Abstract
Sapovirus is a genus of caliciviruses that are known to cause enteric disease in humans and animals. There is considerable genetic diversity among the sapoviruses, which are classified into different genogroups based on phylogenetic analysis of the full-length capsid protein sequence. While several mammalian species, including humans, pigs, minks, and dogs, have been identified as animal hosts for sapoviruses, there were no reports of sapoviruses in bats in spite of their biological diversity. In this report, we present the results of a targeted surveillance study in different bat species in Hong Kong. Five of the 321 specimens from the bat species, Hipposideros pomona, were found to be positive for sapoviruses by RT-PCR. Complete or nearly full-length genome sequences of approximately 7.7 kb in length were obtained for three strains, which showed similar organization of the genome compared to other sapoviruses. Interestingly, they possess many genomic features atypical of most sapoviruses, like high G+C content and minimal CpG suppression. Phylogenetic analysis of the viral proteins suggested that the bat sapovirus descended from an ancestral sapovirus lineage and is most closely related to the porcine sapoviruses. Codon usage analysis showed that the bat sapovirus genome has greater codon usage bias relative to other sapovirus genomes. In summary, we report the discovery and genomic characterization of the first bat calicivirus, which appears to have evolved under different conditions after early divergence from other sapovirus lineages.
Highlights
The caliciviruses are a family of small non-enveloped viruses, and can be classified into five genera: Vesivirus, Lagovirus, Norovirus, Sapovirus and Nebovirus
RT-PCR using broadly reactive degenerate primers for a 185 nt fragment in the 3D-like RNA-dependent RNA polymerase (RdRp) region of the calicivirus ORF1 gene was positive in two specimens
A phylogenetic tree was constructed from the nucleotide alignment based on the length of the partial RdRp sequence obtained from bat SaV/TLC72 (GenBank accession number JQ267527) (Figure S2)
Summary
The caliciviruses are a family of small non-enveloped viruses, and can be classified into five genera: Vesivirus, Lagovirus, Norovirus, Sapovirus and Nebovirus. They possess a non-segmented, polyadenylated, positive-sense ssRNA genome of about 7.5 to 8.5 kb in length, enclosed in an icosahedral capsid of 27 to 40 nm in diameter. A putative sixth genus, Recovirus, has been proposed for a novel calicivirus detected in stool specimens from rhesus monkeys [4,5]. Another new genus, Valovirus, has been proposed for a novel group of swine caliciviruses known as the St-Valerien-like viruses [6]. There exist other unclassified caliciviruses, such as the recently described chicken calicivirus [7]
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