Whole Genome Sequence Analysis of a Prototype Strain of the Novel Putative Rotavirus Species L

Abstract

Rotaviruses infect humans and animals and are a main cause of diarrhea. They are non-enveloped viruses with a genome of 11 double-stranded RNA segments. Based on genome analysis and amino acid sequence identities of the capsid protein VP6, the rotavirus species A to J (RVA-RVJ) have been defined so far. In addition, rotaviruses putatively assigned to the novel rotavirus species K (RVK) and L (RVL) have been recently identified in common shrews (Sorex araneus), based on partial genome sequences. Here, the complete genome sequence of strain KS14/0241, a prototype strain of RVL, is presented. The deduced amino acid sequence for VP6 of this strain shows only up to 47% identity to that of RVA to RVJ reference strains. Phylogenetic analyses indicate a clustering separated from the established rotavirus species for all 11 genome segments of RVL, with the closest relationship to RVH and RVJ within the phylogenetic RVB-like clade. The non-coding genome segment termini of RVL showed conserved sequences at the 5'-end (positive-sense RNA strand), which are common to all rotaviruses, and those conserved among the RVB-like clade at the 3'-end. The results are consistent with a classification of the virus into a novel rotavirus species L.

Keywords: genome sequence; phylogeny; rotavirus; taxonomy; virus species.

Figure 1

Phylogenetic relationship of RVL with other rotavirus species. The complete deduced amino acid sequences of the encoded proteins of RVL were compared with those of reference strains of the other rotavirus species (as specified in Supplementary Data S1) by the Neighbor-joining method using MEGA X. RVL is marked in red and bootstrap values > 50% are shown. Scaled in amino acid substitutions per site.