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Liu Y, Liu L, Wang J, Wang T, Gao Y, Sun X, Yuan W, Li R, Wang J. Development of a new TaqMan-based real-time RT-PCR assay for the specific detection of bovine kobuvirus. Front Vet Sci 2022; 9:953599. [PMID: 35990282 PMCID: PMC9386250 DOI: 10.3389/fvets.2022.953599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/07/2022] [Indexed: 11/24/2022] Open
Abstract
Bovine kobuvirus (BKV) is a novel kobuvirus considered to be closely related to calf diarrhea and has become a worldwide epidemic. Currently, the BKV lacks an efficient and convenient detection method to assist the research on BKV prevalence. In this study, a new and specific TaqMan-based real-time RT-PCR for the detection of BKV was developed using the conserved region of the 3D gene. The assay was highly specific for BKV, without cross-amplification with other non-targeted pathogens. The limit of detection of this assay was 102 copies. Standard curves showed a strong linear correlation from 102 to 106 copies of BKV standard RNA per reaction, and the parameters revealed as a slope of −3.54, efficiency of 91.64%, and regression coefficients (R2) of 0.998. The assay was also reproducible, with the intra-assay and inter-assay coefficient of variation <1.0%. The newly developed real-time RT-PCR was validated using 243 fecal samples collected from diarrheic or non-diarrheic cattle from nine regions in Hebei province and revealed the positive detection of BKV at a ratio of 19.34% (47/243). Sequencing of partial 3D genes from 13 positive samples and the following phylogenetic analysis demonstrated the reliability of the assay. In conclusion, the newly developed TaqMan-based real-time RT-PCR could be used for the screening and epidemic monitoring of BKV.
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Affiliation(s)
- Yuelin Liu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
- Department of Animal and Plant Quarantine, Technology Center of Shijiazhuang Customs District, Shijiazhuang, China
| | - Libing Liu
- Department of Animal and Plant Quarantine, Technology Center of Shijiazhuang Customs District, Shijiazhuang, China
| | - Jinfeng Wang
- Department of Animal and Plant Quarantine, Technology Center of Shijiazhuang Customs District, Shijiazhuang, China
| | - Ting Wang
- Department of Animal Genetics and Breeding, Hebei Mountain Agricultural Technology Innovation Center, Hebei Agricultural University, Baoding, China
| | - Yaxin Gao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Xiaoxia Sun
- Department of Animal and Plant Quarantine, Technology Center of Shijiazhuang Customs District, Shijiazhuang, China
| | - Wanzhe Yuan
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Ruiwen Li
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
- *Correspondence: Ruiwen Li
| | - Jianchang Wang
- Department of Animal and Plant Quarantine, Technology Center of Shijiazhuang Customs District, Shijiazhuang, China
- Jianchang Wang
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Savard C, Ariel O, Fredrickson R, Wang L, Broes A. Detection and genome characterization of bovine kobuvirus (BKV) in faecal samples from diarrhoeic calves in Quebec, Canada. Transbound Emerg Dis 2022; 69:1649-1655. [PMID: 33788413 PMCID: PMC8938984 DOI: 10.1111/tbed.14086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/17/2021] [Accepted: 03/26/2021] [Indexed: 02/05/2023]
Abstract
Kobuviruses are known to infect the gastrointestinal tract of different animal species. Since its discovery in 2003, bovine kobuvirus (BKV) has been identified in faecal samples from diarrhoeic cattle in many countries, but only recently in North America. Although its possible role as an agent of calf diarrhoea remains to be determined, evidence is mounting. Our study reports for the first time the detection of BKV in faecal samples from diarrhoeic calves raised in Quebec, Canada. BKV was more commonly identified than eight known and common enteric calf pathogens. Further sequence analysis revealed that Canada BKV strain 1,043,507 was more closely correlated with the US BKV IL35164 strain than other BKV strains with complete genome. Continued surveillance and genomic characterization are needed to monitor BKV in the cattle around the world.
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Affiliation(s)
| | | | - Richard Fredrickson
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
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Hao L, Chen C, Bailey K, Wang L. Bovine kobuvirus-A comprehensive review. Transbound Emerg Dis 2021; 68:1886-1894. [PMID: 33146459 DOI: 10.1111/tbed.13909] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 10/14/2020] [Accepted: 10/30/2020] [Indexed: 02/05/2023]
Abstract
Bovine kobuvirus (BKV) is a single-stranded, positive sense, non-enveloped RNA virus in genus Kobuvirus of family Picornavirus. BKV was first identified in the culture media of HeLa cell containing calf serum in 2003. Since then, BKV has been detected in 13 countries of four different continents, suggesting widespread in the world. Herein, we review the detection and genomic characterization of BKV in 13 countries. All studies tested bovine faecal samples for BKV. These studies provide evidence that BKV might be a causative agent for neonatal calf diarrhoea. Therefore, further efforts including animal challenge study are urgently needed to unveil the pathogenicity of BKV.
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Affiliation(s)
- Lili Hao
- College of Life Science and Technology, Southwest Minzu University, Chengdu, China
| | - Chaoxi Chen
- College of Life Science and Technology, Southwest Minzu University, Chengdu, China
| | - Keith Bailey
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Leyi Wang
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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Wang L, Fredrickson R, Duncan M, Samuelson J, Hsiao SH. Bovine Kobuvirus in Calves with Diarrhea, United States. Emerg Infect Dis 2020; 26:176-178. [PMID: 31855534 PMCID: PMC6924891 DOI: 10.3201/eid2601.191227] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We detected bovine kobuvirus (BKV) in calves with diarrhea in the United States. The strain identified is related genetically to BKVs detected in other countries. Histopathologic findings also confirmed viral infection in 2 BKV cases. Our data show BKV is a potential causative agent for diarrhea in calves.
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Li H, Tang C, Yue H. Molecular detection and genomic characteristics of bovine kobuvirus from dairy calves in China. INFECTION GENETICS AND EVOLUTION 2019; 74:103939. [PMID: 31247336 PMCID: PMC7106006 DOI: 10.1016/j.meegid.2019.103939] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/11/2019] [Accepted: 06/22/2019] [Indexed: 11/18/2022]
Abstract
In this study, 96 diarrheic and 77 non-diarrheic fecal samples from dairy calves were collected from 14 dairy farms in 4 provinces to investigate the molecular prevalence and genomic characteristics of Bovine Kobuvirus (BKoV) in China. The results showed that the BKoV positive rate for the diarrheic feces (35.42%) was significantly higher than that for the non-diarrheic feces (11.69%, p < 0.001). Interestingly, three potential novel VP1 lineages were identified from 15 complete VP1 sequences, and a unique triple nucleotide insertion which can result in an aa insertion, was first observed in the 11/12 VP0 fragments with 660 bp long in this study, compared with known BKoV VP0 sequences. Moreover, the first Chinese BKoV genome was successfully obtained from a diarrheic fecal sample, named CHZ/CHINA. The open reading frame (ORF) of the genome from strain CHZ/China shares 87.4%–88.3% nucleotide (nt) and 93.7%–96.4% amino acid (aa) identity, compared with the three known genomes of BKoV. Interestingly, phylogenetic tree based on aa sequences of these genomes showed that CHZ/CHINA was clustered into an independent branch, suggesting the strain may represent a novel BKoV strain. The findings contribute to better understanding the molecular characteristics and evolution of BKoV. Three potential novel VP1 lineages in BKoV. A unique VP0 sequence type in BKoV. The first BKoV genome from China which may represent a novel BKoV strain. Contributing to better understanding the molecular characteristics of BKoV.
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Affiliation(s)
- Huiping Li
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China
| | - Cheng Tang
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China; Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Chengdu, China
| | - Hua Yue
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China; Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Chengdu, China.
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Viral metagenomics reveals significant viruses in the genital tract of apparently healthy dairy cows. Arch Virol 2019; 164:1059-1067. [PMID: 30783771 DOI: 10.1007/s00705-019-04158-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 01/03/2019] [Indexed: 01/03/2023]
Abstract
The virome in genital tract secretion samples collected from 80 dairy cattle in Shanghai, China, was characterized. Viruses detected included members of the families Papillomaviridae, Polyomaviridae, Hepeviridae, Parvoviridae, Astroviridae, Picornaviridae, and Picobirnaviridae. A member of a new species within the genus Dyoxipapillomavirus and six circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viral genomes were fully sequenced and phylogenetically analyzed. The prevalence of bovine polyomaviruses 1 and 2 was measured by PCR to be 10% (8/80) and 6.25% (5/80), respectively. PCR screening also indicated that the novel papillomavirus ujs-21015 and bovine herpesvirus 6 were present in three and two out of the 80 samples, respectively.
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Mohamed FF, Mansour SMG, Orabi A, El-Araby IE, Ng TFF, Mor SK, Goyal SM. Detection and genetic characterization of bovine kobuvirus from calves in Egypt. Arch Virol 2018; 163:1439-1447. [PMID: 29423548 PMCID: PMC7087207 DOI: 10.1007/s00705-018-3758-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 01/11/2018] [Indexed: 11/28/2022]
Abstract
Kobuviruses are small non-enveloped RNA viruses that probably cause diarrhea in cattle and swine. Since its discovery in 2003, few studies have addressed bovine kobuvirus (BKoV; a species of Aichivirus B) infections. BKoV has been reported in Europe, Asia, and South America, suggesting a worldwide distribution. To investigate the presence of BKoV in Egypt, 36 fecal specimens from diarrheic calves in two different Egyptian provinces (Cairo and Sharkia) were screened by RT-PCR and 24 (66.7%) were found positive for BKoV. RNA from one of the positive samples (BKoV/Egy-1/KY407744) was subjected to next-generation sequencing to determine the complete BKoV genome sequence. When compared to the only recorded BKoV genome sequence (BKoV/U-1/AB084788), the studied strain showed 94 amino acid (aa) substitutions through its entire polyprotein (2463 aa), one nucleotide (nt) insertion and one nt deletion in the 2B gene and 4-nt deletions in the UTRs (2 each). Additionally, five VP1 and seven 3D sequences were obtained from other samples by using RT-PCR and Sanger sequencing. A discrepancy in the phylogenetic topography of VP1 and 3D was observed, where the Egyptian VP1 sequences were classified as a distinct cluster within the proposed lineage 1 (genotype A), which also contained strains from the UK, Brazil, and Japan. While, the 3D sequences from Cairo were related to those of Chinese strains unlike Sharkia ones that were more closer to Korean strains. To the best of our knowledge, this is the first detection and genomic characterization of BKoV in Egypt or indeed Africa.
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Affiliation(s)
- Fakry F Mohamed
- Department of Virology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia, 44511, Egypt.,Department of Veterinary Population Medicine and Veterinary Diagnostic Laboratory, University of Minnesota, St. Paul, Minnesota, 55108, USA
| | - Shimaa M G Mansour
- Department of Virology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia, 44511, Egypt
| | - Ahmed Orabi
- Department of Virology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia, 44511, Egypt
| | - Iman E El-Araby
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia, 44511, Egypt
| | - Terry Fei Fan Ng
- College of Veterinary Medicine, University of Georgia Athens, Athens, GA, 30602, USA
| | - Sunil K Mor
- Department of Veterinary Population Medicine and Veterinary Diagnostic Laboratory, University of Minnesota, St. Paul, Minnesota, 55108, USA.
| | - Sagar M Goyal
- Department of Veterinary Population Medicine and Veterinary Diagnostic Laboratory, University of Minnesota, St. Paul, Minnesota, 55108, USA
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Ribeiro J, Lorenzetti E, Júnior JCR, da Silva Medeiros TN, Alfieri AF, Alfieri AA. Phylogenetic analysis of VP1 and RdRP genes of Brazilian aichivirus B strains involved in a diarrhea outbreak in dairy calves. Arch Virol 2017; 162:3691-3696. [PMID: 28849283 PMCID: PMC7086745 DOI: 10.1007/s00705-017-3531-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/23/2017] [Indexed: 02/07/2023]
Abstract
Aichivirus B has been reported worldwide in calves and adult cattle with and without diarrhea. The aim of this study was to describe the molecular characteristics of the RdRP and VP1 genes of aichivirus B strains identified as the most frequent etiologic agent in a neonatal diarrhea outbreak in a high-production Brazilian dairy cattle herd. Preliminary laboratory analysis ruled out important enteropathogens (Cryptosporidium spp; Eimeria spp., E. coli F5, and bovine coronavirus). Fecal samples from diarrheic (n = 24) and asymptomatic (n = 5) calves up to 30 days old were collected for virological analysis. RT-PCR assays were performed for the detection of aichivirus B RdRP and VP1 genes and for rotavirus A VP7 and VP4 genes in fecal samples. Asymptomatic calves (control group) were negative for both viruses. Aichivirus B and rotavirus A G10P[11] genotypes were found in 54.2% (13/24) and 25% (6/24) of the diarrheic fecal samples, respectively. Aichivirus B was only identified (83.3%, 10/12) in calves up to two weeks old. Phylogenetic analysis based on the RdRP gene grouped the Brazilian strains in a new branch within the aichivirus B group. Comparative analysis of the nucleotide sequence of the VP1 gene of Brazilian and Chinese aichivirus B strains allowed the strains identified in this study to be classified in the putative lineage 1. This is the first description of a high rate of aichivirus B detection in a diarrhea outbreak in dairy calves, and the first phylogenetic study of the VP1 gene of aichivirus B wild-type strains performed in South America.
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Affiliation(s)
- Juliane Ribeiro
- Laboratory of Animal Virology, Molecular Biology Unit, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, Campus Universitário, PO Box 10011, CEP 86057-970, Londrina, PR, Brazil
| | - Elis Lorenzetti
- Multi-User Animal Health Laboratory, Molecular Biology Unit, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, Campus Universitário, PO Box 10011, CEP 86057-970, Londrina, PR, Brazil
| | - José Carlos Ribeiro Júnior
- Multi-User Animal Health Laboratory, Molecular Biology Unit, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, Campus Universitário, PO Box 10011, CEP 86057-970, Londrina, PR, Brazil
| | - Thais Neris da Silva Medeiros
- Laboratory of Animal Virology, Molecular Biology Unit, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, Campus Universitário, PO Box 10011, CEP 86057-970, Londrina, PR, Brazil
| | - Alice Fernandes Alfieri
- Multi-User Animal Health Laboratory, Molecular Biology Unit, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, Campus Universitário, PO Box 10011, CEP 86057-970, Londrina, PR, Brazil
| | - Amauri Alcindo Alfieri
- Laboratory of Animal Virology, Molecular Biology Unit, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, Campus Universitário, PO Box 10011, CEP 86057-970, Londrina, PR, Brazil. .,National Institute of Science and Technology for the Dairy Production Chain (INCT - Leite), Rodovia Celso Garcia Cid, Campus Universitário, PO Box 10011, CEP 86057-970, Londrina, PR, Brazil.
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Candido M, Batinga MCA, Alencar ALF, de Almeida-Queiroz SR, da Glória Buzinaro M, Livonesi MC, Fernandes AM, de Sousa RLM. Molecular characterization and genetic diversity of bovine Kobuvirus, Brazil. Virus Genes 2016; 53:105-110. [PMID: 27623839 DOI: 10.1007/s11262-016-1391-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 09/06/2016] [Indexed: 12/01/2022]
Abstract
It is suggested that Bovine kobuvirus (BKV) is involved in the etiology of gastroenteric diseases especially among calves; however, this association remains unknown. This study evaluated 216 fecal samples from cattle with and without diarrhea symptoms obtained from different regions of Brazil. A 216 bp fragment of the BKV 3D gene was amplified by RT-PCR in 14.4 % (31/216) of the studied samples, and 17 samples were subjected to nucleotide sequencing. All positive samples were obtained from animals aged less than 5 months, and most of animals presented diarrhea (p < 0.05). Phylogenetic analyses showed that the obtained sequences were grouped within the genogroup 2 of BKV forming subclades specific for each Brazilian municipality sampled. In addition, the alignment of the sequences revealed differences of nucleotides between sequences from different locations. Our results indicate for the first time that there is a regional genotypic differentiation of BKV in Brazil.
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Affiliation(s)
- Marcelo Candido
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Avenida Duque de Caxias Norte, 225, Jardim Elite, Pirassununga, São Paulo, 13635-900, Brazil.
| | - Maria Cryskely Agra Batinga
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Avenida Duque de Caxias Norte, 225, Jardim Elite, Pirassununga, São Paulo, 13635-900, Brazil
| | - Anna Luiza Farias Alencar
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Avenida Duque de Caxias Norte, 225, Jardim Elite, Pirassununga, São Paulo, 13635-900, Brazil
| | - Sabrina Ribeiro de Almeida-Queiroz
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Avenida Duque de Caxias Norte, 225, Jardim Elite, Pirassununga, São Paulo, 13635-900, Brazil
| | - Maria da Glória Buzinaro
- Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castellani, Rural, Jaboticabal, São Paulo, 14884-900, Brazil
| | - Márcia Cristina Livonesi
- Department of Clinical Analysis, Alfenas Federal University (UNIFAL), Rua Gabriel Monteiro da Silva, 700, Centro, Alfenas, Minas Gerais, 37130-000, Brazil
| | - Andrezza Maria Fernandes
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Avenida Duque de Caxias Norte, 225, Jardim Elite, Pirassununga, São Paulo, 13635-900, Brazil
| | - Ricardo Luiz Moro de Sousa
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Avenida Duque de Caxias Norte, 225, Jardim Elite, Pirassununga, São Paulo, 13635-900, Brazil
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