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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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Wei R, Shang R, Cheng K, Wang S, Yuan X, Wu J, Yu Z. Phylogenetic analysis and molecular characterization of the co-infection of the new variant of the porcine epidemic diarrhea virus and the novel porcine kobuvirus isolated from piglets with diarrhea. Braz J Microbiol 2023; 54:2527-2534. [PMID: 37344656 PMCID: PMC10484880 DOI: 10.1007/s42770-023-01025-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/30/2023] [Indexed: 06/23/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is a virus that can cause diarrhea in pigs, resulting in significant economic losses to the pig industry. The mutation of the virus and its co-infection with other enteroviruses leads to poor control of PEDV infection. In this study, we found that the diarrhea outbreak in a pig farm in Shandong Province was mainly caused by PEDV infection. Through high-throughput sequencing, we also detected one other diarrhea-related virus (porcine kobuvirus). In the phylogenetic analysis and molecular characterization of the detected PEDV S gene and PKV, it was found that the S gene of the PEDV strain detected in this study (named SD22-2) had more mutations than the CV777 strain. The highest homology between PKV (named SD/2022/China) detected in this study and other strains was only 89.66%. Based on polyprotein, we divided SD/2022/China strains into a new grouping (designated group 4) and detected recombination signals. In summary, SD22-2 detected in this study is a new PEDV variant strain, and SD/2022/China strain might be a novel PKV strain. We also found the co-infection of the new PEDV variant and the novel PKV isolated from piglets with diarrhea. Our data suggested the importance of continuous surveillance of PEDV and PKV.
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Affiliation(s)
- Ran Wei
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Rui Shang
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Kaihui Cheng
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Song Wang
- Medical Integration and Practice Center, Shandong University, Jinan, 250012, China
| | - Xiaoyuan Yuan
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Jiaqiang Wu
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Zhijun Yu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
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3
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Eriksen EØ. A Systematic Review: Is Porcine Kobuvirus Causing Gastrointestinal Disease in Young Pigs? Vet Sci 2023; 10:286. [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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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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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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KOBUVIRUS DETECTION IN THE CRITICALLY ENDANGERED PYGMY HOG ( PORCULA SALVANIA), INDIA. J Zoo Wildl Med 2021; 52:343-347. [PMID: 33827197 DOI: 10.1638/2019-0104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2020] [Indexed: 11/21/2022] Open
Abstract
Pygmy hogs (Porcula salvania) are the smallest and rarest wild suid. It is categorized as a Critically Endangered species as per the Red List of the International Union for Conservation of Nature. This study reports the first detection of a single-stranded RNA virus species, Aichivirus C, belonging to the genus Kobuvirus (KobV) and the family Picornaviridae, in pygmy hogs. KobV species are identified as a cause of acute gastroenteritis among children in India. As of now, there exists no report on the detection of KobV in animals from India. We used a detection assay based on reverse transcription-polymerase chain reaction for KobV screening in pygmy hogs from a conservation center in India. The 3D polymerase gene-based molecular analysis revealed KobV presence in the Indian wild suid, pygmy hogs. Of the 15 samples tested, three were found positive for picornaviruses and were negative for rotavirus A, rotavirus C, astrovirus, picobirnavirus and caliciviruses. Nucleotide-based sequence analysis of the partial 3D polymerase gene revealed close identity with porcine KobV from the Czech Republic (JX232619, 90.6%-91.6%) and Hungary (NC_011829, 89.8%-91.6%), wherein one of the current study strains clustered with the Czech Republic JX232619 strain in the phylogenetic tree. Further investigation of the role of KobV in health and disease of pygmy hogs is warranted.
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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: 14] [Impact Index Per Article: 4.7] [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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Ding G, Fu Y, Li B, Chen J, Wang J, Yin B, Sha W, Liu G. Development of a multiplex RT-PCR for the detection of major diarrhoeal viruses in pig herds in China. Transbound Emerg Dis 2019; 67:678-685. [PMID: 31597013 PMCID: PMC7168528 DOI: 10.1111/tbed.13385] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/30/2019] [Accepted: 09/26/2019] [Indexed: 01/09/2023]
Abstract
The major enteric RNA viruses in pigs include porcine epidemic diarrhoea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine rotavirus A (PRV‐A), porcine kobuvirus (PKV), porcine sapovirus (PSaV) and porcine deltacoronavirus (PDCoV). For differential diagnosis, a multiplex RT‐PCR method was established on the basis of the N genes of TGEV, PEDV and PDCoV, the VP7 gene of PRV‐A, and the polyprotein genes of PKV and PSaV. This multiplex RT‐PCR could specifically detect TGEV, PEDV, PDCoV, PRV‐A, PKV and PSaV without cross‐reaction to any other major viruses circulating in Chinese pig farms. The limit of detection of this method was as low as 100–101 ng cDNA of each virus. A total of 398 swine faecal samples collected from nine provinces of China between October 2015 and April 2017 were analysed by this established multiplex RT‐PCR. The results demonstrated that PDCoV (144/398), PSaV (114/398), PEDV (78/398) and PRV‐A (70/398) were the main pathogens, but TGEV was not found in the pig herds in China. In addition, dual infections, for example, PDCoV + PSaV, PDCoV + PRV‐A, PRA‐V + PSaV and PEDV + PDCoV, and triple infections, for example, PDCoV + PRV‐A + PSaV and PEDV + PDCoV + PKV, were found among the collected samples. The multiplex RT‐PCR provided a valuable tool for the differential diagnosis of swine enteric viruses circulating in Chinese pig farms and will facilitate the prevention and control of swine diarrhoea in China.
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Affiliation(s)
- Guangming Ding
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.,School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yuguang Fu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Baoyu Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianing Chen
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianlin Wang
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Baishuang Yin
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin, China
| | - Wanli Sha
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin, China
| | - Guangliang Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
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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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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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Complete Genome Sequence of a Porcine Kobuvirus Variant Strain from Jiangxi, China. GENOME ANNOUNCEMENTS 2017; 5:5/5/e01580-16. [PMID: 28153909 PMCID: PMC5289695 DOI: 10.1128/genomea.01580-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The complete genome sequence of a porcine kobuvirus (PKoV) variant strain, CH/KB-1/2014 from Jiangxi, China, with a 90-nucleotide deletion in the 2B gene, was determined and characterized. This study provides a better understanding of the molecular characteristics and evolution of PKoV in Jiangxi, China.
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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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Diseases of the Alimentary Tract. Vet Med (Auckl) 2017. [PMCID: PMC7167529 DOI: 10.1016/b978-0-7020-5246-0.00007-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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17
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Lau SKP, Woo PCY, Li KSM, Zhang HJ, Fan RYY, Zhang AJX, Chan BCC, Lam CSF, Yip CCY, Yuen MC, Chan KH, Chen ZW, Yuen KY. Identification of Novel Rosavirus Species That Infects Diverse Rodent Species and Causes Multisystemic Dissemination in Mouse Model. PLoS Pathog 2016; 12:e1005911. [PMID: 27737017 PMCID: PMC5063349 DOI: 10.1371/journal.ppat.1005911] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/02/2016] [Indexed: 01/14/2023] Open
Abstract
While novel picornaviruses are being discovered in rodents, their host range and pathogenicity are largely unknown. We identified two novel picornaviruses, rosavirus B from the street rat, Norway rat, and rosavirus C from five different wild rat species (chestnut spiny rat, greater bandicoot rat, Indochinese forest rat, roof rat and Coxing's white-bellied rat) in China. Analysis of 13 complete genome sequences showed that “Rosavirus B” and “Rosavirus C” represent two potentially novel picornavirus species infecting different rodents. Though being most closely related to rosavirus A, rosavirus B and C possessed distinct protease cleavage sites and variations in Yn-Xm-AUG sequence in 5’UTR and myristylation site in VP4. Anti-rosavirus B VP1 antibodies were detected in Norway rats, whereas anti-rosavirus C VP1 and neutralizing antibodies were detected in Indochinese forest rats and Coxing's white-bellied rats. While the highest prevalence was observed in Coxing's white-bellied rats by RT-PCR, the detection of rosavirus C from different rat species suggests potential interspecies transmission. Rosavirus C isolated from 3T3 cells causes multisystemic diseases in a mouse model, with high viral loads and positive viral antigen expression in organs of infected mice after oral or intracerebral inoculation. Histological examination revealed alveolar fluid exudation, interstitial infiltration, alveolar fluid exudate and wall thickening in lungs, and hepatocyte degeneration and lymphocytic/monocytic inflammatory infiltrates with giant cell formation in liver sections of sacrificed mice. Since rosavirus A2 has been detected in fecal samples of children, further studies should elucidate the pathogenicity and emergence potential of different rosaviruses. We identified two novel picornaviruses, rosavirus B and C, infecting street and wild rats respectively in China. While rosavirus B was detected from Norway rats, rosavirus C was detected from five different wild rat species (chestnut spiny rat, greater bandicoot rat, Indochinese forest rat, roof rat and Coxing's white-bellied rat) by RT-PCR. Anti-rosavirus B antibodies were detected in Norway rats, whereas anti-rosavirus C antibodies were detected in Indochinese forest rats and Coxing's white-bellied rats, supporting potential interspecies transmission of rosavirus C. Genome analysis supported the classification of rosavirus B and C as two novel picornavirus species, with genome features distinct from rosavirus A. Rosavirus C isolated from 3T3 cells causes multisystemic diseases in a mouse model, with viruses and pathologies detected in various organs of infected mice after oral or intracerebral inoculation. Our results extend our knowledge on the host range and pathogenicity of rodent picornaviruses.
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Affiliation(s)
- Susanna K. P. Lau
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Patrick C. Y. Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Kenneth S. M. Li
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Hao-Ji Zhang
- Department of Veterinary Medicine, Foshan University, Foshan, China
| | - Rachel Y. Y. Fan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Anna J. X. Zhang
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Brandon C. C. Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Carol S. F. Lam
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Cyril C. Y. Yip
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Ming-Chi Yuen
- Food and Environmental Hygiene Department, Hong Kong, China
| | - Kwok-Hung Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Zhi-Wei Chen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- * E-mail:
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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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20
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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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21
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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: 36] [Impact Index Per Article: 4.5] [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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22
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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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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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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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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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Genetic characterization of porcine kobuvirus and detection of coinfecting pathogens in diarrheic pigs in Jiangsu Province, China. Arch Virol 2014; 159:3407-12. [PMID: 25119679 DOI: 10.1007/s00705-014-2204-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 08/04/2014] [Indexed: 01/19/2023]
Abstract
In this study, 396 samples from diarrheic pigs on 46 pig farms in Jiangsu Province, China, were analyzed by RT-PCR. One-hundred eighty-one pigs from 37 farms tested positive for porcine kobuvirus (PKV). Phylogenetic analysis of the 3D gene from 19 isolates showed sequence homology of 88.0 %-100 % and 69.4 %-100 % for nucleotides and amino acids, respectively, while similarity to isolates of other kobuviruses was 69.6 %-78.8 % and 27.8 %-56.9 %, respectively. One-hundred eighty-five samples contained two or more pathogens, and 31/68 PKV-positive samples tested positive for other diarrheic pathogens, confirming the existence of PKV infection and coinfection.
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28
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Zhang B, Tang C, Yue H, Ren Y, Song Z. Viral metagenomics analysis demonstrates the diversity of viral flora in piglet diarrhoeic faeces in China. J Gen Virol 2014; 95:1603-1611. [DOI: 10.1099/vir.0.063743-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
To investigate the diversity of viral flora, we used metagenomics to study the viral communities in a pooled faecal sample of 27 diarrhoeic piglets from intensive commercial farms in China. The 15 distinct mammalian viruses identified in the pooled diarrhoeic sample were, in order of abundance of nucleic acid sequence, Porcine epidemic diarrhea virus (PEDV), sapovirus, porcine bocavirus-4 (PBoV-4), sapelovirus, torovirus, coronavirus, PBoV-2, stool-associated single-stranded DNA virus (poSCV), astrovirus (AstV), kobuvirus, posavirus-1, porcine enterovirus-9 (PEV-9), porcine circovirus-like (po-circo-like) virus, picobirnavirus (PBV) and Torque teno sus virus 2 (TTSuV-2). The prevalence rate of each virus was verified from diarrhoeic and healthy piglets by PCR assay. A mean of 5.5 different viruses were shed in diarrhoeic piglets, and one piglet was in fact co-infected with 11 different viruses. By contrast, healthy piglets shed a mean of 3.2 different viruses. Compared with samples from healthy piglets, the co-infection of PEDV and PBoV had a high prevalence rate in diarrhoea samples, suggesting a correlation with the appearance of diarrhoea in piglets. Furthermore, we report here for the first time the presence of several recently described viruses in China, and the identification of novel genotypes. Therefore, our investigation results provide an unbiased survey of viral communities and prevalence in faecal samples of piglets.
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Affiliation(s)
- Bin Zhang
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu 610041, PR China
| | - Cheng Tang
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu 610041, PR China
| | - Hua Yue
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu 610041, PR China
| | - Yupeng Ren
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu 610041, PR China
| | - Zhigang Song
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu 610041, PR China
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Molecular characterization and sequence analysis of the 2B region of Aichivirus C strains in Japan and Thailand. INFECTION GENETICS AND EVOLUTION 2014; 26:89-94. [PMID: 24837671 DOI: 10.1016/j.meegid.2014.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 04/17/2014] [Accepted: 05/05/2014] [Indexed: 11/20/2022]
Abstract
Aichivirus C is the third species in the genus Kobuvirus, family Picornaviridae, and the virus is circulating in pigs worldwide. Aichivirus A in humans and Aichivirus B in cows have been shown to associate with diarrheal diseases, however, the pathogenesis of Aichivirus C has not been demonstrated clearly. In this study, the full genome nucleotide sequence of the Thai strain, CMP06/2007/THA collected from stool sample of a diarrheal piglet was analyzed and identified as a variant type with a 90-nt deletion in the 2B-coding region. In addition, molecular characterization of nucleotide sequences of the 2B-coding region of Aichivirus C strains from six diarrheal and six healthy piglets in Thailand, and four strains from healthy pigs in Japan revealed that all of the strains in this study were variant types. These findings indicate that variant strains of Aichivirus C are circulating in Asian countries such as China, Thailand and Japan, and deletion of tandem repeat of 2B-region is unlikely to associate with the pathogenesis of the virus.
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30
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Wang E, Yang B, Liu W, Liu J, Ma X, Lan X. Complete sequencing and phylogenetic analysis of porcine kobuvirus in domestic pigs in Northwest China. Arch Virol 2014; 159:2533-5. [PMID: 24777826 DOI: 10.1007/s00705-014-2087-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 04/09/2014] [Indexed: 11/28/2022]
Abstract
Porcine kobuvirus, a member of the genus Kobuvirus that is associated with diarrhea, has been reported in many countries. We determined the complete genome sequence and investigated the genetic evolution of the kobuvirus strain swKoV CH441, which was detected in the highland of Gansu province in Northwest China. The viral genome is 8149 nucleotides (nt) long, including a 29-nt poly(A) tail of the 3' end, and is 90 nt shorter in the 2B coding region than those of other kobuvirus strains whose sequences are available in the GenBank database. Phylogenetic analysis showed that swKoV CH441 was most closely related to porcine kobuvirus CH/HNXX-4 but more distantly related to other strains, including the strains GS-1/2012/CH and GS-2/2012/CH, which were detected in Gansu province, indicating that porcine kobuvirus may have geographic and host differences in evolution.
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Affiliation(s)
- Enli Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Grazing Animal Diseases, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
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Li C, Chen J, Shi H, Zhang X, Shi D, Han X, Chi Y, Feng L. Rapid detection of porcine kobuvirus in feces by reverse transcription loop-mediated isothermal amplification. Virol J 2014; 11:73. [PMID: 24755372 PMCID: PMC4026823 DOI: 10.1186/1743-422x-11-73] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/09/2014] [Indexed: 03/02/2023] Open
Abstract
Background PKV is a new emerging pathogen detected in diarrhea pigs. At present, no more detection methods were reported except RT-PCR method. this study was to develop a fast diagnostic method based on the LAMP reaction for rapid detection of PKV nucleic acid in fecal samples. Findings Two pairs of primers were designed to amplify the conservative 3D gene of PKV genome. The PKV RT-LAMP method possessed well specificity and had 100 times higher sensitivity than common reverse transcription PCR (RT-PCR), which could detect up to 10 RNA copies of the target gene. Conclusions The results showed that the optimal reaction condition for RT-LAMP was achieved at 64°C for 50 min. Furthermore, the RT-LAMP procedure does not demand special equipment and is time-saving.
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Affiliation(s)
| | | | | | | | | | | | | | - Li Feng
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of the Chinese Academy of Agricultural Sciences, No,427 Maduan Street, Nangang District, Harbin 150001, China.
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Khamrin P, Maneekarn N, Okitsu S, Ushijima H. Epidemiology of human and animal kobuviruses. Virusdisease 2014; 25:195-200. [PMID: 25674585 DOI: 10.1007/s13337-014-0200-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 01/31/2014] [Indexed: 11/28/2022] Open
Abstract
Kobuviruses are member of the family Picornaviridae. Initially, members in Kobuvirus genus were named according to the basis of their host species. The viruses found in humans called "Aichi virus", the viruses from cattle called "bovine kobuvirus", and the viruses isolated from pigs called "porcine kobuvirus". Currently, taxonomy of kobuviruses has been proposed and the virus species have been renamed. The "Aichi virus" has been renamed as "Aichivirus A", "bovine kobuvirus" has been renamed as "Aichivirus B", and "porcine kobuvirus" has been changed to "Aichivirus C". Among Aichivirus A, three distinct members, including Aichi virus 1 (Aichivirus in human), canine kobuvirus 1, and murine kobuvirus 1, have been described. Aichi virus 1 in human is globally distributed and has been identified at low incidence (0-3 %) in sporadic acute gastroenteritis cases. Aichi virus 1 has been reported to be associated with variety types of clinical illnesses including diarrhea, vomiting, fever, purulent conjunctivitis, and respiratory symptoms. The studies from Japan, Spain, Germany, and Tunisia demonstrated that high antibody prevalence against Aichi virus 1 were found in the populations. Aichivirus B or previously known as bovine kobuvirus was first reported in 2003. Since then, Aichivirus B has also been reported from several countries worldwide. An overall prevalence of Aichivirus B varies from 1 to 34.5 %, and the highest prevalence was found in cattle with diarrhea in Korea. Aichivirus C or porcine kobuvirus is widely distributed in pigs. Aichivirus C has been found in both diarrhea and healthy pigs and the positive rate of this virus varies from 3.9 up to 100 %. It was reported that Aichivirus C was found with high prevalence in wild boars in Hungary. The accumulated data of the biological, pathological, as well as epidemiological studies of kobuviruses are still limited. Comprehensive global investigations of the prevalence and diversity are required and will be helpful for providing further insight into pathogenicity, genetic heterogeneity, interspecies transmission, and global distribution of kobuviruses.
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Affiliation(s)
- Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, 110 Intawaroros, Sriphoom, Muang, Chiang Mai, 50200 Thailand
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, 110 Intawaroros, Sriphoom, Muang, Chiang Mai, 50200 Thailand
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
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Chang J, Wang Q, Wang F, Jiang Z, Liu Y, Yu L. Prevalence and genetic diversity of bovine kobuvirus in China. Arch Virol 2013; 159:1505-10. [PMID: 24366549 DOI: 10.1007/s00705-013-1961-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 11/20/2013] [Indexed: 12/01/2022]
Abstract
A total of 166 faecal specimens from diarrheic cattle were collected in China for detection of bovine kobuvirus (BKV) by reverse transcription PCR (RT-PCR) targeting the region a portion of the 3D nonstructural protein, with an amplicon size of 631 bp. The RNA corresponding to the BKV 3D region was detected in 34.9 % of faecal samples (58/166) in four major dairy-cattle-production areas in China, and sequence analysis based on the partial 3D sequences (35/58) indicated that the Chinese BKVs shared 88.9-96.2 % nucleotide sequence identity to BKV reference strains. Further phylogenetic analysis based on the complete VP1-encoding sequences (17/35) revealed that the Chinese BKVs shared 81-83.4 % nucleotide sequence identity to the U-1 strain, and these Chinese BKV strains, together with the U-1 strain, are apparently divided into four lineages, representing four genotypes of BKV, designated as A, B, C and D. Our results show that BKV infection is widely distributed, with high genetic diversity in China.
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Affiliation(s)
- Jitao Chang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, People's Republic of China
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Identification and characterization of porcine kobuvirus variant isolated from suckling piglet in Gansu province, China. Viruses 2013; 5:2548-60. [PMID: 24145960 PMCID: PMC3814603 DOI: 10.3390/v5102548] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 10/11/2013] [Accepted: 10/15/2013] [Indexed: 01/28/2023] Open
Abstract
Kobuviruses comprise three species, the Aichivirus A, Aichivirus B, and Aichivirus C (porcine kobuvirus). Porcine kobuvirus is endemic to pig farms and is not restricted geographically but, rather, is distributed worldwide. The complete genomic sequences of four porcine kobuvirus strains isolated during a diarrhea outbreak in piglets in the Gansu province of China were determined. Two of these strains exhibited variations relative to the traditional strains. The potential 3C/3D cleavage sites of the variant strains were Q/C, which differed from the Q/S in the traditional porcine kobuvirus genome. A 90-nucleotide deletion in the 2B protein and a single nucleotide insertion in the 3′UTR were found in the variant strains. The VP1 regions of all four porcine kobuviruses in our study were highly variable (81%–86%). Ten common amino acid mutations were found specifically at certain positions within the VP1 region. Significant recombination sites were identified using SimPlot scans of whole genome sequences. Porcine kobuviruses were also detected in pig serum, indicating that the virus can escape the gastrointestinal tract and travel to the circulatory system. These findings suggest that mutations and recombination events may have contributed to the high level of genetic diversity of porcine kobuviruses and serve as a driving force in its evolution.
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35
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Molecular detection of porcine kobuviruses in Italian swine. Res Vet Sci 2013; 95:782-5. [DOI: 10.1016/j.rvsc.2013.06.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 06/19/2013] [Accepted: 06/23/2013] [Indexed: 11/19/2022]
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36
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Chen L, Zhu L, Zhou YC, Xu ZW, Guo WZ, Yang WY. Molecular and phylogenetic analysis of the porcine kobuvirus VP1 region using infected pigs from Sichuan Province, China. Virol J 2013; 10:281. [PMID: 24025093 PMCID: PMC3847588 DOI: 10.1186/1743-422x-10-281] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 09/10/2013] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Porcine kobuvirus (PKoV) is a member of the Kobuvirus genus within the Picornaviridae family. PKoV is distributed worldwide with high prevalence in clinically healthy pigs and those with diarrhea. METHODS Fecal and intestinal samples (n = 163) from pig farms in Sichuan Province, China were obtained to determine the presence of PKoV using reverse transcription polymerase chain reaction assays. Specific primers were used for the amplification of the gene encoding the PKoV VP1 protein sequence. Sequence and phylogenetic analyses were conducted to clarify evolutionary relationships with other PKoV strains. RESULTS Approximately 53% (87/163) of pigs tested positive for PKoV. PKoV was widespread in asymptomatic pigs and those with diarrhea. A high prevalence of PKoV was observed in pigs younger than 4 weeks and in pigs with diarrhea. Phylogenetic analysis of 36 PKoV VP1 protein sequences showed that Sichuan PKoV strains formed four distinct clusters. Two pigs with diarrhea were found to be co-infected with multiple PKoV strains. Sequence and phylogenetic analyses revealed diversity within the same host and between different hosts. Significant recombination breakpoints were observed between the CHN/SC/31-A1 and CHN/SC/31-A3 strains in the VP1 region, which were isolated from the same sample. CONCLUSION PKoV was endemic in Sichuan Province regardless of whether pigs were healthy or suffering from diarrhea. Based on our statistical analyses, we suggest that PKoV was the likely causative agent of high-mortality diarrhea in China from 2010. For the first time, we provide evidence for the co-existence of multiple PKoV strains in one pig, and possible recombination events in the VP1 region. Our findings provide further insights into the molecular properties of PKoV, along with its epidemiology.
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Affiliation(s)
- Lei Chen
- Animal Biotechnology Center, College of Veterinary Medicine of Sichuan Agricultural University, 46# Xinkang Road, Yucheng District, Ya'an 625014Sichuan province, P,R, China.
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Ribeiro J, de Arruda Leme R, Alfieri AF, Alfieri AA. High frequency of Aichivirus C (porcine kobuvirus) infection in piglets from different geographic regions of Brazil. Trop Anim Health Prod 2013; 45:1757-62. [DOI: 10.1007/s11250-013-0428-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2013] [Indexed: 01/26/2023]
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38
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Shi D, Zhang S, Chen J, Shi H, Zhang X, Feng L. Molecular characterization of a porcine kobuvirus variant strain in China. Arch Virol 2013; 158:2379-83. [DOI: 10.1007/s00705-013-1736-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 04/14/2013] [Indexed: 10/26/2022]
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39
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Sisay Z, Wang Q, Oka T, Saif L. Prevalence and molecular characterization of porcine enteric caliciviruses and first detection of porcine kobuviruses in US swine. Arch Virol 2013; 158:1583-8. [PMID: 23456421 DOI: 10.1007/s00705-013-1619-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 12/17/2012] [Indexed: 02/04/2023]
Abstract
The prevalence of porcine sapoviruses (SaVs) and noroviruses (NoVs) in nursing piglets on three pig farms in Ohio was studied. Fecal samples (n = 139) were collected from individual pigs and screened for caliciviruses by RT-PCR. Phylogenetic analysis was conducted using partial sequences of the RNA polymerase region. Three different SaV genogroups, including a newly emerging one (DO19 Korea-like) were detected. No NoVs were detected. Kobuviruses, emerging members of the family Picornaviridae, were detected by primers designed for SaV. To our knowledge, this is the first report of porcine DO19 Korea-like SaV and kobuvirus in the United States.
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Affiliation(s)
- Zufan Sisay
- Department of Veterinary Preventive Medicine, Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
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40
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Yu JM, Li JS, Ao YY, Duan ZJ. Detection of novel viruses in porcine fecal samples from China. Virol J 2013; 10:39. [PMID: 23363449 PMCID: PMC3598965 DOI: 10.1186/1743-422x-10-39] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 11/26/2012] [Indexed: 11/10/2022] Open
Abstract
Background Pigs are well known source of human infectious disease. To better understand the spectrum of viruses present in pigs, we utilized the 454 Life Sciences GS-FLX high-throughput sequencing platform to sequence stool samples from healthy pigs. Findings Total nucleic acid was extracted from stool samples of healthy piglets and randomly amplified. The amplified materials were pooled and processed using a high-throughput pyrosequencing technique. The raw sequences were deconvoluted on the basis of the barcode and then processed through a standardized bioinformatics pipeline. The unique reads (348, 70 and 13) had limited similarity to known astroviruses, bocaviruses and parechoviruses. Specific primers were synthesized to assess the prevalence of the viruses in healthy piglets. Our results indicate extremely high rates of positivity. Conclusions Several novel astroviruses, bocaviruses and Ljungan-like viruses were identified in stool samples from healthy pigs. The rates of isolation for the new viruses were high. The high detection rate, diverse sequences and categories indicate that pigs are well-established reservoirs for and likely sources of different enteric viruses.
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Affiliation(s)
- Jie-mei Yu
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
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41
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Abstract
Porcine kobuvirus, an emerging virus, may be the underlying etiological cause of a large-scale outbreak of diarrhea in suckling piglets in China that started in 2010. We report the complete genome sequence of the porcine kobuvirus variant CH/HNXX-4/2012 with a 30-amino-acid deletion in its 2B-coding region that was isolated in this outbreak. This will help the phenotypic variation and evolutionary characteristics of porcine kobuvirus to be understood.
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42
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Genetic diversity of porcine sapoviruses, kobuviruses, and astroviruses in asymptomatic pigs: an emerging new sapovirus GIII genotype. Arch Virol 2012; 158:549-58. [DOI: 10.1007/s00705-012-1528-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 09/25/2012] [Indexed: 12/13/2022]
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43
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Molecular detection of bovine kobuviruses in Italy. Arch Virol 2012; 157:2393-6. [PMID: 22886185 DOI: 10.1007/s00705-012-1439-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 06/29/2012] [Indexed: 10/28/2022]
Abstract
Faecal samples obtained from either asymptomatic or diarrhoeic calves in Italy were screened for bovine kobuviruses (BKVs) using specific primers. BKV RNA was detected in 4.9 % of the samples, with higher positivity rates in diarrhoeic calves (5.3 %) than in asymptomatic animals (4.8 %), although the difference was not statistically significant. Upon sequence analysis, all of the Italian viruses formed a tight group along with BKV-like sequences previously detected in Thailand and Japan.
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Abstract
Porcine kobuvirus, an emerging virus, was first identified in Hungary in 2007. We report here the complete genome sequence of porcine kobuvirus strain WUH1 isolated from piglets with severe diarrhea, which will help toward understanding the molecular and evolutionary characteristics of the porcine kobuvirus.
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45
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Wang C, Lan D, Cui L, Yang Z, Yuan C, Hua X. Molecular characterization of a porcine kobuvirus strain in China. Arch Virol 2011; 157:573-8. [DOI: 10.1007/s00705-011-1205-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 11/22/2011] [Indexed: 01/11/2023]
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Sequence analysis of porcine kobuvirus VP1 region detected in pigs in Japan and Thailand. Virus Genes 2011; 44:253-7. [DOI: 10.1007/s11262-011-0692-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Barry AF, Ribeiro J, Alfieri AF, van der Poel WH, Alfieri AA. First detection of kobuvirus in farm animals in Brazil and the Netherlands. INFECTION GENETICS AND EVOLUTION 2011; 11:1811-4. [DOI: 10.1016/j.meegid.2011.06.020] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 06/28/2011] [Accepted: 06/29/2011] [Indexed: 11/27/2022]
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Wang C, Lan D, Hua X. Porcine kobuvirus from pig stool specimens in Shanghai, China. Virus Genes 2011; 43:350-2. [DOI: 10.1007/s11262-011-0643-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 07/09/2011] [Indexed: 11/28/2022]
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Li L, Pesavento PA, Shan T, Leutenegger CM, Wang C, Delwart E. Viruses in diarrhoeic dogs include novel kobuviruses and sapoviruses. J Gen Virol 2011; 92:2534-2541. [PMID: 21775584 DOI: 10.1099/vir.0.034611-0] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The close interactions of dogs with humans and surrounding wildlife provide frequent opportunities for cross-species virus transmissions. In order to initiate an unbiased characterization of the eukaryotic viruses in the gut of dogs, this study used deep sequencing of partially purified viral capsid-protected nucleic acids from the faeces of 18 diarrhoeic dogs. Known canine parvoviruses, coronaviruses and rotaviruses were identified, and the genomes of the first reported canine kobuvirus and sapovirus were characterized. Canine kobuvirus, the first sequenced canine picornavirus and the closest genetic relative of the diarrhoea-causing human Aichi virus, was detected at high frequency in the faeces of both healthy and diarrhoeic dogs. Canine sapovirus constituted a novel genogroup within the genus Sapovirus, a group of viruses also associated with human and animal diarrhoea. These results highlight the high frequency of new virus detection possible even in extensively studied animal species using metagenomics approaches, and provide viral genomes for further disease-association studies.
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Affiliation(s)
- Linlin Li
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Patricia A Pesavento
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Tongling Shan
- Zoonosis and Comparative Medicine Group, Shanghai Jiao Tong University, Shanghai, Republic of China
- Blood Systems Research Institute, San Francisco, CA, USA
| | | | - Chunlin Wang
- Stanford Genome Technology Center, Stanford, CA, USA
| | - Eric Delwart
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- Blood Systems Research Institute, San Francisco, CA, USA
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Abstract
Kobuviruses are members of the large and growing family Picornaviridae. Until now, two official, Aichi virus and Bovine kobuvirus, and one candidate kobuvirus species, 'porcine kobuvirus', have been identified in human, cattle and swine, respectively. In addition, kobu-like viruses were detected very recently in the bat. Aichi virus could be one of the causative agents of gastroenteritis in humans, and kobuviruses probably also cause diarrhoea in cattle and swine. Although Aichi virus has been detected relatively infrequently (0-3%) in human diarrhoea, high seroprevalence, up to 80-95% at the age of 30-40, was found indicating the general nature of infection in different human populations. In the previous years, much new information has accumulated relating to kobuviruses and their host species. This review summarises the current knowledge on kobuviruses including taxonomy, biology and viral characteristics, and covers all aspects of infection including epidemiology, clinical picture, host species diversity, laboratory diagnosis and it gives a summary about possible future perspectives.
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Affiliation(s)
- Gábor Reuter
- National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary.
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