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Boros Á, Pankovics P, László Z, Urbán P, Herczeg R, Gáspár G, Tóth F, Reuter G. The genomic and epidemiological investigations of enteric viruses of domestic caprine ( Capra hircus) revealed the presence of multiple novel viruses related to known strains of humans and ruminant livestock species. Microbiol Spectr 2023; 11:e0253323. [PMID: 37823638 PMCID: PMC10714811 DOI: 10.1128/spectrum.02533-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/04/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Compared with other domestic animals, the virome and viral diversity of small ruminants especially in caprine are less studied even of its zoonotic potential. In this study, the enteric virome of caprine was investigated in detail using next-generation sequencing and reverse transcription PCR techniques. The complete or nearly complete genomes of seven novel viruses were determined which show a close phylogenetic relationship to known human and ruminant viruses. The high similarity between the identified caprine tusavirus (family Parvoviridae) and an unassigned CRESS DNA virus with closely related human strains could indicate the (reverse) zoonotic potential of these viruses. Others, like astroviruses (family Astroviridae), enteroviruses, or novel caripiviruses (named after the term caprine picornavirus) of family Picornaviridae found mostly in multiple co-infections in caprine and ovine, could indicate the cross-species transmission capabilities of these viruses between small ruminants.
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Affiliation(s)
- Ákos Boros
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Pankovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Zoltán László
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Urbán
- János Szentágothai Research Centre of the University of Pécs, Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Pécs, Hungary
| | - Róbert Herczeg
- János Szentágothai Research Centre of the University of Pécs, Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Pécs, Hungary
| | - Gábor Gáspár
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Fruzsina Tóth
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
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Huang M, Gan J, Xu Z, Guo Y, Chen Z, Gao GF, Liang H, Liu WJ. A black goat-derived novel genotype of Aichi virus C blurs the boundary between caprine and porcine kobuviruses. Virology 2023; 585:215-221. [PMID: 37384968 DOI: 10.1016/j.virol.2023.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/12/2023] [Accepted: 06/21/2023] [Indexed: 07/01/2023]
Abstract
Aichi virus C, a species in the genus Kobuvirus, causes diarrhea diseases in pigs and goats and pose health threat and economic loss for stock farming. A nearly complete genome sequence of caprine kobuvirus GCCDC14 was obtained from an anal swab of a black goat died from diarrhea collected in Hubei, China in 2019. Phylogenetic analyses suggested that GCCDC14 is a novel genotype of Aichi virus C, forming a sister branch to other caprine kobuviruses, with P1 and VP0 genes more closely related to porcine kobuviruses and VP3 in an independent branch. Compared to previous caprine kobuviruses, unique amino acid changes in the poly-l-proline type II helix structure of VP0 and VP1 were found, which may affect the cellular machinery of host and pathogenicity. This study indicates the presence of the kobuvirus with continuously evolving features and emphasizes the surveillance and genetic evolution investigation of kobuviruses for safety of husbandry.
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Affiliation(s)
- Mengkun Huang
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed By the Province and Ministry, Guangxi Medical University, Nanning, 530000, China; NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Jinxian Gan
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed By the Province and Ministry, Guangxi Medical University, Nanning, 530000, China; NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Ziqian Xu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Yuanyuan Guo
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China; School of Public Health, Shandong University, Jinan, 250012, China
| | - Zhangfu Chen
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China; School of Public Health, Shandong University, Jinan, 250012, China
| | - George F Gao
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed By the Province and Ministry, Guangxi Medical University, Nanning, 530000, China; NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China; School of Public Health, Shandong University, Jinan, 250012, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China; Research Unit of Adaptive Evolution and Control of Emerging Viruses (2018RU009), Chinese Academy of Medical Sciences, Beijing, 102206, China.
| | - Hao Liang
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed By the Province and Ministry, Guangxi Medical University, Nanning, 530000, China.
| | - William J Liu
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed By the Province and Ministry, Guangxi Medical University, Nanning, 530000, China; NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China; Research Unit of Adaptive Evolution and Control of Emerging Viruses (2018RU009), Chinese Academy of Medical Sciences, Beijing, 102206, China.
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Yang Y, Abi K, Li Y, Yang C, Yang F. First detection and molecular characteristics of bopivirus from goats in China. Front Vet Sci 2022; 9:1033011. [PMID: 36532341 PMCID: PMC9753977 DOI: 10.3389/fvets.2022.1033011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/14/2022] [Indexed: 10/13/2023] Open
Abstract
A metavirome analysis was performed and detected bopivirus in the diarrhoeal fecal samples of goats in China. A total of 136 fecal samples were collected from yeanlings between the dates of June 2021 and January 2022 in Sichuan province, China. Moreover, "Bopivirus B" strains were detected by a specific RT-PCR targeting the 3D gene of the virus. The results showed that the overall detection rate of "Bopivirus B" was 19.12% (26/136). Additionally, there was a higher detection rate (24.05%, 19/79) in the fecal samples collected from yeanlings with diarrhea compared to those from asymptomatic animals (12.28%, 7/57). In these samples, no other common diarrhea-causing pathogens were detected except for three enteric viruses, namely caprine enterovirus, caprine kobuvirus and caprine hunnivirus (with detection rates of 13.97, 13.97, and 8.82%, respectively). Subsequently, full-length VP4, VP2, VP3, and VP1 genes from "Bopivirus B"-positive samples were amplified, cloned, sequenced, and analyzed. The phylogenetic analysis performed on the VP1 genes revealed that the identified bopivirus belonged to genotype B1 (seven strains) and B2 (three strains) and presented a high genetic diversity. Furthermore, a complete genome sequence of a "Bopivirus B" strain (SWUN/B1/2022) was obtained using PCR from fecal sample of a diarrhoeal yeanling. The complete genome was 7,309 nucleotides in length with a standard picornavirus genome organization, and shares 93.10% and 91.10% nucleotide similarity with bopivirus B1 genotype strain ovine/TB14/2010-HUN and bopivirus B2 genotype strain goat/AGK16/2020-HUN, respectively. According to the species classification criteria put forward by the International Committee on Taxonomy of Viruses and VP1 genotype, the strain SWUN/B1/2022 belongs to the bopivirus B1. This strain has unique amino acid substitutions in the VP4, VP2, VP3, and VP1 genes. Moreover, genomic recombination analysis revealed that this strain may be a minor parental strain of bopivirus B1 ovine/TB14/2010-HUN. Evolutionary analysis based on the 2C and 3CD genes revealed that the new bopivirus B1 strain SWUN/B1/2022 presents a unique evolutionary pattern. This study provided evidence to suggest that "Bopivirus B" is circulating with substantial genetic diversity in goats in China at present, and the mixed infection of "Bopivirus B" with other enteric viruses should be considered to be a composite factor in the occurrence of viral diarrhea in goats.
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Affiliation(s)
- Youwen Yang
- Department of Veterinary Medicine, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Kehamo Abi
- Department of Veterinary Medicine, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Yanmin Li
- Department of Veterinary Medicine, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Chen Yang
- Department of Veterinary Medicine, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Falong Yang
- Department of Veterinary Medicine, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China
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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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Abi KM, Yang C, Tang C, Jing ZZ. Aichivirus C isolate is a diarrhea-causing pathogen in goats. Transbound Emerg Dis 2022; 69:e2268-e2275. [PMID: 35502695 DOI: 10.1111/tbed.14566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/07/2022] [Accepted: 04/19/2022] [Indexed: 11/28/2022]
Abstract
Aichivirus C is an emerging virus in goats, but its biological significance remains unknown. In this study, 18 diarrheic and 16 non-diarrheic fecal samples of kids were collected from a farm with an ongoing diarrheic outbreak in Sichuan Province, China in May 2021. Of these samples, 77.8% (14/18) of diarrheic samples were detected as Aichivirus C positive by RT-PCR, which was significantly higher than that of non-diarrheic feces (0%, p<0.001); meanwhile, other common diarrhea-causing pathogens in goats were not detected in diarrheic samples, except for two samples that were detected as caprine enterovirus positive, suggesting that Aichivirus C was associated with goat diarrhea. Furthermore, five Aichivirus C strains were successfully isolated from positive samples using Vero cell lines and two isolates further plaque-purified, named SWUN/F5/2021(10-6.7 TCID50 /0.1ml) and SWUN/F6/2021(10-7 TCID50 /0.1ml). Interestingly, Aichivirus C strain could cause systemic infection in experimental kids via oral administration, with the main clinical manifestation being severe watery diarrhea. Histopathological changes observed in the duodenum and jejunum were characteristic, with shedding of mucosal epithelial cells. In addition, the virus was detected in tissues of diarrhea kids naturally infected with Aichivirus C, exhibiting pathological changes similar to those of experimental infections. Overall, this study first isolated Aichivirus C and confirmed its pathogenicity on kids, with further study needed to better understand virus pathogenicity. As Aichivirus C has been detected in South Korea, Italy, and the USA and widely prevalent in southwest China, the results obtained here have significant implications for the diagnosis and control of diarrhea in goats. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Keha-Mo Abi
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, PR China.,State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Chen Yang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, PR China
| | - Cheng Tang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, PR China
| | - Zhi Zhong Jing
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
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Gao Y, He W, Fu J, Li Y, He H, Chen Q. Epidemiological Evidence for Fecal-Oral Transmission of Murine Kobuvirus. Front Public Health 2022; 10:865605. [PMID: 35517645 PMCID: PMC9062591 DOI: 10.3389/fpubh.2022.865605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundMurine Kobuvirus (MuKV) is a novel picornavirus of the genus Kobuvirus, and was first identified in the feces of murine rodents in the USA in 2011. There is limited information on the transmission route of MuKV. Thus, we conducted a study to investigate virus detection rates in fecal, serum, throat, and lung tissue samples from murine rodents.ResultsA total of 413 fecal samples, 385 lung samples, 269 throat swab samples, and 183 serum samples were collected from 413 murine rodents (Rattus norvegicus, Rattus tanezumi, and Rattus rattus) captured in urban Shenzhen. Kobuviruses were detected via RT-PCR. Only fecal samples were positive, with prevalence rates of 34.9% in Rattus norvegicus and 29.4% in Rattus tanezumi. Phylogenetic analysis based on partial 3D and complete VP1 sequence regions indicated that all of the MuKV sequences obtained belonged to Aichivirus A, and were genetically closely related to other MuKVs reported in China, Hungary, and the USA. Twenty-eight full-length MuKV sequences were acquired. Phylogenetic analysis of two sequences randomly selected from the two species (SZ59 and SZ171) indicated that they shared very high nucleotide and amino acid identity with one another (94.0 and 99.3%, respectively), and comparison with human Kobuvirus revealed amino acid identity values of ~80%. Additionally, a sewage-derived sequence shared high similarity with the rat-derived sequences identified in this study, with respective nucleotide and amino acid identity values from 86.5 and 90.7% to 87.2 and 91.1%.ConclusionThe results of the current study provide evidence that murine Kobuvirus is transmitted via the fecal-oral route.
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Di Martino B, Di Profio F, Robetto S, Fruci P, Sarchese V, Palombieri A, Melegari I, Orusa R, Martella V, Marsilio F. Molecular Survey on Kobuviruses in Domestic and Wild Ungulates From Northwestern Italian Alps. Front Vet Sci 2021; 8:679337. [PMID: 34195249 PMCID: PMC8237713 DOI: 10.3389/fvets.2021.679337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
Since the first identification in 1989 in humans, kobuviruses (KoVs) have been identified from a wide range of animal species including carnivores, rodents, birds, ungulates, rabbits, and bats. Several studies have described the identification of genetically related KoVs in the fecal virome of domestic and wild animals suggesting a mutual exchange of viruses. By screening a total of 231 fecal samples from wild and domestic ungulates, KoVs RNA was detected in wild boars (3.2%; 2/63), chamois (4.6%; 2/43), and goats (2.6%; 2/77). On phylogenetic analysis of the partial RdRp sequence, the wild boar strains clustered within the species Aichivirus C whilst the strains identified in domestic and wild ruminants grouped into the species Aichivirus B. The complete VP1 gene was obtained for chamois and goat KoVs. Interestingly, upon phylogenetic analysis the strains grouped together with a KoV of ovine origin within a distinct genetic type (B3) of the species Aichivirus B.
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Affiliation(s)
- Barbara Di Martino
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Federica Di Profio
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Serena Robetto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Centro di Referenza Nazionale per le Malattie degli Animali Selvatici (CeRMAS), Aosta, Italy
| | - Paola Fruci
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Vittorio Sarchese
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Andrea Palombieri
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Irene Melegari
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Riccardo Orusa
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Centro di Referenza Nazionale per le Malattie degli Animali Selvatici (CeRMAS), Aosta, Italy
| | - Vito Martella
- Department of Veterinary Medicine, Università Aldo Moro di Bari, Valenzano, Italy
| | - Fulvio Marsilio
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
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