# ent

id: cord-010053-kniq2mbw
type: PROTEIN
entity:
  truncated S cytoplasmic tail 0 100 0 nsp10 405 100 0 100 0 100 0 100 0 100 0 100 0 99 2 1 nsp11 54 100 0 100 0 100 0 100 0 100 0 100 0 100 0 nsp12


id: cord-260212-m80dkzm4
type: DNA
entity:
  nucleocapsid protein coding gene PDCoV 587F 5 0 CCCAGCTCAAGGTTTCAGAG 3 0 PDCoV 587R 5 0 CCC AATCCTGTTTGTCTGCT 3 0


id: cord-274773-3jhka8wl
type: PERSON
entity:
  Zhang Jialin Chen Jianfei Liu Ye Da Shi Shi Hongyan Zhang Xin Liu Jianbo Cao Liyan Zhu Xiangdong Wang Xiaobo


id: cord-289584-rbp7p8s9
type: PROTEIN
entity:
  PDCoV CHJXNI2 2015 KR131621 1 Porcine coronavirus HKU15 strain HKU15 44 NC016990 Bulbul coronavirus HKU11 796


id: cord-294698-mtfrbn87
type: DISEASE
entity:
  acute respiratory syndrome coronavirus SARS CoV Middle East respiratory syndrome coronavirus MERS CoV Nipah


id: cord-294698-mtfrbn87
type: DISEASE
entity:
  acute respiratory syndrome coronavirus SARS CoV Middle East respiratory syndrome coronavirus MERS CoV Nipah virus Hendra virus and Ebola virus


id: cord-294021-x8avmtef
type: DNA
entity:
  5 untranslated region UTR replicase ORF 1ab spike gene S envelope gene E membrane gene M nonstructural gene 6


id: cord-294021-x8avmtef
type: DISEASE
entity:
  Pérez Rivera Claudia Ramírez Mendoza Humberto Mendoza Elvira Susana Segura Velázquez Rene Sánchez Betancourt José


id: cord-317455-6qx0v28w
type: PROTEIN
entity:
  European Turkey coronavirus XIIIth Nidovirus 2014 Symposium p 104 Salamanca Spain First complete genome sequence


id: cord-318237-22s13v2y
type: PROTEIN
entity:
  cord 318237 22s13v2y authors Mira Francesco Purpari Giuseppa Di Bella Santina Colaianni Maria Loredana Schirò Giorgia Chiaramonte Gabriele Gucciardi Francesca Pisano Patrizia Lastra Antonio Decaro Nicola Guercio Annalisa title Spreading


id: cord-302819-oj33i2ma
type: DNA
entity:
  PEDS mod 1581 F 5 0 CCAACCTTATTGCATCT GAC 3 0 map positions 22214 22233 and S R1 5 0 CAT CTT TGACAACTGTGT 3 0 map positions 24825 24842


id: cord-331932-oujdl459
type: DISEASE
entity:
  respiratory syndrome virus PRRSV influenza A virus porcine circovirus type 2 porcine respiratory corona virus four bacteria Mycoplasma


id: cord-352211-3ps5o8ji
type: DNA
entity:
  primers PDCoV S1 5 0 ATGCAGAGAGCTCTATTG 3 0 and 5 0 TATTT CAACTTCGCCATC 3 0 PDCoV S2 5 0 CGACCATCCATAGTTTCA 3 0 and PDCoV S2 5 0 CTACCATTCCTTAAACTT 3 0 and PDCoV N 5 0 ATGGCCGCACCAGTAGTC 3 0 and 5 0 CTACGCTGCTGATTCCTG 3 0


id: cord-326596-8ux1q9xw
type: PROTEIN
entity:
  nucleocapsid protein NP 128 1 525 1 398 nt phosphoprotein P 1 687 2 979 1 293 nt matrix protein M 3 235 4 335 1 101 nt fusion protein F 4 265 1 668 nt or 4 265 1 638 nt 7 963 or 7 957 1 842 nt and large polymerase protein L 9 278 16 003 or 9 272 15 997 6 726 nt In addition the small hydrophobic protein SH 6 970 or 6 964 429 nt that AAvV 6


id: cord-343949-zmuvq6e3
type: DNA
entity:
  Aichi virus canine kobuvirus murine kobuvirus Kathmandu sewage kobuvirus roller kobuvirus and feline kobuvirus FeKoV Adams


id: cord-284377-hsju2shr
type: PROTEIN
entity:
  cord 284377 hsju2shr authors Li Meng Zhao Lin Ma Jiajun Zhao Na Luo Jing Wang Chengmin Chen Lin Ma Guoyao


id: cord-331740-yjt3q9ph
type: CELL_LINE
entity:
  MagNA Pure LC Total Nucleic Acid Isolation kit Roche Burgess Hill West Sussex UK Nucleic acid extractions were prepared from 200 ll of sample


id: cord-331740-yjt3q9ph
type: CELL_LINE
entity:
  primer CTA TCG CCA GGG AAA TGT C IBVRT2 reverse primer GCG TCC TAG TGC TGT ACC C IBVRT3 TaqMan Ò probe FAM CCT GGA AAC GAA CGG TAG ACC CT TAMRA


id: cord-331740-yjt3q9ph
type: CHEMICAL
entity:
  MgCl 2 1 ll 10 mm dNTP mix 0 8 lm IBVRT1 primer 0 8 lm IBVRT2 primer 0 2 lm IBVRT3 TaqMan probe 0 25 ll RNasin


id: cord-331740-yjt3q9ph
type: CHEMICAL
entity:
  MgCl 2 1 ll 10 mm dNTP mix 0 4 lm of primer S1for2 0 4 lm of primer S1rev3 0 04 lm of each of the remaining primers 0 25 ll RNasin


id: cord-293082-fw7deem8
type: WORK_OF_ART
entity:
  Tracking Changes in SARS CoV 2 Spike Evidence that D614G Increases Infectivity of the COVID 19 Virus


id: cord-293082-fw7deem8
type: ORG
entity:
  Decade Long Structural Studies of SARS Coronavirus Molecular Mechanism for Antibody Dependent Enhancement of Coronavirus Entry Development


# bib

id: cord-010053-kniq2mbw
author: Lee, Sunhee
date: 2019-05-20
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7168548/
doi: 10.1111/tbed.13219
title:
  Molecular characteristics and pathogenic assessment of porcine epidemic diarrhoea virus isolates from the 2018 endemic outbreaks on Jeju Island, South Korea

abstract:
  Since the 2013–2014 incursion of the virulent G2b porcine epidemic diarrhoea virus (PEDV) pandemic strains in South Korea, frequent moderate‐scale regional outbreaks have recurred. In particular, areas of Jeju Island with extensive swine production have faced repeated epidemics since the re‐emergence in 2014. The current study reports the complete genome sequences and molecular characterization of the representative PEDV strains responsible for the 2018 endemic outbreaks on Jeju Island. All isolates were determined to belong genetically to the highly pathogenic pandemic G2b group. Full‐length genome sizes of four isolates differed from that of the G2b epidemic field strain due to insertion or deletion (DEL) mutations in the non‐structural protein (nsp)‐ or spike (S) protein‐coding regions. The 2018 Jeju isolates shared 96.7%–98.7% and 98.5%–99.4% identity at the S gene and whole‐genome levels, respectively, compared to global G2b PEDV strains. Genetic and phylogenetic analyses indicated that the 2018 isolates were closest to the 2014 G2b re‐emergent Jeju strains, but appeared to have undergone substantial rapid independent evolution. Among the isolates, a notable nsp3 DEL variant strain, KOR/KNU‐1807/2018, was isolated and propagated by continuous passages in Vero cells, and displayed typical PEDV‐induced syncytia formation. Genomic sequencing identified a unique 8‐nt DEL in the extreme C‐terminal region of the S gene at the 4th passage (KNU‐1807‐P4) compared to its original sample. This DEL resulted in the premature termination of S by nine amino acid residues (EVFEKVHVQ), which contained a KxHxx motif that is a potential endoplasmic reticulum retrieval signal. In vivo animal studies showed that variant strain KNU‐1807 had decreased virulence in suckling piglets. These results advance our knowledge regarding the genetic variation and pathogenicity of the G2b PEDV endemic strains prevalent in Jeju swine herds in South Korea.


id: cord-011411-hufxjf5p
author: Oliveira, Thalita Evani Silva
date: 2019-06-24
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7228412/
doi: 10.1111/tbed.13223
title:
  Mycoplasma bovis and viral agents associated with the development of bovine respiratory disease in adult dairy cows

abstract:
  The etiology and pathologic findings of bovine respiratory disease (BRD) in adult dairy cows (n = 35) from a commercial dairy herd in Southern Brazil were investigated. Pulmonary samples were examined for histopathologic patterns and specific features within these patterns, while immunohistochemical (IHC) assays were designed to detect the intralesional antigens of viral infectious disease agents and Mycoplasma bovis. Pneumonia was diagnosed in 91.4% (32/35) of these cases; neither pneumonia nor any of the infectious disease pathogens evaluated occurred in three cows. The presence of multiple respiratory pathogens in 75% (24/32) of these cases indicated the complex origin of pneumonia in cattle. Interstitial pneumonia, necrosuppurative bronchopneumonia and suppurative bronchopneumonia were the principal patterns of pulmonary disease identified by histopathology. The most frequent pathogens identified by IHC were bovine viral diarrhea virus (BVDV; n = 18), M. bovis (n = 16) and bovine alphaherpesvirus type 1 (BoHV‐1; n = 14), followed by bovine respiratory syncytial virus (BRSV; n = 11) and bovine parainfluenza virus type 3 (BPIV‐3; n = 5). Obliterative bronchiolitis and peribronchial lymphocytic cuffings were the characteristic histopathologic features associated with M. bovis. Necrohemorrhagic bronchitis with bronchial angiogenesis was associated with BoHV‐1. Necrotizing bronchitis and bronchiolitis were associated with BVDV, BoHV‐1 and BRSV. Ballooning degeneration of the bronchial and bronchiolar epithelia was associated with BRSV and BoHV‐1. This is the first report from Brazil that correlated the histopathologic findings of BRD with the associated infectious disease agents by immunohistochemistry. M. bovis was frequently detected in the tissues of cows with fatal pulmonary disease during this study and may be a possible primary disease pathogen associated with the development of BRD in dairy cows. Additionally, the histopathologic features identified within patterns of pulmonary disease during this investigation may be an efficient diagnostic tool to associate histopathologic findings with specific agents of BRD in dairy cows.


id: cord-253450-k7p510p4
author: keha, Abi
date: 2019-05-31
url: https://doi.org/10.1111/tbed.13228
doi: 10.1111/tbed.13228
title:
  Prevalence of a novel bovine coronavirus strain with a recombinant hemagglutinin/esterase gene in dairy calves in China

abstract:
  Bovine coronavirus (BCoV) is the causative agent of diarrhoea in newborn calves, winter dysentery in adult cattle and respiratory tract illnesses in cattle across the world. In this study, a total of 190 faecal samples from dairy calves with diarrhoea were collected from 14 farms in six Chinese provinces, and BCoV was detected in 18.95% (36/190) of the samples by reverse transcriptase polymerase chain reaction. Full‐length spike, hemagglutinin/esterase (HE), nucleocapsid and transmembrane genes were simultaneously cloned from 13 clinical samples (eight farms in four provinces), and most of the BCoV strains showed a unique evolutionary pattern based on the phylogenetic analysis of these genes. Interesting, 10 of the 13 strains were identified as HE recombinant strains, and these strains had experienced the same recombination event and carried the same recombination sites located between the esterase and lectin domain. They also shared an identical aa variant (F181V) in the R2‐loop. Moreover, 9/10 strains displayed another identical aa variant (P, S158A) in the adjacent R1‐loop of the HE gene, which differs from the other available BCoV HE sequences in the GenBank database. Our results showed that BCoV is widely circulating in dairy cattle in China, contributing to the diagnosis and control of dairy calves diarrhoea. Furthermore, a BCoV strain that carries a recombinant HE gene has spread in dairy calves in China. To the best of our knowledge, this is the first description of an HE recombination event occurring in BCoV; this is also the first description of the molecular prevalence of BCoV in China. Our findings will enhance current understanding about the genetic evolution of BCoV.


id: cord-253850-e3l5xtc2
author: Wang, M.
date: 2018-01-23
url: https://www.ncbi.nlm.nih.gov/pubmed/29363281/
doi: 10.1111/tbed.12819
title:
  Detection and genetic characterization of porcine deltacoronavirus in Tibetan pigs surrounding the Qinghai–Tibet Plateau of China

abstract:
  Porcine deltacoronavirus (PDCoV) is a recently discovered RNA virus that belongs to the family Coronaviridae and genus Deltacoronavirus. This virus causes enteric disease in piglets that is characterized by enteritis and diarrhoea. In our present investigation, 189 diarrhoeic samples were collected between July 2016 and May 2017 from Tibetan pigs inhabiting in three different provinces surrounding the Qinghai–Tibet Plateau of China. We then applied the molecular‐based method of reverse transcription polymerase chain reactions (RT‐PCRs) to detect the presence of PDCoV in collected samples, and RT‐PCR indicated that the prevalence of PDCoV was 3.70% (7/189) in Tibetan pigs. Four of 7 PDCoV‐positive pigs were monoinfections of PDCoV, three samples were co‐infections of PDCoV with porcine epidemic diarrhoea virus (PEDV), and 52 (27.51%) samples were positive for PEDV. Four strains with different full‐length genomes were identified (CHN/GS/2016/1, CHN/GS/2016/2, CHN/GS‐/2017/1 and CHN/QH/2017/1), and their genomes were used to analyse the characteristics of PDCoV currently prevalent in Tibetan pigs. We found a 3‐nt insertion in the spike gene in four strains in Tibetan pigs. Phylogenetic analysis of the complete genome and spike and nucleocapsid gene sequences revealed that these strains shared ancestors with the strain CHN‐AH‐2004, which was found in pigs from the Anhui province of China mainland. However, PDCoV strains from Tibetan pigs formed different branches within the same cluster, implying continuous evolution in the field. Our present findings highlight the importance of epidemiologic surveillance to limit the spread of PDCoV in livestock at high altitudes in China.


id: cord-260212-m80dkzm4
title: Detection and Phylogenetic Analysis of Porcine Deltacoronavirus in Korean Swine Farms, 2015
author: Lee, J. H.
date: 2016-03-10
txt: ./txt/cord-260212-m80dkzm4.txt
cache: ./cache/cord-260212-m80dkzm4.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26968326/
doi: 10.1111/tbed.12490
summary:
  In this study, faecal samples of pigs showing signs of diarrhoea (n = 681) collected from January 2013 to March 2015 were screened for the presence of porcine deltacoronavirus (PDCoV). The phylogenetic trees showed that Korean PCDoV isolates in 2014 (KNU14.04) and in 2015 (SL2, SL5) were grouped within US PDCoV cluster, but they located at different branches (highlights). For the genetic characterization, the maximum likelihood phylogenetic trees reconstructed from the S and N genes (Fig. 1a, b) showed a clear separation between Chinese and US strains of PDCoV and is similar to the previous studies (Marthaler et al., 2014; Wang et al., 2016) . Based on the S gene, the inferred ancestral amino acid changes along the nodes of the phylogeny (Fig. 2a) showed that the branches leading to Korean PDCoV isolates in 2014 and in 2015 shared 1 back substitution (node #40: Q106L, node #37: L106Q) and four unique substitutions (node #39: S697A, node #38: V550A, I669L and node #37: I1014V).

abstract:
  This study applied molecular‐based method to investigate the presence of porcine deltacoronavirus (PDCoV) in 59 commercial pig farms in South Korea. The results of RT‐PCR screening on a relatively large collection of faeces samples (n = 681) from January 2013 to March 2015 did not reveal the presence of PDCoV until the end of 2014. However, on March 2015, PDCoV‐positive samples (SL2, SL5) were detected from SL swine farm in Gyeongbuk province. The phylogenetic trees based on the complete spike‐ and nucleocapsid protein‐coding genes showed that SL2 and SL5 closely related to the US PDCoV strains rather than those in China. Thought Korean strains of PDCoV isolated in 2014 (KNU14.04) and in 2015 (SL2 and SL5) grouped within US PDCoV cluster, the reconstruction of ancestral amino acid changes suggested that they are different.


id: cord-263094-5zbzm1b0
title: Detection of influenza D virus in bovine respiratory disease samples, UK
author: Dane, Hannah
date: 2019-07-07
url: https://www.ncbi.nlm.nih.gov/pubmed/31228318/
doi: 10.1111/tbed.13273
abstract:
  Influenza D is a newly described virus of cattle, pigs and small ruminants first detected in North America during 2011. Cattle have been shown to be the main viral reservoir and mounting evidence indicates that infection with influenza D may contribute to the development of bovine respiratory disease. The virus has been detected across the United States, Europe and Asia. To date, influenza D has not been reported in the UK. During the winter and spring of 2017/2018, we performed molecular testing of cattle submitted for post‐mortem examination where respiratory disease signs were present. We detected influenza D virus in 8.7% of cases, often as the sole viral agent and always in conjunction with bacterial co‐infection with one or more agents. Viral RNA was present in both the upper and lower respiratory tract and pathological changes in lung tissues were observed alongside signs of concurrent bacterial infections. Sequencing of one UK isolate revealed that it is similar to viruses from the Republic of Ireland and Italy.


id: cord-269287-vbuepdm4
title: Nearly full‐length genome characterization of canine parvovirus strains circulating in Nigeria
author: Ogbu, Kenneth Ikejiofor
date: 2019-10-16
url: https://doi.org/10.1111/tbed.13379
doi: 10.1111/tbed.13379
abstract:
  Canine parvovirus type 2 (CPV‐2) emerged suddenly in the late 1970s as pathogen of dogs, causing a severe and often fatal gastroenteric disease. The original CPV‐2 was replaced by three antigenic variants, CPV‐2a, CPV‐2b and CPV‐2c, which to date have gained a worldwide distribution with different relative proportions. All previous studies conducted in Africa were based on partial VP2 gene sequences. The aim of this study was to provide a genome analysis to characterize the CPV strains collected in Nigeria, Africa. Rectal swab samples (n = 320) were collected in 2018 and tested by means of an immunochromatographic assay. Among the 144 positive samples, 59 were selected for further analyses using different molecular assays. The results revealed a high prevalence of CPV‐2c (91.5%) compared to the CPV‐2a variant (8.5%). The VP2 gene sequences showed a divergence from the strains analysed in 2010 in Nigeria and a closer connection with CPV strains of Asian origin. The non‐structural gene analysis evidenced amino acid changes never previously reported. The molecular analysis based on genomic sequences evidenced a geographical pattern of distribution of the analysed strains, suggesting a potential common evolutionary origin with CPV of Asian origin. This study represents the first CPV molecular characterization including all the encoding gene sequences conducted in the African continent and contributes to define the current geographical spread of the CPV variants worldwide.


id: cord-274773-3jhka8wl
author: Zhang, Jialin
date: 2019-09-30
txt: ./txt/cord-274773-3jhka8wl.txt
cache: ./cache/cord-274773-3jhka8wl.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/tbed.13369
doi: 10.1111/tbed.13369
summary:
  title: Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5‐day‐old neonatal piglets from virulent challenge High levels of IgG antibodies and NA were also detected in the serum of neonatal piglets born to immunized sows, which suggests that the antibodies were successfully transferred through the colostrum and milk. The protective efficacy of passive immunity elicited by the inactivated PDCoV vaccine against challenge with a highly pathogenic virulent strain in neonatal piglets born to immunized sows was investigated. These results suggest that within the first week, IgG antibodies in colostrum and milk of immunized sows could provide protection for piglets against TGEV virulent challenge. Moreover, high levels of IgG antibodies and NA responses were detected in serum, which protected the piglets against virulent PDCoV challenge. Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5-day-old neonatal piglets from virulent challenge

title:
  Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5‐day‐old neonatal piglets from virulent challenge

abstract:
  In this study, the pathogenicity of porcine deltacoronavirus (PDCoV) strain NH (passage 10, P10) was evaluated. We found that PDCoV strain NH is enteropathogenic in 5‐day‐old pigs. Pathogenicity experiments provided a challenge model for studying the protection efficiency of passive immunity. In order to investigate the protective efficacy of passive immunity in newborn piglets, pregnant sows were vaccinated with either a PDCoV‐inactivated vaccine at the Houhai acupoint (n = 5) or DMEM as a negative control (n = 2) using a prime/boost strategy 20 and 40 days before delivery. PDCoV spike (S)‐specific IgG and neutralizing antibody (NA) responses were detected in immunized sows and piglets born to immunized sows. PDCoV spike (S)‐specific sIgA was also detected in the colostrum and milk of immunized sows. Five days post‐farrowing, piglets were orally challenged with PDCoV strain NH (10(5) TCID(50)/piglet). Severe diarrhoea, high levels of viral RNA copies and substantial intestinal villus atrophy were detected in piglets born to unimmunized sows. Only 4 of 31 piglets (12.9%) born to immunized sows in the challenge group displayed mild to moderate diarrhoea, lower viral RNA copies and minor intestinal villi damage compared to piglets born to unimmunized sows post‐challenge. Mock piglets exhibited no typical clinical symptoms. The challenge experiment results indicated that the inactivated PDCoV vaccine exhibited 87.1% protective efficacy in the piglets. These findings suggest that the inactivated PDCoV vaccine has the potential to be an effective vaccine, providing protection against virulent PDCoV.


id: cord-278154-oenuy07r
author: Gallien, Sarah
date: 2018-07-02
txt: ./txt/cord-278154-oenuy07r.txt
cache: ./cache/cord-278154-oenuy07r.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/tbed.12945
doi: 10.1111/tbed.12945
summary:
  Although viral RNA was detected in air samples with both strains, the indirect contact pigs remained free from infection with the InDel strain in contrast to the non‐InDel group in which airborne transmission occurred in the indirect contact pigs. In the non-InDel strain groups, all animals involved in the experiment showed clinical signs (including indirect contact pigs), with more severe clinical signs compared to the InDel inoculated groups. In case of infection with a non-InDel and an InDel strain, 100% of morbidity (except for the InDel indirect contact pigs) was observed, but clinical signs were not apparent at the same time among the two types of PEDV-infected groups. In fact, in a recent study using a different non-InDel strain from ours, airborne transmission to pigs in indirect contact was not effective even when PEDV RNA was detected in nasal swabs of infected pigs but at low levels (Niederwerder et al., 2016) .

title:
  Better horizontal transmission of a US non‐InDel strain compared with a French InDel strain of porcine epidemic diarrhoea virus

abstract:
  From the severe porcine epidemic diarrhoea (PED) epidemics that struck in 2013 in the United States of America and other countries of North and South America, two types of porcine epidemic diarrhoea virus (PEDV) were isolated, namely the InDel and the non‐InDel strains. They are differentiated by insertions/deletions in the S1 nucleotide sequence of the S gene, and differences in virulence were observed from the clinical cases. In 2014, a PED outbreak occurred in a pig farm in France, from which an InDel strain was isolated. This study aimed at comparing, under experimental conditions, the pathogenicity and the direct and indirect transmissions between a non‐InDel strain isolated from a PED‐affected piglet in 2014 in the USA and the French InDel strain. All infected pigs showed clinical signs with the non‐InDel strain although only the inoculated and direct contact pigs showed clinical signs in the InDel strain group. Although viral RNA was detected in air samples with both strains, the indirect contact pigs remained free from infection with the InDel strain in contrast to the non‐InDel group in which airborne transmission occurred in the indirect contact pigs. All infected pigs shed virus in faeces regardless of PEDV strain with 9 of 30 pigs showing intermittent faecal shedding. The transmission rate by direct contact was found to be 2.17‐fold higher than the non‐InDel strain compared with the InDel. In conclusion, the InDel strain was less pathogenic than the non‐InDel strain in our experimental conditions. The transmission route differed between the two strains. Direct contact was the main transmission route for the InDel strain, although the non‐InDel strain was transmitted through direct contact and indirectly through the air.


id: cord-279794-hn5vmic0
title: Evolutionary and genotypic analyses of global porcine epidemic diarrhea virus strains
author: Guo, Jiahui
date: 2018-08-27
txt: ./txt/cord-279794-hn5vmic0.txt
cache: ./cache/cord-279794-hn5vmic0.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/tbed.12991
doi: 10.1111/tbed.12991
summary:
  Molecular clock analysis showed that divergence of the GII‐c subgroup spike gene occurred in April 2010, suggesting that the subgroup originated from recombination events before the PEDV re‐emergence outbreaks. Consistent with our previous research (Wang, Fang, & Xiao, 2016a) , the phylogenetic tree indicated that the complete PEDV genomes evolved into two separate genogroups, GI (classical) and GII (variant), as presented in Figure 1a . Genetic variation of nucleocapsid genes of porcine epidemic diarrhea virus field strains in China Detection and molecular diversity of spike gene of porcine epidemic diarrhea virus in China Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China Complete genome sequence of a recombinant porcine epidemic diarrhea virus strain Evolutionary and epidemiological analyses based on spike genes of porcine epidemic diarrhea virus circulating in Thailand

abstract:
  Porcine epidemic diarrhea virus (PEDV), which re‐emerged in China in October 2010, has spread rapidly worldwide. Detailed analyses of the complete genomes of different PEDV strains are essential to understand the relationships among re‐emerging and historic strains worldwide. Here, we analysed the complete genomes of 409 strains from different countries, which were classified into five subgroup strains (i.e., GI‐a, GI‐b, GII‐a, GII‐b, and GII‐c). Phylogenetic study of different genes in the PEDV strains revealed that the newly discovered subgroup GII‐c exhibited inconsistent topologies between the spike gene and other genes. Furthermore, recombination analysis indicated that GII‐c viruses evolved from a recombinant virus that acquired the 5′ part of the spike gene from the GI‐a subgroup and the remaining genomic regions from the GII‐a subgroup. Molecular clock analysis showed that divergence of the GII‐c subgroup spike gene occurred in April 2010, suggesting that the subgroup originated from recombination events before the PEDV re‐emergence outbreaks. Interestingly, Ascaris suum, a large roundworm occurring in pigs, was found to be an unusual PEDV host, providing potential support for cross‐host transmission. This study has significant implications for understanding ongoing global PEDV outbreaks and will guide future efforts to develop effective preventative measures against PEDV.


id: cord-280328-16fpiuc2
title: One Health needs a vision beyond zoonoses
author: Villanueva‐Cabezas, JP
date: 2020-08-12
txt: ./txt/cord-280328-16fpiuc2.txt
cache: ./cache/cord-280328-16fpiuc2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32786137/
doi: 10.1111/tbed.13782
summary:
  We propose that the United Nation''s sustainable development goals provide an adequate multidimensional set of targets that can help researchers and policymakers contextualise emerging diseases, and guide One Health long‐term solutions that are equitable, efficacious, and sustainable. All rights reserved farming supports food security (SDG 2), and underpins peri-urban and urban sustainability (SDG 11) (Costard et al., 2009) , smallholders respond to ASF outbreaks by selling or consuming infected pigs (Chenais et al., 2017) . All rights reserved If after COVID-19 the community resumes the trade of wildlife, positive SDG effects associated with the trading ban will be lost (C  B) to improved human population wellbeing (C  C). If in contrast, the systems lack resilience and ASF outbreaks result in pathogen-centric approaches (for example, culling of animals with minimum or no compensation), the positive SDGs effects associated with the pig value chain are severely undermined (E  D).

abstract:
  The unprecedented pandemic events that currently affect animals and humans have fueled calls for One Health action. We argue that the One Health framework must be accompanied by ‘rich outcomes’ to avoid a reductionist One Health focus on zoonotic pathogens, that forgoes the benefits of the framework. We propose that the United Nation’s sustainable development goals provide an adequate multidimensional set of targets that can help researchers and policymakers contextualise emerging diseases, and guide One Health long‐term solutions that are equitable, efficacious, and sustainable.


id: cord-281081-rifr5uub
author: Deng, Junhua
date: 2020-05-07
txt: ./txt/cord-281081-rifr5uub.txt
cache: ./cache/cord-281081-rifr5uub.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/tbed.13577
doi: 10.1111/tbed.13577
summary:
  In this study, 1,914 serum samples from 35 animal species were used for detection of SARS‐CoV‐2‐specific antibodies using double‐antigen sandwich ELISA after validating its specificity and sensitivity. The results showed that no SARS‐CoV‐2‐specific antibodies were detected in above samples which excluded the possibility of 35 animal species as intermediate host for SARS‐CoV‐2. The results showed that no SARS-CoV-2-specific antibodies were detected in above species of animals including pangolin which has been reported as an intermediate host of SARS-CoV-2 (Kangpeng Xiao, 2020) . After confirming the specificity, sensitivity and suitability of SARS-CoV-2 ELISA kit for different species of experimental animals, clinical serum samples from domestic livestock (pig, cow, sheep, horse), poultry (chicken, duck, goose), experimental animal (mice, rat and rhesus monkey), companion animal (dog and cat) and wild animals (camel, fox, mink, alpaca, ferret, bamboo rat, peacock, eagle, tiger rhinoceros, pangolin, leopard cat, jackal, giant panda, masked civet, porcupine, bear, yellow-throated marten, weasel, red pandas and wild boar) were used for antibody detection.

title:
  Serological survey of SARS‐CoV‐2 for experimental, domestic, companion and wild animals excludes intermediate hosts of 35 different species of animals

abstract:
  The pandemic SARS‐CoV‐2 has been reported in 123 countries with more than 5,000 patients died from it. However, the original and intermediate hosts of the virus remain unknown. In this study, 1,914 serum samples from 35 animal species were used for detection of SARS‐CoV‐2‐specific antibodies using double‐antigen sandwich ELISA after validating its specificity and sensitivity. The results showed that no SARS‐CoV‐2‐specific antibodies were detected in above samples which excluded the possibility of 35 animal species as intermediate host for SARS‐CoV‐2. More importantly, companion animals including pet dogs (including one dog the SARS‐CoV‐2 patient kept and two dogs which had close contact with it) and cats, street dogs and cats also showed serological negative to SARS‐CoV‐2, which relieved the public concerns for the pets as SARS‐CoV‐2 carriers.


id: cord-283316-a8jewy2h
author: Bianchini, Juana
date: 2019-10-09
txt: ./txt/cord-283316-a8jewy2h.txt
cache: ./cache/cord-283316-a8jewy2h.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/tbed.13356
doi: 10.1111/tbed.13356
summary:
  Score 2 Low: increased (il)legal imports of animal subproducts such as skin, meat and edible products from EU member states have a low influence on the pathogen/disease (re)emergence in Belgium. Score 0 Score 1 Negligible: increased (il)legal imports of NON-animal products such as tires, wood, furniture from EU member states have a negligible influence on the pathogen/disease (re)emergence in Belgium. Score 2 Low: increased (il)legal imports of NON-animal products such as tires, wood, furniture from EU member states have a low influence on the pathogen/disease (re)emergence in Belgium. Score 2 Low: Increased imports of animal subproducts such as skin, meat and edible products from Third countries have a low influence on the pathogen/disease (re)emergence in Belgium. Score 2 Low: increased (il)legal imports of NON-animal products such as tires, wood, furniture from Third countries have a low influence on the pathogen/disease (re)emergence in Belgium.

title:
  Prioritization of livestock transboundary diseases in Belgium using a multicriteria decision analysis tool based on drivers of emergence

abstract:
  During the past decade, livestock diseases have (re‐)emerged in areas where they had been previously eradicated or never been recorded before. Drivers (i.e. factors of (re‐)emergence) have been identified. Livestock diseases spread irrespective of borders, and therefore, reliable methods are required to help decision‐makers to identify potential threats and try stopping their (re‐)emergence. Ranking methods and multicriteria approaches are cost‐effective tools for such purpose and were applied to prioritize a list of selected diseases (N = 29 including 6 zoonoses) based on the opinion of 62 experts in accordance with 50 drivers‐related criteria. Diseases appearing in the upper ranking were porcine epidemic diarrhoea, foot‐and‐mouth disease, low pathogenic avian influenza, African horse sickness and highly pathogenic avian influenza. The tool proposed uses a multicriteria decision analysis approach to prioritize pathogens according to drivers and can be applied to other countries or diseases.


id: cord-284377-hsju2shr
title: Vibrio vulnificus in aquariums is a novel threat to marine mammals and public health
author: Li, Meng
date: 2018-07-26
txt: ./txt/cord-284377-hsju2shr.txt
cache: ./cache/cord-284377-hsju2shr.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30047566/
doi: 10.1111/tbed.12967
summary:
  title: Vibrio vulnificus in aquariums is a novel threat to marine mammals and public health vulnificus is frequently distributed in aquariums, thus constituting a threat to captive marine mammals and to public health. Several known viral pathogens that have been reported to infect marine mammals were also detected by virus-specific PCR, including type A influenza virus (IAV), phocine distemper virus (PDV), coronavirus, and rotavirus. In this analysis, we successfully collected 54 samples from six aquariums in northern China ( genotypes based on its virulence-correlated gene (vcg) (Warner & Oliver, 2008) ; our analysis showed that 11 of the 12 isolated V. vulnificus strains display a potential threat to mammals, including marine animals and humans. vulnificus is not the only threat to marine animals and public health in aquariums. Wound infections caused by Vibrio vulnificus and other marine bacteria Vibrio vulnificus in aquariums is a novel threat to marine mammals and public health

abstract:
  Vibrio vulnificus is a Gram‐negative, curved, obligate halophilic marine bacterium that exclusively exists in coastal seawaters. Previous studies revealed that V. vulnificus is one of the most dangerous foodborne zoonotic pathogens for human beings. However, it remains unknown whether marine mammals can be infected by V. vulnificus. In May 2016, a captive spotted seal (Phoca largha) died due to septicemia induced by V. vulnificus. Upon post‐mortem examination, V. vulnificus was isolated, identified, and named as BJ‐PH01. Further analysis showed that BJ‐PH01 belongs to biotype 1 and the Clinical genotype. Furthermore, we performed an epidemiological investigation of V. vulnificus in six aquariums in northern China. As a result, V. vulnificus was successfully isolated from all investigated aquariums. The positive rates ranged from 20% to 100% in each investigated aquarium. During the investigation, 12 strains of V. vulnificus were isolated, and all 12 isolates were classified into biotype 1. Eleven of the 12 isolates belonged to the Clinical genotype, and one isolate belonged to the Environmental genotype. All 12 isolated V. vulnificus strains showed limited antibiotic resistance. Overall, our work demonstrated that V. vulnificus is frequently distributed in aquariums, thus constituting a threat to captive marine mammals and to public health.


id: cord-284398-rhfwbyav
author: Aboubakr, Hamada A.
date: 2020-07-14
txt: ./txt/cord-284398-rhfwbyav.txt
cache: ./cache/cord-284398-rhfwbyav.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/tbed.13707
doi: 10.1111/tbed.13707
summary:
  In another study, aerosolized SARS-CoV-2 retained its infectivity for a period of 16h at room temperature and the authors concluded that the virus can be considered as an airborne pathogen (Fears et al., 2020 and was infectious after 72 hr of aerosolization (Ijaz, Brunner, Sattar, Nair, & Johnson-Lussenburg, 1985) . In the first study, SARS-CoV-2 retained its infectivity for 4 days but was completely decayed after 7 days on plastic surface at room temperature and 65% RH (Chin et al., 2020) . Although this study reported longer virus survival, it has been shown that the survivability of SARS-CoV-1 on plastic surface is drastically affected by increases in temperature and RH as described below. In another study, a this virus with a higher initial load (5.5 log TCID 50 ) retained its infectivity for 4 days and was completely inactivated after 7 days on stainless steel at room temperature and RH of 65% (Chin et al., 2020) .

title:
  Stability of SARS‐CoV‐2 and other coronaviruses in the environment and on common touch surfaces and the influence of climatic conditions: A review

abstract:
  Although the unprecedented efforts the world has been taking to control the spread of the human coronavirus disease (COVID‐19) and its causative aetiology [severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2)], the number of confirmed cases has been increasing drastically. Therefore, there is an urgent need for devising more efficient preventive measures, to limit the spread of the infection until an effective treatment or vaccine is available. The preventive measures depend mainly on the understanding of the transmission routes of this virus, its environmental stability, and its persistence on common touch surfaces. Due to the very limited knowledge about SARS‐CoV‐2, we can speculate its stability in the light of previous studies conducted on other human and animal coronaviruses. In this review, we present the available data on the stability of coronaviruses (CoVs), including SARS‐CoV‐2, from previous reports to help understand its environmental survival. According to available data, possible airborne transmission of SARS‐CoV‐2 has been suggested. SARS‐CoV‐2 and other human and animal CoVs have remarkably short persistence on copper, latex and surfaces with low porosity as compared to other surfaces like stainless steel, plastics, glass and highly porous fabrics. It has also been reported that SARS‐CoV‐2 is associated with diarrhoea and that it is shed in the faeces of COVID‐19 patients. Some CoVs show persistence in human excrement, sewage and waters for a few days. These findings suggest a possible risk of faecal–oral, foodborne and waterborne transmission of SARS‐CoV‐2 in developing countries that often use sewage‐polluted waters in irrigation and have poor water treatment systems. CoVs survive longer in the environment at lower temperatures and lower relative humidity. It has been suggested that large numbers of COVID‐19 cases are associated with cold and dry climates in temperate regions of the world and that seasonality of the virus spread is suspected.


id: cord-289584-rbp7p8s9
author: Zhou, Ling
date: 2019-01-09
txt: ./txt/cord-289584-rbp7p8s9.txt
cache: ./cache/cord-289584-rbp7p8s9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30171801/
doi: 10.1111/tbed.13008
summary:
  So far, six coronaviruses have been identified from pigs, which include porcine epidemic diarrhoea virus (PEDV), porcine respiratory coronavirus (PRCV), SADS-CoV and transmissible gastroenteritis virus (TGEV) that all belong to the Alphacoronavirus genus, as well as one betacoronavirus, porcine hemagglutinating encephalomyelitis virus (PHEV) and one deltacoronavirus, porcine deltacoronavirus (PDCoV) (Lin, Saif, Marthaler, & Wang, 2016; Wesley, Woods, & Cheung, 1991; Woo et al., 2010) . Our results also indicated that both the complete genomes, N genes and S genes of all SADS-CoV strains shared the highest nucleotides identifies with those corresponding sequences of four bat coronavirus HKU2 strains. In this work, The phylogenetic trees of full length genomes and S genes of SADS-CoV sequences showed that the SADS-CoV branch clustered with these four HKU2 strains, which is same to previous results (Gong et al., 2017; Pan et al., 2017; Zhou et al., 2018) .

title:
  Retrospective detection and phylogenetic analysis of swine acute diarrhoea syndrome coronavirus in pigs in southern China

abstract:
  Swine acute diarrhoea syndrome coronavirus (SADS‐CoV), a novel coronavirus, was first discovered in southern China in January 2017 and caused a large scale outbreak of fatal diarrheal disease in piglets. Here, we conducted a retrospective investigation of 236 samples from 45 swine farms with a clinical history of diarrheal disease to evaluate the emergence and the distribution of SADS‐CoV in pigs in China. Our results suggest that SADS‐CoV has emerged in China at least since August 2016. Meanwhile, we detected a prevalence of SADS‐CoV (43.53%), porcine deltacoronavirus (8.83%), porcine epidemic diarrhoea virus (PEDV) (78.25%), rotavirus (21.77%), and transmissible gastroenteritis virus (0%), and we also found the co‐infection of SADS‐CoV and PEDV occurred most frequently with the rate of 17.65%. We screened and obtained two new complete genomes, five N and five S genes of SADS‐CoV. Phylogenetic analysis based on these sequences revealed that all SADS‐CoV sequences in this study clustered with previously reported SADS‐CoV strains to form a well defined branch that grouped with the bat coronavirus HKU2 strains. This study is the first retrospective investigation for SADS‐CoV and provides the epidemiological information of this new virus in China, which highlights the urgency to develop effective measures to control SADS‐CoV.


id: cord-291026-99cit4ig
author: Lung, O.
date: 2015-01-27
txt: ./txt/cord-291026-99cit4ig.txt
cache: ./cache/cord-291026-99cit4ig.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/tbed.12318
doi: 10.1111/tbed.12318
summary:
  In this study, we describe validation of a new probe‐based insulated isothermal reverse transcriptase PCR (iiRT‐PCR) assay for rapid detection of classical swine fever virus (CSFV) on a compact, user‐friendly device (POCKIT (™) Nucleic Acid Analyzer) that does not need data interpretation by the user. Archived viral nucleic acid from 18 laboratory-amplified non-CSF viruses including eight other pestiviruses (BVDV 1-Hastings, Singer and NY1 strains; BVDV 2-Ames 125c, 890, 24515 strains; BDV-Coos Bay; HoBi atypical pestivirus), African swine fever virus-Lisbon, swine vesicular disease virus-ITL 19/92, porcine respiratory and reproductive syndrome virus-YNL, swine influenza virus (H3N2), porcine circovirus 1 (PCV1, derived from infectious clone based on GenBank accession no. The iiRT-PCR assay accurately detected all CSFV RNA samples which represented all three genotypes, and eight of 11 subgenotypes that were available for testing and gave negative results for three BVDV type 1 strains, three BVDV type 2 strains, BDV, HoBi atypical pestivirus, ASFV and nine other viruses that affect livestock.

title:
  Insulated Isothermal Reverse Transcriptase PCR (iiRT‐PCR) for Rapid and Sensitive Detection of Classical Swine Fever Virus

abstract:
  Classical swine fever (CSF) is an OIE‐listed disease that can have a severe impact on the swine industry. User‐friendly, sensitive, rapid diagnostic tests that utilize low‐cost field‐deployable instruments for CSF diagnosis can be useful for disease surveillance and outbreak monitoring. In this study, we describe validation of a new probe‐based insulated isothermal reverse transcriptase PCR (iiRT‐PCR) assay for rapid detection of classical swine fever virus (CSFV) on a compact, user‐friendly device (POCKIT (™) Nucleic Acid Analyzer) that does not need data interpretation by the user. The assay accurately detected CSFV RNA from a diverse panel of 33 CSFV strains representing all three genotypes plus an additional in vitro‐transcribed RNA from cloned sequences representing a vaccine strain. No cross‐reactivity was observed with a panel of 18 viruses associated with livestock including eight other pestivirus strains (bovine viral diarrhoea virus type 1 and type 2, border disease virus, HoBi atypical pestivirus), African swine fever virus, swine vesicular disease virus, swine influenza virus, porcine respiratory and reproductive syndrome virus, porcine circovirus 1, porcine circovirus 2, porcine respiratory coronavirus, vesicular exanthema of swine virus, bovine herpes virus type 1 and vesicular stomatitis virus. The iiRT‐PCR assay accurately detected CSFV as early as 2 days post‐inoculation in RNA extracted from serum samples of experimentally infected pigs, before appearance of clinical signs. The limit of detection (LOD (95%)) calculated by probit regression analysis was 23 copies per reaction. The assay has a sample to answer turnaround time of less than an hour using extracted RNA or diluted or low volume of neat serum. The user‐friendly, compact device that automatically analyses and displays results could potentially be a useful tool for surveillance and monitoring of CSF in a disease outbreak.


id: cord-293082-fw7deem8
title: Animal coronaviruses and SARS‐CoV‐2
author: Zhang, Guangzhi
date: 2020-08-16
txt: ./txt/cord-293082-fw7deem8.txt
cache: ./cache/cord-293082-fw7deem8.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/tbed.13791
doi: 10.1111/tbed.13791
summary:
  As of April 7, just four months since its first outbreak, more 48 than 3.4 million confirmed cases and 238,000 deaths have been recorded in 215 countries, areas, 49 and territories, and moreover it seems that severe acute respiratory syndrome coronavirus 2 50 (SARS-CoV-2) that causes COVID-19 will probably continue to circulate around the globe 51 (https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/). The health 52 authorities and governments of affected countries have paid attention to current pandemic and 53 have taken immediate measures to block COVID-19 transmission, including utilization of personal 54 protective equipment, quarantine, epidemiological investigation, isolation, clinical data analysis 55 and sharing, public health education, maintaining social distance, the creation of diagnostics, 56 therapeutics, and vaccines, etc (Xiao and Torok 2020) . Human Kidney is a Target for Novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain

abstract:
  COVID‐19 is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). It has rapidly spread to 216 countries and territories since first outbreak in December of 2019, posing a substantial economic losses and extraordinary threats to the public health worldwide. Although bats have been suggested as the natural host of SARS‐CoV‐2, transmission chains of this virus, role of animals during cross‐species transmission, and future concerns remain unclear. Diverse animal coronaviruses have extensively been studied since the discovery of avian coronavirus in 1930s. The current article comprehensively reviews and discusses the current understanding about animal coronaviruses and SARS‐CoV‐2 for their emergence, transmission, zoonotic potential, alteration of tissue/host tropism, evolution, status of vaccines, and surveillance. This study aims at providing guidance for control of COVID‐19 and preventative strategies for possible future outbreaks of zoonotic coronavirus via cross‐species transmission.


id: cord-294021-x8avmtef
title: First report and phylogenetic analysis of porcine deltacoronavirus in Mexico
author: Pérez‐Rivera, Claudia
date: 2019-04-16
txt: ./txt/cord-294021-x8avmtef.txt
cache: ./cache/cord-294021-x8avmtef.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30941894/
doi: 10.1111/tbed.13193
summary:
  Subsequently, in early 2014, PDCoV was reported from the United States of America (USA) and Canada, and it caused heavy economic losses to the swine industry due to the presentation of a clinical enteric disease Song et al., 2015; Wang et al., 2014) . The authors note that PDCoV infections are common in pigs and that coinfections are frequent, especially with the porcine epidemic diarrhoea virus and rotavirus C (Hu et al., 2015; Marthaler, Raymond, et al., 2014; Song et al., 2015) . The most common coinfection was PDCoV/PEDV, found in 54.1% of the total deltacoronavirus-positive cases (46/85), a result that coincides with that reported by other authors (Song et al., 2015; Zhang, 2016 Figure 1 ). Newly emerged porcine deltacoronavirus associated with diarrhoea in swine in China: Identification, prevalence and full-length genome sequence analysis First report and phylogenetic analysis of porcine deltacoronavirus in Mexico

abstract:
  Porcine deltacoronavirus has caused great economic losses in the swine industry worldwide. In this study, we carried out the first detection, sequencing and characterization of this virus in Mexico. We analysed 885 rectal samples by multiplex RT‐PCR to determine coinfections. In addition, the Spike gene was amplified, sequenced and analysed phylogenetically. We found 85 positive samples for porcine deltacoronavirus, representing 9.6% of the total samples, and we determined that the most frequent coinfection was with porcine epidemic diarrhoea virus (54.1%). Four sequences of Mexican isolates were most closely related to those of the United States. The antigenic regions and the glycosylation site of the strains obtained coincide with those previously reported. This relationship is probably related to the commercial exchange of pigs between the US and Mexico and the geographical proximity of these two countries.


id: cord-294468-0v4grqa7
author: Kasilingam, Dharun
date: 2020-08-04
txt: ./txt/cord-294468-0v4grqa7.txt
cache: ./cache/cord-294468-0v4grqa7.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/tbed.13764
doi: 10.1111/tbed.13764
summary:
  This research uses exponential growth modelling studies to understand the spreading patterns of the COVID‐19 virus and identifies countries that have shown early signs of containment until 26(th) March 2020. Machine learning models based on logistic regression, decision tree, random forest, and support vector machines are developed and show accuracies between 76.2% to 92.9% to predict early signs of infection containment. The objective of the research is to develop a mathematical model using exponential growth analysis coupled with machine learning, to predict worldwide COVID-19 early containment signs. Secondly, the research aims at building supervised machine learning models with high accuracies for predicting signs of early containment with infrastructure availability, environmental factors, infection severity factors, and government policies of countries as independent variables. The research presents machine learning models based on variables such as infrastructure, environment, policies, and the infection itself, to predict early signs of containment in the country.

title:
  Exploring the Growth of COVID‐19 Cases using Exponential Modelling Across 42 Countries and Predicting Signs of Early Containment using Machine Learning

abstract:
  COVID‐19 pandemic disease spread by the SARS‐COV‐2 single‐strand structure RNA virus, belongs to the 7(th) generation of the coronavirus family. Following an unusual replication mechanism, it’s extreme ease of transmissivity has put many counties under lockdown. With uncertainty of developing a cure/vaccine for the infection in the near future, the onus currently lies on healthcare infrastructure, policies, government activities, and behaviour of the people to contain the virus. This research uses exponential growth modelling studies to understand the spreading patterns of the COVID‐19 virus and identifies countries that have shown early signs of containment until 26(th) March 2020. Predictive supervised machine learning models are built using infrastructure, environment, policies, and infection‐related independent variables to predict early containment. COVID‐19 infection data across 42 countries are used. Logistic regression results show a positive significant relationship between healthcare infrastructure and lockdown policies, and signs of early containment. Machine learning models based on logistic regression, decision tree, random forest, and support vector machines are developed and show accuracies between 76.2% to 92.9% to predict early signs of infection containment. Other policies and the decisions taken by countries to contain the infection are also discussed.


id: cord-294698-mtfrbn87
author: Kim, H. K.
date: 2016-05-23
txt: ./txt/cord-294698-mtfrbn87.txt
cache: ./cache/cord-294698-mtfrbn87.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/tbed.12515
doi: 10.1111/tbed.12515
summary:
  In this study, consensus primer‐based reverse transcriptase polymerase chain reactions (RT‐PCRs) and high‐throughput sequencing were performed to investigate viruses in bat faecal samples collected at 11 natural bat habitat sites from July to December 2015 in Korea. Therefore, in this study, we investigated viruses in bat species in Korea, using 49 faecal samples collected from July to December 2015 in 11 sites in natural bat habitats. So far, group H rotaviruses have only been reported in human and pigs (Molinari et al., 2015) , but this study provides evidence that bat species may be a host of group H RVs. To confirm that, there should be follow-up studies including virus isolation and characterization, genomic analysis, continuous surveillance and VP6-based classification (Matthijnssens et al., 2012) to find its prevalence, epidemiology and zoonotic potential. In this study, SARS-CoV-like and MERS-CoV-like bat CoVs and group H rotavirus were detected for this first time in Korea, which may be of interest because of their zoonosis potential.

title:
  Detection of Severe Acute Respiratory Syndrome‐Like, Middle East Respiratory Syndrome‐Like Bat Coronaviruses and Group H Rotavirus in Faeces of Korean Bats

abstract:
  Bat species around the world have recently been recognized as major reservoirs of several zoonotic viruses, such as severe acute respiratory syndrome coronavirus (SARS‐CoV), Middle East respiratory syndrome coronavirus (MERS‐CoV), Nipah virus and Hendra virus. In this study, consensus primer‐based reverse transcriptase polymerase chain reactions (RT‐PCRs) and high‐throughput sequencing were performed to investigate viruses in bat faecal samples collected at 11 natural bat habitat sites from July to December 2015 in Korea. Diverse coronaviruses were first detected in Korean bat faeces, including alphacoronaviruses, SARS‐CoV‐like and MERS‐CoV‐like betacoronaviruses. In addition, we identified a novel bat rotavirus belonging to group H rotavirus which has only been described in human and pigs until now. Therefore, our results suggest the need for continuing surveillance and additional virological studies in domestic bat.


id: cord-302819-oj33i2ma
author: Pasick, J
date: 2014-08-07
txt: ./txt/cord-302819-oj33i2ma.txt
cache: ./cache/cord-302819-oj33i2ma.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25098383/
doi: 10.1111/tbed.12269
summary:
  On the SDPP sample that was tested, the following N gene rRT-PCR results were observed: C t of 35.84 for PBS supernatant after 10 000 g, C t of 36.74 for the PBS pellet after 10 000 g, C t of 38.83 for the PBS + Nonidet P-40 Comparison of S protein gene sequences obtained from bioassay piglets versus those of field cases. No significant difference was observed in the kinetics of N gene rRT-PCR positivity in animals that were inoculated with the three SDPP samples that were tested, suggesting that each contained infectious virus. Negative contrast staining electron microscopy of fecal samples collected at 4 dpi from the SDPP-inoculated piglets and the positive control group piglets showed the presence of virus-like particles consistent with coronavirus virions. Similar virus-like particles were also found in the content of the small intestine of a SDPP-inoculated piglet at 7 dpi and a positive control group contact piglet at 5 days post-contact.

title:
  Investigation into the Role of Potentially Contaminated Feed as a Source of the First-Detected Outbreaks of Porcine Epidemic Diarrhea in Canada

abstract:
  SUMMARY: In January 2014, approximately 9 months following the initial detection of porcine epidemic diarrhea (PED) in the USA, the first case of PED was confirmed in a swine herd in south-western Ontario. A follow-up epidemiological investigation carried out on the initial and 10 subsequent Ontario PED cases pointed to feed as a common risk factor. As a result, several lots of feed and spray-dried porcine plasma (SDPP) used as a feed supplement were tested for the presence of PEDV genome by real-time RT-PCR assay. Several of these tested positive, supporting the notion that contaminated feed may have been responsible for the introduction of PEDV into Canada. These findings led us to conduct a bioassay experiment in which three PEDV-positive SDPP samples (from a single lot) and two PEDV-positive feed samples supplemented with this SDPP were used to orally inoculate 3-week-old piglets. Although the feed-inoculated piglets did not show any significant excretion of PEDV, the SDPP-inoculated piglets shed PEDV at a relatively high level for ≥9 days. Despite the fact that the tested PEDV genome positive feed did not result in obvious piglet infection in our bioassay experiment, contaminated feed cannot be ruled out as a likely source of this introduction in the field where many other variables may play a contributing role.


id: cord-303289-qoukiqr7
title: Coronavirus infections in horses in Saudi Arabia and Oman
author: Hemida, M. G.
date: 2017-03-13
txt: ./txt/cord-303289-qoukiqr7.txt
cache: ./cache/cord-303289-qoukiqr7.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/tbed.12630
doi: 10.1111/tbed.12630
summary:
  We carried out RT‐PCR on 306 nasal and 315 rectal swabs and tested 243 sera for antibodies to detect coronavirus infections in apparently healthy horses in Saudi Arabia and Oman. RNA extracts were tested for evidence of conserved coronavirus nucleic acid genetic sequences using previously reported RT-PCR assays (Chu et al., 2014) , RTqPCR assay for MERS-CoV upE gene (Corman et al., 2012) , RTqPCR assay for ECoV (Miszczak et al., 2014) , and a RTqPCR assay for HKU23 reported below. T A B L E 5 Cross-neutralization titres (denoted as reciprocal titres) for Middle East respiratory coronavirus (MERS-CoV), bovine coronavirus (BCoV) and equine coronavirus (ECoV) in hyperimmune or naturally infected sera known to be positive for different coronaviruses NR460pig antiserum to porcine respiratory coronavirus 1,200 a <20 <20 <20 <20 Similarly, a BCoV immune serum from an experimentally infected gnotobiotic calf showed detectable, but 16-fold reduced antibody titre with ECoV but no cross-reaction with MERS-CoV.

abstract:
  Equine coronaviruses (ECoV) are the only coronavirus known to infect horses. So far, data on ECoV infection in horses remain limited to the USA, France and Japan and its geographic distribution is not well understood. We carried out RT‐PCR on 306 nasal and 315 rectal swabs and tested 243 sera for antibodies to detect coronavirus infections in apparently healthy horses in Saudi Arabia and Oman. We document evidence of infection with ECoV and HKU23 coronavirus by RT‐PCR. There was no conclusive evidence of Middle East respiratory syndrome coronavirus infection in horses. Serological data suggest that lineage A betacoronavirus infections are commonly infecting horses in Saudi Arabia and Oman but antibody cross‐reactivities between these viruses do not permit us to use serological data alone to identify which coronaviruses are causing these infections.


id: cord-309734-m8miwtha
title: Middle East respiratory syndrome coronavirus experimental transmission using a pig model
author: Vergara‐Alert, J.
date: 2017-06-26
txt: ./txt/cord-309734-m8miwtha.txt
cache: ./cache/cord-309734-m8miwtha.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28653496/
doi: 10.1111/tbed.12668
summary:
  Dromedary camels are the main reservoir of Middle East respiratory syndrome coronavirus (MERS‐CoV), but other livestock species (i.e., alpacas, llamas, and pigs) are also susceptible to infection with MERS‐CoV. Virus was present in nasal swabs of infected animals, and limited amounts of viral RNA, but no infectious virus were detected in the direct contact pigs. However, other animal species such as non-human primates (rhesus macaques and common marmosets), members of the family Camelidae (alpacas and llamas), rabbits and pigs have been demonstrated to be susceptible to MERS-CoV infection (Crameri et al., 2016; Falzarano et al., 2014; Haagmans et al., 2015; Vergara-Alert, van den Brand, et al., 2017; de Wit et al., 2013 de Wit et al., , 2017 . To study whether MERS-CoV might be transmitted between pigs, an experimental transmission study in this animal model was designed and performed under direct and indirect contact settings.

abstract:
  Dromedary camels are the main reservoir of Middle East respiratory syndrome coronavirus (MERS‐CoV), but other livestock species (i.e., alpacas, llamas, and pigs) are also susceptible to infection with MERS‐CoV. Animal‐to‐animal transmission in alpacas was reported, but evidence for transmission in other species has not been proved. This study explored pig‐to‐pig MERS‐CoV transmission experimentally. Virus was present in nasal swabs of infected animals, and limited amounts of viral RNA, but no infectious virus were detected in the direct contact pigs. No virus was detected in the indirect contact group. Furthermore, direct and indirect contact pigs did not develop specific antibodies against MERS‐CoV. Therefore, the role of pigs as reservoir is probably negligible, although it deserves further confirmation.


id: cord-316006-t080mykk
title: Clusters of 2019 coronavirus disease (COVID‐19) cases in Chinese tour groups
author: Kong, Dechuan
date: 2020-07-27
txt: ./txt/cord-316006-t080mykk.txt
cache: ./cache/cord-316006-t080mykk.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32657548/
doi: 10.1111/tbed.13729
summary:
  Our study describes clusters of COVID-19 cases within tour groups travelling in European countries from January 16 through 28. Tour group transmission may have occurred in the following sceParis-Shanghai, all of the confirmed and suspected cases had seats within two rows ( Figure 3 ). We reported three clusters of COVID-19 confirmed cases in three tour groups travelling in European countries and one cluster of suspected cases on one flight in late January 2020. In group A, the cluster was initiated by a familial transmission, followed by spread of disease to 13 out of 34 members in the 12-day tour. In conclusion, we reported a cluster of 13 COVID-19 cases, which was initiated by within-family transmission followed by propagative transmission into tour groups travelling in European countries. The study findings show that clustered cases in tour groups may be more propagative than simple familial transmission. Clusters of 2019 coronavirus disease (COVID-19) cases in Chinese tour groups

abstract:
  International travel may facilitate the spread of the novel coronavirus disease (COVID‐19). The study describes clusters of COVID‐19 cases within Chinese tour groups travelling in Europe January 16–28. We compared characteristics of cases and non‐cases to determine transmission dynamics. The index case travelled from Wuhan, China, to Europe on 16 January 2020, and to Shanghai, China, on 27 January 2020, within a tour group (group A). Tour groups with the same outbound flight (group B) or the same tourism venue (group D) and all Chinese passengers on the inbound flight (group C) were investigated. The outbreak involved 11 confirmed cases, 10 suspected cases and six tourists who remained healthy. Group A, involving seven confirmed cases and six suspected cases, consisted of familial transmission followed by propagative transmission. There was less pathogenicity with propagative transmission than with familial transmission. Disease was transmitted in shared outbound flights, shopping venues within Europe and inbound flight back to China. The novel coronavirus caused clustered cases of COVID‐19 in tour groups. When tourism and travel opens up, governments will need to improve screening at airports and consider increased surveillance of tour groups—particularly those with older tour members.


id: cord-316617-8cqxz3wi
title: SARS‐CoV‐2, where to now?
author: Ward, Michael P.
date: 2020-06-19
txt: ./txt/cord-316617-8cqxz3wi.txt
cache: ./cache/cord-316617-8cqxz3wi.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32562349/
doi: 10.1111/tbed.13654
abstract: nan
summary:
  (2020) present the results of a SARS-CoV-2 serological survey in 35 animal species in China, including the dog of a COVID-19 patient and an additional two in-contact dogs. Tests available for the detection of SARS-CoV-2 are comprehensively described in this issue of Transboundary and Emerging Diseases (Li & Ren, 2020) . In addition to the publication of new knowledge about SARS-CoV-2 in this issue of Transboundary and Emerging Diseases, new ideas are also presented. A key enabler of such a shift in our thinking and approach to disease emergence and spread is a One Health workforce capable of undertaking integrated monitoring, surveillance, risk assessment and response activities. The COVID-19 pandemic could be a catalyst for such a seismic shift in how we approach emerging infectious diseases and One Health. We can be sure, even when the current COVID-19 pandemic is resolved, that the need for surveillance, response and prevention of transboundary and emerging diseases will remain.


id: cord-317455-6qx0v28w
author: Brown, Paul A.
date: 2018-09-10
txt: ./txt/cord-317455-6qx0v28w.txt
cache: ./cache/cord-317455-6qx0v28w.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/tbed.13006
doi: 10.1111/tbed.13006
summary:
  Turkey coronavirus, originally identified in the USA in the 1970s as one of the agents responsible for an acute enteritis named bluecomb (Panigrahy, Naqi, & Hall, 1973; Ritchie, Deshmukh, Larsen, & Pomeroy, 1973) and since with a multifactorial disease known as poult enteritis complex of turkeys (PEC) , has now been detected in most areas where turkeys are farmed Cavanagh et al., 2001; Dea & Tijssen, 1988; Domańska-Blicharz, Seroka, Lisowska, Tomczyk, & Minta, 2010; Martin, Vinco, Cordioli, & Lavazza, 2002; Maurel et al., 2009; Teixeira et al., 2007) , although TCoVs isolated in Europe have been shown to have a different genetic lineage to those isolated in the USA (Brown et al., 2016; Maurel et al., 2011) . At 1-day post-inoculation (dpi), two SPF turkey contacts were introduced into groups 1-4 as sentinels to demonstrate horizontal transmission of infectious virus. They were housed in a negative pressure room, under the same rearing conditions as in Exp 2, with three 11-day-old SPF turkeys introduced as contact-birds at 1 dpi to demonstrate horizontal transmission.

title:
  Transmission Kinetics and histopathology induced by European Turkey Coronavirus during experimental infection of specific pathogen free turkeys

abstract:
  Numerous viruses, mostly in mixed infections, have been associated worldwide with poult enteritis complex (PEC). In 2008 a coronavirus (Fr‐TCoV 080385d) was isolated in France from turkey poults exhibiting clinical signs compatible with this syndrome. In the present study, the median infectious dose (ID (50))(,) transmission kinetics and pathogenicity of Fr‐TCoV were investigated in 10‐day‐old SPF turkeys. Results revealed a titre of 10(4.88) ID (50)/ml with 1 ID (50)/ml being beyond the limit of genome detection using a well‐characterized qRT‐PCR for avian coronaviruses. Horizontal transmission of the virus via the airborne route was not observed however, via the oro‐faecal route this proved to be extremely rapid (one infectious individual infecting another every 2.5 hr) and infectious virus was excreted for at least 6 weeks in several birds. Histological examination of different zones of the intestinal tract of the Fr‐TCoV‐infected turkeys showed that the virus had a preference for the lower part of the intestinal tract with an abundance of viral antigen being present in epithelial cells of the ileum, caecum and bursa of Fabricius. Viral antigen was also detected in dendritic cells, monocytes and macrophages in these areas, which may indicate a potential for Fr‐TCoV to replicate in antigen‐presenting cells. Together these results highlight the importance of good sanitary practices in turkey farms to avoid introducing minute amounts of virus that could suffice to initiate an outbreak, and the need to consider that infected individuals may still be infectious long after a clinical episode, to avoid virus dissemination through the movements of apparently recovered birds.


id: cord-318237-22s13v2y
title: Spreading of canine parvovirus type 2c mutants of Asian origin in southern Italy
author: Mira, Francesco
date: 2019-07-14
txt: ./txt/cord-318237-22s13v2y.txt
cache: ./cache/cord-318237-22s13v2y.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/tbed.13283
doi: 10.1111/tbed.13283
summary:
  Although to date CPV‐2 is circulating in all continents, most of the current studies have analysed the amino acid changes accounted in the VP2 gene sequence, with limited information on virus introductions from other countries. The aim of this study was the detection and molecular analysis of CPV strains displaying genetic features of Asian viruses spreading in southern Italy. More recently, a CPV-2c strain displaying genetic signatures typical of Asian viruses was detected in southern Italy (Mira, Purpari, Lorusso, et al., 2018) , thus suggesting the introduction of the virus from other countries, as reported for other canine viruses (Decaro, Campolo, et al., 2007; Martella et al., 2006; .

abstract:
  Canine parvovirus type 2 (CPV‐2) emerged as dog pathogen in the late 1970s, causing severe and often fatal epizootics of gastroenteritis in the canine population worldwide. Although to date CPV‐2 is circulating in all continents, most of the current studies have analysed the amino acid changes accounted in the VP2 gene sequence, with limited information on virus introductions from other countries. The aim of this study was to analyse the genetic features of CPV‐2c strains currently spreading in Italy. Swabs and tissue samples were collected from dogs suspected of CPV infection. The nearly complete genome sequence from the CPV‐positive samples was obtained. The co‐circulation of two different but related CPV‐2c strains, with amino acid changes characteristic of CPV strains of Asian origin (NS1: 60V, 544F, 545F, 630P – NS2: 60V, 151N, 152V ‐ VP2: 5A/G, 267Y, 297A, 324I, 370R), were observed. The phylogenetic analyses inferred from the NS1 and VP2 gene sequences confirmed the relationship with Asian CPV‐2c strains. This study reports the spread of novel CPV‐2c mutants in Italy and supports further studies to evaluate the coexistence of genetically divergent CPV strains in the same geographical environment.


id: cord-326596-8ux1q9xw
author: Chen, Yanyu
date: 2018-09-08
txt: ./txt/cord-326596-8ux1q9xw.txt
cache: ./cache/cord-326596-8ux1q9xw.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/tbed.13005
doi: 10.1111/tbed.13005
summary:
  To better further explore the relationships among above factors, an AAvV‐6 epidemiological surveillance of domestic poultry and wild birds in six provinces of China suspected of sites of inter‐species transmission and being intercontinental flyways during the year 2013–2017 was conducted. Despite this, knowledge about the regularities of transmission, genetic and biological characteristics of AAvV-6 viruses in commercial poultry and wild birds in the China recent years remains limited. Therefore, in this study, an AAvV-6 surveillance of domestic poultry and wild birds in six provinces of China suspected of sites of inter-species transmission and being intercontinental flyways from December 2013 to June 2017 was conducted. Complete genome sequence of a novel avian paramyxovirus isolated from wild birds in South Korea Complete nucleotide sequence of avian paramyxovirus type 6 strain JL isolated from mallard ducks in China Completion of full length genome sequence of novel avian paramyxovirus strain APMV/Shimane67 isolated from migratory wild geese in Japan

title:
  Biological and phylogenetic characterization of a novel hemagglutination‐negative avian avulavirus 6 isolated from wild waterfowl in China

abstract:
  Up to now only nine whole genome sequences of avian avulavirus 6 (AAvV‐6) had been documented in the world since the first discovery of AAvV‐6 (AAvV‐6/duck/HongKong/18/199/77) at a domestic duck in 1977 from Hong Kong of China. Very limited information is known about the regularities of transmission, genetic and biological characteristics of AAvV‐6 because of the lower isolation rate and mild losses for poultry industry. To better further explore the relationships among above factors, an AAvV‐6 epidemiological surveillance of domestic poultry and wild birds in six provinces of China suspected of sites of inter‐species transmission and being intercontinental flyways during the year 2013–2017 was conducted. Therefore, 9,872 faecal samples from wild birds and 1,642 cloacal and tracheal swab samples from clinically healthy poultry of live bird market (LBM) were collected respectively. However, only one novel hemagglutination‐negative AAvV‐6 isolate (AAvV‐6/mallard/Hubei/2015) was isolated from a fresh faecal sample obtained from mallard at a wetland of Hubei province. Sequencing and phylogenetic analyses of this AAvV‐6 isolate (AAvV‐6/mallard/Hubei/2015) indicated that this isolate grouping to genotype I were epidemiological intercontinentally linked with viruses from the wild birds in Europe and America. Meanwhile, at least two genotypes (I and II) are existed within serotype AAvV‐6. In additional, this novel hemagglutination‐negative AAvV‐6 isolate in chicken embryos restored its hemagglutination when pre‐treated with trypsin. These findings, together with data from other AAvV‐6, suggest potential epidemiological intercontinental spreads among AAvV‐6 transmission by wild migratory birds, and reveal potential threats to wild birds and domestic poultry worldwide.


id: cord-330364-ye02hwhy
title: Systemic resilience to cross‐border infectious disease threat events in Europe
author: Semenza, Jan C.
date: 2019-05-17
url: https://doi.org/10.1111/tbed.13211
doi: 10.1111/tbed.13211
abstract:
  Recurrent health emergencies threaten global health security. International Health Regulations (IHR) aim to prevent, detect and respond to such threats, through increase in national public health core capacities, but whether IHR core capacity implementation is necessary and sufficient has been contested. With a longitudinal study we relate changes in national IHR core capacities to changes in cross‐border infectious disease threat events (IDTE) between 2010 and 2016, collected through epidemic intelligence at the European Centre for Disease Prevention and Control (ECDC). By combining all IHR core capacities into one composite measure we found that a 10% increase in the mean of this composite IHR core capacity to be associated with a 19% decrease (p = 0.017) in the incidence of cross‐border IDTE in the EU. With respect to specific IHR core capacities, an individual increase in national legislation, policy & financing; coordination and communication with relevant sectors; surveillance; response; preparedness; risk communication; human resource capacity; or laboratory capacity was associated with a significant decrease in cross‐border IDTE incidence. In contrast, our analysis showed that IHR core capacities relating to point‐of‐entry, zoonotic events or food safety were not associated with IDTE in the EU. Due to high internal correlations between core capacities, we conducted a principal component analysis which confirmed a 20% decrease in risk of IDTE for every 10% increase in the core capacity score (95% CI: 0.73, 0.88). Globally (EU excluded), a 10% increase in the mean of all IHR core capacities combined was associated with a 14% decrease (p = 0.077) in cross‐border IDTE incidence. We provide quantitative evidence that improvements in IHR core capacities at country‐level are associated with fewer cross‐border IDTE in the EU, which may also hold true for other parts of the world.


id: cord-331740-yjt3q9ph
author: Jones, R. M.
date: 2011-04-07
txt: ./txt/cord-331740-yjt3q9ph.txt
cache: ./cache/cord-331740-yjt3q9ph.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/j.1865-1682.2011.01222.x
doi: 10.1111/j.1865-1682.2011.01222.x
summary:
  This real-time RT-PCR test was used to examine a panel of field samples and its performance compared to virus isolation in embryonated fowls'' eggs. Design and calibration of IBV real-time RT-PCR To confirm that the modified test was suitable for detecting contemporary UK field strains of IBV, a panel of laboratory isolates of IBV representing the major genotypes currently circulating in the UK was tested . The validity of the result obtained for 38 of the 173 real-time RT-PCR positive, virus isolation negative samples could be confirmed by sequencing of the amplicon generated by the diagnostic RT-PCR. Infectious bronchitis virus RNA has been detected in tracheal swab samples by other real-time RT-PCRs for at least 21 days post-vaccination (Callison et al., 2006) and has been isolated from faecal samples in some infected birds as long as 227 days post-infection Gough, 1977, 1978) , making it essential to be able to differentiate between vaccine and field strains for diagnostic purposes.

title:
  Development and Validation of RT‐PCR Tests for the Detection and S1 Genotyping of Infectious Bronchitis Virus and Other Closely Related Gammacoronaviruses Within Clinical Samples

abstract:
  Two tests were developed that allow the detection and genotyping of infectious bronchitis virus (IBV) and other closely related gammacoronaviruses. The first test employs a one‐step, reverse transcription‐polymerase chain reaction (RT‐PCR) assay in which the amplification is monitored in real time using a TaqMan(®) probe. This real‐time RT‐PCR test was used to examine a panel of field samples and its performance compared to virus isolation in embryonated fowls’ eggs. A total of 323 field samples were tested; 176 samples were positive using the real‐time RT‐PCR method, but only three were positive by virus isolation. Sequencing was used to confirm the positive real‐time RT‐PCR results for a subset of samples. The test is suitable for swabs and post‐mortem samples and has been shown to be highly sensitive and specific. The second test, a genotyping method, was developed for identification of the strain of IBV present in field samples based on nucleotide variations within the gene encoding the S1 subunit of the surface spike (S) glycoprotein. This method was developed to provide a tool to inform vaccination decisions and for ongoing surveillance to detect new and emerging strains of IBV within the UK. The performance of the test was evaluated using laboratory isolates of IBV and field samples. Both tests are suitable for use in a high‐throughput diagnostic laboratory.


id: cord-331932-oujdl459
title: Multiplex PCR and Microarray for Detection of Swine Respiratory Pathogens
author: Lung, O.
date: 2015-12-12
url: https://doi.org/10.1111/tbed.12449
doi: 10.1111/tbed.12449
abstract:
  Porcine respiratory disease complex (PRDC) is one of the most important health concerns for pig producers and can involve multiple viral and bacterial pathogens. No simple, single‐reaction diagnostic test currently exists for the simultaneous detection of major pathogens commonly associated with PRDC. Furthermore, the detection of most of the bacterial pathogens implicated in PRDC currently requires time‐consuming culture‐based methods that can take several days to obtain results. In this study, a novel prototype automated microarray that integrates and automates all steps of post‐PCR microarray processing for the simultaneous detection and typing of eight bacteria and viruses commonly associated with PRDC is described along with associated multiplex reverse transcriptase PCR. The user‐friendly assay detected and differentiated between four viruses [porcine reproductive and respiratory syndrome virus (PRRSV), influenza A virus, porcine circovirus type 2, porcine respiratory corona virus], four bacteria (Mycoplasma hyopneumoniae, Pasteurella multocida, Salmonella enterica serovar Choleraesuis, Streptococcus suis), and further differentiated between type 1 and type 2 PRRSV as well as toxigenic and non‐toxigenic P. multocida. The assay accurately identified and typed a panel of 34 strains representing the eight targeted pathogens and was negative when tested with 34 relevant and/or closely related non‐target bacterial and viral species. All targets were also identified singly or in combination in a panel of clinical lung samples and/or experimentally inoculated biological material.


id: cord-339871-jso21mbx
author: Lee, Sunhee
date: 2018-05-16
txt: ./txt/cord-339871-jso21mbx.txt
cache: ./cache/cord-339871-jso21mbx.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/tbed.12904
doi: 10.1111/tbed.12904
summary:
  To investigate the diversity of PEDVs responsible for the ongoing outbreaks in South Korea, in this study, we determined the full-length sequences of the S proteins of field isolates and complete genome sequences of representative strains identified throughout 2017. Based on the S gene sequences, therefore, PEDV can be genetically separated into two genogroup clusters, genogroup 1 (G1, classical and recombinant: low-pathogenic) and genogroup 2 (G2, field epizootic or panzootic: high-pathogenic), which are further divided into subgroups 1a and F I G U R E 1 Phylogenetic analysis based on nucleotide sequences of the spike genes (a) and full-length genomes (b) of porcine epidemic diarrhoea virus strains. Molecular characterization and phylogenetic analysis of membrane protein genes of porcine epidemic diarrhea virus isolates in China Full-genome sequence analysis of a variant strain of porcine epidemic diarrhea virus in South Korea Genomic and antigenic characterization of Porcine epidemic diarrhoea virus strains isolated from South Korea

title:
  Genomic and antigenic characterization of porcine epidemic diarrhoea virus strains isolated from South Korea, 2017

abstract:
  Porcine epidemic diarrhoea virus (PEDV) is a globally emerging and re‐emerging enteric coronavirus in pigs causing serious economic threats to the world swine industry. Since the re‐emergence of massive PEDV outbreaks in South Korea in 2013−2014, domestic pig farms have continued to experience PED epidemics or endemics. This study represents the molecular characterization of PEDV isolates identified in diarrhoeic animals collected across the country in 2017. Initial sequencing analysis of the full‐length S genes revealed that 70% of the 2017 isolates (7/10) belong to the G2b subgroup, while the remaining isolates were classified as G1b. The data indicated that both variant G1b and global epidemic G2b strains were responsible for current PED outbreaks in South Korea. The 2017 G1b and G2b isolates shared 98.7%–99.4% and 98.1%–99.2% amino acid sequence identity at the S gene level and 99.3% and 99.0%–99.6% nucleotide sequence homology at the genome level compared to the corresponding Korean prototype G1b and G2b strains, respectively. In an interesting manner, one G2b‐like KNU‐1705 strain was found to possess a large 39‐nucleotide deletion in the ORF1a region theoretically encoding nonstructural protein 3. Phylogenetic analysis based on the entire genome and spike protein sequences indicated that the 2017 isolates were most closely related to other global G1b or G2b strains but formed different branches within the same genogroup. These results indicate that PEDVs undergo continuous evolution in the field. In addition, one 2017 PEDV strain, KOR/KNU‐1705/2017, was successfully isolated and propagated in Vero cells. The antisera raised against the Korean prototype 2014 G2b strain efficiently neutralized KNU‐1705 virus infection, suggesting antigenic homology between the 2014 and 2017 PEDV strains. Our data advance the understanding of the molecular epidemiology and antigenicity of PEDV circulating in South Korea.


id: cord-342766-ndzhlf3k
title: Identification and genetic characterization of porcine circovirus type 3 in China
author: Ku, X.
date: 2017-03-19
txt: ./txt/cord-342766-ndzhlf3k.txt
cache: ./cache/cord-342766-ndzhlf3k.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28317326/
doi: 10.1111/tbed.12638
summary:
  title: Identification and genetic characterization of porcine circovirus type 3 in China This study reports on the first identification, widely epidemic, different phylogenetic clusters, potential role in sow reproductive failure and possible origins of PCV3 in China. PCV3 is associated with porcine dermatitis, nephropathy syndrome and reproductive failure (Palinski et al., 2016) and cardiac and multisystemic inflammation (Phan et al., 2016) . To better understand the infection status, epidemic status, geographical distribution, potential pathogenicity and genetic characteristics of PCV3 in China, a total of 222 samples (i.e., stillborn, tissues, semen and serum) were collected from 35 farms in 11 provinces or districts (i.e., Anhui, Chongqing, Fujian, Hebei, Henan, Hunan, Jiangsu, Jiangxi, Liaoning, Shenyang and Zhejiang) in China. Genetic variability of porcine circovirus 2 (PCV2) field isolates from vaccinated and nonvaccinated pig herds in Germany Similarity plot of the whole genome of 10 PCV3 isolates with 5 Bat circovirus isolates.

abstract:
  A novel circovirus called porcine circovirus type 3 (PCV3) was recently reported to exist in the USA. This circovirus is associated with porcine dermatitis, nephropathy syndrome and reproductive failure. This study reports on the first identification, widely epidemic, different phylogenetic clusters, potential role in sow reproductive failure and possible origins of PCV3 in China.


id: cord-343949-zmuvq6e3
title: First report and genetic characterization of feline kobuvirus in diarrhoeic cats in China
author: Lu, Gang
date: 2018-06-06
url: https://www.ncbi.nlm.nih.gov/pubmed/29873199/
doi: 10.1111/tbed.12916
abstract:
  Feline kobuvirus (FeKoV) is a newly discovered organism, classified under the species Aichivirus A of the genus Kobuvirus. Since it was first reported in 2013, molecular evidence for FeKoV in the feline population has been restricted to two countries: Korea and Italy. In this study, we collected faecal samples from cats in southern China and detected the FeKoV RNA in these samples. A prevalence rate of 9.9% (8/81) was identified by RT‐PCR, and all positive samples were obtained from diarrhoeic animals. In addition, FeKoV was shown positive associated with diarrhoea in cats, with a correlation coefficient of 0.25. Next, we designed three primer pairs with degenerate bases, which targeted the conservative overlapping region of the entire published FeKoV genome, and sequenced the near‐complete genome of the first Chinese field FeKoV strain, WHJ‐1, using long‐fragment PCR. Finally, we analysed WHJ‐1's homology and phylogeny using the polyprotein gene. The results indicated that FeKoV has rapidly mutated since it was first discovered. This study will help to better understand FeKoV's epidemiology, evolutionary pattern and genetic diversity.


id: cord-347475-ttmactz0
title: Outbreak of Porcine Epidemic Diarrhea Virus in Portugal, 2015
author: Mesquita, J. R.
date: 2015-09-07
txt: ./txt/cord-347475-ttmactz0.txt
cache: ./cache/cord-347475-ttmactz0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26344708/
doi: 10.1111/tbed.12409
summary:
  An outbreak of porcine epidemic diarrhea virus (PEDV) in the South of Portugal in January 2015 and the spread of PEDV northwards in the territory are described. Comparative analysis of the amplified sequences showed a very high (99.0%) identity with the PEDV variant most recently reported in the United States and also show complete (100%) identity to the strains recently reported in Germany, supporting the hypothesis that a unique strain is currently circulating in Europe. Typical clinical symptoms of PED include watery diarrhea, vomiting, dehydration, and Porcine epidemic diarrhea virus (PEDV; family Coronaviridae, subfamily Coronavirinae, genus Alphacoronavirus) is a highly contagious virus responsible for enteric disease in swine characterized by an acute onset of symptoms including severe watery diarrhea, vomiting, dehydration, and high mortality in suckling piglets (ICTV, 2012; Song and Park, 2012) . 2013: Emergence of porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences

abstract:
  An outbreak of porcine epidemic diarrhea virus (PEDV) in the South of Portugal in January 2015 and the spread of PEDV northwards in the territory are described. Comparative analysis of the amplified sequences showed a very high (99.0%) identity with the PEDV variant most recently reported in the United States and also show complete (100%) identity to the strains recently reported in Germany, supporting the hypothesis that a unique strain is currently circulating in Europe. The origin of this PEDV variant still needs to be elucidated and further studies in the remaining European countries may contribute to the knowledge.


id: cord-351564-nikcd44o
author: Zhang, Xiaozhan
date: 2020-01-24
url: https://www.ncbi.nlm.nih.gov/pubmed/31943814/
doi: 10.1111/tbed.13477
title:
  Molecular characterization of variant infectious bronchitis virus in China, 2019: Implications for control programmes

abstract:
  Infectious bronchitis virus (IBV), an ongoing emergence enveloped virus with a single‐stranded positive‐sense RNA genome, belongs to the Gammacoronavirus genus in the Coronaviridae family. IBV‐associated tracheitis, nephritis, salpingitis, proventriculitis and egg drop have caused devastating economic losses to poultry industry worldwide. Since the end of 2018, a remarkably increasing number of commercial broilers and layers, vaccinated or not, were infected with IBV in China. Here, we described two IB outbreaks with severe respiratory system or kidney injury in IBV‐vaccinated commercial poultry farms in central China. Other possible causative viral pathogens, including avian influenza virus (AIV), Newcastle disease virus (NDV) and Kedah fatal kidney syndrome virus (KFKSV), were excluded by reverse transcription‐polymerase chain reaction (RT‐PCR), and three virulent IBV strains, HeN‐1/China/2019, HeN‐2/China/2019 and HeN‐101/China/2019, were identified. Although the gross pathologic appearance of these two IB outbreaks was different, the newly identified IBV strains were all closely related to the ck/China/I0529/17 strain and grouped into GI‐19 genotype clade based on the sequencing and phylogenetic analysis of the complete S1 genes. Moreover, there are still some evolutionary distance between the newly identified IBV strains, HeN‐101/China/2019 in particular, and other GI‐19 strains, suggesting that Chinese IBV strains constantly emerge and evolve towards different directions. In conclusion, this study provided an insight of the recently emerging IBV outbreaks in IBV‐vaccinated commercial poultry farms and identified the genetic characteristics of three virulent GI‐19 IBV strains, which shows the need to carry out proper preventive measures and control strategies.


id: cord-351584-380s4j70
title: The role of climate during the COVID‐19 epidemic in New South Wales, Australia
author: Ward, Michael P.
date: 2020-06-01
url: https://www.ncbi.nlm.nih.gov/pubmed/32438520/
doi: 10.1111/tbed.13631
abstract:
  Previous research has identified a relationship between climate and occurrence of SARS‐CoV and MERS‐CoV cases, information that can be used to reduce the risk of infection. Using COVID‐19 notification and postcode data from New South Wales, Australia during the exponential phase of the epidemic in 2020, we used time series analysis to investigate the relationship between 749 cases of locally acquired COVID‐19 and daily rainfall, 9 a.m. and 3 p.m. temperature, and 9 a.m. and 3 p.m. relative humidity. Lower 9 a.m. relative humidity (but not rainfall or temperature) was associated with increased case occurrence; a reduction in relative humidity of 1% was predicted to be associated with an increase of COVID‐19 cases by 6.11%. During periods of low relative humidity, the public health system should anticipate an increased number of COVID‐19 cases.


id: cord-352211-3ps5o8ji
author: Mai, K.
date: 2017-03-27
txt: ./txt/cord-352211-3ps5o8ji.txt
cache: ./cache/cord-352211-3ps5o8ji.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28345292/
doi: 10.1111/tbed.12644
summary:
  A previous study (Zhai et al., 2016) reported that the current prevalence in Southern China was 1.54% (5/390), and three of the five detected strains were from Guangdong Province, revealing that the information regarding the molecular epidemiology of PDCoVs in Guangdong was still limited. T A B L E 3 Detection of porcine enteric pathogens from 13 tissue cultured purified PDCoV-positive samples from 11 swine farms in Guangdong Two pairs of strains 07 and 08 from farm G and 10 and 11 from farm I were isolated from the same commercial swine farms, but at different times. Complete genome sequence of strain SDCV/USA/Illinois121/2014, a porcine deltacoronavirus from the United States Rapid detection, complete genome sequencing, and phylogenetic analysis of porcine deltacoronavirus. Newly emerged porcine deltacoronavirus associated with diarrhoea in swine in China: Identification, prevalence and full-length genome sequence analysis Complete genome sequence of porcine deltacoronavirus strain CH/Sichuan/S27/2012 from Mainland China

title:
  The detection and phylogenetic analysis of porcine deltacoronavirus from Guangdong Province in Southern China

abstract:
  Porcine deltacoronavirus (PDCoV) is a newly discovered coronavirus that causes diarrhoea, vomiting and dehydration in sucking and nursing piglets. It was first reported in Hong Kong in 2012 and has since been discovered in the United States, Canada, South Korea, mainland China, Thailand and Laos. PDCoV has been experimentally proved to lead to diarrhoea in swine and it was detected positive in pigs in Guangdong, southern China. In our study, 252 faecal and intestinal samples from sucking piglets and sows with diarrhoea were surveyed for common enteric viruses. We found a prevalence of PDCoV (21.8%), porcine epidemic diarrhoea virus (65.5%), transmissible gastroenteritis virus (0%), rotavirus group A (25.0%) and porcine kobuvirus (68.7%). We isolated 13 PDCoV strains and discovered that PDCoV infections were often co‐infections with kobuvirus rather than the commonly linked porcine epidemic diarrhoea virus. Phylogenetic analysis of S gene and N gene revealed that 11 of 13 PDCoV strains belonged to Chinese lineage. As for the left two strains, one single strain (CHN‐GD16‐05) belonged to American and Korean lineages while another strain (CHN‐GD16‐03) was similar to a Thai strain, but only in the S gene. This suggested a possible recombination event between the Thai and the newly described Chinese strain.


id: cord-354729-dpaz01np
author: Huan, Changchao
date: 2019-08-22
url: https://doi.org/10.1111/tbed.13321
doi: 10.1111/tbed.13321
title:
  Characterization and evolution of the coronavirus porcine epidemic diarrhoea virus HLJBY isolated in China

abstract:
  A strain of porcine epidemic diarrhoea virus (PEDV), namely HLJBY, was isolated in Heilongjiang province, China. To provide insight into the understanding of the phylogenetic and the current epidemiological status of PEDV, PEDV HLJBY was compared with CV777 and other PEDV strains deposited in the GenBank. The homology between the entire genomic nucleotide sequences of PEDV HLJBY and CV777 was 97.7%. The homology of M gene was the highest (99.0%). However, the homology of ORF3 gene was 97.7%, and protein of ORF3 was 90.1%. In addition, HLJBY showed the highest nucleotide identity (99.9%) with PEDV‐SX/China/2017 strain and lowest similarity (91.2%) to PEDV/Belgorod/dom/2008 strain. We analysed the changes in S gene and its protein of PEDV HLJBY with 65 historic PEDV strains. The highest nucleotide identity was 99.9% compared with PEDV‐SX/China/2017 strain, and the lowest nucleotide identity was 60.0% compared with PEDV/Belgorod/dom/2008 strain. The length of deduced amino acid sequences of S proteins varied from 1,372 to 1,390 amino acids (aa). Compared with most aa sequences of S proteins, HLJBY exhibited 5 aa deletions (position 55, 59–61, 144). Analysis and comparison of open reading frame 3 (ORF3) proteins between HLJBY strain and other PEDV strains were also focused in this study. We revealed that the length of deduced amino acid sequences of ORF3 proteins was 80–224 aa among tested strains and the identity of HLJBY ORF3 amino acids with other PEDV strains was 71.4%–98.9%. ORF3 protein of both HLJBY strain and PEDV‐SX/China/2017 strain consists of 91 aa, with 133 aa deletions at their C' end in relation to the other tested PEDV strains. The phylogenetic tree based on different proteins or genes resulted in different phylogenetic groups. For pathogenicity evaluation of PEDV HLJBY strain, colostrum deprivation piglets were challenged with PEDV HLJBY, and PEDV reference strain CV777 as a control, the results showed that animals challenged with either of these PEDV strains developed diarrhoea, and histopathological examination of small intestines of challenged animals showed acute viral enteritis with villous atrophy in either PEDV HLJBY‐P10 or PEDV CV777‐P8 inoculated piglets.


