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Open AccessArticle

Genomic Analyses of Human Sapoviruses Detected over a 40-Year Period Reveal Disparate Patterns of Evolution among Genotypes and Genome Regions

1
Division of Viral Products, CBER, FDA, Silver Spring, MD 20993, USA
2
Division of Molecular Biology, CFSAN, FDA, Laurel, MD 20993, USA
3
National Virus Reference Laboratory, UC-Dublin, Dublin 4, Ireland
4
Laboratory of Infectious Diseases, NIH, Bethesda, MD 20993, USA
*
Authors to whom correspondence should be addressed.
Viruses 2020, 12(5), 516; https://doi.org/10.3390/v12050516
Received: 10 April 2020 / Revised: 4 May 2020 / Accepted: 6 May 2020 / Published: 7 May 2020
(This article belongs to the Section Animal Viruses)
Human sapovirus is a causative agent of acute gastroenteritis in all age groups. The use of full-length viral genomes has proven beneficial to investigate evolutionary dynamics and transmission chains. In this study, we developed a full-length genome sequencing platform for human sapovirus and sequenced the oldest available strains (collected in the 1970s) to analyse diversification of sapoviruses. Sequence analyses from five major genotypes (GI.1, GI.2, GII.1, GII.3, and GIV.1) showed limited intra-genotypic diversification for over 20–40 years. The accumulation of amino acid mutations in VP1 was detected for GI.2 and GIV.1 viruses, while having a similar rate of nucleotide evolution to the other genotypes. Differences in the phylogenetic clustering were detected between RdRp and VP1 sequences of our archival strains as well as other reported putative recombinants. However, the lack of the parental strains and differences in diversification among genomic regions suggest that discrepancies in the phylogenetic clustering of sapoviruses could be explained, not only by recombination, but also by disparate nucleotide substitution patterns between RdRp and VP1 sequences. Together, this study shows that, contrary to noroviruses, sapoviruses present limited diversification by means of intra-genotype variation and recombination. View Full-Text
Keywords: sapovirus; calicivirus; genetic diversity; evolution; recombination; norovirus sapovirus; calicivirus; genetic diversity; evolution; recombination; norovirus
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Tohma, K.; Kulka, M.; Coughlan, S.; Green, K.Y.; Parra, G.I. Genomic Analyses of Human Sapoviruses Detected over a 40-Year Period Reveal Disparate Patterns of Evolution among Genotypes and Genome Regions. Viruses 2020, 12, 516.

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