Marta Diez-Valcarce1, Christina J Castro1, Rachel L Marine2, Natasha Halasa3, Holger Mayta4, Mayuko Saito5, Laura Tsaknaridis6, Chao-Yang Pan7, Filemon Bucardo8, Sylvia Becker-Dreps9, Maria Renee Lopez10, Laura Cristal Magaña1, Terry Fei Fan Ng2, Jan Vinjé11. 1. Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA. 2. Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA. 3. Vanderbilt University, Nashville, TN, 37332, USA. 4. Department of Cellular and Molecular Sciences, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru. 5. Department of Cellular and Molecular Sciences, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru; Department of Virology, Tohoku University, Graduate School of Medicine, Sendai, Japan. 6. Oregon State Public Health Laboratory, Hillsboro, OR, 97124, USA. 7. California Department of Public Health, Richmond, CA, USA. 8. Department of Microbiology, University of Leon, Leon, Nicaragua. 9. Department of Family Medicine and Epidemiology, University of North Carolina, Chapel Hill, NC, USA. 10. Universidad del Valle de Guatemala, Guatemala City, Guatemala. 11. Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA. Electronic address: jvinje@cdc.gov.
Abstract
BACKGROUND: Sapoviruses are responsible for sporadic and epidemic acute gastroenteritis worldwide. Sapovirus typing protocols have a success rate as low as 43% and relatively few complete sapovirus genome sequences are available to improve current typing protocols. OBJECTIVE/STUDY DESIGN: To increase the number of complete sapovirus genomes to better understand the molecular epidemiology of human sapovirus and to improve the success rate of current sapovirus typing methods, we used deep metagenomics shotgun sequencing to obtain the complete genomes of 68 sapovirus samples from four different countries across the Americas (Guatemala, Nicaragua, Peru and the US). RESULTS: VP1 genotyping showed that all sapovirus sequences could be grouped in the four established genogroups (GI (n = 13), GII (n = 30), GIV (n = 23), GV (n = 2)) that infect humans. They include the near-complete genome of a GI.6 virus and a recently reported novel GII.8 virus. Sequences of the complete RNA-dependent RNA polymerase gene could be grouped into three major genetic clusters or polymerase (P) types (GI.P, GII.P and GV.P) with all GIV viruses harboring a GII polymerase. One (GII.P-GII.4) of the new 68 sequences was a recombinant virus with the hotspot between the NS7 and VP1 regions. CONCLUSIONS: Analyses of this expanded database of near-complete sapovirus sequences showed several mismatches in the genotyping primers, suggesting opportunities to revisit and update current sapovirus typing methods.
BACKGROUND: Sapoviruses are responsible for sporadic and epidemic acute gastroenteritis worldwide. Sapovirus typing protocols have a success rate as low as 43% and relatively few complete sapovirus genome sequences are available to improve current typing protocols. OBJECTIVE/STUDY DESIGN: To increase the number of complete sapovirus genomes to better understand the molecular epidemiology of human sapovirus and to improve the success rate of current sapovirus typing methods, we used deep metagenomics shotgun sequencing to obtain the complete genomes of 68 sapovirus samples from four different countries across the Americas (Guatemala, Nicaragua, Peru and the US). RESULTS: VP1 genotyping showed that all sapovirus sequences could be grouped in the four established genogroups (GI (n = 13), GII (n = 30), GIV (n = 23), GV (n = 2)) that infect humans. They include the near-complete genome of a GI.6 virus and a recently reported novel GII.8 virus. Sequences of the complete RNA-dependent RNA polymerase gene could be grouped into three major genetic clusters or polymerase (P) types (GI.P, GII.P and GV.P) with all GIV viruses harboring a GII polymerase. One (GII.P-GII.4) of the new 68 sequences was a recombinant virus with the hotspot between the NS7 and VP1 regions. CONCLUSIONS: Analyses of this expanded database of near-complete sapovirus sequences showed several mismatches in the genotyping primers, suggesting opportunities to revisit and update current sapovirus typing methods.
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