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

Kentaro Tohma,Michael Kulka,Kim Y Green,Gabriel I Parra,Suzie Coughlan

doi:10.3390/v12050516

Abstract

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.

Highlights

Human sapovirus is a causative agent of acute gastroenteritis in people from all age-groups.A member of the family Caliciviridae, sapoviruses are non-enveloped and their viral capsid has icosahedral symmetry
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, by recombination, and by disparate nucleotide substitution patterns between RNA dependent RNA polymerase (RdRp) and VP1 sequences
We designed a primer that annealed to the first 27 nucleotide of the 5’-end of the sapovirus genome, which is highly conserved among strains, and together with a poly-T primer, would allow full-length viral RNA genome amplification (Figure 1a,b)

Summary

Introduction

Human sapovirus is a causative agent of acute gastroenteritis in people from all age-groups. A member of the family Caliciviridae, sapoviruses are non-enveloped and their viral capsid has icosahedral symmetry. Their genomes are single-stranded, positive-sense, 3’-polyadenylated RNA molecules of approximately 7.4 kb in length. The genome is organized into two open reading frames (ORFs), which are flanked by a short 5’-end and a long 3’-end non-coding regions. An ORF3 has been predicted in some sapovirus strains, but its function is still unknown [1]. The ORF1 encodes the nonstructural proteins, including the RNA dependent RNA polymerase (RdRp), and the major viral capsid protein (VP1) [1,2].

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