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Chang X, Lin Q, Zhang Q, Hu J, Tursun G, Deng Y, Guo C, Wang X. Molecular Analysis of Caprine Enterovirus Circulating in China during 2016–2021: Evolutionary Significance. Viruses 2022; 14:v14051051. [PMID: 35632794 PMCID: PMC9143109 DOI: 10.3390/v14051051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 11/18/2022] Open
Abstract
Here, we report the characterization of 13 novel caprine/ovine enterovirus strains isolated from different regions in China during 2016–2021. Immunoperoxidase monolayer assay showed that these viral strains shared strong cross-reaction with the previously reported caprine enterovirus CEV-JL14. Alignment analysis of the complete nucleotide sequences revealed 79.2%–87.8% and 75.0%–76.7% sequence identity of these novel caprine enterovirus strains to CEV-JL14 and TB4-OEV, respectively. Phylogenetic analyses clustered these novel strains to EV-G based on the amino acid sequences of P1 and 2C+3CD. Moreover, phylogenetic analysis of these caprine enterovirus strains identified three new EV-G types using VP1 sequences. These results demonstrate the genetic variations and the evolution of caprine enterovirus.
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Wang I, Gupta SK, Ems G, Jayawardena N, Strauss M, Bostina M. Cryo-EM Structure of a Possum Enterovirus. Viruses 2022; 14:v14020318. [PMID: 35215909 PMCID: PMC8879876 DOI: 10.3390/v14020318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/24/2022] [Accepted: 02/01/2022] [Indexed: 01/27/2023] Open
Abstract
Enteroviruses (EVs) represent a substantial concern to global health. Here, we present the cryo-EM structure of a non-human enterovirus, EV-F4, isolated from the Australian brushtail possum to assess the structural diversity of these picornaviruses. The capsid structure, determined to ~3 Å resolution by single particle analysis, exhibits a largely smooth surface, similar to EV-F3 (formerly BEV-2). Although the cellular receptor is not known, the absence of charged residues on the outer surface of the canyon suggest a different receptor type than for EV-F3. Density for the pocket factor is clear, with the entrance to the pocket being smaller than for other enteroviruses.
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Affiliation(s)
- Ivy Wang
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7, Canada;
| | | | - Guillaume Ems
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand; (G.E.); (N.J.)
- Faculté des Sciences, Université de Namur, 5000 Namur, Belgium
| | - Nadishka Jayawardena
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand; (G.E.); (N.J.)
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Mike Strauss
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7, Canada;
- Correspondence: (M.S.); (M.B.)
| | - Mihnea Bostina
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand; (G.E.); (N.J.)
- Otago Micro and Nano Imaging, University of Otago, Dunedin 9016, New Zealand
- Correspondence: (M.S.); (M.B.)
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Ji C, Zhang Y, Sun R, Ma J, Pan Z, Yao H. Isolation and Identification of Type F Bovine Enterovirus from Clinical Cattle with Diarrhoea. Viruses 2021; 13:v13112217. [PMID: 34835023 PMCID: PMC8617846 DOI: 10.3390/v13112217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 12/15/2022] Open
Abstract
Recently, bovine enterovirus (BEV) has caused several respiratory and gastrointestinal diseases outbreaks in cattle. Monitoring the epidemiological and pathogenic characteristics of this virus is crucial to controlling its spread. We isolated a BEV strain with typical cytopathic effects from the faeces of cows with significant diarrhoeal symptoms in China and observed the viral particles within 20–30 nm through transmission electron microscopy. Then, we designated this strain as HB19-1 in this study. The multistep growth curves showed that the virus propagated well in the MDBK cells. Molecular genetic analysis of VP1 indicated that HB19-1 belonged to the BEV-F1 group. Although the challenged ICR mice did not exhibit typical disease symptoms in animal infection assay, we observed significant pathological damage in the lungs, intestines, and muscle tissues. In summary, we isolated a BEV strain HB19-1 causing severe diarrhoea in cattle and proposed reinforcing the epidemiological surveillance of this virus.
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Affiliation(s)
- Chengyuan Ji
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (C.J.); (Y.Z.); (R.S.); (J.M.); (Z.P.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing 210095, China
| | - Yao Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (C.J.); (Y.Z.); (R.S.); (J.M.); (Z.P.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing 210095, China
| | - Ruini Sun
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (C.J.); (Y.Z.); (R.S.); (J.M.); (Z.P.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing 210095, China
| | - Jiale Ma
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (C.J.); (Y.Z.); (R.S.); (J.M.); (Z.P.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing 210095, China
| | - Zihao Pan
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (C.J.); (Y.Z.); (R.S.); (J.M.); (Z.P.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing 210095, China
| | - Huochun Yao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (C.J.); (Y.Z.); (R.S.); (J.M.); (Z.P.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing 210095, China
- Correspondence: ; Tel.: +86-025-84395328
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Zhu J, Qi M, Jiang C, Peng Y, Peng Q, Chen Y, Hu C, Chen J, Chen X, Chen H, Guo A. Prevalence of bovine astroviruses and their genotypes in sampled Chinese calves with and without diarrhoea. J Gen Virol 2021; 102. [PMID: 34424158 PMCID: PMC8513638 DOI: 10.1099/jgv.0.001640] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Bovine astrovirus (BoAstV) belongs to genus Mamastravirus (MAstV). It can be detected in the faeces of both diarrhoeal and healthy calves. However, its prevalence, genetic diversity, and association with cattle diarrhoea are poorly understood. In this study, faecal samples of 87 diarrhoeal and 77 asymptomatic calves from 20 farms in 12 provinces were collected, and BoAstV was detected with reverse transcription-polymerase chain reaction (RT-PCR). The overall prevalence rate of this virus in diarrhoeal and asymptomatic calves was 55.17 % (95 % CI: 44.13, 65.85 %) and 36.36 % (95 % CI: 25.70, 48.12 %), respectively, indicating a correlation between BoAstV infection and calf diarrhoea (OR=2.15, P=0.024). BoAstV existed mainly in the form of co-infection (85.53 %) with one to five of nine viruses, and there was a strong positive correlation between BoAstV co-infection and calf diarrhoea (OR=2.83, P=0.004). Binary logistic regression analysis confirmed this correlation between BoAstV co-infection and calf diarrhoea (OR=2.41, P=0.038). The co-infection of BoAstV and bovine rotavirus (BRV) with or without other viruses accounted for 70.77 % of all the co-infection cases. The diarrhoea risk for the calves co-infected with BoAstV and BRV was 8.14-fold higher than that for the calves co-infected with BoAstV and other viruses (OR=8.14, P=0.001). Further, the co-infection of BoAstV/BRV/bovine kobuvirus (BKoV) might increase the risk of calf diarrhoea by 14.82-fold, compared with that of BoAstV and other viruses (OR=14.82, P <0.001). Then, nearly complete genomic sequences of nine BoAstV strains were assembled by using next-generation sequencing (NGS) method. Sequence alignment against known astrovirus (AstV) strains at the levels of both amino acids and nucleotides showed a high genetic diversity. Four genotypes were identified, including two known genotypes MAstV-28 (n=3) and MAstV-33 (n=2) and two novel genotypes designated tentatively as MAstV-34 (n=1) and MAstV-35 (n=3). In addition, seven out of nine BoAstV strains showed possible inter-genotype recombination and cross-species recombination. Therefore, our results increase the knowledge about the prevalence and the genetic evolution of BoAstV and provide evidence for the association between BoAstV infection and calf diarrhoea.
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Affiliation(s)
- Jie Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China
| | - Mingpu Qi
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China
| | - Chuanwen Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China
| | - Yongchong Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China
| | - Qingjie Peng
- Wuhan Keqian Biology Co.Ltd, Wuhan, 430070, PR China
| | - Yingyu Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, PR China.,Key Laboratory of Ruminant Bio-products of Ministry of Agriculture and and Rural Affairs, Huazhong Agriculture University, Wuhan 430070, PR China
| | - Changmin Hu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Jianguo Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Xi Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China.,Wuhan Keqian Biology Co.Ltd, Wuhan, 430070, PR China
| | - Aizhen Guo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, PR China.,Key Laboratory of Ruminant Bio-products of Ministry of Agriculture and and Rural Affairs, Huazhong Agriculture University, Wuhan 430070, PR China
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Molecular Identification of Enteroviruses from Cattle and Goat Feces and Environment in Thailand. Appl Environ Microbiol 2019; 85:AEM.02420-18. [PMID: 30552188 DOI: 10.1128/aem.02420-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/07/2018] [Indexed: 12/29/2022] Open
Abstract
The identification and characterization of viruses of the genus Enterovirus in healthy and infected livestock, including cattle and goats, have been increasing. Enterovirus E (EV-E) and Enterovirus F (EV-F) are commonly found in cattle, whereas Enterovirus G (EV-G) is found in goats. In this study, molecular and phylogenetic analyses were performed to determine the prevalence of EVs in cattle and goat feces from Kanchanaburi Province, Thailand. The presence of EVs in water samples and the feces of other animals collected from the areas surrounding cattle and goat farms was also investigated. By use of 5'-untranslated region (5' UTR) real-time reverse transcription-PCR (RT-PCR), EVs were detected in 39.5% of cattle samples, 47% of goat samples, 35.3% of water samples, and one pool of chicken feces. Phylogenetic analysis revealed the presence of EV-E and EV-F in cattle, EV-E and EV-G in goats, and EV-F in water samples and chicken feces. Analysis of enteroviral VP1 sequences from cattle revealed that the EV-E genotypes circulating in the study region were EV-E1, with a possible new genotype that is closely related to EV-E2. Analysis of enteroviral VP1 sequences from goats suggested the circulation of EV-G5 and a possible new genotype that is closely related to EV-G20. Sequence analyses also suggested that although the VP1 sequences from goats were closely related to those of EV-G, which were considered porcine enterovirus sequences, their 5' UTRs form a separated cluster with sequences of sheep and goat origin, suggesting a new classification of the ovine/caprine-specific enterovirus group.IMPORTANCE Possible new EV-E and EV-G genotypes were identified for EVs detected in this study. The EV-E viruses were also successfully isolated from MDBK cells. The goat EV sequence analysis suggested the presence of an ovine/caprine-specific EV group that is different from EV-G of porcine origin. The significance of our research is that it identifies and characterizes possible novel EVs, thereby indicating that enteroviruses in animals are continually evolving. The facts that enteroviruses can persist in the environment, contaminate it for long periods, and be transmitted between animals raise serious concerns regarding this group of viruses as emerging livestock pathogens.
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Gomez DE, Weese JS. Viral enteritis in calves. THE CANADIAN VETERINARY JOURNAL = LA REVUE VETERINAIRE CANADIENNE 2017; 58:1267-1274. [PMID: 29203935 PMCID: PMC5680732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A complex community of bacteria, viruses, fungi, protists, and other microorganisms inhabit the gastrointestinal tract of calves and play important roles in gut health and disease. The viral component of the microbiome (the virome) is receiving increasing attention for its role in neonatal calf diarrhea (NCD). Rotavirus and coronavirus have for a long time been associated with NCD and commercial vaccines have been produced against these agents. Recently, several other viruses which may play a role in diarrhea have been discovered in calf fecal samples, mostly by sequence-based methods. These viruses include torovirus, norovirus, nebovirus, astrovirus, kobuvirus, and enterovirus. Most studies have involved epidemiologic investigations seeking to show association with diarrhea for each virus alone or in combination with potential pathogens. However, determining the contribution of these viruses to calf diarrhea has been challenging and much uncertainty remains concerning their roles as primary pathogens, co-infection agents, or commensals.
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Affiliation(s)
- Diego E. Gomez
- Address all correspondence to Dr. Diego E. Gomez; e-mail:
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A novel enterovirus species identified from severe diarrheal goats. PLoS One 2017; 12:e0174600. [PMID: 28376123 PMCID: PMC5380325 DOI: 10.1371/journal.pone.0174600] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 03/07/2017] [Indexed: 11/23/2022] Open
Abstract
Backgrounds The Enterovirus genus of the family of Picornaviridae consists of 9 species of Enteroviruses and 3 species of Rhinoviruses based on the latest virus taxonomy. Those viruses contribute significantly to respiratory and digestive disorders in human and animals. Out of 9 Enterovirus species, Enterovirus E-G are closely related to diseases affecting on livestock industry. While enterovirus infection has been increasingly reported in cattle and swine, the enterovirus infections in small ruminants remain largely unknown. Methods Virology, molecular and bioinformatics methods were employed to characterize a novel enterovirus CEV-JL14 from goats manifesting severe diarrhea with morbidity and mortality respectively up to 84% and 54% in China. Results CEV-JL14 was defined and proposed as a new Enterovirus species L within the genus of Enterovirus of the family Picornaviridae. CEV-JL14 had a complete genome sequence of 7461 nucleotides with an ORF encoding 2172 amino acids, and shared 77.1% of genomic sequence identity with TB4-OEV, an ovine enterovirus. Comparison of 5’-UTR and structural genes of CEV-JL14 with known Enterovirus species revealed highly genetic variations among CEV-JL14 with known Enterovirus species. VP1 nucleotide sequence identities of CEV-14 were 51.8%-53.5% with those of Enterovirus E and F, 30.9%-65.3% with Enterovirus G, and 43.8–51. 5% with Enterovirus A-D, respectively. CEV-JL14 was proposed as a novel species within the genus of Enterovirus according to the current ICTV demarcation criteria of enteroviruses. Conclusions CEV-JL14 clustered phylogenetically to neither Enterovirus E and F, nor to Enterovirus G. It was defined and proposed as novel species L within the genus of Enterovirus. This is the first report of caprine enterovirus in China, the first complete genomic sequence of a caprine enterovirus revealed, and the unveiling of significant genetic variations between ovine enterovirus and caprine enterovirus, thus broadening the current understanding of enteroviruses.
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Tsuchiaka S, Rahpaya SS, Otomaru K, Aoki H, Kishimoto M, Naoi Y, Omatsu T, Sano K, Okazaki-Terashima S, Katayama Y, Oba M, Nagai M, Mizutani T. Identification of a novel bovine enterovirus possessing highly divergent amino acid sequences in capsid protein. BMC Microbiol 2017; 17:18. [PMID: 28095784 PMCID: PMC5240211 DOI: 10.1186/s12866-016-0923-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/28/2016] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Bovine enterovirus (BEV) belongs to the species Enterovirus E or F, genus Enterovirus and family Picornaviridae. Although numerous studies have identified BEVs in the feces of cattle with diarrhea, the pathogenicity of BEVs remains unclear. Previously, we reported the detection of novel kobu-like virus in calf feces, by metagenomics analysis. In the present study, we identified a novel BEV in diarrheal feces collected for that survey. Complete genome sequences were determined by deep sequencing in feces. Secondary RNA structure analysis of the 5' untranslated region (UTR), phylogenetic tree construction and pairwise identity analysis were conducted. RESULTS The complete genome sequences of BEV were genetically distant from other EVs and the VP1 coding region contained novel and unique amino acid sequences. We named this strain as BEV AN12/Bos taurus/JPN/2014 (referred to as BEV-AN12). According to genome analysis, the genome length of this virus is 7414 nucleotides excluding the poly (A) tail and its genome consists of a 5'UTR, open reading frame encoding a single polyprotein, and 3'UTR. The results of secondary RNA structure analysis showed that in the 5'UTR, BEV-AN12 had an additional clover leaf structure and small stem loop structure, similarly to other BEVs. In pairwise identity analysis, BEV-AN12 showed high amino acid (aa) identities to Enterovirus F in the polyprotein, P2 and P3 regions (aa identity ≥82.4%). Therefore, BEV-AN12 is closely related to Enterovirus F. However, aa sequences in the capsid protein regions, particularly the VP1 encoding region, showed significantly low aa identity to other viruses in genus Enterovirus (VP1 aa identity ≤58.6%). In addition, BEV-AN12 branched separately from Enterovirus E and F in phylogenetic trees based on the aa sequences of P1 and VP1, although it clustered with Enterovirus F in trees based on sequences in the P2 and P3 genome region. CONCLUSIONS We identified novel BEV possessing highly divergent aa sequences in the VP1 coding region in Japan. According to species definition, we proposed naming this strain as "Enterovirus K", which is a novel species within genus Enterovirus. Further genomic studies are needed to understand the pathogenicity of BEVs.
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Affiliation(s)
- Shinobu Tsuchiaka
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagito, Gifu-shi, Gifu, 501-1193, Japan.,Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Sayed Samim Rahpaya
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagito, Gifu-shi, Gifu, 501-1193, Japan.,Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Konosuke Otomaru
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima-shi, Kagoshima, 890-0065, Japan
| | - Hiroshi Aoki
- Faculty of Veterinary Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Mai Kishimoto
- Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Yuki Naoi
- Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Tsutomu Omatsu
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagito, Gifu-shi, Gifu, 501-1193, Japan.,Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Kaori Sano
- Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Sachiko Okazaki-Terashima
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagito, Gifu-shi, Gifu, 501-1193, Japan.,Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Yukie Katayama
- Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Mami Oba
- Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Makoto Nagai
- Faculty of Bioresources and Environmental Sciences, Ishikawa prefectural University, 1-308, Suematsu, Nonoichi-shi, Ishikawa, 921-8836, Japan
| | - Tetsuya Mizutani
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagito, Gifu-shi, Gifu, 501-1193, Japan. .,Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan.
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Isolation and characterization of a new enterovirus F in yak feces in the Qinghai-Tibetan Plateau. Arch Virol 2016; 162:523-527. [DOI: 10.1007/s00705-016-3119-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/11/2016] [Indexed: 10/20/2022]
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Kosoltanapiwat N, Yindee M, Chavez IF, Leaungwutiwong P, Adisakwattana P, Singhasivanon P, Thawornkuno C, Thippornchai N, Rungruengkitkun A, Soontorn J, Pearsiriwuttipong S. Genetic variations in regions of bovine and bovine-like enteroviral 5'UTR from cattle, Indian bison and goat feces. Virol J 2016; 13:13. [PMID: 26811239 PMCID: PMC4727389 DOI: 10.1186/s12985-016-0468-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 01/17/2016] [Indexed: 11/16/2022] Open
Abstract
Background Bovine enteroviruses (BEV) are members of the genus Enterovirus in the family Picornaviridae. They are predominantly isolated from cattle feces, but also are detected in feces of other animals, including goats and deer. These viruses are found in apparently healthy animals, as well as in animals with clinical signs and several studies reported recently suggest a potential role of BEV in causing disease in animals. In this study, we surveyed the presence of BEV in domestic and wild animals in Thailand, and assessed their genetic variability. Methods Viral RNA was extracted from fecal samples of cattle, domestic goats, Indian bison (gaurs), and deer. The 5’ untranslated region (5’UTR) was amplified by nested reverse transcription-polymerase chain reaction (RT-PCR) with primers specific to BEV 5’UTR. PCR products were sequenced and analyzed phylogenetically using the neighbor-joining algorithm to observe genetic variations in regions of the bovine and bovine-like enteroviral 5’UTR found in this study. Results BEV and BEV-like sequences were detected in the fecal samples of cattle (40/60, 67 %), gaurs (3/30, 10 %), and goats (11/46, 24 %). Phylogenetic analyses of the partial 5’UTR sequences indicated that different BEV variants (both EV-E and EV-F species) co-circulated in the domestic cattle, whereas the sequences from gaurs and goats clustered according to the animal species, suggesting that these viruses are host species-specific. Conclusions Varieties of BEV and BEV-like 5’UTR sequences were detected in fecal samples from both domestic and wild animals. To our knowledge, this is the first report of the genetic variability of BEV in Thailand.
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Affiliation(s)
- Nathamon Kosoltanapiwat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Marnoch Yindee
- Faculty of Veterinary Science, Mahidol University, Bangkok, Thailand.
| | - Irwin Fernandez Chavez
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Pornsawan Leaungwutiwong
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Pratap Singhasivanon
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Charin Thawornkuno
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Narin Thippornchai
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Amporn Rungruengkitkun
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Juthamas Soontorn
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Sasipan Pearsiriwuttipong
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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Sobhy NM, Mor SK, Mohammed MEM, Bastawecy IM, Fakhry HM, Youssef CRB, Abouzeid NZ, Goyal SM. Isolation and molecular characterization of bovine enteroviruses in Egypt. Vet J 2015; 206:317-21. [PMID: 26586212 PMCID: PMC7129267 DOI: 10.1016/j.tvjl.2015.10.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 09/29/2015] [Accepted: 10/04/2015] [Indexed: 01/07/2023]
Abstract
Bovine enterovirus (BEV) was isolated from diarrheic calves in Egypt. Sequencing revealed of BEV/Egypt/2014//KM667941 to have 7417 nucleotides (nt). The organization of nt was typical of the BEV genome including 822 nt in 5′NTR, 6498 nt in ORF, and 97 nt in 3′NTR. Phylogenetic analysis revealed clustering of BEV/Egypt/2014/KM667941 with BEV-F. A specific RT-PCR for BEV was developed to detect this pathogen in cattle.
Enteroviruses belong to the Picornaviridae family and infect a wide range of mammals including cattle. Bovine enterovirus (BEV) has recently been reclassified into E and F serotypes. BEV was first isolated in Egypt in 1966 although it has been known in other countries since the 1950s. In this study, BEV-F2 was isolated from calves with severe diarrhea and the isolated viruses were subjected to molecular characterization. Illumina sequencing of one of the isolates revealed the presence of a complete BEV-F genome sequence. The phylogenetic analysis revealed nucleotide substitutions along the genome in comparison with other known strains of BEV-F (HQ663846, AY508697 and DQ092795). Two primer sets were designed from the 3D and 5′NTR regions and used for the examination of the remaining isolates, which were confirmed to be of the BEV-F2 serotype. The availability of the complete genome sequence of this virus adds to the sequence database of the members of Picornaviridae and should be useful in future molecular studies of BEV.
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Affiliation(s)
- N M Sobhy
- Department of Animal Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia 44511, Egypt
| | - S K Mor
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - M E M Mohammed
- Department of Animal Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia 44511, Egypt
| | - I M Bastawecy
- Department of Virology, Animal Health Research Institute, Dokki, Giza 12618, Egypt
| | - H M Fakhry
- Veterinary Serum and Vaccine Research Institute, East of Cairo 131, Egypt
| | - C R B Youssef
- Department of Microbiology, Faculty of Pharmacy, Zagazig University, Zagazig, Sharkia 44519, Egypt
| | - N Z Abouzeid
- Department of Animal Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia 44511, Egypt
| | - S M Goyal
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55108, USA.
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12
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Shaukat S, Angez M, Alam MM, Jebbink MF, Deijs M, Canuti M, Sharif S, de Vries M, Khurshid A, Mahmood T, van der Hoek L, Zaidi SSZ. Identification and characterization of unrecognized viruses in stool samples of non-polio acute flaccid paralysis children by simplified VIDISCA. Virol J 2014; 11:146. [PMID: 25112200 PMCID: PMC4254409 DOI: 10.1186/1743-422x-11-146] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/30/2014] [Indexed: 12/22/2022] Open
Abstract
Background The use of sequence independent methods combined with next generation sequencing for identification purposes in clinical samples appears promising and exciting results have been achieved to understand unexplained infections. One sequence independent method, Virus Discovery based on cDNA Amplified Fragment Length Polymorphism (VIDISCA) is capable of identifying viruses that would have remained unidentified in standard diagnostics or cell cultures. Methods VIDISCA is normally combined with next generation sequencing, however, we set up a simplified VIDISCA which can be used in case next generation sequencing is not possible. Stool samples of 10 patients with unexplained acute flaccid paralysis showing cytopathic effect in rhabdomyosarcoma cells and/or mouse cells were used to test the efficiency of this method. To further characterize the viruses, VIDISCA-positive samples were amplified and sequenced with gene specific primers. Results Simplified VIDISCA detected seven viruses (70%) and the proportion of eukaryotic viral sequences from each sample ranged from 8.3 to 45.8%. Human enterovirus EV-B97, EV-B100, echovirus-9 and echovirus-21, human parechovirus type-3, human astrovirus probably a type-3/5 recombinant, and tetnovirus-1 were identified. Phylogenetic analysis based on the VP1 region demonstrated that the human enteroviruses are more divergent isolates circulating in the community. Conclusion Our data support that a simplified VIDISCA protocol can efficiently identify unrecognized viruses grown in cell culture with low cost, limited time without need of advanced technical expertise. Also complex data interpretation is avoided thus the method can be used as a powerful diagnostic tool in limited resources. Redesigning the routine diagnostics might lead to additional detection of previously undiagnosed viruses in clinical samples of patients. Electronic supplementary material The online version of this article (doi:10.1186/1743-422X-11-146) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Syed Sohail Zahoor Zaidi
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 45500, Pakistan.
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