Analysis of the full genome of human group C rotaviruses reveals lineage diversification and reassortment

Abstract

Group C rotaviruses (RVC) are enteric pathogens of humans and animals. Whole-genome sequences are available only for few RVCs, leaving gaps in our knowledge about their genetic diversity. We determined the full-length genome sequence of two human RVCs (PR2593/ 2004 and PR713/2012), detected in Italy from hospital-based surveillance for rotavirus infection in 2004 and 2012. In the 11 RNA genomic segments, the two Italian RVCs segregated within separate intra-genotypic lineages showed variation ranging from 1.9 % (VP6) to 15.9 % (VP3) at the nucleotide level. Comprehensive analysis of human RVC sequences available in the databases allowed us to reveal the existence of at least two major genome configurations, defined as type I and type II. Human RVCs of type I were all associated with the M3 VP3 genotype, including the Italian strain PR2593/2004. Conversely, human RVCs of type II were all associated with the M2 VP3 genotype, including the Italian strain PR713/2012. Reassortant RVC strains between these major genome configurations were identified. Although only a few full-genome sequences of human RVCs, mostly of Asian origin, are available, the analysis of human RVC sequences retrieved from the databases indicates that at least two intra-genotypic RVC lineages circulate in European countries. Gathering more sequence data is necessary to develop a standardized genotype and intragenotypic lineage classification system useful for epidemiological investigations and avoiding confusion in the literature.

Evolution of rotavirus C in humans and several domestic animal species

“…Serological typing of RVC is limited, owing to the difficulty of cultivating RVC strains in cell culture, and RVC genotypes are determined by sequence data (Fujii et al, ; Jeong et al, ; Marthaler et al, ; Moutelikova, Prodelalova, & Dufkova, ; Saif, Terrett, Miller, & Cross, ; Soma et al, ; Suzuki, Hasebe, Miyazaki, & Tsunemitsu, ; Tsunemitsu et al, ). At the time of this study, the availability of whole‐genome sequence (WGS) data for RVC is limited for all hosts: swine ( n = 1), canine ( n = 1), bovine ( n = 7) and human ( n = 13) (Baek, Than, Kim, Lim, & Kim, ; Chen, Lambden, Lau, Caul, & Clarke, ; Doan et al, ; Mawatari, Hirano, Tsunemitsu, & Suzuki, ; Marton et al, ; Soma et al, ; Yamamoto et al, ; Zhirakovskaia et al, ).…”