Analysis of Genetic Diversity and Sites of Recombination in Human Rhinovirus Species C

Abstract

Human rhinoviruses (HRVs) are a highly prevalent and diverse group of respiratory viruses. Although HRV-A and HRV-B are traditionally detected by virus isolation, a series of unculturable HRV variants have recently been described and assigned as a new species (HRV-C) within the picornavirus Enterovirus genus. To investigate their genetic diversity and occurrence of recombination, we have performed comprehensive phylogenetic analysis of sequences from the 5 untranslated region (5 UTR), VP4/VP2, VP1, and 3Dpol regions amplified from 89 HRV-C-positive respiratory samples and available published sequences. Branching orders of VP4/VP2, VP1, and 3Dpol trees were identical, consistent with the absence of intraspecies recombination in the coding regions. However, numerous tree topology changes were apparent in the 5 UTR, where >60% of analyzed HRV-C variants showed recombination with species A sequences. Two recombination hot spots in stem-loop 5 and the polypyrimidine tract in the 5 UTR were mapped using the program GroupingScan. Available HRV-C sequences showed evidence for additional interspecies recombination with HRV-A in the 2A gene, with breakpoints mapping precisely to the boundaries of the C-terminal domain of the encoded proteinase. Pairwise distances between HRV-C variants in VP1 and VP4/VP2 regions fell into two separate distributions, resembling inter-and intraserotype distances of species A and B. These observations suggest that, without serological cross-neutralization data, HRV-C genetic groups may be equivalently classified into types using divergence thresholds derived from distance distributions. The extensive sequence data from multiple genome regions of HRV-C and analyses of recombination in the current study will assist future formulation of consensus criteria for HRV-C type assignment and identification.

Toward Genetics-Based Virus Taxonomy: Comparative Analysis of a Genetics-Based Classification and the Taxonomy of Picornaviruses

“…Specifics of both HRV-C evolution and the two classification frameworks could play a role. The genetic diversity of these viruses in capsid (1A, also known as VP4, and 1D proteins) and nonstructural (3D) regions was previously reported to exceed those of other rhinoviruses (51,69). In the 1D protein, this difference is smallest, and the entire HRV-C diversity was considered to be below the species divergence limit, paving the way for the recognition of HRV-C as a single species.…”

Genetic analysis of the VP4/VP2 coding region in human rhinovirus species C in patients with acute respiratory infection in Japan

“…In the present study, HRV-C strains were detected in patients with various ARIs such as URI and bronchitis. In addition, previous reports have suggested that~30 genotypes with high genetic divergence are found in various HRV-C strains (McIntyre et al, 2010;Simmonds et al, 2010). The present strains were also classified into 11 genotypes with a relatively wide divergence, although only a small number of HRV-C strains were examined in the current study.…”

“…To assign genotypes to each of the present strains, we used the 28 HRV-C reference strains (Arakawa et al, 2012;Simmonds et al, 2010). In addition, to assess interspecies frequency distributions of HRV-C, we calculated pairwise distances for all of the HRV-C strains, both present strains and reference strains, as described previously (Arakawa et al, 2012;Mizuta et al, 2010).…”

“…For genotypic assignment of the HRV-strains -the 19 HRV-C strains analysed in this study and 28 reference strains (Simmonds et al, 2010) phylogenetic analysis using the NJ method was performed as described previously (Arakawa et al, 2012). Evolutionary distances were estimated according to Kimura's two-parameter method, and the reliability of the tree was estimated with 1000 bootstrap replications (Kimura, 1980;Saitou & Nei, 1987).…”

“…Indeed, our previous report suggested that the genomes of HRV-C detected in Japanese subjects with various ARIs showed .30 % divergence based on sequences in the VP4/VP2 coding region, and these strains could be classified into many genotypes by phylogenetic analysis (Arakawa et al, 2012). Furthermore, studies of the VP4/VP2 coding region have allowed detailed phylogenetic analysis of the genotypes of HRV-A to -C (Arakawa et al, 2012;Cuevas et al, 2012;McIntyre et al, 2010;Simmonds et al, 2010). It appears, then, that this region could be useful for the detailed genetic analysis of HRV-C, although the evolution of the region is not fully understood.…”