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?' ---------------------------------------------------------- 102 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 5038 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 55 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 11 PEDV 10 PRRSV 10 IBV 8 RNA 7 PCR 6 China 5 TGEV 5 Fig 5 ELISA 4 virus 4 rotavirus 4 PCV2 3 dna 3 day 3 ORF 3 Escherichia 3 Decaro 3 DPI 3 BVDV 2 type 2 swedish 2 strain 2 pig 2 isolate 2 dog 2 cpv 2 cell 2 canine 2 Vero 2 PRRSV-1 2 PMWS 2 PID 2 FIP 2 BRV 2 ASFV 1 zooepidemicus 1 western 1 tp1 1 theaflavin 1 spf 1 s1δ197 1 rig 1 respiratory 1 r191 1 pwd 1 protein 1 porcine 1 ped 1 page 1 nucleic Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 3962 virus 2292 strain 2095 cell 1902 pig 1792 infection 1544 % 1460 protein 1267 group 1185 gene 1151 sample 1150 study 1082 antibody 1002 vaccine 981 type 898 sequence 854 disease 823 coronavirus 772 day 723 isolate 707 animal 695 calf 690 analysis 626 ml 600 piglet 596 dog 595 result 586 serum 580 syndrome 578 diarrhea 537 tissue 532 assay 524 genome 493 rotavirus 491 time 452 cat 449 control 446 p 445 genotype 443 culture 440 detection 419 acid 412 region 401 swine 393 c 386 h 378 lesion 376 coli 375 number 373 datum 372 antigen Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 4508 al 3963 . 3571 et 991 PRRSV 846 PEDV 790 RNA 712 Fig 692 PCR 552 IBV 334 China 328 RT 323 S 290 E. 281 PCV2 242 II 234 N 230 ELISA 229 USA 225 S1 220 TGEV 214 Table 213 M 199 C 193 BVDV 188 sera 180 Decaro 176 Escherichia 170 CH 168 SARS 167 Vero 165 FCoV 150 DPI 149 PBS 148 CCoV 147 PRRS 135 IFN 134 aa 131 SPF 128 H120 127 Veterinary 126 PMWS 126 AE 123 US 123 ORF 117 icPC22A 116 CoVs 116 CoV 112 ® 111 A 110 TW Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 600 it 521 we 310 i 215 they 65 them 25 he 22 us 13 itself 8 one 4 themselves 3 you 3 isu-64 3 him 2 she 2 mrnas 1 s 1 pc92.9 1 ourselves 1 isu3927 1 icpc22a 1 hku4-covs 1 himself 1 ch/ 1 caspase-7 1 ayn 1 a`corona Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 15318 be 2092 have 1719 use 970 show 853 infect 779 detect 710 isolate 523 observe 503 include 440 inoculate 429 contain 424 describe 408 cause 405 associate 397 indicate 397 base 394 find 373 test 366 determine 364 follow 356 compare 345 perform 320 do 319 induce 316 report 312 collect 303 identify 301 obtain 300 suggest 248 demonstrate 244 strain 242 develop 240 produce 221 remain 221 increase 220 occur 217 provide 216 result 209 incubate 206 bind 194 confirm 191 relate 190 reveal 188 consider 186 neutralize 180 represent 177 know 173 vaccinate 171 express 164 select Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 1247 porcine 1153 not 994 viral 946 respiratory 868 - 758 high 702 positive 698 other 695 also 666 infectious 625 different 592 clinical 507 bovine 496 canine 486 only 486 however 453 reproductive 452 specific 436 more 415 negative 379 low 355 most 340 old 332 severe 329 respectively 328 previously 319 genetic 317 feline 313 first 298 similar 291 immune 291 anti 288 present 288 experimental 286 new 285 well 284 molecular 283 human 279 further 276 non 272 same 263 then 257 such 256 like 239 infected 230 intestinal 229 fecal 224 enteric 222 significant 222 recombinant Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 126 most 95 high 61 least 24 large 23 Most 20 good 14 low 11 close 10 great 7 ® 7 early 5 small 4 young 3 severe 3 old 3 long 3 late 3 ClustalW 2 strong 2 strict 2 new 1 ≈200 1 tremeGENE 1 t.t 1 simple 1 safe 1 ret 1 near 1 few 1 cvaA 1 chi2-t 1 big 1 -t 1 -CGATTTTGCGCTT Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 229 most 50 least 9 well 2 oldest 1 lowest 1 highest Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 9 doi.org 4 dx.doi.org 4 blast.ncbi.nlm.nih.gov 3 talk.ictvonline.org 2 www.ncbi.nlm.nih.gov 2 www.mbio.ncsu.edu 2 www 1 www.who.int 1 www.swissmodel.expasy.org 1 www.qiagen.com 1 www.qgenetics.com 1 www.pymol.org 1 www.picornastudygroup.com 1 www.oie.int 1 www.ncbi.nim.nih.gov 1 www.megasoftware.net 1 www.megasof 1 www.eng.uiowa.edu 1 www.dfvf.dk 1 sray.med.som.jhmi.edu 1 rotac 1 opal.biology.gatech.edu 1 imagej.nih 1 hcv.lanl.gov 1 enterobase.warwick.ac 1 enterobase 1 cge.cbs.dtu.dk 1 blast.ncbi.nlm.nih.gove 1 blast.ncbi.nlm 1 asparagin.cenargen.embrapa.br 1 apps.who.int Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 3 http://dx.doi.org/10.1016/ 3 http://blast.ncbi.nlm.nih.gov/Blast.cgi 2 http://www.ncbi.nlm.nih.gov 2 http://www 2 http://doi.org/10.1016/j.vetmic.2020.108693 2 http://doi.org/10.1016/j.vetmic.2019.01.020 1 http://www.who.int/ 1 http://www.swissmodel.expasy.org/ 1 http://www.qiagen.com 1 http://www.qgenetics.com 1 http://www.pymol.org 1 http://www.picornastudygroup.com/definitions7genus_ 1 http://www.oie.int/international-standard-setting/terrestrialmanual/access-online/ 1 http://www.ncbi.nim.nih.gov/orffinder/ 1 http://www.megasoftware.net/ 1 http://www.megasof 1 http://www.mbio.ncsu.edu/bioedit.htm 1 http://www.mbio.ncsu.edu/bioEdit/bioedit 1 http://www.eng.uiowa.edu/$tscheetz/ 1 http://www.dfvf.dk 1 http://talk.ictvonline.org/taxonomy/ 1 http://talk.ictvonline.org/ictv-reports/ 1 http://talk.ictvonline.org/ 1 http://sray.med.som.jhmi.edu/SCRopftware/simplot/ 1 http://rotac 1 http://opal.biology.gatech.edu/ 1 http://imagej.nih 1 http://hcv.lanl.gov/content/sequence/SNAP/SNAP.html 1 http://enterobase.warwick.ac 1 http://enterobase 1 http://dx.doi.org/10.1016/j 1 http://doi.org/http://dx.doi.org/10.1016/j.vetmic 1 http://doi.org/10.1016/j.vetmic.2019.08.003 1 http://doi.org/10.1016/j.vetmic.2019.02.015 1 http://doi.org/10.1016/j.vetmic.2018.11.025 1 http://doi.org/10.1016/j.vetmic.2018.05.014 1 http://cge.cbs.dtu.dk/ 1 http://blast.ncbi.nlm.nih.gove/Blast.cgi 1 http://blast.ncbi.nlm.nih.gov/ 1 http://blast.ncbi.nlm 1 http://asparagin.cenargen.embrapa.br 1 http://apps.who.int/iris/bitstream/handle/10665/ Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 21 samples were positive 10 pigs were negative 8 pigs did not 8 samples were also 7 pigs were positive 6 cells were then 6 pigs had significantly 6 pigs were randomly 6 sample containing rifampicin 6 samples tested positive 6 samples were infectious 6 virus induced cpe 6 virus infected cells 6 virus is not 5 % were positive 5 calves were orally 5 cells were also 5 groups were significantly 5 pigs were vi 5 vaccines are still 5 virus was not 4 cells were co 4 cells were mock 4 group was orally 4 pedv was not 4 pigs were also 4 pigs were seropositive 4 samples were subsequently 4 samples were then 4 sequenced using conventional 4 strains are more 4 virus did not 3 % base pair 3 animals did not 3 calves following oral 3 cells was not 3 days following inoculation 3 groups were negative 3 groups were not 3 infection did not 3 infections are sporadic 3 pigs had higher 3 pigs had mild 3 pigs were seronegative 3 protein is not 3 proteins were then 3 rna was not 3 samples contained infectious 3 samples were negative 3 sequences are available Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 2 days showed no evidence 2 groups were not significant 2 pedv was not infectious 2 pigs had not yet 1 % showed no clinical 1 analysis is not able 1 cells had no changes 1 cells showed no protein 1 cells was not due 1 disease is not well 1 group showed no common 1 group were not significant 1 groups were not significantly 1 infection is not always 1 infections are not infrequent 1 isolate did not fig 1 isolate was not pathogenic 1 isolates have no correlation 1 pcr was not possible 1 pedv had no replication 1 pedv had no tissue 1 pigs are not susceptible 1 pigs is not ubiquitous 1 pigs showed no clinical 1 pigs were not serologically 1 pigs were not systematically 1 protein is not clear 1 proteins are not available 1 prrsv did not completely 1 samples is not probable 1 strain has no ifn 1 strains have not yet 1 strains was not possible 1 strains were not able 1 vaccine does not organization 1 vaccine is not clinically 1 vaccines are not yet 1 vaccines did not significantly 1 virus is not essential 1 virus was not infectious 1 virus was not present 1 viruses are not available A rudimentary bibliography -------------------------- id = cord-319168-i23pqiwx author = Abro, Shahid Hussain title = Emergence of novel strains of avian infectious bronchitis virus in Sweden date = 2012-03-23 keywords = IBV; Sweden; isolate; swedish summary = Nucleotide and amino acid sequence comparisons have shown that the recent isolates bear 98.97% genetic similarity with strains of the QX-like genotype. Twenty Swedish IBV isolates from different outbreaks were selected for comprehensive study of the complete spike gene of the virus. Analysis of the nucleotide sequences of spike glycoprotein of Swedish isolates from 1995 to 2010 showed that they comprise distinct sets of IBV variants; differing among themselves along that timeline (Table 3 ). The phylogenetic studies, based on the partial S1 gene regions, showed that Swedish IBV isolates from 1995 to 1999 were related to the Massachusetts genotype. Taken together, the complete spike sequence data revealed different isolates of IBV of the Massachusetts type and European D388/QX-like strains circulating over a time-line in Sweden. Complete genome sequence analysis of a predominant infectious bronchitis virus (IBV) strain in China doi = 10.1016/j.vetmic.2011.09.022 id = cord-299539-f7i4lq2w author = Bachofen, Claudia title = Clinical appearance and pathology of cattle persistently infected with bovine viral diarrhoea virus of different genetic subgroups date = 2010-03-24 keywords = BVDV; animal summary = doi = 10.1016/j.vetmic.2009.09.022 id = cord-277364-vy2yirek author = Baró, J. title = Porcine circovirus type 2 (PCV2) enteric disease: An independent condition or part of the systemic disease? date = 2015-03-23 keywords = PCV2; PCV2-SD summary = doi = 10.1016/j.vetmic.2015.01.006 id = cord-315094-pzixgqcy author = Benetka, Viviane title = Prevalence of feline coronavirus types I and II in cats with histopathologically verified feline infectious peritonitis date = 2004-03-26 keywords = FIP; PCR; type summary = doi = 10.1016/j.vetmic.2003.07.010 id = cord-337369-2ceq42av author = Blum, Shlomo title = Outbreak of Streptococcus equi subsp. zooepidemicus infections in cats date = 2010-07-29 keywords = zooepidemicus summary = doi = 10.1016/j.vetmic.2009.12.040 id = cord-007472-ydrnanug author = Brock, K.V. title = Detection of bovine viral diarrhea virus in serum from cattle by dot blot hybridization assay date = 2002-11-13 keywords = BVDV; Harkness; hybridization summary = doi = 10.1016/0378-1135(90)90179-y id = cord-301382-zlr4nwc2 author = Burimuah, Vitus title = Sero-prevalence, cross-species infection and serological determinants of prevalence of Bovine Coronavirus in Cattle, Sheep and Goats in Ghana date = 2019-12-03 keywords = Ghana summary = doi = 10.1016/j.vetmic.2019.108544 id = cord-257645-6fxfmn1i author = Chang, Ji-Tao title = Ovine rotavirus strain LLR-85-based bovine rotavirus candidate vaccines: Construction, characterization and immunogenicity evaluation date = 2010-11-20 keywords = LLR-85; r191; rotavirus summary = doi = 10.1016/j.vetmic.2010.04.016 id = cord-258433-n50joeda author = Chang, Long title = β-cantenin is potentially involved in the regulation of c-Jun signaling following bovine herpesvirus 1 infection date = 2020-08-08 keywords = JNK; Jun; figure summary = Interestingly, β-catenin was found to be involved in the regulation of c-Jun signaling in virus-infected cells as iCRT14, a β-catenin-specific inhibitor that can inhibit β-catenin-dependent transcriptional activity, was able to decrease protein expression and phosphorylation of c-Jun. Furthermore, we suggest that BoHV-1 infection stimulates c-Jun phosphorylation regulated by β-catenin via both c-Jun NH2-terminal kinase (JNK)-dependent and JNK-independent mechanisms. Similarly, BoHV-1 infection activates the JNK/c-Jun cascade, with inhibition of this pathway via the chemical inhibitor SP600125 significantly blocking productive infection in cell cultures (Zhu et al., 2016) . In order to understand the effects that β-catenin had on the activation of c-Jun signaling stimulated by BoHV-1 infection, we detected the protein levels of both c-Jun and p-c-Jun(S73) in the presence of β-catenin-specific inhibitor iCRT14 via Western blot. Taken together, these data suggest that in BoHV-1-infected MDBK cells, β-catenin is potentially involved in the phosphorylation of c-Jun signaling partially through the activation of JNK. doi = 10.1016/j.vetmic.2020.108804 id = cord-007481-4mj5isyl author = Chanter, N. title = Dysentery in calves caused by an atypical strain of Escherichia coli (S102-9) date = 2002-11-13 keywords = S102; calf summary = doi = 10.1016/0378-1135(86)90053-2 id = cord-278641-8lh5y7j0 author = Chen, Jianing title = Identification and characterization of PEDV infection in rat crypt epithelial cells date = 2020-09-17 keywords = IEC-6; PEDV; cell summary = Porcine epidemic diarrhea virus (PEDV), as the PED causative agent, has been commonly propagated and investigated in Vero cells, as well as in IPEC-J2, a porcine epithelial cell-jejunum 2. Besides that, PEDV infection in IEC-6 cells can induce the production of inflammatory cytokines and interferon, especially the type III IFNs. Collectively, our findings suggest that IEC-6 is an ideal cell line for PEDV replication and immune response studies. PEDV CV777 strain reached its most elevated viral titers in both Vero and IEC-6 cells but poorly replicated in IPEC-J2 cells (Fig. 1E) . The results showed that both type I and type III interferon responses were significantly activated in PEDV infected IEC-6 and IPEC-J2 cells while the type I interferon were absent in Vero cells ( Fig. 2A, 2B, 2D, 2E ). For type II interferon, PEDV infection led to a significant upregulation in IEC-6 cells but not in IPEC-J2 and Vero cells (Fig. 2C) . doi = 10.1016/j.vetmic.2020.108848 id = cord-305684-ipeup5mp author = Chen, Yuqiu title = Identification and molecular characterization of a novel serotype infectious bronchitis virus (GI-28) in China date = 2016-12-16 keywords = China; IBV; LGX/111119 summary = doi = 10.1016/j.vetmic.2016.12.017 id = cord-331868-xbszmiql author = Clark, K.J title = An in vitro study of theaflavins extracted from black tea to neutralize bovine rotavirus and bovine coronavirus infections date = 1998-10-01 keywords = theaflavin summary = title: An in vitro study of theaflavins extracted from black tea to neutralize bovine rotavirus and bovine coronavirus infections Crude theaflavin was extracted from black tea and then fractionated by HPLC into five components (initial peaks (IP), TF(1), TF(2A), TF(2B), and TF(3)). Therefore, although the use of phyllosilicate clays and charcoal are an ideal method of concentrating virus particles, they do not appear to be an effective method of eliminating the infectivity of rotavirus or coronavirus as judged from in vitro studies (Clark et al., 1998) . In our studies, the crude extract of theaflavin and each of the purified derivatives were studied (individually and in combination) for their antiviral effect against rotavirus and coronavirus. Crude theaflavin extractions were later made from Indian and Chinese black tea and compared to the U.S. source for inactivation activity against bovine rotavirus. doi = 10.1016/s0378-1135(98)00242-9 id = cord-350467-18bvwxci author = Clark, K.J title = In vitro studies on the use of clay, clay minerals and charcoal to adsorb bovine rotavirus and bovine coronavirus date = 1998-10-01 keywords = HSCAS; rotavirus; virus summary = doi = 10.1016/s0378-1135(98)00241-7 id = cord-285585-tigj7fhc author = Cleveland, Christopher A. title = Survey for selected pathogens in wild pigs (Sus scrofa) from Guam, Marianna Islands, USA date = 2017-05-03 keywords = Guam; Leptospira; pig summary = doi = 10.1016/j.vetmic.2017.05.001 id = cord-284514-b7no0yrv author = Davies, Robert L title = Diversity of avian Pasteurella multocida strains based on capsular PCR typing and variation of the OmpA and OmpH outer membrane proteins date = 2003-02-02 keywords = OMP; Pasteurella; type summary = title: Diversity of avian Pasteurella multocida strains based on capsular PCR typing and variation of the OmpA and OmpH outer membrane proteins One hundred avian Pasteurella multocida isolates recovered from cases of fowl cholera and related infections in England and Wales over a 13-year period were characterised by capsular PCR typing and analysis of outer membrane protein (OMP) profiles. Nineteen distinct OMP profiles (OMP-types) were identified based mainly on molecular mass heterogeneity of the heat-modifiable (OmpA) and porin (OmpH) proteins. Strains of capsular types B, D and F, as well as the untypable isolates, were associated exclusively with specific OMP-types and represent distinct and widely disseminated clonal groups. The molecular mass of OmpA (A) varied from 36.9 to 37.9 kDa and that of OmpH (H) varied from 33.1 to 38.3 kDa. The distribution of OMP-types among the avian isolates is shown in Table 1 . doi = 10.1016/s0378-1135(02)00300-0 id = cord-270563-fm6j7thy author = Decaro, N. title = Canine parvovirus vaccination and immunisation failures: are we far from disease eradication? date = 2020-06-15 keywords = MDA; canine; cpv summary = Taking into account the reduced circulation of canine distemper virus and canine adenovirus type 1 in countries where extensive vaccination is carried out, more effort should be made to aim for CPV eradication, including antibody testing to determine the optimal time for vaccinations of pups and adults and homogeneous vaccine coverage of dog population. In a recent study (Altman et al., 2017) , inactivated vaccines were more frequently associated with immunisation failures than MLV vaccines in pups of less than twelve weeks of age, likely as a consequence of a better ability of replicating MLV to override residual maternally-derived antibodies (MDA). Dogs vaccinated against CPV, canine distemper virus (CDV) and canine adenovirus (CAdV) were protected from disease and/or infection after challenge 9 years from vaccination (Schultz et al., 2010) . doi = 10.1016/j.vetmic.2020.108760 id = cord-258696-01wj76es author = Decaro, Nicola title = Experimental infection of dogs with a novel strain of canine coronavirus causing systemic disease and lymphopenia date = 2008-04-30 keywords = RNA; day; dog summary = The dogs, three 2.5-month-old and two 6-month-old pups, were successfully infected, shedding viral RNA with their faeces for the entire observation period (21 days) and displaying systemic clinical signs resembling those observed during the course of natural infection. At postmortem examination, remarkable lesions were observed in the internal organs of the euthanized pups, that tested positive for CCoV by real-time RT-PCR and virus isolation on cell cultures. Unexpectedly, CCoV type II RNA was detected at very high titres in the internal organs of the dead pups and the virus (strain CB/05) was isolated on canine cell cultures. (last day of observation) reaching the maximal mean value of 6.79 Â 10 5 RNA copy numbers/ml of template at day 10 p.i. Surprisingly, CCoV RNA was never detected in the blood of the 6-month-old pups, as well as in the euthanized animals, in whose organs remarkable viral RNA titres were found. doi = 10.1016/j.vetmic.2007.10.008 id = cord-259988-3s7b5ovi author = Decaro, Nicola title = Virological and molecular characterization of a mammalian orthoreovirus type 3 strain isolated from a dog in Italy date = 2005-08-10 keywords = MRV; PCR summary = doi = 10.1016/j.vetmic.2005.05.014 id = cord-298499-a2vblbbz author = Decaro, Nicola title = Canine parvovirus—A review of epidemiological and diagnostic aspects, with emphasis on type 2c date = 2012-02-24 keywords = CPV-2; Decaro; cpv summary = In comparison to the original type CPV-2, the antigenic variants display increased pathogenicity in dogs and extended host range, being able to infect and cause disease in cats. In comparison to the original type CPV-2, the antigenic variants display increased pathogenicity in dogs and extended host range, being able to infect and cause disease in cats. Nothing is know about the protection induced by the original type against CPV-2c (as well as against the other variants) after a long period interval between vaccination and challenge, when the type-2 antibody titers could be not high enough to efficiently prevent infection and disease caused by a field strain. A real-time PCR assay for rapid detection and quantitation of canine parvovirus type 2 DNA in the feces of dogs A minor groove binder probe real-time PCR assay for discrimination between type 2-based vaccines and field strains of canine parvovirus doi = 10.1016/j.vetmic.2011.09.007 id = cord-308315-g6udfu2a author = Decaro, Nicola title = Characterisation of bubaline coronavirus strains associated with gastroenteritis in water buffalo (Bubalus bubalis) calves date = 2010-10-26 keywords = Decaro; PCR summary = doi = 10.1016/j.vetmic.2010.04.010 id = cord-324324-8ybfiz8f author = Decaro, Nicola title = Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses date = 2020-04-14 keywords = China; East; IBV; MERS; RNA; SARS; bat; coronavirus summary = In addition, the close contact between human beings and different animal species sold at the wet markets of East Asia represents the optimal situation for the host species jump and adaptation to humans of potentially zoonotic agents like CoVs. It is not a coincidence that two of the most severe zoonoses of the last two decades (highly pathogenic H5N1 avian influenza and SARS) have emerged in the same Chinese province of Guangdong where the contact between humans and animals is closer (Lorusso et al., 2020) . All these viruses as well as analogous IBV-like CoVs detected in other birds including penguins, pigeons, peafowl, parrots, waterfowl, teal, quail, duck and whooper swan (Cavanagh et al., 2002; Circella et al., 2007; Domanska-Blicharz et al., 2014; Torres et al., 2013; Hughes et al., 2009; Liu et al., 2005; Wille et al., 2016; Jordan et al., 2015; Bande et al., 2016; Suryaman et al., 2019) have been assigned to the same viral species known as Avian coronavirus (ACoV) within the subgenus Igacovirus of genus Gammacoronavirus. doi = 10.1016/j.vetmic.2020.108693 id = cord-327170-rv0efgg2 author = Decaro, Nicola title = Tissue distribution of the antigenic variants of canine parvovirus type 2 in dogs date = 2007-03-31 keywords = Decaro; dna summary = doi = 10.1016/j.vetmic.2006.11.005 id = cord-312867-fxgx9c4v author = Di Martino, Barbara title = Canine kobuviruses in diarrhoeic dogs in Italy date = 2013-09-27 keywords = Aichi summary = doi = 10.1016/j.vetmic.2013.05.007 id = cord-320559-up1q3k6q author = Dortmans, J.C.F.M. title = Porcine epidemic diarrhea virus (PEDV) introduction into a naive Dutch pig population in 2014 date = 2018-05-24 keywords = ELISA; Netherlands; PEDV summary = doi = 10.1016/j.vetmic.2018.05.014 id = cord-015722-0w3crrf9 author = Fey, H. title = Proceedings of minisymposium on neonatal diarrhea in calves and pigs: Saskatoon, Sask., 3–4 May 1976. Veterinary Infectious Diseae Organization (VIDO), University of Saskatchewan, Saskatoon, University Publications Office, 1976, 155pp., $5.00, ISBN 0-88880-004-5 date = 2002-12-09 keywords = author; manuscript summary = 3. Manuscripts should be typewritten, typed on one side of the paper, with wide margins and double spacing throughout, including abstracts, footnotes and references. Every page of the manuscript should be numbered in the upper right-hand corner, including title page, references, tables, etc. If Greek letters or uncommon symbols are used in the manuscript, they should be written very clearly, and if necessary a note such as "Greek lower-case chi" should be put in the margin and encircled. Elsevier reserves the privilege of returning to the author for revision accepted manuscripts and illustrations which are not in the proper form given in this guide. The manuscript should be carefully checked to ensure that the spelling of authors'' names and dates are exactly the same in the text as in the reference list If reference is made in the text to a publication written by more than two authors the name of the first autilor should be used followed by "et al doi = 10.1016/0378-1135(78)90020-2 id = cord-297283-o1oauxex author = Fritzen, Juliana T.T. title = Longitudinal surveillance of rotavirus A genotypes circulating in a high milk yield dairy cattle herd after the introduction of a rotavirus vaccine date = 2019-02-18 keywords = RVA summary = This study aimed to determine the frequency and intensity of neonatal diarrhea and the incidence of RVA and attempted to monitor the G and P genotypes present in the RVA strains circulating in a high milk yield cattle herd vaccinated with RVA G6P[5] strain. The aim of this study was to determine the frequency and intensity of neonatal diarrhea and the incidence of RVA and to identify the RVA G and P genotypes circulating in dairy calves born from cows that are regularly vaccinated with the RVA G6P[5] strain in a high milk yield dairy cattle herd. Other longitudinal studies that have been conducted in Brazil to determine the level of RVA infection in calves born from vaccinated dairy cows had percentages of RVA-positive diarrheic fecal samples that were 5.7% (49/850) (Coura et al., 2015) and 3.9% (11/281) (Rocha et al., 2017) . doi = 10.1016/j.vetmic.2019.02.022 id = cord-305156-w6iqeayr author = Gallien, Sarah title = Limited shedding of an S-InDel strain of porcine epidemic diarrhea virus (PEDV) in semen and questions regarding the infectivity of the detected virus date = 2018-10-11 keywords = DPI; PEDV summary = doi = 10.1016/j.vetmic.2018.09.025 id = cord-306976-p2521bl4 author = Gao, Mengying title = Serotype, antigenicity, and pathogenicity of a naturally recombinant TW I genotype infectious bronchitis coronavirus in China date = 2016-08-15 keywords = China; IBV; strain summary = Furthermore, neither the vaccine strains nor the attenuated viruses could provide complete respiratory protection of chickens against a challenge with the ck/CH/LDL/140520 strain, indicating that it is necessary to develop new live vaccines or to evaluate the use of established vaccines in combination to control naturally recombinant TW I-type IBV strains in the future. Our results showed that strain ck/CH/LDL/140520 is very pathogenic, and that it is able to cause cystic oviducts in a high percentage of birds, as well as mortality due to nephritis and respiratory distress with complete tracheal ciliostasis, especially in chickens infected at 1 day of age. In contrast, respiratory signs (sneezing, nasal discharge, and tracheal rales) developed at 3-4 dpc and lasted until 10 dpc in some of the chickens in the groups that were vaccinated with the H120, 4/91, and Conn vaccines, and the attenuated LSD/120720 and LGX/ 100508 viruses when challenged with the nrTW I IBV strain at 20 days of age. doi = 10.1016/j.vetmic.2016.05.018 id = cord-007497-nn5l5rai author = Garcia-Sanchez, J. title = Survey of rotavirus infection in a dairy herd: comparison between polycrylamide gel electrophoresis and two commercial tests date = 2002-11-13 keywords = ELISA; page; rotavirus summary = doi = 10.1016/0378-1135(93)90057-e id = cord-015742-nt44jcjm author = Garwes, D.J. title = Antigenicity of structural components from porcine transmissible gastroenteritis virus date = 2002-11-13 keywords = TGEV; antibody summary = doi = 10.1016/0378-1135(79)90034-8 id = cord-293458-jb7u9xn6 author = Gerdts, Volker title = Vaccines for porcine epidemic diarrhea virus and other swine coronaviruses date = 2016-12-02 keywords = PEDV; TGEV; porcine summary = doi = 10.1016/j.vetmic.2016.11.029 id = cord-306948-wkisfz1m author = Han, Mingyuan title = Engineering the PRRS virus genome: Updates and perspectives date = 2014-12-05 keywords = PRRSV; RNA; virus summary = doi = 10.1016/j.vetmic.2014.10.007 id = cord-301136-7odc5un9 author = Hasslung, F. title = Experimental reproduction of postweaning multisystemic wasting syndrome (PMWS) in pigs in Sweden and Denmark with a Swedish isolate of porcine circovirus type 2 date = 2005-03-20 keywords = PCV2; PMWS; PPV; swedish summary = doi = 10.1016/j.vetmic.2004.12.011 id = cord-265765-zpf1bla8 author = Holland, Robert E title = Characterization of eae(+)Escherichia coli isolated from healthy and diarrheic calves date = 1999-05-14 keywords = Escherichia; Shiga summary = Strains of Escherichia coli from 101 healthy and 114 diarrheic calves were screened by PCR for the eae (intimin) gene and Shiga toxin genes (stx). Moreover, Shiga toxin antigens were detected significantly more (p = 0.001) often among the eae/stx(+) strains from healthy calves when compared to eae/stx(+) strains from diarrheic calves. No significant difference (p ≥ 0.05) was detected among the eae(+) and eae/stx(+) strains from healthy and diarrheic calves for enterohemolysin production. In this study, the Premier EHEC assay was used to detect Shiga toxin antigens associated with eae/stx strains. When examined in the immunoassay, Shiga toxin antigens were detected for all 20 eae/stx (100%) strains from healthy calves and in 8 of 11 (73.0%) strains from diarrheic calves. Detection and characterization of the eae gene of shiga-like toxin-producing Escherichia coli using polymerase chain reaction Shiga toxin-producing Escherichia coli strains from bovines: association of adhesion with carriage of eae and other genes doi = 10.1016/s0378-1135(99)00013-9 id = cord-316592-a1uhy2ex author = Huang, Fen title = RNA interference inhibits hepatitis E virus mRNA accumulation and protein synthesis in vitro date = 2010-05-19 keywords = HEV; ORF2; a549 summary = To exploit the possibility of using RNA interference (RNAi) as a strategy against HEV infection, four small interference RNA (siRNA) duplex targeting ORF2 gene were constructed. Real-Time quantitative polymerase chain reaction (Real-Time qPCR) and Western blot assay demonstrated that four HEV specific siRNAs (si-ORF2-1, si-ORF2-2, si-ORF2-3 and si-ORF2-4) were capable of protecting cells against HEV infection with very high specificity and efficiency. Real-Time quantitative polymerase chain reaction (Real-Time qPCR) and Western blot assay demonstrated that four HEV specific siRNAs (si-ORF2-1, si-ORF2-2, si-ORF2-3 and si-ORF2-4) were capable of protecting cells against HEV infection with very high specificity and efficiency. The efficiency of suppression of the HEV ORF2 gene by various HEV specific siRNAs was evaluated by fluorescence microscopy, Real-Time qPCR and Western blot. RNA interference effectively inhibits mRNA accumulation and protein expression of hepatitis C virus core and E2 genes in human cells doi = 10.1016/j.vetmic.2009.10.023 id = cord-007474-ckqghr3b author = Johnson, Michael E. title = Development of specific nucleic acid probes for the differentiation of porcine rotavirus serotypes date = 2002-11-13 keywords = Gottfried; OSU; RNA summary = doi = 10.1016/0378-1135(90)90180-4 id = cord-292101-lnap47kp author = Jung, Kwonil title = Structural alteration of tight and adherens junctions in villous and crypt epithelium of the small and large intestine of conventional nursing piglets infected with porcine epidemic diarrhea virus date = 2015-06-12 keywords = Cadherin; PEDV; PID summary = doi = 10.1016/j.vetmic.2015.03.022 id = cord-268918-6l02una0 author = Kapil, Sanjay title = Characterization of bovine coronavirus isolates/from eight different states in the USA date = 1999-06-30 keywords = BCV; isolate summary = Antigenic differences were observed among the isolates in a one-way hemagglutination-inhibition (HI) test using a polyclonal antiserum against the Mebus bovine coronavirus isolate. Minor antigenic and biological differences have been observed among BCV isolates from calf diarrhea and winter dysentery cases from the USA (Tsunemitsu and Saif, 1995) and Canada (Dea et al., 1995) . We compared antigenic differences on one-way hemagglutination-inhibition (HI) test, isoelectric focusing of BCV proteins, and relative susceptibility of BCV isolates to hygromycin B. We observed some differences in cytopathic effects among the calf diarrhea isolates; however, passage number, plaque purification, and the presence of trypsin and pancreatin in the cell culture medium greatly affected the cytopathology of BCV isolates. Antiserum against cell culture propagated bovine coronavirus isolates: on the basis of a one way HI test, 77 BCV isolates were inhibited from 1 : 2 up to 1 : 1024. doi = 10.1016/s0378-1135(99)00042-5 id = cord-007476-wu9tuvy9 author = Katz, Jonathan B. title = Antigenic differences between European and American isolates of porcine reproductive and respiratory syndrome virus (PRRSV) are encoded by the carboxyterminal portion of viral open reading frame 3 date = 2000-03-10 keywords = Lelystad; PRRSV; american; european summary = doi = 10.1016/0378-1135(94)00113-b id = cord-285335-agm4zbcx author = Kennedy, Melissa title = Deletions in the 7a ORF of feline coronavirus associated with an epidemic of feline infectious peritonitis date = 2001-08-08 keywords = FIP; ORF summary = A population of Persian cats experienced an epidemic of feline infectious peritonitis (FIP) over 2 years. Feline coronavirus (FCoV) genomic RNA was detected consistently in this study in biologic samples from adult cats, kittens suffering from FIP, and their siblings. Analysis of viral 7a/7b open reading frame (ORFs) were analyzed and revealed two distinct virus variants circulating in the population, one with an intact 7a ORF and one with two major deletions in the 7a ORF. Both virus variants were identified in one cat, the sire ''''Dan'''', as sequence analysis of clones from a single PCR from this animal revealed the presence of the 7a deletion mutant as well as the intact isolate (Dan 1 and 2 in Fig. 2 ). The sire of the majority of FIP kittens was dually infected with both virus variants as revealed by sequence analysis of cloned 7a/7b genes from this cat. doi = 10.1016/s0378-1135(01)00354-6 id = cord-308953-4mhjtitv author = Kim, Hyun-Jeong title = Detection and genotyping of Korean porcine rotaviruses date = 2010-08-26 keywords = GARV summary = To obtain genomic data on the G and P genotypes of Korean porcine GARVs, porcine GARVs isolated from the diarrheic fecal samples were subjected to RT-PCR with primer pairs specific to each VP7 and VP4 gene of GARVs (Table 1) . In order to determine the prevalence of porcine GARVs in diarrheic Korean piglets, a total of 475 fecal samples from diarrheic pigs in 143 farms across South Korea were screened by RT-PCR and nested PCR using two sets of primer pairs (Table 1) . A comparison of the nucleotide and deduced amino acid sequences of the VP7 gene between all Korean porcine GARV strains and the GARV strains representing all 23 G genotypes was performed with a 1020 bp fragment (excluding the primer sequences) (Tables 4 and 5). doi = 10.1016/j.vetmic.2010.01.019 id = cord-007480-grndfx7b author = Koopmans, M. title = Seroepidemiology of Breda virus in cattle using ELISA date = 2002-11-13 keywords = BRV; Breda; ELISA summary = doi = 10.1016/0378-1135(89)90069-2 id = cord-255619-5h3l6nh6 author = Kuo, Shu-Ming title = Evolution of infectious bronchitis virus in Taiwan: Positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity date = 2013-03-23 keywords = Fig; IBV; RNA summary = doi = 10.1016/j.vetmic.2012.10.020 id = cord-321261-3lp54mmu author = Kuo, Shu-Ming title = Evolution of infectious bronchitis virus in Taiwan: Characterisation of RNA recombination in the nucleocapsid gene date = 2010-08-26 keywords = IBV summary = doi = 10.1016/j.vetmic.2010.02.027 id = cord-329274-ncvvmkca author = Labarque, G title = Porcine reproductive–respiratory syndrome virus infection predisposes pigs for respiratory signs upon exposure to bacterial lipopolysaccharide date = 2002-08-02 keywords = LPS; PRRSV summary = doi = 10.1016/s0378-1135(02)00104-9 id = cord-257046-er5orx8s author = Ladekjær-Mikkelsen, A.-S title = Reproduction of postweaning multisystemic wasting syndrome (PMWS) in immunostimulated and non-immunostimulated 3-week-old piglets experimentally infected with porcine circovirus type 2 (PCV2) date = 2002-10-22 keywords = PCV2; PID; PMWS; dna summary = title: Reproduction of postweaning multisystemic wasting syndrome (PMWS) in immunostimulated and non-immunostimulated 3-week-old piglets experimentally infected with porcine circovirus type 2 (PCV2) Reproduction of postweaning multisystemic wasting syndrome (PMWS) in immunostimulated and non-immunostimulated 3-week-old piglets experimentally infected with porcine circovirus type 2 (PCV2) PCV1 is considered to be a non-pathogenic virus (Tischer et al., 1986; Allan et al., 1995) , whereas infection of swine with PCV2 is causally associated with development of postweaning multisystemic wasting syndrome (PMWS) in weaned 5-to 12-week-old piglets (Allan et al., 1998; Ellis et al., 1998) . In contrast, dual infection with PCV2 and porcine parvovirus (PPV) or porcine reproductive and respiratory syndrome virus (PRRSV) potentiates the replication and distribution of PCV2 and induces clinical disease in addition to more severe histopathological lesions Kennedy et al., 2000; Krakowka et al., 2000; Harms et al., 2001) . doi = 10.1016/s0378-1135(02)00174-8 id = cord-301655-6nxhvvm4 author = Lei, Xi-Mei title = Specific recombinant proteins of porcine epidemic diarrhea virus are immunogenic, revealing their potential use as diagnostic markers date = 2019-08-10 keywords = ELISA; Fig; ORF3C; PEDV summary = doi = 10.1016/j.vetmic.2019.108387 id = cord-260869-rym2ik0o author = Lemmermeyer, Tanja title = Characterization of monoclonal antibodies against feline coronavirus accessory protein 7b date = 2016-02-29 keywords = Fig; ORF; protein; western summary = The 7b protein has a molecular mass of $26 kDa, it is secreted from the cell and contains (i) a Cterminal KDEL-like endoplasmic reticulum (ER) retention signal, (ii) an N-terminal signal sequence of 17 amino acids and (iii) a potential N-glycosylation site at aa position 68 (Vennema et al., 1992a) . The identity of the purified protein was confirmed by SDS-PAGE and Western blotting using anti-His mAb. The protein had an apparent molecular mass of 24 kDa as judged by SDS-PAGE analysis, which is predicted for this protein, and was recognized by the His-tag-specific antibody (Fig. 1a) . Two additional minor bands in the SDS-PAGE were specifically recognized by Western blotting using the His-tag-specific mAb. These bands are consistent with a dimer and a 37-kDa degradation product, respectively, of the GST-7bDSS-His protein (Fig. 1b) . The results outlined above show that the anti-7b mAbs recognize exclusively the nonglycosylated form of the viral protein in FCoV-infected cells. doi = 10.1016/j.vetmic.2015.12.009 id = cord-260217-bne77cap author = Letellier, C title = Detection and genotyping of bovine diarrhea virus by reverse transcription-polymerase chain amplification of the 5′ untranslated region date = 1999-01-01 keywords = BVDV summary = doi = 10.1016/s0378-1135(98)00267-3 id = cord-312119-wzcas4zd author = Lu, Ti title = Mapping the neutralizing epitopes of F18 fimbrial adhesin subunit FedF of enterotoxigenic Escherichia coli (ETEC) date = 2019-02-06 keywords = Escherichia; f18; pwd summary = A vaccine that induces broad immunity to prevent K88 and F18 fimbrial ETEC bacterial attachment and colonization in pig small intestines and to neutralize enterotoxin enterotoxicity would be effective for PWD. In this study, we in silico identified immunodominant epitopes from F18 FedF subunit, fused individual epitopes to protein carrier CfaB (a structural subunit of heterologous human ETEC fimbria CFA/I), immunized mice with each epitope fusion protein, measured mouse anti-F18 antibody response, and examined epitope-derived antibodies for neutralizing activities against F18 fimbria adherence to determine FedF neutralizing epitopes. Furthermore, CfaB-epitope fusions were examined as competitive agents to prevent anti-F18 antibodies from inhibiting adherence of F18fimbrial bacteria to pig intestine cell line IPEC-2. Competitive ELISA and bacteria adherence inhibition assay to show CfaB-epitope fusion proteins blocking binding of anti-F18 antiserum with F18 fimbriae or F18-fimbrial E. A tripartite fusion, FaeG-FedF-LT(192)A2:B, of enterotoxigenic Escherichia coli (ETEC) elicits antibodies that neutralize cholera toxin, inhibit adherence of K88 (F4) and F18 fimbriae, and protect pigs against K88ac/heat-labile toxin infection doi = 10.1016/j.vetmic.2019.02.015 id = cord-007479-2z6crx22 author = Lu, Wei title = Serological and genotypic characterization of group a rotavirus reassortants from diarrheic calves born to dams vaccinated against rotavirus() date = 2002-11-13 keywords = BRV; NCDV; NS-1 summary = doi = 10.1016/0378-1135(94)90015-9 id = cord-296611-ma32oz4o author = Ma, Tianxin title = Novel genotype of infectious bronchitis virus isolated in China date = 2019-01-29 keywords = China; I0636/16; IBV; strain summary = Further comparative genomic analysis revealed at least two recombination sites that replaced the spike gene in a lineage 18 within genotype I (GI-18)-like virus with an as-yet-unidentified sequence, likely derived from another IBV strain, resulting a novel serotype with a lower affinity to the respiratory tract in chickens. To the best of our knowledge, this provides the first evidence for recombination leading to replacement of the complete spike gene and the emergence of a novel genotype/serotype with a lower affinity to the respiratory tract in chickens comparing to one of its parental virus ck/CH/LGX/111119. To confirm these recombination breakpoints, three phylogenetic trees were constructed on the basis of the results of similarity plot (SimPlot) analysis for the nucleotide fragments 1-20,265 (5′ untranslated region (UTR) to 3′ end of Gene 1), 20,266-24,151 (3′ end of Gene 1 to 5′ end of Gene 3), and 24,152-27,629 (5′ end of Gene 3 to 3′ UTR), from nine IBV strains, including I0636/16, five strains (LGX/ 111119, CK/CH/GD/GZ14, γCoV/ck/China/I0114/14 (I0114/14), GX-YL9, and GX-YL5) showing close relationships with I0636/16 based on the complete genomic sequence analysis, and three Mass strains (Beaudette, H120, and M41) as an outgroup. doi = 10.1016/j.vetmic.2019.01.020 id = cord-260799-kx6hfpu0 author = Mahmood, Zana H. title = Isolation and molecular characterization of Sul/01/09 avian infectious bronchitis virus, indicates the emergence of a new genotype in the Middle East date = 2011-05-12 keywords = IBV; Iraq summary = title: Isolation and molecular characterization of Sul/01/09 avian infectious bronchitis virus, indicates the emergence of a new genotype in the Middle East Infectious bronchitis virus (IBV) was isolated from trachea and kidney tissues of eight broiler farms in Kurdistan region of North Iraq from 2008 to 2010. Veterinary Microbiology 150 (2011) 21-27 Infectious bronchitis virus (IBV) was isolated from trachea and kidney tissues of eight broiler farms in Kurdistan region of North Iraq from 2008 to 2010. In order to investigate IBV genotypes in Iraq, where the disease is endemic and widely spread in vaccinated and unvaccinated poultry farms mainly associated with kidney damage and urolethiasis, identification and molecular characterization of IBV (Sul/01/09) isolated from eight infected broiler farms was conducted and the deduced amino acid sequence of the S1 subunit of the virus was compared with geographically related isolates. doi = 10.1016/j.vetmic.2010.12.015 id = cord-259744-r9j5yzfc author = McDonagh, Phillip title = Identification and characterisation of small molecule inhibitors of feline coronavirus replication date = 2014-12-05 keywords = CPE; antiviral; compound; effect summary = Plaque reduction and virus yield reduction assays were performed to confirm antiviral effects of candidate compounds identified during screening, and the possible antiviral mechanisms of action of these compounds were investigated using virucidal suspension assays and CPE inhibition and IFA-based time of addition assays. Plaque reduction and virus yield reduction assays were performed to confirm antiviral effects of candidate compounds identified during screening, and the possible antiviral mechanisms of action of these compounds were investigated using virucidal suspension assays and CPE inhibition and IFA-based time of addition assays. This study identifies three compounds (chloroquine, mefloquine, and hexamethylene amiloride) demonstrating a marked inhibitory effect on FCoV replication in vitro by significant reductions in virus induced CPE and viral titres at low micromolar concentrations when present during the early stages of viral replication. This study has identified three compounds demonstrating marked in vitro inhibition of FCoV in an immortalised cell line at low micromolar concentrations, including the first demonstration of antiviral effects of mefloquine against a coronavirus. doi = 10.1016/j.vetmic.2014.10.030 id = cord-312208-8ydh6jev author = Meng, X.J title = Heterogeneity of porcine reproductive and respiratory syndrome virus: implications for current vaccine efficacy and future vaccine development date = 2000-06-12 keywords = ORF; PRRSV; U.S. summary = doi = 10.1016/s0378-1135(00)00196-6 id = cord-285096-g9y3au1a author = Mitchell, Judy A. title = Tropism and pathological findings associated with canine respiratory coronavirus (CRCoV) date = 2013-03-23 keywords = CIRD; crcov; day; dog; respiratory summary = doi = 10.1016/j.vetmic.2012.11.025 id = cord-290442-rrj684c4 author = Moutinho Costa, Erika title = Molecular characterization of canine coronavirus strains circulating in Brazil date = 2014-01-10 keywords = CCoV summary = doi = 10.1016/j.vetmic.2013.10.002 id = cord-007461-v3tff2gk author = Nguyen, T.D. title = Transmissible gastroenteritis (TGE) of swine: In vitro virus attachment and effects of polyanions and polycations date = 2002-11-12 keywords = TGEV; cell summary = doi = 10.1016/0378-1135(87)90026-5 id = cord-256180-xpdtt0ej author = Ohshima, T. title = A minute virus of canines (MVC: canine bocavirus) isolated from an elderly dog with severe gastroenteritis, and phylogenetic analysis of MVC strains date = 2010-10-26 keywords = MVC summary = doi = 10.1016/j.vetmic.2010.03.033 id = cord-260840-tudl9k1g author = Opriessnig, Tanja title = Effect of porcine circovirus type 2a or 2b on infection kinetics and pathogenicity of two genetically divergent strains of porcine reproductive and respiratory syndrome virus in the conventional pig model date = 2012-07-06 keywords = PCV2; PRRSV; pig summary = More recently, attention has focused on the occurrence of high mortality in Chinese swine herds which Veterinary Microbiology 158 (2012) [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] To determine differences in infection kinetics of two temporally and genetically different type 2 porcine reproductive and respiratory syndrome virus (PRRSV) isolates in vivo with and without concurrent porcine circovirus (PCV) type 2a or 2b infection, 62 pigs were randomly assigned to one of seven groups: negative controls (n = 8); pigs coinfected with a 1992 PRRSV strain (VR-2385) and PCV2a (CoI-92-2a; n = 9), pigs coinfected with VR-2385 and PCV2b (CoI-92-2b; n = 9), pigs coinfected with a 2006 PRRSV strain (NC16845b) and PCV2a (CoI-06-2a; n = 9), pigs coinfected with NC16845b and PCV2b (CoI-06-2b; n = 9), pigs infected with VR-2385 (n = 9), and pigs infected with NC16845b (n = 9). doi = 10.1016/j.vetmic.2012.02.010 id = cord-272375-c4ut7vn7 author = Palombieri, Andrea title = Molecular detection and characterization of Carnivore chaphamaparvovirus 1 in dogs date = 2020-10-01 keywords = canine summary = Recent advances in molecular technologies have been allowed the discovery of novel parvoviruses in dogs, including two additional bocaparvoviruses species, CBoV-2 and CBoV-3 identified respectively from healthy and sick dogs respiratory samples (Kapoor et al., 2012) and from the liver of a dog with multiorgan failure (Li et al., 2013) , and the still unclassified carnivore protoparvoviruses likebufaviruses (CBuVs) detected in stool samples of dogs with or without enteric disease and in the nasal and oropharyngeal swabs of animals with respiratory signs. In order to gather additional information on the distribution of this novel parvovirus in dogs and to investigate its possible association with enteritis, during the year 2019 a surveillance study was initiated by implementing with CaChPV-specific assays the diagnostic algorithms of cases of acute gastro-enteritis admitted to the veterinary hospital of the Faculty of Veterinary Medicine, University of Teramo (Italy). doi = 10.1016/j.vetmic.2020.108878 id = cord-255238-adpn5fb9 author = Pan, Yongfei title = Discovery of a novel swine enteric alphacoronavirus (SeACoV) in southern China date = 2017-09-28 keywords = HKU2; PEDV; TGEV summary = doi = 10.1016/j.vetmic.2017.09.020 id = cord-320769-qcpua9ck author = Park, Su-Jin title = Molecular epidemiology of bovine toroviruses circulating in South Korea date = 2008-01-25 keywords = PCR; korean summary = doi = 10.1016/j.vetmic.2007.07.012 id = cord-007506-swx3kqob author = Paul, Prem S. title = Applications of nucleic acid probes in veterinary infectious diseases date = 2002-11-13 keywords = dna; nucleic summary = doi = 10.1016/0378-1135(90)90187-z id = cord-283946-ts2lyy4p author = Pedersen, N.C title = An isolated epizootic of hemorrhagic-like fever in cats caused by a novel and highly virulent strain of feline calicivirus date = 2000-05-11 keywords = Ari; FCV; October; cat summary = doi = 10.1016/s0378-1135(00)00183-8 id = cord-007463-8g0zklzy author = Pocock, D.H. title = Characterisation of rotavirus isolates from sub-clinically infected calves by genome profile analysis date = 2002-11-13 keywords = RNA; rotavirus summary = doi = 10.1016/0378-1135(87)90095-2 id = cord-319712-3dikelw6 author = Pujols, Joan title = Survivability of porcine epidemic diarrhea virus (PEDV) in bovine plasma submitted to spray drying processing and held at different time by temperature storage conditions date = 2014-12-05 keywords = PEDV summary = doi = 10.1016/j.vetmic.2014.10.021 id = cord-007484-nvhu7blo author = Richard Dorn, C. title = Characteristics of vero cytotoxin producing Escherichia coli associated with intestinal colonization and diarrhea in calves date = 2002-11-13 keywords = Escherichia; SLT summary = title: Characteristics of vero cytotoxin producing Escherichia coli associated with intestinal colonization and diarrhea in calves Isolates of Escherichia coli which produce Vero cytotoxin (VTEC) were obtained during 1983–1989 from calves raised in 5 north-central states of the USA. E. coli producing Vero cytotoxin (VTEC) have been isolated from cattle, beef, other meats, milk and milk products (Karmali, 1989; Giffin and Tauxe, 1991 ) . Serotypes which were isolated from calves in this study and which have been reported from HC in humans include O11 I:NM, O45:H2, O26:H11 and O5:NM (Bopp et al., 1987) Other 05 : NM strains of bovine origin have been associated with hemorrhagic enteritis in cattle. This O5:NM strain produced a toxin active on Vero cells which was neutralized by anti VT 1 and hybridized with the VT 1 and CVD419 probes (Dorn et al., 1989) . Production of toxins by Escherichia coli strains isolated from calves with diarrhea in Galicia doi = 10.1016/0378-1135(93)90136-u id = cord-270727-2dd3b7di author = Rivera-Benitez, José Francisco title = Co-infection of classic swine H1N1 influenza virus in pigs persistently infected with porcine rubulavirus date = 2016-02-29 keywords = DPI; Mock; PorPV; group summary = A Student''s t-test assuming unequal variance and a significance level of P 0.05 was used to compare rectal temperatures and the viral load of PorPV and swH1N1 in different samples (nasal and oral swabs, respiratory tissues and SLO) between the single-infected groups to the co-infected group. In the nasal swabs, samples that tested positive for PorPV were detected from 24 h post-infection up to 28 DPI (PorPV/Mock and PorPV/swH1N1 groups) (Fig. 3a) , and there were no differences (P > 0.05) in the mean of viral loads at any time analysed for these two groups. The pigs in the Mock/swH1N1 group presented the lowest respiratory signs and rectal temperatures, with no pigs showing a difference in respiration or temperature after experimental infection, a finding that is in accordance with studies that used low-virulence swine influenza virus strains (Busquets et al., 2010) . doi = 10.1016/j.vetmic.2016.01.005 id = cord-290540-r0d6oaez author = Rottier, Peter J.M. title = The molecular dynamics of feline coronaviruses date = 1999-09-01 keywords = FIPV; PCR; virus summary = Special attention is given to the genetic dynamics of the viruses as these now allow us to begin to understand the origin of the different phenotypes, in particular the genesis of virulence during persistent infection. The conclusion from these experiments is that feline coronaviruses may persist in the lower intestinal tract where the virus continues to replicate at low levels. Conceivably, the persisting virus confers to its host resistance against superinfection by the closely related feline coronaviruses, which were infecting the other cats. The idea was that''feline enteric coronaviruses'' are indeed restricted in tropism, while''FIP viruses'' would cross the epithelium, infect macrophages and go systemically. The result of all these studies is that generally there is no protection when an antibody response to the spike protein is induced there is rather an enhancement of the infection, with an''early death'' phenomenon. Detection of feline coronavirus RNA in feces, tissues and body fluids of naturally infected cats by reverse transcriptase PCR doi = 10.1016/s0378-1135(99)00099-1 id = cord-261160-g92zhv19 author = Rowland, Raymond R.R title = Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero date = 2003-10-30 keywords = PCR; PRRSV; RNA; virus summary = doi = 10.1016/j.vetmic.2003.07.006 id = cord-279975-542qbbgp author = Shibata, Isao title = Isolation of porcine epidemic diarrhea virus in porcine cell cultures and experimental infection of pigs of different ages date = 2000-03-15 keywords = Vero; ped summary = doi = 10.1016/s0378-1135(99)00199-6 id = cord-274892-a6fscyjf author = Smith, Joseph A. title = Identification and isolation of a novel herpesvirus in a captive mob of eastern grey kangaroos (Macropus giganteus) date = 2008-06-22 keywords = PCR; herpesvirus; kangaroo summary = doi = 10.1016/j.vetmic.2007.11.019 id = cord-323845-s78t5qxj author = Soliman, H. title = Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of viral hemorrhagic septicaemia virus (VHS) date = 2006-05-31 keywords = LAMP; RNA; VHS summary = doi = 10.1016/j.vetmic.2005.11.063 id = cord-269560-vq462fh2 author = Stadejek, Tomasz title = Pathogenicity of three genetically diverse strains of PRRSV Type 1 in specific pathogen free pigs date = 2017-05-16 keywords = BOR59; DPI; PRRSV; PRRSV-1 summary = doi = 10.1016/j.vetmic.2017.05.011 id = cord-254317-n2knqj4z author = Su, Yunfang title = The enhanced replication of an S-intact PEDV during coinfection with an S1 NTD-del PEDV in piglets date = 2018-11-27 keywords = PEDV; Vero; s1δ197 summary = Porcine epidemic diarrhea virus (PEDV) variants having a large deletion in the N-terminal domain of the S1 subunit of spike (S) protein were designated as S1 NTD-del PEDVs. They replicate well in experimentally infected pigs. Effect of mucin, bile and bile acids on the infection of PEDV icPC22A and icPC22A-S1Δ197 in Vero and IPEC-DQ cells Viruses (icPC22A or icPC22A-S1Δ197) were mixed with different concentrations of BM (0, 0.1, 0.3, 0.5 mg/mL) or PGM (0, 0.5, 1.0, 2.5, 5.0 mg/mL). Compared with the peak fecal PEDV N gene shedding titer (11.6 ± 0.2 log 10 copies/mL) of piglets in the icPC22A group (1 dpi), pigs in the coinfection group had a significantly higher peak titer (13.6 ± 0.7 log 10 copies/mL) ( Fig. 1B and Table 2 ) at a delayed time point (1.5 dpi). S1 NTD-del PEDV replicated to a lower peak titer in coinfection than that in single virus infection in both Vero cells and IPEC-DQ cells. doi = 10.1016/j.vetmic.2018.11.025 id = cord-289629-9p9ld4ur author = Suzuki, Kazuhiko title = Equine coronavirus induces apoptosis in cultured cells date = 2008-06-22 keywords = MDBK; hat summary = doi = 10.1016/j.vetmic.2007.11.034 id = cord-264598-2u8bm2fz author = Sánchez-Carvajal, J.M. title = Activation of pro- and anti-inflammatory responses in lung tissue injury during the acute phase of PRRSV-1 infection with the virulent strain Lena date = 2020-06-02 keywords = Lena; PRRSV; PRRSV-1 summary = doi = 10.1016/j.vetmic.2020.108744 id = cord-299751-2drhoz70 author = Tabynov, Kairat title = Inactivated porcine reproductive and respiratory syndrome virus vaccine adjuvanted with Montanide™ Gel 01 ST elicits virus-specific cross-protective inter-genotypic response in piglets date = 2016-08-30 keywords = ADJ; PRRSV summary = The efficacy of a novel BEI-inactivated porcine reproductive and respiratory syndrome virus (PRRSV) candidate vaccine in pigs, developed at RIBSP Republic of Kazakhstan and delivered with an adjuvant Montanide™ Gel 01 ST (D/KV/ADJ) was compared with a commercial killed PRRSV vaccine (NVDC-JXA1, C/KV/ADJ) used widely in swine herds of the Republic of Kazakhstan. Clinical parameters (body temperature and respiratory disease scores), virological and immunological profiles [ELISA and virus neutralizing (VN) antibody titers], macroscopic lung lesions and viral load in the lungs (quantitative real-time PCR and cell culture assay) were assessed in vaccinated and both genotype 1 and 2 PRRSV challenged pigs. The challenge virus strains LKZ/2010 and CM/08 were propagated in MARC-145 cells, and confirmed as type 1 and type 2 viruses by EZ-PRRSV TM MPX 4.0 Real Time RT-PCR using Target-Specific Reagents kit for the Rapid Identification & Differentiation of North American and European PRRS Viral RNA (Tetracore, MD, USA). doi = 10.1016/j.vetmic.2016.06.014 id = cord-277746-rllxa6fj author = Takano, Tomomi title = Molecular characterization and pathogenicity of a genogroup GVI feline norovirus date = 2015-08-05 keywords = M49 summary = In addition, specific pathogen-free cats inoculated with FNoV gene-positive-fecal samples developed diarrhea symptoms, and the viral gene was detected in their feces and blood. The FNoV gene was detected in samples collected from Cat No. 49-2012, as confirmed by RT-PCR described below, and these samples were subsequently used in this study. When the FNoV gene-positive PCR products of fecal samples collected on days 4, 9, 18, and 21 were subjected to a sequencing analysis, all were identical with the ORF1 gene of the FNoV M49-1 strain. A Simplot analysis was performed to compare gene sequences including the recombination breaking point among the FNoV M49-1 strain, GIV FNoV, GIV lion norovirus, GIV canine NoV (CNoV), and GVI CNoV. FNoV was detected with the development of clinical symptoms in SPF cats orally inoculated with fecal samples containing the FNoV M49-1 strain. doi = 10.1016/j.vetmic.2015.05.018 id = cord-007456-acbo4zs2 author = Thomas, L.H. title = Growth of Mycoplasma bovis in organ cultures of bovine foetal trachea and comparison with Mycoplasma dispar date = 2002-11-13 keywords = day summary = doi = 10.1016/0378-1135(87)90044-7 id = cord-258107-s53f25sb author = Wattrang, Eva title = Exudative epidermitis and porcine circovirus-2 infection in a Swedish SPF-herd date = 2002-05-24 keywords = PCV-2; spf summary = In addition, 3-week-old piglets from three litters (n=24) farrowed close after the initial EE outbreak were closely monitored for clinical signs of skin disease, sampled for Staphylococcus hyicus, tested for antibodies to porcine parvovirus and in sequentially collected serum samples tested for interferon-α (IFN-α) and interleukin-6. All tested serum samples from the SPF-herd collected in 1990, 1992 and February 1993, i.e., up to 2 months prior to the EE outbreak, were negative for antibodies to PCV-2 both in ELISA n 22 and IIF (n 10, February 1993 samples). Thus, after being sero-negative to PCV-2 earlier in 1993, pigs in the SPF-herd had varying levels of antibodies to this virus 2 weeks after the ®rst outbreak of EE. Piglets in litter 3 were also sero-positive to PCV-2 at 3 days of age but had lower levels of antibodies compared to the offspring of sow no. doi = 10.1016/s0378-1135(02)00024-x id = cord-007491-yxz69nil author = Weingartl, H.M. title = Binding of porcine transmissible gastroenteritis virus by enterocytes from newborn and weaned piglets date = 2002-11-13 keywords = TGEV summary = doi = 10.1016/0378-1135(93)90113-l id = cord-007495-gpz4gkv3 author = Weiss, M. title = Antibodies to berne virus in horses and other animals date = 2002-11-13 keywords = Berne; ELISA summary = doi = 10.1016/0378-1135(84)90014-2 id = cord-277187-rcxjjxw3 author = Xu, Zhichao title = Attenuation and characterization of porcine enteric alphacoronavirus strain GDS04 via serial cell passage date = 2019-11-04 keywords = P100; P15; P67; PEAV summary = doi = 10.1016/j.vetmic.2019.108489 id = cord-292690-1p1gnpgf author = Zang, Yue title = Recombinant Lactobacillus acidophilus expressing S(1) and S(2) domains of porcine epidemic diarrhea virus could improve the humoral and mucosal immune levels in mice and sows inoculated orally date = 2020-08-16 keywords = China; PEDV summary = doi = 10.1016/j.vetmic.2020.108827 id = cord-343036-vmprhd9g author = Zhang, Li title = Efficient inactivation of African swine fever virus by ozonized water date = 2020-07-10 keywords = ASFV summary = doi = 10.1016/j.vetmic.2020.108796 id = cord-322683-wkrj6n1d author = Zhang, Pengfei title = Cellular Poly(C) Binding Protein 2 Interacts with porcine epidemic diarrhea virus Papain-Like Protease 1 and Supports Viral Replication date = 2020-07-13 keywords = IFN; PCBP2; PEDV; PLP1 summary = doi = 10.1016/j.vetmic.2020.108793 id = cord-333366-j3yh5v1g author = Zhao, Dongmin title = Peptide inhibitors of tembusu virus infection derived from the envelope protein date = 2020-05-07 keywords = TMUV; TP2; tp1 summary = DN59, an inhibitory peptide corresponding to the stem region of dengue virus (DENV) E protein, almost completely inhibited DENV infection in LLC-MK2 cells and exhibited cross-inhibitory activity against West Nile virus (WNV) infection. The data demonstrated that TP1 inhibited TMUV infection through destroying the integrity of the viral particles, while both TP1 and TP2 exerted inhibitory effects by interfering with the binding of TMUV to cells. At 24 h post-infection, qRT-PCR, plaque assays, and western blotting were conducted to detect virus production with peptide treatment. To explore the mechanism of the inhibitory effects of TP2, a virus binding inhibition assay was performed to determine whether the peptides interfered with the binding between TMUV and cells. The direct binding of TP1 or TP2 to TMUV, but not to target cells, might explain why both peptides exhibited similar inhibitory effects in the different cell types BHK-21 cells, CEFs, DF-1 cells and DEFs. The mechanism by which flavivirus infection is inhibited by peptide inhibitors is not clearly understood. doi = 10.1016/j.vetmic.2020.108708 id = cord-257886-ytlnhyxr author = Zhao, Kuan title = Nucleocapsid protein of porcine reproductive and respiratory syndrome virus antagonizes the antiviral activity of TRIM25 by interfering with TRIM25-mediated RIG-I ubiquitination date = 2019-05-03 keywords = PRRSV; TRIM25; rig summary = title: Nucleocapsid protein of porcine reproductive and respiratory syndrome virus antagonizes the antiviral activity of TRIM25 by interfering with TRIM25-mediated RIG-I ubiquitination These results indicate for the first time that TRIM25 inhibits PRRSV replication and that the N protein antagonizes the antiviral activity by interfering with TRIM25-mediated RIG-I ubiquitination. The cells were lysed in RIPA lysis buffer after 36 h of transfection and the effects of siRNAs were analyzed by WB using an anti-TRIM25 monoclonal antibody (cat. To investigate whether TRIM25-mediated RIG-I ubiquitination is regulated by the PRRSV N protein, HEK293T cells grown in 6-well plates were co-transfected with pCAGGS-Flag-RIG-I (0.5 μg per well) and HA-ubiquitin (0.5 μg per well), and the indicated amounts of the Myc-N expression plasmids. The experiment revealed that TRIM25-mediated RIG-I ubiquitination was potentiated by Sendai virus (SEV) infection but was substantially suppressed by increasing the PRRSV N protein expression, in a dose-dependent manner (Fig. 5) . doi = 10.1016/j.vetmic.2019.05.003 id = cord-293781-7so4gqc8 author = Zhao, Shanshan title = Effects of virulent and attenuated transmissible gastroenteritis virus on the ability of porcine dendritic cells to sample and present antigen date = 2014-06-25 keywords = SHXB; STC3 summary = In this study, an attenuated TGEV (STC3) and a virulent TGEV (SHXB) were used to determine whether porcine DCs play an important role in pathogenetic differences between these two TGEVs. Our results showed that immature and mature monocyte-derived dendritic cells (Mo-DCs) were susceptible to infection with SHXB and STC3. In this study, an attenuated TGEV (STC3) and a virulent TGEV (SHXB) were used to determine whether porcine DCs play an important role in pathogenetic differences between these two TGEVs. Our results showed that immature and mature monocyte-derived dendritic cells (Mo-DCs) were susceptible to infection with SHXB and STC3. Second, the SHXB and STC3 strains were used to infect the piglets in vivo in order to further determine whether they could damage the ability of intestinal DCs to sample the heat-inactivated Escherichia coli, migrate, and stimulate CD3 + , CD4 + and CD8 + T-cell proliferation at 48 h postinfection. doi = 10.1016/j.vetmic.2014.03.017 id = cord-272305-eniovfwy author = Zhao, Ye title = Safety and efficacy of an attenuated Chinese QX-like infectious bronchitis virus strain as a candidate vaccine date = 2015-10-22 keywords = China; Fig; IBV summary = Strain YN-inoculated birds had clinical signs of varying severity with 30% mortality, while the attenuated group appeared healthy, with less tissue damage. The resulting attenuated YN strain was shorted as aYN and was titrated by inoculating 10-fold serial dilutions with phosphate-buffered saline (PBS) of the virus stocks into the allantoic sac of 10-day-old SPF embryonated eggs. Gross changes were noted and samples of trachea, kidney, lung, proventriculus, duodenum, and bursa of Fabricius were collected for virus detection via real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) and in 10% neutral formalin for histopathological examination. In terms of the real-time RT-qPCR examination, both strains were detected in respiratory and non-respiratory tissues, including the kidney, trachea, lungs, proventriculus, duodenum, and bursa of Fabricius, indicating viral replication in these organs; however, this was relatively limited in the birds infected with the YN attenuated strain. Efficacy and safety of an attenuated live QX-like infectious bronchitis virus strain as a vaccine for chickens doi = 10.1016/j.vetmic.2015.07.036 id = cord-328032-unwehrr5 author = Zhou, Haisheng title = Identification of a novel recombinant virulent avian infectious bronchitis virus date = 2017-01-03 keywords = CH/2010; JT-1 summary = Whole-genome sequence analysis showed that CK/CH/2010/JT-1 originated from multiple template switches among QX-like, CK/CH/LSC/99I-, tl/CH/LDT3/03and 4/91-type IBVs. All of these data demonstrated that CK/CH/2010/JT-1 is a new recombinant genotype IBV with high virulence. The complete genome and gene sequences of isolate CK/CH/ 2010/JT-1 and of IBV reference strains obtained from GenBank were aligned and analysed using the ClustalW multiple alignment method in the MegAlign program of DNASTAR software (version 7.1; DNAstar, Madison, USA). Phylogenetic analysis of the S1 gene of IBVs revealed that CK/CH/2010/JT-1 and 31 other isolates described in BLASTN analysis are grouped as a new cluster (Fig. 1) , which is separated from the previously identified serotypes and genotypes. Phylogenetic analysis of the S1 gene showed these strains could be grouped as a new genotypic cluster which was different from the previously identified genotypes IBV in China. Complete genome sequence of a recombinant nephropathogenic infectious bronchitis virus strain in China doi = 10.1016/j.vetmic.2016.12.038 id = cord-305079-foifc8ch author = Zhou, Ying Shun title = Establishment of reverse genetics system for infectious bronchitis virus attenuated vaccine strain H120 date = 2013-02-22 keywords = H120; IBV summary = doi = 10.1016/j.vetmic.2012.08.013 id = cord-317640-61crnh6a author = Zhu, Zhaozhong title = Homologous recombination shapes the genetic diversity of African swine fever viruses date = 2019-08-10 keywords = ASFV; Fig; african summary = doi = 10.1016/j.vetmic.2019.08.003 id = cord-257572-dh4jvbmi author = van Kasteren, Puck B. title = In vivo assessment of equine arteritis virus vaccine improvement by disabling the deubiquitinase activity of papain-like protease 2 date = 2015-07-09 keywords = EAV; PLP2; dub summary = Both viruses have been thoroughly characterized in cell[ 6 _ T D $ D I F F ] culture experiments, revealing no differences in replication kinetics, yet a strongly decreased DUB activity and an enhanced induction of interferon beta mRNA expression (a hallmark of innate immune activation) of the mutant virus compared to its parental counterpart (van Kasteren et al., 2013) . Upon challenge with the[ 4 _ T D $ D I F F ] virulent EAV KY84 strain, both nonvaccinated control horses (Group 3) showed virus replication, with amounts of viral RNA reaching levels comparable to those produced by the vaccine viruses (Fig. 3A) . We have previously shown that mutant EAV lacking PLP2 DUB activity induces a more potent innate immune response than its DUB-competent parental virus upon infection in cell culture (van Kasteren et al., 2013) , and hypothesized that this feature might be included in an improved arterivirus vaccine. doi = 10.1016/j.vetmic.2015.04.018