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Wu S, Gou F, Meng J, Jin X, Liu W, Ding W, Xu W, Gu C, Hu X, Cheng G, Tao P, Zhang W. Porcine kobuvirus enhances porcine epidemic diarrhea virus pathogenicity and alters the number of intestinal lymphocytes in piglets. Vet Microbiol 2024; 293:110100. [PMID: 38718527 DOI: 10.1016/j.vetmic.2024.110100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/25/2024] [Accepted: 04/25/2024] [Indexed: 05/15/2024]
Abstract
Recent epidemiological studies have discovered that a lot of cases of porcine epidemic diarrhea virus (PEDV) infection are frequently accompanied by porcine kobuvirus (PKV) infection, suggesting a potential relationship between the two viruses in the development of diarrhea. To investigate the impact of PKV on PEDV pathogenicity and the number of intestinal lymphocytes, piglets were infected with PKV or PEDV or co-infected with both viruses. Our findings demonstrate that co-infected piglets exhibit more severe symptoms, acute gastroenteritis, and higher PEDV replication compared to those infected with PEDV alone. Notably, PKV alone does not cause significant intestinal damage but enhances PEDV's pathogenicity and alters the number of intestinal lymphocytes. These results underscore the complexity of viral interactions in swine diseases and highlight the need for comprehensive diagnostic and treatment strategies addressing co-infections.
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Affiliation(s)
- Simin Wu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Fang Gou
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Jie Meng
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Xin Jin
- Hubei Animal Disease Prevention and Control Center, Wuhan 430070, China.
| | - Wanchen Liu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Weishuai Ding
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Weihang Xu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Changqin Gu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Xueying Hu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Guofu Cheng
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Pan Tao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Wanpo Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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Zang Y, Feng B, Huang Z, Zhao D, Qi W, Qiu Y, Qiu M, Li C, Lin H, Zheng W, Zhu J, Chen N. Epidemiologic and Genomic Characterizations of Porcine Kobuviruses in Diarrheic and Healthy Pigs. Animals (Basel) 2023; 13:3129. [PMID: 37835735 PMCID: PMC10571770 DOI: 10.3390/ani13193129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/30/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023] Open
Abstract
Porcine kobuvirus (PKV) is an enteric virus commonly detected in both diarrheic and healthy pigs. Little is known about the role of PKV in enteric diseases. In this study, an epidemiological investigation based on 324 intestinal samples collected from six provinces of China during the period of 2018 to 2022 was performed, and showed that PKV has an overall 65.43% (212/324) positive rate. Noticeably, 89.47% (17/19) of PKV and porcine epidemic diarrhea virus (PEDV) double-positive pigs were clinically diseased, while 91.71% (177/193) of PKV-positive but PEDV-negative pigs were clinically healthy, suggesting that PKV infection in itself is unlikely to cause enteric diseases. In addition, three PKV genomes were obtained from both diseased and healthy pigs. Phylogenetic analysis showed that Chinese PKV strains could be divided into three groups (SH-W-CHN-like, S-1-HUN-like and JXAT2015-like strains). All three obtained PKV genomes belong to SH-W-CHN-like strains and JSYZ1806-158 was detected as a recombinant virus. Furthermore, multiple comparisons showed that nucleotide similarities are clearly lower than amino acid similarities for PKV polyproteins. Selective pressure analysis indicated that Chinese PKV polyproteins are predominantly under negative selection. Overall, this study provided new insights into the prevalence and evolution of PKV in both diarrheic and healthy pigs in China.
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Affiliation(s)
- Yu Zang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
| | - Binghui Feng
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
| | - Zitao Huang
- Animal Health Supervision Institute of Fengxi District, Chaozhou 521031, China;
| | - Dashi Zhao
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
| | - Wenhao Qi
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
| | - Yuejia Qiu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
| | - Ming Qiu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
| | - Chen Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
| | - Hong Lin
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
| | - Wanglong Zheng
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
| | - Jianzhong Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou 225009, China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou 225009, China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Nanhua Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou 225009, China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou 225009, China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, Fuzhou 350002, China
- Fujian Provincial Key Laboratory for Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan University, Longyan 364012, China
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3
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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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4
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Yan N, Yue H, Liu Q, Wang G, Tang C, Liao M. Isolation and Characteristics of a Novel Aichivirus D from Yak. Microbiol Spectr 2023; 11:e0009923. [PMID: 37097198 PMCID: PMC10269754 DOI: 10.1128/spectrum.00099-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/05/2023] [Indexed: 04/26/2023] Open
Abstract
Aichivirus D (AiV-D) is a newly emerging Kobuvirus detected in bovine and sheep, and information is limited regarding its biological significance and prevalence. This study aimed to explore both the prevalence and characteristics of AiV-D in yaks. From May to August 2021, 117 fecal samples were collected from yaks with diarrhea in three provinces of China's Qinghai-Tibet Plateau, 15 of which were selected and pooled for metagenomic analysis. A high abundance of AiV-D sequences was obtained. Of the 117 diarrhea samples, 29 (24.8%) tested AiV-D-positive, including 33.3% (14/42) from Sichuan, 21.1% (8/38) from Qinghai, and 18.9% (7/37) from Tibet, respectively, suggesting a wide geographical distribution of the AiV-D in yaks in the Qinghai-Tibet Plateau. Furthermore, three AiV-D strains were successfully isolated using Vero cells. Significantly, the AiV-D strain could cause diarrhea, intestinal bleeding, and inflammation in yak calves via oral inoculation. The virus was distributed in the ileum, jejunum, duodenum, colon, cecum, and rectum. Based on phylogenetic analysis of the genome and capsid protein P1 (VP0, VP3, and VP1 genes), the yak AiV-D strains likely represent a novel genotype of AiV-D. On the whole, this study identified a novel genotype of AiV-D from yaks, which was successfully isolated, and confirmed that this virus is a diarrhea pathogen in yaks and has a wide geographical distribution in the Qinghai-Tibet Plateau. Our results expand the host range of AiV-D and the pathogen spectrum of yaks and have significant implications for diagnosing and controlling diarrhea in yaks. IMPORTANCE In this study, we identified and successfully isolated a novel genotype of AiV-D from yaks. Animal infection confirmed that this virus can cause diarrhea, intestinal bleeding, and inflammation in yak calves via oral inoculation. The virus was distributed in the ileum, jejunum, cecum, duodenum, colon, and rectum. All of these results have significant implications for diagnosing and controlling diarrhea in yaks. These novel AiV-D strains have a wide geographical distribution in yaks from the Qinghai-Tibet Plateau in China. In addition to expanding the host range of AiV-D and the pathogen spectrum of yaks, these findings can increase knowledge of the prevalence and diversity of AiV-D.
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Affiliation(s)
- Nan Yan
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Hua Yue
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Quan Liu
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Gang Wang
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Guangzhou, China
- Field Observation and Experiment Station on Animal Blight of Guangdong Province, Guangzhou, China
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Cheng Tang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Ming Liao
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Guangzhou, China
- Field Observation and Experiment Station on Animal Blight of Guangdong Province, Guangzhou, China
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Eriksen EØ. A Systematic Review: Is Porcine Kobuvirus Causing Gastrointestinal Disease in Young Pigs? Vet Sci 2023; 10:vetsci10040286. [PMID: 37104441 PMCID: PMC10144032 DOI: 10.3390/vetsci10040286] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/31/2023] [Accepted: 04/05/2023] [Indexed: 04/28/2023] Open
Abstract
Since porcine kobuvirus (PKV) was first described in 2008, researchers have speculated whether the virus is of clinical importance. This systematic literature review answers the question: Is porcine kobuvirus a cause of gastrointestinal disease in young pigs? A case-control study showed that PKV was not associated with neonatal diarrhea. A cohort study suffered from a very small sample size (n = 5), and in an experimental trial, the effect of PKV inoculation could not be separated from the effect of being inoculated with porcine epidemic diarrhea virus. In 13 poorly defined observational studies, more than 4000 young pigs had been assigned a diarrhea status and their feces analyzed for PKV. Unfortunately, the studies lacked well-characterized unbiased samples, and thus the strongest possible inference from these studies was that a very strong association between PKV and diarrhea is unlikely. PKV was commonly detected in non-diarrheic pigs, and this could indicate that PKV is not a sufficient cause in itself or that reinfection of individuals with some immunological protection due to previous infections is common. Conclusively, there is a lack of good evidence of PKV being a cause of gastrointestinal disease, but the sparse available evidence suggests that PKV is of limited clinical importance.
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Affiliation(s)
- Esben Østergaard Eriksen
- Section for Production, Nutrition and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
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6
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Cui Y, Li J, Guo J, Pan Y, Tong X, Liu C, Wang D, Xu W, Shi Y, Ji Y, Qiu Y, Yang X, Hou L, Zhou J, Feng X, Wang Y, Liu J. Evolutionary Origin, Genetic Recombination, and Phylogeography of Porcine Kobuvirus. Viruses 2023; 15:240. [PMID: 36680281 PMCID: PMC9867129 DOI: 10.3390/v15010240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
The newly identified porcine Kobuvirus (PKV) has raised concerns owing to its association with diarrheal symptom in pigs worldwide. The process involving the emergence and global spread of PKV remains largely unknown. Here, the origin, genetic diversity, and geographic distribution of PKV were determined based on the available PKV sequence information. PKV might be derived from the rabbit Kobuvirus and sheep were an important intermediate host. The most recent ancestor of PKV could be traced back to 1975. Two major clades are identified, PKVa and PKVb, and recombination events increase PKV genetic diversity. Cross-species transmission of PKV might be linked to interspecies conserved amino acids at 13-17 and 25-40 residue motifs of Kobuvirus VP1 proteins. Phylogeographic analysis showed that Spain was the most likely location of PKV origin, which then spread to pig-rearing countries in Asia, Africa, and Europe. Within China, the Hubei province was identified as a primary hub of PKV, transmitting to the east, southwest, and northeast regions of the country. Taken together, our findings have important implications for understanding the evolutionary origin, genetic recombination, and geographic distribution of PKV thereby facilitating the design of preventive and containment measures to combat PKV infection.
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Affiliation(s)
- Yongqiu Cui
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jingyi Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jinshuo Guo
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yang Pan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xinxin Tong
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Changzhe Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Dedong Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Weiyin Xu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yongyan Shi
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Ying Ji
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yonghui Qiu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyu Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Lei Hou
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jianwei Zhou
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Xufei Feng
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yong Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Jue Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
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7
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Li Y, Liang J, Wu S, Yan Z, Zhang W. Complete genomic sequence analysis and intestinal tissue localization of a porcine Kobuvirus variant in China. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 104:105362. [PMID: 36084837 DOI: 10.1016/j.meegid.2022.105362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/19/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Porcine kobuvirus (PKV) infection is very common in both healthy pigs and diarrhea pigs throughout the world. However, there is no proof that it causes diarrhea, and little is known about its role in diarrhea. There are only a few reports concerning porcine kobuvirus separation at present, which makes investigating its invasion and pathogenesis mechanisms difficult. This study sequenced the entire genome of a porcine kobuvirus strain termed "Wuhan2020" after it was isolated from intestinal tissue samples of healthy piglets. The analysis results revealed that it shared the most resemblance with the WUH1 strain (89.5%) and belonged to the same evolutionary branch as the Hungarian strain S-1-SUN. The PKV was located using the in situ hybridization (ISH) approach, which revealed that it was colonized in intestinal villus epithelial cells and lymphocytes in the Peyer's patch. In general, we analyzed the genetic evolution of PKV, discovered PKV susceptible cells and determined PKV localization in the intestine of infected pigs, providing a reference for future research.
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Affiliation(s)
- Yang Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China; Veterinary Pathology Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Jixiang Liang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Simin Wu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China; Veterinary Pathology Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Zhishan Yan
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China; Veterinary Pathology Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Wanpo Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China; Veterinary Pathology Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China.
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8
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Aftab G, Arfaee F, Akhtardanesh B, Nikbakht Brojeni G. Molecular characterization of canine and feline kobuvirus infections in Iran. VETERINARY RESEARCH FORUM : AN INTERNATIONAL QUARTERLY JOURNAL 2022; 13:447-450. [PMID: 36320293 PMCID: PMC9548235 DOI: 10.30466/vrf.2020.128667.2975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/25/2020] [Indexed: 11/14/2022]
Abstract
Kobuviruses are viral pathogens with broad host range presented in human gastroenteritis cases; but, the pathogenesis of these viruses in companion animals is not well described. In the present study, the presence of canine (CaKVs) and feline kobuviruses (FeKVs) was detected in the 100 fecal samples of diarrhoeic and healthy companion dogs and cats by polymerase chain reaction in Tehran, Iran. The prevalence of infection was estimated as 8.00% and 4.00% in dogs and cats, respectively. All positive samples were belonged to non-diarrhoeic animals except for a feline sample being co-infected with panleukopenia. Sequence analysis showed multiple point mutations in canine and feline Iranian strains and new feline strain was detected in the present study. This is the first detection of CaKVs and FeKVs in Iran; but, the exact role of these enteric viral pathogens and their zoonotic risks are better to be clarified in all endemic regions.
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Affiliation(s)
- Ghazal Aftab
- Department of Clinical Sciences, Faculty of Specialized Veterinary Science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Farnoosh Arfaee
- Department of Clinical Sciences, Faculty of Specialized Veterinary Science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Baharak Akhtardanesh
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran; ,Correspondence Baharak Akhtardanesh. DVM, DVSc Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran. E-mail:
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Pathogenic and metagenomic evaluations reveal the correlations of porcine epidemic diarrhea virus, porcine kobuvirus and porcine astroviruses with neonatal piglet diarrhea. Microb Pathog 2022; 170:105703. [DOI: 10.1016/j.micpath.2022.105703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/20/2022] [Accepted: 07/31/2022] [Indexed: 11/17/2022]
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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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Capai L, Piorkowski G, Maestrini O, Casabianca F, Masse S, de Lamballerie X, Charrel RN, Falchi A. Detection of porcine enteric viruses (Kobuvirus, Mamastrovirus and Sapelovirus) in domestic pigs in Corsica, France. PLoS One 2022; 17:e0260161. [PMID: 35030164 PMCID: PMC8759673 DOI: 10.1371/journal.pone.0260161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 11/03/2021] [Indexed: 11/19/2022] Open
Abstract
Many enteric viruses are found in pig farms around the world and can cause death of animals or important production losses for breeders. Among the wide spectrum of enteric viral species, porcine Sapelovirus (PSV), porcine Kobuvirus (PKoV) and porcine Astrovirus (PAstV) are frequently found in pig feces. In this study we investigated sixteen pig farms in Corsica, France, to evaluate the circulation of three enteric viruses (PKoV, PAstV-1 and PSV). In addition to the three viruses studied by RT–qPCR (908 pig feces samples), 26 stool samples were tested using the Next Generation Sequencing method (NGS). Our results showed viral RNA detection rates (i) of 62.0% [58.7–65.1] (n = 563/908) for PSV, (ii) of 44.8% [41.5–48.1] (n = 407/908) for PKoV and (iii) of 8.6% [6.8–10.6] (n = 78/908) for PAstV-1. Significant differences were observed for all three viruses according to age (P-value = 2.4e–13 for PAstV-1; 2.4e–12 for PKoV and 0.005 for PSV). The type of breeding was significantly associated with RNA detection only for PAstV-1 (P-value = 9.6e–6). Among the 26 samples tested with NGS method, consensus sequences corresponding to 10 different species of virus were detected. This study provides first insight on the presence of three common porcine enteric viruses in France. We also showed that they are frequently encountered in pigs born and bred in Corsica, which demonstrates endemic local circulation.
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Affiliation(s)
- Lisandru Capai
- UR 7310, Laboratoire de Virologie, Université de Corse, Corte, France
- * E-mail: (LC); (AF)
| | - Géraldine Piorkowski
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Oscar Maestrini
- Laboratoire de Recherche sur le Développement de l’Elevage (LRDE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Corte, France
| | - François Casabianca
- Laboratoire de Recherche sur le Développement de l’Elevage (LRDE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Corte, France
| | - Shirley Masse
- UR 7310, Laboratoire de Virologie, Université de Corse, Corte, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Rémi N. Charrel
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Alessandra Falchi
- UR 7310, Laboratoire de Virologie, Université de Corse, Corte, France
- * E-mail: (LC); (AF)
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Kaiser FK, van Dyck L, Jo WK, Schreiner T, Pfankuche VM, Wohlsein P, Baumann I, Peters M, Baumgärtner W, Osterhaus ADME, Ludlow M. Detection of Systemic Canine Kobuvirus Infection in Peripheral Tissues and the Central Nervous System of a Fox Infected with Canine Distemper Virus. Microorganisms 2021; 9:microorganisms9122521. [PMID: 34946122 PMCID: PMC8705045 DOI: 10.3390/microorganisms9122521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/17/2021] [Accepted: 12/03/2021] [Indexed: 12/13/2022] Open
Abstract
Canine kobuvirus (CaKV) is a globally distributed pathogen of dogs and is predominantly associated with infection of the gastrointestinal tract. However, an etiological link to enteric disease has not been established since CaKV has been identified in both asymptomatic dogs and animals with diarrheic symptoms. In this study, an extraintestinal CaKV infection was detected by next-generation sequencing in a fox (Vulpes vulpes) in Germany concomitant with a canine distemper virus (canine morbillivirus; CDV) co-infection. Phylogenetic analysis of the complete coding region sequence showed that this strain was most closely related to a CaKV strain detected in a dog in the United Kingdom in 2008. The tissue and cellular tropism of CaKV was characterized by the detection of viral antigens and RNA. CaKV RNA was detected by in situ hybridization in different tissues, including epithelial cells of the stomach and ependymal cells in the brain. The use of a new RT-qPCR assay for CaKV confirmed the systemic distribution of CaKV with viral RNA also detected in the lymph nodes, bladder, trachea, and brain. The detection of a CDV infection in this fox suggests that immunosuppression should be further investigated as a contributing factor to the enhanced extraintestinal spread of CaKV.
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Affiliation(s)
- Franziska K. Kaiser
- Research Center for Infectious Disease and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (F.K.K.); (W.K.J.); (I.B.); (A.D.M.E.O.)
| | - Lydia van Dyck
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (L.v.D.); (T.S.); (V.M.P.); (P.W.); (W.B.)
| | - Wendy K. Jo
- Research Center for Infectious Disease and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (F.K.K.); (W.K.J.); (I.B.); (A.D.M.E.O.)
| | - Tom Schreiner
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (L.v.D.); (T.S.); (V.M.P.); (P.W.); (W.B.)
| | - Vanessa M. Pfankuche
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (L.v.D.); (T.S.); (V.M.P.); (P.W.); (W.B.)
| | - Peter Wohlsein
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (L.v.D.); (T.S.); (V.M.P.); (P.W.); (W.B.)
| | - Ilka Baumann
- Research Center for Infectious Disease and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (F.K.K.); (W.K.J.); (I.B.); (A.D.M.E.O.)
| | - Martin Peters
- Chemisches und Veterinäruntersuchungsamt Westfalen, 59821 Arnsberg, Germany;
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (L.v.D.); (T.S.); (V.M.P.); (P.W.); (W.B.)
| | - Albert D. M. E. Osterhaus
- Research Center for Infectious Disease and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (F.K.K.); (W.K.J.); (I.B.); (A.D.M.E.O.)
| | - Martin Ludlow
- Research Center for Infectious Disease and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (F.K.K.); (W.K.J.); (I.B.); (A.D.M.E.O.)
- Correspondence:
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Zhang M, You F, Wu F, He H, Li Q, Chen Q. Epidemiology and genetic characteristics of murine kobuvirus from faecal samples of Rattus losea, Rattus tanezumi and Rattus norvegicus in southern China. J Gen Virol 2021; 102. [PMID: 34486970 PMCID: PMC8567428 DOI: 10.1099/jgv.0.001646] [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] [Indexed: 01/05/2023] Open
Abstract
Recently, murine kobuvirus (MuKV), a novel member of the family Picornaviridae, was identified in faecal samples of Rattus norvegicus in China. The limited information on the circulation of MuKV in other murine rodent species prompted us to investigate its prevalence and conduct a genetic characterization of MuKV in Rattus losea, Rattus tanezumi and Rattus norvegicus in China. Between 2015 and 2017, 243 faecal samples of these three murine rodent species from three regions in southern China were screened for the presence of MuKV. The overall prevalence was 23.0% (56/243). Three complete MuKV polyprotein sequences were acquired, and the genome organization was determined. Phylogenetic analyses suggested that our sequences were closely related to Chinese strains and belong to the species Aichivirus A in the genus Kobuvirus. Additional studies are required to understand the true prevalence of MuKV in murine rodent populations in China.
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Affiliation(s)
- Minyi Zhang
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou 510515, PR China
| | - Fangfei You
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou 510515, PR China
| | - Fei Wu
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou 510515, PR China
| | - Huan He
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou 510515, PR China
| | - Qiushuang Li
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou 510515, PR China
| | - Qing Chen
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou 510515, PR China
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Phylogenetic analysis of kobuviruses and astroviruses from Korean wild boars: 2016-2018. Arch Virol 2021; 166:2591-2596. [PMID: 34244861 DOI: 10.1007/s00705-021-05164-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/20/2021] [Indexed: 10/20/2022]
Abstract
Between 2016 and 2018, the prevalence of porcine kobuvirus (PKoV) and porcine astrovirus (PAstV) in Korean wild boars (n = 845) was 28.0% and 10.7%, respectively. Coinfection by both viruses was detected in 5.1% of boars. Phylogenetic analysis revealed that 134 PKoV isolates belonged to diverse lineages within the species Aichivirus C; however, one strain (WKoV16CN-8627) clustered with bovine kobuvirus (Aichivirus B). Forty-seven PAstVs belonged to lineage PAstV4, and only one strain (WAst17JN-10931) was a novel addition to lineage PAstV2. The two viruses were more prevalent in boars weighing ≤ 60 kg than in boars weighing > 61 kg.
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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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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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Sadiq A, Yinda CK, Deboutte W, Matthijnssens J, Bostan N. Whole genome analysis of Aichivirus A, isolated from a child, suffering from gastroenteritis, in Pakistan. Virus Res 2021; 299:198437. [PMID: 33901591 DOI: 10.1016/j.virusres.2021.198437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/30/2021] [Accepted: 04/20/2021] [Indexed: 11/19/2022]
Abstract
Viruses are the primary cause of acute gastroenteritis in children all over the world. Understanding the emergence and genetic variation of these viruses may help to prevent infections. Aichivirus (AiV) is a member of the Kobuvirus genus, which currently contains six officially recognized species: Aichivirus A-F. The species AiV A contains six types including Aichivirus 1 (AiV 1) and eventually, three genotypes have been identified in the human AiV 1 (named A to C). The present study describes the identification and sequencing of the polyprotein gene of a human AiV 1 strain PAK419 via NGS in Pakistani children with acute gastroenteritis. Our study strain PAK419 was classified as AiV 1 genotype A, most commonly found in Japan and Europe, and closely related to non-Japanese and European strains on the phylogenetic tree. PAK419 showed 95-98 % nucleotide sequence identity with strains isolated from Ethiopia (ETH/2016/P4), Australia (FSS693) and China (Chshc7). On phylogenetic observation PAK419 formed a distinct cluster in the AiV 1 genotype A with the above mentioned and other human AiV strains detected around the world (Germany, Brazil, Japan, Thailand, Korea and Vietnam). The data clearly showed that Pakistani AiV strains and human strains identified from all over the world are distinct from Aichivirus strains found in bovine, swine, canine, feline, caprine, ferret, bat, and environmental samples. The distinguishing characteristics of the AiV genome showed a lower probability of inter-genotypic recombination events, which may support the lack of AiV serotypes. PAK419 also had a high content of C nucleotide (37.4 %), as found in previous studies, which could also restrict the possible genetic variation of AiV. This study demonstrate the power of NGS in uncovering unknown gastroenteric etiological agents circulating in the population.
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Affiliation(s)
- Asma Sadiq
- Department of Biosciences, COMSATS University (CUI), Park Road, Tarlai Kalan, Chak Shahzad, Islamabad, 45550, Pakistan
| | - Claude Kwe Yinda
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Ward Deboutte
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Jelle Matthijnssens
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Nazish Bostan
- Department of Biosciences, COMSATS University (CUI), Park Road, Tarlai Kalan, Chak Shahzad, Islamabad, 45550, Pakistan.
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García-Hernández ME, Trujillo-Ortega ME, Alcaraz-Estrada SL, Lozano-Aguirre-Beltrán L, Sandoval-Jaime C, Taboada-Ramírez BI, Sarmiento-Silva RE. Molecular Detection and Characterization of Porcine Epidemic Diarrhea Virus and Porcine Aichivirus C Coinfection in México. Viruses 2021; 13:v13050738. [PMID: 33922604 PMCID: PMC8146670 DOI: 10.3390/v13050738] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/11/2021] [Accepted: 04/14/2021] [Indexed: 11/16/2022] Open
Abstract
Swine enteric viral infections are responsible for substantial economic losses in the pork industry worldwide. Porcine epidemic diarrhea (PEDV) is one of the main causative agents of diarrhea in lactating pigs, and reports of PEDV coinfection with other enteric viruses highlight the importance of viral interactions for disease presentation and outcomes. Using next-generation sequencing (NGS) and sequence analyses from samples taken from piglets with acute diarrhea, we explored the possible interactions between PEDV and other less reported pathogens. PEDV coinfection with porcine kobuvirus (PKV) was detected in 36.4% (27/74) of samples. Full genomes from porcine coronavirus and kobuvirus were obtained, as was a partial porcine sapovirus genome (PSaV). The phylogenetic results show the clustering of these strains corresponding to the geographical relationship. To our knowledge, this is the first full genome and isolation report for porcine kobuvirus in México, as well as the first phylogenetic analysis for porcine sapovirus in the country. The NGS approach provides a better perspective of circulating viruses and other pathogens in affected production units.
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Affiliation(s)
- Montserrat-Elemi García-Hernández
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad #3000, Ciudad de México 04510, Mexico;
| | - María-Elena Trujillo-Ortega
- Departamento de Medicina y Zootecnia de Cerdos, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad #3000, Ciudad de México 04510, Mexico;
| | - Sofía-Lizbeth Alcaraz-Estrada
- División de Medicina Genómica y Genética Clínica, Centro Médico Nacional “20 de Noviembre”, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Av. Félix Cuevas #540, Ciudad de México 03100, Mexico;
| | - Luis Lozano-Aguirre-Beltrán
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca 62209, Mexico;
| | - Carlos Sandoval-Jaime
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca 62209, Mexico; (C.S.-J.); (B.I.T.-R.)
| | - Blanca Itzel Taboada-Ramírez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca 62209, Mexico; (C.S.-J.); (B.I.T.-R.)
| | - Rosa-Elena Sarmiento-Silva
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad #3000, Ciudad de México 04510, Mexico;
- Correspondence: ; Tel.: +55-56225900 (ext. 33)
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Shi Y, Li B, Tao J, Cheng J, Liu H. The Complex Co-infections of Multiple Porcine Diarrhea Viruses in Local Area Based on the Luminex xTAG Multiplex Detection Method. Front Vet Sci 2021; 8:602866. [PMID: 33585617 PMCID: PMC7876553 DOI: 10.3389/fvets.2021.602866] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 01/05/2021] [Indexed: 01/17/2023] Open
Abstract
The large-scale outbreaks of severe diarrhea caused by viruses have occurred in pigs since 2010, resulting in great damage to the pig industry. However, multiple infections have contributed to the outbreak of the disease and also resulted in great difficulties in diagnosis and control of the disease. Thus, a Luminex xTAG multiplex detection method, which was more sensitive and specific than general multiplex PCR method, was developed for the detection of 11 viral diarrhea pathogens, including PKoV, PAstV, PEDV, PSaV, PSV, PTV, PDCoV, TGEV, BVDV, PoRV, and PToV. To investigate the prevalence of diarrhea-associated viruses responsible for the outbreaks, a total of 753 porcine stool specimens collected from 9 pig farms in Shanghai during 2015-2018 were tested and the pathogen spectrums and co-infections were analyzed. As a result, PKoV, PAstV and PEDV were most commonly detected viruses in diarrheal pigs with the rate of 38.65% (291/753), 20.32% (153/753), and 15.54% (117/753), respectively. Furthermore, multiple infections were commonly seen, with positive rate of 28.42%. Infection pattern of the viral diarrhea pathogens in a specific farm was changing, and different farms had the various diarrhea infection patterns. A longitudinal investigation showed that PEDV was the key pathogen which was closely related to the death of diarrhea piglets. Other pathogens might play synergistic roles in the pathogenesis of diarrhea disease. Furthermore, the surveillance confirmed that variant enteropathogenic viruses were leading etiologic agents of porcine diarrhea, either mono-infection or co-infections of PKoV were common in pigs in Shanghai, but PEDV was still the key pathogen and multiple pathogens synergistically complicated the infection status, suggesting that controlling porcine diarrhea might be more complex than previously thought. The study provides a better understanding of diarrhea viruses in piglets, which will aid in better preventing and controlling epidemics of viral porcine diarrhea.
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Affiliation(s)
- Ying Shi
- Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Engineering Research Center of Pig Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Benqiang Li
- Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Engineering Research Center of Pig Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jie Tao
- Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Engineering Research Center of Pig Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jinghua Cheng
- Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Engineering Research Center of Pig Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Huili Liu
- Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Engineering Research Center of Pig Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
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Shahhosseini N, Frederick C, Letourneau-Montminy MP, Marie-Odile BB, Kobinger GP, Wong G. Computational genomics of Torque teno sus virus and Porcine circovirus in swine samples from Canada. Res Vet Sci 2020; 134:171-180. [PMID: 33387757 DOI: 10.1016/j.rvsc.2020.12.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/06/2020] [Accepted: 12/18/2020] [Indexed: 11/26/2022]
Abstract
Emerging viral diseases include pathogens that can threaten the health of the Canadian swineherd. Anelloviruses and Circoviruses comprise of pathogens with veterinary significance. The aim of this study was to determine the genomic organization and phylogenetic relationships of Torque teno sus virus (TTsusV) and Porcine circovirus (PCV) from Canadian pig samples. Fecal and tissue specimens were collected during the winter, spring and summer of 2018. We utilized either virus- or genus-specific PCR assays to characterize the occurrence and genetic diversity of TTsusV and PCV in Canadian pigs. Pairwise comparison of all partial sequences and identity calculation was performed using MAFFT algorithm implemented in Sequence Demarcation Tool (SDT). The obtained full-length sequences were aligned using ClustalW, and phylogeny was inferred using a Maximum likelihood (ML) method by Geneious software. The PCR detection results revealed that the overall positive rate of TTsusV type-1 and type-2 was 45.6% and 32.6%, respectively. The TTsusV isolate MK990454 from Canada clustered in the subtype TTsusV1b, while the TTsusV isolate MK872392 fell in the subtype TTsusV2c, and all showed similarity to known American and Chinese isolates. In addition, our screening PCR showed that 2.7% of stool samples were positive for PCV1. Phylogenetic analysis using the full-length sequence demonstrated that PCV1 (MK872393) isolated from Quebec clustered with other Chinese PCV1 strains. Despite the far geographical distance between Canada and China, the close similarity between Canadian and Chinese TTsusV1 and 2, and PCV1 sequences may be explained by a considerable amount of pig trade between these two nations.
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Affiliation(s)
- Nariman Shahhosseini
- Département de Microbiologie-Infectiologie et d'Immunologie, Université Laval, Québec City, Québec, Canada
| | - Christina Frederick
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec City, Québec, Canada
| | | | - Benoit-Biancamano Marie-Odile
- Research Group on Infectious Diseases in Production Animals (GREMIP) and Swine and Poultry Infectious Disease Research Center (CRIPA), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Gary P Kobinger
- Département de Microbiologie-Infectiologie et d'Immunologie, Université Laval, Québec City, Québec, Canada; Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada; Department of Immunology, University of Manitoba, Winnipeg, Manitoba, Canada; Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Gary Wong
- Département de Microbiologie-Infectiologie et d'Immunologie, Université Laval, Québec City, Québec, Canada; Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.
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21
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Valkó A, Marosi A, Cságola A, Farkas R, Rónai Z, Dán Á. Frequency of diarrhoea-associated viruses in swine of various ages in Hungary. Acta Vet Hung 2019; 67:140-150. [PMID: 30922088 DOI: 10.1556/004.2019.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Enteric viral diseases of swine are one of the most frequent disorders causing huge economic losses in pork production. After the reappearance of an emerging enteropathogen, porcine epidemic diarrhoea virus (PEDV) in Hungary in 2016, an extensive survey was initiated in an attempt to identify diarrhoea-related porcine viruses, including adeno-, astro-, boca-, calici-, circo-, corona-, kobu-, rota- and Torque teno viruses. A total of 384 faecal samples collected during a twoyear period from diarrhoeic and asymptomatic pigs of various ages in 17 farms were screened by conventional and real-time PCR methods. Half of the samples contained at least one examined virus with the dominance of kobuvirus (55.1%) followed by bocaviruses (33.2%) and rotavirus groups A and C together (20.9%), while coronaviruses including PEDV were not found in this set of samples. Statistical analysis showed a highly significant difference (P < 0.0001) in the frequency of single infections compared to mixed ones with the exception of weaned pigs, in which group additionally most viruses were detected. The results of this study suggest that the complexity of this disease may vary with age, which makes the prevention of diarrhoea a challenge, especially in weaned pigs.
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Affiliation(s)
- Anna Valkó
- 1 Department of Microbiology and Infectious Diseases, University of Veterinary Medicine Budapest, Hungária krt. 23–25, H-1143 Budapest, Hungary
| | - András Marosi
- 1 Department of Microbiology and Infectious Diseases, University of Veterinary Medicine Budapest, Hungária krt. 23–25, H-1143 Budapest, Hungary
| | | | - Rózsa Farkas
- 3 National Food Chain Safety Office, Veterinary Diagnostic Directorate, Budapest, Hungary
| | - Zsuzsanna Rónai
- 3 National Food Chain Safety Office, Veterinary Diagnostic Directorate, Budapest, Hungary
| | - Ádám Dán
- 3 National Food Chain Safety Office, Veterinary Diagnostic Directorate, Budapest, Hungary
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Niu TJ, Yi SS, Wang X, Wang LH, Guo BY, Zhao LY, Zhang S, Dong H, Wang K, Hu XG. Detection and genetic characterization of kobuvirus in cats: The first molecular evidence from Northeast China. INFECTION GENETICS AND EVOLUTION 2018; 68:58-67. [PMID: 30529719 PMCID: PMC7185515 DOI: 10.1016/j.meegid.2018.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 11/16/2022]
Abstract
Feline kobuvirus (FeKoV), a novel picornavirus of the genus kobuvirus, was initially identified in the feces of cats with diarrhea in South Korea in 2013. To date, there is only one report of the circulation of kobuvirus in cats in southern China. To investigate the presence and genetic variability of FeKoV in northeast China, 197 fecal samples were collected from 105 cats with obvious diarrhea and 92 asymptomatic cats in Shenyang, Jinzhou, Changchun, Jilin and Harbin regions, Northeast China, and viruses were detected by RT-PCR with universal primers targeting all kobuviruses. Kobuvirus was identified in 28 fecal samples with an overall prevalence of 14.2% (28/197) of which 20 samples were co-infected with feline parvovirus (FPV) and/or feline bocavirus (FBoV). Diarrhoeic cats had a higher kobuvirus prevalence (19.1%, 20/105) than asymptomatic cats (8.7%, 8/92). By genetic analysis based on partial 3D gene, all kobuvirus-positive samples were more closely related to previous FeKoV strains with high identities of 90.5%-97.8% and 96.6%-100% at the nucleotide and amino acid levels. Additionally, phylogenetic analysis based on the complete VP1 gene indicated that all FeKoV strains identified in this study were placed into a cluster, which separated from other reference strains previously reported, and three identical amino acid substitutions were present at the C-terminal of the VP1 protein for these FeKoV strains. Furthermore, two complete FeKoV polyprotein genomes were successfully obtained from two positive samples and designated 16JZ0605 and 17CC0811, respectively. The two strains shared 92.9%-94.9% nucleotide identities and 96.8%-98.4% amino acid identities to FeKoV prototype strains. Phylogenetic analysis indicated that FeKoVs were clustered according to their geographical regions, albeit with limited sequences support. This study provides the first molecular evidence that FeKoV circulates in cats in northeast China, and these FeKoVs exhibit genetic diversity and unique evolutionary trend.
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Affiliation(s)
- Ting-Jiang Niu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province 130118, China
| | - Shuai-Shu Yi
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province 130118, China
| | - Xin Wang
- Sinovet (Jiangsu) Biopharmaceuticals Co., Ltd, Taizhou 225300, China
| | - Lei-Hua Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Research Institute, Academy of Military Medical Sciences, Changchun 130122, China
| | - Bing-Yan Guo
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province 130118, China; Jilin Institute of Animal Husbandry and Veterinary Science, Changchun, Jilin Province 130062, China
| | - Li-Yan Zhao
- Library, Jilin Agricultural University, Changchun, Jilin Province 130118, China
| | - Shuang Zhang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province 130118, China
| | - Hao Dong
- College of life Science and Technology, Jilin Agricultural University, Changchun, Jilin Province 130118, China.
| | - Kai Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province 130118, China
| | - Xue-Gui Hu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province 130118, China.
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Bergallo M, Galliano I, Montanari P, Rassu M, Daprà V. Aichivirus in Children with Diarrhea in Northern Italy. Intervirology 2018; 60:196-200. [PMID: 29502122 DOI: 10.1159/000487051] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/22/2018] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVE Since its discovery, Aichivirus (AiV) A has been detected, with an incidence of 0.9-4.1%, primarily when studying outbreaks of diarrhea in children or young adults. In this paper, we report the first detection of AiV in Piedmont, Italy, in pediatric patients. METHODS A total of 159 fecal specimens (from 96 males and 63 females) previously screened for rotaviruses, adenoviruses, noroviruses, human parechoviruses, saliviruses, and sapoviruses were collected from infants and children with acute gastroenteritis. RESULTS The most commonly detected virus was norovirus GII (33.80%), fol lowed by rotavirus (21.30%), astrovirus (18.87%), boca virus (13.92%), sapovirus (10.90%), parechovirus (8%), norovirus GI (6.70%), adenovirus (1%), and salivirus (0.52%). Real-time polymerase chain reaction detected AiV A in 1 (0.62%) case subjects. AiV A was detected in monoinfection only in January. CONCLUSIONS Our results indicate that AiV may be associated with a limited number of diarrhea cases in pediatric patients.
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Affiliation(s)
- Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, University of Turin Medical School, Turin, Italy.,SC Pediatric U Regina Margherita Hospital, Turin, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, University of Turin Medical School, Turin, Italy.,SC Pediatric U Regina Margherita Hospital, Turin, Italy
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, University of Turin Medical School, Turin, Italy.,SC Pediatric U Regina Margherita Hospital, Turin, Italy
| | - Marco Rassu
- Department of Public Health and Pediatric Sciences, University of Turin Medical School, Turin, Italy
| | - Valentina Daprà
- Department of Public Health and Pediatric Sciences, University of Turin Medical School, Turin, Italy
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24
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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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Lu L, Van Dung N, Ivens A, Bogaardt C, O’Toole A, Bryant JE, Carrique-Mas J, Van Cuong N, Anh PH, Rabaa MA, Tue NT, Thwaites GE, Baker S, Simmonds P, Woolhouse ME. Genetic diversity and cross-species transmission of kobuviruses in Vietnam. Virus Evol 2018; 4:vey002. [PMID: 29449965 PMCID: PMC5810437 DOI: 10.1093/ve/vey002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cross-species transmission of viruses poses a sustained threat to public health. Due to increased contact between humans and other animal species the possibility exists for cross-species transmissions and ensuing disease outbreaks. By using conventional PCR amplification and next generation sequencing, we obtained 130 partial or full genome kobuvirus sequences from humans in a sentinel cohort in Vietnam and various mammalian hosts including bats, rodents, pigs, cats, and civets. The evolution of kobuviruses in different hosts was analysed using Bayesian phylogenetic methods. We estimated and compared time of origin of kobuviruses in different host orders; we also examined the cross-species transmission of kobuviruses within the same host order and between different host orders. Our data provide new knowledge of rodent and bat kobuviruses, which are most closely related to human kobuviruses. The novel bat kobuviruses isolated from bat roosts in Southern Vietnam were genetically distinct from previously described bat kobuviruses, but closely related to kobuviruses found in rodents. We additionally found evidence of frequent cross-species transmissions of kobuviruses within rodents. Overall, our phylogenetic analyses reveal multiple cross-species transmissions both within and among mammalian species, which increases our understanding of kobuviruses genetic diversity and the complexity of their evolutionary history.
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Affiliation(s)
- Lu Lu
- Ashworth Laboratories, Centre for Immunity, Infection and Evolution, University of Edinburgh, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Nguyen Van Dung
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
| | - Alasdair Ivens
- Ashworth Laboratories, Centre for Immunity, Infection and Evolution, University of Edinburgh, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Carlijn Bogaardt
- Ashworth Laboratories, Centre for Immunity, Infection and Evolution, University of Edinburgh, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Aine O’Toole
- Ashworth Laboratories, Centre for Immunity, Infection and Evolution, University of Edinburgh, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Juliet E Bryant
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, National Hospital for Tropical Diseases, Hanoi, Vietnam
| | - Juan Carrique-Mas
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Nguyen Van Cuong
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Pham Hong Anh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Maia A Rabaa
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Ngo Tri Tue
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Guy E Thwaites
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
- The Department of Medicine, University of Cambridge, Hills Rd, Cambridge CB2 0SP, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
| | - Mark Ej Woolhouse
- Ashworth Laboratories, Centre for Immunity, Infection and Evolution, University of Edinburgh, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
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Peng Q, Lan X, Wang C, Ren Y, Yue N, Wang J, Zhong B, Zhu Q. Kobuvirus VP3 protein restricts the IFN-β-triggered signaling pathway by inhibiting STAT2-IRF9 and STAT2-STAT2 complex formation. Virology 2017; 507:161-169. [DOI: 10.1016/j.virol.2017.04.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/15/2017] [Accepted: 04/19/2017] [Indexed: 11/25/2022]
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Is Porcine Kobuvirus 1 a Typical Diarrhoeic Pathogen of Piglets? FOLIA VETERINARIA 2017. [DOI: 10.1515/fv-2017-0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
The objective of this study was to show if porcine kobuvirus 1 (PKV-1) participates in the development of diarrhoea in piglets. The experiments were focused on comparing the occurrence of PKV-1 with the occurrence of rotavirus A (RVA) infection in suckling pigs on Slovak pig farms. A total of 91 rectal swabs of piglets (age < 28 days) were collected from 8 pig farms. RT-PCR was employed to detect PKV-1 through amplification of the 495 bp fragment of the 3D gene using primers KoVF/ KoVR, and RVA was detected through amplification of the 309 bp fragment of the VP6 gene using primers rot3 and rot5. As expected, the detection of RVA in diarrhoeic piglets was 56.8 % (P < 0.01), while only 14.8 % in healthy animals. These results confirm that RVA is one of the main causes of diarrhoea in young piglets. Comparatively, PKV-1 was detected in approximately equal numbers in the same group of both healthy and diarrhoeic pigs, with 74.1 % in healthy animals and 81.1 % in diarrhoeic animals, which was not statistically significant (P < 0.05). The level of co-infection of both viruses was 11.1 % in healthy animals. A portion of 48.6 % (P < 0.01) of diarrhoeic animals were found with RVA and PKV-1 coinfections. The results of this study indicate that while RVA is an enteric virus, PKV-1 cannot confidently be confirmed as an enteric pathogen.
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Zhai SL, Zhang H, Lin T, Chen SN, Zhou X, Chen QL, Lv DH, Wen XH, Zhou XR, Jia CL, Wei WK. A novel porcine kobuvirus emerged in piglets with severe diarrhoea in China. Transbound Emerg Dis 2017; 64:1030-1036. [DOI: 10.1111/tbed.12663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Indexed: 11/29/2022]
Affiliation(s)
- S.-L. Zhai
- Guangdong Key Laboratory of Animal Disease Prevention; Animal Disease Diagnostic Center; Institute of Animal Health; Guangdong Academy of Agricultural Sciences; Guangzhou China
| | - H. Zhang
- College of Veterinary Medicine; South China Agricultural University; Guangzhou China
| | - T. Lin
- Department of Chemistry and Biochemistry; South Dakota State University; Brookings SD USA
| | - S.-N. Chen
- Department of Chemistry and Biochemistry; South Dakota State University; Brookings SD USA
| | - X. Zhou
- College of Veterinary Medicine; South China Agricultural University; Guangzhou China
| | - Q.-L. Chen
- Guangdong Key Laboratory of Animal Disease Prevention; Animal Disease Diagnostic Center; Institute of Animal Health; Guangdong Academy of Agricultural Sciences; Guangzhou China
| | - D.-H. Lv
- Guangdong Key Laboratory of Animal Disease Prevention; Animal Disease Diagnostic Center; Institute of Animal Health; Guangdong Academy of Agricultural Sciences; Guangzhou China
| | - X.-H. Wen
- Guangdong Key Laboratory of Animal Disease Prevention; Animal Disease Diagnostic Center; Institute of Animal Health; Guangdong Academy of Agricultural Sciences; Guangzhou China
| | - X.-R. Zhou
- Guangdong Key Laboratory of Animal Disease Prevention; Animal Disease Diagnostic Center; Institute of Animal Health; Guangdong Academy of Agricultural Sciences; Guangzhou China
| | - C.-L. Jia
- Guangdong Key Laboratory of Animal Disease Prevention; Animal Disease Diagnostic Center; Institute of Animal Health; Guangdong Academy of Agricultural Sciences; Guangzhou China
| | - W.-K. Wei
- Guangdong Key Laboratory of Animal Disease Prevention; Animal Disease Diagnostic Center; Institute of Animal Health; Guangdong Academy of Agricultural Sciences; Guangzhou China
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Complete genome analysis of porcine kobuviruses from the feces of pigs in Japan. Virus Genes 2017; 53:593-602. [PMID: 28484931 DOI: 10.1007/s11262-017-1464-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/24/2017] [Indexed: 10/19/2022]
Abstract
Porcine kobuviruses (PoKoVs) are ubiquitously distributed in pig populations worldwide and are thought to be enteric viruses in swine. Although PoKoVs have been detected in pigs in Japan, no complete genome data for Japanese PoKoVs are available. In the present study, 24 nearly complete or complete sequences of the PoKoV genome obtained from 10 diarrheic feces and 14 non-diarrheic feces of Japanese pigs were analyzed using a metagenomics approach. Japanese PoKoVs shared 85.2-100% identity with the complete coding nucleotide (nt) sequences and the closest relationship of 85.1-98.3% with PoKoVs from other countries. Twenty of 24 Japanese PoKoVs carried a deletion of 90 nt in the 2B coding region. Phylogenetic tree analyses revealed that PoKoVs were not grouped according to their geographical region of origin and the phylogenetic trees of the L, P1, P2, and P3 genetic regions showed topologies different from each other. Similarity plot analysis using strains from a single farm revealed partially different similarity patterns among strains from identical farm origins, suggesting that recombination events had occurred. These results indicate that various PoKoV strains are prevalent and not restricted geographically on pig farms worldwide and the coexistence of multiple strains leads to recombination events of PoKoVs and contributes to the genetic diversity and evolution of PoKoVs.
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Detection and molecular characterization of porcine kobuvirus in piglets in 2009-2013 in northern Thailand. Trop Anim Health Prod 2017; 49:1077-1080. [PMID: 28466239 DOI: 10.1007/s11250-017-1298-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 04/24/2017] [Indexed: 10/19/2022]
Abstract
A total of 636 fecal samples collected from piglets with and without diarrhea during 2009 to 2013 were tested for porcine kobuvirus by RT-PCR. From a total of 528 fecal samples collected from piglets with diarrhea and 108 from healthy controls, 505 (95.6%) and 104 (96.3%) were positive for porcine kobuvirus, respectively. The detection rates of porcine kobuvirus were remarkable equally high in both diarrheic and healthy piglets. Phylogenetic analysis revealed that porcine kobuvirus strains detected in both symptomatic and asymptomatic piglets were genetically closely related to each other and also to other porcine kobuviruses reported worldwide. It was interesting to point out that one of the porcine kobuvirus strains isolated from piglet in our study was similar to a porcine-like bovine kobuvirus reference strain isolated previously in South Korea. This finding provided the evidence to support the interspecies transmission of kobuviruses between cattle and swine.
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Moreira ASD, Raabis SM, Graham ME, Dreyfus JM, Sibley SD, Godhardt-Cooper JA, Toohey-Kurth KL, Goldberg TL, Peek SF. Identification by next-generation sequencing of Aichivirus B in a calf with enterocolitis and neurologic signs. J Vet Diagn Invest 2017; 29:208-211. [PMID: 28176615 DOI: 10.1177/1040638716685597] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
An 11-d-old Holstein bull calf was presented to the Veterinary Medical Teaching Hospital at the University of Wisconsin-Madison because of a 4-d history of diarrhea and persistent low-grade fever. Initial diagnosis was enteritis caused by Cryptosporidium and rotavirus. During hospitalization, the calf became stuporous and was only responsive to noxious stimuli, with hypotonia of all 4 limbs, tail, head, and neck. A cerebrospinal fluid analysis revealed xanthochromia, with marked lymphocytic pleocytosis, which was suggestive of viral meningitis and/or encephalitis. Aichivirus B, which belongs to the Kobuvirus genus, was tentatively identified in spinal fluid by next-generation DNA sequencing. This virus can affect a multitude of species, including humans and cattle, and has been isolated from both healthy and diarrheic individuals. However, to date, a possible connection with neurologic disease has not been described, to our knowledge.
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Affiliation(s)
- Ana S D Moreira
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Sarah M Raabis
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Melissa E Graham
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Jennifer M Dreyfus
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Samuel D Sibley
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Jennifer A Godhardt-Cooper
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Kathy L Toohey-Kurth
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Tony L Goldberg
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Simon F Peek
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
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Molecular detection of kobuviruses in livestock in Northern Ireland and the Republic of Ireland. Arch Virol 2017; 162:1275-1279. [DOI: 10.1007/s00705-017-3223-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 12/07/2016] [Indexed: 10/20/2022]
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Jackova A, Sliz I, Mandelik R, Salamunova S, Novotny J, Kolesarova M, Vlasakova M, Vilcek S. Porcine kobuvirus 1 in healthy and diarrheic pigs: Genetic detection and characterization of virus and co-infection with rotavirus A. INFECTION GENETICS AND EVOLUTION 2017; 49:73-77. [PMID: 28087494 DOI: 10.1016/j.meegid.2017.01.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 01/04/2017] [Accepted: 01/09/2017] [Indexed: 12/16/2022]
Abstract
The porcine kobuvirus 1 (PKV-1) is believed to be an enteric virus. To investigate the prevalence of PKV-1 in pigs, virus was detected by RT-PCR in rectal swabs originating from 414 healthy and diarrheic pigs of different age categories on farms in Slovakia. Among all ages of animals, PKV-1 was detected equally in diarrheic (63.8%) and clinically healthy (62.9%) pigs. PKV-1 was more often detected in diarrheic (74.6%) than in healthy (64.4%) suckling piglets (<28days) but data was not statistically significant. Results in weaned (28-70days) and fattening (>70days) of both healthy and diarrheic pigs were inconsistent ranging in interval 56.2% to 67.9%. This study did not confirm a clear relationship of PKV-1 infection with diarrhea in pigs. Rotavirus A infection was detected among the same animals in 39% diarrheic and 9.2% healthy suckling piglets (p<0.001) confirming rotavirus as a causative agent of diarrhea in this age group. The difference was not significant in older pigs with both diarrheic and healthy pigs being infected within a range of 0% to 12.2%. Co-infection with PKV-1 and rotavirus A was detected overall in 5.6% of healthy and in 13.5% of diarrheic pigs and was highest in suckling piglets (33.9%). The PKV-1sequences from pigs in Slovakia were analyzed at the genetic level in the partial 3D gene region for the first time. The viral sequences were grouped in phylogenetic clusters according to their farm of origin. When compared with 157 nucleotide sequences originating from pig samples of different countries around the world Slovakian PKV-1 sequences were clustered in the phylogenetic tree with Asian sequences but not with nucleotide sequences from the neighbouring countries of Czech Republic or Hungary.
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Affiliation(s)
- Anna Jackova
- University of Veterinary Medicine and Pharmacy, Komenskeho 73, SK-041 81 Kosice, Slovakia.
| | - Ivan Sliz
- University of Veterinary Medicine and Pharmacy, Komenskeho 73, SK-041 81 Kosice, Slovakia.
| | - Rene Mandelik
- University of Veterinary Medicine and Pharmacy, Komenskeho 73, SK-041 81 Kosice, Slovakia.
| | - Slavomira Salamunova
- University of Veterinary Medicine and Pharmacy, Komenskeho 73, SK-041 81 Kosice, Slovakia.
| | - Jaroslav Novotny
- University of Veterinary Medicine and Pharmacy, Komenskeho 73, SK-041 81 Kosice, Slovakia.
| | - Mariana Kolesarova
- Faculty of Science, P.J. Safarik University, Srobarova 2, SK-041 80 Kosice, Slovakia.
| | - Michaela Vlasakova
- University of Veterinary Medicine and Pharmacy, Komenskeho 73, SK-041 81 Kosice, Slovakia.
| | - Stefan Vilcek
- University of Veterinary Medicine and Pharmacy, Komenskeho 73, SK-041 81 Kosice, Slovakia.
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Kong N, Zuo Y, Wang Z, Yu H, Zhou EM, Shan T, Tong G. Molecular characterization of new described kobuvirus in dogs with diarrhea in China. SPRINGERPLUS 2016; 5:2047. [PMID: 27995024 PMCID: PMC5130936 DOI: 10.1186/s40064-016-3738-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 11/25/2016] [Indexed: 11/13/2022]
Abstract
Canine kobuvirus (CaKVs) was a newly described virus detected in dogs in the US and Italy. To learn more about CaKVs, 5 of 106 fecal samples from diarrhea dogs were positive with CaKVs in China, and the full genome of CaKVs strain CH-1 isolated from dog with diarrhea was sequenced. The genome consists of 8186 nucleotides, excluding the 3′ poly (A) tail, and an open reading frame that maps between nucleotide positions 601 and 7943 which encodes a 2446 amino acid polyprotein. Based on the complete amino acid sequence of polyprotein, phylogenetic analysis showed that CH-1 was grouped along with other canine kobuvirus strains detected in the USA (US-PC0082, AN211D).
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Affiliation(s)
- Ning Kong
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241 China ; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009 China ; Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100 China
| | - Yewen Zuo
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241 China
| | - Zhongze Wang
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241 China
| | - Hai Yu
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241 China ; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009 China
| | - En-Min Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100 China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241 China ; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009 China
| | - Guangzhi Tong
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241 China ; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009 China
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36
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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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Abstract
To investigate whether kokuvirus is present in Japanese dogs, we examined the fecal
samples obtained from 94 diarrheal household dogs and 50 clinically healthy kenneled dogs
by RT-PCR. The gene was detected in 37.2% and 48.0% in the former and the latter,
respectively, suggesting that canine kobuvirus (CaKoV) is circulating among Japanese dogs.
From the result of the latter, however, CaKoV may not be a primary pathogen. Furthermore,
all gene-positive dogs were purebreds aged four months or younger. This finding suggests
that CaKoV endemic is confined in multi-dog environments, and the dogs have a strong
age-dependent resistance to CaKoV.
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Affiliation(s)
- Takehisa Soma
- Veterinary Diagnostic Laboratory, Marupi Lifetech Co., Ltd., 103 Fushiocho, Ikeda, Osaka 563-0011, Japan
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38
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Chuchaona W, Khamrin P, Yodmeeklin A, Kumthip K, Saikruang W, Thongprachum A, Okitsu S, Ushijima H, Maneekarn N. Detection and characterization of Aichi virus 1 in pediatric patients with diarrhea in Thailand. J Med Virol 2016; 89:234-238. [PMID: 27420653 DOI: 10.1002/jmv.24630] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2016] [Indexed: 11/06/2022]
Abstract
Kobuvirus is a newly discovered virus that belongs to the Kobuvirus genus in Picornaviridae family, which comprised of three species including Aichivirus A, Aichivirus B, and Aichivirus C. The kobuvirus isolated from human has been classified as Aichi virus 1 and belongs to Aichivirus A species. The present study aimed to assess the epidemiology and to perform molecular characterization of Aichi virus 1 in children admitted to hospitals with acute gastroenteritis in Chiang Mai, Thailand. A total of 923 fecal specimens collected from January, 2011 to December, 2013 were screened for the presence of Aichi virus 1 by RT semi-nested PCR. Out of 923 fecal specimens tested, Aichi virus 1 was detected with the prevalence of 2.6% (24/923). Of these, 0.3% (3/923) was genotype A and 2.3% (21/923) were genotype B. It is interesting to note that the genotype A showed the nucleotide sequence closely related to the Aichi virus reference strain isolated from sewage in Tunisia, while genotype B was most closely related to other human Aichi virus B reference strains. The results suggest that Aichi virus 1 of both genotypes A and B are circulating in pediatric patients in Thailand. J. Med. Virol. 89:234-238, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Watchaporn Chuchaona
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Arpaporn Yodmeeklin
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Kattareeya Kumthip
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Wilaiporn Saikruang
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Aksara Thongprachum
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Shoko Okitsu
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Hiroshi Ushijima
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
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Molecular Epidemiological Investigation of Porcine kobuvirus and Its Coinfection Rate with PEDV and SaV in Northwest China. BIOMED RESEARCH INTERNATIONAL 2016; 2016:7590569. [PMID: 27294133 PMCID: PMC4884858 DOI: 10.1155/2016/7590569] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 04/15/2016] [Accepted: 04/28/2016] [Indexed: 11/17/2022]
Abstract
Porcine kobuvirus (PKV) has circulated throughout China in recent years. Although many studies have detected it throughout the world, its molecular epidemiology has not been characterized in northwest China. To understand its prevalence, 203 fecal samples were collected from different regions of Gansu Province and tested with reverse transcription-polymerase chain reaction. In this study, we tested these samples for PKV, porcine epidemic diarrhea virus (PEDV), and sapovirus and analyzed the amplified 2C gene fragments of PKV. Overall, 126 (62.1%) samples were positive for PKV. Of the 74 piglets samples among the 203 fecal samples, 65 (87.8%) were positive for PKV. PKV infection was often accompanied by PEDV, but the relationship between the two viruses must be confirmed. A phylogenetic analysis indicated that the PKV strains isolated from the same regions clustered on the same branches. This investigation shows that PKV infections are highly prevalent in pigs in northwest China, especially in piglets with symptoms of diarrhea.
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40
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Naoi Y, Kishimoto M, Masuda T, Ito M, Tsuchiaka S, Sano K, Yamasato H, Omatsu T, Aoki H, Furuya T, Katayama Y, Oba M, Okada T, Shirai J, Mizutani T, Nagai M. Characterization and phylogenetic analysis of a novel picornavirus from swine feces in Japan. Arch Virol 2016; 161:1685-90. [DOI: 10.1007/s00705-016-2834-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/16/2016] [Indexed: 01/10/2023]
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41
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Amimo JO, El Zowalaty ME, Githae D, Wamalwa M, Djikeng A, Nasrallah GK. Metagenomic analysis demonstrates the diversity of the fecal virome in asymptomatic pigs in East Africa. Arch Virol 2016; 161:887-97. [PMID: 26965436 DOI: 10.1007/s00705-016-2819-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 03/03/2016] [Indexed: 01/01/2023]
Abstract
Pigs harbor a variety of viruses that are closely related to human viruses and are suspected to have zoonotic potential. Little is known about the presence of viruses in smallholder farms where pigs are in close contact with humans and wildlife. This study provides insight into viral communities and the prevalence and characteristics of enteric viral co-infections in smallholder pigs in East Africa. Sequence-independent amplification and high-throughput sequencing were applied to the metagenomics analysis of viruses in feces collected from asymptomatic pigs. A total of 47,213 de novo-assembled contigs were constructed and compared with sequences from the GenBank database. Blastx search results revealed that 1039 contigs (>200 nt) were related to viral sequences in the GenBank database. Of the 1039 contigs, 612 were not assigned to any viral taxa because they had little similarity to known viral genomic or protein sequences, while 427 contigs had a high level of sequence similarity to known viruses and were assigned to viral taxa. The most frequent contigs related to mammalian viruses resembling members of the viral genera Astrovirus, Rotavirus, Bocavirus, Circovirus, and Kobuvirus. Other less abundant contigs were related to members of the genera Sapelovirus, Pasivirus, Posavirus, Teschovirus and Picobirnavirus. This is the first report on the diversity of the fecal virome of pig populations in East Africa. The findings of the present study help to elucidate the etiology of diarrheal diseases in pigs and identify potential zoonotic and emerging viruses in the region. Further investigations are required to compare the incidence of these viruses in healthy and diseased pigs in order to better elucidate their pathogenic role.
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Affiliation(s)
- Joshua O Amimo
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, P.O Box 29053, Nairobi, 00625, Kenya. .,Bioscieces of Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI), Hub, Nairobi, P.O Box 30709, Nairobi, 00100, Kenya.
| | | | - Dedan Githae
- Bioscieces of Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI), Hub, Nairobi, P.O Box 30709, Nairobi, 00100, Kenya
| | - Mark Wamalwa
- Bioscieces of Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI), Hub, Nairobi, P.O Box 30709, Nairobi, 00100, Kenya
| | - Apollinaire Djikeng
- Bioscieces of Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI), Hub, Nairobi, P.O Box 30709, Nairobi, 00100, Kenya
| | - Gheyath K Nasrallah
- Biomedical Research Center, Qatar University, Doha, 2713, Qatar. .,Department of Health Sciences, College of Arts and Sciences, Qatar University, Doha, 2713, Qatar.
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Lu L, Van Dung N, Bryant JE, Carrique-Mas J, Van Cuong N, Anh PH, Rabaa MA, Baker S, Simmonds P, Woolhouse ME. Evolution and phylogeographic dissemination of endemic porcine picornaviruses in Vietnam. Virus Evol 2016; 2:vew001. [PMID: 27774295 PMCID: PMC4989877 DOI: 10.1093/ve/vew001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Members of the Picornaviridae are important and often zoonotic viruses responsible for a variety of human and animal diseases. However, the evolution and spatial dissemination of different picornaviruses circulating in domestic animals are not well studied. We examined the rate of evolution and time of origin of porcine enterovirus G (EV-G) and porcine kobuvirus species C lineages (PKV-C) circulating in pig farms in Vietnam and from other countries. We further explored the spatiotemporal spread of EV-G and PKV-C in Southwest Vietnam using phylogeographic models. Multiple types of EV-G are co-circulating in Vietnam. The two dominant EV-G types among isolates from Vietnam (G1 and G6) showed strong phylogenetic clustering. Three clades of PKV-C (PKV-C1-3) represent more recent introductions into Vietnam; PKV-C2 is closely related to PKV-C from Southwest China, indicating possible cross-border dissemination. In addition, high virus lineage migration rates were estimated within four districts in Dong Thap province in Vietnam for both EV-G types (G1, G6) and all PKV-C (C1-3) clades. We found that Chau Thanh district is a primary source of both EV-G and PKV-C clades, consistent with extensive pig trading in and out of the district. Understanding the evolution and spatial dissemination of endemic picornaviruses in pigs may inform future strategies for the surveillance and control of picornaviruses.
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Affiliation(s)
- Lu Lu
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Nguyen Van Dung
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - Juliet E Bryant
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam,; Nuffield Department of Medicine, Oxford University, Old Rd, Oxford OX3 7LF, UK and
| | - Juan Carrique-Mas
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Nguyen Van Cuong
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Pham Honh Anh
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Maia A Rabaa
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam,; Nuffield Department of Medicine, Oxford University, Old Rd, Oxford OX3 7LF, UK and; The London School of Hygiene and Tropical Medicine, Keppel St, Bloomsbury, London WC1E 7HT, UK
| | - Peter Simmonds
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK,; Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - Mark E Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
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43
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Zhu X, Wang Y, Chen J, Zhang X, Shi H, Shi D, Gao J, Feng L. Development of TaqMan real-time reverse transcription-polymerase chain reaction for the detection and quantitation of porcine kobuvirus. J Virol Methods 2016; 234:132-6. [PMID: 26912233 DOI: 10.1016/j.jviromet.2016.01.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/14/2016] [Accepted: 01/24/2016] [Indexed: 10/22/2022]
Abstract
Porcine kobuvirus (PKV) is a newly emerging virus that has been detected in diarrheic pigs. Presently, reverse transcription-polymerase chain reaction (RT-PCR) and RT-loop-mediated amplification are the only methods that can be used to detect PKV. To develop a TaqMan real-time RT-PCR for the rapid detection and quantitation of PKV nucleic acid in fecal samples, a pair of primers and a probe were designed to amplify the conserved 3D region of the PKV genome. After optimization, the TaqMan real-time RT-PCR was highly specific and ∼1000 times more sensitive than conventional RT-PCR, and the detection limit was as low as 30 DNA copies. Among the 148 intestinal samples from piglets with diarrhea, 136 and 118 were positive based on the TaqMan and conventional RT-PCR methods, respectively, indicating that the TaqMan RT-PCR was more sensitive than conventional RT-PCR, and the total concordance of the two methods was approximately 87.84%. Thus, the TaqMan real-time RT-PCR should be a useful tool for the early detection and quantitation of PKV.
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Affiliation(s)
- Xiangdong Zhu
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No.427 Maduan Street, Nangang District, Harbin 150001, China.
| | - Yufei Wang
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No.427 Maduan Street, Nangang District, Harbin 150001, China; College of Life Science, Northeast Agricultural University, Harbin 150030, China.
| | - Jianfei Chen
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No.427 Maduan Street, Nangang District, Harbin 150001, China.
| | - Xin Zhang
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No.427 Maduan Street, Nangang District, Harbin 150001, China.
| | - Hongyan Shi
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No.427 Maduan Street, Nangang District, Harbin 150001, China.
| | - Da Shi
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No.427 Maduan Street, Nangang District, Harbin 150001, China.
| | - Jing Gao
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No.427 Maduan Street, Nangang District, Harbin 150001, China; College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 2 Xinyang Road, Sartu District, Daqing 163319, China.
| | - Li Feng
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No.427 Maduan Street, Nangang District, Harbin 150001, China.
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Van Dung N, Anh PH, Van Cuong N, Hoa NT, Carrique-Mas J, Hien VB, Sharp C, Rabaa M, Berto A, Campbell J, Baker S, Farrar J, Woolhouse ME, Bryant JE, Simmonds P. Large-scale screening and characterization of enteroviruses and kobuviruses infecting pigs in Vietnam. J Gen Virol 2015; 97:378-388. [PMID: 26653281 DOI: 10.1099/jgv.0.000366] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A recent survey of pigs in Dong Thap province, Vietnam identified a high frequency of enterovirus species G (EV-G) infection (144/198; 72.7%). Amongst these was a plethora of EV-G types (EV-G1, EV-G6 and four new types EV-G8-EV-G11). To better characterize the genetic diversity of EV-G and investigate the possible existence of further circulating types, we performed a larger-scale study on 484 pig and 45 farm-bred boar faecal samples collected in 2012 and 2014, respectively. All samples from the previous and current studies were also screened for kobuviruses. The overall EV infection frequency remained extremely high (395/484; 81.6%), but with comparable detection rates and viral loads between healthy and diarrhoeic pigs; this contrasted with less frequent detection of EV-G in boars (4/45; 8.9%). EV was most frequently detected in pigs ≤ 14 weeks old (∼ 95%) and declined in older pigs. Infections with EV-G1 and EV-G6 were most frequent, whilst less commonly detected types included EV-G3, EV-G4 and EV-G8-EV-G11, and five new types (EV-G12-EV-G16). In contrast, kobuvirus infection frequency was significantly higher in diarrhoeic pigs (40.9 versus 27.6%; P = 0.01). Kobuviruses also showed contrasting epizootiologies and age associations; a higher prevalence was found in boars (42%) compared with domestic pigs (29%), with the highest infection frequency amongst pigs >52 weeks old. Although genetically diverse, all kobuviruses identified belonged to the species Aichivirus C. In summary, this study confirms infection with EV-G was endemic in Vietnamese domestic pigs and exhibits high genetic diversity and extensive inter-type recombination.
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Affiliation(s)
- Nguyen Van Dung
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - Pham Hong Anh
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Van Cuong
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam.,Nuffield Department of Medicine, Oxford University, Oxford OX3 7BN, UK
| | - Juan Carrique-Mas
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - Vo Be Hien
- Subdepartment of Animal Health, Dong Thap Province, Vietnam
| | - C Sharp
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - M Rabaa
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - A Berto
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - James Campbell
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam.,Nuffield Department of Medicine, Oxford University, Oxford OX3 7BN, UK.,London School of Hygiene and Tropical Medicine, Keppel Street, Bloomsbury, London WC1E 7HT, UK
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - Mark E Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
| | - Juliet E Bryant
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam.,Nuffield Department of Medicine, Oxford University, Oxford OX3 7BN, UK
| | - Peter Simmonds
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK.,Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
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45
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Liu P, Li P, Lyu W, Li X, Li S, Yang F, Huang J, Xu Z, Zhu L. Epidemiological study and variation analysis of the porcine kobuvirus 3D gene in Sichuan province, China. Virol Sin 2015; 30:460-3. [PMID: 26637336 DOI: 10.1007/s12250-015-3632-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Affiliation(s)
- Pengjuan Liu
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611134, China
| | - Ping Li
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611134, China
| | - Wenting Lyu
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611134, China
| | - Xinqiong Li
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611134, China
| | - Song Li
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611134, China
| | - Fan Yang
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611134, China
| | - Jianbo Huang
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611134, China
| | - Zhiwen Xu
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611134, China
| | - Ling Zhu
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611134, China.
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Otomaru K, Naoi Y, Haga K, Omatsu T, Uto T, Koizumi M, Masuda T, Yamasato H, Takai H, Aoki H, Tsuchiaka S, Sano K, Okazaki S, Katayama Y, Oba M, Furuya T, Shirai J, Katayama K, Mizutani T, Nagai M. Detection of novel kobu-like viruses in Japanese black cattle in Japan. J Vet Med Sci 2015; 78:321-4. [PMID: 26369290 PMCID: PMC4785127 DOI: 10.1292/jvms.15-0447] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
During surveillance for bovine diarrhea of unknown causes in Japanese black cattle in Kagoshima Prefecture,
Japan, we found two types of novel kobu-like viruses in fecal samples of calves. Sequence analyses revealed
that they had L protein and 2A protein with H-box/NC sequence motif, which are present in kobuviruses.
Phylogenetic analysis revealed that they were related to kobuviruses; however, they clustered apart from other
kobuviruses. In the prevalence study of two types of novel kobu-like viruses, 16.9% and 10.4% prevalence of
these viruses were observed in the feces of diarrheal calves in this area.
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Affiliation(s)
- Konosuke Otomaru
- Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima 890-0065, Japan
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47
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Liu X, Oka T, Wang Q. Genomic characterization of a US porcine kobuvirus strain. Arch Microbiol 2015; 197:1033-40. [PMID: 26316163 DOI: 10.1007/s00203-015-1139-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 06/22/2015] [Accepted: 08/02/2015] [Indexed: 12/14/2022]
Abstract
Porcine kobuvirus has been detected from pig fecal samples in the USA, but there is still no information on the full-length genomes. In this study, we characterized the first complete genomic sequence of a US porcine kobuvirus strain OH/RV50/2011. The viral genome is 8123 nucleotides (nt) long, including a 576-nt 5'-untranslated region (UTR), a 7380-nt polyprotein encoding sequence, and a 167-nt 3'-UTR. A complete genome sequence alignment suggested that two types of porcine kobuviruses were found based on whether a 30-aa deletion existed in the 2B encoding region. Furthermore, several conserved motifs that can be used for the design of universal kobuvirus or porcine kobuvirus-specific primers were verified in non-structural protein genes. Phylogenetic analysis based on the complete genome sequence showed that RV50 was grouped with other porcine kobuviruses and more closely related to Chinese strains. Secondary structure analysis of the 5'-UTR showed that RV50 has three stem-loop domains in the first 108 nt and has a potential hepacivirus-/pestivirus-like type IV group-B-like internal ribosomal entry site, like the porcine kobuvirus prototype strain S-1. Codon usage analysis showed that the most preferred usage tends to be C or U at the end of a codon in a porcine kobuvirus genome. These results will be useful in understanding the evolution of porcine kobuviruses .
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Affiliation(s)
- Xinsheng Liu
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agricultural and Environmental Sciences, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH, USA,
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48
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Jin WJ, Yang Z, Zhao ZP, Wang WY, Yang J, Qin AJ, Yang HC. Genetic characterization of porcine kobuvirus variants identified from healthy piglets in China. INFECTION GENETICS AND EVOLUTION 2015; 35:89-95. [PMID: 26238210 DOI: 10.1016/j.meegid.2015.07.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/28/2015] [Accepted: 07/29/2015] [Indexed: 01/20/2023]
Abstract
In this study, two porcine kobuvirus strains, JS-01-CHN and JS-02a-CHN were detected from piglets with diarrhea and asymptomatic, respectively. The sequences of the two strains were analyzed using a bioinformatics software package. The full-length genome of JS-02a-CHN, was detected in healthy piglets was 8121 nucleotides (nt) long excluding the poly(A) tail. There was a 30 amino acid deletion in the 2B-coding region of JS-02a-CHN. We are the first to report a 30 amino acid deletion in porcine kobuvirus from asymptomatic piglets, indicating that porcine kobuvirus may have evolved differently based on geography and host differences. Fecal samples were obtained from pigs with diarrhea (n=91) and healthy (n=126) pigs and analyzed using RT-PCR. Of these, 64.8% (59/91) of diarrheic piglets and 19.8% (25/126) of healthy piglets were positive for PKV using VP1 specific primers. Twenty-eight (28) virus positive samples were randomly selected and the VP1 gene was analyzed. Phylogenetic analysis indicated that the 15 strains isolated from pigs with diarrhea clustered into different branches, while the VP1 sequences from clinically healthy pigs clustered into a single large group. These results indicate that the VP1 gene is diverse in pigs with diarrhea but conserved in healthy pigs in the Jiangsu Province.
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Affiliation(s)
- Wen-Jie Jin
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China; College of Veterinary Medicine, Yangzhou University, Ministry of Education Key Lab for Avian Preventive Medicine, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, PR China.
| | - Zhen Yang
- College of Veterinary Medicine, Yangzhou University, Ministry of Education Key Lab for Avian Preventive Medicine, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, PR China
| | - Zhen-Peng Zhao
- College of Veterinary Medicine, Yangzhou University, Ministry of Education Key Lab for Avian Preventive Medicine, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, PR China
| | - Wan-Yi Wang
- College of Veterinary Medicine, Yangzhou University, Ministry of Education Key Lab for Avian Preventive Medicine, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, PR China
| | - Juan Yang
- College of Veterinary Medicine, Yangzhou University, Ministry of Education Key Lab for Avian Preventive Medicine, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, PR China
| | - Ai-Jian Qin
- College of Veterinary Medicine, Yangzhou University, Ministry of Education Key Lab for Avian Preventive Medicine, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, PR China.
| | - Han-Chun Yang
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China.
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49
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Infection of farmed pigs with porcine kobuviruses in Italy. Arch Virol 2015; 160:1533-6. [PMID: 25809018 DOI: 10.1007/s00705-015-2397-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/08/2015] [Indexed: 12/18/2022]
Abstract
Two-hundred eight swine fecal samples from six Italian farms were tested using a kobuvirus-specific RT-PCR with primers that amplify a region within the 3D gene. All farms were kobuvirus positive, with prevalence rates ranging between 24 % and 84 %. Overall, 57.5 % of asymptomatic pigs and 49.7 % of animals with diarrhea were positive for kobuvirus. Sequence analysis showed a different predominant strain circulating on each farm and indicated that the strains detected were related to both European and Asiatic strains. A possible pathogenic role of kobuvirus should be investigated further, since infections with this virus occur frequently in pigs of different ages.
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50
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Choi JW, Lee MH, Lee KK, Oem JK. Genetic characteristics of the complete feline kobuvirus genome. Virus Genes 2014; 50:52-7. [PMID: 25404141 DOI: 10.1007/s11262-014-1144-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 11/08/2014] [Indexed: 11/30/2022]
Abstract
We sequenced the complete genome of a feline kobuvirus and determined relationships with other kobuviruses. This kobuvirus has an 8,269-nucleotide-long RNA genome, excluding the poly(A) tail. The genome contains a 7,311-bp open reading frame (ORF) encoding a putative polyprotein precursor of 2,437 amino acids, a 717-bp 5'-untranslated region (UTR), and a 241-bp 3'-UTR. The L protein sequence was found to be the most variable region in the feline kobuvirus genome. Interestingly, the 5'-UTR B and C stem-loops were conserved as observed with other kobuviruses; however, a secondary structure corresponding to stem-loop A was not found in the full length 5'-UTR sequence. Phylogenetic tree analysis showed that kobuviruses can be divided into 3 main groups. The feline kobuvirus belongs to the Aichivirus A species containing Aichivirus, mouse kobuvirus, and canine kobuvirus.
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Affiliation(s)
- Jeong-Won Choi
- Viral Disease Diagnostic Laboratory, Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, 480 Anyang-6-Dong, Anyang, 430-824, Republic of Korea
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