Whole-genome analysis of two bovine rotavirus C strains: Shintoku and Toyama

Abstract

Rotavirus C (RVC) has been detected frequently in epidemic cases and/or outbreaks of diarrhoea in humans and animals worldwide. Because it is difficult to cultivate RVCs serially in cell culture, the sequence data available for RVCs are limited, despite their potential economical and epidemiological impact. Although whole-genome sequences of one porcine RVC and seven human RVC strains have been analysed, this has not yet been done for a bovine RVC strain. In the present study, we first determined the nucleotide sequences for five as-yet underresearched genes, including the NSP4 gene, from a cultivable bovine RVC, the Shintoku strain, identified in Hokkaido Prefecture, Japan, in 1991. In addition, we elucidated the ORF sequences of all segments from another bovine RVC, the Toyama strain, detected in Toyama Prefecture, Japan, in 2010, in order to investigate genetic divergence among bovine RVCs. Comparison of segmental nucleotide and deduced amino acid sequences among RVCs indicates high identity among bovine RVCs and low identity between human and porcine RVCs. Phylogenetic analysis of each gene showed that the two bovine RVCs belong to a cluster distinct from human and porcine RVCs. These data demonstrate that RVCs can be classified into different genotypes according to host species. Moreover, RVC NSP1, NSP2 and VP1 amino acid sequences contain a unique motif that is highly conserved among rotavirus A (RVA) strains and, hence, several proteins from bovine RVCs are suggested to play important roles that are similar to those of RVAs.

Whole genome sequences of Japanese porcine species C rotaviruses reveal a high diversity of genotypes of individual genes and will contribute to a comprehensive, generally accepted classification system

“…According to our cut-off value for VP7 and the result of phylogenetic analysis, Tottori-KT and Ishi-1 represent a novel genotype of RVC, provisionally named G12 and G13, respectively. Soma et al (2013) proposed cut-off values for VP1-3 and NSP1-5; however, these values were based on limited sequence numbers. Thus, we calculated cut-off values including the new data.…”

“…Gene specific cut-off values for demarcation of individual genotypes were proposed for RVA (Matthijnssens et al, 2008a). For RVC, cut-off values for VP7 (84% or 85% in nt), VP4 (77% or 83% in nt), and VP6 (85%, 87%, or 90% in nt) were proposed by some researchers (Jeong et al, 2015;Marthaler et al, 2013;Soma et al, 2013;Suzuki et al, 2014Suzuki et al, , 2015. According to our cut-off value for VP7 and the result of phylogenetic analysis, Tottori-KT and Ishi-1 represent a novel genotype of RVC, provisionally named G12 and G13, respectively.…”

“…Whole genome analyses are useful for researching rotavirus evolution, including gene reassortment events and interspecies transmission, as well as following up epidemic and nosocomial transmission events. To our knowledge, whole genome sequences of many strains were analyzed in human RVC (Baek et al, 2013;Chen et al, 2015;; however only a few RVC whole genome sequences are available in animals (Marton et al, 2015a, b;Soma et al, 2013). In porcine RVC, only one whole genome sequence is available to date (Bremont et al, 1992;Bremont et al, 1993;Qian et al, 1991).…”

Analysis of genetic divergence among strains of porcine rotavirus C, with focus on VP4 and VP7 genotypes in Japan

“…To date, the genome of hundreds of RVA strains have been sequenced completely (Matthijnssens et al, 2012). Nonetheless, complete sequences are still limited in several human and bovine RVC strains, and one porcine RVC strain, Cowden (Chen et al, 2002;Bremont et al, 1992;Soma et al, 2013;Yamamoto et al, 2011). Moreover, phylogenetic analyses of individual genes among the strains revealed the presence of a single genotype grouped according to host species in each gene, except in the VP3 and VP7 genes (Martella et al, 2007a;Soma et al, 2013).…”

VP6 gene diversity in 11 Brazilian strains of porcine group C rotavirus

“…The porcine RVC strains have been demonstrated to have higher diversity upon VP6 gene analysis [17,18] compared with human [34,35] and bovine [36] strains. Additionally, previous studies have described high nucleotide similarity between strains from different host species [15,20].…”