Genetic diversity of human sapovirus across the Americas

Marta Diez-Valcarce, Christina J. Castro, Rachel L. Marine, Natasha Halasa, Holger Mayta, Mayuko Saito, Laura Tsaknaridis, Chao Yang Pan, Filemon Bucardo, Sylvia Becker-Dreps, Maria Renee Lopez, Laura Cristal Magaña, Terry Fei Fan Ng, Jan Vinjé

Research output: Contribution to journalArticle

13 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)65-72
Number of pages8
JournalJournal of Clinical Virology
Volume104
DOIs
Publication statusPublished - 2018 Jul

Keywords

  • Genotypes
  • Next generation sequencing
  • Sapovirus
  • Viral gastroenteritis

ASJC Scopus subject areas

  • Virology
  • Infectious Diseases

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    Diez-Valcarce, M., Castro, C. J., Marine, R. L., Halasa, N., Mayta, H., Saito, M., Tsaknaridis, L., Pan, C. Y., Bucardo, F., Becker-Dreps, S., Lopez, M. R., Magaña, L. C., Ng, T. F. F., & Vinjé, J. (2018). Genetic diversity of human sapovirus across the Americas. Journal of Clinical Virology, 104, 65-72. https://doi.org/10.1016/j.jcv.2018.05.003