Spike (RBD) protein. Therefore, targeting 106 the interaction between human ACE2 receptor and the RBD in S protein of SARS-CoV-2 could 107 serve as a promising approach for the development of effective entry inhibitors for potential 108 prevention and/or treatment of COVID-19. Activity of Clioquinol (CLQ) and Analogues against ACE2 Exopeptidase Activity and 725 ACE2 and SARS-CoV-2 Spike (RBD) Protein Interaction doi = 10.1101/2020.08.14.250480 id = cord-255997-oer5lxxr author = Onodi, Fanny title = SARS-CoV-2 induces activation and diversification of human plasmacytoid pre-dendritic cells date = 2020-07-10 keywords = CoV-2; Fig; IFN; SARS summary = Here, we have studied the interaction of isolated primary SARS-CoV-2 viral strains with human plasmacytoid pre-dendritic cells (pDC), a key player in antiviral immunity. Importantly, all major aspects of SARS-CoV-2-induced pDC activation were inhibited by hydroxychloroquine, including P2and P3-pDC differentiation, the expression of maturation markers, and the production of interferon-α and inflammatory cytokines. Interestingly, pDC responded to SARS-CoV-2 by a complete activation program, including diversification into effector subsets, production of type I and type III IFN, as well as inflammatory cytokines. We also showed that hydroxychloroquine, an antimalarial drug proposed for treatment of COVID-19 patients (Das et al., 2020; Mahévas et al., 2020) , inhibits SARS-CoV-2-induced pDC activation and IFN production in a dose-dependent manner. Following 24 hours of culture, we found that HCQ inhibited pDC diversification in response to SARS-CoV-2, which is similar to the decrease observed with Flu, used as a positive control ( Fig 4A) . doi = 10.1101/2020.07.10.197343 id = cord-262119-s6hc7fxs author = Ostaszewski, Marek title = COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms date = 2020-10-27 keywords = ACE2; COVID-19; CoV-2; Coronavirus; Disease; Map; SARS; SBML; cell; pathway; protein summary = title: COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms The molecular pathophysiology that links SARS-CoV-2 infection to the clinical manifestations and course of COVID-19 is complex and spans multiple biological pathways, cell types and organs [2, 3] . With this goal in mind, we initiated a collaborative effort involving over 230 biocurators, domain experts, modelers and data analysts from 120 institutions in 30 countries to develop the COVID-19 Disease Map, an open-access collection of curated computational diagrams and models of molecular mechanisms implicated in the disease [4] . The COVID-19 Disease Map diagrams, available in layout-aware systems biology formats and integrated with external repositories, are available in several formats allowing a range of computational analyses, including network analysis and Boolean, kinetic or multiscale simulations. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms doi = 10.1101/2020.10.26.356014 id = cord-342015-bz2vab6e author = Ouadfeul, Sid-Ali title = Multifractal Analysis of SARS-CoV-2 Coronavirus genomes using the wavelet transform date = 2020-08-16 keywords = dna summary = In this paper, the 1D Wavelet Transform Modulus Maxima lines (WTMM) method is used to investigate the Long-Range Correlation (LRC) and to estimate the so-called Hurst exponent of 21 isolate RNA sequence downloaded from the NCBI database of patients infected by SARS-CoV-2, Coronavirus, the Knucleotidic, Purine, Pyramidine, Ameno, Keto and GC DNA coding are used. Arneodo et al (1996) published a paper deals with the study of the Long-Range Correlation (LRC) character of DNA sequences using the 1D continuous wavelet transform method. Audit et al (2004) published a paper deals with wavelet Analysis of DNA bending profiles reveals structural constraints on the evolution of genomic sequences, Voss (1996) published a paper deals with the evolution of Long-Range fractal correlations and 1/f noise in DNA base sequences. In this paper the 1D Wavelet Transform Modulus Maxima Lines (WTMM) method is used to demonstrate the monofractal behavior of SARS-CoV-2 RNA sequences downloaded from the NCBI database and to estimate the so-called Hurst exponent, the goal is to investigate the LRC character in these sequences. doi = 10.1101/2020.08.15.252411 id = cord-277648-9kxwkcbl author = Overholt, Kalon J. title = Dissecting the common and compartment-specific features of COVID-19 severity in the lung and periphery with single-cell resolution date = 2020-06-19 keywords = ARDS; BALF; cell; covid-19; figure summary = Bulk RNA sequencing (bulk RNA-seq) and single-cell RNA sequencing (scRNA-seq) studies have identified stark transcriptional differences between bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cell (PBMC) samples in hospitalized COVID-19 patients, indicating that immunological responses may be highly compartment-specific [21, 22] . We used identical methods to separately analyze multi-donor scRNA-seq datasets from bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells (PBMCs) in COVID-19 patients classified by severity strata as well as healthy control subjects to investigate severity-specific immune dysregulation in the lung and periphery. When we increased this analysis to include all of the cell types found in the BALF (Figure 3A We next investigated pathway-level changes occurring in PBMCs and found that differential gene expression between ARDS and non-ARDS patients supported the detection of statistically enriched pathways through GSEA. doi = 10.1101/2020.06.15.147470 id = cord-339772-q814d6l7 author = Pach, Szymon title = ACE2-Variants Indicate Potential SARS-CoV-2-Susceptibility in Animals: An Extensive Molecular Dynamics Study date = 2020-05-14 keywords = ACE2; SARS summary = To investigate the reason for the variable susceptibility observed in different species, we have developed molecular descriptors to efficiently analyze our dynamic simulation models of complexes between SARS-CoV-2 S and ACE2. Moreover, we compared ACE2 sequences from rodents (mouse, rat, hamster, and red squirrel) to sample additional binding pockets in the ACE2-RBD interface and predict susceptibility to SARS-CoV-2 of the red squirrel (Sciurus vulgaris). To compare three-dimensional binding interfaces of animal ACE2-RBD complexes, we developed homology models of dog, cat, ferret, hamster, mouse, rat, and red squirrel proteins. Both outlier residues are located on flexible loops of ACE2 distal to the S binding site and represent polymorphic mutations from glycine in human crystal structure to serine in homology models. Based on known susceptibility of animal species to SARS-CoV-2 and the comparison of MD trajectories, we were able to develop models for prediction of RBD binding to ACE2. doi = 10.1101/2020.05.14.092767 id = cord-273083-xrydkiu4 author = Pahmeier, Felix title = A versatile reporter system to monitor virus infected cells and its application to dengue virus and SARS-CoV-2 date = 2020-09-01 keywords = SARS summary = Here, we describe the generation and characterization of a reporter system to visualize dengue virus and SARS-CoV-2 replication in live cells. The system is based on viral protease activity causing cleavage and nuclear translocation of an engineered fluorescent protein that is expressed in the infected cells. Here we describe a reporter system that takes advantage of virus-encoded proteases that are expressed in infected cells to cleave an ER-anchored fluorescent protein fused to a nuclear localization sequence. Using this system, we demonstrate reliable reporting activity for two major human pathogens from the Flaviviridae and the Coronaviridae families: dengue virus and SARS-CoV-2. In order to generate a reporter system that can specifically indicate virus infection, we 219 designed a construct expressing a GFP fusion protein that could selectively be cleaved 220 by viral proteases. However, since no fluorescent 304 protein coding sequence is incorporated into the construct, expression of the DENV 305 polyprotein cannot be followed by live cell imaging. doi = 10.1101/2020.08.31.276683 id = cord-254772-1xzkfl8g author = Pandolfi, Laura title = Neutrophil extracellular traps induce the epithelial-mesenchymal transition: implications in post-COVID-19 fibrosis date = 2020-11-09 keywords = EMT; Fig; Neu; PMA summary = Bronchoalveolar lavage fluid of severe COVID-19 patients showed high concentration of NETs. Thus, we tested in an in vitro alveolar model the hypothesis that virus-induced NET may drive EMT. Co-culturing A549 at air-liquid interface with alveolar macrophages, neutrophils and SARS-CoV2, we demonstrated a significant induction of the EMT in A549 together with high concentration of NETs, IL8 and IL1β, best-known inducers of NETosis. Because of the high levels of NETs in the BAL of COVID-19 patients and their potential role in inducing the EMT, we next focused on the correlation between NETs and the EMT by setting up an in vitro alveolar model that we infected with SARS-CoV-2. In particular, we would like to propose a model in which macrophages, by releasing IL8 and IL1β, two cytokines significantly increased in the plasma (32, 33) and BAL-fluid of severe COVID-19 patients (14), potentiate the capacity of NETs released by Neu to amplify the noxious activity on lung cells, favoring the EMT. doi = 10.1101/2020.11.09.374769 id = cord-284045-scd3f8vk author = Pape, Constantin title = Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera date = 2020-10-07 keywords = ELISA; Fig; SARS; cell summary = Here we describe the development of a semi-quantitative high-content microscopy-based assay for detection of three major classes (IgG, IgA and IgM) of SARS-CoV-2 specific antibodies in human samples. The possibility to detect antibodies against the entire viral proteome together with a robust semi-automated image analysis workflow resulted in specific, sensitive and unbiased assay which complements the portfolio of SARS-CoV-2 serological assays. The dsRNA co-localizing pattern 213 observed for sera from the negative control cohort is by definition non-specific for SARS-CoV-2, 214 but would be classified as a positive hit based on staining intensity alone. The high information content of the IF data (differential staining patterns) 363 together with a machine learning-based approach [45] and the implementation of stable cell lines 364 expressing selected viral antigens in the IF assay will provide additional parameters for 365 classification of patient sera and further improve sensitivity and specificity of the presented IF 366 assay. doi = 10.1101/2020.06.15.152587 id = cord-309411-2dfiwo65 author = Paris, Kristina A. title = Loss of pH switch unique to SARS-CoV2 supports unfamiliar virus pathology date = 2020-06-23 keywords = ACE2; Fig; RBD; SARS summary = On the other hand, the loss of this pH-switch, which sequence alignments show is unique to CoV2, eliminates the transition state and allows the virus to stay bound to the ACE2 receptor for time scales compatible with the recruitment of additional ACE2 receptors diffusing in the cell membrane. Work on SARS-CoV (CoV1) has already determined that the virus enters cells via receptormediated endocytosis in a pH-dependent manner (Wang et al., 2008) that is characterized by cotranslocation of the viral spike glycoprotein and its specific functional receptor, the angiotensinconverting enzyme 2 (ACE2), from the cell surface to early endosomes. This newly discovered difference in protein sequence in the receptor binding domain of the spike glycoprotein and its impact on receptor binding reveals a mechanism that allows SARS-CoV2 internalization to take advantage of the high expression of ACE2 in the nasal epithelium¾resulting in increased retention times in the upper respiratory tract and augmented infectivity. doi = 10.1101/2020.06.16.155457 id = cord-318253-vp22xd8p author = Parisi, Ortensia Ilaria title = “Monoclonal-type” plastic antibodies for SARS-CoV-2 based on Molecularly Imprinted Polymers date = 2020-05-28 keywords = SARS summary = Our idea is focused on the development of "monoclonal-type" plastic antibodies based on Molecularly Imprinted Polymers (MIPs) able to selectively bind a portion of the novel coronavirus SARS-CoV-2 spike protein to block its function and, thus, the infection process. In the present study, the developed imprinted polymeric nanoparticles were characterized in terms of particles size and distribution by Dynamic Light Scattering (DLS) and the imprinting effect and selectivity were investigated by performing binding experiments using the receptor-binding domain (RBD) of the novel coronavirus and the RBD of SARS-CoV spike protein, respectively. In this context, our idea is to develop "monoclonal-type" plastic antibodies based on Molecularly Imprinted Polymers (MIPs) for the selective recognition and binding of the RBD of the novel coronavirus SARS-CoV-2 in the aim to block the function of its spike protein (Figure 1.) . doi = 10.1101/2020.05.28.120709 id = cord-347441-8ow952d8 author = Parvez, Md Sorwer Alam title = Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: insights into the origin, mutation spectrum, and possible pathomechanism date = 2020-06-07 keywords = SARS summary = title: Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: insights into the origin, mutation spectrum, and possible pathomechanism Molecular docking analysis to evaluate the effect of the mutations on the interaction between the viral spike proteins and the human ACE2 receptor, though no significant interaction was observed. This study provides some preliminary insights into the origin of Bangladeshi SARS-CoV-2 isolates, mutation spectrum and its possible pathomechanism, which may give an essential clue for designing therapeutics and management of COVID-19 in Bangladesh. As many of the Bangladeshi people return during the COVID-19 39 outbreak mainly from China, India, Saudi Arabia, Spain, Italy, Japan, Qatar, Canada, Kuwait, USA, 40 France, Sweden, and Switzerland, the first deposited genome sequence of those countries were also 41 retrieved. In total, three models were generated using the template PDB ID: 6VSB; one model for the spike protein 118 of reference strain, and the two others were for two different mutant isolates from Bangladesh (Fig 3) . doi = 10.1101/2020.06.07.138800 id = cord-339665-nwwutduy author = Patel, Ami title = Intradermal-delivered DNA vaccine provides anamnestic protection in a rhesus macaque SARS-CoV-2 challenge model date = 2020-07-29 keywords = COVID-19; CoV-2; SARS summary = Prior work with the related coronaviruses, SARS-CoV and MERS-CoV, delineated that the Spike protein of these viruses was an important target for development of neutralizing antibodies, and in animal viral challenges vaccine targeted immunity (reviewed in (Du et al., 2009; Roper and Rehm, 2009; Thanh Le et al., 2020) (Liu et al., 2018; Muthumani et al., 2015; van Doremalen et al., 2020a) . These memory titers were comparable to those observed in other reported protection studies in macaques performed at the acute phase of the vaccine-induced immune response (Gao et al., 2020; van Doremalen et al., 2020b; Yu et al., 2020) and those reported in the sera of convalescent patients (Ni et al., 2020; Robbiani et al., 2020) . Our study and other published reports show that DNA vaccination with candidates targeting the full-length SARS-CoV-2 spike protein likely increase the availability of T cell immunodominant epitopes leading to a broader and more potent immune response, compared to partial domains and truncated immunogens. doi = 10.1101/2020.07.28.225649 id = cord-102976-cic1gxrk author = Patel, Roosheel S. title = Single cell resolution landscape of equine peripheral blood mononuclear cells reveals diverse immune cell subtypes including T-bet+ B cells date = 2020-05-07 keywords = Fig; PBMC; cell; seq summary = Single cell RNA-Sequencing (scRNA-Seq) offers an alternative to flow cytometry as it defines different cell types (and their functional states) by gene expression patterns rather than surface marker expression. To characterize equine PBMC at high resolution and establish a corresponding peripheral blood immune cell atlas, we independently analyzed scRNA-Seq data for the constituent clusters of each major cell group, except Basophils due to the low number of cells. Additional genes with significantly elevated expression levels in cluster 28 include NR4A1 (transcription factor necessary for differentiation of non-classical monocytes in mice) (23) , CX3CR1 (chemokine receptor characteristic of nonclassical monocytes in humans and mice) (24, 25) , and HES4 (target of NOTCH signaling implicated in non-classical monocyte generation) (26) (Fig. 2E ). To further support our cell type annotations and assess potential differences in monocyte/DC subsets between horses and humans, we performed cross-species hierarchical clustering with a human PBMC public reference scRNA-Seq data set ( Fig. S2A-B, Fig. 2G ). doi = 10.1101/2020.05.05.077362 id = cord-259246-azt5sr9w author = Peng, Qi title = Structural basis of SARS-CoV-2 polymerase inhibition by Favipiravir date = 2020-10-19 keywords = Favipiravir; Fig; RNA summary = This structure provides a missing snapshot for visualizing the catalysis dynamics of coronavirus polymerase, and reveals an unexpected base-pairing pattern between Favipiravir and pyrimidine residues which may explain its capacity for mimicking both adenine and guanine nucleotides. Recently, we and other groups have determined the structures of SARS-CoV-2 core polymerase complex in both apo and RNA-bound states 26-30 , providing important information for structure-based antiviral drug design. Similar observations were also reported recently that SARS-CoV-2 polymerase is more tolerant for mismatches between template and product residues than other viral RdRps 5 , which further highlights the requirement for the proofreading nuclease nsp14 to maintain the integrity of viral genome. Interestingly, Favipiravir could be incorporated into the RNA product with similar efficiencies to those of ATP or GTP substrates guided by U or C template residues, respectively (Fig. 1c) . doi = 10.1101/2020.10.19.345470 id = cord-280994-w8dtfjel author = Peng, Qi title = Structural and biochemical characterization of nsp12-nsp7-nsp8 core polymerase complex from COVID-19 virus date = 2020-04-23 keywords = RNA; SARS; polymerase summary = Here, we describe the near-atomic resolution structure of its core polymerase complex, consisting of nsp12 catalytic subunit and nsp7-nsp8 cofactors. This structure highly resembles the counterpart of SARS-CoV with conserved motifs for all viral RNA-dependent RNA polymerases, and suggests the mechanism for activation by cofactors. Biochemical studies revealed reduced activity of the core polymerase complex and lower thermostability of individual subunits of COVID-19 virus as compared to that of SARS-CoV. Simultaneous 193 replacement of the nsp7 and nsp8 cofactors further enhanced the efficiency for RNA synthesis 194 to ~2.2 times of that for the SARS-CoV-2 homologous complex ( Figure 4B ). After 3 rounds of extensive 2D classification, ~924,000 particles 437 were selected for 3D classification with the density map of SARS-CoV nsp12-nsp7-nsp8 438 complex (EMDB-0520) as the reference which was low-pass filtered to 60 Å resolution. One severe acute respiratory syndrome 631 coronavirus protein complex integrates processive RNA polymerase and exonuclease activities doi = 10.1101/2020.04.23.057265 id = cord-293274-ysr1l557 author = Perisé-Barrios, Ana Judith title = Humoral response to SARS-CoV-2 by healthy and sick dogs during COVID-19 pandemic in Spain date = 2020-09-22 keywords = CoV-2; SARS; dog summary = Infection of animals with SARS-CoV-2 are being reported during last months, and also an increase of severe lung pathologies in domestic dogs has been detected by veterinarians in Spain. Infection of animals with SARS-CoV-2 are being reported during last months, and also an increase of severe lung pathologies in domestic dogs has been detected by veterinarians in Spain. Here we report that despite detecting dogs with IgG α-SARS-CoV-2, we never obtained a positive RT-qPCR, not even in dogs with severe pulmonary disease; suggesting that even in the case of a canine infection transmission would be unlikely. Here we report that despite detecting dogs with IgG α-SARS-CoV-2, we never obtained a positive RT-qPCR, not even in dogs with severe pulmonary disease; suggesting that even in the case of a canine infection transmission would be unlikely. doi = 10.1101/2020.09.22.308023 id = cord-102219-d3gkfo7s author = Perzel Mandell, Kira A. title = Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex date = 2019-10-30 keywords = dna; figure; gene; methylation summary = In the present report, we describe the use of whole genome bisulfite sequencing (WGBS) to capture an unbiased map of the DNAm landscape, and to characterize both CpG and CpH methylation during prenatal brain development. We performed whole genome bisulfite sequencing (WGBS) to better characterize the shifting DNAm landscape in the developing human dorsolateral prefrontal cortex (DLPFC) in 20 prenatal samples during the second trimester in utero (Table S1 ). We found that DNAm changes were abundant even during this relatively restricted period in prenatal development, with 36,546 CpG sites differentially methylated across the ages of 14-20 post-conception weeks (PCW, at FDR < 0.05, Table S3 ). The top biological processes associated with genes containing differentially methylated CpGs across age were related to axon development and guidance, and regulation of neuron projection ( Figure S4 , Table S8 ). doi = 10.1101/823781 id = cord-353911-hp6s6ebh author = Petráš, Marek title = Early immune response in mice immunized with a semi-split inactivated vaccine against SARS-CoV-2 containing S protein-free particles and subunit S protein date = 2020-11-03 keywords = SARS; vaccine summary = title: Early immune response in mice immunized with a semi-split inactivated vaccine against SARS-CoV-2 containing S protein-free particles and subunit S protein Our aim was to design a semi-split inactivated vaccine offering a wide range of multi-epitope determinants important for the immune system including not only the spike (S) protein but also the envelope, membrane and nucleocapsid proteins. The above laboratory procedure generated a semi-split inactivated vaccine, i.e., a vaccine with 307 the S protein separated from the viral particle exhibiting an early, both humoral and cellular, 308 immune response. Safety and immunogenicity of the ChAdOx1 nCoV-386 19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, 387 randomised controlled trial An in-depth investigation of the safety and immunogenicity of an 468 inactivated SARS-CoV-2 vaccine A double-inactivated 499 whole virus candidate SARS coronavirus vaccine stimulates neutralising and 500 protective antibody responses. Inactivated Vaccine Against SARS-CoV-2 on Safety and Immunogenicity 526 doi = 10.1101/2020.11.03.366641 id = cord-349684-2tioh80m author = Pezzotti, Giuseppe title = Rapid Inactivation of SARS-CoV-2 by Silicon Nitride, Copper, and Aluminum Nitride date = 2020-06-20 keywords = Fig; Nitride; RNA; SARS; Si3N4 summary = The present study compared the effects of exposing SARS-CoV-2 to aqueous suspensions of Si3N4 and aluminum nitride (AlN) particles and two controls, (i.e., a suspension of copper (Cu) particles (positive control) and a sham treatment (negative control)). In (c) and (d), results of RT-PCR tests for supernatants after 10 min exposure of virus suspension to Cu, AlN, and Si3N4 powders for viral N gene "set 1" and "set 2" primers are shown, respectively. The present work is the first to show that compounds capable of endogenous nitrogen-release, such as Si3N4 and AlN, can inactivate the SARS-CoV-2 virus at least as effectively as Cu. These results suggest that multiple antiviral mechanisms may be operative, such as RNA fragmentation, and in the case of Cu, direct metal ion toxicity; but while Cu and AlN supernatants demonstrated strong and partial cellular lysis, respectively, Si3N4 provoked no metabolic alterations. doi = 10.1101/2020.06.19.159970 id = cord-104161-jvbgouv8 author = Pfrieger, Frank W. title = Insight into the workforce advancing fields of science and technology date = 2020-06-02 keywords = Fig; TTA; team summary = Context-specific, but citation-independent metrics gauge team impact and reveal key contributors valuing publication output, mentorship and collaboration. Based on scientific articles related to a specific topic, this approach reveals instantly the teams working in a research field, visualizes workforce growth, delineates family and collaborative connections and gauges team performance in a citation-independent manner. A PubMed query using the term "circadian clock" (Clock) yielded a list of articles published between 1960 and 2020, from which TTA identified principal investigators (PIs)/teams working in the field based on last author names (Table 1 ; Supplementary Data 1). The Clock field expanded steadily in terms of workforce and of publication output as indicated by annual counts of newly entering teams and of published articles, respectively (Fig. 1A) . Individual PIs/teams published up to 113 articles (PC, publication count) as last authors (Last) with a maximum annual output of nearly 7 papers per year. doi = 10.1101/2020.06.01.128355 id = cord-103830-pu6v53oy author = Pichon, Fabien title = Analysis and annotation of genome-wide DNA methylation patterns in two nonhuman primate species using the Infinium Human Methylation 450K and EPIC BeadChips date = 2020-05-10 keywords = Infinium; dna; probe summary = In the present study, we evaluated the use of the Infinium 450K and Infinium EPIC BeadChips for genome-wide DNA methylation analyses in samples from Chlorocebus sabaeus and Macaca mulatta and conducted an in-depth analysis of the available probes for these two old world monkey genomes. We provide for each species and each microarray a list of annotated probes that can be used by the scientific community for genome-wide DNA methylation studies in Chlorocebus sabaeus or Macaca mulatta. We then mapped all the 50 bp probe sequences targeting CpG positions in the human genome from the Infinium 450K and EPIC arrays to Chlorocebus sabaeus (CS) and Macaca mulatta (MM) genomes, consecutively, using Bowtie [39], allowing only a unique position on the respective genome and up to 3 mismatches. doi = 10.1101/2020.05.09.081547 id = cord-275173-ely3aen3 author = Pickering, Brad S. title = Susceptibility of domestic swine to experimental infection with SARS-CoV-2 date = 2020-09-10 keywords = DPI; SARS summary = The work reported here aims to determine whether domestic swine are susceptible to 63 SARS-CoV-2 infection, providing critical information to aid public health risk assessments. The data presented in 66 this study provides evidence live SARS-CoV-2 virus can persist in swine for at least 13 days 67 following experimental inoculation. Two pigs (20-10, 20-11) displayed low 237 levels of viral RNA by RT-qPCR at 3 DPI (Table 2, Detection of SARS-CoV-2 was also attempted from whole blood by RT-qPCR, following 253 the sampling schedule outlined in Table 1 . To identify potential target tissues or gross lesions consistent with SARS-CoV-2 disease, 261 necropsy was performed on two animals starting at 3 DPI and every other day up to day 15; with 262 an additional two pigs necropsied at both 22 and 29 DPI (Table 1) (Table 2) . The results presented in this study define domestic swine as a susceptible species albeit at 293 low levels to SARS-CoV-2 viral infection. doi = 10.1101/2020.09.10.288548 id = cord-261718-zqoggwnk author = Pietschmann, Jan title = Brief Communication: Magnetic Immuno-Detection of SARS-CoV-2 specific Antibodies date = 2020-06-03 keywords = CoV-2; SARS summary = Available point-of-care diagnostic systems as lateral flow assays have high potential for fast and easy on-site antibody testing but are lacking specificity, sensitivity or possibility for quantitative measurements. Here, a new point-of-care approach for SARS-CoV-2 specific antibody detection in human serum based on magnetic immuno-detection is described and compared to standard ELISA. For magnetic immuno-detection, immunofiltration columns were coated with a SARS-CoV-2 spike protein peptide. After addition of 176 biotinylated GaR and subsequent labelling with streptavidin-AP, the ELISA plate was read out at 177 405 nm and obtained measuring values were used to generate calibration curves for SARS-CoV-2 178 specific antibody concentrations in PBS (Fig 1, black curve) and in human serum samples (Fig 1, red 179 curve). Same calibration measurements employing dilutions of SARS-CoV-2 specific antibody were 211 done with our PoC MInD-based setup (Fig 2 and 3) . Comparable to laboratory-based ELISA, the same 212 dilutions of SARS-CoV-2 spike protein peptide specific antibody in PBS-buffer (Fig 3, black doi = 10.1101/2020.06.02.131102 id = cord-262958-tmp6yxlv author = Pinto, Dora title = Structural and functional analysis of a potent sarbecovirus neutralizing antibody date = 2020-04-09 keywords = CoV-2; S309; SARS summary = The SARS-CoV-2 spike (S) glycoprotein 26 promotes entry into host cells and is the main target of neutralizing antibodies. None of the mAbs studied bound to 97 prefusion OC43 S or MERS-CoV S ectodomain trimers, indicating a lack of cross-98 reactivity outside the sarbecovirus subgenus (Extended Data Fig.1) . The structural data explain the S309 cross-reactivity between SARS-CoV-2 and 148 SARS-CoV as 19 out of 24 residues of the epitope are strictly conserved ( Fig. 2f and 149 Extended Data Fig. 6a To further investigate the mechanism of S309-mediated neutralization, we 175 compared side-by-side transduction of SARS-CoV-2-MLV in the presence of either 176 S309 Fab or S309 IgG. This analysis 208 identified at least four antigenic sites within the S B domain of SARS-CoV targeted by 209 our panel of mAbs. The receptor-binding motif, which is targeted by S230, S227 and 210 S110, is termed site I. doi = 10.1101/2020.04.07.023903 id = cord-313247-55loucvc author = Pipes, Lenore title = Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny date = 2020-10-07 keywords = SARS summary = We investigate several different strategies for rooting the SARS-CoV-2 tree and provide measures of statistical uncertainty for all methods. Our results suggest that inferences on the origin and early spread of SARS-CoV-2 based on rooted trees should be interpreted with caution. There are many different methods for inferring the root of a phylogenetic tree, but they largely depend on three possible sources of information: outgroups, the molecular clock, and non-reversibility. To investigate the possible rootings of the SARS-CoV-2 phylogeny we used six different methods and quantified the uncertainty in the placement of the root for each method on the inferred maximum likelihood topology. We note that while interpretation of bootstrap proportions in phylogenetics can be problematic (see Efron et al., 1996) we performed 1,000 parametric simulations using pyvolve (Spielman and Wilke, 2015) using maximum likelihood estimates, from the original data set, of the model of molecular evolution and the phylogenetic tree, including branch lengths (see Table S2 ). doi = 10.1101/2020.06.19.160630 id = cord-272626-bw9lbzvt author = Pizzorno, Andrés title = Characterization and treatment of SARS-CoV-2 in nasal and bronchial human airway epithelia date = 2020-04-02 keywords = Fig; HAE; SARS summary = Here, we advantageously used human reconstituted airway epithelial models of nasal or bronchial origin to characterize viral infection kinetics, tissue-level remodeling of the cellular ultrastructure and transcriptional immune signatures induced by SARS-CoV-2. Developed from biopsies of nasal or bronchial cells differentiated in the air/liquid interphase, these models reproduce with high fidelity most of the main structural, functional and innate immune features of the human respiratory epithelium that play a central role 70 in the early stages of infection and constitute robust surrogates to study airway disease mechanisms and for drug discovery (10) . Comparably, daily treatment with 20 µM remdesivir resulted in 7.3 log10 and 7.9 log10 reductions of intracellular SARS-CoV-2 viral titers at 48 hpi in nasal and bronchial HAE, respectively (Fig. 4D, upper panel) . doi = 10.1101/2020.03.31.017889 id = cord-287205-k64svq6n author = Pollet, Jeroen title = SARS-CoV-2 RBD219-N1C1: A Yeast-Expressed SARS-CoV-2 Recombinant Receptor-Binding Domain Candidate Vaccine Stimulates Virus Neutralizing Antibodies and T-cell Immunity in Mice date = 2020-11-05 keywords = Alhydrogel; RBD; RBD219-N1C1; SARS summary = title: SARS-CoV-2 RBD219-N1C1: A Yeast-Expressed SARS-CoV-2 Recombinant Receptor-Binding Domain Candidate Vaccine Stimulates Virus Neutralizing Antibodies and T-cell Immunity in Mice Here we report on the development of a SARS-CoV-2 receptor-binding domain (RBD) protein, expressed at high levels in yeast (Pichia pastoris), as a suitable vaccine candidate against COVID-19. The modified SARS-CoV-2 antigen, 264 RBD219-N1C1, when formulated on Alhydrogel ® , was shown to induce virus-neutralizing antibodies 265 in mice, equivalent to those levels elicited by the wild-type (RBD219-WT) recombinant protein 266 counterpart. Here we report on a yeast-expressed SARS-CoV-2 RBD219-N1C1 protein and its potential as a 397 vaccine candidate antigen for preventing COVID-19. In a mouse virus challenge model for the SARS CoV RBD recombinant protein vaccine, we 422 found that Alhydrogel ® formulations induced high levels of protective immunity but did not 423 stimulate eosinophilic immune enhancement, suggesting that Alhydrogel ® may even reduce immune The selection of the P. doi = 10.1101/2020.11.04.367359 id = cord-310477-vniokol0 author = Pontes, Camila title = Unraveling the molecular basis of host cell receptor usage in SARS-CoV-2 and other human pathogenic β-CoVs date = 2020-08-21 keywords = ACE2; SARS; Sarbecovirus summary = More precisely, our results indicate that host cell receptor usage is encoded in the amino acid sequences of different CoV spike proteins in the form of a set of specificity determining positions (SDPs). In summary, the SDPs found within these β-CoV subgenera define a specific region of the receptor binding domains: they are part of, or in direct contact with, the ACE2 interacting surface ( A second S3Det analysis was performed on the full β-CoV MSA. On the other hand, the analysis performed on individual β-CoV subgenera, i.e. Sarbecovirus, Merbecovirus and Embecovirus subgroups, allowed a fine-grained classification into subfamily clusters that clearly reflect the functional diversification of the spike protein family, that is, the specificity to different host-cell receptors (Figure 2-3) . doi = 10.1101/2020.08.21.260745 id = cord-310017-c8rd714a author = Popa, Alexandra title = Mutational dynamics and transmission properties of SARS-CoV-2 superspreading events in Austria date = 2020-07-17 keywords = CoV-2; Fig; SARS; austrian; mutation summary = Moreover, we combined our deep viral genome sequencing data with epidemiologically identified chains of transmissions and family clusters together with biomathematical analyses to study genetic bottlenecks and the dynamics of genome evolution of SARS-CoV-2. We assembled SARS-CoV-2 genome sequences, constructed phylogenies and identified low 15 frequency mutations based on high-quality sequencing results with >5 million reads per sample and >80% of mapped viral reads (Fig. S2A-B) . Our pipeline was validated by experimental controls involving sample titration and technical sample replicates ( Fig. S2CTo investigate the link between local outbreaks in Austria and the global pandemic, we 20 performed phylogenetic analysis of 305 SARS-CoV-2 genomes from the Austrian cases (>96% genome coverage, >80% aligned viral reads) and 7,695 global genomes from the GISAID database (Fig. 1B, Table S1 ). 7 Dynamics of low frequency and fixed mutations in clusters Next, we sought to gain insights into the fundamental processes of SARS-CoV-2 infection by integrative analysis of viral genomes. doi = 10.1101/2020.07.15.204339 id = cord-325610-n3zb36am author = Postlethwait, John H. title = An intestinal cell type in zebrafish is the nexus for the SARS-CoV-2 receptor and the Renin-Angiotensin-Aldosterone System that contributes to COVID-19 comorbidities date = 2020-09-02 keywords = Ang; Angiotensin summary = title: An intestinal cell type in zebrafish is the nexus for the SARS-CoV-2 receptor and the Renin-Angiotensin-Aldosterone System that contributes to COVID-19 comorbidities To exploit zebrafish (Danio rerio) as a disease model to understand mechanisms regulating the RAAS and its relationship to COVID-19 comorbidities, we must first identify zebrafish orthologs and co-orthologs of human RAAS genes, and second, understand where and when these genes are expressed in specific cells in zebrafish development. Results further identified a specific intestinal cell type in zebrafish larvae as the site of expression for key RAAS components, including Ace, Ace2, the coronavirus co-receptor Slc6a19, and the Angiotensin-related peptide cleaving enzymes Anpep and Enpep. These results identify specific genes and cell types to exploit zebrafish as a disease model for understanding the mechanisms leading to COVID-19 comorbidities. SUMMARY STATEMENT Genomic analyses identify zebrafish orthologs of the Renin-Angiotensin-Aldosterone System that contribute to COVID-19 comorbidities and single-cell transcriptomics show that they act in a specialized intestinal cell type. doi = 10.1101/2020.09.01.278366 id = cord-273882-tqdcb3oo author = Pratibha, title = Ubiquitous Forbidden Order in R-group classified protein sequence of SARS-CoV-2 and other viruses date = 2020-08-21 keywords = SARS; figure summary = title: Ubiquitous Forbidden Order in R-group classified protein sequence of SARS-CoV-2 and other viruses We report here a novel method of species characterization based upon the order of these R-group classified amino acids in the linear sequence of the side chains associated with the codon triplets. These ubiquitous forbidden orders (UFO) are unique structures of the viruses that may provide an insight into viruses'' chemical behavior and the folding patterns of the proteins. Next, we analyzed protein sequences of 26 viruses (Figures 2, 3 , and Supplementary Figures 1 -4) to search for a ubiquitous forbidden order in each one of them. Among the 26 viruses studied, we noted that the forbidden order BPAB is unique to SARS CoV-2, Rubella, and Avian IB (Figure 3) . We found that at R-group classified sequences of N, B, A, and P in these two samples are identical up to level 4 of the amino acid ordering in the protein structures (Figures 4a, d, g) . doi = 10.1101/2020.08.21.261289 id = cord-258914-g6pv8zz9 author = Proud, Pamela C. title = Prophylactic intranasal administration of a TLR2 agonist reduces upper respiratory tract viral shedding in a SARS-CoV-2 challenge ferret model date = 2020-09-25 keywords = CoV-2; SARS summary = title: Prophylactic intranasal administration of a TLR2 agonist reduces upper respiratory tract viral shedding in a SARS-CoV-2 challenge ferret model We show that prophylactic intra-nasal administration of the TLR2/6 agonist INNA-051 in a SARS-CoV-2 ferret infection model effectively reduces levels of viral RNA in the nose and throat. The results of our study support clinical development of a therapy based on prophylactic TLR2/6 innate immune activation in the URT to reduce SARS-CoV-2 transmission and provide protection against COVID-19. The TLRs are key microbe-recognition receptors with a crucial role in 97 activation of host defence and protection from infections and therefore attractive drug 98 targets against infectious diseases [12] [13] [14] To determine whether TLR2/6 agonists are also active against SARS-CoV-2, we used In life samples were taken at days 1, 3, 5, 7, 10 and 12, with scheduled culls at days 137 3 (n=6) and end of study days 12-14 (n=18) (Fig 1A) . doi = 10.1101/2020.09.25.309914 id = cord-255791-ghrlj6b2 author = Pruijssers, Andrea J. title = Remdesivir potently inhibits SARS-CoV-2 in human lung cells and chimeric SARS-CoV expressing the SARS-CoV-2 RNA polymerase in mice date = 2020-04-27 keywords = EC50; Fig; RDV; SARS summary = doi = 10.1101/2020.04.27.064279 id = cord-275252-4e3cn50u author = Rad SM, Ali Hosseini title = Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting date = 2020-05-16 keywords = CoV-2; RNA; SARS; mutation summary = In addition to amino acid changes, mutations could affect RNA secondary structure critical to viral life cycle, or interfere with sequences targeted by host miRNAs. We have analysed subsets of genomes from SARS-CoV-2 isolates from around the globe and show that several mutations introduce changes in Watson-Crick pairing, with resultant changes in predicted secondary structure. The impact of these and further mutations on secondary structures, miRNA targets or potential splice sites offers a new context in which to view future SARS-CoV-2 evolution, and a potential platform for engineered viral attenuation and antigen presentation. A common primary focus of mutational analysis of emerging viruses is the alteration in amino acid sequence of viral proteins that may provide enhanced or new functions for virus replication, immune avoidance, or spread. However, the potential of these mutations to impact upon RNA structure and miRNA recognition provides a basis for ongoing monitoring of viral evolution at these sites in the SARS-CoV-2 genome. doi = 10.1101/2020.05.15.098947 id = cord-311114-ggcpsjk8 author = Radhakrishnan, Chandni title = Initial insights into the genetic epidemiology of SARS-CoV-2 isolates from Kerala suggest local spread from limited introductions date = 2020-09-09 keywords = CoV-2; India; Kerala; SARS summary = The rapid increase in the COVID-19 cases in the state of Kerala has necessitated the understanding of the genetic epidemiology of circulating virus, evolution, and mutations in SARS-CoV-2. The analysis identified 166 unique high-quality variants encompassing 4 novel variants and 89 new variants identified for the first time in SARS-CoV-2 samples isolated from India. Phylogenetic and haplotype analysis revealed that the circulating population of the virus was dominated (94.6% of genomes) by three distinct introductions followed by local spread, apart from identifying polytomies suggesting recent outbreaks. Further analysis of the functional variants revealed two variants in the S gene of the virus reportedly associated with increased infectivity and 5 variants that mapped to five primer/probe binding sites that could potentially compromise the efficacy of RT-PCR detection. In our analysis, we mapped the SARS-CoV-2 genetic variants obtained from Kerala genomes to the 132 primer or probes sequence and calculated the melting temperature (Tm) of the mutant with the wild type sequence. doi = 10.1101/2020.09.09.289892 id = cord-103683-xcsal8vk author = Rafie, K. title = The structure of enteric human adenovirus 41 - a leading cause of diarrhea in children date = 2020-10-16 keywords = F41; Fig; HAdV; Supplementary summary = The structure also provides new insights into conserved aspects of HAdV architecture such as a proposed location of protein V, which links the viral DNA to the capsid, and assembly-induced conformational changes in the penton base protein. Compared to the two other reported structures of human adenoviruses, HAdV-C5 (PDB: 6B1T (20) ) and HAdV-D26 (PDB: 5TX1(21)), the sequence identity of the capsid proteins ranges from 30-80% (Supplementary Table 3 ). The HAdV-F41 penton base undergoes assembly-induced conformational changes Located on the five-fold symmetry axes of adenovirus capsids, the penton base (PB) protein forms a homopentamer that contains integrin-binding motifs and serves as an assembly hub connecting the icosahedral capsid to the fibers (Fig. 1A) . The DNA-binding protein V is located at a conserved position at the inner face of the capsid After initial model building of the virion at pH=7.4, the asymmetric unit contained five peptide chains that still had not been assigned an identity. doi = 10.1101/2020.07.01.181735 id = cord-323654-9nnjex9y author = Ramachandran, Ashwin title = Electric-field-driven microfluidics for rapid CRISPR-based diagnostics and its application to detection of SARS-CoV-2 date = 2020-05-22 keywords = CRISPR; ITP summary = Unlike previous CRISPR diagnostic assays, we also use ITP for automated purification of target RNA from raw nasopharyngeal swab sample. We here combine this ITP purification with loop-mediated isothermal amplification, and the ITP-enhanced CRISPR assay to achieve detection of SARS-CoV-2 RNA (from raw sample to result) in 30 min for both contrived and clinical nasopharyngeal swab samples. We also demonstrated on-chip ITP extraction of total nucleic acids from raw clinical 175 positive and negative nasopharyngeal swab samples (Figs. We observed that ITP-extracted nucleic acids showed E gene amplification on positive qPCR-based detection approaches is provided in Table 1 . We propose here 520 the concept that such a system can integrate ITP-based nucleic acid extraction, 521 multiplexed isothermal amplification of target cDNA of N and E genes of SARS-CoV-2 522 and RNase P control, followed by ITP-CRISPR-based cDNA detection in three separate 523 channels using photodiodes. doi = 10.1101/2020.05.21.109637 id = cord-103625-p55ew8w7 author = Ramana, Chilakamarti V. title = Regulation of early growth response-1 (Egr-1) gene expression by Stat1-independent type I interferon signaling and respiratory viruses date = 2020-08-14 keywords = Egr-1; IFN; TNF summary = Transcriptional factor profiling in the transcriptome and RNA analysis revealed that Early growth response-1 (Egr-1) was rapidly induced by IFN-α/β and Toll-like receptor (TLR) ligands in multiple cell types. Furthermore, Egr-1 inducible genes including transcription factors, mediators of cell growth, and chemokines were differentially regulated in the human lung cell lines after coronavirus infection, and in the lung biopsies of COVID-19 patients. In this study, transcription factor profiling in interferon-mediated gene expression data sets and RT-PCR revealed that Egr-1 was rapidly induced by IFN-α/β and TLR ligands in multiple cell types. Respiratory pathogens including coronaviruses (SARS-CoV-1 and 2) and influenza viruses regulated the expression of Egr-1 in human lung cell lines and in lung biopsies and peripheral blood cells of COVID-19 patients, These studies suggest that the regulation of Egr-1 may play an important role in the antiviral response and inflammatory disease. doi = 10.1101/2020.08.14.244897 id = cord-252597-ea78sjcs author = Ramazzotti, Daniele title = VERSO: a comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples date = 2020-10-19 keywords = Material; SARS; Supplementary; VERSO; step; variant summary = Moreover, the in-depth analysis of the mutational landscape of SARS-CoV-2 confirms a statistically significant increase of genomic diversity in time and allows us to identify a number of variants that are transiting from minor to clonal state in the population, as well as several homoplasies, some of which might indicate ongoing positive selection processes. The outbreak of coronavirus disease 2019 (COVID19) , which started in late 2019 in Wuhan (China) [1, 2] and was declared pandemic by the World Health Organization, is fueling the publication of an increasing number of studies aimed at exploiting the information provided by the viral genome of SARS-CoV-2 virus to identify its proximal origin, characterize the mode and timing of its evolution, as well as to define descriptive and predictive models of geographical spread and evaluate the related clinical impact [3, 4, 5] . doi = 10.1101/2020.04.22.044404 id = cord-260315-uau554jj author = Ramirez, Santseharay title = Efficient culture of SARS-CoV-2 in human hepatoma cells enhances viability of the virus in human lung cancer cell lines permitting the screening of antiviral compounds date = 2020-10-04 keywords = Huh7.5; SARS summary = title: Efficient culture of SARS-CoV-2 in human hepatoma cells enhances viability of the virus in human lung cancer cell lines permitting the screening of antiviral compounds Culture adaptation in Huh7.5 cells further permitted efficient infection of the otherwise SARS-CoV-2 refractory human lung cancer cell line A549, with titers of ~6 Log10TCID50/mL. Importance The cell culture adapted variant of the SARS-CoV-2 virus obtained in the present study, showed significantly enhanced replication and propagation in various human cell lines, including lung derived cells otherwise refractory for infection with the original virus. Further, as shown here with the use of remdesivir and EIDD-2801, two nucs with significant inhibitory effect against SARS-CoV-2, large differences in the antiviral activity are observed depending on the cell line. 137 We performed a comparative titration in various cells of the P2 VeroE6 and the P5 Huh7.5 viruses ( Figure 138 1b) and found that the infectivity titers in Huh7.5 cells after culture adaptation had increased by more 139 than 3 logs (mean of 4.7 and 8.0 Log 10 TCID 50 /mL, respectively). doi = 10.1101/2020.10.04.325316 id = cord-346978-ubkqny8j author = Ranoa, Diana Rose E. title = Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction date = 2020-06-18 keywords = MS2; RNA; SARS summary = 35 Using intact, γ-irradiated SARS-CoV-2 spiked into fresh human saliva, which was then heat treated at 95°C for 30 min, we observed outstanding virus detection when saliva samples were combined with either Tris-Borate-EDTA (TBE) or TE buffer ( Figure 3A) . Similar results were observed with heat-inactivated SARS-CoV-2, whereby the LOD was measured to be 5000 viral copies/mL for both RNA extraction of saliva samples and direct saliva-to-RT-qPCR, with greater detection if the virus was directly analyzed in water (Supporting Limit of Detection (LOD) for assessment of SARS-CoV-2 from saliva, comparing a process utilizing RNA isolation/purification to one that bypasses RNA isolation/purification. Altogether, these findings indicate that the optimized protocol (heat treatment of saliva samples at 95°C for 30 min / addition of TBE buffer and Tween 20) yields a LOD that is comparable to reported clinical viral shedding concentrations in oral fluid, thus emphasizing the translatability of the protocol to detecting SARS-CoV-2 in patient samples. doi = 10.1101/2020.06.18.159434 id = cord-329395-4k8js9v2 author = Ratcliff, Jeremy title = Evaluation of Different PCR Assay Formats for Sensitive and Specific Detection of SARS-CoV-2 RNA date = 2020-07-01 keywords = PCR; SARS summary = Polymerase chain reaction (PCR)-based assays are the gold standard for detecting viral RNA in patient samples and are used extensively in clinical settings. To enable the application of PCR in resource-poor or non-specialist laboratories, we have developed and evaluated a nested PCR method for SARS-CoV-2 RNA using simple agarose gel electrophoresis for product detection. Using clinical samples tested by conventional qPCR methods and RNA transcripts of defined RNA copy number, the nested PCR based on the RdRP gene demonstrated high sensitivity and specificity for SARS-CoV-2 RNA detection in clinical samples, but showed variable and transcript length-dependent sensitivity for RNA transcripts. The sensitivity of the nested PCR and two RT-qPCR methods was compared by measuring the 118 50% endpoints (50EP) of detection for serial dilutions of the four transcripts described above 119 (Table 1, Figure 2 ). Protocol: Real-time RT-PCR assays for the detection of SARS-CoV-2 doi = 10.1101/2020.06.24.168013 id = cord-300194-nsp53lv6 author = Rath, Soumya Lipsa title = Investigation of the effect of temperature on the structure of SARS-Cov-2 Spike Protein by Molecular Dynamics Simulations date = 2020-06-19 keywords = NTD; SARS; Spike summary = Spike protein is the outermost structural protein of the SARS-CoV-2 virus which interacts with the Angiotensin Converting Enzyme 2 (ACE2), a human receptor, and enters the respiratory system. Here, we study the influence of temperature on the structure of the Spike glycoprotein, the outermost structural protein, of the virus which binds to the human receptor ACE2. and S2 domains individually, with respect to the starting structure, to understand the ause for higher R S values o served at and igure The R S values of S1 domain at and were found to e around nm nearly nm more than simulations at 1 and respe tively similar trend was o served in the R S of S domain ut the differen e in values was only 1 nm lthough in this study we haven''t considered the bilayer lipid membrane of the SARS-COV-2 envelope inside which the Spike 9 glycoprotein resides, the S2 domain shows remarkable stability in its RMSD values ( Figure 2 ). doi = 10.1101/2020.06.10.145086 id = cord-103055-071a5b0x author = Rathbun, LI title = PLK1- and PLK4-mediated asymmetric mitotic centrosome size and positioning in the early zebrafish embryo date = 2020-04-14 keywords = cell; figure summary = We propose a model in which uniquely large centrosomes direct spindle placement within the disproportionately large zebrafish embryo cells to orchestrate cell divisions during early embryogenesis. This is clearly visualized through the use of a fluorescent microtubule transgenic zebrafish line (EMTB-3xGFP) [7] , where the 16-cell stage embryo contains mitotic spindles oriented perpendicular to the previous division at the 8 In early development, rapid rounds of division result in a stark decrease in cell size during the cleavage stage [8] . Strikingly, mitotic centrosomes in zebrafish embryos were extremely large with g-tubulin organized into a wheel-like structure (246.44±11.93μm 2 at 8-cell stage, Figure 1E ), compared to g-tubulin in C. elegans and zebrafish embryos, cell length and mitotic centrosome area decreased by 30-40% over time. In order to determine the importance of PLK1/4-dependent asymmetric mitotic centrosome size placement in early zebrafish divisions, we raised embryos after injection of 1% DMSO, 1μM BI2536, or 1μM centrinone ( Figure 4F ). doi = 10.1101/2020.04.13.039362 id = cord-278869-7zr1118b author = Ravichandran, Supriya title = Antibody repertoire induced by SARS-CoV-2 spike protein immunogens date = 2020-05-13 keywords = RBD; S1+S2 summary = To better understand antibody response induced by spike protein-based vaccines, we immunized rabbits with various SARS-CoV-2 spike protein antigens: S-ectodomain (S1+S2) (aa 16-1213), which lacks the cytoplasmic and transmembrane domains (CT-TM), the S1 domain (aa 16-685), the receptor-binding domain (RBD) (aa 319-541), and the S2 domain (aa 686-1213 as control). The spike ectodomain (S1+S2) generated antibodies that predominantly bound to S1+S2 108 6 (black bar), followed by the S1 protein (blue bar), and 3-fold lower antibody binding to the RBD 109 and the S2 domain (red and green bars, respectively) (Fig. 1D ). Antibody off-rate constants, which describe the fraction of antigen-antibody complexes 119 that decay per second, were determined directly from the serum sample interaction with SARS-120 CoV-2 spike ectodomain (S1+S2), S1, S2, and RBD using SPR in the dissociation phase only for 121 sensorgrams with Max RU in the range of 20-100 RU (Suppl. doi = 10.1101/2020.05.12.091918 id = cord-310464-lkdkdque author = Rayko, Mikhail title = Quality control of low-frequency variants in SARS-CoV-2 genomes date = 2020-05-07 keywords = GISAID; SARS summary = During the current outbreak of COVID-19, research labs around the globe submit sequences of the local SARS-CoV-2 genomes to the GISAID database to provide a comprehensive analysis of the variability and spread of the virus during the outbreak. As a result of the collaborative efforts of the researchers worldwide, on April 14, 2020 it contained over 8,000 SARS-nCoV-2 genomes from different countries, sequenced and assembled using various technologies and approaches. GISAID database curators do a tremendous job of filtering submitted sequences, but sometimes it is difficult to distinguish real variants from errors, especially at the lack of information about coverage. Dataset 8,053 full-length (>29,000 bp) sequences of the SARS-CoV-2 were downloaded from the GISAID database ( www.epicov.org ) on April 14, 2020, including 5,556 genomes marked as "high coverage". Full table with percentage of singleton-containing genomes depending on sequencing and assembly method. doi = 10.1101/2020.04.26.062422 id = cord-261435-wcn4bjnw author = Ren, Xianwen title = Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients date = 2020-10-29 keywords = SARS; cell; covid-19; figure summary = doi = 10.1101/2020.10.29.360479 id = cord-267845-18hb5ndr author = Resende, Paola Cristina title = SARS-CoV-2 genomes recovered by long amplicon tiling multiplex approach using nanopore sequencing and applicable to other sequencing platforms date = 2020-05-01 keywords = Illumina; SARS summary = Here, we describe three protocols using a unique primer set designed to recover long reads of SARS-CoV-2 directly from total RNA extracted from clinical samples. Despite those limitations, we developed a sequencing protocol that successfully obtained whole genomes from SARS-CoV-2 positive samples referred to the National Reference laboratory at FIOCRUZ in Brazil. The tiling amplicon multiplex PCR method has been previously used for virus sequencing directly from clinical samples to obtain consensus genome sequences (3). Here, we describe three protocols using a primer set designed to sequence SARS-CoV-2 directly from total RNA extracted from clinical samples, which were initially diagnosed using real-time RT-PCR (7, 8) . Here we introduce a versatile sequencing protocol to recover the complete SARS-CoV-2 genome based on reverse transcription plus an overlapping long amplicon multiplex PCR strategy, and associated with pipelines to report the data, and recover the consensus files. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples doi = 10.1101/2020.04.30.069039 id = cord-313505-2lr4xara author = Resende, Paola Cristina title = Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil date = 2020-06-18 keywords = CoV-2; SARS summary = title: Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil Phylogenetic analyses revealed multiple introductions of SARS-CoV-2 in Brazil and the community transmission of a major B.1.1 lineage defined by two amino acid substitutions in the Nucleocapsid and ORF6. Introduction 59 COVID-19, the disease caused by Severe Acute Respiratory Syndrome Coronavirus-2 60 (SARS-CoV-2), is leading to high rates of acute respiratory syndrome, hospitalization, and death 61 genomes (> 10% of ambiguous positions), we obtained a final dataset of 7,674 sequences. The prevalence of the sub-clade 211 B.1.1 in our sample (92%) was much higher than that observed in other Brazilian sequences 212 available in GISAID (36%) (Fig. 1C) phylogenetic tree, consistent with the hypothesis of multiple independent introductions (Fig. 2) (Fig. 2) . Revealing COVID-19 Transmission by SARS-CoV-2 Genome 410 Sequencing and Agent Based Modelling. doi = 10.1101/2020.06.17.158006 id = cord-102444-n4vdxdhp author = Rhea, Elizabeth M. title = The S1 protein of SARS-CoV-2 crosses the blood-brain barrier: Kinetics, distribution, mechanisms, and influence of ApoE genotype, sex, and inflammation date = 2020-07-15 keywords = Alb; BBB; Raybiotech summary = doi = 10.1101/2020.07.15.205229 id = cord-102565-egtbzhg7 author = Richards, Gareth title = Assortative Mating, Autistic Traits, Empathizing, and Systemizing date = 2020-10-28 keywords = Cohen summary = doi = 10.1101/2020.10.28.358895 id = cord-103432-cdmoazrl author = Richardson, Eve title = A computational method for immune repertoire mining that identifies novel binders from different clonotypes, demonstrated by identifying anti-Pertussis toxoid antibodies date = 2020-06-02 keywords = antibody; cdrh3; clonotype summary = To test the ability of paratyping and clonotyping to group antibodies that target the same epitope we performed a test in a single-cell (paired VH/VL) data set of 1290 antibodies isolated from genetically engineered mice that have a full set of human immunoglobulin variable region genes [31] immunised with Pertussis toxoid (PTx). Each of the PTx-binders is referred to as a "probe" antibody; sequences that are within the same paratype or clonotype as the probe are predicted to bind PTx. The precision and recall of the two methods (calculated over the aggregate of predictions) for repertoire mining are comparable ( Figure 2 , Table 1 ). In a test system of transgenic mice immunised with Pertussis toxoid (PTx), we show for the first time that prediction and comparison of paratopes can be used to group antigen-specific antibodies in both an enriched, single-cell data set and non-enriched bulk heavy chain repertoires. doi = 10.1101/2020.06.02.121129 id = cord-342599-558yn6pu author = Rinchai, Darawan title = A modular framework for the development of targeted Covid-19 blood transcript profiling panels date = 2020-05-22 keywords = SARS; covid-19; figure; module; transcript summary = Here we aimed to develop an approach to support the design of focused blood transcriptome panels for profiling the immune response to SARS-CoV-2 infection. As a proof of principle, we designed three targeted blood transcript panels, each with a different translational connotation: therapeutic development relevance, SARS biology relevance and immunological relevance. In this proof of principle study, we used the available transcript profiling data from two separate studies to select Covid-19 relevant sets of modules (8, 9) . One of these applications provides access to module-level transcript abundance profiles for available Covid-19 blood transcriptome profiling datasets. Despite large differences between the two studies in terms of design, range of clinical severity, technology platforms and module coverage, the combined overall changes (detected at a high-level perspective) are consistent with those observed in known acute infections, such as those caused by influenza, respiratory syncytial virus (RSV) or S. doi = 10.1101/2020.05.20.107243 id = cord-102898-eyyd7ent author = Rizvi, Vaseef A. title = Translation regulation of Japanese encephalitis virus revealed by ribosome profiling date = 2020-07-17 keywords = JEV; RNA; UTR; virus summary = doi = 10.1101/2020.07.16.206920 id = cord-343586-28ezisog author = Rocca, María Florencia title = A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs date = 2020-05-07 keywords = MALDI; SARS summary = title: A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs Here, we exploit the potential of mass spectrometry technology combined with machine learning algorithms as an alternative fast tool for SARS-CoV-2 detection from nasopharyngeal swabs samples. According to our preliminary results, mass spectrometry-based methods combined with multivariate analysis showed an interesting potential as a complementary diagnostic tool and further steps should be focused on sample preparation protocols and the improvement of the technology applied. These preliminary results suggest that MALDI-TOF MS coupled with ClinProTools software represents an interesting alternative as a screening tool for diagnosis of SARS-CoV-2, especially because of the good performance and accuracy obtained with samples in which viral presence was not detected. doi = 10.1101/2020.05.07.082925 id = cord-288644-ywaefpe8 author = Rodon, Jordi title = Pre-clinical search of SARS-CoV-2 inhibitors and their combinations in approved drugs to tackle COVID-19 pandemic date = 2020-10-20 keywords = SARS; Supp; Vero; table summary = We have tested the antiviral activity of different clinically available compounds and their combinations by assessing their ability to inhibit viral induced cytopathic effect in vitro. Drug selection criteria first focused on compounds already being tested in clinical trials, along with well-known human immunodeficiency virus-1 (HIV-1) and hepatitis C virus (HCV) protease inhibitors, as well as other compounds suggested to have potential activity against SARS-CoV-2 in molecular docking analysis or in vitro assays. Additional Food and Drug Administration (FDA)-approved compounds previously used to abrogate viral entry via clathrin-mediated endocytosis were also tested in this SARS-CoV-2-induced cytotoxicity assay (Supp . Cytopathic effect on Vero E6 cells exposed to a fixed concentration of SARS-CoV-2 in the presence of increasing concentrations of plitidepsin and its combinations with hydroxychloroquine and remdesivir. doi = 10.1101/2020.04.23.055756 id = cord-353161-mtq6yh25 author = Rodrigues, João PGLM title = Insights on cross-species transmission of SARS-CoV-2 from structural modeling date = 2020-06-05 keywords = ACE2; HADDOCK; RBD; SARS summary = We found that species known not to be susceptible to SARS-CoV-2 infection have non-conservative mutations in several ACE2 amino acid residues that disrupt key polar and charged contacts with the viral spike protein. Collectively, our results provide a structural framework that explains why certain animal species are not susceptible to SARS-CoV-2 infection, and also suggests potential mutations that can enhance binding to the viral RBD. Although it is well-known that docking scores do not quantitatively correlate with experimental binding affinities [19] , these scores suggest that SARS-CoV-2 neg species lack one or more key ACE2 residues that contribute significantly to the interaction with RBD. Models of SARS-CoV-2 neg species -chicken, duck, guinea pig, mouse, and rat -generally have higher (worse) HADDOCK scores than average (Figure 2 ), suggesting that these species'' non-susceptibility to infection could stem from deficient RBD binding to ACE2. doi = 10.1101/2020.06.05.136861 id = cord-102383-m5ahicqb author = Romano, Alessandra title = Energy dynamics for systemic configurations of virus-host co-evolution date = 2020-05-15 keywords = host; system; virus summary = A systems-thinking representation, based on stock-flow diagramming of virus-host interaction at the cellular level, is used here for the first time to simulate the system energy dynamics. A systems-thinking representation, based on stock-flow diagramming of virus-host interaction at the cellular level, is used here for the first time to simulate the system energy dynamics. A systems-thinking representation, based on stock-flow diagramming of virus-host interaction at the cellular level, is used here for the first time to simulate the system energy dynamics. Viral load and early addressing (in the first two days from infection) of leverage points are the most effective strategies on stock dynamics to minimize virion assembly and preserve host-cell bioenergetics. Viral load and early addressing (in the first two days from infection) of leverage points are the most effective strategies on stock dynamics to minimize virion assembly and preserve host-cell bioenergetics. doi = 10.1101/2020.05.13.092866 id = cord-347472-n6811ens author = Rosebrock, Adam P. title = Patient DNA cross-reactivity of the CDC SARS-CoV-2 extraction control leads to an inherent potential for false negative results date = 2020-05-15 keywords = CDC; RNA; SARS; dna summary = The US Centers for Disease Control and Prevention (CDC) have specified and given emergency use authorization (EUA) for a SARS-CoV-2 molecular diagnostic used to detect viral RNA in clinical samples (2) . Genomic DNA is co-purified in quantities sufficient to generate strong positive signals for the CDC-specified extraction control during work-up of clinical RNA specimens. To test for the presence of control-affecting DNA, qPCR reactions lacking reverse transcriptase were performed on SARS-CoV-2-positive clinical samples using the CDC-specified RP primer and probe. All clinical samples tested generated unambiguous extraction control positive signals in the absence of reverse transcription, a reaction context that could not have detected virus an RNA virus ( Fig. 2A) Single-digit copies of genomic DNA are sufficient to generate a positive control signal using the CDC-designed assay. Due to the presence of co-purifying genomic DNA in clinical samples, loss of RNA integrity leads to false-negative results using the CDC-specified control. doi = 10.1101/2020.05.13.094839 id = cord-336522-y9nzsv95 author = Rosenke, Kyle title = Inhibition of SARS-CoV-2 in Vero cell cultures by peptide-conjugated morpholino-oligomers date = 2020-09-30 keywords = PPMO; SARS summary = title: Inhibition of SARS-CoV-2 in Vero cell cultures by peptide-conjugated morpholino-oligomers Cell viability was 33 evaluated with an ATP-based method and viral growth was measured with quantitative RT-PCR 34 and TCID50 infectivity assays. Results: PPMO designed to base-pair with sequence in the 5''-terminal region or the leader 36 transcription regulatory sequence-region of SARS-CoV-2 genomic RNA were highly 37 efficacious, reducing viral titers by up to 4-6 log10 in cell cultures at 48-72 hours post-infection, 38 in a non-toxic and dose-responsive manner. Results: PPMO designed to base-pair with sequence in the 5''-terminal region or the leader 36 transcription regulatory sequence-region of SARS-CoV-2 genomic RNA were highly 37 efficacious, reducing viral titers by up to 4-6 log10 in cell cultures at 48-72 hours post-infection, 38 in a non-toxic and dose-responsive manner. In this study, five PPMO were designed to target the 5'' UTR 107 and first translation start site-region of SARS-CoV-2 positive sense genomic RNA ( Table 1) . doi = 10.1101/2020.09.29.319731 id = cord-309289-vm0k7hfx author = Rothan, Hussin A. title = The FDA- approved gold drug Auranofin inhibits novel coronavirus (SARS-COV-2) replication and attenuates inflammation in human cells date = 2020-04-14 keywords = COV-2; SARS summary = title: The FDAapproved gold drug Auranofin inhibits novel coronavirus (SARS-COV-2) replication and attenuates inflammation in human cells These data indicate that auranofin could be a useful drug to limit SARS-CoV-2 infection and associated lung injury due to its anti-viral, anti-inflammatory and anti-ROS properties. Herein, we report that the FDA-approved gold drug, auranofin, inhibits SARS-COV-2 replication in human cells at low micro molar concentration. Herein, we report that the FDA-approved gold drug, auranofin, inhibits SARS-COV-2 replication in human cells at low micro molar concentration. These data indicate that auranofin could be a useful drug to limit SARS-CoV-2 infection and associated lung injury due to its anti-viral, antiinflammatory and anti-ROS properties. We investigated the anti-viral activity of auranofin against SARS-CoV-2 and its effect on virus-induced inflammation in human cells. These data indicate that auranofin could be a useful drug to limit SARS-CoV-2 infection and associated lung injury. doi = 10.1101/2020.04.14.041228 id = cord-263090-29n9tsk9 author = Roy, Susmita title = Dynamical asymmetry exposes 2019-nCoV prefusion spike date = 2020-04-21 keywords = Fig; RBD; SARS summary = In this study, a structural-topology based model Hamiltonian of C3 symmetric trimeric spike is developed to explore its complete conformational energy landscape using molecular dynamic simulations. B. Side and top views of the homo-trimeric structure of SARS-CoV-2 spike protein with one RBD of the S1 subunit head rotated in the up conformation. A number of Cryo-EM structures captured the ''up'' and ''down'' conformations of the RBD domain of spike proteins of other coronaviruses including SARS-CoV-2 where the S1 subunit undergoes a hinge-like conformational movement prerequisite for receptor binding (Fig. 2C) (7, 8, 10, 17) . Analysis of all the simulations yields the 2-D free energy landscape of the trimeric spike protein of SARS-CoV-2 ( Fig 3B) with its all possible conformations. This generates a homo-trimeric SARS-CoV-2 spike where this initial structure has important components in terms of intra and inter-chain contacts (interaction) leading to an ''S1-head-up'' and an ''S1-head-down'' conformation for each protomer. doi = 10.1101/2020.04.20.052290 id = cord-306901-uuwgpuhw author = Roy, Sylvie title = Efficient production of Moloney murine leukemia virus-like particles pseudotyped with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein date = 2020-09-16 keywords = SARS summary = title: Efficient production of Moloney murine leukemia virus-like particles pseudotyped with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein Several investigational vaccines that have already been tested in animals and humans were able to induce neutralizing antibodies against the SARS-CoV-2 spike (S) protein, however protection and long-term efficacy in humans remain to be demonstrated. We have investigated if a virus-like particle (VLP) derived from Moloney murine leukemia virus (MLV) could be engineered to become a candidate SARS-CoV-2 vaccine amenable to mass production. High amounts of SARS-CoV-2 DS protein are incorporated into MLV VLPs released 142 from stable producer cells. A VLP-derived SARS CoV-2 vaccine will be a viable option if 143 sufficient amounts of S protein are incorporated at the surface of the released particles. In conclusion, we have developed and characterized a new MLV VLP platform that can 243 efficiently incorporate the S protein from SARS-CoV-2, and that has the potential to produce a pan-244 coronavirus vaccine. doi = 10.1101/2020.09.16.298992 id = cord-302160-4yfvspaq author = Ruetalo, Natalia title = Rapid and efficient inactivation of surface dried SARS-CoV-2 by UV-C irradiation date = 2020-10-07 keywords = SARS summary = Strikingly, short exposure of high titer surface dried virus (3*10^6 IU/ml) with UV-C light (16 mJ/cm2) resulted in a total reduction of SARS-CoV-2 infectivity. We hence conducted a "real-life" application approach simulating the 66 inactivation of dried surface residing infectious SARS-CoV-2 by a mobile handheld UV-C 67 emitting device and an UV-C box designed to decontaminate medium-size objects. Simulating the situation that exhaled droplets or aerosols from infected 115 individuals contaminate surfaces, we produced a high-titer SARS-CoV-2 infectious stock and 116 dried 35µL of this stock corresponding to ~4*10^6 IU/ml in each well of a 6-well plate. Of note, even short UV-C treatment of the dried virus in the context of the moving "fast" 135 regimen completely inactivated SARS-CoV-2, as no infected cells were detected based on 136 fluorescence protein expression (Fig. 1b) . Altogether, our data 143 demonstrate that UV-C regimens that expose high-titer SARS-CoV-2 to doses down to 16 144 mJ/cm² are sufficient to achieve complete inactivation of the virus. doi = 10.1101/2020.09.22.308098 id = cord-267482-afqfymbq author = Ryu, Seungjin title = Ketogenesis restrains aging-induced exacerbation of COVID in a mouse model date = 2020-09-12 keywords = A59; COVID-19; SARS; cell; figure; mouse summary = Aged mCoV-A59-infected mice have increased mortality and higher systemic inflammation in the heart, adipose tissue and hypothalamus, including neutrophilia and loss of γδ T cells in lungs. Also, initial studies that employ lung ciliated epithelial cell-specific HFH4/FOXJ1 promoter driven hACE2 transgenic mice show SARS-CoV-2 infection induces weight loss, lung inflammation and approximately 50% mortality rate, suggesting the usefulness of this model to understand the mechanism of immune dysregulation (Jiang et al., 2020) . Moreover, given our recent findings that ketogenesis inhibits inflammation and expands tissue resident ϒδ T cells (Goldberg et al., 2019) while SARS-CoV-2 infection in patients is associated with depletion of ϒδ T cells (Lei et al., 2020; Rijkers et al., 2020) , we next tested whether elevating BHB by feeding a ketogenic diet (KD) protects against mCoV-A59-driven inflammatory damage in aged mice. doi = 10.1101/2020.09.11.294363 id = cord-292985-w62xaa4f author = Römer, Rudolf A. title = Flexibility and mobility of SARS-CoV-2-related protein structures date = 2020-07-12 keywords = SARS; protein; structure summary = We are using a recent protein flexibility modelling approach, combining protein structural rigidity with possible motion consistent with chemical bonds and sterics. 34 We have performed our analysis through multiple conformational steps starting from the crystal structures of SARS-CoV-2-related proteins as currently deposited in the PDB. In Fig. 1 (a) we see that for the crystal structure of SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain (PDB:6m3m), the largest rigid cluster in the pristine structure, i.e. at E cut = 0, largely remains rigid through the dilution process of consecutively lowering E cut values. Last, a protein with 2nd-order rigidity should have the most complex behaviour in terms of flexibility since new possible mobility can be expected throughout the range of E cut values. Moving along directions proposed by an elastic normal model analysis of the crystal structure, we can therefore construct possible motion trajectories that are fully consistent with the bond network and steric constraints. doi = 10.1101/2020.07.12.199364 id = cord-300783-pvn2qq0f author = Sadykov, Mukhtar title = Short sequence motif dynamics in the SARS-CoV-2 genome suggest a role for cytosine deamination in CpG reduction date = 2020-08-07 keywords = SARS summary = title: Short sequence motif dynamics in the SARS-CoV-2 genome suggest a role for cytosine deamination in CpG reduction RNA viruses use CpG reduction to evade the host cell defense, but the driving mechanisms are still largely unknown. Remarkably, by simply ordering SARS-CoV-2 genomes by their date of collection, we find a progressive increase of C-to-U substitutions resulting in 5''-UCG-3'' motif reduction that in turn have reduced the CpG frequency over just a few months of observation. Our results thus link the dynamics of target sequences in the viral genome for two known host molecular defense mechanisms, mediated by the APOBEC and ZAP proteins. One such 34 mechanism is the CpG dinucleotide reduction observed in many single-stranded RNA 35 fraction of the observed C>U changes represent multiple, independent events ( Figure S3 ). CpG Dinucleotides in SARS-CoV-2 Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host 396 antiviral defense Multi-site co-398 mutations and 5''UTR CpG immunity escape drive the evolution of SARS-CoV-2 doi = 10.1101/2020.06.19.161687 id = cord-255755-5jccb3nh author = Saha, Sovan title = Detection of spreader nodes and ranking of interacting edges in Human-SARS-CoV protein interaction network date = 2020-04-23 keywords = PPIN; SARS summary = title: Detection of spreader nodes and ranking of interacting edges in Human-SARS-CoV protein interaction network The new network attribute spreadability index along with generated SIS values of selected top spreader nodes when compared with the other network centrality based methodologies like Degree centrality (DC), Closeness centrality (CC), Local average centrality (LAC) and Betweeness centrality (BC) is found to perform relatively better than the existing-state-of-art. In the proposed methodology, Protein-protein interaction network (PPIN) has been used as the central component in identification of spreader nodes in SARS-CoV. Once it is formed, spreader nodes are identified in each of SARS-CoV proteins, its level 1 and level 2 of human network by the application of a new network attribute i.e. spreadability index which is a combination of three terminologies: 1) edge ratio [28] 2) neighborhood density [28] and 3) node weight [29] . doi = 10.1101/2020.04.12.038216 id = cord-315702-pn8247j2 author = Sahakijpijarn, Sawittree title = Development of Remdesivir as a Dry Powder for Inhalation by Thin Film Freezing date = 2020-09-22 keywords = TFF; drug; remdesivir summary = Remdesivir exhibits in vitro activity against SARS-CoV-2 and was granted approval for Emergency Use. To maximize delivery to the lungs, we formulated remdesivir as a dry powder for inhalation using thin film freezing (TFF). In conclusion, TFF technology produces high potency remdesivir dry powder formulations for inhalation suitable to treat patients with COVID-19 on an outpatient basis and earlier in the disease course where effective antiviral therapy can reduce related morbidity and mortality. Although several techniques have been used to prepare inhalable powders, including 116 mechanical milling and spray drying, the advantages of thin film freezing (TFF) over other techniques 5 of 39 rely on the ability to produce aerosolizable particles composed of brittle matrix, nanostructured 118 aggregates. This shows that the 530 TFF technology can be used to minimize the need of excipient(s) in the formulation, thus maximizing 531 the amount of remdesivir being delivered to the lungs by dry powder inhalation. doi = 10.1101/2020.07.26.222109 id = cord-335652-v98gv5uf author = Salazar, Cecilia title = Multiple introductions, regional spread and local differentiation during the first week of COVID-19 epidemic in Montevideo, Uruguay date = 2020-05-10 keywords = CoV-2; SARS; Uruguay summary = Methods We performed whole-genome sequencing of 10 SARS-CoV-2 from patients diagnosed during the first week (March 16th to 19th) of COVID-19 outbreak in Uruguay. Our analysis set the bases for future genomic epidemiology studies to understand the dynamics of SARS-CoV-2 in Uruguay and the Latin America and the Caribbean region. This global health emergency has deployed international efforts to apply genomic epidemiology to track the spread of SARS-CoV-2 in real time. The recent development of targeted sequencing protocols by the ARTIC Network [3] , open sharing of genomic data through the GISAID (www.gisaid.org) database and straightforward bioinformatic tools for viral phylogenomics [4] , provides the opportunity to reconstruct global spatio-temporal dynamics of the COVID-19 pandemic with unprecedented comprehensiveness and resolution. We therefore aimed to characterize the spatio-temporal dynamics of SARS-CoV-2 by sequencing around 10% of cases occurred during the first week of outbreak in Montevideo, allowing us to identify transmission patterns, geographic origins and genetic variation among local strains. doi = 10.1101/2020.05.09.086223 id = cord-338543-q6cl5kjp author = Salguero, Francisco J. title = Comparison of Rhesus and Cynomolgus macaques as an authentic model for COVID-19 date = 2020-09-17 keywords = SARS summary = Here, we show that SARS-CoV-2 replicates in the upper and lower respiratory tract and causes pulmonary lesions in both rhesus and cynomolgus macaques, resembling the mild clinical cases of COVID-19 in humans. In contrast to prior publications, in which rhesus are accepted to be the optimal study species, we provide convincing evidence that both macaque species authentically represent mild to moderate forms of COVID-19 observed in the majority of the human population and both species should be used to evaluate the safety and efficacy of novel and repurposed interventions against SARS-CoV-2. Throat swabs from cynomolgus macaques contained 147 higher levels of viral RNA early in infection (one to three dpc) and remained ≥4.5 x 148 10 4 copies/ml for all animals between four and nine dpc. However viral RNA 159 levels above the LLOQ were detected at both three dpc and five dpc in cynomolgus 160 macaques in comparison to two dpc and three dpc in rhesus macaques ( Figure 2D ). doi = 10.1101/2020.09.17.301093 id = cord-346299-2s9j01q7 author = Salim Khan, S Muhammad title = Seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar, northern India – a cross-sectional study date = 2020-09-04 keywords = District; SARS summary = title: Seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar, northern India – a cross-sectional study Background Prevalence of IgG antibodies against SARS-CoV-2 infection provides essential information for deciding disease prevention and mitigation measures. We estimate the seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar. 65 Besides, assuming that antibodies provide partial or total immunity, seroprevalence surveys give Here, we present the results of a cross-sectional seroprevalence study in District Srinagar, 70 conducted between 1 st and 15 th July 2020, to estimate the prevalence of IgG antibodies against 71 SARS-CoV-2 among adults using a sensitive and specific chemiluminescent microparticle 72 immunoassay (CMIA)-based test. 156 We estimated the number of infections till two weeks before the study period, i.e., 15 th June 2020 157 to 30 th June 2020, by applying the age-and gender-specific seroprevalence rates found in the Table) . doi = 10.1101/2020.09.04.282640 id = cord-102920-z5q3wo7v author = Sang, Eric R. title = Integrate Structural Analysis, Isoform Diversity, and Interferon-Inductive Propensity of ACE2 to Refine SARS-CoV2 Susceptibility Prediction in Vertebrates date = 2020-06-28 keywords = ACE2; Fig; RBD; SARS summary = Previous reports using structural analysis of the viral spike protein (S) binding its cell receptor of angiotensin-converting enzyme 2 (ACE2), indicate a broad SARS-CoV2 susceptibility in wild and particularly domestic animals. In addition to showing a broad susceptibility potential across mammalian species based on structural analysis, our results also reveal that domestic animals including dogs, pigs, cattle and goats may evolve ACE2-related immunogenetic diversity to restrict SARS-CoV2 infections. Along with showing a broad susceptibility potential across mammalian species based on structural analysis [26] [27] [28] , our results further reveal that domestic animals including dogs, pigs, cattle and goats may evolve previously unexamined immunogenetic diversity to restrict SARS-CoV2 infections. In addition to structural analysis of simulated S-RBD-ACE2 interaction, we propose that several immunogenetic factors, including the evolution of S-binding-void ACE2 isoforms in some domestic animals, the species-specific IFN system, and epigenetic regulation of IFN-stimulated property of host ACE2 genes, contribute to the viral susceptibility and the development of COVID-19-like symptoms in certain animal species [15, 38, 39, 49] . doi = 10.1101/2020.06.27.174961 id = cord-348159-v5hrcl5k author = Sang, Eric R. title = Epigenetic Evolution of ACE2 and IL-6 Genes as Non-Canonical Interferon-Stimulated Genes Correlate to COVID-19 Susceptibility in Vertebrates date = 2020-09-10 keywords = ACE2; IL-6 summary = Furthermore, significantly higher positive histone modification markers and position weight matrix (PWM) scores of key cis-elements corresponding to inflammatory and IFN signaling, were discovered in both ACE2 and IL6 gene promoters across representative COVID-19-susceptible species compared to unsusceptible ones. Third, we found that the evolutionary increase of 147 ACE2, and especially the IL-6 genes response to inflammatory and IFN signaling may 148 serve as epigenetic marker for COVID-19 susceptibility in some animal species including 149 humans. . This shows that ACE2 and especially IL-6 genes from CoV2(+) species contain CREs with significantly higher mPWM scores, indicating that in some vertebrate species, non-ISGs like ACE2 and especially IL-6 genes evolved to obtain high inductive propensity by inflammatory and IFN signaling, and may serve as epigenetic biomarkers (or triggers) for susceptibility prediction for COVID-19 and other ARD syndromes. doi = 10.1101/2020.09.09.273268 id = cord-268795-tjmx6msm author = Sardar, Rahila title = Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis date = 2020-03-21 keywords = SARS; genome summary = title: Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis We have performed an integrated sequence-based analysis of SARS-CoV2 genomes from different geographical locations in order to identify its unique features absent in SARS-CoV and other related coronavirus family genomes, conferring unique infection, facilitation of transmission, virulence and immunogenic features to the virus. Our analysis reveals nine host miRNAs which can potentially target SARS-CoV2 genes. Our analysis shows unique host-miRNAs targeting SARS-CoV2 virus genes. CELLO2GO (7)server was used to infer biological function for each protein of SARS-CoV2 genome with their localization prediction. Assembled SARS-CoV2 genomes sequences in FASTA format from India, USA, China, Italy and Nepal used for coronavirus typing tool analysis. For the phylogenetic analysis, we compared the sequences of 6 SARS-CoV2 isolates from different countries namely, Wuhan, India, Italy, USA and Nepal along with other corona virus species ( Figure 1 ). doi = 10.1101/2020.03.21.001586 id = cord-323839-a4oejky0 author = Sasaki, Michihito title = SARS-CoV-2 variants with mutations at the S1/S2 cleavage site are generated in vitro during propagation in TMPRSS2-deficient cells date = 2020-08-28 keywords = SARS; Vero summary = These results indicated that S gene mutants are resistant to the 1 5 9 treatment with TMPRRSS2 inhibitors, but are sensitive to antivirals that target post entry In an effort to understand the selection mechanisms underlying the generation of these 1 6 4 mutant variants, we estimated the frequency of S gene mutants in virus population of 1 6 5 SARS-CoV-2 that had undergone serial passage in cultured cells. In contrast, nucleotide sequence 1 7 2 deletions around the S1/S2 cleavage site corresponding to del1 and del2 mutants were 1 7 3 observed in all three biological replicates of SARS-CoV-2 populations passaged in Vero 1 7 4 cells (Fig. 5a) . Moreover, we must be very objective when interpreting the results 2 3 0 from studies using Vero-passaged virus, especially those focused on S protein cleavage, Cells were infected with either WT or S mutants of SARS-CoV-2 at an MOI of 1. doi = 10.1101/2020.08.28.271163 id = cord-104169-2sbc1guz author = Satish, Swarup title = The impact of preprint servers in the formation of novel ideas date = 2020-10-08 keywords = figure; phrase summary = Our proposed Bayesian Approach to Novelty Detection (BAND) finds the time interval τ that maximizes the observed series of publication frequency for a phrase (Figure 1 ). Our motivation for finding τ using BAND is to compare the impact of different publication venues (i.e. preprint servers and peer-reviewed journals) that cover overlapping research topics. In our analysis (Section 5.2), we compare these methods to BAND not only for finding the first clear inflection point, but also how relevant τ is for the end goal of novelty detection and comparing research impact. • Can we find the point τ in time when a phrase is determined novel using our Bayesian Approach to Novelty Detection (BAND)? Our findings indicate that novel phrases, which we use as a proxy for new ideas, in most cases appear on pre-print servers and in peer reviewed journals. doi = 10.1101/2020.10.08.330696 id = cord-310752-zl2g9wqo author = Sato, Taku title = Expression of ACE2 and TMPRSS2 proteins in the upper and lower aerodigestive tracts of rats date = 2020-05-15 keywords = ACE2; TMPRSS2 summary = Methods To elucidate the underlying histological mechanisms of the aerodigestive disorders caused by SARS-CoV-2, we investigated the expression of ACE2 and TMPRSS2 proteins in the aerodigestive tracts of the tongue, hard palate with partial nasal tissue, larynx with hypopharynx, trachea, esophagus, lung, and kidney of rats through immunohistochemistry. Results Strong co-expression of ACE2 and TMPRSS2 proteins was observed in the nasal respiratory epithelium, trachea, bronchioles, alveoli, kidney, and taste buds of the tongue. Notably, strong co-expression of ACE2 and TMPRSS2 proteins was observed in the taste buds of the tongue, nasal respiratory epithelium, trachea, bronchioles, alveoli, and the kidney. The strong co-expression of ACE2 and TMPRSS2 in the taste buds may explain the high incidence of ageusia or dysgeusia in patients with SARS-CoV-2 infection. Unlike that in the nasal respiratory epithelium, TMPRSS2 was more strongly expressed in the cytoplasm of tracheal epithelium, hence suggesting the trachea to be more prone to developing clinical symptoms after SARS-CoV-2 infection than the nasal tissue. doi = 10.1101/2020.05.14.097204 id = cord-103421-46owvqw8 author = Saunders, Jaclyn K. title = METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies - Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses date = 2020-05-21 keywords = LCA; METATRYP; peptide; share summary = Improvements include: ingestion of complex sequence assembly data categories (metagenomic and metatranscriptomic assemblies, single cell amplified genomes, and metagenome assembled genomes), prediction of the Least Common Ancestor (LCA) for a peptide shared across multiple organisms, increased performance through updates to the backend architecture, and development of a web portal (https://metatryp.whoi.edu). Improvements include: ingestion of complex sequence assembly data categories (metagenomic and metatranscriptomic assemblies, single cell amplified genomes, and metagenome assembled genomes), prediction of the Least Common Ancestor (LCA) for a peptide shared across multiple organisms, increased performance through updates to the backend architecture, and development of a web portal (https://metatryp.whoi.edu). This feature previously existed in METATRYP v 1 for generating peptide redundancy tables within the "Genome" sequencing data category and was used to show the relatively low occurrence of shared peptides across disparate taxa in the open ocean microbiome [1] . doi = 10.1101/2020.05.20.107490 id = cord-264296-0x90yubt author = Sawmya, Shashata title = Analyzing hCov genome sequences: Applying Machine Intelligence and beyond date = 2020-06-03 keywords = China; Coronavirus; India; sequence summary = We present here an analysis pipeline comprising phylogenetic analysis on strains of this novel virus to track its evolutionary history among the countries uncovering several interesting relationships, followed by a classification exercise to identify the virulence of the strains and extraction of important features from its genetic material that are used subsequently to predict mutation at those interesting sites using deep learning techniques. C. Several CNN-RNN based models are used to predict mutations at specific Sites of Interest (SoIs) of the sars-cov-2 genome sequence followed by further analyses of the same on several South-Asian countries. D. Overall, we present an analysis pipeline that can be further utilized as well as extended and revised (a) to study where a newly discovered genome sequence lies in relation to its predecessors in different regions of the world; (b) to analyse its virulence with respect to the number of deaths its predecessors have caused in their respective countries and (c) to analyse the mutation at specific important sites of the viral genome. doi = 10.1101/2020.06.03.131987 id = cord-339431-kyr5lv15 author = Saçar Demirci, Müşerref Duygu title = Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection date = 2020-03-17 keywords = RNA; SARS summary = In the case of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there are several mechanisms that would make miRNAs impact the virus, like interfering with replication, translation and even modulating the host expression. In this study, we performed a machine learning based miRNA prediction analysis for the SARS-CoV-2 genome to identify miRNA-like hairpins and searched for potential miRNA – based interactions between the viral miRNAs and human genes and human miRNAs and viral genes. Although there are studies regarding to the viral replication and their interaction with host innate immune system, the role of miRNA-mediated RNA-silencing in SARS-CoV-2 infection has not been enlightened yet. In this study, SARS-CoV-2 genome was searched for miRNA-like sequences and potential host-virus interactions based on miRNA actions were analyzed. In our study, we have also identified possible miRNA like small RNAs from SARS-CoV-2 genome which target important human genes. doi = 10.1101/2020.03.15.992438 id = cord-102505-g37ti2jj author = Schaworonkow, Natalie title = EEG-triggered TMS reveals stronger brain state-dependent modulation of motor evoked potentials at weaker stimulation intensities date = 2018-01-22 keywords = EEG; MEP; TMS summary = doi = 10.1101/251363 id = cord-296649-h6oyjz56 author = Scherf-Clavel, Oliver title = Tissue Level Profiling of SARS-CoV-2 antivirals in mice to predict their effects: comparing Remdesivir’s active metabolite GS-441 524 vs. the clinically failed Hydroxychloroquine date = 2020-11-06 keywords = HCQ; SARS; gs-441 summary = In this study, an adapted mouse model was chosen to demonstrate its suitability to provide sufficient information on the model substances GS-441 524 and HCQ regarding plasma concentration and distribution into relevant tissues a prerequisite for treatment effectiveness. Blood and organ samples were taken at several time points and drug concentrations were quantified in plasma and tissue homogenates by two liquid chromatography/tandem mass spectrometry methods. For GS-441 524, measured tissue concentrations exceeded the reported in vitro EC50 values by more than 10-fold and in consideration of its high efficacy against feline infectious peritonitis, GS-441 524 could indeed be effective against SARS-CoV-2 in vivo. The value obtained from our experiments falls in that range and is comparable to the V z obtained in mice from blood concentrations and to plasma V z measured in humans (see Table 4 ). doi = 10.1101/2020.09.16.299537 id = cord-103465-6udhvl9n author = Schierding, William title = Low tolerance for transcriptional variation at cohesin genes is accompanied by functional links to disease-relevant pathways date = 2020-04-13 keywords = GWAS; cohesin; gene; variant summary = Results 140 genetic variants with regulatory potential are associated with cohesin loci Mitotic cohesin genes (SMC1A, SMC3, STAG1, STAG2, and RAD21), meiotic cohesin genes (SMC1B, STAG3, REC8, and RAD21L1), cohesin support genes (WAPL, NIPBL, PDS5A, PDS5B, and MAU2) and CTCF were investigated to determine if they contain non-coding genetic variants (SNPs) that make contact in 3D with genes and therefore could directly affect gene expression (GWAS-attributed and eQTL-attributed; Table 1, Table S1 ). Intriguingly, Haploreg motif prediction identified 16 of the 209 variants (7 different loci: MAU2, PDS5B, REC8, SMC1B, STAG3, RAD21L1, STAG1) as residing within protein binding domains associated with cohesin-related DNA interactions (i.e. RAD21, SMC3, and CTCF). Pathway enrichment implicates coordinated regulation of cohesin with essential cell cycle genes CoDeS3D identified 140 variants as being physically connected to, and associated with the expression levels of 310 genes (243 genes from eQTL-attributed variants, 141 from GWAS-attributed variants, and 74 overlap) across 6,795 significant tissue-specific regulatory connections (FDR p<0.05). doi = 10.1101/2020.04.11.037358 id = cord-103112-m6cg67lz author = Schloer, Sebastian title = Targeting the endolysosomal host-SARS-CoV-2 interface by clinically licensed functional inhibitors of acid sphingomyelinase (FIASMA) including the antidepressant fluoxetine date = 2020-08-16 keywords = SARS; cell summary = As the FIASMA group consists of a large number of small compounds that are well-tolerated and widely used for a broad range of clinical applications, exploring these licensed pharmaceuticals may offer a variety of promising antivirals for host-directed therapy to counteract enveloped viruses, including SARS-CoV-2 and COVID 19. We find that fluoxetine, a widely used antidepressant and a functional inhibitor of 27 acid sphingomyelinase (FIASMA), efficiently inhibited the entry and propagation of SARS-CoV-28 2 in the cell culture model without cytotoxic effects and also exerted potent antiviral activity 29 against two currently circulating influenza A virus subtypes, an effect which was also observed 30 upon treatment with the FIASMAs amiodarone and imipramine. We find that fluoxetine, a widely used antidepressant and a functional inhibitor of 27 acid sphingomyelinase (FIASMA), efficiently inhibited the entry and propagation of SARS-CoV-28 2 in the cell culture model without cytotoxic effects and also exerted potent antiviral activity 29 against two currently circulating influenza A virus subtypes, an effect which was also observed 30 upon treatment with the FIASMAs amiodarone and imipramine. doi = 10.1101/2020.07.27.222836 id = cord-270329-t60t639i author = Schloer, Sebastian title = Drug synergy of combinatory treatment with remdesivir and the repurposed drugs fluoxetine and itraconazole effectively impairs SARS-CoV-2 infection in vitro date = 2020-10-16 keywords = SARS summary = title: Drug synergy of combinatory treatment with remdesivir and the repurposed drugs fluoxetine and itraconazole effectively impairs SARS-CoV-2 infection in vitro We tested the antiviral potential of repurposing the antifungal itraconazole and the antidepressant fluoxetine on the production of infectious SARS-CoV-2 particles in the polarized Calu-3 cell culture model and evaluated the added benefit of a combinatory use of these host-directed drugs with remdesivir, an inhibitor of viral RNA polymerase. Importantly, both itraconazole-remdesivir and fluoxetine-remdesivir combinations inhibited the production of infectious SARS-CoV-2 particles > 90% and displayed synergistic effects in commonly used reference models for drug interaction. While drugs 87 directly acting on virus structures are much more likely to completely eliminate the 88 pathogens in shorter treatment time, emerging viral resistance to these antivirals is a major 89 concern, as observed with the influenza neuraminidase inhibitor oseltamivir (Kim et al., itraconazole antiviral activity in SARS-CoV-2 infected Vero cells (Fig. 1b) . doi = 10.1101/2020.10.16.342410 id = cord-355728-wivk0bm0 author = Schoof, Michael title = An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation date = 2020-08-17 keywords = Fig; RBD; SARS; Spike summary = Here, we develop single-domain antibodies (nanobodies) that potently disrupt the interaction between the SARS-CoV-2 Spike and ACE2. Cryogenic electron microscopy (cryo-EM) revealed that one exceptionally stable nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains (RBDs) locked into their inaccessible down-state, incapable of binding ACE2. Class I nanobodies emerged with highly 144 variable activity in this assay with Nb6 and Nb11 as two of the most potent clones with IC50 145 values of 370 and 540 nM, respectively (Table 1) To define the binding sites of Nb6 and Nb11, we determined their cryogenic electron 156 microscopy (cryo-EM) structures bound to Spike* ( Fig. 2A state RBDs only contacts a single RBD (Fig. 2D) . 277 278 mNb6-tri displays further gains in potency in both pseudovirus and live SARS-CoV-2 infection 279 assays with IC50 values of 120 pM (5.0 ng/mL) and 54 pM (2.3 ng/mL), respectively (Fig. 4H-I, 280 Table 1). doi = 10.1101/2020.08.08.238469 id = cord-305589-ofpna4k1 author = Schubert, Katharina title = SARS-CoV-2 Nsp1 binds ribosomal mRNA channel to inhibit translation date = 2020-07-07 keywords = Fig; Nsp1; SARS; translation summary = By combining cryo-electron microscopy and biochemical experiments, we show that SARS-CoV-2 Nsp1 binds to the human 40S subunit in ribosomal complexes including the 43S pre-initiation complex. Based on these results we assembled in vitro a 40S-Nsp1 complex and determined its structure at 2.8 Å resolution using cryo-EM (Extended Data Fig. 2 ). As observed in the high-resolution structure of the 40S-Nsp1 complex, the C-terminal part of Nsp1 in the mRNA entrance channel (Fig. 1e ) folds into two helices that interact with h18 of the 18S rRNA as well as proteins uS3 in the head and uS5 and eS30 in the body, respectively ( Fig. 1f; Fig. 2a ). Our structural data suggest that SARS-CoV-2 Nsp1 inhibits translation by sterically occluding the entrance region of the mRNA channel and interfering with binding of cellular mRNAs (Fig. 4a,b) . doi = 10.1101/2020.07.07.191676 id = cord-103813-w2sb6h94 author = Schumacher, Garrett J. title = Genetic information insecurity as state of the art date = 2020-07-10 keywords = datum; dna; genetic; information; security summary = Therefore, human genetic information is a uniquely confidential form of data that requires increased security controls and scrutiny. Sensitive genetic information, which includes both biological material and digital genetic data, is the primary asset of concern, and associated assets, such as metadata, electronic health records and intellectual property, are also vulnerable within this ecosystem. ❖ Private Sensitive Genetic Information can be expected to cause a moderate level of risk to a nation, ethnic group, individual, or stakeholder if it is disclosed, modified, or destroyed without authorization. The genetic information ecosystem is a distributed cyber-physical system containing numerous stakeholders (Supplementary Material, Appendix 1), personnel, and devices for computing and networking purposes. Genetic information security is a shared responsibility between sequencing laboratories and device vendors, as well as all other involved stakeholders. Examples include biorepositories, DNA sequencing laboratories, researchers, cloud and other service providers, and supply chain entities responsible for devices, software and materials. doi = 10.1101/2020.07.08.192666 id = cord-103085-vf4qyvft author = Seitz, Christian title = Multiscale simulations examining glycan shield effects on drug binding to influenza neuraminidase date = 2020-11-02 keywords = Influenza; figure; glycan; site summary = Using Brownian dynamics simulations, we observe a twoto eight-fold decrease in the rate of ligand binding to the primary binding site of neuraminidase due to the presence of glycans. We have utilized BD to estimate the rates of binding of small molecules to the primary (i.e. active/catalytic) and secondary (i.e. hemadsorption) binding sites of influenza neuraminidase in glycosylated and unglycosylated states. The protein-ligand atom pairs were taken from crystal structures of ligands in the primary and secondary sites of neuraminidase for each monomer, and simulations were run for the full tetramer. Keeping in mind the primary and secondary binding sites are located just beneath the glycans (Figure 1) , the size and flexibility of the glycans here shows that they have the capability to "shield" the binding sites from ligand association. (A) The glycan structures from the MD simulations show a moderate association rate inhibition to the primary binding site irrespective of ligand chosen. doi = 10.1101/2020.08.12.248690 id = cord-280922-w6a5ec06 author = Sen, Sanjana title = Predicting COVID-19 Severity with a Specific Nucleocapsid Antibody plus Disease Risk Factor Score date = 2020-10-29 keywords = SARS; abs; covid-19; ep9 summary = Here, ELISA and coronavirus antigen microarray (COVAM) analysis mapped antibody epitopes in the plasma of COVID-19 patients (n = 86) experiencing a wide-range of disease states. Here, ELISA and coronavirus antigen microarray (COVAM) analysis mapped antibody epitopes in the plasma of COVID-19 patients (n = 86) experiencing a wide-range of disease states. Furthermore, a recent review on antibody-dependent enhancement of SARS-CoV-2 stated, "At present, there are no known clinical findings, immunological assays or biomarkers that can differentiate any severe infection from immune-enhanced disease, whether by measuring antibodies, T cells or intrinsic host responses (7) ." This conclusion inspired our study. The results demonstrate that Abs to a specific epitope from N protein plus disease risk factors strongly correlate with COVID-19 disease severity. The DRFS of patients with αEp9 Abs strongly correlates with COVID-19 disease severity (Pearson''s r = 0.72, p-value <0.0001, and R 2 = 0.52) (Fig. 4A) . doi = 10.1101/2020.10.15.341743 id = cord-103306-1wc3f1rl author = Sengupta, Sourodip title = Matrix metalloproteinases and tissue inhibitors of metalloproteinases in murine coronavirus-induced neuroinflammation date = 2020-09-18 keywords = A59; MHV; rsa59 summary = Elevated mRNA and protein levels of tissue inhibitors of metalloproteinases 1 (TIMP-1) in MHV-A59 infection are suggestive of a TIMP-1 mediated host antiviral response. Total RNA was isolated from mock and virus-infected brain tissues 238 for expression analysis of viral nucleocapsid and Mmp genes through RT-qPCR. MMPs. To understand the regulation of MMPs upon MHV-A59 infection, we also 254 considered the gene expression of TIMPs. As described above, total RNA from brain samples 255 of mock and MHV-A59 infected mice were subjected to RT-qPCR using specific primers 256 12 (Table 1) to determine the transcript levels of Timp1, Timp2, Timp3, and Timp4. While Timp1 mRNA 260 followed a similar expression pattern as the Mmps following MHV-A59 infection-induced 261 inflammation, its protein levels remained high throughout post-infection, as shown in the 262 representative figure (Fig. 2, B) . Transcript levels of Parkinson''s disease 7 312 (Park7) gene were significantly upregulated following RSA59 infection and remained 313 elevated p.i compared to mock-infected samples (Fig. 7, A; p<0.05). doi = 10.1101/2020.09.17.302877 id = cord-102778-b1ul7zug author = Serrao, Juliet.M. title = Alfaxalone activates Human Pregnane-X Receptors with greater efficacy than Allopregnanolone: an in-vitro study with implications for neuroprotection during anesthesia date = 2020-09-06 keywords = PXR; alfaxalone; allopregnanolone summary = doi = 10.1101/2020.09.05.284075 id = cord-102206-mb0qcd0b author = Seymour, Elif title = Configurable Digital Virus Counter on Robust Universal DNA Chips date = 2020-10-22 keywords = EBOV; IRIS; dna summary = doi = 10.1101/2020.10.22.350579 id = cord-350558-qfdp4ov9 author = Shaban, Mohammed Samer title = Inhibiting coronavirus replication in cultured cells by chemical ER stress date = 2020-08-26 keywords = Fig; cell; protein summary = We found that the ER stress inducer thapsigargin efficiently inhibits coronavirus (HCoV-229E, MERS-CoV, SARS-CoV-2) replication in different cell types, (partially) restores the virus-induced translational shut-down, and counteracts the CoV-mediated downregulation of IRE1α and the ER chaperone BiP. A detailed proteomics analysis reveals multiple thapsigargin-78 regulated pathways and a network of proteins that are suppressed by CoV but (re)activated by 79 chemically stressed infected cells. we determined the expression levels of 166 components of the ER stress pathway KEGG 04141 85 "protein processing in endoplasmic reticulum" in human HuH7 liver cells, a commonly used cellular 86 model for CoV replication, in response to infections with HCoV-229E and MERS-CoV, respectively. The highly inducible HERPUD1 protein has an essential scaffolding function for the organization of searching our proteomics data for further ERAD factors we were able to retrieve a total of 34 (for 284 MERS-CoV) and 20 (for SARS-CoV-2) proteins of the canonical ERQC and ERAD pathways for 285 which a differential expression was observed in virus-infected cells treated with thapsigargin (Fig. 286 5H) . doi = 10.1101/2020.08.26.266304 id = cord-324480-7u5lh4jx author = Sharma, A. title = Structural stability of SARS-CoV-2 degrades with temperature date = 2020-10-14 keywords = CoV-2; SARS summary = Here we have used atomic force microscopy to examine the structural stability of individual SARS-CoV-2 virus like particles at different temperatures. This is consistent with other existing non-mechanistic studies of viral infectivity, provides a single particle perspective on viral seasonality, and strengthens the case for a resurgence of COVID-19 in winter. However an understanding of how SARS-CoV-2 survives different environmental conditions is still incomplete and mechanisms of virus particle degradation are poorly mapped out. A key challenge in studying SARS-CoV-2 is the extreme level of threat associated with the live virus and the resultant need for high safety standards for such work. Here we used this technology to study the stability of the viral envelope and associated proteins (M, E, and S) under different environmental conditions. Environmental stability of SARS-CoV-2 on different types of surfaces under indoor and seasonal climate conditions doi = 10.1101/2020.10.12.336818 id = cord-103523-46hn2249 author = Shaw, Dario R. title = Extracellular electron transfer-dependent anaerobic oxidation of ammonium by anammox bacteria date = 2019-11-26 keywords = EET; Fig; NH4 summary = Here we show using complementary approaches that in the absence of NO2−, freshwater and marine anammox bacteria couple the oxidation of NH4+ with transfer of electrons to carbon-based insoluble extracellular electron acceptors such as graphene oxide (GO) or electrodes poised at a certain potential in microbial electrolysis cells (MECs). However, it is still unknown whether anammox bacteria have EET 27 capability and can couple the oxidation of NH4 + with transfer of electrons to carbon-based 28 insoluble extracellular electron acceptors. However, it is still unknown whether anammox bacteria have EET 27 capability and can couple the oxidation of NH4 + with transfer of electrons to carbon-based 28 insoluble extracellular electron acceptors. Here we show using complementary approaches that in 29 the absence of NO2 -, freshwater and marine anammox bacteria couple the oxidation of NH4 + with 30 transfer of electrons to carbon-based insoluble extracellular electron acceptors such as graphene 31 oxide (GO) or electrodes poised at a certain potential in microbial electrolysis cells (MECs). doi = 10.1101/855817 id = cord-102358-kf04tra6 author = Sheffield, Lakbira title = Age-dependent impairment of disease tolerance is associated with a robust transcriptional response following RNA virus infection in Drosophila date = 2020-09-21 keywords = Drosophila; FHV; figure summary = doi = 10.1101/2020.09.21.307017 id = cord-103015-3dxwbmd2 author = Shengjuler, Djoshkun title = The RNA-binding site of poliovirus 3C protein doubles as a phosphoinositide-binding domain date = 2017-08-04 keywords = PI4P; PIP; RNA; figure summary = Molecular-docking simulations revealed a putative site of PIP binding to poliovirus (PV) 3C protein that was validated using NMR spectroscopy. 93 Validation of PIP-binding sites by NMR 94 In order to test the validity of our docking observations, we titrated 15 N-labeled 3C protein 95 with soluble dibutyl-PI4P to observe potential NMR chemical shift perturbations (CSPs), which 96 would indicate chemical environment changes in the presence of PI4P (Figure 2) . Out of the three 97 basic residues of the major cluster that were predicted to interact with the PI4P, R13 showed the 98 largest CSP (Figure 2A ). Titration of PI4P into a solution containing 3C caused CSPs that were consistent 249 with the major PI4P-binding site observed computationally (Figure 2A) . doi = 10.1101/172742 id = cord-103940-a2cqw8kg author = Shi, Yuejun title = Insight into vaccine development for Alpha-coronaviruses based on structural and immunological analyses of spike proteins date = 2020-06-09 keywords = RBD; SARS summary = Currently, structural studies have shown that Alpha-coronavirus (HCoV-229E) and Beta-coronavirus (SARS-CoV and SARS-CoV-2) RBDs are in lying and standing state, respectively. In this study, 130 we selected SARS-CoV, SARS-CoV-2, and HCoV-229E as models, which adopt the 131 two RBD states, and evaluated and compared immune responses to the S trimers and 132 7 RBDs of these coronaviruses through immunological and bioinformatics approaches. 133 We also investigated the mechanism through which the HCoV-229E S trimer 134 produced effective nAbs. Finally, we provide possible vaccine strategies for alphaTo address this issue, we performed B-cell epitope predictions for the S trimers 152 and RBDs of alpha-CoV (HCoV-229E) and beta-CoVs (SARS-CoV and 153 SARS-CoV-2). Taken together, these results showed that the intact and stable S1 subunit of 240 HCoV-229E is a prerequisite for the production of effective nAbs. Furthermore, our experimental results show that RBD has a higher ability to bind 242 12 to the receptor hAPN (Fig. 4B) , which indicates that the characteristics of RBD itself 243 may lead to the generation of less neutralizing antibodies. doi = 10.1101/2020.06.09.141580 id = cord-103924-mhgnqi80 author = Shin, Donghyuk title = Novel class of OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection date = 2020-04-28 keywords = Fig; OTU summary = MS analysis of catalytically inactive LotB and LotC identified different categories of host-substrates for these two related DUBs. Together, our results provide new structural insights of bacterial OTU deubiquitinases and indicate distinct roles of bacterial deubiquitinases in host-pathogen interactions. Whereas the overall fold of the 174 catalytic core of LotB and LotC resembles that of other OTU-deubiquitinases, both showed clear 175 differences in the helical arm region, which has been shown to interact with ubiquitin and it serves 176 as an S1 binding site (Mevissen et al., 2013) . To address this, we performed ubiquitin 192 docking into both LotB and LotC, followed by molecular dynamics (MD) simulations for 600 ns 193 ( Fig. 4aTo gain better insights into the physiological roles of LotB and LotC, we decided to identify their 216 interacting proteins or substrates. doi = 10.1101/2020.04.25.060954 id = cord-254636-3lr008th author = Shishir, Tushar Ahmed title = In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh date = 2020-08-16 keywords = Bangladesh; CoV-2; SARS summary = We conducted comparative analysis of publicly available whole-genome sequences of 64 SARS-CoV-2 isolates in Bangladesh and 371 isolates from another 27 countries to predict possible transmission routes of COVID19 to Bangladesh and genomic variations among the viruses. Compared to the ancestral SARS-CoV-2 sequence reported from China, the isolates in Bangladesh had a total of 180 mutations in the coding region of the genome, and 110 of these were missense. We conducted comparative analysis of publicly available genome sequences of SARS-CoV-2 from 27 countries to predict the origin of viruses in Bangladesh by studying a time-4 resolved phylogenetic relationship. Later, we analyzed the variants present in different isolates of Bangladesh to understand the pattern of mutations in relation to the ancestral Wuhan strain, find unique mutations, and possible effect of these mutations on the stability of encoded proteins, and selection pressure on genes. doi = 10.1101/2020.07.20.212563 id = cord-331611-pwj226j0 author = Shrimp, Jonathan H. title = An Enzymatic TMPRSS2 Assay for Assessment of Clinical Candidates and Discovery of Inhibitors as Potential Treatment of COVID-19 date = 2020-06-23 keywords = AMC; SARS; TMPRSS2 summary = We demonstrate effectiveness to quantify inhibition down to subnanomolar concentrations by assessing the inhibition of camostat, nafamostat and gabexate, clinically approved agents in Japan for pancreatitis due to their inhibition of trypsin-like proteases. The structurally related trypsin-like serine protease inhibitor nafamostat was shown to similarly inhibit spike protein-mediated cell fusion of MERS-CoV 7 . Herein we report the development of a TMPRSS2 fluorogenic biochemical assay and testing of clinical repurposing candidates for COVID19. To identify inhibitors of TMPRSS2 that may be used to validate its role in SARS-CoV-2 entry and potentially expedite to clinical trials, we developed a biochemical assay using active TMPRSS2 protease and a fluorogenic peptide substrate ( Figure 1B) . We developed a fluorogenic biochemical assay for measuring recombinant human TMPRSS2 activity for high-throughput screening that can be readily replicated and used to demonstrate that nafamostat is a more potent inhibitor than camostat and gabexate. doi = 10.1101/2020.06.23.167544 id = cord-102809-06izdji8 author = Siddiqui, Nabil A. title = Radiolabelled Bacterial Metallophores as Targeted PET Imaging Contrast Agents for Accurate Identification of Bacteria and Outer Membrane Vesicles in vivo date = 2020-08-06 keywords = Fig; pet summary = doi = 10.1101/2020.08.06.240119 id = cord-102668-1yc38ok1 author = Siddiqui, Shoib S. title = Acidosis, Zinc and HMGB1 in Sepsis: A Common Connection Involving Sialoglycan Recognition date = 2020-07-15 keywords = HMGB1; blood; figure summary = doi = 10.1101/2020.07.15.198010 id = cord-312473-7i7efdp2 author = Sidhom, John-William title = Analysis of SARS-CoV-2 specific T-cell receptors in ImmuneCode reveals cross-reactivity to immunodominant Influenza M1 epitope date = 2020-06-20 keywords = SARS summary = We first examined the distribution of TCRs within the McPas database over the types of pathogens present in the database and cross-referenced the SARS-CoV-2 specific TCRs into the McPas database ( Figure 1A) , and we noted that there was a statistically significant enrichment (from 17.3% to 32.9%) of SARS-CoV-2 specific TCRs that had known specificity to the immunodominant M1 GILGFVFTL epitope We then examined the distribution of TCRs within the ImmuneCode database across the various open readings frames (orfs) and mapped the M1 specific TCRs within this database ( Figure 1B) . In conclusion, while these results are preliminary in a small cohort of individuals, we have identified a set of TCRs that is known to both recognize an immunodominant epitope derived from Influenza and SARS-CoV-2, suggesting that immune control of one infection may play a role in the control of the other. doi = 10.1101/2020.06.20.160499 id = cord-296997-ba7f2mf3 author = Sikora, Mateusz title = Map of SARS-CoV-2 spike epitopes not shielded by glycans date = 2020-07-03 keywords = Appendix; Fig; SARS summary = To identify possible antibody binding sites not shielded by glycans, we performed multi-microsecond molecular dynamics simulations of a 4.1 million atom system containing a patch of viral membrane with four full-length, fully glycosylated and palmitoylated S proteins. By mapping steric accessibility, structural rigidity, sequence conservation and generic antibody binding signatures, we recover known epitopes on S and reveal promising epitope candidates for vaccine development. Our simulation system contained four membrane-embedded SARS-CoV-2 S proteins assembled from resolved structures where available and models for the missing parts (SI Appendix, Fig. S5 ). In the ray analysis, we illuminated the protein model by diffuse light; in the Fab docking analysis, we performed rigid body Monte Carlo simulations of S and the SARS-CoV-2 antibody CR3022 Fab to determine the steric accessibility to an antibody Fab. To account for protein and glycan mobility, we performed both analyses individually for 4 × 193 snapshots taken at 10 ns time intervals from the 1.93 µs MD simulation with four glycosylated S proteins. doi = 10.1101/2020.07.03.186825 id = cord-295765-c7o2ukm6 author = Silvas, Jesus A. title = Inhibitors of VPS34 and lipid metabolism suppress SARS-CoV-2 replication date = 2020-07-20 keywords = SARS summary = VPS34 inhibitors, Orlistat and Triacsin C inhibited virus growth in Vero E6 cells and in the human airway epithelial cell line Calu-3, acting at a post-entry step in the virus replication cycle. As SARS-CoV-2 replication 174 damages the cell monolayer, impedance measurements decrease over time, providing a detailed 175 assessment of infection kinetics. Based on the toxicity window of 1-20 221 h.p.t. determined with the VPS34 inhibitors, neither Triacsin C nor Orlistat induced early 222 cytotoxic effects, even at the highest concentrations of 50uM and 500uM, respectively ( Figure 223 3A and 3C). Here, we demonstrate that two VPS34 inhibitors, Orlistat, and Triacsin C each have clear effects 308 on SARS-CoV-2 replication and the morphology of viral replication centers. In contrast, the compounds did not exhibit any activity against 384 SARS-CoV-2 in Vero E6 cells whereas Triacsin C did. doi = 10.1101/2020.07.18.210211 id = cord-326257-rcv8sh22 author = Simmonds, P. title = Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses – causes and consequences for their short and long evolutionary trajectories date = 2020-05-01 keywords = RNA; SARS; c->u summary = C->U transitions underpinned almost half of the amino acid differences between SARS-CoV-2 variants, and occurred preferentially in both 5''U/A and 3''U/A flanking sequence contexts comparable to favoured motifs of human APOBEC3 proteins. Importance The evidence that much of sequence change in SARS-CoV-2 and other coronaviruses may be driven by a host APOBEC-like editing process has profound implications for understanding their short and long term evolution. The possibility that the initial diversity within a viral population was largely host-induced would have major implications for 70 evolutionary reconstruction of SARS-CoV-2 variants in the current pandemic, as well as in our understanding both of host antiviral pathways against coronaviruses and the longer term shaping effects on their genome composition. To formally analyse 105 the excess of C->U transitions we calculated an index of asymmetry (frequency[C->U] / f[U->C]) x (fU/fC) and compared this with degrees of sequence divergence and dN/dS ratio in SARS-CoV-2 and other coronavirus datasets (Fig. 2B, 2C ). doi = 10.1101/2020.05.01.072330 id = cord-290290-wyx9ib7s author = Sinegubova, Maria V. title = High-level expression of the monomeric SARS-CoV-2 S protein RBD 320-537 in stably transfected CHO cells by the EEF1A1-based plasmid vector date = 2020-11-05 keywords = CHO; CoV-2; RBD; SARS; cell; protein summary = title: High-level expression of the monomeric SARS-CoV-2 S protein RBD 320-537 in stably transfected CHO cells by the EEF1A1-based plasmid vector Based on the previously developed p1.1 vector, containing the regulatory sequences of the Eukaryotic translation elongation factor 1 alpha gene (EEF1A1) from Chinese hamster, we created two expression constructs encoding SARS-CoV-2 RBD with C-terminal c-myc and polyhistidine tags. Previously we have developed the plasmid vector p1.1, containing large fragments of non-coding DNA from the EEF1A1 gene of the Chinese hamster and fragment of the Epstein-Barr virus long terminal repeat concatemer [21] and employed it for unusually high-level expression of various proteins in CHO cells, including blood clotting factors VIII [22] , IX [23] , and heterodimeric follicle-stimulating hormone [24] . We have proposed that SARS-CoV-2 RBD, suitable for in vitro diagnostics use, may be expressed in large quantities by stably transfected CHO cells, bearing the EEF1A1-based plasmid. doi = 10.1101/2020.11.04.368092 id = cord-288705-f3zqhpx1 author = Slaine, Patrick title = Thiopurines activate an antiviral unfolded protein response that blocks viral glycoprotein accumulation in cell culture infection model date = 2020-10-01 keywords = Fig; IAV; UPR summary = title: Thiopurines activate an antiviral unfolded protein response that blocks viral glycoprotein accumulation in cell culture infection model Selective disruption of IAV glycoprotein processing and accumulation by 6-TG and 6-TGo correlated with unfolded protein response (UPR) activation and HA accumulation could be partially restored by the chemical chaperone 4-phenylbutyrate (4PBA). Thiopurines inhibited replication of the human coronavirus OC43 (HCoV-OC43), which also correlated with UPR/ISR activation and diminished accumulation of ORF1ab and nucleocapsid (N) mRNAs and N protein, which suggests broader disruption of coronavirus gene expression in ER-derived cytoplasmic compartments. Our results suggest that 406 the effects are unlikely to be mediated through DNA or RNA incorporation of 6-TG because 1) 407 replicative stress does not specifically induce UPR; 2) among viral proteins, glycoprotein 408 accumulation and processing was preferentially disrupted; 3) messenger RNA levels of HA and 409 NA were not affected. doi = 10.1101/2020.09.30.319863 id = cord-103538-vh6ma7k7 author = Smaldino, Paul E. title = Coupled Dynamics of Behavior and Disease Contagion Among Antagonistic Groups date = 2020-10-05 keywords = behavior; figure; group summary = We analyze a simple model of coupled behavior-change and infection in a structured population characterized by homophily and outgroup aversion. While we might expect strong selection-both biological and cultural-for adaptive responses to epidemics, complications such as the potentially differing time 33 scales of culture and disease transmission and the existence of social structures that shape adoption may complicate convergence to adaptive behavioral solutions. Unlike a disease, which is reasonably modeled as equally transmissible between any susceptible-infected pairing, where behavior is concerned, susceptible individuals are more likely to adopt when interacting with in-126 group adopters, but less likely to adopt when interacting with outgroup adopters. Not so with outgroup aversion, in which the peak infection rates increase relative to the low homophily case ( Figure 3E , F). However, when R 0 is high enough and outgroup aversion induces 258 group differences in behavior adoption, strong homophily among group 2 can lead to larger, albeit delayed, epidemics in the initially-uninfected segment of the population. doi = 10.1101/2020.06.17.157511 id = cord-103163-0rreoh4o author = Smith, Sydni Caet title = Reovirus RNA recombination is sequence directed and generates internally deleted defective genome segments during passage date = 2020-10-22 keywords = DVG; PCR; RNA; Reoviridae summary = We determined the titers and RNA segment profiles of reovirus (rsT1L and rsT3D I ) and rotavirus (rsSA11) laboratory strains that had been rescued by reverse genetics then serially passaged ten times, each in triplicate lineages, in cultured cells. The two reoviruses accumulated non-canonical RNAs that retain 5′ and 3′ termini and feature one or more large internal deletions, while the rotavirus rarely accumulated such DVGs. Analyses of next-generation RNA-sequencing data sets from purified rsT1L reovirus RNA revealed many junctions, with hot spots for recombination in specific viral gene segments. Taken together, lin1 RNA profiles suggest non-canonical RNA species that differ in length but have identical termini to the parental segments accumulate variably during reovirus and rotavirus serial passage in cultured cells. doi = 10.1101/2020.10.19.346031 id = cord-103739-mmkrwj8t author = Snijder, Eric J. title = A unifying structural and functional model of the coronavirus replication organelle: tracking down RNA synthesis date = 2020-03-24 keywords = MERS; RNA; membrane; replication summary = Metabolic labelling of newly-synthesized viral RNA followed by quantitative EM autoradiography revealed abundant viral RNA synthesis associated with DMVs in cells infected with the beta-CoVs MERS-CoV and SARS-CoV, and the gamma-CoV infectious bronchitis virus. In infected cells, the CoV RNA-23 synthesizing machinery associates with modified endoplasmic reticulum membranes that are 24 transformed into the viral replication organelle (RO). In infected cells, the CoV RNA-23 synthesizing machinery associates with modified endoplasmic reticulum membranes that are 24 transformed into the viral replication organelle (RO). 106 double-membrane spherules (DMSs) 107 We first set out to analyse the ultrastructure of MERS-CoV-infected Huh7 cells under sample 108 preparation conditions favourable for autoradiography (see Materials and Methods) (Fig 1, S1 109 Video). Association of polioviral proteins of the P2 89 genomic region with the viral replication complex and virus-induced membrane synthesis as 90 visualized by electron microscopic immunocytochemistry and autoradiography doi = 10.1101/2020.03.24.005298 id = cord-305858-gp1u4kh7 author = Song, Xiang title = High expression of angiotensin-converting enzyme-2 (ACE2) on tissue macrophages that may be targeted by virus SARS-CoV-2 in COVID-19 patients date = 2020-07-19 keywords = ACE2; COVID-19; SARS; USA; figure summary = To better understand the pathogenesis of COVID-19 and build up the host anti-viral immunity, we examined the levels of ACE2 expression on different types of immune cells including tissue macrophages. To determine whether platelets were directly targeted by SARS-CoV-2 or trigged by viral inflammatory reactions, we examined the ACE2 expression on the highly-purified CD41b + CD42a + platelets from human peripheral blood ( Figure 3A Our previous work established that platelets could release mitochondria contributing to the immune modulation and islet b-cell regeneration [13] . Thus, the virus-infected alveolar macrophages play a critical role in the pathogenesis of COVID-19 and SARS [28] [29] [30] and may recruit the lung infiltration of additional immune cells through predominantly releasing cytokines and chemokines [31, 32] , resulting in pulmonary edema and hypoxemia: the hallmark of acute respiratory distress syndrome (ARDS) ( Figure 6 ). doi = 10.1101/2020.07.18.210120 id = cord-102486-llmfgavd author = Sprenger, Kayla G. title = Optimizing immunization protocols to elicit broadly neutralizing antibodies date = 2020-01-06 keywords = Ags; Fig summary = doi = 10.1101/2020.01.04.894857 id = cord-340432-vm6m0kb4 author = Srivastava, Sukrit title = Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch Vaccines designed by reverse epitomics approach, shows potential to cover large ethnically distributed human population worldwide date = 2020-09-06 keywords = Patches; SARS summary = title: Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch Vaccines designed by reverse epitomics approach, shows potential to cover large ethnically distributed human population worldwide Methodology A novel reverse epitomics approach, "overlapping-epitope-clusters-to-patches" method is utilized to identify multiple antigenic regions from the SARS-CoV-2 proteome. Multi-Patch Vaccine designing to combat SARS-CoV-2 infection by reverse epitomics approach, "Overlapping-epitope-clusters-to-patches" method. In the present study, we have reported a novel method to design a 1170 vaccine against SARS-CoV-2 by utilizing multiple antigenic patches from the viral 1171 proteins. The designed MPVs from the antigenic patches of SARS-CoV-2 proteins 1182 have several advantages over to the subunit and multi-epitope based vaccines. Design of multi epitope-based peptide vaccine against E 1409 protein of human 2019-nCoV: An immunoinformatics approach Multi-epitope based peptide 1549 vaccine design against SARS-CoV-2 using its spike protein In silico approach for designing of a multi-epitope based 1587 vaccine against novel Coronavirus (SARS-COV-2) doi = 10.1101/2020.09.06.284992 id = cord-261961-u4d0vvmq author = St-Germain, Jonathan R. title = A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research date = 2020-08-28 keywords = SARS; protein; virus summary = To this end, we conducted a mass spectrometry-based characterization of the SARS-CoV-2 virion and infected cell lysates, identifying 189 unique high-confidence virus tryptic peptides derived from 17 different virus proteins, to create a high quality resource for use in targeted proteomics approaches. The resulting viral tryptic peptides were identified using nanoflow liquid chromatography -tandem mass spectrometry (LC-MS/MS; Fig 1A, Together, these data confirm and expand upon previous proteomic analyses of SARS-CoV-2 virions, infected cells 4, 7-11 and patient samples [12] [13] [14] , and provide a library of high quality virus peptide spectra covering 17 virus proteins that can be used for the creation of peptide spectral libraries and targeted proteomics approaches. To this end, we also undertook an analysis of SARS-CoV-2 virions and infected Vero cell lsyates using data-dependent acquisition tandem mass spectrometry, and identified 189 unique tryptic peptides, assigned to 17 different virus proteins. doi = 10.1101/2020.08.28.269175 id = cord-342942-1s32o9m8 author = Stamatakis, George title = Generation of SARS-CoV-2 S1 spike glycoprotein putative antigenic epitopes in vitro by intracellular aminopeptidases date = 2020-06-22 keywords = HLA; SARS; erap1 summary = Here, we analyzed the proteolytic processing of overlapping precursor peptides spanning the entire sequence of the S1 spike glycoprotein of SARS-CoV-2, by three key enzymes that generate antigenic peptides, aminopeptidases ERAP1, ERAP2 and IRAP. In this study, we utilized a novel approach to analyze antigen trimming by intracellular aminopeptidases ERAP1, ERAP2 and IRAP, focusing on the largest antigen of SARS-CoV-2, namely S1 spike glycoprotein. To investigate the trimming of antigenic epitope precursors by intracellular aminopeptidases that generate antigenic peptides, we used a mixture of 315 synthetic peptides derived from the sequence of the SARS-CoV-2 S1 spike glycoprotein. Our analysis of the largest antigen of SARS-CoV-2, S1 spike glycoprotein, suggests that aminopeptidase trimming can be a significant filter that helps shape which peptides will be presented by HLA. doi = 10.1101/2020.06.22.164681 id = cord-275690-83nrzfon author = Stanifer, Megan L. title = Critical role of type III interferon in controlling SARS-CoV-2 infection, replication and spread in primary human intestinal epithelial cells date = 2020-04-24 keywords = CoV-2; Fig; IFN; SARS summary = title: Critical role of type III interferon in controlling SARS-CoV-2 infection, replication and spread in primary human intestinal epithelial cells Our results demonstrate that human intestinal epithelial cells fully support SARS-CoV-2 infection, replication and production of infectious de-novo virus particles. Importantly, and in agreement with the results observed in cells depleted of the type III IFN receptor, this increase in infectivity was also associated with an increase in infectious denovo virus particle production ( Fig. 3G ). All together, these results strongly support a model where the type III IFN mediated signaling controls SARS-CoV-2 infection in human intestinal epithelial cells. All together these results show that human colon organoids can support SARS-CoV-2 infection, replication and spread and that the type III IFN response plays a critical role in controlling virus replication. doi = 10.1101/2020.04.24.059667 id = cord-303868-aes92l6s author = Steffen, Tara L. title = The receptor binding domain of SARS-CoV-2 spike is the key target of neutralizing antibody in human polyclonal sera date = 2020-08-22 keywords = RBD; SARS summary = In this study, we identify the spike protein subunits that contain antigenic determinants and examine the neutralization capacity of polyclonal sera from a cohort of patients that tested qRT-PCR-positive for SARS-CoV-2. In this study, we identify the spike protein subunits that contain antigenic determinants and examine the neutralization capacity of polyclonal sera from a cohort of patients that tested qRT-PCR-positive for SARS-CoV-2. This suggests that polyclonal antibody binding to the RBD domain of the spike protein represents the key target of neutralizing antibody to SARS-CoV-2 after natural infection. Most importantly, our antigen-specific antibody depletion approach demonstrated that the RBD domain of the spike protein is responsible for 70% +/-18.9% of the human polyclonal neutralizing antibody activity to spike after natural SARS-CoV-2 infection. Although our study shows that the dominant target of IgG neutralizing antibody response after natural SARS-CoV-2 infection is the RBD domain of the spike protein, we have evaluated a limited number (n=10) of patients by antigen-specific antibody depletion. doi = 10.1101/2020.08.21.261727 id = cord-353209-qkhfp66l author = Steiner, Daniel J. title = Array-based analysis of SARS-CoV-2, other coronaviruses, and influenza antibodies in convalescent COVID-19 patients date = 2020-06-16 keywords = CoV-2; SARS; air summary = We report a multiplex label-free antigen microarray on the Arrayed Imaging Reflectometry (AIR) platform for detection of antibodies to SARS-CoV-2, SARS-CoV-1, MERS, three circulating coronavirus strains (HKU1, 229E, OC43) and three strains of influenza. Aminereactive substrates for fabrication of AIR arrays were provided by Adarza BioSystems, Inc. For ELISA assays, SARS-CoV-2 full-length spike and RBD were produced in-house using a mammalian expression system, 20,21 as was influenza A/H1N1/California 2009 hemagglutinin. To that end, we have presented preliminary data on a 15-plex array on the AIR platform, developed in response to the need to study SARS-CoV-2 but incorporating antigens for other coronaviruses and influenza. Responses to SARS-CoV-2 antigens on the array effectively discriminated between serum samples from uninfected and COVID-19 convalescent subjects, with generally good correlation to ELISA data. doi = 10.1101/2020.06.15.153064 id = cord-305496-t8ykkekl author = Stone, E. Taylor title = Characterization of cells susceptible to SARS-COV-2 and methods for detection of neutralizing antibody by focus forming assay date = 2020-08-21 keywords = HPI; SARS; Vero summary = One such tool for evaluating neutralizing antibody response is a 88 plaque/focus neutralization reduction test (PRNT/FRNT), which evaluates the ability of polyclonal 89 sera samples to prevent or reduce infection of a cell monolayer in vitro. We examined the impact of cell density on foci formation for both Vero WHO and Vero E6 cells 144 by plating identical dilutions of SARS-CoV-2 virus stocks on 96-well plates seeded with differing 145 numbers of WHO or E6 cells (3 × 104, 1.5 × 104 or 3 × 104 cells/well) one day prior to infection 146 of the cell monolayer. To determine the optimal time frame for infection of SARS-CoV-2 on a Vero WHO cell 172 monolayer to form individual foci, we tested a variety of incubation times. The FFA relies on an immunostaining protocol of an infected cell monolayer in order to 197 quantify infectious virus titer and is therefore dependent upon SARS-CoV-2-specific antibody 198 doi = 10.1101/2020.08.20.259838 id = cord-303399-s1hbpvn7 author = Straus, Marco R. title = SPINT2 inhibits proteases involved in activation of both influenza viruses and metapneumoviruses date = 2019-08-31 keywords = HMPV; SPINT2 summary = SPINT2 treatment resulted in the cleavage and fusion inhibition of full-length influenza A/CA/04/09 (H1N1) HA, A/Aichi/68 (H3N2) HA, A/Shanghai/2/2013 (H7N9) HA and HMPV F when activated by trypsin, recombinant matriptase or KLK5. https://doi.org/10.1101/752592 doi: bioRxiv preprint vivo situation and requires validation by expressing the full-length fusion proteins in a cell culture model 3 to test cleavage and cleavage inhibition of the respective protease (39). To test SPINT2-mediated cleavage inhibition of full-length HA we expressed the HAs of A/CA/04/09 9 (H1N1), A/x31 (H3N2) and A/Shanghai/2/2013 (H7N9) in 293T cells and added recombinant matriptase or 10 KLK5 protease that were pre-incubated with 10nM or 500nM SPINT2. To understand whether SPINT2 was able to inhibit or reduce the growth of virus in a cell culture 20 model over the course of 48 hours we transfected cells with human TMPRSS2 and human matriptase, two 21 major proteases that have been shown to be responsible for the activation of distinct influenza A subtype 22 doi = 10.1101/752592 id = cord-346532-4xpnd93d author = Strömich, Léonie title = Allosteric Hotspots in the Main Protease of SARS-CoV-2 date = 2020-11-06 keywords = SARS; site summary = Here, we report the allosteric communication pathways in the main protease dimer by using two novel fully atomistic graph theoretical methods: Bond-to-bond propensity analysis, which has been previously successful in identifying allosteric sites without a priori knowledge in benchmark data sets, and, Markov transient analysis, which has previously aided in finding novel drug targets in catalytic protein families. Bond-to-bond propensities have been shown to successfully detect allosteric sites on proteins [43] and we here present 141 the results in the SARS-CoV-2 M pro to that effect. After a full Bond-to-bond propensity analysis and quantile regression to rank all residues, we are able to score the active 156 site to obtain a measure for the connectivity towards the catalytic center (Tab. S8). A complementary, node-based method, Markov Transient analysis (MTA) 276 identifies areas of the protein that are significantly connected to a site of interest, the source, such as the active site, and 277 obtains the signal propagation that connects the two sites at the atomistic level. doi = 10.1101/2020.11.06.369439 id = cord-291710-ixun0c8g author = Su, Haixia title = Discovery of baicalin and baicalein as novel, natural product inhibitors of SARS-CoV-2 3CL protease in vitro date = 2020-04-14 keywords = CoV-2; SARS; baicalein summary = A crystal structure of SARS-CoV-2 3CLpro in complex with baicalein, the first non-covalent, non-peptidomimetic small-molecule inhibitor, was also determined, revealing a unique binding mode of this natural product with the protease. To validate the binding of baicalin and baicalein with SARS-CoV-2 3CLpro and exclude the suspicion of being the pan-assay interference compounds (PAINS) (15) , their binding affinities with the protease were measured by isothermal titration calorimetry (ITC), widely known as an invaluable tool used to determine thermodynamic parameters of protein-ligand interactions such as Kd (Fig. 1, A and B ; Table 1 ). Moreover, the ITC profiles in combination with their chemical structures suggest that baicalin and baicalein act as noncovalent inhibitors of SARS-CoV-2 3CLpro with a high ligand binding efficiency. The mode of action of baicalein and the structural determinants associated with its binding with SARS-CoV-2 3CLpro were further explored using X-ray protein crystallography. doi = 10.1101/2020.04.13.038687 id = cord-103046-w8bm4p44 author = Suarez, David L. title = Lack of susceptibility of poultry to SARS-CoV-2 and MERS-CoV date = 2020-06-16 keywords = MERS summary = Multiple studies have examined the susceptibility of domestic animals to CoV-2 to establish the risk of zoonotic transmission and two studies have shown chickens and 24 Middle East Respiratory Syndrome coronavirus (MERS-CoV), another coronavirus of 26 high concern associated with zoonotic infection, was first detected in patients with severe acute 27 lower respiratory tract disease in Saudi Arabia in 2012. For MERS-CoV, dromedary 35 camels appear to be the primary natural reservoir of infection to humans, but other domestic 36 animals seem to be susceptible to infection (7, 8) . Because poultry are so widespread and have close and extended contact with humans, 39 and other mammals in many production systems, including live animal markets, susceptibility 40 were conducted with SARS-CoV-2 and MERS-CoV in five common poultry species. Susceptibility of ferrets, cats, 109 dogs, and other domesticated animals to SARS-coronavirus 2. Middle East Respiratory Syndrome (MERS), and SARS-114 Middle East 118 respiratory syndrome coronavirus infection in non-camelid domestic mammals. doi = 10.1101/2020.06.16.154658 id = cord-319447-xanewi59 author = Sun, Jiya title = Comparative transcriptome analysis reveals the intensive early-stage responses of host cells to SARS-CoV-2 infection date = 2020-05-01 keywords = MERS; SARS; figure summary = To gain insights, we performed high-throughput sequencing that generated time-series data simultaneously for bioinformatics analysis of virus genomes and host transcriptomes implicated in SARS-CoV-2 infection. The early rapid host responses were potentially attributed to the high efficiency of SARS-CoV-2 entry into host cells, underscored by evidence of a remarkably up-regulated gene expression of TPRMSS2 soon after infection. In this study, we used the SARS-CoV-2 strain isolated from patients [11] to infect in vitro Calu-3 cells, and performed RNA sequencing to determine the time-series transcriptome profiling data of the host. Next, to gain possible explanations for the distinct patterns in host antiviral capacity and cytokine production during SARS-CoV-2 infection, dynamic expression of four types of key genes were evaluated, including virus receptors for cell entry, pathogen recognition receptors (PRRs) for an innate immune startup, regulator genes for induction of antiviral-related genes and interferon production (Figure 4) . doi = 10.1101/2020.04.30.071274 id = cord-312305-ll29frwc author = Sun, Shihui title = Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2 date = 2020-11-11 keywords = COVID-19; CoV-2; Fig; SARS; mouse summary = Herein, we generated and characterized a novel mouse-adapted SARS-CoV-2 strain named MASCp36 that causes acute respiratory symptoms and mortality in standard laboratory mice. We further characterized the in vivo replication dynamics of MASCp6 in both young and aged mice, and the results from qRT-PCR showed that high levels of SARS-CoV-2 subgenomic RNAs were persistent in the lung and tracheas till 4 day post infection (dpi) in aged mice (Fig. 1E) . The skewed age distribution of COVID-19 disease was reproduced in the MASCp36 infected mouse model where more severe symptoms were observed in aged mice when compared to young mice. In addition to the age-related skewed distribution of COVID-19, gender-related differences in distribution of COVID-19 disease is also recapitulated in this MASCp36 infected mouse model with increased susceptibility and enhanced pathogenicity observed in male mice when compared to their female counterparts. doi = 10.1101/2020.11.10.377333 id = cord-326666-melz5fq4 author = Sun, Weitao title = The discovery of gene mutations making SARS-CoV-2 well adapted for humans: host-genome similarity analysis of 2594 genomes from China, the USA and Europe date = 2020-09-03 keywords = HGS; SARS summary = title: The discovery of gene mutations making SARS-CoV-2 well adapted for humans: host-genome similarity analysis of 2594 genomes from China, the USA and Europe This study shows that the host-genome similarity (HGS) of SARS-CoV-2 is significantly higher than that of SARS-CoV, especially in the ORF6 and ORF8 genes encoding proteins antagonizing innate immunity in vivo. This finding implies that high HGS of SARS-CoV-2 genome may further inhibit IFN I synthesis and cause delayed host innate immunity. An ORF1ab mutation, 10818G>T, which occurred in virus populations with high HGS but rarely in low-HGS populations, was identified in 2594 genomes with geolocations of China, the USA and Europe. 578 shown with special markers at the top of colored blocks representing ORFs. Mutation 623 10818G>T in ORF1ab (codon TTG>TTT) occurred in populations with high HGS, which 624 results in amino acid M37F mutation in transmembrane protein nsp6. ORF1ab (codon TTG>TTT) occurred in populations with high HGS, which results in amino 631 acid M37F mutation in transmembrane protein nsp6. doi = 10.1101/2020.09.03.280727 id = cord-102808-c7ajfvt5 author = Sundqvist, Martina title = Barbadin selectively modulates FPR2-mediated neutrophil functions independent of receptor endocytosis date = 2020-05-01 keywords = Barbadin; FPR2; Fig; ROS summary = doi = 10.1101/2020.04.30.070011 id = cord-313805-6mnclfeg author = Suzuki, Yuichiro J. title = SARS-CoV-2 spike protein-mediated cell signaling in lung vascular cells date = 2020-10-12 keywords = MEK; SARS summary = Currently, the world is suffering from the pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that uses angiotensin-converting enzyme 2 (ACE2) as a receptor to enter the host cells. The treatment of human pulmonary artery smooth muscle cells or human pulmonary artery endothelial cells with recombinant SARS-CoV-2 spike protein S1 subunit (Val16 – Gln690) at 10 ng/ml (0.13 nM) caused an activation of MEK phosphorylation. Our results showing that SARS-CoV-2 spike protein is capable of activating the MEK/ERK pathway in pulmonary artery smooth muscle and endothelial cells suggest that cell growth signaling may be triggered in the pulmonary vascular walls in response to SARS-CoV-2. The major finding of this study is that the SARS-CoV-2 spike protein without the rest of the virus can elicit cell signaling, specifically the activation of the MEK/ERK pathway, in human host lung vascular smooth muscle and endothelial cells. doi = 10.1101/2020.10.12.335083 id = cord-327912-wfjdxgxh author = Swann, Heather title = Minimal system for assembly of SARS-CoV-2 virus like particles date = 2020-08-24 keywords = SARS summary = Here we demonstrate that non-infectious SARS-CoV-2 virus like particles (VLPs) can be assembled by co-expressing the viral proteins S, M and E in mammalian cells. Non-infectious virus like particles (VLPs) displaying essential viral proteins can be used to study the structural properties of the SARS-CoV-2 virions and due to their maximum immunogenicity are also vaccine candidates 2, 3 . Similarly, expression of M, E and S proteins are shown to result in release of morphologically identical particles to wild type SARS-CoV virus 9, 10 . We then tested the structural integrity of the SARS-CoV-2 VLPs attached to dry glass using Atomic Force Microscopy (AFM), since SARS-CoV-2 virions have been reported to survive on solid surfaces in dry conditions for many hours 13 . SARS-CoV-2 M, S and E protein genes were identified from the full genome sequence of the virus 1 , these genes were then humanized and inserted in CMV driven mammalian expression vectors (see supplement for complete plasmid sequences). doi = 10.1101/2020.06.01.128058 id = cord-102892-nt1zoktv author = Sweeney, Blake A. title = R2DT: computational framework for template-based RNA secondary structure visualisation across non-coding RNA types date = 2020-09-11 keywords = R2DT; RNA summary = Consensus tRNA primary 213 sequence with 2D structure for each isotype of each taxonomic domain was generated based 214 on the tRNA alignments used for building the isotype-specific covariance models in tRNAscan-215 SE 2.0 16 . 270 R2DT templates model the conserved core of most structured RNAs We classified each nucleotide in the resulting diagrams according to whether it matched a 282 template and found that 90.6% of nucleotides were displayed using the nucleotide locations 283 encoded in the templates, while 6.0% of nucleotides represented insertions compared to the 284 templates, and 3.4% of nucleotides matched the templates but required automatic repositioning 285 by the Traveler software (Table 2) . In addition, R2DT will benefit from the ongoing development Isotype-specific consensus tRNA sequences and 2D structures were generated using R-scape 52 389 from the alignments that were used to train and build the corresponding covariance models in 390 tRNAscan-SE 16 . doi = 10.1101/2020.09.10.290924 id = cord-102451-pcuzylva author = Swoger, Maxx title = Vimentin intermediate filaments mediate cell shape on visco-elastic substrates date = 2020-09-08 keywords = cell; substrate; vimentin summary = doi = 10.1101/2020.09.07.286237 id = cord-253987-83h861lp author = Tada, Takuya title = A soluble ACE2 microbody protein fused to a single immunoglobulin Fc domain is a potent inhibitor of SARS-CoV-2 infection in cell culture date = 2020-09-17 keywords = ACE2; SARS; figure; protein summary = The disulfide-bonded ACE2 microbody protein inhibited entry of lentiviral SARS-CoV-2 spike protein pseudotyped virus and live SARS-CoV-2 with a potency 10-fold higher than unmodified soluble ACE2 and was active after initial virus binding to the cell. In SARS-CoV-2 entry, the virus attaches to the target cell through the interaction of the spike glycoprotein (S) with its receptor, the angiotensin-converting enzyme 2 (ACE2) (Li, 2015; Li et al., 2005; Li et al., 2003) , a plasma membrane protein carboxypeptidase that degrades angiotensin II to angiotensin-(1-7) [Ang-(1-7)] a vasodilator that promotes sodium transport in the regulation of cardiac function and blood pressure (Kuba et al., 2010; Riordan, 2003; Tikellis and Thomas, 2012) . To determine the relative antiviral activity of soluble ACE2 and the ACE2 microbody proteins, we tested their ability to block the infection SARS-CoV-2 Δ19 S protein pseudotyped GFP/luciferase reporter virus. doi = 10.1101/2020.09.16.300319 id = cord-335118-oa9jfots author = Taka, E. title = Critical Interactions Between the SARS-CoV-2 Spike Glycoprotein and the Human ACE2 Receptor date = 2020-09-21 keywords = ACE2; RBD; SARS summary = By performing all-atom Molecular Dynamics (MD) simulations, we identified an extended network of salt bridges, hydrophobic and electrostatic interactions, and hydrogen bonding between the receptor-binding domain (RBD) of the S protein and ACE2. Initial studies have constructed a homology model of SARS-CoV-2 RBD in complex with ACE2, based on the SARS-CoV crystal structure (8, 14) and performed conventional MD (cMD) simulations totaling 10 ns (15, 16) and 100 ns (17, 18) in length to estimate binding free energies (15, 16) and interaction scores (18) . In this study, we performed a comprehensive set of all-atom MD simulations totaling 16.5 µs in length using the recently-solved structure of the RBD of the SARS-CoV-2 S protein in complex with the PD of ACE2 (7) . In 20 SMD simulations (each 15 ns, totaling 300 ns in length, table S1), the average work applied to unbind RBD from PD was 71.1 ± 12.7 kcal/mol (mean ± s.d.), demonstrating that the S protein binds stably to ACE2 (Fig. 3B) . doi = 10.1101/2020.09.21.305490 id = cord-312414-g5px0b65 author = Takagi, Akira title = An immunodominance hierarchy exists in CD8+ T cell responses to HLA-A*02:01-restricted epitopes identified from the non-structural polyprotein 1a of SARS-CoV-2 date = 2020-09-19 keywords = CD8; SARS summary = As shown in Fig. 2 , the intracellular cytokine staining (ICS) assay showed that 173 significant numbers of IFN--producing CD8+ T cells were elicited in mice immunized 174 with 18 liposomal peptides including pp1a-38, -52, -84, -103, -445, -597, -641, -1675, 175 -2785, -2884, -3083, -3403, -3467, -3583, -3662, -3710, -3732, and -3886, revealing that 176 these 18 peptides are HLA-A*02:01-restricted CTL epitopes derived from SARS-CoV-2 177 pp1a. However, any of 18 185 epitopes are not found in the amino acid sequence of either MERS-CoV or the four 186 common cold human coronaviruses involving HCoV-OC43, In the 18 positive peptides, 10 peptides including pp1a-38, -84, -641, -1675, -2884, 189 -3467, -3583, -3662, -3710, and -3732 were selected for the following analyses because 190 of the high ratios of IFN- + cells in CD8 + T cells (Fig. 2) . At first glance, the graphs of CD107a ( Taken together, 10 peptides differed significantly in their ability to induce 226 SARS-CoV-2 pp1a-specific CTLs when mice were immunized with the mixture of 10 227 peptides in liposomes. doi = 10.1101/2020.09.18.304493 id = cord-104092-yau3r79c author = Tamming, Renee J. title = Atrx deletion in neurons leads to sexually-dimorphic dysregulation of miR-137 and spatial learning and memory deficits date = 2019-04-13 keywords = Atrx; figure; memory; mouse summary = Mechanistically, we identify ATRX-dependent and sex-specific alterations in synaptic gene expression linked to Mir137 levels, a known regulator of presynaptic processes and spatial memory. Summary statement Ablation of the ATRX chromatin remodeler specifically in forebrain excitatory neurons of mice causes male-specific deficits in long-term spatial memory associated with miR-137 overexpression, transcriptional changes and structural alterations corresponding to preand post-synaptic abnormalities. A comprehensive analysis of these mice reveals that ATRX promotes long-term spatial learning and memory associated with morphological and synaptic ultrastructural changes in the hippocampus. We show that female mice lacking ATRX in neurons are protected from spatial learning and memory defects and identify sex-specific effects of ATRX loss on the expression of synaptic genes and miR-137. This study presents evidence that ATRX is required in a sex-specific manner in excitatory forebrain neurons for normal spatial learning and memory (Figure 8) [75] [76] [77] . doi = 10.1101/606442 id = cord-346335-el45v0a5 author = Tan, H.S. title = Fourier spectral density of the coronavirus genome date = 2020-08-11 keywords = SARS; Spike; genome summary = We uncover an interesting, new scaling law for the coronavirus genome: the complexity of the genome scales linearly with the power-law exponent that characterizes the enveloping curve of the low-frequency domain of the spectral density. An example of a seminal paper in this subject is that of Voss in [2] where the author found that the spectral density of the genome of many different species follows a power law of the form 1/k β in the low-frequency domain, with the exponent β potentially related to the organism''s evolutionary category. We develop a few models to characterize the typical spectrum, and in the process stumble upon a linear scaling law between a measure of the complexity of each genome and the power-law exponent that describes the enveloping curve of the low-frequency domain. doi = 10.1101/2020.06.30.180034 id = cord-317123-0tdfvlqd author = Tan, Xiaotian title = Rapid and quantitative detection of COVID-19 markers in micro-liter sized samples date = 2020-04-21 keywords = ELISA; SARS summary = Here, we present a microfluidic ELISA technology for rapid (15-20 minutes), quantitative, sensitive detection of SARS-CoV-2 biomarkers using SARS-CoV-2 specific IgG and viral antigen – S protein in serum. We also characterized various humanized monoclonal IgG, and identified a candidate with a high binding affinity towards SARS-CoV-2 S1 protein that can serve as the calibration standard of anti-SARS-CoV-2 S1 IgG in serological analyses. In this work, we present a microfluidic ELISA technology for rapid (15-20 minutes), quantitative, and sensitive detection of SARS-CoV-2 biomarkers using SARS-CoV-2 specific IgG and viral antigen -S protein, both of which are spiked in serum, as a model system. For the anti-S1 IgG detection experiments (see Figure S2 (B) for the detailed protocol), various concentrations of monoclonal antibodies were prepared by diluting the stock solutions with 50 times diluted human serum (the serum was diluted with 1× reagent diluent, which correlates to 1% BSA). doi = 10.1101/2020.04.20.052233 id = cord-353099-38bz0acw author = Tang, Mei San title = Association between SARS-CoV-2 neutralizing antibodies and commercial serological assays date = 2020-07-02 keywords = SARS summary = Methods 67 specimens from 48 patients with PCR-confirmed COVID-19 and a positive result by the Roche Elecsys SARS-CoV-2, Abbott SARS-CoV-2 IgG, or EUROIMMUN SARS-CoV-2 IgG assays and 5 control specimens were analyzed for the presence of neutralizing antibodies to SARS-CoV-2. Results The correlation between SARS-CoV-2 neutralizing titer (EC50) and the Roche, Abbott, and EUROIMMUN assays was 0.29, 0.47, and 0.46 respectively. Conclusion COVID-19 patients generate an antibody response to multiple viral proteins such that the calibrator ratios on the Roche, Abbott, and EUROIMMUN assays are all associated with SARS-CoV-2 neutralization. The correlation of the SARS-CoV-2 neutralizing titer with the ratio reported by the 162 Roche, Abbott, and EI assays was 0.29, 0.47, and 0.46 respectively (Figure 2A-C) . Increased neutralizing antibody titers were also higher in patients that were intubated, 201 had cardiac injury, or AKI relative to those with milder COVID-19 symptoms ( Figure 202 4B-D). doi = 10.1101/2020.07.01.182220 id = cord-103350-jj9pc4a6 author = Tang, Pingtao title = An HIV-Tat inducible mouse model system of childhood HIV-associated nephropathy date = 2020-05-08 keywords = HIV; HIVAN; Tat summary = rAd-Tat and LacZ control vectors (2 × 109) were expressed in the kidney of newborn wild type and HIV-transgenic (Tg26) FVB/N mice without significant proteinuria (n = 5 8 per group). Results HIV-Tat induced the expression of HIV-1 genes (env) and heparin binding growth factors in the kidney of HIV-Tg26 mice, and precipitated HIVAN in the first month of life. Summary statement We developed a new inducible mouse model system of childhood HIV-associated nephropathy, and demonstrated that HIV-Tat plays a critical role in this renal disease acting in synergy with other HIV-1 genes and heparin binding cytokines. Therefore, we carried out this study to determine whether the HIV-1 trans-activator (Tat) gene precipitates HIVAN in young mice, and define whether this approach could be used to generate an inducible mouse model system of childhood HIVAN. Our study showed that the activation and basic binding domains of Tat are sufficient to induce the renal expression of HIV-genes and precipitate HIVAN in young mice. doi = 10.1101/2020.05.06.081851 id = cord-104081-a3fx8tyd author = Tang, Tiffany title = Proteolytic activation of the SARS-CoV-2 spike S1/S2 site: a re-evaluation of furin cleavage date = 2020-10-05 keywords = SARS summary = The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses its spike (S) protein to mediate viral entry into host cells. Our results demonstrate that S1/S2 pre-cleavage is essential for plasma membrane entry into Calu-3 cells, a model lung epithelial cell line, but not for endosomal entry Vero E6 cells, a model cell culture line, and that other proteases in addition to furin are responsible for processing SARS-CoV-2 S1/S2. dec-RVKR-CMK treatment had no significant impact on SARS-CoV S mediated infection of Vero E6 and Calu-3 cells (Figure 6A and 6B) , suggesting that dec-RVKR-CMK impacts on SARS-CoV-2 S is due to inhibiting the S1/S2 pre-cleavage and not due to some general effect on protein expression. Different residues in the SARS-CoV spike protein determine cleavage and activation by the host cell protease TMPRSS2 Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells doi = 10.1101/2020.10.04.325522 id = cord-286466-scokdxp2 author = Tani, Hideki title = Evaluation of SARS-CoV-2 neutralizing antibodies using a vesicular stomatitis virus possessing SARS-CoV-2 spike protein date = 2020-08-23 keywords = CRNT; SARS summary = The neutralization values of the serum samples collected from hospitalized patients with COVID-19 or SARS-CoV-2 PCR-negative donors against the pseudotyped virus infection evaluated by the CRNT were compared with antibody titers determined from an immunofluorescence assay (IFA). The neutralization values of the serum 31 samples collected from hospitalized patients with COVID-19 or SARS-CoV-2 PCR-negative 32 donors against the pseudotyped virus infection evaluated by the CRNT were compared with 33 was designated as pCAG-SARS-CoV-2. Vero cells were treated with serially diluted sera or whole blood of convalescent patients with 145 COVID-19 or PCR-negative donors and then inoculated with Sfullpv, St19pv, or VSVpv. To 146 remove hematopoietic cells from whole blood samples, centrifugation was performed at 2,000 × g 147 for 5 min. To determine the specificity of infection of Sfullpv and St19pv, a neutralization assay of the 183 pseudotyped viruses was performed using sera of two hospitalized COVID-19 patients. doi = 10.1101/2020.08.21.262295 id = cord-352073-rdhjj72g author = Taniwaki, S.A title = Resource optimization in COVID-19 diagnosis date = 2020-06-26 keywords = SARS summary = The emergence and rapid dissemination worldwide of a novel Coronavirus (SARS-CoV-2) results in decrease of swabs availability for clinical samples collection, as well as, reagents for RT-qPCR diagnostic kits considered a confirmatory test for COVID-19 infection. This manuscript reports on the optimization of the Charité and the CDC RT-qPCR protocols for SARS-CoV-2 detection regarding concentration and volumes of reagents for both probe and intercalant agent-based platforms, as well as on the substitution of rayon swabs for cotton swabs for sample collection. Performance of E and RdRp genes of SARS-CoV-2 RT-qPCRs, based on final reaction volume of 10 µL with 2 µL of RNA (Table 1) , were verified with a relative standard curve built with 10 -2 to 10 -8 dilutions of positive RNA control. Tabela 4 -Probe-based RT-qPCR to the E gene of serial dilutions of SARS-CoV-2 sampled with cotton and rayon swabs. doi = 10.1101/2020.06.25.172528 id = cord-102376-wk70iipl author = Tausch, Simon H. title = PathoLive – Real-time pathogen identification from metagenomic Illumina datasets date = 2020-04-14 keywords = Fig; Illumina; sequencing summary = doi = 10.1101/402370 id = cord-104122-klvx927g author = Tayfuroglu, Omer title = An Accurate Free Energy Method for Solvation of Organic Compounds and Binding to Proteins date = 2020-05-28 keywords = Free; Molecular; energy summary = The method is adopted from ANI-1ccx neural network potentials (Machine Learning) for the Atomic Simulation Environment (ASE) and predicts the single point energies at the accuracy of CCSD(T)/CBS level for the entire configurational space that is sampled by Molecular Dynamics (MD) simulations. [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] More sophisticated methods to calculate the potential binding free energy of inhibitor candidate to the protein ranges from post molecular dynamics simulations such as Molecular 57 Recently several models using active learning such as ANI-1, 58 ANI-1x 59 and ANI-1cxx 60 Here, we introduce a new strategy to estimate free energies of solvation of small organic compounds and binding to proteins in explicit solvent using single end-state MD simulations. The method is adopted from ANI-1ccx neural network potentials (Machine Learning) for the The insertion of the ligand to an environment of solvent (solvation free energy) or receptor (binding free energy) can be defined by a coupling parameter, λ. doi = 10.1101/2020.05.26.116459 id = cord-103345-v555a2ll author = Taylor, Adrian title = The novel roles of choline transporter-like 1 and 2 in ethanolamine transport date = 2020-08-28 keywords = CTL1; CTL2; Etn summary = These data firmly established that CTL1 and CTL2 are the first identified ethanolamine transporters in the whole cells and mitochondria, with intrinsic roles in de novo PE synthesis by the CDP-Etn Kennedy pathway and compartmentation of intracellular ethanolamine. PC and PE are synthesized de novo by CDP-Cho and CDP-Etn branches of the Kennedy pathway in which the extracellular substrates choline (Cho) and ethanolamine (Etn) are actively transported into the cell, phosphorylated and coupled with diacylglycerols (DAG) to form the final phospholipid product. While multiple transport systems have been established for Cho, Etn transport is poorly characterized and there is no single gene/protein assigned a transport function for mammalian Etn. Cho transport for membrane phospholipid synthesis is mediated by Cho transporter like protein CTL1/SLC44A1 (3) . M1 and M2 cells only express CTL2 and at levels similar to Ctrl and Cos 7 cells, and do not have a functional CTL1 protein ( Fig. 2A,D) , strongly implicating CTL2 as responsible for the low affinity Etn transport. doi = 10.1101/2020.08.27.270223 id = cord-102412-cnlvyey4 author = Tekman, Mehmet title = A single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework date = 2020-08-28 keywords = Galaxy; RNA; analysis; cell; single summary = Results Here we outline several Galaxy workflows and learning resources for scRNA-seq, with the aim of providing a comprehensive analysis environment paired with a thorough user learning experience that bridges the knowledge gap between the computational methods and the underlying cell biology. The analysis of scRNA-seq within Galaxy was a two-pronged e ort concentrated on bringing high quality single-cell tools into Galaxy, and providing the necessary work ows and training to accompany them. The training pictographically guides users through the concepts of extracting cell barcodes from the protocol, explains the signi cance of UMIs in the process of read deduplication with illustrative examples, and instructs the user in the process of performing further quality controls on their data during the post-mapping process via RNA STAR and other tools that are native to Galaxy. A Galaxy-based training resource for single-cell RNA-sequencing quality control and analyses doi = 10.1101/2020.06.06.137570 id = cord-315760-9g8901v6 author = Teng, Xufei title = Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades date = 2020-08-30 keywords = SARS summary = Here, we describe an analysis procedure where genome composition and its variables are related, through the genetic code, to molecular mechanisms based on understanding of RNA replication and its feedback loop from mutation to viral proteome sequence fraternity including effective sites on replicase-transcriptase complex. Our analysis starts with primary sequence information and identity-based phylogeny based on 22,051 SARS-CoV-2 genome sequences and evaluation of sequence variation patterns as mutation spectrum and its 12 permutations among organized clades tailored to two key mechanisms: strand-biased and function-associated mutations. Our findings include: (1) The most dominant mutation is C-to-U permutation whose abundant second-codon-position counts alter amino acid composition toward higher molecular weight and lower hydrophobicity albeit assumed most slightly deleterious. We have further examined the compositional subtleties among the clades and clusters with 304 a focus on G+C and purine content variability as both contents appear drifting toward optima 305 in SARS-CoV-2 and its relatives ( Figure 5C and 5D). doi = 10.1101/2020.08.26.267781 id = cord-328695-nptfd6c2 author = Tengs, Torstein title = A mobile genetic element in the SARS-CoV-2 genome is shared with multiple insect species date = 2020-06-29 keywords = SARS summary = title: A mobile genetic element in the SARS-CoV-2 genome is shared with multiple insect species We document here the presence of s2m, a highly conserved, mobile genetic element with unknown function, in both the SARS-CoV-2 genome and a large number of insect genomes. Although s2m is not universally present among coronaviruses and appears to undergo horizontal transfer, the high sequence conservation and universal presence of s2m among isolates of SARS-CoV-2 indicate that, when present, the element is essential for viral function. The presence of s2m in the SARS-CoV-2 genome (GenBank accession MN908947, position 29727-29768) and other members of this group is probably the result of a single horizontal transfer event, predating the divergence of the SARS-related viruses (Tengs, et al. The insect species that contain s2m (and the associated protein) are distantly related, indicating either a deep evolutionary origin with multiple losses or that this genetic construct is also a mobile element, perhaps using viruses as a vector . doi = 10.1101/2020.06.29.177030 id = cord-336938-03366q9t author = Thacker, Vivek V title = Rapid endothelialitis and vascular inflammation characterise SARS-CoV-2 infection in a human lung-on-chip model date = 2020-08-10 keywords = Fig; SARS; cell summary = title: Rapid endothelialitis and vascular inflammation characterise SARS-CoV-2 infection in a human lung-on-chip model A combination of qRT-PCR, RNAscope, immunofluorescence, and ELISA measurements are used to study the dynamics of viral replication and host responses to a low dose infection of SARS-CoV-2 delivered to the apical surface of the epithelial face maintained at an air-liquid interface. We therefore establish a human lung-on-chip model for SARS-CoV-2 infections, and probe the viral growth kinetics, cellular localization and responses to a low dose infection using qRT-PCR, ELISA, RNAscope, immunofluorescence and confocal imaging (Fig. 1J) . Nevertheless, total RNA extracted from the apical and vascular channels of an infected LoC without macrophages at 1 dpi revealed >10 4 genomes in both epithelial and endothelial cells (Fig. 2C ) and genome copy numbers exceeded those for cellular housekeeping gene RNAseP (Fig. 2D ). Human iPSC-derived alveolar and airway epithelial cells can be cultured at air-liquid interface and express SARS-CoV-2 host factors doi = 10.1101/2020.08.10.243220 id = cord-321166-nvphu1fm author = Thomson, Emma C. title = The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity date = 2020-11-05 keywords = CoV-2; N439; RBD; RBM; SARS; d614; figure summary = We find that the N439K mutation is associated with a similar clinical spectrum of disease and slightly higher viral loads in vivo compared with isolates with the wild-type N439 residue, and that it results in immune escape from polyclonal sera from a proportion of recovered individuals and a panel of neutralizing mAbs. N439K provides a sentinel example of immune escape, indicating that RBM variants must be evaluated when considering vaccines and the therapeutic or prophylactic use of mAbs. Long term control of the pandemic will require systematic monitoring of immune escape variants and selection of strategies that address the variants circulating in targeted populations. Fitness of this variant, N439K, was demonstrated by repeated emergence by convergent evolution, spread to multiple countries and significant representation in the SARS-CoV-2 sequence databases, the fact that the N439K RBD retains a high affinity interaction with the hACE2 receptor, efficient viral replication in cultured cells, and no disease attenuation in a large cohort of infected individuals. doi = 10.1101/2020.11.04.355842 id = cord-300272-95o8yd7h author = Thépaut, Michel title = DC/L-SIGN recognition of spike glycoprotein promotes SARS-CoV-2 trans-infection and can be inhibited by a glycomimetic antagonist date = 2020-08-10 keywords = SARS; SIGN summary = In the context of the current COVID-19 pandemic, attention is now focused on the SARS-CoV-2 virus Zhou et al., 2020) .Coronaviruses use a homotrimeric glycosylated spike (S) protein protruding from their viral envelope to interact with cell membranes and promote fusion upon proteolytic activation. Additionally, in the case of SARS-CoV-2, a new paradigm is needed to untangle the complex clinical picture, resulting in a vast range of possible symptoms and in a spectrum of disease severity associated on one hand with active viral replication and cell infection through interaction with ACE2 along the respiratory tract, and, on the other hand, to the development of excessive immune activation, i.e. the so called "cytokine storm", that is related to additional tissue damage and potential fatal outcomes. These observations prompted us to investigate the potential interaction of C-type lectins receptors, notably DC/L-SIGN with SARS-CoV-2, through glycan recognition of the spike envelope glycoprotein, as well at their potential role in SARS-CoV-2 transmission. doi = 10.1101/2020.08.09.242917 id = cord-297826-2nruf2g7 author = Tian, Jing-Hui title = SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 elicits immunogenicity in baboons and protection in mice date = 2020-06-30 keywords = Matrix; NVX; SARS summary = In mice and baboons, low-dose NVX-CoV2373 with saponin-based Matrix-M adjuvant elicits high titer anti-S IgG that is associated with blockade of hACE2 receptor binding, virus neutralization, and protection against SARS-CoV-2 challenge in mice with no evidence of vaccine-associated enhanced respiratory disease (VAERD). Mice 171 immunized with 10 μg dose of NVX-CoV2373/Matrix-M induced antibodies that blocked 172 hACE2 receptor binding to S-protein and virus neutralizing antibodies 21-28-days after 173 a single priming dose ( Fig. 4B and 4C ). Importantly, we found the frequency 254 of IFN-γ + , TNF-α + , and IL-2 + cytokine-secreting CD4 + and CD8 + T cells was 255 significantly higher (p <0.0001) in spleens from the NVX-CoV2373/Matrix-M immunized 256 mice compared to mice immunized without adjuvant ( Fig. 6B and 6C) . Anti-S protein IgG titers were detected within 21-days of a single priming immunization 288 in animals immunized with NVX-CoV2373/Matrix-M across all the dose levels (GMT = 289 1,249-19,000). doi = 10.1101/2020.06.29.178509 id = cord-255440-ls1l2mlg author = Tindle, Courtney title = Adult Stem Cell-derived Complete Lung Organoid Models Emulate Lung Disease in COVID-19 date = 2020-10-18 keywords = ALI; COVID-19; Fig; SARS; at2; cell summary = Besides the approaches described so far, there are a few more approaches used for modeling COVID-19-(i) 3D organoids from bronchospheres and tracheospheres have been established before (Hild and Jaffe, 2016; Rock et al., 2009; Tadokoro et al., 2016) and are now used in apical-out cultures for infection with SARS-COV-2 (Suzuki et al., 2020); (ii) the most common model used for drug screening is the air-liquid interphase (ALI model) in which pseudo-stratified primary bronchial or small airway epithelial cells are used to recreate the multilayered mucociliary epithelium (Mou et al., 2016; Randell et al., 2011) ; (iii) several groups have also generated 3D airway models from iPSCs or tissue-resident stem cells (Dye et al., 2015; Ghaedi et al., 2013; Konishi et al., 2016; McCauley et al., 2017; Miller et al., 2019; Wong et al., 2012) ; (iv) others have generated AT2 cells from iPSCs using closely overlapping protocols of sequential differentiation starting with definitive endoderm, anterior foregut endoderm, and distal alveolar expression (Chen et al., 2017; Gotoh et al., 2014; Huang et al., 2014; Jacob et al., 2017; Jacob et al., 2019; Yamamoto et al., 2017) . doi = 10.1101/2020.10.17.344002 id = cord-102199-mc6zruyx author = Toksvang, Linea Natalie title = Hepatotoxicity during 6-thioguanine treatment in inflammatory bowel disease and childhood acute lymphoblastic leukaemia: a systematic review date = 2019-01-30 keywords = disease; patient summary = title: Hepatotoxicity during 6-thioguanine treatment in inflammatory bowel disease and childhood acute lymphoblastic leukaemia: a systematic review Hepatotoxicity in the form of sinusoidal obstruction syndrome (SOS) occurred in 9–25% of the ALL patients in two of the four included RCTs using 6TG doses of 40–60 mg/m2/day, and long-term hepatotoxicity in the form of nodular regenerative hyperplasia (NRH) was reported in 2.5%. Oral 6-mercaptopurine versus oral 6-thioguanine and veno-occlusive disease in children with standard-risk acute lymphoblastic leukemia: report of the Children''s Oncology Group CCG-1952 clinical trial 6-Thioguanine associated nodular regenerative hyperplasia in patients with inflammatory bowel disease may induce portal hypertension Splitting a therapeutic dose of thioguanine may avoid liver toxicity and be an efficacious treatment for severe inflammatory bowel disease: a 2-center observational cohort study Early nodular hyperplasia of the liver occurring with inflammatory bowel diseases in association with thioguanine therapy doi = 10.1101/535518 id = cord-102749-tgka0pl0 author = Tovo, Anna title = Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju date = 2020-05-01 keywords = 16S; Kaiju; community; core; number summary = In this study, we first apply and compare different bioinformatics methods based on 16S ribosomal RNA gene and whole genome shotgun sequencing for taxonomic classification to three small mock communities of bacteria, of which the compositions are known. In particular, we propose an updated version of Kaiju, which combines the power of shotgun metagenomics data with a more focused marker gene classification method, similar to 16S rRNA, but based on core protein domain families (40, 41, 42, 43) from the PFAM database (44) . As shown in (27) , where different amplicon sequencing methods are tested on both simulated and real data and the results are compared to those obtained with metagenomic pipelines, the whole genome approach resulted to outperform the previous ones in terms of both number of identified strains, taxonomic and functional resolution and reliability on estimates of microbial relative abundance distribution in samples. doi = 10.1101/2020.01.08.898395 id = cord-345405-ngpsgn63 author = Tremiliosi, Guilherme C. title = Ag nanoparticles-based antimicrobial polycotton fabrics to prevent the transmission and spread of SARS-CoV-2 date = 2020-06-26 keywords = SARS; fabric; nanoparticle; polycotton summary = An adaptation of ISO 18184 Determination of antiviral activity of textile products Standard Method [23] was used as a reference for a quantitative method to evaluate the treated polycotton''s ability to inactivate the SARS-CoV-2 virus particles (SARS-CoV-2/human/BRA/SP02cc/2020 -MT350282), under the tested conditions, at two different time intervals (2 and 5 minutes of contact time). The antiviral activity test was designed to determine the inactivation of viral particles upon short exposure to the products, which in this case were the Ag-based treated polycotton samples incubated in liquid media. Table 6 shows the number of copies of the control media without any fabric sample, non-treated polycotton, and the two Ag-based treated polycotton samples at the two different tested time periods. Application of silver nanoparticles to cotton fabric as an antibacterial textile finish Fibers Polym Antibacterial properties of cotton fabric treated with silver nanoparticles doi = 10.1101/2020.06.26.152520 id = cord-293640-pgrrurrc author = Tripathi, Satyendra C title = Renal carcinoma is associated with increased risk of coronavirus infections date = 2020-07-06 keywords = ACE2; DPP4; TMPRSS2 summary = We took a bioinformatics approach to analyze the gene and protein expression data of these coronavirus receptors in human normal and cancer tissues of multiple organs. TCGA data analysis also showed increased expression of all receptors except TMPRSS2 in renal tumor tissues as compared to their adjacent normal (Sup Fig 1) . Further, we specifically analyzed ACE2, which is a primary SARS-CoV receptor and DPP4, highly correlated to ACE2 across the kidney cancer subtypes along with immune cell signatures (innate and adaptive immunity, inflammatory cytokines and chemokines). ACE2, DPP4, ANPEP, and ENPEP each associated with a high level of immune infiltration, inflammatory chemokines, cytokines and markers of an immunosuppressive microenvironment and T cell exhaustion in KIRC tumors. The Tumor Immune System Interaction database (TISIDB) (http://cis.hku.hk/TISIDB/) platform was used to analyze the correlation of ACE2 with other CoV receptors (DPP4, ANPEP, ENPEP, TMPRSS2) expression in different renal carcinoma subtypes. doi = 10.1101/2020.07.02.184663 id = cord-102734-ltuqoa2b author = Tsai, Hsiang-Yu title = Antagonistic Effects of Intraspecific Cooperation and Interspecific Competition on Thermal Performance date = 2020-05-04 keywords = TPC; beetle; temperature summary = doi = 10.1101/2020.05.03.075325 id = cord-323685-gjocoa60 author = Tsai, Shang-Jui title = Exosome-Mediated mRNA Delivery For SARS-CoV-2 Vaccination date = 2020-11-06 keywords = LSNME; SARS; cell summary = The resulting combinatorial vaccine, LSNME/SW1, was injected into thirteen weeks-old, male C57BL/6J mice, followed by interrogation of humoral and cellular immune responses to the SARS-CoV-2 nucleocapsid and spike proteins, as well as hematological and histological analysis to interrogate animals for possible adverse effects. Conclusion Taken together, these results validate the use of exosomes for delivering functional mRNAs into target cells in vitro and in vivo, and more specifically, establish that the LSNME/SW1 vaccine induced broad immunity to multiple SARS-CoV-2 proteins. These antigen-responsive CD4+ and CD8+ populations were present nearly two months after the final boost injection, indicating that LSNME/S W1 vaccination had elicited a sustained cellular immune response to both of these SARS-CoV-2 structural proteins. As for the future development of the LSNME/S W1 vaccine, we anticipate that follow-on studies in larger animal models at doses comparable to other mRNA vaccines will demonstrate a desirable combination of safety, balanced immune responses, and when challenged, protection against SARS-CoV-2 infection and/or disease. doi = 10.1101/2020.11.06.371419 id = cord-351559-az4pgi9k author = Turjya, Rafeed Rahman title = Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection date = 2020-06-29 keywords = RNA; SARS; protein summary = Regulatory roles of long non-coding RNAs (lncRNAs) during viral infection and associated antagonism of host antiviral immune responses has become more evident in last decade. To elucidate possible functions of lncRNAs in the COVID-19 pathobiology, we have utilized RNA-seq dataset of SARS-CoV-2 infected lung epithelial cells. By network enrichment analysis we find that these lncRNAs can directly interact with differentially expressed protein-coding genes ADAR, EDN1, KYNU, MALL, TLR2 and YWHAG; and also AKAP8L, EXOSC5, GDF15, HECTD1, LARP4B, LARP7, MIPOL1, UPF1, MOV10 and PRKAR2A, host genes that interact with SARS-CoV-2 proteins. Conclusions Our investigation determines that deregulated lncRNAs in SARS-CoV-2 infection are involved in viral proliferation, cellular survival, and immune response, ultimately determining disease outcome and this information could drive the search for novel RNA therapeutics as a treatment option. doi = 10.1101/2020.06.29.177204 id = cord-321050-yabt72jf author = Tuttle, Kathryn D. title = JAK1 inhibition blocks lethal sterile immune responses: implications for COVID-19 therapy date = 2020-04-09 keywords = Dp16; IFN; P(I summary = Increasing evidence supports the notion that mortality during infections with SARS-CoV-2, which causes coronavirus disease of 2019 , is driven by the exacerbated immune response to the virus, leading to a cascade of events involving a cytokine storm and acute respiratory distress syndrome (ARDS), often accompanied by myocardial damage and multiple organ failure (5, 6) . Overall, these results have potential far-reaching significance for the treatment of COVID-19, justifying a deeper study of JAK inhibitors as a therapeutic strategy to attenuate the cytokine storm and downstream organ failure in this condition, while also indicating that individuals with DS should be considered a high-risk population during the COVID-19 pandemic. This analysis revealed that Dp16 mice have increased liver pathology even before P(I:C) treatment, as demonstrated by significantly higher levels of cell injury, inflammation, and reactive changes relative to their WT littermates (Figure 4B,C) . doi = 10.1101/2020.04.07.024455 id = cord-260481-twk5kvd3 author = Täufer, Matthias title = Rapid, large-scale, and effective detection of COVID-19 via non-adaptive testing date = 2020-08-18 keywords = PCR; pool summary = doi = 10.1101/2020.04.06.028431 id = cord-292670-12prczym author = Urra, José Miguel title = The antibody response to the glycan α-Gal correlates with COVID-19 disease symptoms date = 2020-07-14 keywords = Gal summary = Humans evolved by losing the capacity to synthesize the glycan Galα1-3Galβ1-(3)4GlcNAc-R (α-Gal), which resulted in the development of a protective response against pathogenic viruses and other microorganisms containing this modification on membrane proteins mediated by anti-α-Gal IgM/IgG antibodies produced in response to bacterial microbiota. These results support the proposal of developing interventions such as probiotics based on commensal bacteria with α-Gal epitopes to modify the microbiota and increase the α-Gal-induced protective immune response and reduce the severity of COVID-19. Although more severe symptoms have been associated with elderly patients, herein older 199 patients were recorded in the hospitalized and not the ICU group (p < 0.001; Table 1 The serum IgA, IgE, IgM and IgG antibody response to α-Gal was characterized in healthy 226 individuals and COVID-19 patients at different disease stages (Figures 2 and 3a) . doi = 10.1101/2020.07.14.201954 id = cord-102661-lh7992rl author = Valentine, Charles C. title = Direct Quantification of in vivo Mutagenesis and Carcinogenesis Using Duplex Sequencing date = 2020-11-03 keywords = Duplex; Sequencing; TGR; dna; mutation summary = doi = 10.1101/2020.06.28.176685 id = cord-103181-my4n0vye author = Valle-Casuso, José Carlos title = Replication of Equine arteritis virus is efficiently suppressed by purine and pyrimidine biosynthesis inhibitors date = 2020-04-10 keywords = EAV; cell summary = Using this assay, we identified three molecules that impair EAV infection in equine cells: the broad-spectrum antiviral and nucleoside analog ribavirin, and two compounds previously described as inhibitors of dihydroorotate dehydrogenase (DHODH), the fourth enzyme of the pyrimidine biosynthesis pathway. We were also interested in exploring the antiviral capacity of two new BSA, IPPA17-04 and GAC50 163 that impair viral replication through inhibition of de novo pyrimidine biosynthesis in host cells. These results show that cell cultures treated with pyrimidine biosynthesis inhibitors did not 175 exhibit cytopathic effects associated to EAV infection, suggesting that EAV replication is also impaired. To verify that ribavirin, IPPA17-A04 and GAC50 actually block EAV replication, viral genome copies 180 were quantified at 48 h.p.i. Culture supernatants of infected ED cells treated or not with the 181 compounds at different concentrations were analyzed by RT-qPCR. doi = 10.1101/2020.04.10.035402 id = cord-103567-nh9i28lu author = Vanachayangkul, Pattaraporn title = Safety, pharmacokinetics, and liver-stage Plasmodium cynomolgi effect of high-dose ivermectin and chloroquine in Rhesus Macaques date = 2020-04-29 keywords = ivermectin summary = title: Safety, pharmacokinetics, and liver-stage Plasmodium cynomolgi effect of high-dose ivermectin and chloroquine in Rhesus Macaques Here, ivermectin showed inhibition of the in vitro development of Plasmodium cynomolgi schizonts (IC50 = 10.42 μM) and hypnozoites (IC50 = 29.24 μM) in primary macaque hepatocytes when administered in high-dose prophylactically but not when administered in radical cure mode. The safety, pharmacokinetics, and efficacy of oral ivermectin (0.3, 0.6, and 1.2 mg/kg) with and without chloroquine (10 mg/kg) administered for seven consecutive days was evaluated for prophylaxis or radical cure of Plasmodium cynomolgi liver-stages in Rhesus macaques. Approximately 3 weeks later, a second relapse occurred 174 in all negative control and ivermectin high-and low-dose treated macaques with no significant 175 differences for time to blood-stage parasitemia or treatment (Log-Rank (Mantel Cox) test P > 176 0.05). If a relapse occurs, 397 and blood-stage parasitemia reaches >5,000 parasites per µl, then macaques received seven 398 days of chloroquine (10mg/kg) plus ivermectin (1.2 mg/kg) for both the low-and high-dose 399 groups. doi = 10.1101/2020.04.27.065409 id = cord-103108-vmze2mdx author = Vanheer, Lotte title = Revealing the Key Regulators of Cell Identity in the Human Adult Pancreas date = 2020-09-25 keywords = cell; figure; human; pancreatic; type summary = HIGHLIGHTS Reconstruction of gene regulatory networks for human adult pancreatic cell types An interactive resource to explore and visualize gene expression and regulatory states Predicting putative transcription factors driving pancreatic cell identity HEYL and JUND as candidate regulators of acinar and alpha cell identity, respectively Because TFs recognize DNA motifs in the genome, one can measure if inferred target genes are expressed within single cells, and therefore quantify the activity of TFs. Such approaches have revealed the regulatory programs in distinct systems including the Drosophila brain (Davie et al , 2018) , cancer (Wouters et al., 2020) , during early mouse embryonic development (Peng et al , 2019) , in a mouse cell atlas (Suo et al., 2018 ) and a human cell atlas (Han et al., 2020) . doi = 10.1101/2020.09.23.310094 id = cord-334300-hnrmaytm author = Ventura Fernandes, Bianca H title = Zebrafish studies on the vaccine candidate to COVID-19, the Spike protein: Production of antibody and adverse reaction date = 2020-10-20 keywords = SARS; covid-19 summary = Establishing new experimental animal models to assess the safety and immune response to the antigen used in the development of COVID-19 vaccine is an imperative issue. Based on the advantages of using zebrafish as a model in research, herein we suggest doing this to test the safety of the putative vaccine candidates and to study immune response against the virus. Based on the in vivo and in silico results presented here, we propose the zebrafish as a model for translational research into the safety of the vaccine and the immune response of the vertebrate organism to the SARS-CoV-2 virus. 169 In the global task to develop the vaccine and possible therapeutic approaches for 170 COVID-19, several animal models have been proposed, such as mice 10 , hACE2 171 transgenic mice 11 , alpaca 12 , golden Syrian hamsters, ferrets, dogs, pigs, chickens, and 172 cats 9 , and species of non-human primates 10 . doi = 10.1101/2020.10.20.346262 id = cord-284102-rovyvv45 author = Wagner, Teresa R. title = NeutrobodyPlex - Nanobodies to monitor a SARS-CoV-2 neutralizing immune response date = 2020-09-28 keywords = ACE2; RBD; SARS summary = Here we identified 11 unique nanobodies (Nbs) with high binding affinities to the SARS-CoV-2 spike receptor domain (RBD). Considering that Nbs targeting diverse epitopes within the RBD:ACE2 interface are beneficial 201 in both reducing viral infectivity and preventing mutational escape, we next combined the most 202 potent inhibitory and neutralizing candidates derived from Nb-Set1 (NM1226, NM1228) and 203 We incubated our previously generated color-coded beads 232 comprising RBD, S1 domain or homotrimeric spike with serum samples from patients or non-233 infected individuals, in addition to dilution series of the combinations NM1226/ NM1230 or 234 NM1228/ NM1230 and used this to detect patient-derived IgGs bound to the respective 235 antigens. As a result, we modified our previously described multiplex immunoassay 303 (MULTICOV-AB, 20 ) and developed a novel diagnostic test called NeutrobodyPlex to monitor 304 the presence and the emergence of neutralizing antibodies in serum samples of SARS-CoV-2 305 infected individuals. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block 681 interaction with ACE2 doi = 10.1101/2020.09.22.308338 id = cord-261855-qpbgq5d8 author = Walker, Susanne N. title = SARS-CoV-2 assays to detect functional antibody responses that block ACE2 recognition in vaccinated animals and infected patients date = 2020-06-18 keywords = ACE2; Fig summary = title: SARS-CoV-2 assays to detect functional antibody responses that block ACE2 recognition in vaccinated animals and infected patients Here we describe a rapid serological diagnostic assay for determining antibody receptor blocking and demonstrate the broad utility of the assay by measuring the antibody functionality of sera from small animals and non-human primates immunized with an experimental SARS-CoV-2 vaccine and using sera from infected patients. Here, we describe a competition ELISA assay and a SPR 100 assay developed to rapidly detect ACE2 receptor blocking antibodies in IgGs and sera of 101 vaccinated mice, guinea pigs, rabbits and non-human primates, as well as, human samples (Fig. 1B) . Next, using Enzyme-Linked Immunosorbent Assays (ELISAs) we immobilized full-length 120 SARS-CoV-2 spike protein (containing both the S1 and S2 subunits) and incubated a dilution 121 series of ACE2-IgHu (Fig. 1D) . The proof-of-concept competition ELISA displayed a full blocking curve, so we sought to utilize 140 this assay for animals immunized with SARS-CoV-2 spike protein. doi = 10.1101/2020.06.17.158527 id = cord-308428-zw26usmh author = Walter, Justin D. title = Highly potent bispecific sybodies neutralize SARS-CoV-2 date = 2020-11-10 keywords = ACE2; Fig; RBD; S-2P; SARS; Sb#15; Sb#68 summary = Here, we report the generation of synthetic nanobodies, known as sybodies, against the receptor-binding domain (RBD) of SARS-CoV-2 spike protein. We identified a sybody pair (Sb#15 and Sb#68) that can bind simultaneously to the RBD, and block ACE2 binding, thereby neutralizing pseudotyped and live SARS-CoV-2 viruses. However, binders of the isolated RBD may not effectively engage the aforementioned pre-fusion conformation of the spike protein, which could account for the poor neutralization ability of recently described single-domain antibodies that were raised against the RBD of SARS-CoV-2 spike protein [29] . Since Sb#15 and Sb#68 can bind simultaneously to the RBD and the full-length spike protein, we mixed Sb#15 and Sb#68 together to investigate potential additive or synergistic neutralizing activity of these two independent sybodies. To gain structural insights into how Sb#15 and Sb#68 recognize the RBD, we performed single particle cryo-EM analysis of the spike protein in complex with the sybodies. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2 doi = 10.1101/2020.11.10.376822 id = cord-318444-sgm24q1i author = Walter, Justin D. title = Sybodies targeting the SARS-CoV-2 receptor-binding domain date = 2020-05-16 keywords = ECD; ELISA; RBD; SARS; TBS summary = Two independently prepared RBD constructs were used for in vitro sybody selections, and resulting single clones that could bind the full spike ectodomain were sequenced, expressed, and purified. Six unique sybodies show favorable binding affinity to the SARS-CoV-2 spike, and five of these were also found to substantially attenuate the interaction between the viral RBD and human ACE2. While this purified pre-fusion spike (PFS) had not yet been available for binder selections and characterization by grating-coupled interferometry, it was used to conduct ELISAs in order to identify selected sybodies which recognize the RBD in the pre-fusion context (see below). Since virulence of SARS-CoV-2 is dependent on the ability of the viral RBD to bind to human ACE2 (hACE2), we sought to determine which of the 57 selected sybodies that were well-behaved upon purification could inhibit interaction between the isolated RBD and purified hACE2. doi = 10.1101/2020.04.16.045419 id = cord-285088-krim73zt author = Wang, Deguo title = One-pot Detection of COVID-19 with Real-time Reverse-transcription Loop-mediated Isothermal Amplification (RT-LAMP) Assay and Visual RT-LAMP Assay date = 2020-04-21 keywords = LAMP summary = title: One-pot Detection of COVID-19 with Real-time Reverse-transcription Loop-mediated Isothermal Amplification (RT-LAMP) Assay and Visual RT-LAMP Assay Objective This study was to establish one-pot real-time reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay and one-pot visual RT-LAMP assay for the detection of COVID-19. The analytic sensitivities of the newly developed real-time RT-LAMP assay and visual RT-LAMP assay were determined with pUC57-N DNA ranging from 2-0.02 fg, and the reaction mixtures were heated at the optimal temperature for 60 min in a StepOneTM System (Applied Biosystems, Foster City, CA, USA) or in a water bath, when water bath was used, the reaction tube was sunk into water. The detection limits of the one-pot real-time RT-LAMP assay and the one-pot visual RT-LAMP assay were determined using pUC57-N DNA ranging from 2-0.02 fg at 59 °C for 60 min in a StepOneTM System (Applied Biosystems, Foster City, CA, USA) or in a water bath. doi = 10.1101/2020.04.21.052530 id = cord-320417-01l27d99 author = Wang, Hai-Long title = The emergence of inter-clade hybrid SARS-CoV-2 lineages revealed by 2D nucleotide variation mapping date = 2020-10-14 keywords = SARS; SNP; clade summary = I proposed a novel illustrating method using a 2D map to display populations of co-occurring nucleotide variants for intraand inter-viral clades. Using this method, I revealed the emergence of inter-clade hybrid SARS-CoV-2 lineages that are potentially caused by homologous genetic recombination. SARS-CoV-2 is an RNA virus with limited genome length, but its high mutation rate and homologous genetic recombination nonetheless gave rise to exponentially increased variants. This is why all previously reported recombination events of SARS-Cov-2 have relied on clade-defining SNPs. The 2D co-occurring variant mapping is a simple way to display inter-clade hybrid lineages, and it can be used to directly compare distributions of populations for intra-and inter-clade from different geographic locations or the same location but at a different time point. I downloaded ~18,000 SARS-CoV-2 genome sequences from NCBI (on September 2 nd ) and used the same criterion as before to search for inter-clade co-occurring SNP pairs (see method for details). doi = 10.1101/2020.10.13.338038 id = cord-260508-z11exbyu author = Wang, Hongru title = Synonymous mutations and the molecular evolution of SARS-Cov-2 origins date = 2020-10-12 keywords = CoV-2; GD410721; SARS summary = Phylogenetic analyses (Fig. 2 ) in genomic regions with all recombination tracts 6 (Supplementary Table 5 ) masked using Maximum-likelihood (Fig. 2a) and Neighbor-joining 7 based on synonymous (Fig. 2b ) or non-synoymous (Fig. 2c ) mutation distance metrics, 8 consistently support RmYN02 as the nearest outgroup to human SARS-CoV-2, in contrast to 9 previous analyses before the discovery of RmYN02, which instead found RaTG13 to be the 10 nearest outgroup ). Notice that the divergences 14 between human SARS-CoV-2 and the bat viral sequences, RaTG13 and RmYN02, in most 15 regions of the genome, are quite low compared to the other comparisons. While the overall divergence in the S gene encoding the spike protein could suggest the 10 presence of recombination in the region, previous study ) reported that the tree 11 based on synonymous substitutions supported RaTG13 as the sister taxon to the human SARS-12 doi = 10.1101/2020.04.20.052019 id = cord-103688-n7hzpbyf author = Wang, Lina title = VirusDIP: Virus Data Integration Platform date = 2020-06-09 keywords = Yang; virus summary = Results To facilitate virus research and promote the global sharing of virus data, we present here VirusDIP, a one-stop service platform for archive, integration, access, analysis of virus data. It accepts the submission of viral sequence data from all over the world and currently integrates data resources from the National GeneBank Database (CNGBdb), Global initiative on sharing all influenza data (GISAID), and National Center for Biotechnology Information (NCBI). Moreover, based on the comprehensive data resources, BLAST sequence alignment tool and multi-party security computing tools are deployed for multi-sequence alignment, phylogenetic tree building and global trusted sharing. For data compatibility, the virus data standard integrates the virus and pathogen sample data standard of The International Nucleotide Sequence Database Collaboration (INSDC) (Karsch-Mizrachi et al., 2018) , the hCoV-19 data standard of GISAID, and the sample data standard of COVID-19 Genomics UK (COG-UK) Consortium. VirusDIP is committed to building a comprehensive virus data platform for archive, integration, access, and analysis. doi = 10.1101/2020.06.08.139451 id = cord-263780-8jejswuk author = Wang, Nan title = Chloroquine and hydroxychloroquine as ACE2 blockers to inhibit viropexis of 2019-nCoV Spike pseudotyped virus date = 2020-08-14 keywords = ACE2 summary = title: Chloroquine and hydroxychloroquine as ACE2 blockers to inhibit viropexis of 2019-nCoV Spike pseudotyped virus Purpose The objective of this study is to investigate whether CQ and HCQ could be ACE2 blockers and used to inhibit 2019-nCoV virus infection. We further analyzed the binding character of CQ and HCQ to ACE2 by molecular docking and surface plasmon resonance (SPR) assays, 2019-nCoV spike pseudotyped virus was also used to observe the viropexis effect of CQ and HCQ in ACE2h cells. Conclusions CQ and HCQ both inhibit the entrance 2019-nCoV into cells by blocking the binding of the virus with ACE2. In this study, we found that CQ and HCQ can antagonize ACE2 and inhibit the entry of 2019-nCoV 103 spike pseudotyped virus into ACE2 expressed HEK293T cells (ACE2 h cells). It can be concluded that the toxicity 216 of HCQ was higher than that of CQ on ACE2 h cells at different time points at the same 217 concentrations (Figure 1C) . doi = 10.1101/2020.06.22.164665 id = cord-103462-z3d9lcar author = Wang, Shiyu title = CD4+ T cell subsets present stable relationships in their T cell receptor repertoires date = 2020-11-02 keywords = TCRB summary = Here, we examined the features of TCR beta (TCRB) repertoire of the top clones within naïve, memory and regular T cell (Treg) subsets: repertoire structure, gene usage, length distribution and sequence composition. To unveil the influence of differentiation on TCR repertoire, we analyzed the sequencing 68 data of TCR beta (TCRB) chain of NT, ET, EMT, CMT, Tscm and Treg. It suggests 232 that the length distribution of TCRB repertoire of NT is highly skewed in these less-233 differentiated memory cells ( Figure 4B ). We detected the 320 relationships among the TCRB repertoire of top1000 clones of naïve, memory and Treg subsets 321 (including NT, ET, Tcm, Tem, Tscm ET and Treg) by estimating the repertoire structure, the 322 germline gene usage, the sequence composition (K-mer) and public CDR3 clone usage. In our study, public clones from NT are less maintained in 359 differentiated subsets, and SVM analyses indicate that sequence composition in memory 360 doi = 10.1101/2020.11.01.364224 id = cord-104001-5clslvqb author = Wang, Xiaoqi title = selfRL: Two-Level Self-Supervised Transformer Representation Learning for Link Prediction of Heterogeneous Biomedical Networks date = 2020-10-21 keywords = network; path; prediction; representation summary = The meta path detection-based self-supervised learning task is proposed to learn representation vectors that can capture the global-level structure and semantic feature in HBNs. The vertex entity mask-based self-supervised learning mechanism is designed to enhance local association of vertices. First, a meta path detection self-supervised learning mechanism is developed to train a deep Transformer encoder for learning low-dimensional representations that capture the path-level information on HBNs. Meanwhile, sel-fRL integrates the vertex entity mask task to learn local association of vertices in HBNs. Finally, the representations from the entity mask and meta path detection is concatenated for generating the embedding vectors of nodes in HBNs. The results of link prediction on six datasets show that the proposed selfRL is superior to 25 state-of-the-art methods. • We proposed a two-level self-supervised representation learning method for HBNs, where this study integrates the meta path detection and vertex entity mask selfsupervised learning task based on a great number of unlabeled data to learn high quality representation vector of vertices. doi = 10.1101/2020.10.20.347153 id = cord-104073-vsa5y7ip author = Warner, Emily F. title = Cross kingdom analysis of putative quadruplex-forming sequences in fungal genomes: novel antifungal targets to ameliorate fungal pathogenicity? date = 2020-09-23 keywords = PQS; figure; gene summary = PQS in the clinically important pathogens Aspergillus fumigatus, Cryptococcus neoformans, and Candida albicans were located within genes (particularly coding regions), mRNA, repeat regions, mobile elements, tRNA, ncRNA, rRNA, and the centromere. Finally, PQS were found in over 100 genes associated with virulence, drug resistance, or key biological processes in these pathogenic fungi and were found in genes which were highly upregulated during germination, hypoxia, oxidative stress, iron limitation, and in biofilms. Using a computational approach, we identified putative quadruplex-forming 30 sequences (PQS) in 1362 genomes across the fungal kingdom and explored their potential 31 involvement in virulence, drug resistance, and pathogenicity. Using a computational approach, we identified putative quadruplex-forming 30 sequences (PQS) in 1362 genomes across the fungal kingdom and explored their potential 31 involvement in virulence, drug resistance, and pathogenicity. PQS in the 35 clinically important pathogens Aspergillus fumigatus, Cryptococcus neoformans, and Candida 36 albicans were located within genes (particularly coding regions), mRNA, repeat regions, 37 doi = 10.1101/2020.09.23.310581 id = cord-103876-2rg2qtdq author = Watkins, Laura C. title = Influenza A M2 Inhibitor Binding Understood through Mechanisms of Excess Proton Stabilization and Channel Dynamics date = 2020-06-20 keywords = channel; drug; proton summary = In this work, we test the hypothesis that these drugs act primarily as mechanism-based inhibitors by comparing hydrated excess proton stabilization during proton transport in M2 with the interactions revealed in the crystal structures, using the Multiscale Reactive Molecular Dynamics (MS-RMD) methodology. Along with an earlier qualitative MD simulation study that guided the design of the spiro-adamantyl amine inhibitors, 41 the crystallographic analysis provided potential insights into the mechanism of inhibition, suggesting that the backbone carbonyls of pore-lining residues act as physiochemical chameleons, able to engage in both hydrophobic and hydrophilic interactions, and that the drug is tilted off the channel''s axis and interacts with waters in the Ala30 layer. Most recently, we further analyzed the MS-RMD simulations to explore the detailed interactions between the hydrated excess proton and the channel and found that the proton dynamically, as a function of its position, alters several properties of the protein and pore waters, including the hydrogen-bonding network and the protein structure. doi = 10.1101/2020.06.19.162248 id = cord-103853-ar09nzmw author = Wayment-Steele, Hannah K. title = RNA secondary structure packages ranked and improved by high-throughput experiments date = 2020-05-31 keywords = Eterna; RNA; figure summary = 20 In this work, we evaluate the performance of commonly-used packages capable of making thermodynamic predictions in two tasks that have been crowdsourced on Eterna and are emerging as central to RNA characterization and design: 1) predicting chemical reactivity data through calculating probabilities that nucleotides are unpaired, and 2) predicting relative stabilities of multiple structural states that underlie the functions of riboswitch molecules, a task that involves predicting affinities of both small molecules and proteins of interest. We evaluated commonly used secondary structure modeling packages in their ability to make thermodynamic predictions on a compilation of large datasets of diverse synthetic molecules from Eterna, which we termed EternaBench ( Figure 1A ). We trained models with a variety of combinations of data types to explore interactions in multitask training (Table 1) and evaluated performance on held-out test sets for single-structure prediction accuracy, chemical mapping prediction accuracy, and riboswitch fold change prediction. doi = 10.1101/2020.05.29.124511 id = cord-327520-qj7coqfr author = Wei, Yulong title = Coronavirus genomes carry the signatures of their habitats date = 2020-06-13 keywords = Fig; SARS summary = Coronaviruses such as SARS-CoV-2 regularly infect host tissues that express antiviral proteins (AVPs) in abundance. Two AVPs that may shape viral genomes are the zinc finger antiviral protein (ZAP) and the apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3 protein (APOBEC3). We tested the hypothesis that both APOBEC3 and ZAP may act as primary selective pressures that shape the genome of an infecting coronavirus by considering a comprehensive number of publicly available genomes for seven coronaviruses (SARS-CoV-2, SARS-CoV, MERS, Bovine CoV, Murine MHV, Porcine HEV, and Canine CoV). In SARS-CoV-2, CpG is most deficient in the S protein region to evaded ZAP-mediated antiviral defense during cell entry. Here we compared the CpG and U content 327 of these coronaviruses and found that viruses that regularly infect AVP-rich tissues tend to Based on global sequence comparison, figure 4a shows that most SNPs are C->U substitutions. doi = 10.1101/2020.06.13.149591 id = cord-314329-rzda8x62 author = Wells, Stephen A. title = Rigidity, normal modes and flexible motion of a SARS-CoV-2 (COVID-19) protease structure date = 2020-03-12 keywords = PDB; motion; structure summary = A judicious combination of simplified methodologiesrigidity analysis, elastic network modelling, and geometric simulation of flexible motioncan work together to extract valuable information on the large-amplitude, low-frequency motions of a protein structure, at a fraction of the computational cost (in resources and time) of molecular dynamics (MD) approaches [3] . The simulations reported here suggest that the protease structure is capable of substantial flexible motions which alter domain orientations, open and close clefts, and affect the geometry of an inhibitor-binding site. The rigidity and flexibility of two recently reported crystal structures (PDB entries 6Y2E and 6LU7) of a protease from the SARS-CoV-2 virus, the infectious agent of the COVID-19 respiratory disease, has been investigated using pebble-game rigidity analysis, elastic network model normal mode analysis, and all-atom geometric simulations. The rigidity and flexibility of two recently reported crystal structures (PDB entries 6Y2E and 6LU7) of a protease from the SARS-CoV-2 virus, the infectious agent of the COVID-19 respiratory disease, has been investigated using pebble-game rigidity analysis, elastic network model normal mode analysis, and all-atom geometric simulations. doi = 10.1101/2020.03.10.986190 id = cord-103029-nc5yf6x4 author = Wichmann, Stefan title = Computational design of genes encoding completely overlapping protein domains: Influence of genetic code and taxonomic rank date = 2020-09-25 keywords = Fig; OLG; SGC; sequence summary = In this study the artificially designed sequences are compared to their original sequences in terms of amino acid identity, amino acid similarity, Hidden Markov Model profile and secondary structure in order to determine the impact of OLG construction and which sequences are potentially functional. While the previous study [30] tried to estimate an upper limit of how many domains can be successfully overlapped in at least one reading frame and position, here the average success rate for OLG construction is determined instead, which is more relevant in relation to both understanding constraints on the formation rate of naturally occuring OLGs and in assessing the likelihood of successful synthetic creation of OLGs. These results in one sense give an upper estimate of the ease of creating overlaps as the difficulty of obtaining an overlapping gene pair naturally is not directly addressed here. doi = 10.1101/2020.09.25.312959 id = cord-103297-4stnx8dw author = Widrich, Michael title = Modern Hopfield Networks and Attention for Immune Repertoire Classification date = 2020-08-17 keywords = CMV; CNN; Hopfield; LSTM; MIL; sequence summary = In this work, we present our novel method DeepRC that integrates transformer-like attention, or equivalently modern Hopfield networks, into deep learning architectures for massive MIL such as immune repertoire classification. DeepRC sets out to avoid the above-mentioned constraints of current methods by (a) applying transformer-like attention-pooling instead of max-pooling and learning a classifier on the repertoire rather than on the sequence-representation, (b) pooling learned representations rather than predictions, and (c) using less rigid feature extractors, such as 1D convolutions or LSTMs. In this work, we contribute the following: We demonstrate that continuous generalizations of binary modern Hopfield-networks (Krotov & Hopfield, 2016 Demircigil et al., 2017) have an update rule that is known as the attention mechanisms in the transformer. We evaluate the predictive performance of DeepRC and other machine learning approaches for the classification of immune repertoires in a large comparative study (Section "Experimental Results") Exponential storage capacity of continuous state modern Hopfield networks with transformer attention as update rule doi = 10.1101/2020.04.12.038158 id = cord-264031-0y7xbgun author = Wierbowski, Shayne D. title = A 3D Structural Interactome to Explore the Impact of Evolutionary Divergence, Population Variation, and Small-molecule Drugs on SARS-CoV-2-Human Protein-Protein Interactions date = 2020-10-13 keywords = CoV-2; SARS; human; interface; protein summary = title: A 3D Structural Interactome to Explore the Impact of Evolutionary Divergence, Population Variation, and Small-molecule Drugs on SARS-CoV-2-Human Protein-Protein Interactions This resource includes docked structures for all interactions with protein structures, enrichment analysis of variation along interfaces, predicted ΔΔG between SARS-CoV and SARS-CoV-2 variants for each interaction, predicted impact of natural human population variation on binding affinity, and a further prioritized set of drug repurposing candidates predicted to overlap with protein interfaces†. Further, we explore the utility of our interactome modeling approach in identifying key 99 interactions undergoing evolution along viral protein interfaces, highlighting population variants on 100 human interfaces that could modulate the strength of viral-host interactions to confer protection from or 101 susceptibility to COVID-19, and prioritizing drug candidates predicted to bind competitively at viral-102 human interaction interfaces. doi = 10.1101/2020.10.13.308676 id = cord-291677-zcbyhsf1 author = Wilamowski, M. title = Methylation of RNA Cap in SARS-CoV-2 captured by serial crystallography date = 2020-08-16 keywords = Nsp16; RNA; SAM; SARS; nsp10/16 summary = To investigate the 2′-O methyltransferase activity of SARS-CoV-2 Nsp10/16, we applied fixed-target serial synchrotron crystallography (SSX) which allows for physiological temperature data collection from thousands of crystals, significantly reducing the x-ray dose while maintaining a biologically relevant temperature. We conducted serial synchrotron crystallography (SSX) experiments at 297 K to test whether low radiation dose could help uncover the structure of Nsp10/16 in a complex with Cap-1. The SARS-CoV-2 Nsp10/16 2′-O MTase complex provides a molecular arrangement for binding of the mRNA Cap-0 and subsequent methylation of the first transcribed nucleotide. The further development of SSX and implementation of time-resolved SSX crystallography is an approach that could visualize chemical processes and protein molecular dynamics -such as of the transfer of the methyl group catalyzed by Nsp10/16 2′O-MTase from SARS-CoV-2. Crystal structure and functional analysis of the SARS-coronavirus RNA cap 2′-o-methyltransferase nsp10/nsp16 complex doi = 10.1101/2020.08.14.251421 id = cord-102634-0n42h72w author = Willforss, Jakob title = OmicLoupe: Facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons date = 2020-10-22 keywords = dataset; datum; feature; figure summary = doi = 10.1101/2020.10.22.349944 id = cord-102145-bi8jyz6r author = Wilson, Audrey E title = Spatial heterogeneity in resources alters selective dynamics in Drosophila melanogaster date = 2020-09-05 keywords = Drosophila; SCT; selection; treatment summary = doi = 10.1101/2020.09.05.283705 id = cord-306924-dw35dlx3 author = Wohlers, Inken title = COVID-19 risk haplogroups differ between populations, deviate from Neanderthal haplotypes and compromise risk assessment in non-Europeans date = 2020-11-03 keywords = Europeans summary = title: COVID-19 risk haplogroups differ between populations, deviate from Neanderthal haplotypes and compromise risk assessment in non-Europeans Recent genome wide association studies (GWAS) have identified genetic risk factors for developing severe COVID-19 symptoms. We show that (i) COVID-19-related genetic factors of Neanderthals deviate from those of modern humans and that (ii) they differ among world-wide human populations, which compromises risk prediction in non-Europeans. Currently, caution is thus advised in the genetic risk assessment of non-Europeans during this world-wide COVID-19 pandemic. However, as two positions carry protective alleles the risk probability of the 51 previously assessed Vindija Neanderthal haplotype is only 52%. 82 83 All human risk haplogroups differ from Neanderthal haplotypes (Fig. 1c) If this variant was causal (2% probability) using lead variants such as rs11385942 or 120 rs35044562 would incorrectly classify individuals carrying these haplogroups to be at 121 risk. The major genetic risk factor for severe COVID-19 is 142 inherited from Neanderthals doi = 10.1101/2020.11.02.365551 id = cord-103509-hynnba03 author = Wong, Ten-Tsao title = A self-assembled protein nanoparticle serving as a one-shot vaccine carrier date = 2020-09-18 keywords = AH3-GFP; Fig; protein summary = From these two clues, it was hypothesized that AH3-GFP fusion protein form stable protein complex through hydrophobic interaction mediated by N-terminal AH3 peptide. Using the same protocol, AH3-GFP was found to co-sedimented with the bacterial membrane (Fig. S3A) as well as the AH3-sfGFP-hM2e fusion protein but not a free GFP protein (Fig S3B) These results are consistent with our protein structure modeling that Arg11 serves as a main contact point for dimer stacking also it mediates the electrostatic interaction with mutated Glu13 (Fig. 3E ). These results suggest that the two point mutations of AH3 in I8L and K13E enable the formation of a stable, high antigenic protein complex that stimulates long lasting immune responses in a single immunization. The result suggests that although carrier protein AH3-sfGFP also has high antigenicity, it did not interfere with the immune response against the heterologous protein, hM2e (Fig. 5B, 5C) doi = 10.1101/2020.09.16.299149 id = cord-102891-0z397ppn author = Wren, Brandi title = Social contact behaviors are associated with infection status for whipworm (Trichuris sp.) in wild vervet monkeys (Chlorocebus pygerythrus) date = 2020-10-07 keywords = Trichuris; grooming; social summary = doi = 10.1101/2020.10.07.329409 id = cord-103041-ymr3e60k author = Wu, Yue title = Homeostatic mechanisms regulate distinct aspects of cortical circuit dynamics date = 2019-10-02 keywords = Fig; correlation; hebbian summary = To understand how neural circuits exploit various synaptic plasticity and homeostatic mechanisms to decrease and recover both firing rates and correlations during MD, we built a plastic recurrent network model consisting of randomly connected excitatory and inhibitory spiking neurons (Methods). Based on these experimental findings, besides Hebbian plasticity during training, we modeled these two distinct homeostatic mechanisms following MD: (1) synaptic scaling which acts only on excitatory synapses (Turrigiano et al., 1998; Hengen et al., 2013) , and (2) intrinsic plasticity which modifies the intrinsic excitability of both excitatory and inhibitory neurons (Grubb and Burrone, 2010; Campanac et al., 2013) (Methods) . We speculated that this failure to recover correlations in the model network, despite the recovery of firing rates, could be the result of perturbing the structured connectivity between excitatory neurons within assemblies generated through training (Fig. 3B) . doi = 10.1101/790410 id = cord-102842-51n5mnjb author = Węglarz-Tomczak, Ewelina title = Ebselen as a highly active inhibitor of PLProCoV2 date = 2020-05-17 keywords = SARS; pro summary = doi = 10.1101/2020.05.17.100768 id = cord-355811-aq7p1uxo author = Węglarz-Tomczak, Ewelina title = Discovery of potent inhibitors of PLproCoV2 by screening a library of selenium-containing compounds date = 2020-05-21 keywords = SARS summary = A collection of twelve organoselenium compounds, structural analogues of antioxidant drug ebselen were screened for inhibition of the papain-like protease (PLpro) from the acute respiratory syndrome coronavirus 2 (SARS-CoV-2, CoV2). In recent studies, peptide analogues [11] and ebselen [12] have been identified as highly active inhibitors for PL pro . We show that some of them indeed possess higher activity than ebselen, that has been recently reported as PL pro CoV2 inhibitor [12] , and, thus, could be considered as novel potential drugs against COVID-19. In this work, we used the ebselen derivatives/analogues library and performed a comprehensive inhibition study of PL pro CoV2. In the case of PL pro SARS, none of the presented ebselen derivatives was able to block the enzyme. Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design Ebselen as a highly active inhibitor of PL pro CoV2 doi = 10.1101/2020.05.20.107052 id = cord-329118-0gq5yusk author = Xiang, Boyu title = ScRNA-seq discover cell cluster change under OAB: ACE2 expression reveal possible alternation of 2019-nCoV infectious pathway date = 2020-06-06 keywords = ACE2; OAB summary = The purpose of our study is to explore cell cluster structure and ACE2 expression pattern in the bladder and use scRNA-seq to infer the effects of human senile lesions, OAB, on umbrella cells and intermediate cells in the bladder epithelium from the results of mice. Because this potential urinary tract infection pathway may be critical to prevent 2019n-Cov, here we used two scRNA-Seq transcriptomes to analyze bladder tissue from normal and OAB mice and combined human and mouse bladder ACE2 expression data from public data base to analyze the impact of underlying disease on this potential infectious system 7 . Single-cell Analysis of ACE2 Expression in Human Kidneys and Bladders Reveals a Potential Route of 2019-nCoV Infection doi = 10.1101/2020.06.05.137380 id = cord-312228-wbyqmvhs author = Xiao, Minfeng title = Multiple approaches for massively parallel sequencing of HCoV-19 (SARS-CoV-2) genomes directly from clinical samples date = 2020-03-19 keywords = Fig; read; sequencing summary = Here we illustrate the application of amplicon and hybrid capture (capture)-based sequencing, as well as ultra-high-throughput metatranscriptomic (meta) sequencing in retrieving complete genomes, inter-individual and intra-individual variations of HCoV-19 from clinical samples covering a range of sample types and viral load. 90 Therefore, we aim to comprehensively compare the sensitivity, inter-individual (variant) and 91 intra-individual (iSNV) accuracy, and other general features of different approaches by sys-92 tematically utilizing ultra-high-throughput metatranscriptomic, hybrid capture-based, and 93 amplicon-based sequencing approaches to obtain genomic information of HCoV-19 from 94 serial dilutions of a cultured isolate and directly from clinical samples. We assessed the correlations between the HCoV-19 genome copies per mL in diluted 396 samples of cultured isolates and the minimum amount of sequencing data for amplicon-397 and capture-based methods using Pearson correlation coefficient (R) with the function 398 scatter from the R package ggpubr (v3.6.1) 38 . doi = 10.1101/2020.03.16.993584 id = cord-325420-e9fjo7tl author = Xiao, Xia title = Identification of potent and safe antiviral therapeutic candidates against SARS-CoV-2 date = 2020-07-06 keywords = SARS summary = Here we performed a high throughput screen of approximately 1700 US FDA approved compounds to identify novel therapeutic agents that can effectively inhibit replication of coronaviruses including SARS-CoV-2. These screens have identified 24 anti-SARS-CoV-2 drugs including previously reported compounds such as hydroxychloroquine, amlodipine, arbidol hydrochloride, tilorone 2HCl, dronedarone hydrochloride, and merfloquine hydrochloride. Positive compounds from the initial screen were tested for their antiviral 120 efficacy against SARS-CoV-2 in Vero cells. Our data show that 24 of these compounds show significant 124 efficacy in inhibiting SARS-CoV-2 replication with sub micromolar IC50 for many of these 125 drugs such as nilotinib, clofazimine and raloxifene. This screen identified five new compounds that 187 are highly efficacious in inhibiting the viral replication of SARS-CoV-2 with SI >600. The positively identified drugs from this screen were used to perform dose response curves 220 against OC43 on LLC-MK2 and against SARS-CoV-2 using Vero cells as described below. doi = 10.1101/2020.07.06.188953 id = cord-337701-56tmg38b author = Xiao, Yan title = Comparison of three TaqMan Real-Time Reverse Transcription-PCR assays in detecting SARS-CoV-2 date = 2020-07-06 keywords = PCR summary = In the present study, we evaluated the sensitivity, specificity, amplification efficiency, and linear detection ranges of three qRT-PCR assays, including the assays developed by our group (IPBCAMS), and the assays recommended by WHO and China CDC (CCDC). No effect of the 152 co-existed other viral nucleic acids on the LOD and the linear detection range was 153 observed, although higher Ct values were generated than those of RNA transcript 154 alone as template in all of the three qRT-PCR assays. Although most of the evaluated 232 assays exhibited good sensitivity, specificity, reproducibility and wide linear detection 233 range, performance test with clinical specimens from suspected COVID-19 patients 234 suggested that the N gene assay in IPBCAMS assays and CCDC assays, and the ORF 235 1b gene assays in IPBCAMS assays were the preferred qRT-PCR assays for accurate 236 detection of SARS-CoV-2. doi = 10.1101/2020.07.06.189860 id = cord-345299-4k7qymqd author = Xiong, Hua-Long title = Several FDA-approved drugs effectively inhibit SARS-CoV-2 infection in vitro date = 2020-06-05 keywords = SARS; VSV summary = To identify drugs that are potentially used for the treatment of COVID-19, the potency of 1403 FDA-approved drugs were evaluated using a robust pseudovirus assay and the candidates were further confirmed by authentic SARS-CoV-2 assay. Four compounds, Clomiphene (citrate), Vortioxetine, Vortioxetine (hydrobromide) and Asenapine (hydrochloride), showed potent inhibitory effects in both pseudovirus and authentic virus assay. In this study, the anti-SARS-Cov-2 potentiality of 1403 FDA approved drugs were quantitatively evaluated by the pseudovirus-based assay. In the second round of screening, inhibition of VSV-SARS-CoV-2-Sdel18 virus infection and cell cytotoxicity were both detected (Supplementary Figure 1) . The robust assay based on VSV-SARS-CoV-2-Sdel18 pseudovirus screened out the potential drugs with high efficiency, then the inhibitory effect was confirmed by authentic SARS-CoV-2 assay. The relative value or inhibition rate of candidate drugs were calculated according to the decrease of GFP positive cell number (for pseudovirus-based assay) or cytopathic effect (for authentic SARS-CoV-2-based assay). doi = 10.1101/2020.06.05.135996 id = cord-345499-hq5um68k author = Xiong, Rui title = Novel and potent inhibitors targeting DHODH, a rate-limiting enzyme in de novo pyrimidine biosynthesis, are broad-spectrum antiviral against RNA viruses including newly emerged coronavirus SARS-CoV-2 date = 2020-03-12 keywords = DHODH; Fig; S312; S416; SARS summary = title: Novel and potent inhibitors targeting DHODH, a rate-limiting enzyme in de novo pyrimidine biosynthesis, are broad-spectrum antiviral against RNA viruses including newly emerged coronavirus SARS-CoV-2 Herein, we identified two potent inhibitors of DHODH, S312 and S416, with favorable drug-like and pharmacokinetic profiles, which all showed broad-spectrum antiviral effects against various RNA viruses, including influenza A virus (H1N1, H3N2, H9N2), Zika virus, Ebola virus, and particularly against the recent novel coronavirus SARS-CoV-2. We also proposed the drug combination of DAA and HTA was a promising strategy for anti-virus treatment and proved that S312 showed more advantageous than Oseltamivir to treat advanced influenza diseases in severely infected animals. We identified that targeting DHODH offers broad-spectrum antiviral efficacies against various RNA viruses, including the DAA-resistant influenza virus and the newly emerged coronavirus SARS-CoV-2. doi = 10.1101/2020.03.11.983056 id = cord-261877-4y37676n author = Xu, Cong title = Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM date = 2020-06-30 keywords = ACE2; Fig; RBD; SARS summary = Recent cryoelectron microscopy (cryo-EM) studies on the stabilized ectodomain of SARS-CoV-2 S protein revealed a closed state of S trimer with three RBD domains in "down" conformation (Walls et al., 2020) , as well as an open state with one RBD in the "up" conformation, corresponding to the receptor-accessible state (Walls et al., 2020; Wrapp et al., 2020) . To gain a thorough picture on how the receptor ACE2 binding induces conformational dynamics of the SARS-CoV-2 S trimer and triggers transition towards the postfusion state, we determine the cryo-EM structure of SARS-CoV-2 S trimer in complex with human ACE2 PD domain to 3.8 Å resolution (termed SARS-CoV-2 S-ACE2, Figs. Based on the data, we put forward a mechanism of ACE2 binding-induced conformational transitions of SARS-CoV-2 S trimer from the tightly closed ground prefusion state transforming towards the postfusion state (Fig. 6) . Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding doi = 10.1101/2020.06.30.177097 id = cord-328257-kl4wh2zg author = Xu, H title = Hydroxychloroquine increased psychiatric-like behaviors and disrupted the expression of related genes in the mouse brain date = 2020-09-28 keywords = Bdnf; HCQ summary = Although this animal study does not prove that HCQ has a similar effect in humans, it indicates that HCQ poses a significant risk to mental health and suggests that further clinical investigation is essential. Less attention has been paid to the effects of HCQ on mental health, although multiple studies have reported severe psychiatric symptoms, including agitation, hallucinations, anxiety, depression, and suicidal ideation, in patients treated with HCQ or chloroquine (9) (10) (11) (12) . To the best of our knowledge, this study is the first to test the psychiatric effect of HCQ in an animal model, and our results suggest that, in healthy mice, HCQ administration can induce persistent behavioral changes and disrupt gene expression in the brain. Our results did not reveal a significant effect of HCQ treatment on working memory, but total exploration time was decreased after HCQ administration, which also suggests that the drugs increased anxiety. doi = 10.1101/2020.09.27.316158 id = cord-317523-idji1l0a author = Xu, Huanzhou title = SARS-CoV-2 viroporin triggers the NLRP3 inflammatory pathway date = 2020-10-27 keywords = SARS summary = With the selective NLRP3 inhibitor MCC950 able to block ORF3a-mediated inflammasome activation and key ORF3a residues needed for virus release and inflammasome activation conserved in SARS-CoV-2 isolates across continents, ORF3a and NLRP3 present prime targets for intervention. In a pared-down system, we investigate the influence of ORF3a, an essential SARS-CoV-2 protein, on the inflammatory machinery and find that it activates NLRP3, the most prominent inflammasome by causing potassium loss across the cell membrane. To assess if ORF3a also 135 mediates activation of other prominent inflammasomes including NLRP1 and NLRC4, we 136 depleted each of these molecules but were unable to block cleavage of pro-caspase 1 (Fig.2G) , 137 indicating that ORF3a predominantly activates the NLRP3 inflammasome. In summary, an essential viroporin required for release of SARS-CoV-2 from infected cells is also 178 able to prime and activate the NLRP3 inflammasome, the machinery responsible for much of the doi = 10.1101/2020.10.27.357731 id = cord-103422-ys846i99 author = Xu, Xinhui title = CRISPR-Assisted DNA Detection, a novel dCas9-based DNA detection technique date = 2020-05-13 keywords = CADD; HCR; dna summary = In this detection, DNA sample is incubated with a pair of capture sgRNAs (sgRNAa and sgRNAb) specific to a target DNA, dCas9, a signal readout-related probe, and an oligo-coated solid support beads or microplate at room temperature for 15 min. When target DNA is bound by a pair of dCas9-sgRNA complexes, the dCas9-sgRNA-DNA complex will be captured on surface of beads or microplate via annealing between an oligonucleotide coupled on solid supports and capture sequence of sgRNAa. Then the captured dCas9-sgRNA-DNA complex is reported by a kind of signal reporter captured by the capture sequence of sgRNAb. This method was validated by detecting DNA of bacteria, cancer cell and virus. We compared the HPV detection results of these 31 clinical samples tested by Beads-HCR CADD and PCR-reverse dot hybridization method that was performed by Jinling Hospital (Fig. 4C ). These results indicate that Beads-HCR CADD can be used to detect hrHPV infections in clinical samples with high sensitivity and specificity. doi = 10.1101/2020.05.13.093062 id = cord-295560-0rpguepv author = Yan, Kexin title = Simple rapid in vitro screening method for SARS-CoV-2 anti-virals that identifies potential cytomorbidity-associated false positives date = 2020-10-14 keywords = CPE summary = The assay clearly illustrated the anti-viral activity of remdesivir, a drug known to inhibit SARS-CoV-2 replication. Here we describe a simple rapid bioassay for drug screening using Vero 20 E6 cells and inhibition of cytopathic effects (CPE) measured using crystal violet staining. A key refinement involves a simple growth assay to identify drug concentrations that 23 cause cellular stress or "cytomorbidity", as distinct from cytotoxicity or loss of viability. A key refinement involves a simple growth assay to identify drug concentrations that 23 cause cellular stress or "cytomorbidity", as distinct from cytotoxicity or loss of viability. Thus a drug that has no specific anti-viral activity, but that 52 is able to induce cellular stress, may therefore inhibit virus replication non-specifically and generate 53 a potential false positive in the screening assay. A simple rapid bioassay for screening drugs for potential antiviral activity against SARS-CoV-2 72 is to determine whether the drug can inhibit virus-induced cytopathic effects (CPE) in Vero E6 cells. doi = 10.1101/2020.10.13.338541 id = cord-259620-qigfstxt author = Yang, Chen title = Kidney injury molecule-1 is a potential receptor for SARS-CoV-2 date = 2020-10-10 keywords = ACE2; KIM1; SARS summary = Presently, it is generally recognized that SARS-CoV-2 initiates invasion through binding of receptor-binding domain (RBD) of spike protein to host cell-membrane receptor ACE2, however, whether there is additional target of SARS-CoV-2 in kidney remains unclear. Studies have indicated direct infection of SARS-CoV-2 in kidney in addition to lung 5, 31 , however, ACE2 remains the only confirmed receptor which may mediate this invasion. Notably, our results suggest that SARS-CoV-2-RBD binds KIM1 and ACE2 via two distinct pockets, implicating that KIM1 and ACE2 may synergistically mediate the invasion of SARS-CoV-2 in kidney cells; which may explain the strong renal tropism, as well as the high incidence of acute kidney injury in COVID-19 patients 5 . ACE2 is the most well-studied receptor for SARS-CoV-2 so far, yet it is not an ideal therapeutic target for COVID-19 since it is widely expresses in multiple organs, and plays crucial roles in regulating blood pressure and preventing heart/kidney injury 36, 37 . doi = 10.1101/2020.10.09.334052 id = cord-293428-8hj06hzt author = Yang, Jianling title = Cytotoxicity evaluation of chloroquine and hydroxychloroquine in multiple cell lines and tissues by dynamic imaging system and PBPK model date = 2020-04-24 keywords = HCQ; Liu summary = To further uncover the toxicity profile of CQ and HCQ in different tissues, we evaluated the cytotoxicity of them in 8 cell lines, and further adopted the physiologically-based pharmacokinetic models (PBPK) to predict the tissue risk respectively. HCQ has the less impact in 7 cell lines proliferation and less toxicity compared to CQ in heart, liver, kidney and lung. Recent 99 publications have demonstrated that chloroquine (CQ) and hydroxychloroquine (HCQ) 100 efficiently inhibited SARS-CoV-2 infection in vitro assay (7-9). The data suggest that HCQ was 127 demonstrated to be much less toxic than CQ, at least at certain key tissues (heart, liver, 128 kidney, and lung). However, the tissue trough concentration of 197 HCQ in lung is the highest level (25.633 μg/ml) compared with liver, kidney and heart 198 (Table 2 and Figure 4 ). Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting 286 SARS-CoV-2 infection in vitro doi = 10.1101/2020.04.22.056762 id = cord-103869-ii6qi1bp author = Yang, Liu title = Defining a Global Map of Functional Group Based 3D Ligand-binding Motifs date = 2020-09-28 keywords = Fig; ligand; motif summary = Current methods based on structural comparison or alignment of protein pockets have identified many well-defined 3D motifs that are conserved across different protein pockets and widely used for protein function annotation, pockets classification and ligand-binding prediction (Gao and Skolnick, 2013; Hoffmann et al., 2010; Hwang et al., 2017; Pires et al., 2013; Pu et al., 2019; Yeturu and Chandra, 2008) . To systematically identify and evaluate 3D binding motifs at FG level, we developed AFTME, an alignment-free method that automatically maps functional atoms to different FGs from a set of protein pockets binding the same ligand using two-dimensional clustering approach. We have developed AFTME, a computational method to dissect protein pockets binding a specific ligand into sectors that interact with different functional groups (FGs). The basic assumption of this method is simple: if conserved binding pattern for a specific FG exists, the pattern-forming atoms should be spatially proximal to the corresponding FG and frequently co-appear, thus can be detected through clustering analysis of functional atoms from diverse protein pockets binding the same ligand. doi = 10.1101/2020.09.27.315762 id = cord-261688-njlxrxv6 author = Yang, Ziwei title = Suppression of MDA5-mediated antiviral immune responses by NSP8 of SARS-CoV-2 date = 2020-08-12 keywords = MDA5; NSP8; SARS summary = Melanoma differentiation-associated gene-5 (MDA5) acts as a cytoplasmic RNA sensor to detect viral dsRNA and mediates type I interferon (IFN) signaling and antiviral innate immune responses to infection by RNA viruses. Here, we report that SARS-CoV-2 nonstructural protein 8 (NSP8) acts as an innate immune suppressor and inhibits type I IFN signaling to promote infection of RNA viruses. Here, we revealed that NSP8 protein of SARS-CoV-2 directly blocks the activation of the cytosolic viral dsRNA sensor MDA5 and significantly downregulates antiviral immune responses. Our study contributes to our understanding of the direct immune evasion mechanism of SARS-CoV-2 by showing that NSP8 suppresses the most upstream sensor of innate immune responses involved in the recognition of viral dsRNA. Based on our existing experimental data, we propose a simple working model to illustrate how NSP8 218 negatively regulates innate immune responses by inhibiting MDA5 K63-linked polyubiquitination (Fig.5c) . doi = 10.1101/2020.08.12.247767 id = cord-102364-t5bt2eb4 author = Yao, Dehui title = Human H-ferritin presenting RBM of spike glycoprotein as potential vaccine of SARS-CoV-2 date = 2020-06-08 keywords = RBM; SARS summary = In an effort of utilizing human ferritin as nanoplatform for drug delivery, we engineered a fusion protein by presenting receptor-binding motif (RBM) of SARS-CoV-2 virus spike glycoprotein on the N-terminus of ferritin subunits. The designed fusion protein with a cage-like structure, similar to that of corona virus, is a potential anti-SARS-CoV-2 vaccine. We hereby show the construction, preparation, and characterization of the fusion protein RBM-HFtn. Our initial affinity study confirmed its biological activity towards ACE2 receptor which suggests its mode of action against SARS-CoV-2 could be either through vaccine therapy or blocking the cellular entry of virus as antagonist of ACE2 receptor. Antibodies targeting the spike glycoprotein of SARS-CoV and MERS-CoV, especially its receptor-binding domain (RBD), was found to efficiently neutralize virus infection [1, 2] . In this work, we engineered a human ferritin heavy chain (HFtn) by fusing and presenting the RBM of its spike glycoprotein as potential vaccine of SARS-CoV-2. doi = 10.1101/2020.05.25.115618 id = cord-354868-pqn59ojj author = Yao, Hebang title = A high-affinity RBD-targeting nanobody improves fusion partner’s potency against SARS-CoV-2 date = 2020-09-25 keywords = RBD; SARS; SR31 summary = title: A high-affinity RBD-targeting nanobody improves fusion partner''s potency against SARS-CoV-2 Considerable research have been devoted to the development of neutralizing antibodies, including llama-derived single-chain nanobodies, to target the receptor-binding motif (RBM) and to block ACE2-RBD binding. A high-affinity RBD binder without neutralizing activity 85 Previously, we generated 99 sybodies from three highly diverse synthetic libraries by ribosome and phage display with in vitro selections against the SARS-CoV-2 RBD. Consistent with its inability to neutralize SARS-CoV-2 pseudovirus, SR31 did not affect RBD-ACE2 binding (Fig. 1C) . Most RBD-targeting neutralizing antibodies, including neutralizing nanobodies characterized so far (8, 13-15, 19, 20, 22-24, 26-28, 34, 35, 37) , engage the RBD at the receptor-binding motif (RBM) (Fig. 3A) , thus competing off ACE2 and preventing viral entry. Taken together, the structural data rationalize the high-affinity binding between SR31 and RBD, and its inability to neutralize SARS-CoV-2. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2 doi = 10.1101/2020.09.24.312595 id = cord-356005-zhwtlik6 author = Yazhini, Arangasamy title = D614G substitution enhances the stability of trimeric SARS-CoV-2 spike protein date = 2020-11-02 keywords = SARS; d614 summary = Here, using in-silico mutagenesis and energy calculations, we analyzed inter-residue interaction energies and thermodynamic stability of the dominant (G614) and the ancestral (D614) variants of spike protein trimer in ''closed'' and ''partially open'' conformations. Such changes in the local interaction energies enhance the thermodynamic stability of the spike protein trimer as free energy difference (ΔΔG) upon glycine substitution is −2.6 kcal/mol for closed conformation and −2.0 kcal/mol for open conformation. Our results on the structural and energetic basis of enhanced stability hint that G614 may confer increased availability of functional form of spike protein trimer and consequent in higher infectivity than the D614 variant. To study the effect of D614G variation on the thermodynamic stability of the spike protein trimer, we calculated free energy changes upon aspartate to glycine substitution using buildmodel function in FoldX (Schymkowitz et al., 2005) . The table contains details of frustration index of inter-residue contacts present at 614th position of spike protein trimer in closed and partially open conformations. doi = 10.1101/2020.11.02.364273 id = cord-291012-y0ufzx93 author = Ye, Qing title = SARS-CoV-2 infection causes transient olfactory dysfunction in mice date = 2020-11-10 keywords = SARS; figure summary = Robust viral nucleocapsid (N) protein was detected in the 89 lung from SARS-CoV-2 infected hACE2 mice, but not from the control animals 90 ( Figure S1B ). Remarkably, a significantly increased latency (152.8 s v.s. 81.8 s; p=0.022) to locate 103 food pellets was observed in SARS-CoV-2 infected mice as compared with the control 104 animals on 2 dpi ( Figure 1D ). Further RT-qPCR assay showed a dozen of 211 OR genes were significantly down regulated in response to SARS-CoV-2 infection 212 ( Figure 5E ), which may also attribute to the observed olfactory dysfunction. Interestingly, SARS-CoV-2 positive signals were also observed in mOSNs and HBCs 245 of infected animals, although we didn''t detect any hACE2 expression in these cells. A) Representative multiplex immunofluorescent staining shows SARS-CoV-2 674 (SARS-CoV-2 N protein-positive) infects sustentacular cells (CK8-positive, yellow 675 arrows), Bowman''s gland cells (Sox9/CK8-positive, white arrows), microvillar cells 676 (CD73/CK8-positive, cyan arrows), HBCs (CK5-postitive, gold arrows) and iOSNs 677 (GAP43-positive doi = 10.1101/2020.11.10.376673 id = cord-321427-bwcpd6im author = Yee, Min title = Neonatal hyperoxia enhances age-dependent expression of SARS-CoV-2 receptors in mice date = 2020-07-22 keywords = ACE2 summary = Instead, we made the surprising discovery that expression of Ace2 and Tmprss2 mRNA increases as mice age and is accelerated by exposing mice to neonatal hyperoxia. Our finding that early life insults such as hyperoxia enhances the age-dependent expression of SARS-CoV-2 receptors in the respiratory epithelium helps explain why COVID-19 lung disease is greater in the elderly and people with pre-existing co-morbidities. When quantified, neonatal hyperoxia increased the number of alveolar cells expressing ACE2 by 148 approximately 50% at 2, 6 and 12 months of age (Figure 4b) . The levels of Tmprss2 mRNA and protein were examined in the lungs of 2-, 12-and 18-month-old mice that were exposed to neonatal hyperoxia and room air from PND0-4 by qRT-PCR 168 and western blotting. As observed for Ace2 expression, 173 exposure to ≥ 60% oxygen from PND4-0 was required to significantly increase the levels of Tmprss2 174 mRNA in the lungs of mice at 2 months of age (Figure 6c ). doi = 10.1101/2020.07.22.215962 id = cord-102350-e1vc2q4j author = Yoon, Hye-Jin title = Signature of N-terminal domain (NTD) structural re-orientation in NPC1 for proper alignment of cholesterol transport: Molecular dynamics study with mutation date = 2020-06-09 keywords = NPC1; NPC2; NTD summary = title: Signature of N-terminal domain (NTD) structural re-orientation in NPC1 for proper alignment of cholesterol transport: Molecular dynamics study with mutation We report the extensive molecular dynamics simulations to gain insight into the structure and motions of NPC1 lumenal domain for cholesterol transport and disease behind the mutation (R518W). In this paper, we present extensive molecular dynamics simulations of NPC1 to understand the structural and dynamical characteristics upon R518W mutation and its effects on overall cholesterol transport efficiency in connection with possible re-location or orientation of NTD and interaction of NPC1 with NPC2. The recent molecular dynamics simulation [30] with full NPC1 when cholesterol is present in NPC1 inhibiting itraconazole binding site, [28] which is at the interface between membrane and lumenal region, shows there is non-negligible distance correlation coefficient between TMD and the rest of the domains. doi = 10.1101/2020.06.09.141630 id = cord-282372-nmii30mc author = Youk, Jeonghwan title = Robust three-dimensional expansion of human adult alveolar stem cells and SARS-CoV-2 infection date = 2020-07-10 keywords = Data; Fig; RNA; SARS; cell summary = Here, we develop a feeder-free, long-term three-dimensional (3D) culture technique for human alveolar type 2 (hAT2) cells, and investigate infection response to SARS-CoV-2. By imaging-based analysis and single-cell transcriptome profiling, we reveal rapid viral replication and the increased expression of interferon-associated genes and pro-inflammatory genes in infected hAT2 cells, indicating robust endogenous innate immune response. Although basic molecular mechanisms in SARS-CoV-2 infection have been identified [5] [6] [7] [8] , most findings have been obtained from experiments using non-physiological cell lines 9 , model animals, such as transgenic mice expressing human angiotensin-converting enzyme 2 (ACE2) 10 , ferrets 11 and golden hamsters 12 , or from observation in clinical cohorts 13 and/or inference from in-silico computational methods [14] [15] [16] . Immunostaining for double-stranded viral RNA (dsRNA) and nucleocapsid protein (NP) of SARS-CoV-2 identified widespread viral infection in hAT2 cells co-expressing pro-SFTPC and ACE2 in hAOs ( Fig. 2a and 2b; Extended Data Fig. 3) . doi = 10.1101/2020.07.10.194498 id = cord-298242-iuskpoug author = Yu, Alvin title = A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion date = 2020-10-02 keywords = SARS; protein summary = Structural data from a combination of cryo-electron microscopy (cryo-EM), x-ray crystallography, and computational predictions were used to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into a complete virion model. In this paper, we construct a largely "bottom-up" coarse-grained (CG) model of the SARS-CoV-2 virion from the currently available structural and atomistic simulation data on SARS-CoV-2 proteins. In this work, we detail several of our CG methods used to iteratively develop a CG model for the full SARS-CoV-2 virion, in which molecular interactions between CG particles are derived using a combination of phenomenological, experimental, and atomistic simulation approaches. In recent cryo-EM images of SARS-CoV-2 particles, the S1 domain of the S protein was found to transiently open and close in order to bind the ACE-2 receptor (3, 5) , which are subtle conformational changes that are difficult to sample in atomistic simulations. doi = 10.1101/2020.10.02.323915 id = cord-330743-o11d0aa1 author = Yu, Xi title = Broad-spectrum virucidal activity of bacterial secreted lipases against flaviviruses, SARS-CoV-2 and other enveloped viruses date = 2020-05-25 keywords = DENV; SARS; ZIKV summary = Herein, we identified 2 secreted bacterial lipases from a Chromobacterium bacterium, named Chromobacterium antiviral effector-1 (CbAE-1) and CbAE-2, with a broad-spectrum virucidal activity against dengue virus (DENV), Zika virus (ZIKV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), human immunodeficiency virus (HIV) and herpes simplex virus (HSV). Incubation of the culture supernatant but not the bacterial lysates resulted in significant suppression of DENV ( Figure 1B ) and ZIKV ( Figure 1C ) infectivity in Vero cells, indicating that an extracellular effector(s) secreted by Csp_BJ was responsible for viral inhibition. DENV, ZIKV, HSV-1 and SARS-CoV-2 virus stocks were diluted to 50 plaque-forming units (pfu) per ml and incubated untreated or with a serial dilution of the CbAEs in five-fold steps at 37°C for 1 hr before being added onto Vero cell monolayers for 2 hr of infection. doi = 10.1101/2020.05.22.109900 id = cord-330473-f03ka7bd author = Yuan, Meng title = A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV date = 2020-03-14 keywords = SARS summary = In this study, we have determined the crystal structure of the receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein in complex with CR3022, a neutralizing antibody previously isolated from a convalescent SARS patient. ONE SENTENCE SUMMARY Structural study of a cross-reactive SARS antibody reveals a conserved epitope on the SARS-CoV-2 receptor-binding domain. A recent study has shown that CR3022, which is a human 49 neutralizing antibody that targets the receptor-binding domain (RBD) of SARS-CoV (4), Nonetheless, despite having a 70 high conservation in the epitope residues, CR3022 Fab binds to SARS-CoV RBD (K d = 1 71 nM) with a much higher affinity than to SARS-CoV-2 RBD (K d = 115 nM) (Table 1 Previous cryo-EM studies have also shown that the recombinant SARS-CoV S 121 protein is mostly found in the none-"up", single-"up", or double-"up" conformations (19, 122 21), but rarely in the triple-"up" conformation, even with ACE2 receptor bound (21, 22) . doi = 10.1101/2020.03.13.991570 id = cord-320054-wqpr8v3p author = Yuan, Xianlin title = The influence of major S protein mutations of SARS-CoV-2 on the potential B cell epitopes date = 2020-08-24 keywords = SARS summary = In this study, we predict neutralizing antibody recognition sites (B cell epitopes) of the prototype S protein of SARS-COV2, along with several common variants using bioinformatics tools. To explore these questions, here we report 94 to used these immuno-bioinformatic tools from the IEDB and related resources to 95 predict the B cell epitopes of S protein from the prototype and mutated strains of 96 SARS-CoV-2 and compare the changes of the likely epitope sites from dominant and 97 rare mutations of S protein. The major variation sequences were available 409 from The Global Initiative for Sharing All Influenza Data (GISAID) [26] and GenBank 446 We used the sequence from early onset SARS-CoV-2 as the wildtype or prototype and 447 the recent variant virus as mutation strains to predict the B-cell epitopes of S protein. doi = 10.1101/2020.08.24.264895 id = cord-286001-pu1fetq7 author = Zang, Ruochen title = TMPRSS2 and TMPRSS4 mediate SARS-CoV-2 infection of human small intestinal enterocytes date = 2020-04-23 keywords = Fig; SARS; TMPRSS4 summary = In addition to TMPRSS2, another mucosa-specific serine protease, TMPRSS4, also enhanced SARS-CoV-2 spike fusogenic activity and mediated viral entry into host cells. Importantly, we found that 160 expression of TMPRSS4 but not ST14 also resulted in a significant increase in the levels of viral RNA and infectious virus titers in the presence of ACE2 ( Fig. 3B and S3C) . Collectively, we have shown that TMPRSS2 and TMPRSS4 activate SARS-CoV-2 S and 187 enhance membrane fusion and viral endocytosis into host cells. Importantly, abrogating TMPRSS4 expression led 209 to a 4-fold reduction in SARS-CoV-2 chimera virus replication in human enteroid, even 210 more significant than TMPRSS2 knockout (Fig. 4B) , highlighting its importance in 211 mediating virus replication in primary cells. It is possible that in the 293 small intestine, whereas SARS-CoV-2 is relatively stable, additional proteases such as 294 trypsin likely enhance viral pathogenesis by triggering more robust IEC fusion (Fig. S2A) . doi = 10.1101/2020.04.21.054015 id = cord-103895-dt0ers70 author = Zeng, Xiangrui title = Comparative Pathway Integrator: a framework of meta-analytic integration of multiple transcriptomic studies for consensual and differential pathway analysis date = 2018-10-16 keywords = CPI; DLPFC; pathway summary = Methods and Results We present a meta-analytic integration tool, Comparative Pathway Integrator (CPI), to address these issues using adaptively weighted Fisher''s method to discover consensual and differential enrichment patterns, consensus clustering to reduce pathway redundancy, and a novel text mining algorithm to assist interpretation of the pathway clusters. In light of this, we proposed a framework of meta-analytical integration of multiple transcriptomic studies for consensual and differential pathway analysis, wrapped in a tool named Comparative Pathway Integrator (CPI). In order to identify both commonly and study-specifically enriched pathways, we applied the adaptively weighted Fisher''s method [14] , which is originally developed to combine p-values from multiple genomic studies for detecting homogeneous and heterogeneous differentially expressed genes. In summary, CPI is a meta-analytic tool for discovering commonly expressed and study specific pattern in transcriptomic studies, that will also reduce pathway redundancy and conduct text mining to increase interpretability of the results. doi = 10.1101/444604 id = cord-253447-4w6caxwu author = Zeng, Xin title = Blocking antibodies against SARS-CoV-2 RBD isolated from a phage display antibody library using a competitive biopanning strategy date = 2020-04-20 keywords = ACE2; RBD; SARS summary = title: Blocking antibodies against SARS-CoV-2 RBD isolated from a phage display antibody library using a competitive biopanning strategy SARS-CoV-2 relies on its spike protein, in particular the receptor binding domain (RBD), to bind human cell receptor angiotensin-converting enzyme 2 (ACE2) for viral entry, and thus targeting RBD holds the promise for preventing SARS-CoV-2 infection. In this work, a competitive biopanning strategy of a phage display antibody library was applied to screen blocking antibodies against RBD. It was proved to competitively block the binding of RBD to ACE2 protein, and potently inhibit SARS-CoV-2 pseudovirus infection of ACE2-overexpressing Hela cells with IC50 values of 12nM. Several high-affinity antibodies targeting SARS-CoV-2 RBD and blocking its binding to ACE2 were isolated, and the top 1 lead exhibited a neutralization activity of SARS-CoV-2 pseudotyped VSV infection. A high-affinity antibody against the target protein can be screened from a phage display antibody library using the standard biopanning process, but its binding epitopes are identified by some extra steps, such as epitope mapping and competitive ELISA. doi = 10.1101/2020.04.19.049643 id = cord-102631-a8fsr6ys author = Zeng, Zipeng title = Generation of kidney ureteric bud and collecting duct organoids that recapitulate kidney branching morphogenesis date = 2020-04-28 keywords = Data; Fig; Matrigel summary = doi = 10.1101/2020.04.27.049031 id = cord-308310-wtmjt3hf author = Zha, Lisha title = Development of a COVID-19 vaccine based on the receptor binding domain displayed on virus-like particles date = 2020-05-14 keywords = RBD; SARS summary = Higly repetitive display of RBD on immunologically optimized virus-like particles derived from cucumber mosaic virus resulted in a vaccine candidate (RBD-CuMVTT) that induced high levels of specific antibodies in mice which were able to block binding of spike protein to ACE2 and potently neutralized the SARS-CoV-2 virus in vitro. Higly repetitive display of RBD on immunologically optimized virus-like particles derived from cucumber mosaic virus resulted in a vaccine candidate (RBD-CuMVTT) that induced high levels of specific antibodies in mice which were able to block binding of spike protein to ACE2 and potently neutralized the SARS-CoV-2 virus in vitro. The receptor binding domain (RBD) of the SARS spike protein binds to ACE2 and is an important target for neutralizing antibodies [5] [6] [7] . Hence, the RBD-CuMVTT vaccine candidate is able to induce high levels of SARS-CoV-2 neutralizing antibodies. Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine doi = 10.1101/2020.05.06.079830 id = cord-104162-fe51v2pt author = Zhang, Chiyu title = Potential Achilles heels of SARS-CoV-2 displayed by the base order-dependent component of RNA folding energy date = 2020-11-02 keywords = HIV-1; RNA; SARS summary = Although SARS-CoV-2 differs in many respects from HIV-1, the same technology displays regions with a high base order-dependent folding energy component, which are also highly conserved. While the regions are often also protein-encoding (e.g. NSP3, ORF3a), we suggest that their nucleic acid level functions – such as the ribosomal frameshifting element (FSE) that facilitates differential expression of 1a and 1ab polyproteins – can be considered potential "Achilles heels" for SARS-CoV-2, perhaps susceptible to therapies like those envisaged for AIDS. Assays of the base order-dependent component of the folding energy have shown that a highly conserved region, in otherwise rapidly mutating HIV-1 genomes, associates with an RNA structure corresponding, not to a protein-encoding function, but to an RNA packaging signal. This high GC% value can obscure the contribution of the base order-dependent component of the folding energy, which provides a sensitive indicator of local intraspecies pressures for the conservation of function within a population (i.e. a mutated organism is eliminated by natural selection so no longer can be assayed for function in the population). doi = 10.1101/2020.10.22.343673 id = cord-103709-86hv27vh author = Zhang, Dong Yan title = Prefusion spike protein stabilization through computational mutagenesis date = 2020-06-19 keywords = SARS; SASA; protein summary = The surface spike protein of SARS-CoV-2 mediates the process of coronavirus entry into human cells by binding angiotensin-converting enzyme 2 (ACE2). Our pipeline integrates bioinformatics analysis of conserved residues, motion dynamics from molecular dynamics simulations, and other structural analysis to identify residues that significantly contribute to the thermodynamic stability of the spike protein. We subject the selected residues to computational redesign using Eris to find the stabilizing mutations by calculating the change in free energy ∆∆ = ∆ − ∆ , where ∆ and ∆ are the free energies of the mutant protein and wild type proteins correspondingly. After the designation of the mutation sites, the pipeline utilizes Eris to determine the changes in free energies of the mutants. We analyze the conservation score, RMSF, and SASA of residues in the spike protein through the pipeline. Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes doi = 10.1101/2020.06.17.157081 id = cord-325348-yi6yu5l1 author = Zhang, G. title = Investigation of ACE2 N-terminal fragments binding to SARS-CoV-2 Spike RBD date = 2020-06-17 keywords = ACE2; SARS; SBP1 summary = Recent cryo-electron microscopy (cryo-EM) structural studies of the SARS-CoV-2 spike protein 68 receptor binding domain (RBD) in complex with full-length human ACE2 receptor revealed key 69 amino acid residues at the contact interface between the two proteins and estimated the binding 70 affinity at ~15 nM [7, 8] . The results of this MD simulation suggest 108 that SBP1 and SBP2 peptides derived from the ACE-PD α1 helix may alone potentially bind the 109 SARS-CoV-2 spike RBD protein with sufficient affinity to disrupt the associated PPI. However, competition was not observed when using non-biotinylated SBP1 pre-140 mixed in solution with Sino Biological insect-derived SARS-CoV-2-RBD, even with a 1000-fold 141 excess of the peptide (Fig. 3C, 3E ). In conclusion, a biotinylated peptide sequence derived from human ACE2 was found to 205 bind Sino Biological insect-derived SARS-CoV-2 spike protein RBD with micromolar affinity, but 206 did not associate with SARS-CoV-2-RBD variants obtained from other commercial sources. doi = 10.1101/2020.03.19.999318 id = cord-321155-dty18esg author = Zhang, Rongxin title = Whole genome identification of potential G-quadruplexes and analysis of the G-quadruplex binding domain for SARS-CoV-2 date = 2020-06-05 keywords = RNA; SARS; SUD summary = We also found that the SUD-like sequence is retained in the SARS-CoV-2 genome, while some other coronaviruses that can infect humans are depleted. To get the potential G-quadruplexes in the SARS-CoV-2 genome, we took the strategy described as follows ( Fig. 2A) : (i) Predicting the PG4s with three software independently. To further characterize the potential canonical secondary structures competitive with Gquadruplexes, the landscape of thermodynamic stability of the SARS-CoV-2 genome was depicted by using ΔG°z-score [55] . The distributions of loop length between the SARS-CoV-2 PG4s and the human two-quartet Gquadruplexes did not show discrepancies (Fig. S1 , Wilcoxon test, p-value = 0.4552). Recent research revealed that the G-quadruplexes in human UTRs (Untranslated Regions) are under selective pressures [58] , and some coronaviruses on bats and pangolins are closely related to SARS-CoV-2. Thus, we started to explore whether the SARS-CoV-2 genome contains the protein-coding sequence similar to SUD and whether SARS-CoV-2 retains the ability to bind RNA G-quadruplexes. doi = 10.1101/2020.06.05.135749 id = cord-332185-a96r1k7a author = Zhang, Shuyuan title = Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution date = 2020-09-22 keywords = RBD; SARS summary = title: Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution Here we determined the cryo-EM structures of the spikes from bat (RaTG13) and pangolin (PCoV_GX) coronaviruses, which are closely related to SARS-CoV-2. However, we found that the PCoV_GX, but not the RaTG13, spike is comparable to the SARS-CoV-2 spike in binding the human ACE2 receptor and supporting pseudovirus cell entry. Through structure and sequence comparisons, we identified critical residues in the RBD that underlie the different activities of the RaTG13 and PCoV_GX/SARS-CoV-2 spikes and propose that N-linked glycans serve as conformational control elements of the RBD. Cryo-electron microscopy structures of the SARS-CoV spike 464 glycoprotein reveal a prerequisite conformational state for receptor binding Cryo-EM structure of the SARS 467 coronavirus spike glycoprotein in complex with its host cell receptor ACE2 Cryo-EM structures of MERS-CoV and SARS-CoV spike 495 glycoproteins reveal the dynamic receptor binding domains doi = 10.1101/2020.09.21.307439 id = cord-328187-9zd79gai author = Zhang, Yali title = Virus-free and live-cell visualizing SARS-CoV-2 cell entry for studies of neutralizing antibodies and compound inhibitors date = 2020-07-22 keywords = CSBT; SARS; figure summary = The new system allows quantitative analyses of the inhibition potentials and detailed influence of COVID-19-convalescent human plasmas, neutralizing antibodies and compounds, providing a versatile tool for high-throughput screening and phenotypic characterization of SARS-CoV-2 entry inhibitors. 22 On 293T-ACE2iRb3 cells, both the SARS-CoV2-RBG and SARS-CoV2-STG 23 probes showed effective-binding to the cells, as membrane-bound and hACE2-24 mRuby3-colocalized mGam signals were observed after a 6-min incubation with the 25 cells ( Figure 2C ). Compared with 3 samples from healthy donors (n=40), all COVID-19-convalescent plasmas showed 4 significant cMFI inhibition on CSBT assay, whereas only 12 samples (37.5%) had 5 detectable CRBT activity ( Figure 3A ). Among the antibody titers derived from various assays, the 10 CSBT titer showed the best correlation with LVppNAT ( Figure 3D and Table S2, 11 r=0.832, p<0.001), and it also well correlated (r=0.959, p<0.001, Figure 3D ) with the 12 neutralization activity against authentic SARS-CoV-2 virus in 12 representative 13 samples (Table S3) . doi = 10.1101/2020.07.22.215236 id = cord-102763-tc1z0nm9 author = Zhang, Yuan title = IgY antibodies against Ebola virus possess post-exposure protection and excellent thermostability date = 2020-05-21 keywords = EBOV; Ebola summary = Lethal dose of virus challenged mice were treated 2 or 24 h post-infection with different doses of anti-EBOV IgY. We developed a highly thermostable therapeutic antibody against EBOV based on chicken immunoglobulin Y (IgY). The newborn mice receiving passive transfer of IgY achieved complete protection against a lethal dose of virus challenge indicating that the anti-EBOV IgY provides a promising countermeasure to solve the current clinical application problems of Ebola antibody-based treatments in Africa. To obtain high titer EBOV NAbs, 5-month-old laying hens were vaccinated with five different 124 immunogens, including 10 3 or 10 4 TCID 50 VSVΔ G/EBOVGP, 100 μ g rEBOVGP, 100 μ g 125 pCAGGS/EBOVGP, 10 μg EBOV-VLP, and 10 11 virus particles (vp) Ad5/EBOVGP (Fig 2a) . Protective 546 monotherapy against lethal Ebola virus infection by a potently neutralizing antibody Protective 546 monotherapy against lethal Ebola virus infection by a potently neutralizing antibody doi = 10.1101/2020.05.21.108159 id = cord-103504-ucqqpra5 author = Zhang, Zhe title = The conserved ER-transmembrane protein TMEM39 coordinates with COPII to promote collagen secretion and prevent ER stress date = 2020-09-20 keywords = COPII; Fig summary = From a genome-wide RNAi screen for 54 genes affecting ER stress response, we previously identified tmem-131 that defines a 55 broadly conserved family of proteins important for procollagen assembly and secretion 56 (22). RNAi knock-down of sec-23 and most other COPII genes 340 recapitulated the tmem-39 loss-of-function phenotypes in constitutively high ER stress 341 response, defective collagen secretion and sensitivity to osmolality stress in C. We also noticed that RNAi knock-down of many COPII related genes, such 343 as sec-23, sec-24.1, npp-20, sar-1, sec-12, rab-5 and trpp-8 caused more severe 344 phenotypes than tmem-39 RNAi, leading to lethality or developmental arrest that 345 prevent collagen phenotype analysis (Table 1) Recent work showed that TMEM39A facilitates the ER-to-Golgi transport of SAC1 and 355 regulates autophagosome formation (28). We found that RNAi knock-down of 356 autophagy related genes, such as sac-1 and let-363, caused autophagy induction but 357 did not affect the ER stress response or collagen secretion (Fig 6) . doi = 10.1101/2020.08.17.253450 id = cord-353554-98uzivsk author = Zhang, Zheng title = Membrane proteins with high N-glycosylation, high expression, and multiple interaction partners were preferred by mammalian viruses as receptors date = 2018-03-08 keywords = receptor; viral summary = title: Membrane proteins with high N-glycosylation, high expression, and multiple interaction partners were preferred by mammalian viruses as receptors Here, by manually curating a high-quality database of 268 pairs of mammalian virus-host receptor interaction, which included 128 unique viral species or sub-species and 119 virus receptors, we found the viral receptors were structurally and functionally diverse, yet they had several common features when compared to other cell membrane proteins: more protein domains, higher level of N-glycosylation, higher ratio of self-interaction and more interaction partners, and higher expression in most tissues of the host. 64 The virus-receptor interaction was reported to be a principal determinant of viral host 65 range, tissue tropism and cross-species infection [11, 16, 22] . However, we found the viral receptor tended not to interact with each 248 other ( Figure S3D 270 Since the virus has to compete with other proteins for binding to the receptor, proteins (Table S5) . doi = 10.1101/271171 id = cord-324344-dxuabscn author = Zhao, Xuesen title = LY6E Restricts the Entry of Human Coronaviruses, including the currently pandemic SARS-CoV-2 date = 2020-04-05 keywords = LY6E; OC43; SARS summary = In an effort to search for the host cellular protein(s) mediating the differential 29 susceptibility of the two cell lines to HCoV-OC43 infection, we found that ADAP2, GILT and 30 LY6E, three cellular proteins with known activity of interfering virus entry, expressed at 31 significantly higher levels in HepG2 cells. In an effort to search for the host cellular protein(s) mediating the differential 29 susceptibility of the two cell lines to HCoV-OC43 infection, we found that ADAP2, GILT and 30 LY6E, three cellular proteins with known activity of interfering virus entry, expressed at 31 significantly higher levels in HepG2 cells. Finally, the findings that LY6E inhibits human CoV entry cannot be evaded by ectopic 284 expression of membrane-associated serine protease TMPRSS2 and compromised by AmphoB 285 treatment strongly indicate that LY6E modulates virus entry via a distinct mechanism from that 286 IFITM proteins do (Figs. doi = 10.1101/2020.04.02.021469 id = cord-350627-4pgish5x author = Zhao, Yu title = Single-cell RNA expression profiling of ACE2,thereceptor of SARS-CoV-2 date = 2020-01-26 keywords = ACE2; SARS summary = Here based on the public database and the state-of-the-art single-cell RNA-Seq technique, we analyzed the ACE2 RNA expression profile in the normal human lungs. These studies showed that in normal human lung, ACE2 is mainly expressed by type II and type I alveolar epithelial cells. In total, we analyzed 43,134 cells derived from normal lung tissue of To further understand the special population of ACE2-expressing AT2, we performed gene ontology enrichment analysis to study which biological processes are involved with this cell population by comparing them with the AT2 cells not expressing ACE2. Of note, the 2 male donors have a higher ACE2-expressing cell ratio than all other 6 female author/funder. We also noticed that the only Asian donor (male) has a much higher ACE2Altogether, in the current study, we report the RNA expression profile of ACE2 in the human lung at single-cell resolution. https://doi.org/10.1101/2020.01.26.919985 doi: bioRxiv preprint author/funder. doi = 10.1101/2020.01.26.919985 id = cord-339720-d1stzy8w author = Zhao, Yuan title = Susceptibility of tree shrew to SARS-CoV-2 infection date = 2020-04-30 keywords = SARS; shrew; tree summary = No clinical signs were observed in SARS-CoV-2 inoculated tree shrews during this experiment except the increasing body temperature (above 39° C) particular in female animals during infection. In three young tree shrews (TS26, TS27 and TS28), we could detect viral RNA from only lungs in TS26 and TS27, but not in any tissue from TS28, although these animal had higher number of viral genomic copy numbers at the earlier stage of SARS-CoV-2 infection. Although SARS-CoV-2 infection didn''t cause severe disease in all three ages of tree shrews, viral replication and mild histopathological changes were still observed in this study. In conclusion, tree shrew is not as susceptible to SARS-CoV-2 infection as the reported animal models of COVID-19, though limited replication of SARS-CoV-2 and mild histopathology was detected and observed in some tissues. Young Old Adult 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Histopathological examination of affected tissues from SARS-CoV-2 infected tree shrews. doi = 10.1101/2020.04.30.029736 id = cord-271693-7tg21up3 author = Zheng, Fan title = Identifying persistent structures in multiscale ‘omics data date = 2020-10-03 keywords = Fig; Supplementary; community; protein summary = Many different approaches have been devised or applied to detect structures in biological data, including standard clustering, network community detection, and low-dimensional data projection [5] [6] [7] , some of which can be tuned for sensitivity to objects of a certain size or scale (so-called ''resolution parameters'') [8, 9] . We first explored the idea of measuring community persistence via analysis of synthetic datasets [15] in which communities were simulated and embedded in the similarity network at two different scales (Supplementary Fig. 1a; Methods) . Application to protein-protein interaction networks from budding yeast and human found that HiDeF captured knowledge in GO more significantly than previous pipelines proposed for this task, including the NeXO approach to hierarchical community detection [23] and standard hierarchical clustering of pairwise protein distances calculated by three recent network embedding approaches [24] [25] [26] (Fig. 3a, Fig. 7) . doi = 10.1101/2020.06.16.151555 id = cord-282795-kje7rn57 author = Zheng, Yue title = Neutralization Assay with SARS-CoV-1 and SARS-CoV-2 Spike Pseudotyped Murine Leukemia Virions date = 2020-09-21 keywords = SARS summary = To easily and rapidly measure titers of neutralizing antibodies in serum or plasma, we developed pseudovirion particles composed of the spike glycoprotein of SARS-CoV-2 incorporated onto murine leukemia virus capsids and a modified minimal MLV genome encoding firefly luciferase. Pseudotyped MLV viruses were tested on HEK293FT, HEK293T-ACE2, Huh7 and SupT1 cells. To test for specificity of neutralization, we asked whether neutralizing antibodies from SARSCoV-2 patients would exhibit cross-reactivity against a pseudotype expressing SARS-CoV-1 ( Figure 112 4). Characterization of 162 spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with 163 SARS-CoV Veesler D: Structure, Function, and 165 Antigenicity of the SARS-CoV-2 Spike Glycoprotein The 167 D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases 168 infectivity High-efficiency gene 170 transfer into CD34+ cells with a human immunodeficiency virus type 1-based retroviral 171 vector pseudotyped with vesicular stomatitis virus envelope glycoprotein G Pseudotyping Viral Vectors With Emerging Virus Envelope 177 Proteins doi = 10.1101/2020.07.17.207563 id = cord-327711-welf0eb1 author = Zhou, Daming title = Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient date = 2020-06-13 keywords = Data; EY6A; Fig; RBD; SARS summary = Cryo-EM analyses of the pre-fusion Spike incubated with EY6A Fab reveal a complex of the intact trimer with three Fabs bound and two further multimeric forms comprising destabilized Spike attached to Fab. EY6A binds what is probably a major neutralising epitope, making it a candidate therapeutic for COVID-19. A neutralisation test for EY6A based on quantitative PCR detection of virus in the supernatant bathing infected Vero E6 cells after 5 days of culture, showed a ~1000-fold reduction in virus signal (Methods, Extended Data Fig. 3 ) indicating that it is highly neutralising. To elucidate the epitope of EY6A, we determined the crystal structures of the deglycosylated SARS-CoV-2 RBD in complex with EY6A Fab alone and in a ternary complex incorporating a nanobody (Nb) which has been shown to compete with ACE2 (for data on a closely related Nb see Huo 2020, submitted), as a crystallisation chaperone. doi = 10.1101/2020.06.12.148387 id = cord-333420-qqyg9um9 author = Zhu, Xun title = idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates date = 2020-10-09 keywords = SARS summary = title: idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates idCOV is a phylogenetic pipeline for quickly identifying the clades of SARS-CoV-2 virus isolates from raw sequencing data based on a selected clade-defining marker list. Using a public dataset, we show that idCOV can make equivalent calls as annotated by Nextstrain.org on all three common clade systems using user uploaded FastQ files directly. The on-going Coronavirus disease 2019 (Covid-19) pandemic has resulted in over 734,000 deaths, affect-20 ing more than 188 countries and territories (CSSE, 2020; Dong, et al., 2020) . Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; previously known as 2019-nCoV) 23 is the pathogenic cause of Covid-19 (Lescure, et al., 2020) . In order to quickly identify the clade of an isolate of SARS-Cov-2 given its sequencing FastQ files, 30 we have developed a bioinformatics pipeline and a user-friendly web interface. doi = 10.1101/2020.10.08.330456 id = cord-307504-cogk5kig author = Zhu, Yuanmei title = Design of potent membrane fusion inhibitors against SARS-CoV-2, an emerging coronavirus with high fusogenic activity date = 2020-03-28 keywords = HR1; SARS summary = title: Design of potent membrane fusion inhibitors against SARS-CoV-2, an emerging coronavirus with high fusogenic activity In this study, we firstly verified that SARS-CoV-2 uses human ACE2 as a cell receptor and its spike (S) protein mediates high membrane fusion activity. Then, we designed a HR2 sequence-based lipopeptide fusion inhibitor, termed IPB02, which showed highly poent activities in inibibiting the SARS-CoV-2 S protein-mediated cell-cell fusion and pseudovirus infection. Taken together, these results suggested that 128 SARS-CoV-2 might evolve an increased interaction between the HR1 and HR2 domains in 129 the S2 fusion protein thus critically determining its high fusogenic activity. Interaction between heptad repeat 1 and 2 regions in spike protein of SARS-associated coronavirus: 354 implications for virus fusogenic mechanism and identification of fusion inhibitors Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition 368 using spike protein heptad repeat-derived peptides Heptad repeat-derived peptides block protease-mediated direct entry from the cell surface of 371 severe acute respiratory syndrome coronavirus but not entry via the endosomal pathway doi = 10.1101/2020.03.26.009233 id = cord-327808-k3jec87p author = Zhu, Yunkai title = The S1/S2 boundary of SARS-CoV-2 spike protein modulates cell entry pathways and transmission date = 2020-08-25 keywords = SARS; Sdel summary = We found that the virus with intact spike (Sfull) preferentially enters cells via fusion at the plasma membrane, whereas a clone (Sdel) with deletion disrupting the multi-basic S1/S2 site instead utilizes a less efficient endosomal entry pathway. The sequence at the S1/S2 boundary contains a cleavage site for the furin protease, 61 which could preactivate the S protein for membrane fusion and potentially reduce the 62 dependence of SARS-CoV-2 on plasma membrane proteases, such as transmembrane 63 serine protease 2 (TMPRSS2), to enable efficient cell entry (Shang et al., 2020) . Intriguingly, 188 these genes edited also significantly inhibited the infection by pseudovirus bearing the 189 spike protein of MERS-CoV in A549-ACE2-DPP4 cells ( Figure 3D ). Although no infectious virus was detected by focus-forming 299 assay (data not shown), viral RNA levels were higher in fecal samples for Sfull (20 and 300 40-fold) than Sdel at days 2 and 4, respectively ( Figure 5B ). doi = 10.1101/2020.08.25.266775 id = cord-318478-fn0gcxbb author = Ziv, Omer title = The short- and long-range RNA-RNA Interactome of SARS-CoV-2 date = 2020-10-07 keywords = RNA; SARS; figure summary = Available models for the RNA structure of SARS-CoV-2 and related viruses are largely confined to short-distance base-pairing which result in local folding of important cis-acting elements (Andrews et al., 2020; Huston et al., 2020; Kelly et al., 2020; Lan et al., 2020; Manfredonia et al., 2020; Ryder, 2020; Sanders et al., 2020; Sun et al., 2020) . In addition to the canonical UTR structures, we provide here a direct in vivo evidence for genome cyclization in SARS-CoV-2, mediated by long-range base-pairing between the 5′ and 3′ UTRs ( Figures 5B and S4B ). The long-distance RNA structure map for SARS-CoV-2 provides a practical starting point to dissect the regulation of discontinuous transcription, as it identifies cis-acting elements that interact with each other to create genome topologies that favour the synthesis of the ensemble of sgmRNAs. RNA viruses evolve sophisticated mechanisms to enhance the functional capacity of their size-restricted genomes and to regulate the expression levels of their replicase components. doi = 10.1101/2020.07.19.211110 id = cord-271978-j5enftje author = Zoltán, Köntös title = In Vitro Efficacy of “Essential Iodine Drops” Against Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) date = 2020-11-10 keywords = EID; SARS; iodine summary = Conclusion Substantial reductions in LRV by Iodine-V in EID confirmed the activity of EID against SARS-CoV-2 in vitro, demonstrating that Iodine-V in EID is effective at inactivating the virus in vitro and therefore suggesting its potential application intranasally to reduce SARS-CoV-2 transmission from known or suspected COVID-19 patients. Enthused by promising findings from a recent study by Pelletier and colleagues (12) , the present study was interested in Essential Iodine Drops (EID) for oral/nasal decontaminant in known or suspected cases of COVID-19 as a potentially better alternative to PVP-I. Briefly, the three dilutions of Essential Iodine Drops (EID) containing SARS-CoV-2 virus solution (1:1; 2:1 and 3:1) were tested in triplicates for virucidal activity as described by Pelletier and colleagues (12) . In vitro virucidal assay in the present study has indeed demonstrated that 75% and 50% of Essential Iodine Drops (EID) solution reduced SARS-CoV-2 virus titre after 60 seconds and 90 seconds of incubation by an LRV of 2.0 (99%). doi = 10.1101/2020.11.07.370726 id = cord-329129-t84pu00z author = Zuo, J title = Robust SARS-CoV-2-specific T-cell immunity is maintained at 6 months following primary infection date = 2020-11-02 keywords = CD4; SARS summary = We analysed the magnitude and phenotype of the SARS-CoV-2 cellular immune response in 100 donors at six months following primary infection and related this to the profile of antibody level against spike, nucleoprotein and RBD over the previous six months. In conclusion, our data are reassuring that functional SARS-CoV-2-specific T-cell responses are retained at six months following infection although the magnitude of this response is related to the clinical features of primary infection. In this study we characterised SARS-CoV-2-specific T cell immune responses in a cohort of 100 donors at 6-months post-infection. Peptide pools from a range of viral proteins, including spike, nucleoprotein and membrane protein, were used to stimulate fresh PBMC and the magnitude of the global SARS-CoV-2-specific T-cell response was determined. Here we undertook, to our knowledge, the first assessment of the SARS-CoV-2-specific T cell immune response at six months following primary infection in a unique cohort of healthy adults with asymptomatic or mild-to-moderate COVID-19. doi = 10.1101/2020.11.01.362319 id = cord-321049-9ozn6il7 author = de Almeida, Paula Rodrigues title = SARS-CoV2 quantification using RT-dPCR: a faster and safer alternative to assist viral genomic copies assessment using RT-qPCR date = 2020-05-01 keywords = SARS summary = title: SARS-CoV2 quantification using RT-dPCR: a faster and safer alternative to assist viral genomic copies assessment using RT-qPCR Narrower confidence intervals, indicating high quantification precision were obtained in 100 and 1000-fold serial dilution and RT-dPCR results were equivalent between different assays in the same dilution. Here, we present a fast, accurate and simple method of viral titration using QuantStudio 3D® microchip based RT-dPCR to titrate SARS-CoV2 genomic copies from controls to be used in RT-qPCR assays for diagnosis and research purposes. A dilution that results in approximately 200 to 2000 target copies in the final reaction usually presents better precision values. Results with precision values below 5% were selected to estimate quantity of SARS-CoV2 genomic copies based on RT-dPCR. RT-dPCR results of 10-fold serial dilution of SARS-CoV2 control using assays for three targets in the Nucleocapsid gene. These results indicate that these primer-probe assays are suitable for SARS-CoV2 quantification through RT-dPCR. doi = 10.1101/2020.05.01.072728 id = cord-267223-pf799wbw author = de Lamballerie, Claire Nicolas title = Transcriptional profiling of immune and inflammatory responses in the context of SARS-CoV-2 fungal superinfection in a human airway epithelial model date = 2020-05-19 keywords = superinfection summary = An increasing number of evidence indicate a relatively high prevalence of superinfections associated with COVID-19, including invasive aspergillosis, but the underlying mechanisms remain to be characterized. Our results also highlight unique transcriptional footprints of SARS-CoV-2 Aspergillus superinfection, such as an imbalanced type I/type III IFN, and an induction of several monocyteand neutrophil associated chemokines, that could be useful for the understanding of Aspergillus-associated COVID-19 and but also management of severe forms of aspergillosis in this specific context. Our results also highlight unique transcriptional 30 footprints of SARS-CoV-2 Aspergillus superinfection, such as an imbalanced type I/type III IFN, 31 and an induction of several monocyte-and neutrophil associated chemokines, that could be 32 useful for the understanding of Aspergillus-associated COVID-19 and but also management 33 of severe forms of aspergillosis in this specific context. doi = 10.1101/2020.05.19.103630 id = cord-104146-pabh3ajb author = de Lussanet de la Sablonière, Marc H. E. title = Robust, general purpose, digital power line hum filter which is free of deformations and which can be applied to large transients date = 2019-11-04 keywords = PMS; filter summary = The resulting periodic median subtraction (PMS) filter reliably removes hum of any harmonic composition, even if the ground frequency is lacking. Even though power 25 line noise is mostly highly regular in frequency, amplitude and wave form, it has proven notoriously difficult to design a filter that is free of artifacts and deformations, which leaves the original signal intact. Subtraction-type filters aim to fit the shape and amplitude of the hum 50 noise directly from the data, sometimes from multiple channels (e.g., in EEG signals) or from a reference channel (e.g. Wan et al., 2006; Lin et al., 2016) . Increasing the filter window of the PMS filter from 50 to 500 periods (10 s) reduced the median absolute error in white noise data to 0.037, which is equivalent to the error in a signal with an HF amplitude of 0.2 (cf. doi = 10.1101/830463 id = cord-331888-lbtuvdv3 author = de Souza, Dalton Garcia Borges title = Forecasting COVID-19 cases at the Amazon region: a comparison of classical and machine learning models date = 2020-10-09 keywords = ARIMA; covid-19 summary = title: Forecasting COVID-19 cases at the Amazon region: a comparison of classical and machine learning models We compare the models autoregressive integrated moving average (ARIMA), Holt-Winters, support vector regression (SVR), k-nearest neighbors regressor (KNN), random trees regressor (RTR), seasonal linear regression with change-points (Prophet), and simple logistic regression (SLR). We evaluate the models according to their capacity to forecast in different historical scenarios of the COVID-19 progression, such as exponential increases, sudden decreases, and stability periods of daily cases. Holt-Winters, support vector regression (SVR), k-nearest neighbors regressor (KNN), 43 random trees regressor (RT), seasonal linear regression with change-points (SLiR) and 44 simple logistic regression (SLR), which dictates the baseline performance in this study. Thus, in this paper, we compared classical and machine learning models to forecast 231 the evolution of COVID-19 in the state. Application of ARIMA and Holt-Winters forecasting model to predict 294 the spreading of COVID-19 for India and its states doi = 10.1101/2020.10.09.332908 id = cord-103435-yufvt44t author = van Aalst, Marvin title = Constructing and analysing dynamic models with modelbase v1.0 - a software update date = 2020-10-02 keywords = Python; model; modelbase; system summary = Background Computational mathematical models of biological and biomedical systems have been successfully applied to advance our understanding of various regulatory processes, metabolic fluxes, effects of drug therapies and disease evolution or transmission. Results and Discussion We provide here the update on the development of modelbase, a free expandable Python package for constructing and analysing ordinary differential equation-based mathematical models of dynamic systems. Most recently, deterministic models simulating the dynamics of infectious diseases gained the interest of the general public during our combat of the Covid-19 pandemic, when a large number of ODE based mathematical models has been developed and discussed even in nonscientific journals (see for example [3] [4] [5] ). Implementation modelbase is a Python package to facilitate construction and analysis of ODE based mathematical models of biological systems. We are presenting here updates of our modelling software that has been developed to simplify the building process of mathematical models based on ODEs. modelbase is fully embedded in the Python programming language. doi = 10.1101/2020.09.30.321380