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?' ---------------------------------------------------------- 58 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 5861 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 49 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 7 RNA 7 Fig 5 virus 5 dna 4 ZIKV 4 SARS 4 PCR 4 COVID-19 4 CHIKV 3 infection 3 cell 3 DENV 2 sample 2 rabies 2 mouse 2 dog 2 covid-19 2 control 2 bat 2 antibody 2 Zika 2 RVFV 2 JEV 2 Ebola 2 CD4 2 Africa 1 ΔTK 1 volvulus 1 vaccination 1 sporotrichosis 1 schenckii 1 rabie 1 r06e 1 protein 1 pfu 1 peptide 1 patient 1 particle 1 monocyte 1 model 1 m1r 1 lamp 1 laboratory 1 housing 1 exposure 1 denv2 1 dengue 1 deficient 1 datum 1 cryptosporidium Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 1864 virus 1728 cell 1374 infection 1344 % 1090 mouse 1045 protein 803 study 735 antibody 617 sample 610 disease 576 patient 567 model 561 control 541 case 505 datum 497 dengue 464 animal 414 vaccine 405 response 393 assay 387 level 384 day 371 time 368 treatment 361 analysis 360 bat 351 detection 345 result 343 group 324 ml 323 host 307 activity 304 region 295 test 294 serum 289 dna 281 vector 279 number 277 fever 277 antigen 264 replication 261 strain 259 - 253 factor 244 outbreak 243 dog 242 rabies 242 particle 236 use 232 method Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 555 Fig 502 RNA 466 CHIKV 347 PCR 273 ZIKV 234 JEV 200 DENV 178 RVFV 161 PRV 157 NSs 154 Africa 151 S. 151 Ebola 146 NanoTrap 144 MO 142 SARS 142 MVA 136 Gc 134 ANDV 129 COVID-19 125 mg 121 DNA 118 Table 117 Zika 117 O. 115 Health 111 ELISA 110 Singapore 110 K 109 T. 107 USA 105 DIII 101 MS 100 E2 99 NT53 99 G6PD 98 NP 97 MDA 95 Virus 95 T 94 L 92 Vero 92 PBS 88 E. 87 R. 87 Nakayama 87 A 86 IFN 84 C 82 C9 Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 760 we 525 it 164 they 62 i 42 them 23 she 21 us 14 itself 6 themselves 6 he 6 bohv-4 5 you 4 one 3 em 1 serotype- 1 mg 1 its 1 him 1 her 1 cord-322943-lvdl7puw 1 cord-004247-lagv3tp7 1 b19v 1 am1840 1 +355.65 Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 10321 be 1391 have 1362 use 585 show 536 infect 376 include 366 follow 313 compare 303 detect 296 do 284 provide 282 report 276 bind 273 perform 266 base 260 determine 259 describe 257 identify 250 increase 241 suggest 238 induce 237 develop 232 observe 226 contain 222 obtain 221 find 216 demonstrate 215 collect 214 associate 207 indicate 205 require 199 incubate 186 reduce 184 test 184 cause 183 neutralize 179 treat 179 confirm 171 occur 160 assess 159 result 151 lead 150 protect 147 evaluate 143 analyze 143 add 141 affect 140 mediate 132 express 127 make Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 857 - 835 not 733 viral 547 also 481 human 471 high 447 other 340 specific 340 only 340 clinical 328 more 318 low 316 such 315 however 287 severe 269 non 267 positive 259 different 254 well 253 immune 237 infected 233 anti 218 then 210 most 206 further 205 early 201 previously 197 significantly 192 significant 174 respectively 174 infectious 172 similar 172 as 170 molecular 169 first 163 new 160 negative 147 acute 141 therefore 140 recombinant 138 fecal 138 diagnostic 133 large 130 likely 127 potential 127 cellular 126 important 125 possible 124 several 124 effective Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 70 most 52 good 37 least 28 high 19 low 12 large 11 Most 8 great 4 early 4 close 2 wide 2 short 2 poor 2 late 2 big 1 vRNA 1 steady 1 simple 1 long 1 easy 1 dense 1 cheap 1 Least Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 140 most 31 least 7 well 2 ckv061 1 vrna Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 14 doi.org 2 www.pasteur.fr 1 wwwn.cdc.gov 1 www2.voozanoo.net 1 www.who.int 1 www.vectoranalytica 1 www.tree-puzzle.de 1 www.ncbi.nlm.nih.gov 1 www.mega 1 www.medcalc.org 1 www.malariagen 1 www.immuneepitope.org 1 www.flowingsoftware.com 1 www.factiva.fr 1 www.ebi.ac.uk 1 www.dcvmn.org 1 www.csbio.sjtu.edu.cn 1 www.cioms.ch 1 www.cbs.dtu.dk 1 web.cbio.uct.ac.za 1 tree.bio.ed.ac.uk 1 recombineering.ncifcrf.gov 1 phobius.sbc.su.se 1 liv.bmc.uu.se 1 index.baidu.com 1 dambe.bio.uottawa.ca 1 cels.uri.edu 1 beast.bio.ed.ac.uk Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 1 http://wwwn.cdc.gov/travel/ 1 http://www2.voozanoo.net/tikiindex.php?page 1 http://www.who.int 1 http://www.vectoranalytica 1 http://www.tree-puzzle.de/ 1 http://www.pasteur.fr/sante/clre/cadrecnr/rage/rageactualites.html 1 http://www.pasteur.fr/sante/clre/cadrecnr/rage/rage-actualites.html 1 http://www.ncbi.nlm.nih.gov/BLAST 1 http://www.mega 1 http://www.medcalc.org 1 http://www.malariagen 1 http://www.immuneepitope.org/ 1 http://www.flowingsoftware.com/ 1 http://www.factiva.fr 1 http://www.ebi.ac.uk/Tools/clustalw2/index.html 1 http://www.dcvmn.org/ 1 http://www.csbio.sjtu.edu.cn/bioinf/Signal-3L/ 1 http://www.cioms.ch/ 1 http://www.cbs.dtu.dk/services/SecretomeP 1 http://web.cbio.uct.ac.za/~darren/rdp.html 1 http://tree.bio.ed.ac.uk/software/figtree/ 1 http://recombineering.ncifcrf.gov 1 http://phobius.sbc.su.se/ 1 http://liv.bmc.uu.se/cgi-bin/emboss/antigenic 1 http://index.baidu.com/v2/#/ 1 http://doi.org/10.1371/journal.pntd.0008737.g005 1 http://doi.org/10.1371/journal.pntd.0008349.g002 1 http://doi.org/10.1371/journal.pntd.0008283.g006 1 http://doi.org/10.1371/journal.pntd.0008283.g002 1 http://doi.org/10.1371/journal.pntd.0006977.g001 1 http://doi.org/10.1371/journal.pntd.0006674.t004 1 http://doi.org/10.1371/journal.pntd.0006674.g006 1 http://doi.org/10.1371/journal.pntd.0006349.g002 1 http://doi.org/10.1371/journal.pntd.0006076.g009Development 1 http://doi.org/10.1371/journal.pntd.0005775.g006 1 http://doi.org/10.1371/journal.pntd.0005775.g005 1 http://doi.org/10.1371/journal.pntd.0005775.g003 1 http://doi.org/10.1371/journal.pntd.0005775.g002 1 http://doi.org/10.1371/journal.pntd.0005775 1 http://dambe.bio.uottawa.ca/DAMBE/dambe.aspx 1 http://cels.uri.edu/gsc/cndna.html 1 http://beast.bio.ed.ac.uk/ Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 9 cells were then 7 samples were positive 7 samples were then 4 cells being arbitrarily 4 infection does not 4 mice did not 4 mice were intranasally 3 % had severe 3 animals did not 3 assays were able 3 cases were also 3 cells were mock 3 chikv infected patients 3 data are available 3 days following challenge 3 levels were also 3 mice following jev 3 mice had significant 3 mice were not 3 mice were significantly 3 mice were then 2 % had dengue 2 analysis using anti 2 animals showed weight 2 antibodies are effective 2 antibodies are not 2 antibody binding studies 2 assay is highly 2 assays are not 2 assays using taqman 2 assays were also 2 cases were due 2 cases were not 2 cells are able 2 cells provide protection 2 cells showed lower 2 cells showed similar 2 cells was then 2 cells were evolutionally 2 cells were first 2 cells were likely 2 cells were sub 2 chikv infected individuals 2 data are mean±sd 2 disease is critical 2 disease were apparent 2 infection did not 2 infection was dramatically 2 infection was not 2 levels were not Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 2 assays are not suitable 2 model is not consistently 2 patients are not possible 1 analysis is not trivial 1 animals do not always 1 antibodies are not essential 1 antibodies are not sufficient 1 antibody had no detectable 1 case had no anti 1 case is no longer 1 cells are not naked 1 cells is not completely 1 dengue is not only 1 infection is not uniformly 1 infection was not due 1 levels were not independent 1 levels were not statistically 1 ml were not statistically 1 mouse was not consistent 1 patient reported no respiratory 1 patients were not available 1 protein are not fully 1 protein is not further 1 responses were not exclusive 1 rna was not detectable 1 samples showed no detectable 1 samples were not heat 1 study was not unusual 1 time was not significantly 1 treatments are not available 1 virus has no genetic 1 viruses showed no dissemination A rudimentary bibliography -------------------------- id = cord-000625-cpjlzutk author = Ablordey, Anthony title = Detection of Mycobacterium ulcerans by the Loop Mediated Isothermal Amplification Method date = 2012-04-03 keywords = dna; lamp summary = In order to develop a field applicable technique that offers high detection sensitivity and specificity for the diagnosis of BU, we explored the use of the pocket warmer LAMP (pwLAMP) technique, a DNA amplification method using isothermal conditions (60uC) provided by a disposable pocket warmer [34] . In order to develop a simple and rapid test that can be used to diagnose Buruli ulcer under field conditions, we modified the conventional LAMP assay by using a disposable pocket warmer as a heating device for generating a constant temperature for the test reaction and employed the use of crude sample preparations consisting of boiled and unboiled extracts of the clinical specimen instead of using purified DNA as the diagnostic specimen. Thirty clinical specimens from suspected Buruli ulcer patients were investigated by the modified LAMP (or pocket warmer LAMP) and the conventional LAMP, as well as IS2404 PCR, a reference method for the detection of Mycobacterium ulcerans. doi = 10.1371/journal.pntd.0001590 id = cord-001484-va0teako author = Ahmed, Sarah A. title = Rapid Identification of Black Grain Eumycetoma Causative Agents Using Rolling Circle Amplification date = 2014-12-04 keywords = RCA; dna summary = A rapid, simple, and highly efficient molecular based method for identification of agents of black grain eumycetoma is introduced, aiming to improve diagnostic in endemic areas. Rolling circle amplification (RCA) is a powerful diagnostic method based on detection of specific nucleic-acid sequences and enzymatic amplification of circularized oligonucleotide probes under isothermal conditions [10] . The specificity of the 8 RCA probes was tested using strains of black-grain mycetoma causative species listed in table 1. Identification of mycetoma agent with phenotypic features is too limited, and physiological and biochemical techniques are laborious, time-consuming and nonspecific, whereas the currently available molecular methods based on DNA sequencing are specific but extremely expensive. We describe rolling circle amplification method for identification of black grain eumycetoma using species-specific padlock probes. In the present study we developed a simple, fast and highly specific molecular method for the identification of agents of black grain mycetoma. doi = 10.1371/journal.pntd.0003368 id = cord-281456-3dlsbr7c author = Al-alimi, Abdullah Ahmed title = Dengue Virus Type 2 (DENV2)-Induced Oxidative Responses in Monocytes from Glucose-6-Phosphate Dehydrogenase (G6PD)-Deficient and G6PD Normal Subjects date = 2014-03-13 keywords = G6PD; deficient; denv2; monocyte summary = doi = 10.1371/journal.pntd.0002711 id = cord-332473-ec8lu2a3 author = Amorim, Raquel title = Zika virus inhibits eIF2α-dependent stress granule assembly date = 2017-07-17 keywords = Fig; ZIKV; cell summary = doi = 10.1371/journal.pntd.0005775 id = cord-268329-apl6n6jl author = Antunes, Douglas Eulálio title = Will cases of leprosy reaction increase with COVID-19 infection? date = 2020-07-17 keywords = SARS; covid-19 summary = The coronavirus disease 2019 (COVID-19)-caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a betacoronavirus (betaCoV)-emerged for the first time as an outbreak of pneumonia in Wuhan, China, and it is now spreading to several countries around the world [1] . Some studies of SARS-CoV-2 infection have reported the presence of a cytokine storm syndrome and a subgroup of patients who progressed to severe forms of the disease, expressing a pro-inflammatory profile in plasma with IL-2, IL-7, TNF-α, and others as significant complications, such as occurs in T1R [10, 11] . In both reactions, we warn of the possible effect that COVID-19 infection may have on the number of cases of these immunological events because the presence of infection is an important risk factor for triggering leprosy reactions [8] . Another disturbing factor, which may contribute to the susceptibility of those affected by leprosy reactions, are the treatments implemented during these events that interfere with the inflammatory response of these patients. doi = 10.1371/journal.pntd.0008460 id = cord-352771-s0hfsxzb author = Barriga, Gonzalo P. title = Inhibition of the Hantavirus Fusion Process by Predicted Domain III and Stem Peptides from Glycoprotein Gc date = 2016-07-14 keywords = ANDV; DIII; Fig summary = Based on our previous homology model structure for Gc from Andes hantavirus (ANDV), here we predicted and generated recombinant DIII and stem peptides to test whether these fragments inhibit hantavirus membrane fusion and cell entry. The Gc fragments interfered in ANDV cell entry by preventing membrane hemifusion and pore formation, retaining Gc in a non-resistant homotrimer stage, as described for DIII and stem peptide inhibitors of class II fusion proteins. Once the predicted DIII and stem fragments were synthesized, purified, and characterized, we measured their inhibitory activity against ANDV during virus cell entry via the native, endosomal infection route. In addition to the DIII of ANDV, peptides derived from the stem region of ANDV also cross-inhibited the PUUV fusion activity, which further corroborates the presence of conserved residues among hantavirus Gc proteins that are involved in the likely binding of this peptide. doi = 10.1371/journal.pntd.0004799 id = cord-305890-mdwjrfzp author = Bönsch, Claudia title = Chloroquine and Its Derivatives Exacerbate B19V-Associated Anemia by Promoting Viral Replication date = 2010-04-27 keywords = Epo; b19v; infection summary = doi = 10.1371/journal.pntd.0000669 id = cord-003006-lk2ny1wd author = Cantoni, Diego title = Ebolaviruses: New roles for old proteins date = 2018-05-03 keywords = Ebola; RNA; VP24 summary = These newly discovered roles are revealing new mechanisms of virus replication and pathogenicity, whilst enhancing our understanding of the broad functions of each ebolavirus viral protein (VP). Lastly, VP35 is a suppressor of RNA silencing, functionally equivalent to the human immunodeficiency virus (HIV-1) Trans-activator of transcription (Tat) protein and important for viral evasion of the innate immune response [34] . The authors propose that this mutation is likely a result of EBOV adaptation to the human host, as several viral variants have been seen to increase human cell infectivity while decreasing virus entry in nonhuman primates [83] [84] [85] . In addition, many ebolavirus proteins are seen to interact with immune cells, causing cell activation and/or cell death and facilitating both viral replication and spread (e.g., by recruiting monocytes to infected cells or by increasing vascular leakage) as well as enabling immune evasion (e.g., antibody neutralisation by sGP and by cleaved GP), roles that were previously solely attributed to VP24 and VP35. doi = 10.1371/journal.pntd.0006349 id = cord-345494-8lcdx719 author = Chao, Chien-Chung title = Development of Recombinase Polymerase Amplification Assays for Detection of Orientia tsutsugamushi or Rickettsia typhi date = 2015-07-10 keywords = RPA; dna summary = title: Development of Recombinase Polymerase Amplification Assays for Detection of Orientia tsutsugamushi or Rickettsia typhi Recombinase polymerase amplification (RPA) assays using a lateral flow test (RPA-nfo) and real-time fluorescent detection (RPA-exo) were developed targeting the 47-kDa gene of O. Almost all antigen/pathogen detection assays for rickettsial diseases are based on polymerase chain reaction (PCR [7, 8] ), quantitative real-time PCR (qPCR) or nested PCR targeting different genes, including 56 kDa [9] , 47kDa [10] , groEL [11] of O. The DNA was used as template for the 17-RPA assay to evaluate its performance and qPCR was used to quantitate the copy number of the 17 kDa gene. honei and R japonica were also evaluated to show that they were not detectable by 17-RPA-nfo unless 10 4 or more copies of DNA were present, same results were obtained using 17-RPA-exo. doi = 10.1371/journal.pntd.0003884 id = cord-327799-ngzvdd8c author = Chaumont, Claire title = The SARS-CoV-2 crisis and its impact on neglected tropical diseases: Threat or opportunity? date = 2020-09-21 keywords = NTD; SARS summary = doi = 10.1371/journal.pntd.0008680 id = cord-345315-y3bdjnhg author = Dai, Yaoyao title = Identifying the outbreak signal of COVID-19 before the response of the traditional disease monitoring system date = 2020-10-01 keywords = COVID-19; China; ILI summary = We performed a comparative study to determine the feasibility of the early detection of the COVID-19 outbreak in China based on influenza surveillance data and the internet-based Baidu search index to evaluate the timelines of the alert signals compared with the traditional case reporting and response systems. The findings from this study suggest that monitoring abnormal surges of ILI and identifying peaks of online searches of key terms can provide early signals of novel disease outbreaks. In this study, we performed a comparative study to discuss the early warning capability, timelines, and validity of alert signals for the first wave of the COVID-19 outbreak in China based on the surveillance data of influenza-like illness (ILI) and the Baidu Search Index (BSI) compared with the traditional case reporting system. doi = 10.1371/journal.pntd.0008758 id = cord-276271-3nz3169p author = Deborggraeve, Stijn title = T. cruzi OligoC-TesT: A Simplified and Standardized Polymerase Chain Reaction Format for Diagnosis of Chagas Disease date = 2009-06-02 keywords = Chagas; PCR; dna summary = cruzi OligoC-TesT: A Simplified and Standardized Polymerase Chain Reaction Format for Diagnosis of Chagas Disease The specificity and sensitivity of the assay were evaluated on blood samples from 60 Chagas non-endemic and 48 endemic control persons and on biological samples from 33 patients, 7 reservoir animals, and 14 vectors collected in Chile. We assessed the diagnostic accuracy of the assay on a broad spectrum of biological samples from Chagas non-endemic and endemic control persons, infected children, adults, reservoir animals and vectors. DNA from 25 different Trypanosoma rangeli isolates (Table 1) and from Leishmania donovani, Trypanosoma brucei gambiense, Mycobacterium tuberculosis, Schistosoma mansoni and Plasmodium falciparum was obtained from other research groups. cruzi OligoC-TesT, a simple and standardized dipstick format for detection of PCR amplified T. cruzi OligoC-TesT, a simple and standardized dipstick format for detection of PCR amplified T. doi = 10.1371/journal.pntd.0000450 id = cord-355469-ojop6i4k author = Egawa, Kazutaka title = Virulence, pathology, and pathogenesis of Pteropine orthoreovirus (PRV) in BALB/c mice: Development of an animal infection model for PRV date = 2017-12-14 keywords = DPI; PRV; pfu summary = doi = 10.1371/journal.pntd.0006076 id = cord-001812-ov1qssnu author = Fan, Yi-Chin title = Formalin Inactivation of Japanese Encephalitis Virus Vaccine Alters the Antigenicity and Immunogenicity of a Neutralization Epitope in Envelope Protein Domain III date = 2015-10-23 keywords = FIV; JEV; Nakayama; T16 summary = doi = 10.1371/journal.pntd.0004167 id = cord-000113-d0eur1hq author = Fooks, Anthony R. title = Emerging Technologies for the Detection of Rabies Virus: Challenges and Hopes in the 21st Century date = 2009-09-29 keywords = PCR; RNA; rabies; virus summary = The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis. The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis. Another method for the detection of rabies virus antigen from postmortem samples is a recently developed rapid immunodiagwww.plosntds.org nostic test (RIDT) based on the principles of immunochromatography [13] . Development of RT-LAMP assays for use in diagnosis and surveillance is challenged by the considerable sequence variation observed within the rabies virus genome [44] that can frustrate specific primer design. Currently, high-throughput rabies virus molecular detection methods augment standard diagnostic tests or are in the process of development and refinement for use alone. doi = 10.1371/journal.pntd.0000530 id = cord-001690-cn21fgug author = Franceschi, Valentina title = BoHV-4-Based Vector Single Heterologous Antigen Delivery Protects STAT1((-/-)) Mice from Monkeypoxvirus Lethal Challenge date = 2015-06-18 keywords = CMV; EF1α; MPXV; m1r; ΔTK summary = In the present study, a new vaccination strategy approach based on three recombinant bovine herpesvirus 4 (BoHV-4) vectors, each expressing different MPXV glycoproteins, A29L, M1R and B6R were investigated in terms of protection from a lethal MPXV challenge in STAT1 knockout mice. In vivo efficacy testing of BoHV-4-A-CMV-A29LgD 106 ΔTK, BoHV-4-A-EF1α-M1RgD 106 ΔTK and BoHV-4-A-EF1α-B6RgD 106 ΔTK To test the efficacy of the vectors in vivo, we sought to determine if they could protect mice against a lethal challenge with MPXV. Since the purpose of this study was to determine the capability of BoHV-4-based viral vectors to protect STAT1 (-/-) mice against a lethal MPXV infection, the first concern was the generation of optimized expression cassettes to be integrated into the BAC-BoHV-4-A genome that were able to efficiently express A29L, M1R and B6R antigens. In summary, our findings have demonstrated that BoHV-4 based vectors can be used as vaccines to protect against a lethal MPXV challenge in mice. doi = 10.1371/journal.pntd.0003850 id = cord-308343-crjjhpl1 author = Graef, Geneva title = Impact of confinement housing on study end-points in the calf model of cryptosporidiosis date = 2018-04-25 keywords = CFC; calf; confinement; cryptosporidium; housing summary = doi = 10.1371/journal.pntd.0006295 id = cord-270481-rrpqz0uy author = Hays, Russell title = Helminth coinfection and COVID-19: An alternate hypothesis date = 2020-08-17 keywords = covid-19 summary = doi = 10.1371/journal.pntd.0008628 id = cord-004247-lagv3tp7 author = Hooft van Huijsduijnen, Rob title = Reassessing therapeutic antibodies for neglected and tropical diseases date = 2020-01-30 keywords = Cryptococcus; HIV; Pneumocystis; antibody; cell; infection summary = This mAb was protective in an in vitro, antigen-dependent, cellular cytotoxicity assay with rat macrophages or eosinophils and also in vivo during the early phase of infection Second, beyond the cell-surface proteins, schistosomes also express a large number of glycans as part of their glycoprotein and glycolipid repertoire, and an antibody response against those glycans is mounted by the infected host [80] . In addition to antibodies that directly target and inhibit the fungal pathogen, mAbs can be directed to checkpoints that control the host immune response. In addition to highlighting the potential of mAbs as therapeutics, these studies have demonstrated the diversity of inhibitory actions that mAbs can perform on cryptococcal cells, which can include opsonization and increased phagocytosis, inhibition of fungal growth, capsular polysaccharide release and biofilm formation, antibody-mediated target cleavage, and augmentation of the host response [104] [105] [106] [107] . doi = 10.1371/journal.pntd.0007860 id = cord-340569-f1odmjcs author = Hossain, Mohammad Sorowar title = Dengue in a crowded megacity: Lessons learnt from 2019 outbreak in Dhaka, Bangladesh date = 2020-08-20 keywords = Dhaka; Eid summary = doi = 10.1371/journal.pntd.0008349 id = cord-256303-bpa571ys author = Hotez, Peter J. title = Will COVID-19 become the next neglected tropical disease? date = 2020-04-10 keywords = SARS summary = doi = 10.1371/journal.pntd.0008271 id = cord-260412-yjr83ef6 author = Hotez, Peter J. title = Developing a low-cost and accessible COVID-19 vaccine for global health date = 2020-07-29 keywords = RBD; SARS summary = doi = 10.1371/journal.pntd.0008548 id = cord-285772-4xt4anq5 author = Huang, Rui title = Clinical findings of patients with coronavirus disease 2019 in Jiangsu province, China: A retrospective, multi-center study date = 2020-05-08 keywords = COVID-19; Wuhan; patient summary = doi = 10.1371/journal.pntd.0008280 id = cord-007383-5yb3dxse author = Kang, Jun-Gu title = Vaccination with single plasmid DNA encoding IL-12 and antigens of severe fever with thrombocytopenia syndrome virus elicits complete protection in IFNAR knockout mice date = 2020-03-20 keywords = SFTSV; USA; dna summary = title: Vaccination with single plasmid DNA encoding IL-12 and antigens of severe fever with thrombocytopenia syndrome virus elicits complete protection in IFNAR knockout mice Immunization of NS antigen with Freund''s adjuvant in C57BL/6 mice, which are naturally resistant to SFTSV but partially mimic human infections [12] , failed to enhance viral clearance, although it induced high titer of anti-NS antibodies and significantly elevated IFN-γ levels in sera upon viral challenge [9] . Vaccination of pSFTSV-IL12 provided complete protection of IFNAR KO mice upon lethal SFTSV challenge, whereas immunization with pSFTSV elicits only partial protection, indicating that antigen-specific cellular immune responses enhanced by co-expression of IL-12 could play a significant role in protection against lethal SFTSV infection. Since we observed significant elevation of T cell responses specific to the viral antigens in IFNAR KO mice immunized with pSFTSV-IL12 DNA vaccine, we tested whether it could provide protective immunity against lethal SFTSV infection. doi = 10.1371/journal.pntd.0007813 id = cord-269004-hj03n13h author = Krähling, Verena title = Establishment of Fruit Bat Cells (Rousettus aegyptiacus) as a Model System for the Investigation of Filoviral Infection date = 2010-08-24 keywords = MARV; Marburg; cell; r06e summary = doi = 10.1371/journal.pntd.0000802 id = cord-322943-lvdl7puw author = Lardon, Zélie title = Imported Episodic Rabies Increases Patient Demand for and Physician Delivery of Antirabies Prophylaxis date = 2010-06-22 keywords = ARMC; France; RPEP summary = doi = 10.1371/journal.pntd.0000723 id = cord-000680-vsgd9v1w author = Lee, Linda K. title = Clinical Relevance and Discriminatory Value of Elevated Liver Aminotransferase Levels for Dengue Severity date = 2012-06-05 keywords = DHF; alt; ast summary = We aimed to assess the clinical relevance and discriminatory value of AST or ALT for dengue hemorrhagic fever (DHF) and severe dengue. There was significant overlap in AST and ALT values among patients with dengue with or without warning signs and severe dengue, and between those with DF and DHF. In this study, we aimed to evaluate the clinical relevance of elevated AST and ALT levels and correlate liver aminotransferase levels with dengue severity according to WHO 1997 and 2009 classifications. We performed a subgroup analysis for median maximum AST and ALT values stratified by febrile (days 1-3 of illness), critical (days 4-6), and convalescent (days 7-10) phases as defined by WHO 2009 [1] and compared across dengue severity classification according to WHO 1997 [9] and 2009 [1] . In conclusion, elevated aminotransferase levels were associated with DHF/DSS and severe dengue in our cohort of adult patients with confirmed dengue. doi = 10.1371/journal.pntd.0001676 id = cord-309587-xc4jaw31 author = Lembo, Tiziana title = The Feasibility of Canine Rabies Elimination in Africa: Dispelling Doubts with Data date = 2010-02-23 keywords = Africa; Tanzania; dog; rabie; vaccination summary = doi = 10.1371/journal.pntd.0000626 id = cord-263044-o8aosx2q author = Lipsitch, Marc title = Potential Biases in Estimating Absolute and Relative Case-Fatality Risks during Outbreaks date = 2015-07-16 keywords = CFR; bias; case summary = doi = 10.1371/journal.pntd.0003846 id = cord-002581-r7mskri0 author = Magnani, Diogo M. title = A human inferred germline antibody binds to an immunodominant epitope and neutralizes Zika virus date = 2017-06-12 keywords = DENV; P1F12; ZIKV; Zika; virus summary = title: A human inferred germline antibody binds to an immunodominant epitope and neutralizes Zika virus The isolation of neutralizing monoclonal antibodies (nmAbs) against the Zika virus (ZIKV) might lead to novel preventative strategies for infections in at-risk individuals, primarily pregnant women. Here we describe the isolation of 18 plasmablast-derived human mAbs, sorted 12 days post onset of symptoms from a ZIKV-patient in São Paulo, Brazil. Interestingly, one of these mAbs (P1F12) exhibited no nucleotide mutations when compared to its corresponding germline sequences, but still recognized a ZIKV immunodominant epitope and neutralized the virus. Virus capture assay and recombinant E protein ELISA P1F12 binding was determined by both virus capture assay (VCA) and recombinant (r)E ELISAs. The VCA plates were coated overnight with the mouse-anti-Flavivirus monoclonal antibody 4G2 (clone D1-4G2-4-15, EMD Millipore) followed by incubation with viral stocks (ZIKV or DENV). Molecular determinants of human neutralizing antibodies isolated from a patient infected with Zika virus doi = 10.1371/journal.pntd.0005655 id = cord-003482-f1uvohf0 author = Malmlov, Ashley title = Experimental Zika virus infection of Jamaican fruit bats (Artibeus jamaicensis) and possible entry of virus into brain via activated microglial cells date = 2019-02-04 keywords = RNA; ZIKV; Zika; bat; virus summary = Quantitative probe-based reverse transcription PCR (qRT-PCR) was performed on seruminoculated Vero cell supernatants, serum, brain, lung, liver, spleen, kidney, urinary bladder, prostate and testes from bats from both studies. Brain and testicular tissues stained with both goat polyclonal goat anti-Iba1 (green) and monoclonal 4G-2 flavivirus E specific antibodies (red) showed co-localization (yellow) of ZIKV antigen in cytoplasm of activated microglial cells with their characteristic morphology in the cerebral cortex of infected bats 10 dpi in the time course study and 28 day dpi in the pilot study (Fig 9) . Two bat infection experiments were conducted in this investigation; 1) a pilot study to determine susceptibility of Jamaican fruit bats to ZIKV infection, and 2) a time course study to better understand pathophysiology and chronology of events pertaining to the dynamics of viremia, viral tropism, replication and shedding of the virus in a New World bat species. doi = 10.1371/journal.pntd.0007071 id = cord-003243-u744apzw author = Michael, Edwin title = Quantifying the value of surveillance data for improving model predictions of lymphatic filariasis elimination date = 2018-10-08 keywords = MDA; datum; model summary = doi = 10.1371/journal.pntd.0006674 id = cord-288202-r3r2bc7v author = Morel, Noelia title = A Monoclonal Antibody-Based Copro-ELISA Kit for Canine Echinococcosis to Support the PAHO Effort for Hydatid Disease Control in South America date = 2013-01-10 keywords = ELISA; dog; sample summary = doi = 10.1371/journal.pntd.0001967 id = cord-000283-7s6283y5 author = Nazmi, Arshed title = Antiviral and Neuroprotective Role of Octaguanidinium Dendrimer-Conjugated Morpholino Oligomers in Japanese Encephalitis date = 2010-11-23 keywords = JEV; JEV+SC; Morpholino; Sham summary = We intend to show that these specifically designed Vivo-Morpholinos are effective in countering the viral load in the body, thereby imparting significant protection to the animals that were infected with a lethal dose of JEV. Similarly, E glycoprotein level showed significant increase in JEV-infected and JEV+SC-MO groups when compared to Sham (p,0.01) which were then drastically reduced following 39 and 59 MO treatments (p,0.01) (Figure 3B-D) . CBA performed to check the proinflammatory cytokines levels in the brain homogenates obtained from different treatments showed that levels of MCP-1, IFN-c, TNF-a, and IL-6 were found to be significantly increased in both JEV and JEV+SC-MO groups when compared to Sham infected groups (p,0.01). doi:10.1371/journal.pntd.0000892.g002 Vivo-Morpholino in Japanese Encephalitis www.plosntds.org JEV+SC-MO groups when compared to Sham (p,0.01). Increases were observed in the ROS levels in the brain samples of JEVinfected and JEV+SC-MO groups in comparison to Sham, that were reduced following 39 and 59 MO treatments. doi = 10.1371/journal.pntd.0000892 id = cord-003389-0yh5k6jk author = Patton, John B. title = Development of Onchocerca volvulus in humanized NSG mice and detection of parasite biomarkers in urine and serum date = 2018-12-12 keywords = NSG; Onchocerca; mouse; volvulus summary = doi = 10.1371/journal.pntd.0006977 id = cord-002394-n85ptr5p author = Reddy, Vijayalakshmi title = Molecular Mimicry between Chikungunya Virus and Host Components: A Possible Mechanism for the Arthritic Manifestations date = 2017-01-26 keywords = CHIKV; Fig; peptide summary = Therefore, in this study we investigated the possible occurrence of molecular mimicry between CHIKV E1 and host components using a three pronged strategy: (i) identification of homologous regions between CHIKV proteins and host tissue components using bioinformatics tools, (ii) establishing cross reactivity between serum samples obtained from CHIKV infected patients and peptides exhibiting molecular mimicry and (iii) validating the ability of the cross reactive peptides in inducing joint and muscle pathology in a mouse model. We investigated molecular mimicry in this study by using a combined approach of identifying homologous regions between CHIKV glycoprotein E1 protein and host tissue components using bioinformatics tools, the ability of these designed peptides to cross react with serum samples from CHIKV infected patients and inducing immune mediated joint and muscle pathology in a mouse model. doi = 10.1371/journal.pntd.0005238 id = cord-303647-c4umbcvn author = Reed, Patricia E. title = A New Approach for Monitoring Ebolavirus in Wild Great Apes date = 2014-09-18 keywords = EBOV; Ebola; ape; sample summary = doi = 10.1371/journal.pntd.0003143 id = cord-272250-asuxx1ln author = Robertson, Kis title = Rabies-Related Knowledge and Practices Among Persons At Risk of Bat Exposures in Thailand date = 2011-06-28 keywords = Thailand; bat; exposure; rabies summary = doi = 10.1371/journal.pntd.0001054 id = cord-276850-tnlyk0wz author = Rodrigues, Anderson Messias title = Proteomics-Based Characterization of the Humoral Immune Response in Sporotrichosis: Toward Discovery of Potential Diagnostic and Vaccine Antigens date = 2015-08-25 keywords = CBS; Sporothrix; schenckii; sporotrichosis summary = doi = 10.1371/journal.pntd.0004016 id = cord-352178-irjhmxsg author = Saxton-Shaw, Kali D. title = O''nyong nyong Virus Molecular Determinants of Unique Vector Specificity Reside in Non-Structural Protein 3 date = 2013-01-24 keywords = CHIKV; ONNV; RNA; infection; virus summary = Fifteen distinct chimeric viruses were constructed to evaluate both structural and non-structural regions of the genome and infection patterns were determined through artificial infectious feeds in An. gambiae with each of these chimeras. When ONNV non-structural protein 3 (nsP3) replaced nsP3 from CHIKV virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. Our study analyzed both structural and non-structural regions of the ONNV genome using chimeric viruses and artificially infected Anopheles gambiae mosquitoes. When ONNV non-structural protein 3 (nsP3) replaced nsP3 from chikungunya virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. Six additional non-structural chimeric viruses were also constructed using a novel type II restriction enzyme cloning strategy to examine the broader genome with respect to ONNV''s unique vector specificity for An. gambiae mosquitoes (Figure 2) . doi = 10.1371/journal.pntd.0001931 id = cord-260693-8mfuwx8l author = Seelig, Frederik title = The COVID-19 pandemic should not derail global vector control efforts date = 2020-08-31 keywords = COVID-19; control summary = However, a similar approach should also be adopted for the control of arboviral diseases of global importance, including dengue, Zika, chikungunya, and yellow fever, as recommended by the Pan-American Health Organization (PAHO) in their interim guidance on control of Aedes aegypti mosquitos during the COVID-19 pandemic [2] . The combined impact of both COVID-19 and epidemics of dengue or other vector-borne diseases (VBDs) could have potentially devastating consequences [6] . • Continue the implementation of the WHO''s global vector control response 2017-2030 (GVCR) strategy and regional policies for vector control [7, 8] , with respect to inter-and intrasectoral collaboration, engagement and mobilisation of communities, and scaling up of vector control if required, according to the implementation plan of vector control activities, while adapting activities as necessary to prevent further spread of COVID-19, in particular vector surveillance, which may need to be scaled down [9, 10] . It is vital that the COVID-19 response does not increase VBD threats in these communities by derailing global vector control efforts. doi = 10.1371/journal.pntd.0008606 id = cord-001074-qevosik3 author = Selvarajah, Suganya title = A Neutralizing Monoclonal Antibody Targeting the Acid-Sensitive Region in Chikungunya Virus E2 Protects from Disease date = 2013-09-12 keywords = CHIKV; antibody summary = C9 was determined to be a potent virus neutralizing antibody and a biosensor antibody binding study demonstrated it recognized residues on intact CHIKV VLPs. Shotgun mutagenesis alanine scanning of 98 percent of the residues in the E1 and E2 glycoproteins of CHIKV envelope showed that the epitope bound by C9 included amino-acid 162 in the acid-sensitive region (ASR) of the CHIKV E2 glycoprotein. The neutralizing epitope bound by C9 mapped to the acid-sensitive region (ASR) that is critical for the rearrangement of CHIKV E2 during fusion and viral entry into host cells. Therefore, C9 is a potent neutralizing antibody that can therapeutically protect wild-type neonate mice from a lethal dose of virus at 8 and 18 hours post CHIKV inoculation. This study describes the isolation and characterization of two human monoclonal antibodies, C9 and E8, from CHIKV infected and recovered individuals. doi = 10.1371/journal.pntd.0002423 id = cord-280030-neqycg6v author = Sewlall, Nivesh H. title = Clinical Features and Patient Management of Lujo Hemorrhagic Fever date = 2014-11-13 keywords = Africa; Lassa; Lujo; Patient; VHF summary = doi = 10.1371/journal.pntd.0003233 id = cord-312223-qgwzgazd author = Shafagati, Nazly title = The Use of NanoTrap Particles as a Sample Enrichment Method to Enhance the Detection of Rift Valley Fever Virus date = 2013-07-04 keywords = NT53; PCR; RNA; RVFV; particle summary = doi = 10.1371/journal.pntd.0002296 id = cord-310870-w8wu8vno author = Shorten, Robert J. title = The risk of transmission of a viral haemorrhagic fever infection in a United Kingdom laboratory date = 2017-05-18 keywords = laboratory; virus summary = doi = 10.1371/journal.pntd.0005358 id = cord-296226-ugeupo3u author = Sim, Shuzhen title = A greener vision for vector control: The example of the Singapore dengue control programme date = 2020-08-27 keywords = Aedes; Health; NEA; Singapore; control; dengue summary = Aedes-borne diseases, in particular, including dengue, chikungunya, yellow fever, and Zika, are increasing at an alarming rate due to urbanisation, population movement, weak vector control programmes, and climate change. The environmental management put in place to implement this high standard of public cleanliness has greatly benefited Singapore''s efforts to tackle VBDs. Underscoring the view that Aedes-borne diseases are environmental diseases, dengue control in Singapore is led by the National Environment Agency (NEA), a statutory board of the Ministry of the Environment and Water Resources (MEWR). In view of the importance of infrastructure maintenance and design, environmental sanitation, people''s behaviours, and use of technologies on dengue prevention, the NEA collaborates closely with other government ministries (e.g., Health, National Development, Education, Finance), town councils (responsible for management and maintenance of the common property of public housing estates, including vector control), community associations, research and academic institutions, and the private sector (Fig 2) . doi = 10.1371/journal.pntd.0008428 id = cord-292157-hrm69640 author = Stull-Lane, Annica R. title = Vitamin A supplementation boosts control of antibiotic-resistant Salmonella infection in malnourished mice date = 2020-10-02 keywords = Fig; Typhimurium; VAD; mouse summary = Typhimurium infection and antibiotic treatment failure, we assessed the potential of two consecutive doses of vitamin A in alleviating infection in male and female mice on a VAD or control diet. We found that subtherapeutic antibiotic treatment synergized with vitamin A treatment in infected VAD male mice, significantly decreasing systemic bacterial levels, mitigating weight loss and improving survival. Typhimurium systemic bacterial levels (CFU) were assessed for male (n = 5) and female (n = 5) mice on a standard diet 5 days post-infection for the following treatment groups: 0 mg/ml, 0.01 mg/ml, 0.05 mg/ml, and 0.10 mg/ml enrofloxacin delivered in the drinking water. Typhimurium D23580 at day 4 post-infection were assessed for male and female mice on either control or VAD diets with the following treatment groups: mocktreated, vitamin A only, enrofloxacin (0.05 mg/ml) only, and vitamin A and enrofloxacin cotreatment (Fig 5A) . doi = 10.1371/journal.pntd.0008737 id = cord-350533-fp1ctpax author = Tchesnokov, Egor P. title = Independent inhibition of the polymerase and deubiquitinase activities of the Crimean-Congo Hemorrhagic Fever Virus full-length L-protein date = 2020-06-04 keywords = CCHFV; Fig; RNA summary = doi = 10.1371/journal.pntd.0008283 id = cord-002248-92pzqj35 author = Terasaki, Kaori title = Mechanistic Insight into the Host Transcription Inhibition Function of Rift Valley Fever Virus NSs and Its Importance in Virulence date = 2016-10-06 keywords = IFN; M250; MP-12; RVFV summary = Importantly, RVFV MP-12-NSs mutant viruses with an impaired general transcription inhibition function showed a reduced cytotoxicity in cell culture and attenuated virulence in young mice, compared with its parental virus MP-12, highlighting the contribution of NSs-mediated general transcription inhibition towards RVFV virulence. Each carried mutations in NSs that specifically targeted its general transcription inhibition function without affecting its ability to degrade PKR and inhibit IFN-β promoter induction, through its interaction with Sin3-associated protein 30, a part of the repressor complex at the IFN-β promoter. Importantly, RVFV MP-12-NSs mutant viruses with an impaired general transcription inhibition function showed a reduced cytotoxicity in cell culture and attenuated virulence in young mice, Both NSs mutants retained some NSs functions, including degradation of PKR and SAP30 binding, and yet these NSs mutants and wt NSs showed different levels of general transcriptional suppression activities in virus-infected cells. doi = 10.1371/journal.pntd.0005047 id = cord-286255-ded5t1ai author = Tomashek, Kay M. title = Clinical and epidemiologic characteristics of dengue and other etiologic agents among patients with acute febrile illness, Puerto Rico, 2012–2015 date = 2017-09-13 keywords = AFI; DENV; Puerto; Rico summary = Blood and oro-nasopharyngeal specimens were tested by RT-PCR and immunodiagnostic methods for infection with dengue viruses (DENV) 1–4, chikungunya virus (CHIKV), influenza A and B viruses (FLU A/B), 12 other respiratory viruses (ORV), enterovirus, Leptospira spp., and Burkholderia pseudomallei. Clinical predictors of laboratory-positive dengue compared to all other AFI etiologies were determined by age and day post-illness onset (DPO) at presentation. By enrolling febrile patients at clinical presentation, we identified unbiased predictors of laboratory-positive dengue as compared to other common causes of AFI. Among 6,349 participants who presented early (<3 DPO) in the clinical course, leukopenia, thrombocytopenia, headache, eye pain, nausea, and dizziness were significant positive predictors of laboratory-positive dengue as compared to all other AFI cases across all age groups ( Table 5 ). Of note, 6% of participants !65 years old had dengue as a cause of AFI, a finding comparable to a Puerto Rico study in which 5% of 17,666 laboratory-positive dengue cases detected by surveillance were !65 years old [36] . doi = 10.1371/journal.pntd.0005859 id = cord-002179-v8lpw4r7 author = Viktorovskaya, Olga V. title = Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements date = 2016-08-24 keywords = DENV; Fig; RNA; UPRT; protein summary = title: Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements Previously, we have described a high-throughput mass spectrometry method termed TUX-MS (thiouracil cross-linking mass spectrometry) to identify host factors that interact with viral RNA during a live infection in cell culture [15] . Development of a quantitative thiouridine cross-linking mass spectrometry (qTUX-MS) method for identification of proteins associated with the DENV RNA TUX-MS can be used to identify host factors by incorporating 4-thiouridine (4sU), a zero-distance cross-linker, into the viral RNA (vRNA) to enable cross-linking of proteins bound to vRNA during a live infection in cell culture [15] . Since some of hnRNPs are known to modulate cellular gene expression in response to dengue infection [60, 61] , we can not rule out that some of the observed effects on virus titers derive from their roles in regulating host mRNAs. Among the numerous qTUX-MS identified factors of interest, our study is the first to demonstrate the involvement of HMCES (or C3orf37) in viral infection. doi = 10.1371/journal.pntd.0004921 id = cord-001642-bom9fk1y author = Wang, Junhua title = Deletion of Fibrinogen-like Protein 2 (FGL-2), a Novel CD4(+) CD25(+) Treg Effector Molecule, Leads to Improved Control of Echinococcus multilocularis Infection in Mice date = 2015-05-08 keywords = CD4; FGL2 summary = We showed that AE-fgl2(-/-) mice exhibited (as compared to AE-WT-animals) (a) a significantly lower parasite load with reduced proliferation activity, (b) an increased T cell proliferative response to ConA, (c) reduced Treg numbers and function, and (d) a persistent capacity of Th1 polarization and DC maturation. multilocularis-infected fgl2 -/mice and control WT littermates were analyzed after 1 and 4 months p.i. with respect to parasite weight and the expression of em14-3-3 as a marker for cellular proliferation activity [24] . Quantitative RT-PCR showed that fgl2 mRNA-levels were significantly increased in CD4 + CD25 + Tregs derived from AE-WT mice, when compared to non-infected controls, while no significant changes were evident with respect to CD4 + Teffs, CD8 + T cells. To further explore the role of VF on Tregs and FGL2 secretion, respectively, spleen cells from AE-WT mice and non-infected WT controls were each cultured in the presence of VF (10 μg/mL). doi = 10.1371/journal.pntd.0003755 id = cord-001365-6u80p5sj author = Weger-Lucarelli, James title = A Novel MVA Vectored Chikungunya Virus Vaccine Elicits Protective Immunity in Mice date = 2014-07-24 keywords = CD4; CHIK; GFP; MVA summary = doi = 10.1371/journal.pntd.0002970 id = cord-294798-ji3p0l4j author = White, Sarah K. title = Detection and phylogenetic characterization of arbovirus dual-infections among persons during a chikungunya fever outbreak, Haiti 2014 date = 2018-05-31 keywords = CHIKV; Haiti; PCR; ZIKV summary = We have previously reported isolation of ZIKV [8] , DENV [9] , Human coronavirus NL63 [10] , and Enterovirus D68 [11] from children in this school cohort; however, the cases/outbreaks in these prior publications did not include CHIKV, or cases within the May-August, 2014, time frame of the current study. Viral genomic RNA that was extracted from CHIKV, DENV1-4, and ZIKV strains that were obtained from the Biodefense and Emerging Infections Research Resource Repository (BEI Resources, Manassas, VA) were used as positive control materials for rtRT-PCR. The six ZIKV sequences obtained in June 2014 from the CHIKV co-infected patients were highly similar (99.9%) to each other and also cluster within a well-supported monophyletic clade, which, interestingly, includes a divergent strain isolated in 2016 from Guadaloupe (Figs 3B and S3B) . doi = 10.1371/journal.pntd.0006505 id = cord-306952-cpltrsa7 author = de Souza, Pedro Mansueto Melo title = Validation of verbal autopsy and nasopharyngeal swab collection for the investigation of deaths at home during the COVID-19 pandemics in Brazil date = 2020-11-04 keywords = COVID-19; SVO summary = doi = 10.1371/journal.pntd.0008830 id = cord-340939-ikomc19t author = van Doremalen, Neeltje title = A single-dose ChAdOx1-vectored vaccine provides complete protection against Nipah Bangladesh and Malaysia in Syrian golden hamsters date = 2019-06-06 keywords = Bangladesh; Fig; Malaysia; Nipah; animal summary = doi = 10.1371/journal.pntd.0007462