Genome analysis of the novel putative rotavirus species K

Abstract

Rotaviruses are causative agents of diarrhea in humans and animals. Currently, the species rotavirus A-J (RVA-RVJ) and the putative species RVK and RVL are defined, mainly based on their genome sequence identities. RVK strains were first identified in 2019 in common shrews (Sorex aranaeus) in Germany; however, only short sequence fragments were available so far. Here, we analyzed the complete coding regions of strain RVK/shrew-wt/GER/KS14-0241/2013, which showed highest sequence identities with RVC. The amino acid sequence identity of VP6, which is used for rotavirus species definition, reached only 51% with other rotavirus reference strains thus confirming classification of RVK as a separate species. Phylogenetic analyses for the deduced amino acid sequences of all 11 virus proteins showed, that for most of them RVK and RVC formed a common branch within the RVA-like phylogenetic clade. Only the tree for the highly variable NSP4 showed a different branching; however, with very low bootstrap support. Comparison of partial nucleotide sequences of other RVK strains from common shrews of different regions in Germany indicated a high degree of sequence variability (61-97% identity) within the putative species. These RVK strains clustered separately from RVC genotype reference strains in phylogenetic trees indicating diversification of RVK independent from RVC. The results indicate that RVK represents a novel rotavirus species, which is most closely related to RVC.

Keywords: Genome sequence; Phylogeny; Rotavirus; Shrew; Taxonomy.

Fig. 1

Phylogenetic relationship of RVK proteins VP1-VP4, VP6-VP7 and NSP1-NSP5 with that of other rotavirus species. The complete deduced amino acid sequences of the encoded proteins of RVK strain RVK/shrew-wt/GER/KS14–0241/2013 were compared with those of reference strains of the other rotavirus species (as specified in Supplementary Data S1) by the Maximum Likelihood method using MEGA X. RVK is marked in red and bootstrap values > 50% are shown. Scaled in amino acid substitutions per site. Rotavirus species belonging to the evolutionary RVA-like clade are shaded in orange, whereas those of the RVB-like clade are shaded in blue. For RVB, RVG and RVI, which encode two forms of NSP1 (NSP1–1 and NSP1–2), only NSP1–2 was used in the NSP1 tree.

Fig. 2

Phylogenetic relationship of rotavirus species based on the concatenated amino acid sequences of VP1-VP4, VP6-VP7 and NSP1-NSP5. The concatenated amino acid sequences of proteins of RVK strain RVK/shrew-wt/GER/KS14–0241/2013 were compared with that of reference strains of the other rotavirus species (as specified in Supplementary Data S1) by the Maximum Likelihood method using MEGA X, and a radiated tree was constructed. Bootstrap values > 50% are shown. Scaled in amino acid substitutions per site. Rotavirus species belonging to the evolutionary RVA-like clade are shaded in orange, whereas those of the RVB-like clade are shaded in blue.

Fig. 3

Phylogenetic relationship of different RVK strains and RVC genotype reference strains. Overlapping partial nucleotide sequences (174 nucleotides for VP1, above, and 153 nucleotides for VP6, below) were compared by the Maximum Likelihood method using MEGA X. The virus species (RVK or RVC), genotype (for RVC only) and the GenBank accession numbers are shown at the branches. Bootstrap values > 50% are shown. Scaled in nucleotide substitutions per site.