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Wu S, Gou F, Meng J, Jin X, Liu W, Ding W, Xu W, Gu C, Hu X, Cheng G, Tao P, Zhang W. Porcine kobuvirus enhances porcine epidemic diarrhea virus pathogenicity and alters the number of intestinal lymphocytes in piglets. Vet Microbiol 2024; 293:110100. [PMID: 38718527 DOI: 10.1016/j.vetmic.2024.110100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/25/2024] [Accepted: 04/25/2024] [Indexed: 05/15/2024]
Abstract
Recent epidemiological studies have discovered that a lot of cases of porcine epidemic diarrhea virus (PEDV) infection are frequently accompanied by porcine kobuvirus (PKV) infection, suggesting a potential relationship between the two viruses in the development of diarrhea. To investigate the impact of PKV on PEDV pathogenicity and the number of intestinal lymphocytes, piglets were infected with PKV or PEDV or co-infected with both viruses. Our findings demonstrate that co-infected piglets exhibit more severe symptoms, acute gastroenteritis, and higher PEDV replication compared to those infected with PEDV alone. Notably, PKV alone does not cause significant intestinal damage but enhances PEDV's pathogenicity and alters the number of intestinal lymphocytes. These results underscore the complexity of viral interactions in swine diseases and highlight the need for comprehensive diagnostic and treatment strategies addressing co-infections.
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Affiliation(s)
- Simin Wu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Fang Gou
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Jie Meng
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Xin Jin
- Hubei Animal Disease Prevention and Control Center, Wuhan 430070, China.
| | - Wanchen Liu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Weishuai Ding
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Weihang Xu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Changqin Gu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Xueying Hu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Guofu Cheng
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Pan Tao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Wanpo Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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Brnić D, Vlahović D, Gudan Kurilj A, Maltar-Strmečki N, Lojkić I, Kunić V, Jemeršić L, Bačani I, Kompes G, Beck R, Mikuletič T, Steyer A. The impact and complete genome characterisation of viruses involved in outbreaks of gastroenteritis in a farrow-to-finish holding. Sci Rep 2023; 13:18780. [PMID: 37907693 PMCID: PMC10618538 DOI: 10.1038/s41598-023-45994-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023] Open
Abstract
Viral enteric pathogens continuously burden intensive pig farming, causing gastrointestinal diseases of epidemic and endemic nature. The present study investigated two diarrhoea outbreaks on a large farrow-to-finish holding and subsequent circulation of outbreak-related enteric viruses. These viruses were characterised by whole genome sequencing, and statistical evaluation of the impact on specific production metrics was performed. The results provided evidence that the Porcine epidemic diarrhoea virus-swine enteric coronavirus (PEDV-SeCoV) S gene recombinant strain was responsible for the first outbreak, whilst Rotavirus A (RVA) in a mixed infection with Rotavirus B (RVB) and porcine kobuvirus (PKV) probably caused the second diarrhoea outbreak. Whole genome characterisation revealed a porcine origin of all viruses involved and significant heterogeneity of RVB strain, proposing four novel genotypes and changes in RVB VP1 genotype classification. The statistical evaluation confirmed only a minor disturbance in the number of weaned pigs per sow, with statistical forecasting showing positive trends. A follow-up study corroborated the endemicity of RVA and PKV, in contrast to PEDV-SeCoV. Punctual, comprehensive and timely investigation of diarrhoea outbreaks is a prerequisite for applying adequate pig health and biosecurity management. Calculating such outbreaks' impact on production metrics can potentially shape future decisions on management improvements.
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Affiliation(s)
- Dragan Brnić
- Croatian Veterinary Institute, Savska cesta 143, 10000, Zagreb, Croatia.
| | - Dunja Vlahović
- Croatian Veterinary Institute, Savska cesta 143, 10000, Zagreb, Croatia
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000, Zagreb, Croatia
| | - Andrea Gudan Kurilj
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000, Zagreb, Croatia
| | - Nadica Maltar-Strmečki
- Laboratory for Electron Spin Spectroscopy, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
| | - Ivana Lojkić
- Croatian Veterinary Institute, Savska cesta 143, 10000, Zagreb, Croatia
| | - Valentina Kunić
- Croatian Veterinary Institute, Savska cesta 143, 10000, Zagreb, Croatia
| | - Lorena Jemeršić
- Croatian Veterinary Institute, Savska cesta 143, 10000, Zagreb, Croatia
| | - Ivica Bačani
- Animal Feed Factory, Dr Ivana Novaka 11, 40000, Čakovec, Croatia
| | - Gordan Kompes
- Croatian Veterinary Institute, Savska cesta 143, 10000, Zagreb, Croatia
| | - Relja Beck
- Croatian Veterinary Institute, Savska cesta 143, 10000, Zagreb, Croatia
| | - Tina Mikuletič
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000, Ljubljana, Slovenia
| | - Andrej Steyer
- Division of Public Health Microbiology, National Laboratory of Health, Environment and Food, Grablovičeva 44, 1000, Ljubljana, Slovenia
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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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Huang M, Gan J, Xu Z, Guo Y, Chen Z, Gao GF, Liang H, Liu WJ. A black goat-derived novel genotype of Aichi virus C blurs the boundary between caprine and porcine kobuviruses. Virology 2023; 585:215-221. [PMID: 37384968 DOI: 10.1016/j.virol.2023.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/12/2023] [Accepted: 06/21/2023] [Indexed: 07/01/2023]
Abstract
Aichi virus C, a species in the genus Kobuvirus, causes diarrhea diseases in pigs and goats and pose health threat and economic loss for stock farming. A nearly complete genome sequence of caprine kobuvirus GCCDC14 was obtained from an anal swab of a black goat died from diarrhea collected in Hubei, China in 2019. Phylogenetic analyses suggested that GCCDC14 is a novel genotype of Aichi virus C, forming a sister branch to other caprine kobuviruses, with P1 and VP0 genes more closely related to porcine kobuviruses and VP3 in an independent branch. Compared to previous caprine kobuviruses, unique amino acid changes in the poly-l-proline type II helix structure of VP0 and VP1 were found, which may affect the cellular machinery of host and pathogenicity. This study indicates the presence of the kobuvirus with continuously evolving features and emphasizes the surveillance and genetic evolution investigation of kobuviruses for safety of husbandry.
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Affiliation(s)
- Mengkun Huang
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed By the Province and Ministry, Guangxi Medical University, Nanning, 530000, China; NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Jinxian Gan
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed By the Province and Ministry, Guangxi Medical University, Nanning, 530000, China; NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Ziqian Xu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Yuanyuan Guo
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China; School of Public Health, Shandong University, Jinan, 250012, China
| | - Zhangfu Chen
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China; School of Public Health, Shandong University, Jinan, 250012, China
| | - George F Gao
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed By the Province and Ministry, Guangxi Medical University, Nanning, 530000, China; NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China; School of Public Health, Shandong University, Jinan, 250012, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China; Research Unit of Adaptive Evolution and Control of Emerging Viruses (2018RU009), Chinese Academy of Medical Sciences, Beijing, 102206, China.
| | - Hao Liang
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed By the Province and Ministry, Guangxi Medical University, Nanning, 530000, China.
| | - William J Liu
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed By the Province and Ministry, Guangxi Medical University, Nanning, 530000, China; NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China; Research Unit of Adaptive Evolution and Control of Emerging Viruses (2018RU009), Chinese Academy of Medical Sciences, Beijing, 102206, China.
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Puente H, Arguello H, Cortey M, Gómez-García M, Mencía-Ares O, Pérez-Perez L, Díaz I, Carvajal A. Detection and genetic characterization of enteric viruses in diarrhoea outbreaks from swine farms in Spain. Porcine Health Manag 2023; 9:29. [PMID: 37349807 DOI: 10.1186/s40813-023-00326-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/18/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND The aim of this work was to study the prevalence and distribution of Porcine astrovirus (PAstV), Porcine kobuvirus (PKoV), Porcine torovirus (PToV), Mammalian orthoreovirus (MRV) and Porcine mastadenovirus (PAdV) as well as their association with widely recognized virus that cause diarrhoea in swine such as coronavirus (CoVs) and rotavirus (RVs) in diarrhoea outbreaks from Spanish swine farms. Furthermore, a selection of the viral strains was genetically characterized. RESULTS PAstV, PKoV, PToV, MRV and PAdV were frequently detected. Particularly, PAstV and PKoV were detected in almost 50% and 30% of the investigated farms, respectively, with an age-dependent distribution; PAstV was mainly detected in postweaning and fattening pigs, while PKoV was more frequent in sucking piglets. Viral co-infections were detected in almost half of the outbreaks, combining CoVs, RVs and the viruses studied, with a maximum of 5 different viral species reported in three investigated farms. Using a next generation sequencing approach, we obtained a total of 24 ARN viral genomes (> 90% genome sequence), characterizing for first time the full genome of circulating strains of PAstV2, PAstV4, PAstV5 and PToV on Spanish farms. Phylogenetic analyses showed that PAstV, PKoV and PToV from Spanish swine farms clustered together with isolates of the same viral species from neighboring pig producing countries. CONCLUSIONS Although further studies to evaluate the role of these enteric viruses in diarrhoea outbreaks are required, their wide distribution and frequent association in co-infections cannot be disregard. Hence, their inclusion into routine diagnostic panels for diarrhoea in swine should be considered.
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Affiliation(s)
- Héctor Puente
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain.
| | - Héctor Arguello
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain
- INDEGSAL, Universidad de León, León, Spain
| | - Martí Cortey
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Manuel Gómez-García
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Oscar Mencía-Ares
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Lucía Pérez-Perez
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Ivan Díaz
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
- Unitat Mixta d'investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
- WOAH Reference Laboratory for Classical Swine Fever, IRTA-CReSA, Bellaterra, Spain
| | - Ana Carvajal
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain
- INDEGSAL, Universidad de León, León, Spain
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Eriksen EØ. A Systematic Review: Is Porcine Kobuvirus Causing Gastrointestinal Disease in Young Pigs? Vet Sci 2023; 10:vetsci10040286. [PMID: 37104441 PMCID: PMC10144032 DOI: 10.3390/vetsci10040286] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/31/2023] [Accepted: 04/05/2023] [Indexed: 04/28/2023] Open
Abstract
Since porcine kobuvirus (PKV) was first described in 2008, researchers have speculated whether the virus is of clinical importance. This systematic literature review answers the question: Is porcine kobuvirus a cause of gastrointestinal disease in young pigs? A case-control study showed that PKV was not associated with neonatal diarrhea. A cohort study suffered from a very small sample size (n = 5), and in an experimental trial, the effect of PKV inoculation could not be separated from the effect of being inoculated with porcine epidemic diarrhea virus. In 13 poorly defined observational studies, more than 4000 young pigs had been assigned a diarrhea status and their feces analyzed for PKV. Unfortunately, the studies lacked well-characterized unbiased samples, and thus the strongest possible inference from these studies was that a very strong association between PKV and diarrhea is unlikely. PKV was commonly detected in non-diarrheic pigs, and this could indicate that PKV is not a sufficient cause in itself or that reinfection of individuals with some immunological protection due to previous infections is common. Conclusively, there is a lack of good evidence of PKV being a cause of gastrointestinal disease, but the sparse available evidence suggests that PKV is of limited clinical importance.
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Affiliation(s)
- Esben Østergaard Eriksen
- Section for Production, Nutrition and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
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Sun Y, Sun L, Sun S, Tu Z, Liu Y, Yi L, Tu C, He B. Virome Profiling of an Eastern Roe Deer Reveals Spillover of Viruses from Domestic Animals to Wildlife. Pathogens 2023; 12:pathogens12020156. [PMID: 36839428 PMCID: PMC9959412 DOI: 10.3390/pathogens12020156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Eastern roe deer (Capreolus pygargus) is a small ruminant and is widespread across China. This creature plays an important role in our ecological system. Although a few studies have been conducted to investigate pathogens harbored by this species, our knowledge of the virus diversity is still very sparse. In this study, we conducted the whole virome profiling of a rescue-failed roe deer, which revealed a kobuvirus (KoV), a bocaparvovirus (BoV), and multiple circular single-stranded viruses. These viruses were mainly recovered from the rectum, but PCR detection showed systematic infection of the KoV. Particularly, the KoV and BoV exhibited closely genetic relationships with bovine and canine viruses, respectively, highly suggesting the spillover of viruses from domestic animals to wildlife. Although these viruses were unlikely to have been responsible for the death of the animal, they provide additional data to understand the virus spectrum harbored by roe deer. The transmission of viruses between domestic animals and wildlife highlights the need for extensive investigation of wildlife viruses.
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Affiliation(s)
- Yue Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Lanshun Sun
- Provincial Wildlife Disease Monitoring Station of Shuanghe, Xunke 164400, China
| | - Sheng Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Zhongzhong Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Yang Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Le Yi
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Changchun Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China
- Correspondence: (C.T.); (B.H.)
| | - Biao He
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China
- Correspondence: (C.T.); (B.H.)
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9
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Abi KM, Yang C, Tang C, Jing ZZ. Aichivirus C isolate is a diarrhea-causing pathogen in goats. Transbound Emerg Dis 2022; 69:e2268-e2275. [PMID: 35502695 DOI: 10.1111/tbed.14566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/07/2022] [Accepted: 04/19/2022] [Indexed: 11/28/2022]
Abstract
Aichivirus C is an emerging virus in goats, but its biological significance remains unknown. In this study, 18 diarrheic and 16 non-diarrheic fecal samples of kids were collected from a farm with an ongoing diarrheic outbreak in Sichuan Province, China in May 2021. Of these samples, 77.8% (14/18) of diarrheic samples were detected as Aichivirus C positive by RT-PCR, which was significantly higher than that of non-diarrheic feces (0%, p<0.001); meanwhile, other common diarrhea-causing pathogens in goats were not detected in diarrheic samples, except for two samples that were detected as caprine enterovirus positive, suggesting that Aichivirus C was associated with goat diarrhea. Furthermore, five Aichivirus C strains were successfully isolated from positive samples using Vero cell lines and two isolates further plaque-purified, named SWUN/F5/2021(10-6.7 TCID50 /0.1ml) and SWUN/F6/2021(10-7 TCID50 /0.1ml). Interestingly, Aichivirus C strain could cause systemic infection in experimental kids via oral administration, with the main clinical manifestation being severe watery diarrhea. Histopathological changes observed in the duodenum and jejunum were characteristic, with shedding of mucosal epithelial cells. In addition, the virus was detected in tissues of diarrhea kids naturally infected with Aichivirus C, exhibiting pathological changes similar to those of experimental infections. Overall, this study first isolated Aichivirus C and confirmed its pathogenicity on kids, with further study needed to better understand virus pathogenicity. As Aichivirus C has been detected in South Korea, Italy, and the USA and widely prevalent in southwest China, the results obtained here have significant implications for the diagnosis and control of diarrhea in goats. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Keha-Mo Abi
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, PR China.,State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Chen Yang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, PR China
| | - Cheng Tang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, PR China
| | - Zhi Zhong Jing
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
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10
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Nantel-Fortier N, Gauthier M, L’Homme Y, Lachapelle V, Fravalo P, Brassard J. The swine enteric virome in a commercial production system and its association with neonatal diarrhea. Vet Microbiol 2022; 266:109366. [DOI: 10.1016/j.vetmic.2022.109366] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/31/2022] [Accepted: 02/06/2022] [Indexed: 11/24/2022]
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11
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Di Martino B, Di Profio F, Robetto S, Fruci P, Sarchese V, Palombieri A, Melegari I, Orusa R, Martella V, Marsilio F. Molecular Survey on Kobuviruses in Domestic and Wild Ungulates From Northwestern Italian Alps. Front Vet Sci 2021; 8:679337. [PMID: 34195249 PMCID: PMC8237713 DOI: 10.3389/fvets.2021.679337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
Since the first identification in 1989 in humans, kobuviruses (KoVs) have been identified from a wide range of animal species including carnivores, rodents, birds, ungulates, rabbits, and bats. Several studies have described the identification of genetically related KoVs in the fecal virome of domestic and wild animals suggesting a mutual exchange of viruses. By screening a total of 231 fecal samples from wild and domestic ungulates, KoVs RNA was detected in wild boars (3.2%; 2/63), chamois (4.6%; 2/43), and goats (2.6%; 2/77). On phylogenetic analysis of the partial RdRp sequence, the wild boar strains clustered within the species Aichivirus C whilst the strains identified in domestic and wild ruminants grouped into the species Aichivirus B. The complete VP1 gene was obtained for chamois and goat KoVs. Interestingly, upon phylogenetic analysis the strains grouped together with a KoV of ovine origin within a distinct genetic type (B3) of the species Aichivirus B.
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Affiliation(s)
- Barbara Di Martino
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Federica Di Profio
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Serena Robetto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Centro di Referenza Nazionale per le Malattie degli Animali Selvatici (CeRMAS), Aosta, Italy
| | - Paola Fruci
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Vittorio Sarchese
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Andrea Palombieri
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Irene Melegari
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Riccardo Orusa
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Centro di Referenza Nazionale per le Malattie degli Animali Selvatici (CeRMAS), Aosta, Italy
| | - Vito Martella
- Department of Veterinary Medicine, Università Aldo Moro di Bari, Valenzano, Italy
| | - Fulvio Marsilio
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
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12
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Interaction between Biofilm Formation, Surface Material and Cleanability Considering Different Materials Used in Pig Facilities—An Overview. SUSTAINABILITY 2021. [DOI: 10.3390/su13115836] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Sometimes the contamination in pig facilities can persist even after the washing and disinfection procedure. Some factors could influence this persistence, such as bacteria type, biofilm formation, material type and washing parameters. Therefore, this review summarizes how the type of surface can influence bacteria colonization and how the washing procedure can impact sanitary aspects, considering the different materials used in pig facilities. Studies have shown that biofilm formation on the surface of different materials is a complex system influenced by environmental conditions and the characteristics of each material’s surface and group of bacteria. These parameters, along with the washing parameters, are the main factors having an impact on the removal or persistence of biofilm in pig facilities even after the cleaning and disinfection processes. Some options are available for proper removal of biofilms, such as chemical treatments (i.e., detergent application), the use of hot water (which is indicated for some materials) and a longer washing time.
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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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14
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Nantel-Fortier N, Gauthier M, L'Homme Y, Fravalo P, Brassard J. Treatments of porcine fecal samples affect high-throughput virome sequencing results. J Virol Methods 2020; 289:114045. [PMID: 33333107 DOI: 10.1016/j.jviromet.2020.114045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 12/17/2022]
Abstract
The porcine enteric microbiota is currently extensively studied, taking advantage of developments in high-throughput sequencing technologies. However, the viral part of the microbiota, the virome, is being lightly explored, and the impact of the pretreatments used before sequencing the viruses is barely considered. In this study, the impacts of filtration, RNase and DNase treatments on virus reads recovery and diversity after sequencing on a MiSeq platform were assessed on fecal samples individually taken at <3, 5, 12 and 20 weeks from two piglets. None of the four pretreatment series affected the virus read averages or influenced diversity, but the samples with the higher proportion of reads corresponding to an entry in the "nt" database were those receiving the least number of pretreatments. The enzymatic pretreatments affected the detection of the single-stranded RNA viruses of Aichivirus C, porcine astrovirus, Sapovirus and posavirus, which is worrisome, as these viruses can be involved in swine diarrhea. If enzymatic pretreatments are used when sequencing using a high-throughput method, it may impact single-stranded RNA virus recovery, but not the overall virome diversity. Therefore, filtrated samples may be the better option, reducing the amount of bacterial genetic material while preserving the virus reads.
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Affiliation(s)
- Nicolas Nantel-Fortier
- Research Chair in Meat Safety, Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Quebec, Canada; Swine and Poultry Infections Disease Research Center (CRIPA-FRQNT), University of Montreal, Canada
| | - Martin Gauthier
- Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, Quebec, Canada
| | - Yvan L'Homme
- Swine and Poultry Infections Disease Research Center (CRIPA-FRQNT), University of Montreal, Canada; CEGEP Garneau, Quebec City, Quebec, Canada
| | - Philippe Fravalo
- Research Chair in Meat Safety, Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Quebec, Canada; Swine and Poultry Infections Disease Research Center (CRIPA-FRQNT), University of Montreal, Canada
| | - Julie Brassard
- Swine and Poultry Infections Disease Research Center (CRIPA-FRQNT), University of Montreal, Canada; Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, Quebec, Canada.
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15
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Su M, Qi S, Yang D, Guo D, Yin B, Sun D. Coinfection and Genetic Characterization of Porcine Astrovirus in Diarrheic Piglets in China From 2015 to 2018. Front Vet Sci 2020; 7:462. [PMID: 32923463 PMCID: PMC7456941 DOI: 10.3389/fvets.2020.00462] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/23/2020] [Indexed: 12/31/2022] Open
Abstract
Porcine astrovirus (PAstV) is broadly distributed globally and exists as at least five distinct genotypes. PAstV, which was recently identified as an important pathogen of diarrhea in piglets, is widely distributed in China. However, few studies have investigated the coinfection and genetic characterization of PAstV in diarrheic piglets in China. In this study, 89 PAstV-positive samples were identified in 543 diarrhea samples in China from 2015 to 2018, of which 75.28% (67/89) were coinfected with three to five different porcine pathogens, while none were positive for PAstV only. Among the 543 diarrhea samples, statistical analysis showed that PAstV-induced diarrhea was potentially associated with coinfection of PEV (p < 0.01) and GARV (p < 0.01). Phylogenetic analysis showed that the 27 identified PAstV strains belong to three different genotypes and that PAstV-2 (81.48%, 22/27) was predominant in diarrheic piglets in China, followed by PAstV-4 (11.11%, 3/27) and PAasV-5 (7.41%, 2/27). Sequence analysis revealed that the 27 RdRp genes identified in this study had nucleotide homologies of 53.8-99.5%. In addition, the RdRp gene of PAstV-4 strain JL/MHK/2018/0115 harbored a unique insert of three nucleotides (GAA) as compared with other known PAstV-4 strains. Furthermore, the genotypes of PAstV varied among different geographical locations, although PAstV-2 was the most widely distributed in China. These data demonstrate that PAstV coinfection with other porcine pathogens was common and there was genetic diversity of PAstV in diarrheic piglets in China.
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Affiliation(s)
- Mingjun Su
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China.,Heilongjiang Province Cultivating Collaborative Innovation Center for the Beidahuang Modern Agricultural Industry Technology, Daqing, China
| | - Shanshan Qi
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China.,Heilongjiang Province Cultivating Collaborative Innovation Center for the Beidahuang Modern Agricultural Industry Technology, Daqing, China
| | - Dan Yang
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China.,Heilongjiang Province Cultivating Collaborative Innovation Center for the Beidahuang Modern Agricultural Industry Technology, Daqing, China
| | - Donghua Guo
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China.,Heilongjiang Province Cultivating Collaborative Innovation Center for the Beidahuang Modern Agricultural Industry Technology, Daqing, China
| | - Baishuang Yin
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin, China
| | - Dongbo Sun
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China.,Heilongjiang Province Cultivating Collaborative Innovation Center for the Beidahuang Modern Agricultural Industry Technology, Daqing, China
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16
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You FF, Zhang MY, He H, He WQ, Li YZ, Chen Q. Kobuviruses carried by Rattus norvegicus in Guangdong, China. BMC Microbiol 2020; 20:94. [PMID: 32295529 PMCID: PMC7161169 DOI: 10.1186/s12866-020-01767-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 03/27/2020] [Indexed: 12/14/2022] Open
Abstract
Background Murine kobuviruses (MuKV) are newly recognized picornaviruses first detected in murine rodents in the USA in 2011. Little information on MuKV epidemiology in murine rodents is available. Therefore, we conducted a survey of the prevalence and genomic characteristics of rat kobuvirus in Guangdong, China. Results Fecal samples from 223 rats (Rattus norvegicus) were collected from Guangdong and kobuviruses were detected in 12.6% (28) of samples. Phylogenetic analysis based on partial 3D and complete VP1 sequence regions showed that rat kobuvirus obtained in this study were genetically closely related to those of rat/mouse kobuvirus reported in other geographical areas. Two near full-length rat kobuvirus genomes (MM33, GZ85) were acquired and phylogenetic analysis of these revealed that they shared very high nucleotide/amino acids identity with one another (95.4%/99.4%) and a sewage-derived sequence (86.9%/93.5% and 87.5%/93.7%, respectively). Comparison with original Aichivirus A strains, such human kobuvirus, revealed amino acid identity values of approximately 80%. Conclusion Our findings indicate that rat kobuvirus have distinctive genetic characteristics from other Aichivirus A viruses. Additionally, rat kobuvirus may spread via sewage.
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Affiliation(s)
- Fang-Fei You
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, 1838 North Road Guangzhou, Guangzhou, 510515, China
| | - Min-Yi Zhang
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, 1838 North Road Guangzhou, Guangzhou, 510515, China
| | - Huan He
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, 1838 North Road Guangzhou, Guangzhou, 510515, China
| | - Wen-Qiao He
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, 1838 North Road Guangzhou, Guangzhou, 510515, China
| | - Yong-Zhi Li
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, 1838 North Road Guangzhou, Guangzhou, 510515, China
| | - Qing Chen
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, 1838 North Road Guangzhou, Guangzhou, 510515, China.
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17
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Su M, Li C, Qi S, Yang D, Jiang N, Yin B, Guo D, Kong F, Yuan D, Feng L, Sun D. A molecular epidemiological investigation of PEDV in China: Characterization of co-infection and genetic diversity of S1-based genes. Transbound Emerg Dis 2019; 67:1129-1140. [PMID: 31785090 PMCID: PMC7233288 DOI: 10.1111/tbed.13439] [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: 07/04/2019] [Revised: 10/30/2019] [Accepted: 11/16/2019] [Indexed: 12/15/2022]
Abstract
Porcine epidemic diarrhoea virus (PEDV) is an emerging and re‐emerging epizootic virus of swine that causes substantial economic losses to the pig industry in China and other countries. The variations in the virus, and its co‐infections with other enteric viruses, have contributed to the poor control of PEDV infection. In the current study, a broad epidemiological investigation of PEDV was carried out in 22 provinces or municipalities of China during 2015–2018. The enteric viruses causing co‐infection with PEDV and the genetic diversity of the PEDV S1 gene were also analysed. The results indicated that, of the 543 diarrhoea samples, 66.85% (363/543) were positive for PEDV, and co‐infection rates of PEDV with 13 enteric viruses ranged from 3.58% (13/363) to 81.55% (296/363). Among these enteric viruses, the signs of diarrhoea induced by PEDV were potentially associated with co‐infections with porcine enterovirus 9/10 (PEV) and torque teno sus virus 2 (TTSuV‐2) (p < .05). The 147 PEDV strains identified in our study belong to Chinese pandemic strains and exhibited genetic diversity. The virulence‐determining S1 proteins of PEDV pandemic strains were undergoing amino acid mutations, in which S58_S58insQGVN–N135dup–D158_I159del‐like mutations were common patterns (97.28%, 143/147). When compared with 2011–2014 PEDV strains, the amino acid mutations of PEDV pandemic strains were mainly located in the N‐terminal domain of S1 (S1‐NTD), and 21 novel mutations occurred in 2017 and 2018. Furthermore, protein homology modelling showed that the mutations in pattern of insertion and deletion mutations of the S1 protein of PEDV pandemic strains may have caused structural changes on the surface of the S1 protein. These data provide a better understanding of the co‐infection and genetic evolution of PEDV in China.
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Affiliation(s)
- Mingjun Su
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Chunqiu Li
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Shanshan Qi
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Dan Yang
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Ning Jiang
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Baishuang Yin
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin, China
| | - Donghua Guo
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Fanzhi Kong
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Dongwei Yuan
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Li Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Dongbo Sun
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
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