Genomic diversity and intragenic recombination of species C rotaviruses

Rotavirus C (RVC) is a major cause of diarrhoea in swine, cattle, and humans worldwide. RVC exhibits sequence diversity in all 11 genes, especially in VP4 and VP7, and all segment-based genotyping has been performed similar to rotavirus A. To date, recombination events have been reported in rotaviru...

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Published in	Journal of general virology Vol. 103; no. 2
Main Authors	Oki, Hisako, Masuda, Tsuneyuki, Hayashi-Miyamoto, Michiko, Kawai, Megumi, Ito, Mika, Madarame, Hiroo, Fukase, Yuka, Takemae, Hitoshi, Sakaguchi, Shoichi, Furuya, Tetsuya, Mizutani, Tetsuya, Oba, Mami, Nagai, Makoto
Format	Journal Article
Language	English
Published	England 17.02.2022
Subjects	Animals Cattle Genetic Variation Genome, Viral Humans Rotavirus - genetics Rotavirus Infections - veterinary Rotavirus Infections - virology Swine Swine Diseases - virology genotypes intragenic recombination rotavirus C complete genome analyses
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Abstract	Rotavirus C (RVC) is a major cause of diarrhoea in swine, cattle, and humans worldwide. RVC exhibits sequence diversity in all 11 genes, especially in VP4 and VP7, and all segment-based genotyping has been performed similar to rotavirus A. To date, recombination events have been reported in rotavirus A and B. However, there are no reports describing gene recombination of RVC, except for recombination in NSP3 between RVC and rotavirus H. In this study, nine porcine RVC strains identified in Japanese pigs were completely sequenced and analysed together with RVC sequences from the GenBank database. The analyses showed that sequences of the VP4, VP2, and NSP1 of several porcine RVC strains did not branch with any of those of the RVC strains in the GenBank database, suggesting new genotypes. Several homologous recombination events, between or within genotypes, were identified in the VP4, VP7, VP2, NSP1, and NSP3 genes. Of these, nine, one, and one intergenotypic recombination events in the VP4, VP2, and NSP3 genes, respectively, were supported with sufficient statistical values. Although these findings suggest occurrences of the intragenic recombination events in the RVC genome, potential sequence errors and poor sequence assemblies in the databases should be watched with care. The results in this study present data about the important recombination events of the RVCs, which influence evolution of the virus by aiding them to gain genetic diversity and plasticity, although further sequence data will be necessary to obtain more comprehensive understanding of such mechanisms.
AbstractList	Rotavirus C (RVC) is a major cause of diarrhoea in swine, cattle, and humans worldwide. RVC exhibits sequence diversity in all 11 genes, especially in VP4 and VP7, and all segment-based genotyping has been performed similar to rotavirus A. To date, recombination events have been reported in rotavirus A and B. However, there are no reports describing gene recombination of RVC, except for recombination in NSP3 between RVC and rotavirus H. In this study, nine porcine RVC strains identified in Japanese pigs were completely sequenced and analysed together with RVC sequences from the GenBank database. The analyses showed that sequences of the VP4, VP2, and NSP1 of several porcine RVC strains did not branch with any of those of the RVC strains in the GenBank database, suggesting new genotypes. Several homologous recombination events, between or within genotypes, were identified in the VP4, VP7, VP2, NSP1, and NSP3 genes. Of these, nine, one, and one intergenotypic recombination events in the VP4, VP2, and NSP3 genes, respectively, were supported with sufficient statistical values. Although these findings suggest occurrences of the intragenic recombination events in the RVC genome, potential sequence errors and poor sequence assemblies in the databases should be watched with care. The results in this study present data about the important recombination events of the RVCs, which influence evolution of the virus by aiding them to gain genetic diversity and plasticity, although further sequence data will be necessary to obtain more comprehensive understanding of such mechanisms. Rotavirus C (RVC) is a major cause of diarrhoea in swine, cattle, and humans worldwide. RVC exhibits sequence diversity in all 11 genes, especially in VP4 and VP7, and all segment-based genotyping has been performed similar to rotavirus A. To date, recombination events have been reported in rotavirus A and B. However, there are no reports describing gene recombination of RVC, except for recombination in NSP3 between RVC and rotavirus H. In this study, nine porcine RVC strains identified in Japanese pigs were completely sequenced and analysed together with RVC sequences from the GenBank database. The analyses showed that sequences of the VP4, VP2, and NSP1 of several porcine RVC strains did not branch with any of those of the RVC strains in the GenBank database, suggesting new genotypes. Several homologous recombination events, between or within genotypes, were identified in the VP4, VP7, VP2, NSP1, and NSP3 genes. Of these, nine, one, and one intergenotypic recombination events in the VP4, VP2, and NSP3 genes, respectively, were supported with sufficient statistical values. Although these findings suggest occurrences of the intragenic recombination events in the RVC genome, potential sequence errors and poor sequence assemblies in the databases should be watched with care. The results in this study present data about the important recombination events of the RVCs, which influence evolution of the virus by aiding them to gain genetic diversity and plasticity, although further sequence data will be necessary to obtain more comprehensive understanding of such mechanisms.Rotavirus C (RVC) is a major cause of diarrhoea in swine, cattle, and humans worldwide. RVC exhibits sequence diversity in all 11 genes, especially in VP4 and VP7, and all segment-based genotyping has been performed similar to rotavirus A. To date, recombination events have been reported in rotavirus A and B. However, there are no reports describing gene recombination of RVC, except for recombination in NSP3 between RVC and rotavirus H. In this study, nine porcine RVC strains identified in Japanese pigs were completely sequenced and analysed together with RVC sequences from the GenBank database. The analyses showed that sequences of the VP4, VP2, and NSP1 of several porcine RVC strains did not branch with any of those of the RVC strains in the GenBank database, suggesting new genotypes. Several homologous recombination events, between or within genotypes, were identified in the VP4, VP7, VP2, NSP1, and NSP3 genes. Of these, nine, one, and one intergenotypic recombination events in the VP4, VP2, and NSP3 genes, respectively, were supported with sufficient statistical values. Although these findings suggest occurrences of the intragenic recombination events in the RVC genome, potential sequence errors and poor sequence assemblies in the databases should be watched with care. The results in this study present data about the important recombination events of the RVCs, which influence evolution of the virus by aiding them to gain genetic diversity and plasticity, although further sequence data will be necessary to obtain more comprehensive understanding of such mechanisms.
Author	Madarame, Hiroo Fukase, Yuka Furuya, Tetsuya Mizutani, Tetsuya Takemae, Hitoshi Nagai, Makoto Hayashi-Miyamoto, Michiko Ito, Mika Masuda, Tsuneyuki Oki, Hisako Kawai, Megumi Oba, Mami Sakaguchi, Shoichi
Author_xml	– sequence: 1 givenname: Hisako surname: Oki fullname: Oki, Hisako organization: Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa 920–3101, Japan – sequence: 2 givenname: Tsuneyuki surname: Masuda fullname: Masuda, Tsuneyuki organization: Seibu Livestock Hygiene Service Center, Houki, Tottori 689-4213, Japan – sequence: 3 givenname: Michiko surname: Hayashi-Miyamoto fullname: Hayashi-Miyamoto, Michiko organization: Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa 920–3101, Japan – sequence: 4 givenname: Megumi surname: Kawai fullname: Kawai, Megumi organization: Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa 920–3101, Japan – sequence: 5 givenname: Mika surname: Ito fullname: Ito, Mika organization: Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa 920–3101, Japan – sequence: 6 givenname: Hiroo surname: Madarame fullname: Madarame, Hiroo organization: School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa 252-5201, Japan – sequence: 7 givenname: Yuka orcidid: 0000-0003-2902-0614 surname: Fukase fullname: Fukase, Yuka organization: School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa 252-5201, Japan – sequence: 8 givenname: Hitoshi orcidid: 0000-0003-3003-970X surname: Takemae fullname: Takemae, Hitoshi organization: Center for Infectious Diseases of Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan – sequence: 9 givenname: Shoichi orcidid: 0000-0003-3650-1221 surname: Sakaguchi fullname: Sakaguchi, Shoichi organization: Department of Microbiology and Infection Control, Osaka Medical College, Osaka 569-8686, Japan – sequence: 10 givenname: Tetsuya orcidid: 0000-0003-3979-7072 surname: Furuya fullname: Furuya, Tetsuya organization: Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan – sequence: 11 givenname: Tetsuya surname: Mizutani fullname: Mizutani, Tetsuya organization: Center for Infectious Diseases of Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan – sequence: 12 givenname: Mami orcidid: 0000-0002-4187-3217 surname: Oba fullname: Oba, Mami organization: Center for Infectious Diseases of Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa 252-5201, Japan – sequence: 13 givenname: Makoto orcidid: 0000-0001-5884-620X surname: Nagai fullname: Nagai, Makoto organization: Center for Infectious Diseases of Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa 252-5201, Japan
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Snippet	Rotavirus C (RVC) is a major cause of diarrhoea in swine, cattle, and humans worldwide. RVC exhibits sequence diversity in all 11 genes, especially in VP4 and...
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SubjectTerms	Animals Cattle Genetic Variation Genome, Viral Humans Rotavirus - genetics Rotavirus Infections - veterinary Rotavirus Infections - virology Swine Swine Diseases - virology
Title	Genomic diversity and intragenic recombination of species C rotaviruses
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