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?' ---------------------------------------------------------- 60 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 4525 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 51 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 11 PEDV 10 PCR 5 PRRSV 4 RPA 3 PCV2 3 ELISA 2 respiratory 2 gene 2 dog 2 bovine 2 TGEV 2 Salmonella 2 RNA 2 IBV 2 China 2 CPV-2 2 CPV 2 CDV 1 vr-2332 1 virus 1 veterinary 1 thai 1 temperature 1 tannin 1 table 1 study 1 strain 1 response 1 professional 1 porcine 1 piglet 1 pig 1 pcv2 1 nsp11 1 new 1 line 1 japanese 1 infection 1 herd 1 group 1 fmt 1 figure 1 feline 1 feed 1 dna 1 difficile 1 diarrhoeic 1 country 1 collaboration 1 clostridium Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 1282 virus 1147 infection 1103 % 1037 study 971 sample 784 strain 715 animal 669 time 652 pig 646 dog 581 disease 554 assay 534 gene 504 group 502 result 497 cell 483 analysis 478 protein 456 detection 439 diarrhea 404 control 395 c 388 antibody 370 calf 364 ° 363 sequence 351 p 349 datum 348 vaccine 343 day 343 cat 323 swine 319 number 310 piglet 307 serum 302 type 294 case 292 farm 290 epidemic 279 test 276 method 275 author 267 response 266 pathogen 264 - 259 mouse 240 outbreak 234 value 228 herd 223 effect Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 734 PEDV 658 PCR 311 PRRSV 257 RPA 251 Fig 247 RT 247 RNA 216 China 181 S. 174 C. 172 ELISA 163 Salmonella 157 CDV 149 M. 142 PCV2 139 TGEV 139 S 122 IFN 120 USA 119 E. 115 SaoA 115 C 103 PBS 103 IBV 100 Table 100 DNA 96 Japan 94 US 94 F 90 • 90 REBOV 89 sera 88 Animal 87 O157 84 ORT 82 NP 82 CPV-2 81 United 79 . 78 al 78 Typhimurium 78 H7 77 Germany 76 BCoV 75 M 75 Health 71 University 71 ICA 70 GSNO 69 et Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 407 it 282 we 177 they 58 them 44 i 31 us 20 you 11 themselves 7 he 6 itself 5 one 3 she 2 rsc0018 2 rsc0012 1 y903mxcj 1 rpos 1 pcv2 1 mg 1 ifit5 1 ifih1 1 himself 1 herself 1 bpiv-3 1 agfa Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 8822 be 1179 have 1119 use 561 show 408 detect 347 include 324 base 286 perform 274 test 267 observe 264 report 254 collect 242 associate 239 find 236 compare 231 infect 215 indicate 204 do 198 cause 192 identify 192 follow 190 determine 187 obtain 176 describe 175 isolate 173 contain 165 provide 163 develop 162 consider 157 evaluate 148 induce 148 increase 138 suggest 128 analyze 127 see 126 confirm 120 affect 117 accord 111 demonstrate 110 investigate 109 result 109 reduce 109 add 106 express 105 occur 105 involve 103 require 101 take 99 relate 98 incubate Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 604 not 572 porcine 532 high 509 positive 487 - 463 other 381 also 379 clinical 374 viral 362 real 334 respiratory 291 more 273 different 262 negative 248 however 233 new 224 only 218 significant 215 canine 214 low 213 first 207 bovine 202 specific 202 present 200 most 172 respectively 170 infectious 169 then 168 immune 166 well 163 veterinary 158 same 158 molecular 153 non 153 feline 151 common 149 highly 147 significantly 145 such 141 available 140 fecal 139 large 137 similar 134 old 128 diagnostic 125 reproductive 125 intestinal 124 therefore 124 small 124 previously Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 53 high 46 most 31 good 30 least 13 low 13 Most 9 great 6 close 5 strong 3 large 2 young 2 old 2 fast 2 early 2 Least 2 AuNPs 1 hot 1 dry 1 cold Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 154 most 29 least 4 well Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 8 doi.org 4 www.ncbi.nlm.nih.gov 2 www.ebi.ac.uk 2 www.cbs.dtu.dk 2 purl.org 2 blast.ncbi.nlm.nih.gov 1 www.onehealthinitiative.com 1 www.ncbi 1 www.maff.go.jp 1 www.ibvr.org 1 www.gesetze-im-internet.de 1 www.geneious.com 1 www.enago.com 1 tree 1 rrndb.umms.med.umich.edu 1 figshare.com 1 ec.europa.eu 1 doi Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 5 http://doi.org/10 2 http://www.ebi.ac.uk/arrayexpress/ 1 http://www.onehealthinitiative.com/about.php 1 http://www.ncbi.nlm.nih.gov/nuccore/ 1 http://www.ncbi.nlm.nih.gov/nuccore 1 http://www.ncbi.nlm.nih.gov/genbank 1 http://www.ncbi.nlm.nih.gov/ 1 http://www.ncbi 1 http://www.maff.go.jp 1 http://www.ibvr.org/Services/CellCultures.aspx 1 http://www.gesetze-im-internet.de/schhalthygv/ 1 http://www.geneious.com 1 http://www.enago.com 1 http://www.cbs.dtu.dk/services/NetPhos 1 http://www.cbs.dtu.dk/services/ 1 http://tree 1 http://rrndb.umms.med.umich.edu/ 1 http://purl.org/phylo/treebase/phylows/study/TB2:S22165 1 http://purl.org/phylo/treebase/phylows/ 1 http://figshare.com/s/97bfdb8d693a8c95ffaf).Ethics 1 http://ec.europa.eu/food/animal/resources/publications_en 1 http://doi.org/10.6084/m9.figshare.12830405.v1 1 http://doi.org/10.5683/SP/BT7HN2 1 http://doi.org/10.1111/TBED.13446 1 http://doi 1 http://blast.ncbi.nlm.nih.gov/Blast.cgi 1 http://blast.ncbi.nlm.nih.gov/ Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 12 study are available 7 samples were negative 6 dogs were positive 5 pigs were positive 5 study was not 4 assay was further 4 pedv was first 3 animals were humanely 3 antibody test kit 3 calves has not 3 calves were randomly 3 cells were then 3 detection using recombination 3 dogs had only 3 dogs tested cdv 3 infection did not 3 pedv using rt 3 pigs following consumption 3 results did not 3 samples were also 3 samples were positive 3 strains containing ps 3 studies did not 3 study is available 2 antibodies were not 2 assay is less 2 assay were also 2 assays were highly 2 calves had tsp 2 data provide proof 2 disease was present 2 dog were available 2 group were significantly 2 groups did not 2 groups were lower 2 groups were significantly 2 infection is generally 2 pcr using sampling 2 pedv infected cells 2 pedv is still 2 pigs were negative 2 result is consistent 2 sampled showed clinical 2 samples collected prior 2 samples containing low 2 samples test pedv 2 samples testing positive 2 samples were pcr 2 samples were pedv 2 samples were then Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 2 result showed no seasonal 2 study are not publicly 1 analyses were not able 1 animals had no vaccination 1 data were not available 1 dogs had no history 1 dogs has not yet 1 dogs was not significant 1 groups does not necessarily 1 groups were not significant 1 pcr is not adequately 1 pigs are not probable 1 pigs had no antibody 1 result was not unexpected 1 results are not conclusive 1 results is not clear 1 sampled are not privately 1 studies indicated no differences 1 studies reported no differences 1 study was not able 1 study was not originally 1 study was not subject A rudimentary bibliography -------------------------- id = cord-316746-toen5nvr author = Alves, F. title = Canine parvovirus: a predicting canine model for sepsis date = 2020-06-15 keywords = PIRO; SIRS; dog; study summary = The possibility of stratifying and classifying septic dogs was assessed using a proposed animal adapted PIRO (Predisposition, Infection, Response and Organ dysfunction) scoring system. RESULTS: The 72 dogs enrolled in this study were scored for each of the PIRO elements, except for Infection, as all were considered to have the same infection score, and subjected to two sets of SIRS criteria, in order to measure their correlation with the outcome. The main objective of the current study was to assess the prognostic value of the presenting vital signs as well as to evaluate the possibility of stratifying and classifying septic animals according to a proposed PIRO classification system, using parvovirus infection as a natural model for sepsis study [10] . Table 1 gathers all leucocyte counts, a selection of clinical examination parameters (Temperature, Heart Rate and Respiratory Rate), all individual variables of PIRO (P=Predisposition, I=Infection, R = Response, O=Organ Dysfunction), the total PIRO score and both SIRS criteria for survivors and non-survivors dogs. doi = 10.1186/s12917-020-02417-0 id = cord-305694-qzf425lw author = Andrés-Lasheras, Sara title = Preliminary studies on isolates of Clostridium difficile from dogs and exotic pets date = 2018-03-09 keywords = PCR; clostridium; difficile summary = CONCLUSIONS: The results obtained in this study suggest the implementation of antimicrobial susceptibility surveillance programs to assess the prevalence of metronidazole resistance in dogs; molecular studies to elucidate C. difficile in canine enteric disease is still unclear due to the presence of toxigenic strains or their toxins in asymptomatic animals and the failure to reproduce CDI in healthy dogs with and without antibiotic treatment [9, 10] . difficile, molecular characterisation of the strains obtained (i.e. tpi housekeeping and toxin genes detection by PCR, identification of non-toxigenic strains, and PCR-ribotyping) and antimicrobial susceptibility testing was performed as described elsewhere [21] . Since the ribotypes found in dogs are also commonly found in humans, it is possible Fig. 2 Metronidazole susceptibility test of Clostridium difficile D24 strain after 48 h of incubation. Antibiotic resistance patterns and PCR-ribotyping of Clostridium difficile strains isolated from swine and dogs in Italy doi = 10.1186/s12917-018-1402-7 id = cord-285746-ndrja7os author = Arjin, Chaiwat title = In vitro screening antiviral activity of Thai medicinal plants against porcine reproductive and respiratory syndrome virus date = 2020-03-30 keywords = PRRSV; thai summary = title: In vitro screening antiviral activity of Thai medicinal plants against porcine reproductive and respiratory syndrome virus Therefore, we investigated the in vitro anti-PRRSV and antioxidant properties of seven Thai medicinal plants: Caesalpinia sappan Linn., Garcinia mangostana Linn., Houttuynia cordata, Perilla frutescens, Clinacanthus nutans, Phyllanthus emblica, and Tiliacora triandra. Thai medicinal plants such as Caesalpinia sappan Linn., Garcinia mangostana Linn., Houttuynia cordata, Perilla frutescens, Clinacanthus nutans, Phyllanthus emblica, and Tiliacora triandra are known to have antioxidant and antiviral activities. Therefore, the aim of this study was to determine the antiviral activities of Thai medicinal plant extracts against PRRSV infection in vitro and to measure their phytochemical contents to develop an alternative anti-PRRSV therapy for use in veterinary medicine. In this study, we investigated the antiviral activity of seven Thai medicinal plant extracts against PRRSV by assessing the inhibition of PRRSV infection and replication in MARC-145 cells. doi = 10.1186/s12917-020-02320-8 id = cord-292033-zkwiag7a author = Balboni, Andrea title = Molecular analysis of carnivore Protoparvovirus detected in white blood cells of naturally infected cats date = 2018-02-05 keywords = CPV; FPV; dna summary = Detection of FPV and CPV variants in apparently healthy cats and their persistence in white blood cells (WBC) and other tissues when neutralising antibodies are simultaneously present, suggest that parvovirus may persist long-term in the tissues of cats post-infection without causing clinical signs. CONCLUSIONS: The identification of FPV and CPV DNA in the WBC of asymptomatic cats, despite the presence of specific antibodies against parvoviruses, and the high genetic heterogeneity detected in one sample, confirmed the relevant epidemiological role of cats in parvovirus infection. Furthermore, the ability of FPV and CPV to persist in the peripheral blood mononuclear cells (PBMC) of cats irrespective of the presence of neutralising antibodies [13] [14] [15] [16] [17] and the presence of parvoviral DNA in the bone marrow of healthy cats [18] , suggests that parvovirus may persist long term in the tissues of cats post-infection without causing clinical signs. doi = 10.1186/s12917-018-1356-9 id = cord-294559-u0r7oh9z author = Bian, Hongfen title = A new immunochromatographic assay for on-site detection of porcine epidemic diarrhea virus based on monoclonal antibodies prepared by using cell surface fluorescence immunosorbent assay date = 2019-01-18 keywords = China; ICA; PEDV; new summary = title: A new immunochromatographic assay for on-site detection of porcine epidemic diarrhea virus based on monoclonal antibodies prepared by using cell surface fluorescence immunosorbent assay For rapid detection of PEDV, a new immunochromatographic assay (ICA) based on monoclonal antibodies (mAbs) was developed in this study. To compare its accuracy to other traditional detection methods, 27 swine stool samples from south of China were investigated with the new developed ICA, commercial strip and RT-PCR. Relying on signals emitted from gold nanoparticles labeled mAb (AuNPs-mAb), a new ICA was developed for sensitive, specific and on-site detection of PEDV in swine stool in China. They were capture and detection mAb, the size of gold nanoparticles, the type of sample pad, the type of conjugate pad, the type of Nitrocellulose membrane, the type of absorbent pad, the amount of tween-20 addition and the spray volume of AuNPs-mAb. The optimization methods are shown in the supplemental materials. doi = 10.1186/s12917-019-1773-4 id = cord-340152-b4vg33ap author = Bonelli, F. title = Oral administration of chestnut tannins to reduce the duration of neonatal calf diarrhea date = 2018-07-28 keywords = DDE; tannin summary = The aim of this study was to evaluate the effect of the oral administration of chestnut tannins (Castanea sativa Mill.) in order to reduce the duration of calf neonatal diarrhea. Administration of tannins in calves with diarrhea seemed to shorten the DDE in T by almost 4 days compared to C, suggesting an effective astringent action of chestnut tannins in the calf, as already reported in humans. The aim of the present study was to evaluate the effect of oral administration of chestnut tannins (Castanea sativa) in the treatment of calf neonatal diarrhea. Data concerning the weight at birth and at the third week of life, the age of diarrhea onset and the T0 fecal scores (T0-FS) recorded for both groups were assessed for normal distribution by the Shapiro-Wilk normality test and then a Mann-Whitney test was applied in order to verify differences between the two groups at the inclusion time [28] . doi = 10.1186/s12917-018-1549-2 id = cord-000820-5b29wtim author = Borriello, Giorgia title = Diversity of Salmonella spp. serovars isolated from the intestines of water buffalo calves with gastroenteritis date = 2012-10-25 keywords = Salmonella; Typhimurium; strain summary = doi = 10.1186/1746-6148-8-201 id = cord-321739-dnuu6jok author = Bowman, Andrew S title = Investigating the introduction of porcine epidemic diarrhea virus into an Ohio swine operation date = 2015-02-15 keywords = PCR; PEDV summary = The Ohio swine operation (Figure 1 ), consisting of 3 multi-site, farrow-to-finish production flows (referred to as flows A-C, each having two breed-wean sites) and a multiplier herd (referred to as D, with a single breedwean site) had no prior cases of PEDV and was determined to have effective biosecurity measures in place evidenced by the absence of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) during more than the prior seven years. Beyond the sow unit, a wean-to-finish barn in flow A that received pigs on January 10 th from both flow A breed-wean units (A1 and A2) reported loose stools on January 12 th and had confirmation of PEDV with RT-PCR positive fecal samples collected the same day. On that same day, an oral fluid sample from one of the nurseries in flow B that received pigs from both flow B breed-wean units (B1 and B2) on January 15 th , 17 th , and 20 th , 2014 tested PEDV PCR positive ( Figure 1B ). doi = 10.1186/s12917-015-0348-2 id = cord-259710-qrht9tq3 author = Burimuah, Vitus title = Molecular-based cross-species evaluation of bovine coronavirus infection in cattle, sheep and goats in Ghana date = 2020-10-27 keywords = BCoV; Ghana; RNA summary = doi = 10.1186/s12917-020-02606-x id = cord-337868-d2uvdnii author = Castanheira, Pedro title = Molecular and serological surveillance of canine enteric viruses in stray dogs from Vila do Maio, Cape Verde date = 2014-04-23 keywords = CDV; CPV; Maio; canine summary = Although a higher mortality rate is observed in animals with multiple infections with other pathogens such as CPV-2, canine adenovirus type 1 and CDV, CCoV represents per si a major infectious agent responsible for several epidemics [13, 14] . In order to detect the presence of canine viruses on Maio island, samples collected from stray dogs from Vila do Maio were tested for canine parvovirus (CPV), canine distemper virus (CDV) and canine coronavirus (CCoV), to estimate the viral prevalence in this population and investigate the role of these animals in the maintenance and potential spread of common viral pathogens. This study describes for the first time, the shedding of three common enteric canine viruses, CPV, CDV and CCoV, in 178 stray dogs from Vila do Maio, Cape Verde and reports data on CPV and CDV seroprevalence. In addition, the high mortality rates caused by CDV contribute to the low virus spread in canine populations since the animals that succumbed to infection stop shedding. doi = 10.1186/1746-6148-10-91 id = cord-343324-qriqtv0y author = Charoenkul, Kamonpan title = First detection and genetic characterization of canine Kobuvirus in domestic dogs in Thailand date = 2019-07-19 keywords = Thai; Thailand summary = Genetic and phylogenetic analyses showed that whole genomes of Thai CaKoVs were closely related to Chinese CaKoVs with highest 99.5% amino acid identity suggesting possible origin of CaKoVs in Thailand. Thai CaKoVs were genetically closely related and grouped with Chinese CaKoVs. Our result raises the concerns to vet practitioners that diarrhea in dogs due to canine Kobuvirus infection should not be ignored. The result of this study provided the first detection and genetic characterization of CaKoV isolated from domestic dogs in Thailand. We compared the nucleotide and deduced amino acid sequences of Thai CaKoVs against those of reference viruses from the US, UK, Italy, China, and Korea (Tables 2 and 3 most variable region of VP1 is position 201-243, especially proline rich region. doi = 10.1186/s12917-019-1994-6 id = cord-285714-u9kv4113 author = Chhetri, Bimal K title = Comparison of the geographical distribution of feline immunodeficiency virus and feline leukemia virus infections in the United States of America (2000–2011) date = 2013-01-05 keywords = FIV; PMR; feline summary = BACKGROUND: Although feline immunodeficiency virus (FIV) and feline leukemia virus (FeLV) have similar risk factors and control measures, infection rates have been speculated to vary in geographic distribution over North America. The proportional morbidity ratio of FIV to FeLV infection was estimated for each administrative region and its geographic distribution pattern was visualized by a choropleth map. The proportional morbidity ratio (PMR) of FIV to FeLV infection was estimated for each administrative region and a choropleth disease map was used to visualize the spatial pattern of PMR. Areas of relative FIV excess identified by the spatial scan statistic were visualized by highlighting the boundaries of the states included in the most likely cluster on a choropleth map of the PMR of FIV to FeLV infection. In this study we have identified geographical patterns in the distribution of the proportional morbidity ratio of FIV to FeLV infection among cats in the 49 administrative regions of the US over the period 2000 to 2011. doi = 10.1186/1746-6148-9-2 id = cord-346467-a0r4xh1c author = Cornelissen, Jan B. W. J. title = Mycoplasma detection by triplex real-time PCR in bronchoalveolar lavage fluid from bovine respiratory disease complex cases date = 2017-04-08 keywords = BALF; Mycoplasma; PCR summary = title: Mycoplasma detection by triplex real-time PCR in bronchoalveolar lavage fluid from bovine respiratory disease complex cases BACKGROUND: In this study we evaluated the RespoCheck Mycoplasma triplex real-time PCR for the detection in bronchoalveolar lavage fluid (BALF) of Mycoplasma (M.) dispar, M. RESULTS: The analytical sensitivity of the RespoCheck triplex real-time PCR was, as determined by spiking experiments of the Mycoplasma strains in Phosphate Buffered Saline, 300 colony forming units (cfu)/mL for M. To enable testing of testing for BRD associated pathogens in a routine setting, real-time PCRs for detection of viral, bacterial and mycoplasma pathogens in bronchoalveolar lavage fluid (BALF) of calves have been set up by the Central Veterinary Institute (Lelystad, The Netherlands) under the name RespoCheck. In this study we used the highly conserved 16S rRNA sequence to set up the RespoCheck Mycoplasma triplex real-time PCR assay for the specific detection of M. doi = 10.1186/s12917-017-1023-6 id = cord-302425-aaxvlktp author = Cortey, Martí title = High levels of unreported intraspecific diversity among RNA viruses in faeces of neonatal piglets with diarrhoea date = 2019-12-05 keywords = RNA; RVA; RVC; virus summary = In contrast, other RNA viruses including Kobuvirus, Astrovirus, Sapovirus, Sapelovirus, Teschovirus, and Torovirus, have been detected in pig faeces but its role as causative agents of neonatal diarrhoea has not so far been fully elucidated [10] [11] [12] [13] [14] . The results reported among the 47 diarrhoeic samples analysed include representatives of 12 virus species corresponding to 8 genera of RNA viruses (Additional file 1): Kobuvirus, Rotavirus (RVA, RVB and RVC), Sapovirus (SAV), Mamastrovirus (Porcine Astrovirus types 3 -AstV3 -, 4 -AstV4 -and 5 -AstV5 -), Alphacoronavirus (PEDV), Enterovirus (Enterovirus G, EntVG), Pasivirus (PasiV) and Posavirus (PosaV). Regarding KobuV, our results also agree with an increased prevalence of this agent observed in cases of diarrhoea in suckling piglets worldwide: Brazil [22] , Korea [29] and Vietnam [30] ; despite several (See figure on previous page.) Fig. 5 Neighbor-joining phylogenetic tree based on the p-distance among the nucleotide sequences of the VP7 segment for Rotavirus B. doi = 10.1186/s12917-019-2204-2 id = cord-306502-jkqg1qal author = Dee, Scott title = An evaluation of contaminated complete feed as a vehicle for porcine epidemic diarrhea virus infection of naïve pigs following consumption via natural feeding behavior: proof of concept date = 2014-08-05 keywords = PCR; PEDV; feed summary = doi = 10.1186/s12917-014-0176-9 id = cord-308170-uqezwbzn author = Dee, Scott title = An evaluation of a liquid antimicrobial (Sal CURB®) for reducing the risk of porcine epidemic diarrhea virus infection of naïve pigs during consumption of contaminated feed date = 2014-09-25 keywords = CURB; PEDV; Sal summary = title: An evaluation of a liquid antimicrobial (Sal CURB®) for reducing the risk of porcine epidemic diarrhea virus infection of naïve pigs during consumption of contaminated feed For the purpose of a positive control, a separate group of piglets was allowed to ingest non-treated (Sal CURB®-free) feed also spiked with stock PEDV (Ct = 25.22). Clinical signs of PEDV infection (vomiting and diarrhea) and viral shedding in feces were observed in the positive control group 2–3 days post-consumption of non-treated feed. Furthermore, the results from the positive control group provide additional proof of concept regarding the ability of contaminated feed to serve as a risk factor for PEDV infection of naïve piglets. The results of this study provide initial proof of concept that the application of a liquid antimicrobial product (Sal CURB®) reduced the risk of PEDV infection through contaminated feed. doi = 10.1186/s12917-014-0220-9 id = cord-348522-r7ev9br6 author = Englund, Stina title = The occurrence of Chlamydia spp. in pigs with and without clinical disease date = 2012-01-26 keywords = Chlamydia; PCR; pig summary = By immunohistochemistry, 32 of 44 samples were positive and a significant relationship was detected between macroscopically visible intestinal lesions and a high degree of infection. The present study aimed to investigate the presence of Chlamydia spp in the intestines of growing pigs and in conjunctival swabs from finisher pigs, and relate those findings to the occurrence of clinical signs. Coronavirus was not included in the study, since Sweden has previously been shown to be free from Table 1 The findings in intestinal specimens from growing pigs with diarrhoea (case), clinically healthy control pigs from the same poor performance herds (casecontrol), and from healthy pigs originating from good performance herds (control), examined by immunohistochemistry (IHC), necropsy, and PCR. Intestinal lesions caused by a strain of Chlamydia suis in weanling pigs infected at 21 days of age doi = 10.1186/1746-6148-8-9 id = cord-271392-u6vme2c8 author = Eussen, Björn G.M. title = Stimulating collaboration between human and veterinary health care professionals date = 2017-06-13 keywords = Common; Health; Ingroup; collaboration; professional summary = RESULTS: Based on Gaertner and Dovidio''s Common Ingroup Identity Model, a number of questionnaires were designed and tested; with PROGRESS, the relation between collaboration and common goal was assessed, mediated by decategorization, recategorization, mutual differentiation and knowledge sharing. However, in terms of making room for the bigger collective goal alongside their responsibilities related to the day-to-day care of their own patients, human and veterinary healthcare professionals often see insufficient added value [14] , even though a greater awareness of the added value associated with collaboration would ultimately result in improved care [5, 15, 16] . The current study will not only indicate whether the Common Ingroup Identity Model is useful for the respective groups of healthcare professionals, but it will also quantitatively assess the relationships between the common goal and collaboration in combination with associated mediating factors. One Health as a common goal has a positive effect on collaboration between human and veterinary healthcare professionals. doi = 10.1186/s12917-017-1072-x id = cord-329148-zs18ez5q author = Geng, Yunyun title = Development of real-time recombinase polymerase amplification assay for rapid and sensitive detection of canine parvovirus 2 date = 2017-11-06 keywords = CPV-2; PCR; RPA summary = title: Development of real-time recombinase polymerase amplification assay for rapid and sensitive detection of canine parvovirus 2 With the advances in molecular detection techniques, a substantial number of gene amplification-based assays have been described for CPV-2 diagnosis such as polymerase chain reaction (PCR), nested PCR, real-time PCR, reverse-transcription loop-mediated isothermal amplification (RT-LAMP) and insulated isothermal PCR (iiPCR) [9] [10] [11] [12] [13] [14] [15] . Based on our previous study, we developed here a real-time RPA assay for simple, rapid, convenient and POC detection of CPV-2, which utilizes an exo probe and a portable, userfriendly POC tube scanner. A probit regression analysis using the results of eight complete molecular standard runs calculated that the limit of detection (LOD) of the real-time RPA was 10 1 copies per reaction in 95% of cases (Fig. 2c) , which was the same as that of the real-time PCR applied in the study (data not shown). doi = 10.1186/s12917-017-1232-z id = cord-271040-wzgjwa2z author = Giacometti, Federica title = Highly suspected cases of salmonellosis in two cats fed with a commercial raw meat-based diet: health risks to animals and zoonotic implications date = 2017-07-24 keywords = RMBD; Salmonella summary = doi = 10.1186/s12917-017-1143-z id = cord-325101-9qslo6qh author = Gizzi, Aline Baumann da Rocha title = Presence of infectious agents and co-infections in diarrheic dogs determined with a real-time polymerase chain reaction-based panel date = 2014-01-16 keywords = CPV-2; PCR summary = Although many pathogens have been individually detected with real-time polymerase chain reaction (PCR), a comprehensive panel of agents that cause diarrhea in privately owned dogs has not yet been established. Therefore, the aim of this study was to investigate pathogenic co-infections in populations of diarrheic and control owned dogs using a real-time PCR analysis of a panel of diarrhea-causing agents. The most prevalent agent involved in co-infections was canine parvovirus type 2 (CPV-2), and 21/36 (58.3%) of the diarrheic samples positive for CPV-2 were associated with others agents, most commonly with Clostridium perfringens alpha toxin (CPA), Cryptosporidium spp., and Giardia spp. The detection of individual pathogens in the panel with real-time PCR (Table 3) showed that CPA was the most prevalent pathogen in the fecal samples, infecting 40/104 (38.5%) diarrheic dogs and 6/43 (14.0%) control dogs, and the difference between the groups was highly statistically significant (P = 0.006). doi = 10.1186/1746-6148-10-23 id = cord-000518-78395e3t author = Gloster, John title = Normal variation in thermal radiated temperature in cattle: implications for foot-and-mouth disease detection date = 2011-11-21 keywords = IRT; temperature summary = doi = 10.1186/1746-6148-7-73 id = cord-336902-iptfle2b author = Harada, Kazuki title = First case of Propionibacterium acnes urinary tract infection in a dog date = 2015-12-21 keywords = UTI summary = title: First case of Propionibacterium acnes urinary tract infection in a dog Urinary tract infections are common in dogs and are typically caused by various commensal bacteria. Here we present the first case report of a urinary tract infection caused by P. CONCLUSION: To the best of our knowledge, this is the first case report of a dog with urinary tract infection caused by P. Propionibacterium acnes is an aerotolerant, anaerobic, Gram-positive, rod-shaped bacterium commonly isolated from humans. acnes has not been previously reported as a causative agent of UTI in dogs. [10] reported a case of a dog with osteomyelitis and arthritis due to Propionibacterium infection caused by a dog bite. This type has been isolated from human cases of acne and meningitis and reported in the MLST database [16] . To the best of our knowledge, this is the first case report of a dog with UTI caused by P. doi = 10.1186/s12917-015-0620-5 id = cord-298052-mbg6e2j1 author = Hardstaff, Jo L title = Livestock trade networks for guiding animal health surveillance date = 2015-04-01 keywords = Europe; animal; country summary = Very few shipments of weaned cattle, sheep and goats require a rest period of 24 hours (Additional file 1), whereas many unweaned animals would require a 24 hour break in their journey from their point of origin to their Figure 1 The outdegree is shown against the indegree for the trade of cattle for different purposes on the left column of the table and the geographical movement across Europe is shown on the right column of the table. Breeding Fattening Slaughter Other Figure 2 The outdegree is shown against the indegree for the trade of pigs for different purposes on the left column of the table and the geographical movement across Europe is shown on the right column of the table. Breeding Fattening Slaughter Other Figure 4 The outdegree is shown against the indegree for the trade of goats for different purposes on the left column of the table and the geographical movement across Europe is shown on the right column of the table. doi = 10.1186/s12917-015-0354-4 id = cord-343390-y903mxcj author = Hoppe, Ingrid Bortolin Affonso Lux title = Bovine respiratory syncytial virus seroprevalence and risk factors in non-vaccinated dairy cattle herds in Brazil date = 2018-06-27 keywords = BRSV; bovine; respiratory summary = title: Bovine respiratory syncytial virus seroprevalence and risk factors in non-vaccinated dairy cattle herds in Brazil This study aimed to characterize the epidemiology of BRSV infection in dairy cattle herds of São Paulo State, Brazil, using serological and risk factors analyses. The analysis of risk factors indicated that the age group and the occurrence of coinfection with bovine herpesvirus 1 (BoHV-1) and bovine viral diarrhea virus 1 (BVDV-1) should be associated with a higher prevalence of BRSV, while natural suckling was considered a protective factor. Due to this, the current study aimed to determine antibody prevalence against BRSV and investigate some risk factors associated with BRSV seroprevalence in herds of an important milk producing region in São Paulo State, Brazil. Bovine respiratory syncytial virus seroprevalence and risk factors in endemic dairy cattle herds Prevalence of and risk factors for bovine respiratory syncytial virus (BRSV) infection in non-vaccinated dairy and dual-purpose cattle herds in Ecuador doi = 10.1186/s12917-018-1535-8 id = cord-341141-bgrgzfoo author = Hou, Peili title = Rapid detection of infectious bovine Rhinotracheitis virus using recombinase polymerase amplification assays date = 2017-12-13 keywords = IBRV; LFD; PCR; RPA summary = In this study, we described the development of a lateral flow dipstrip (LFD) of isothermal recombinase polymerase amplification (RPA) method for rapid detection of IBRV. The assay performance on acute-phase high fever clinical samples collected from cattle with no vaccine against IBRV, which were suspected to be infected with IBRV, was validated by detecting 24 fecal, 36 blood, 38 nasal swab and 8 tissue specimens, and compared with SYBR Green I based real-time PCR. The initial agarose gel result showed that Primer set 4-2F/4-2R/ 4-2LF yielded specific amplification efficiency for the RPA assay, and produced the expected size of the product was 250 base-pairs (Fig. 1a) , while the primers/probe targeting glycoprotein gB of the IBRV genome in this study could not be used to amplify effectively in the initial screen (data not show). doi = 10.1186/s12917-017-1284-0 id = cord-001591-4ic2in3i author = Hu, Xiaoliang title = Molecular characterization and phylogenetic analysis of transmissible gastroenteritis virus HX strain isolated from China date = 2015-03-21 keywords = TGEV summary = doi = 10.1186/s12917-015-0387-8 id = cord-347664-8shnkrto author = Kang, JeongWoo title = National post-market surveillance assessment of veterinary medicines in Korea during the past decade date = 2017-05-22 keywords = Korea; veterinary summary = RESULTS: In this study, 1650 drugs for veterinary use were collected per year from each city and province in Korea and analysed for the quantity of active ingredients according to the "national post-market surveillance (NPMS) system" over the past decade. In Korea, national product quality control measures for veterinary medicine consists of pre-market government testing system (PMGTS) and the National Post-Market Surveillance (NPMS) assessment on veterinary medicine before and after the distribution. The Korea Animal and Plant Quarantine Agency (QIA) and each individual city/ province collects antibiotics, biologics and OCD currently in distribution from manufacturers, importers, and wholesalers of veterinary medicine, veterinary pharmacies, and veterinary hospitals in accordance with these testing plans. In particular, antibiotics have shown very dramatic decrease in noncompliance rates ( Table 2 ), illustrating that veterinary medicine manufacturing facilities and quality control standards have significantly improved over time [3, 4] . doi = 10.1186/s12917-017-1054-z id = cord-299988-jaekryq5 author = Karte, Claudia title = Re-emergence of porcine epidemic diarrhea virus in a piglet-producing farm in northwestern Germany in 2019 date = 2020-09-10 keywords = Germany; PEDV; porcine summary = title: Re-emergence of porcine epidemic diarrhea virus in a piglet-producing farm in northwestern Germany in 2019 After initial confirmation of PEDV by real-time RT-PCR, fecal material and small intestine samples from affected pigs were subjected to metagenomic analyses employing next-generation sequencing. Phylogenetic analyses showed high identities among the PEDV sequences obtained from samples of different animals and a close relation to recent strains from Hungary and France. After reports from Asia, that a new PEDV variant caused considerable losses [12, 13] , that highly virulent PEDV variant emerged also in the United States (US) in 2013, with swine farms experiencing explosive epidemics affecting all age classes of animals, with up to 95% mortality in suckling pigs [2, 14] . Emergence of porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences doi = 10.1186/s12917-020-02548-4 id = cord-346250-9kiekksx author = Khare, Sangeeta title = Vaccination with attenuated Salmonella enterica Dublin expressing E coli O157:H7 outer membrane protein Intimin induces transient reduction of fecal shedding of E coli O157:H7 in cattle date = 2010-07-07 keywords = Dublin; O157 summary = title: Vaccination with attenuated Salmonella enterica Dublin expressing E coli O157:H7 outer membrane protein Intimin induces transient reduction of fecal shedding of E coli O157:H7 in cattle The present study was undertaken to test the hypothesis that an adaptive mucosal immune response directed against intimin will reduce or prevent enteric colonization and fecal shedding of E. During the first 28 days, vaccinated calves shed both the vector strain and the intimin-expressing S. Calves challenged with intimin-deficient mutant bacteria do not develop diarrhea or attaching/ effacing lesions, nor are colonized to the same extent as animals infected with wild type or complemented mutant strains [20] . Fecal samples from all the calves were collected daily from day 0 to day 42 post-inoculation to determine the level of vaccine strain shedding. Immunization of cattle with a combination of purified intimin-531, EspA and Tir significantly reduces shedding of Escherichia coli O157:H7 following oral challenge doi = 10.1186/1746-6148-6-35 id = cord-287386-x8uq7499 author = Kongsted, Hanne title = Microbiological, pathological and histological findings in four Danish pig herds affected by a new neonatal diarrhoea syndrome date = 2013-10-12 keywords = diarrhoeic; herd; piglet summary = CONCLUSIONS: The results of the study supported the hypothesis that a new neonatal porcine diarrhoea was present in the investigated herds, since no known pathogen(s) or management factors could explain the diarrhoeal outbreaks. Based on the findings in the four herds the following case-definition of NNPDS was suggested: Non-haemorrhagic diarrhoea during the first week of life, without detection of known infectious pathogens, characterized by milk-filled stomachs and flaccid intestines at necropsy. The article describes the prevalence of well-known enteric pathogens in age-matched diarrhoeic-and nondiarrhoeic piglets from four herds affected by neonatal diarrhoea with no previously established laboratory conclusion. Herds were recommended by veterinary practitioners and included in accordance with the following criteria: 1) Presence of diarrhoea responding poorly to antibiotics during the first week of life (at least 30% affected litters for a period of minimum 6 months), 2) Routine vaccination of sows against ETEC and CPC, 3) Failure of preventive management interventions, 4) PRRS negative farrowing unit as demonstrated in blood samples tested by ELISA/IPT or PCR and 5) Negative results of routine diagnostic examinations for ETEC, CPC and RV in five diarrhoeic piglets aged one to four days. doi = 10.1186/1746-6148-9-206 id = cord-010648-txh19t3u author = Li, Yu-an title = Live-attenuated Salmonella enterica serotype Choleraesuis vaccine with regulated delayed fur mutation confer protection against Streptococcus suis in mice date = 2020-05-07 keywords = Choleraesuis summary = doi = 10.1186/s12917-020-02340-4 id = cord-001134-8ljgxnhf author = Lin, Chao-Nan title = Comparison of viremia of type II porcine reproductive and respiratory syndrome virus in naturally infected pigs by zip nucleic acid probe-based real-time PCR date = 2013-09-12 keywords = PCR; PRRSV; ZNA summary = doi = 10.1186/1746-6148-9-181 id = cord-344309-6c2wttxg author = Lin, Huixing title = Development and application of an indirect ELISA for the detection of antibodies to porcine epidemic diarrhea virus based on a recombinant spike protein date = 2018-08-20 keywords = ELISA; PEDV summary = title: Development and application of an indirect ELISA for the detection of antibodies to porcine epidemic diarrhea virus based on a recombinant spike protein In this study, an indirect enzyme-linked immunosorbent assay (ELISA) based on the recombinant truncated spike (S) protein of PEDV was developed and validated. This indirect ELISA was compared to indirect immunoinfluscent assay (IFA), and the overall coincidence rate was 96.74% based on testing 368 clinical serum samples with different PEDV antibody levels. Finally, the S1 indirect ELISA was applied to detect serum antibodies of 3304 field samples collected from different pig farms in eastern China, and it presented an overall substantial agreement on the PEDV infection status. Therefore, this study selected a gene fragment within the S1 subunit as a coating antigen to develop an indirect enzyme-linked immunosorbent assay (ELISA) method for the detection of PEDV antibodies. Detection of antibodies against porcine epidemic diarrhea virus in serum and colostrum by indirect ELISA doi = 10.1186/s12917-018-1570-5 id = cord-253308-wgseqk4t author = Liu, Chang title = PCV cap proteins fused with calreticulin expressed into polymers in Escherichia coli with high immunogenicity in mice date = 2020-08-27 keywords = CRT; Cap; PCV2; group summary = doi = 10.1186/s12917-020-02527-9 id = cord-343165-la5sy0vq author = Liu, Chuanmin title = Nitric oxide-generating compound GSNO suppresses porcine circovirus type 2 infection in vitro and in vivo date = 2017-02-21 keywords = GSNO; PK-15; pcv2 summary = This study was conducted to investigate the antiviral activity of NO generated from S-nitrosoglutathione (GSNO), during PCV2 infection of PK-15 cells and BALB/c mice. NO strongly inhibited PCV2 replication in PK-15 cells, and the antiviral effect was reversed by Hb. An in vivo assay indicated that GSNO treatment reduced the progression of PCV2 infection in mice, evident as reductions in the percentages of PCV2-positive sera and tissue samples and in the viral DNA copies in serum samples. CONCLUSIONS: Our data demonstrate that the NO-generating compound GSNO suppresses PCV2 infection in PK-15 cells and BALB/c mice, indicating that NO and its donor, GSNO, have potential value as antiviral drugs against PCV2 infection. The antiviral activity of GSNO was determined from the appearance of PCV2-infected cells, viral titers, and PCV2 DNA copy numbers. In this study, we verified the antiviral activity of the NOgenerating compound GSNO during PCV2 infection in PK-15 cells and BALB/c mice. doi = 10.1186/s12917-017-0976-9 id = cord-275512-7yik78yc author = Lojkić, Ivana title = Detection and molecular characterisation of bovine corona and toroviruses from Croatian cattle date = 2015-08-13 keywords = bovine; respiratory summary = doi = 10.1186/s12917-015-0511-9 id = cord-345516-fgn7rps3 author = Miller, Laura C title = Analysis of the swine tracheobronchial lymph node transcriptomic response to infection with a Chinese highly pathogenic strain of porcine reproductive and respiratory syndrome virus date = 2012-10-30 keywords = PRRSV; TBLN; gene; vr-2332 summary = title: Analysis of the swine tracheobronchial lymph node transcriptomic response to infection with a Chinese highly pathogenic strain of porcine reproductive and respiratory syndrome virus Emergence in 2006 of a novel highly pathogenic PRRSV (HP-PRRSV) isolate in China necessitated a comparative investigation into the host transcriptome response in tracheobronchial lymph nodes (TBLN) 13 days post-infection with HP-PRRSV rJXwn06, PRRSV strain VR-2332 or sham inocula. Gene IDs and log2 fold-change expression values for significant hits, that had FPKM values in both the control and the infected differential expression testing for transcripts (Cuffdiff output files), were then analyzed using the Ingenuity Pathway Analysis software. doi = 10.1186/1746-6148-8-208 id = cord-301175-6alsigxk author = Okda, Faten title = Development of an indirect ELISA, blocking ELISA, fluorescent microsphere immunoassay and fluorescent focus neutralization assay for serologic evaluation of exposure to North American strains of Porcine Epidemic Diarrhea Virus date = 2015-08-01 keywords = ELISA; FFN; FMIA; PEDV summary = title: Development of an indirect ELISA, blocking ELISA, fluorescent microsphere immunoassay and fluorescent focus neutralization assay for serologic evaluation of exposure to North American strains of Porcine Epidemic Diarrhea Virus Therefore, the objective of this study was to develop and validate multiple improved serological assays for PEDV, including an indirect ELISA (iELISA); a highly specific monoclonal antibody-based blocking ELISA (bELISA); fluorescent microsphere immunoassays (FMIA) that can be multiplexed to monitor exposure to multiple antigens and pathogens simultaneously; and a fluorescent focus neutralization assay (FFN) to measure functional virus neutralizing antibodies. RESULTS: A recombinant North American nucleoprotein (NP) based iELISA was developed and validated along with a bELISA using newly developed PEDV-NP specific biotinylated monoclonal antibodies (mAbs) and an FMIA using magnetic beads coupled with expressed NA PEDV-NP. In this study, we report the adaptation of a recombinant, highly purified, NA PEDV-NP antigen to the development of iELISA, bELISA and FMIA platforms for the detection of PEDV antibodies in serum. doi = 10.1186/s12917-015-0500-z id = cord-346685-kldpmws7 author = Pan, Qing title = Co-infection of broilers with Ornithobacterium rhinotracheale and H9N2 avian influenza virus date = 2012-07-02 keywords = H9N2; ORT; Shandong/2011 summary = Typical pneumonia and airsacculitis were observed both in broilers inoculated intraperitoneally with an ORT isolate alone and in those co-infected with ORT and H9N2 virus isolates. In the current report, we present the characterisation of ORT and H9N2 isolates obtained from co-infected broilers, with the objective of understanding the aetiology of severe avian pneumonia. Broilers inoculated intraperitoneally with ORT/chicken/Shandong/2011 alone displayed pneumonia and typical airsacculitis, and coinfection of the broilers with ORT and H9N2 virus isolates induced higher mortality than infection with ORT or H9N2 virus alone. The results of this study strongly suggest that co-infection with ORT and H9N2 virus is responsible for the current severe pneumonia with high mortality in broilers of China. However, the birds infected with the ORT isolated in this study had a 50% mortality rate, and a co-infection with the H9N2 virus resulted in 70% death. Co-infection of broilers with Ornithobacterium rhinotracheale and H9N2 avian influenza virus doi = 10.1186/1746-6148-8-104 id = cord-303012-qbkkhfcb author = Paris, Jasmin K title = Enteropathogen co-infection in UK cats with diarrhoea date = 2014-01-12 keywords = Giardia; figure summary = We studied enteropathogen co-infection in diarrhoeic UK cats using results of a real time PCR assay for 8 enteropathogenic species; feline coronavirus (Co), feline panleukopenia virus (Pa), Clostridium perfringens (Cl), Salmonella enterica (Sa), Giardia spp. The primary objective of this study was therefore to identify and describe feline enteropathogen co-infection in a large population of diarrhoeic UK cats using the results obtained from the same PCR assay used in [12] for a panel of 8 enteropathogens (feline coronavirus, feline panleukopenia virus, Clostridium perfringens, Salmonella enterica, Giardia spp., T. Target genes for enteropathogen detection using real-time PCR were as follows: feline coronavirus 7b gene (DQ010921.1), feline panleukopenia virus VP2 gene (EU252145), Clostridium perfringens alpha toxin gene (AM888388), Salmonella enterica invasion A gene (EU348366), Giardia smallsubunit rRNA gene (DQ836339), Tritrichomonas foetus 5.8S rRNA gene (AF339736), Cryptosporidium smallsubunit rRNA gene (A093489), and Toxoplasma gondii internal transcribed spacer-1 gene (L49390). doi = 10.1186/1746-6148-10-13 id = cord-355991-4zu69e0y author = Piñeyro, Pablo Enrique title = First retrospective studies with etiological confirmation of porcine transmissible gastroenteritis virus infection in Argentina date = 2018-09-24 keywords = Fig; IHC; PEDV; TGEV summary = The epidemiological and clinical presentations of outbreaks of neonatal mortality associated with enteritis and the detection of TGEV started in the gestation units. When TGEV enters in a naïve herds, an epizootic form characterized by a 100% mortality of pre-weaning piglets due to diarrhea and dehydration is normally observed [1, 14] . In this study, although all cases were selected using clinical features and epidemiological information, the histological evaluation consistently showed lesions compatible with viral infection. The application of IHC and ISH-RNA on archived paraffin blocks from cases of neonatal diarrhea with high morbidity and mortality allowed retrospective identification of TGEV infection. During the period when the sows showed gastro-enteric clinical signs, 2-to 4-day-old piglets presented vomiting (75-80%) and diarrhea (90%), and the mortality rate of suckling pigs reached 90%. Emergence of porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences doi = 10.1186/s12917-018-1615-9 id = cord-000870-qdfrjvu1 author = Pomorska-Mól, Małgorzata title = C-reactive protein, haptoglobin, serum amyloid A and pig major acute phase protein response in pigs simultaneously infected with H1N1 swine influenza virus and Pasteurella multocida date = 2013-01-18 keywords = SAA; SIV summary = doi = 10.1186/1746-6148-9-14 id = cord-326770-yoefyowv author = Sayama, Yusuke title = A seroepidemiologic study of Reston ebolavirus in swine in the Philippines date = 2012-06-18 keywords = Philippines; REBOV summary = METHODS: A total of 215 swine sera collected at two REBOV-affected farms in 2008, in Pangasinan and Bulacan, were tested for the presence of REBOV-specific antibodies using multiple serodiagnosis systems. In the IFA, none of the 49 swine sera collected in Japan showed a positive reaction (data not shown), and so they were considered to be REBOV-NP and -GP antibody negative. In the IFA specific to REBOV-NP, antibody positive swine sera showed characteristic granular staining patterns in the cytoplasm ( Figure 1A ), which were indistinguishable from those of REBOV-infected cynomolgus monkey sera [18] and REBOV-NP immunized rabbit sera (data not shown). In total, 158 (73.5%) and 169 (78.6%) of the 215 swine sera collected at the affected farms were REBOV-NP and -GP antibody positive in the IFA, respectively (Table 1) . In total, 177 (82.3%) and 165 (76.7%) of the 215 swine sera collected at the affected farms were REBOV-NP and -GP antibody positive in the IgG-ELISA, respectively (Table 1) . doi = 10.1186/1746-6148-8-82 id = cord-002087-o8kffjw0 author = Shi, Xibao title = Nonstructural protein 11 (nsp11) of porcine reproductive and respiratory syndrome virus (PRRSV) promotes PRRSV infection in MARC-145 cells date = 2016-06-06 keywords = PRRSV; nsp11 summary = title: Nonstructural protein 11 (nsp11) of porcine reproductive and respiratory syndrome virus (PRRSV) promotes PRRSV infection in MARC-145 cells RESULTS: Here, we firstly explored the effect of over-expression of nsp11 on PRRSV infection and found that over-expression of nsp11 enhanced the PRRSV titers while the small interfering RNA (siRNAs) specifically targeting nsp11 could reduce the PRRSV titers in MARC-145 cells. Abbreviations EAV, equine arteritis virus; GAPDH, Glyceraldehyde-3-phosphate dehydrogenase; GFP-nsp11, pcDNA 3.1-GFP-nsp11; MHV, mouse hepatitis virus; MOI, multiplicity of infection; NLRP3, NLR family pyrin domain-containing 3; nsp11, nonstructural protein 11; ORF, open reading frame; PRRSV, porcine reproductive and respiratory syndrome virus ; PVDF, polyvinylidene difluoride; qRT-PCR, quantitative real-time RT-PCR; RNAi, RNA interference; siRNA, small interfering RNA; TCID50, 50 % tissue culture infected dose Identification of two auto-cleavage products of nonstructural protein 1 (nsp1) in porcine reproductive and respiratory syndrome virus infected cells: nsp1 function as interferon antagonist doi = 10.1186/s12917-016-0717-5 id = cord-344297-qqohijqi author = Smith, Jacqueline title = The early immune response to infection of chickens with Infectious Bronchitis Virus (IBV) in susceptible and resistant birds date = 2015-10-09 keywords = IBV; gene; infection; line; response summary = title: The early immune response to infection of chickens with Infectious Bronchitis Virus (IBV) in susceptible and resistant birds RESULTS: Genes and biological pathways involved in the early host response to IBV infection were determined andgene expression differences between susceptible and resistant birds were identified. [18] we used Affymetrix wholegenome chicken microarrays to examine the tracheal gene expression profiles of a line of birds known to be susceptible to IBV infection (line 15I) and a line known to show resistance (line N). Gene expression differences found in the susceptible 15I line between infected and control birds over days 2, 3 and 4 post infection were analysed, with a view to examining the innate host response to infection by IBV. Gene expression seen during the host response to IBV infection in the trachea of susceptible birds. Genes found to be differentially expressed between susceptible and resistant lines in response to IBV infection in the trachea. doi = 10.1186/s12917-015-0575-6 id = cord-350364-kcl401xb author = Soares Magalhães, Ricardo J title = Associations between attributes of live poultry trade and HPAI H5N1 outbreaks: a descriptive and network analysis study in northern Vietnam date = 2010-02-22 keywords = H5N1; LBM; LPT; Vietnam summary = The objective of the present study is to better understand the flow of live poultry, as investigated in a poultry trade network of northern Vietnam, and explore its potential role in the risk for HPAI H5N1 introduction and spread and the resulting implications for disease control policies. The network is very fragmented with 30 components, but there is a highly connected core of communes, consisting of a giant weak component and a sparse periphery (containing numerous Table 1 Attributes of "sell only" and "buy and sell" live poultry traders operating in all (total of 12) authorised live bird markets serving the Northern provinces of Vietnam. In particular, our analyses indicate that new LPT''s (i.e. those trading for less than a year) and those operating in authorised retail LBM''s have increased odds of sourcing poultry from flocks located in communes with past history of H5N1 outbreaks during 2003 to 2006, when compared to older LPT''s (i.e. those trading for more than a year) and to those operating in wholesale markets. doi = 10.1186/1746-6148-6-10 id = cord-333477-slcvbzt9 author = Sugita, Koji title = Oral faecal microbiota transplantation for the treatment of Clostridium difficile-associated diarrhoea in a dog: a case report date = 2019-01-07 keywords = fmt summary = title: Oral faecal microbiota transplantation for the treatment of Clostridium difficile-associated diarrhoea in a dog: a case report BACKGROUND: Successful clinical outcomes of faecal microbiota transplantation (FMT) for recurrent Clostridium difficile infection have been reported in humans and a marmoset. Four months prior to the current presentation, a faecal sample of the dog was subjected to real-time PCR analysis (IDEXX Laboratories, Inc., Tokyo, Japan) for Cryptosporidium spp., Giardia spp., Clostridium perfringens α toxin, Clostridium difficile toxin A&B, Campylobacter jejuni, Campylobacter coli, Salmonella spp., Canine parvovirus type 2, canine distemper virus and canine enteric coronavirus genes by a veterinary practitioner; a positive reaction for Campylobacter jejuni was detected in the analysis. difficile antigen and toxin A&B genes and proteins turned into negative, and stool consistency and frequency and faecal blood and mucus became normal after oral FMT in a dog with large bowel diarrhoea. doi = 10.1186/s12917-018-1754-z id = cord-355465-qjtifwhd author = Van Diep, Nguyen title = Molecular characterization of US-like and Asian non-S INDEL strains of porcine epidemic diarrhea virus (PEDV) that circulated in Japan during 2013–2016 and PEDVs collected from recurrent outbreaks date = 2018-03-14 keywords = Japan; PEDV; japanese summary = title: Molecular characterization of US-like and Asian non-S INDEL strains of porcine epidemic diarrhea virus (PEDV) that circulated in Japan during 2013–2016 and PEDVs collected from recurrent outbreaks RESULTS: Phylogenetic analysis based on S gene sequences revealed that all the recent field PEDVs were genetically distinct from the classical Japanese strains, and were classified into three genotypes: North American (NA), S INDEL, and Asian non-S INDEL. Another subclade, designated as PED-J2, including 14 Japanese strains collected in Miyazaki were also clustered into a segregated branch as shown in Fig. 1 The sequence data revealed that S genes from the Japanese field PEDVs are of 4152-4161 nt long, and encode proteins with 1381-1386 aa residues. Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene doi = 10.1186/s12917-018-1409-0 id = cord-337354-ky8mq4y0 author = Velasquez-Munoz, Ana title = Effect of prebiotic supplementation with stabilized rice bran in milk of pre-weaned organic Holstein calves date = 2019-02-07 keywords = CTR; SRB; calf summary = The objective of this study was to evaluate the effect of prebiotic supplementation with stabilized rice bran (SRB) in milk on health, immunity, and performance of pre-weaned organic dairy calves. CONCLUSIONS: These results indicated that the dietary addition of SRB in milk did not have an effect in health, immunity or performance of pre-weaned dairy calves. We hypothesized that the addition of SRB in milk of pre-weaned calves would reduce the presentation and severity of neonatal diarrhea, improving the immune response and consequently the overall calf performance. The addition of prebiotics via SRB into milk starting at 6-7 days of age was assessed for effects on health and performance of pre-weaned organic dairy calves over a 28 days period. The major finding from this study was that the addition of SRB in the milk of newborn calves for 28 days did not enhance performance, health, or immunity during the first month of life, a period characterized for the presentation of digestive diseases. doi = 10.1186/s12917-019-1802-3 id = cord-332572-9h26mj7w author = Wang, Jinfeng title = Development and validation of the isothermal recombinase polymerase amplification assays for rapid detection of Mycoplasma ovipneumoniae in sheep date = 2020-06-01 keywords = LFS; RPA summary = title: Development and validation of the isothermal recombinase polymerase amplification assays for rapid detection of Mycoplasma ovipneumoniae in sheep ovipneumoniae DNA was detected in 29 samples in the real-time RPA, 31 samples in the LFS RPA and 32 samples in the real-time PCR assay. In this study, a real-time RPA assay using the exo probe and a LFS RPA assay using the nfo probe combined with lateral flow strip were developed for rapid, specific and sensitive detection of M. ovipneumoniae DNA was detected in 29 (26.12%), 31 (27.93%) and 32 (28.83%) samples by the real-time RPA, LFS RPA and real-time PCR, respectively (Table 1 ). The real-time RPA and LFS RPA assays demonstrated the comparable performance in detecting the 111 sheep clinical samples. The developed real-time RPA and LFS RPA assays are highly specific and sensitive for detection of M. doi = 10.1186/s12917-020-02387-3 id = cord-003587-zminzrov author = Wang, Xueyu title = Visual detection of porcine epidemic diarrhea virus using a novel reverse transcription polymerase spiral reaction method date = 2019-04-15 keywords = PEDV; PSR summary = title: Visual detection of porcine epidemic diarrhea virus using a novel reverse transcription polymerase spiral reaction method The aim of this study was to establish a novel reverse transcription polymerase spiral reaction (RT-PSR) assay for the rapid detection of porcine epidemic diarrhea virus (PEDV). This new method for PEDV detection was 10 times more sensitive than the conventional reverse transcription-polymerase chain reaction (RT-PCR) assay. To decrease the time required for PEDV detection, PCR-related methods focused on the amplification of viral nucleic acids have been developed, which have been shown to be more efficient, highly sensitive and specific, even at different stages of the disease, when compared to immunological diagnostic methods. The polymerase spiral reaction (PSR) [14] is a novel nucleic acid isothermal amplification method that has the advantages of simplicity, rapidity, accuracy, and low cost when compared to conventional PCR. doi = 10.1186/s12917-019-1851-7 id = cord-346457-2mq2aije author = Wang, Zhilin title = Rapid differentiation of PEDV wild-type strains and classical attenuated vaccine strains by fluorescent probe-based reverse transcription recombinase polymerase amplification assay date = 2020-06-22 keywords = PEDV; RPA summary = RESULTS: In the study, a differential one-step quantitative real-time fluorescent reverse transcription recombinase polymerase amplification (real-time RT-RPA) method based on the PEDV universal real-time RT-RPA assay was established according to the ORF1 deletion sequences of three classical attenuated vaccine strains (PEDV attenuated vaccine KC189944, attenuated CV777 and DR13) and five Vero cell-adapted isolates (JS2008, SDM, SQ2014, SC1402, HLJBY), which could effectively differentiate PEDV classical attenuated vaccine strains from wild-type strains (PEDV classical wild strains and variant strains). The detection limits of PEDV RNA in the both PEDV real-time RT-RPA assays were 300 copies within 20 min at 39 °C, and the detection limits of classical attenuated vaccine strain CV777, Vero-cell-adapted isolate JS2008, and PEDV wild-type strain DX were 10(0.5) TCID(50)/100 μL, 10(1.1) TCID(50)/100 μL, and 10(1.2) TCID(50)/100 μL, respectively. CONCLUSION: This RPA method we developed is simple, time-effective, and safe and provides a reliable technical tool for the differential diagnosis and clinical epidemic surveillance of PEDV classical attenuated vaccine strains and wild-type strains. doi = 10.1186/s12917-020-02424-1 id = cord-279551-py2awuav author = Willi, Barbara title = Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland date = 2015-07-16 keywords = CDV; PCR; Switzerland; dog; table summary = title: Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland In the present study, we describe a distemper outbreak in 15 rescue dogs that were imported from Hungary to Switzerland by an animal welfare organisation. Canine distemper virus (CDV) is one of the most important viral pathogens in domestic dogs and causes high morbidity and mortality worldwide, particularly in unvaccinated dogs or dogs with incomplete vaccination [1] . The study provides data on vaccination, medical history, clinical examinations and diagnostic imaging of the dogs and CDV testing, testing for canine parvovirus (CPV) and vector-borne infections. The vaccine-specific real-time reverse transcription (RT)quantitative (q)PCR was negative for all ten dogs that were tested, which supports the finding of infection with a wild-type CDV strain. doi = 10.1186/s12917-015-0471-0 id = cord-260348-83ftjqev author = Xu, Yinlan title = Cepharanthine and Curcumin inhibited mitochondrial apoptosis induced by PCV2 date = 2020-09-18 keywords = Cepharanthine; Curcumin; PCV2; ROS summary = The results of qPCR and Western blot showed that, compared with the PCV2 infected group, the expression of Cap in Paeonol (0.4 mg/mL and 0.2 mg/mL), Cepharanthine (0.003 mg/mL, 0.0015 mg/mL and 0.00075 mg/mL) and Curcumin (0.02 mg/mL, 0.001 mg/mL and 0.005 mg/mL) treated groups were significantly lowered in a dose-dependent manner. The results of Annexin V-FITC/PI, JC-1, Western blot and ROS analysis showed that the expression of cleaved caspase-3 and Bax were up-regulated Bcl-2 was down-regulated in Cepharanthine or Curcumin treated groups, while ROS and MMP value were decreased at different degrees and the apoptosis rate was reduced. The results showed that Compared to the PCV2-infected group, the cell apoptosis rates were significantly decreased in the group treated with Cepharanthine, Curcumin or Ribavirin, demonstrating a dose-dependent response except the group of 0.005 mg/mL Paeonol (P < 0.05) ( Fig. 3a and b). doi = 10.1186/s12917-020-02568-0 id = cord-003208-lwirkob3 author = Yan, Liping title = Novel protein chip for the detection of antibodies against infectious bronchitis virus date = 2018-09-17 keywords = ELISA; IBV; RDT summary = RESULTS: We have developed two indirect microarray methods to detect antibodies against IBV: a chemiluminescent immunoassay test (CIT) and a rapid diagnostic test (RDT). Compared with these methods, enzyme-linked immunosorbent assay (ELISA) has been widely used for testing IBV early infection and continuous infection, and this technique can be used for both antigenic and antibody detection. The data showed that 130 serum samples were positive for antibodies against IBV, and 14 samples were negative, similar to the results of the IDEXX IBV Ab Test kit with the nsp5 concentration of 0.2 mg/mL (Table 4 ). The specific experiments of the RDT showed that no cross-reaction Fig. 4 a Distribution of the SNRs of the IDEXX-positive (n = 142) and IDEXX-negative (n = 42) serum samples of the clinical sera obtained from the IBV protein microarray. doi = 10.1186/s12917-018-1586-x id = cord-261446-ro1wm0kf author = Yang, Yifei title = Fatal disease associated with Swine Hepatitis E virus and Porcine circovirus 2 co-infection in four weaned pigs in China date = 2015-03-26 keywords = China; HEV; PCV2 summary = doi = 10.1186/s12917-015-0375-z id = cord-313445-4v7pjqt2 author = Zhao, Jun title = Porcine interferon lambda 3 (IFN-λ3) shows potent anti-PRRSV activity in primary porcine alveolar macrophages (PAMs) date = 2020-10-28 keywords = IFN; PRRSV summary = title: Porcine interferon lambda 3 (IFN-λ3) shows potent anti-PRRSV activity in primary porcine alveolar macrophages (PAMs) In addition, IFN-λ3 in our study was able to induce the expression of interferon-stimulated genes 15 (ISG15), 2′-5′-oligoadenylate synthase 1 (OAS1), IFN-inducible transmembrane 3 (IFITM3), and myxoma resistance protein 1(Mx1) in primary PAMs. CONCLUSIONS: IFN-λ3 had antiviral activity against PRRSV and can stimulate the expression of pivotal interferon-stimulated genes (ISGs), i.e., ISG15, Mx1, OAS1, and IFITM3. The virus titre was significantly reduced with the increase of IFN-λ3 treatment dose (10, Fig. 1 The CPE of primary PAMs treated with Porcine IFN-λ3 and infected with PRRSV. The expression of mRNA for ISG15, Mx1, OAS1, and IFIT M3 was up-regulated by 70, 70, 160, and 15 times respectively at the concentration of 1000 ng/ml in primary PAMs. As shown in Fig. 3e and f (The full-length blots are presented in Supplementary file 2), a dosedependent induction of the antiviral proteins ISG15, Mx1 and OAS1 has been observed in primary PAMs treated with IFN-λ3. doi = 10.1186/s12917-020-02627-6