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Corrigendum: Updated classification of norovirus genogroups and genotypes
Updated classification of norovirus genogroups and genotypes
Noroviruses are genetically diverse RNA viruses associated with acute gastroenteritis in mammalian hosts. Phylogenetically they can be segregated into different genogroups as well as P (polymerase)-groups and further into genotypes and P-types based on amino acid diversity of the complete VP1 gene and nucleotide diversity of the RNA-dependent RNA polymerase (RdRp) region of ORF1 respectively. In recent years several new noroviruses have been reported that warrant an update of the existing classification scheme. Using previously described 2× standard deviation (sd) criteria to group sequences into separate clusters we expanded the number of genogroups to 10 (GI-GX) and the number of genotypes to 49 (9 GI 27 GII 3 GIII 2 GIV 2 GV 2 GVI and 1 genotype each for GVII GVIII GIX [formerly GII.15] and GX). Viruses for which currently only one sequence is available in public databases were classified into tentative new genogroups (GNA1 and GNA2) and genotypes (GII.NA1 GII.NA2 and GIV.NA1) with their definitive assignment awaiting additional related sequences. Based on nucleotide diversity in the RdRp region noroviruses can be divided into 60 P-types (14 GI 37 GII 2 GIII 1 GIV 2 GV 2 GVI 1 GVII and 1 GX) 2 tentative P-groups and 14 tentative P-types. Future classification and nomenclature updates will be based on complete genome sequences and will be coordinated and disseminated by the international norovirus classification-working group.
Evolutionary dynamics of non-GII genotype 4 (GII.4) noroviruses reveal limited and independent diversification of variants
Noroviruses are extremely diverse with ≥30 genotypes infecting humans. GII genotype 4 (GII.4) noroviruses the most prevalent genotype present a constant accumulation of mutations on the major capsid protein (VP1) resulting in the chronological emergence of new variants every 2–8 years. On the other hand non-GII.4 noroviruses present a limited number of changes on the capsid protein over time. Despite limited diversification non-GII.4 viruses can also be associated with large outbreaks. To gain insights into the evolutionary dynamics of non-GII.4 viruses we performed variant-specific phylogenetic analyses on a comprehensive dataset of 13 genotypes. Although the genotypes with a single variant presented a linear (clock-like) evolution maximum-likelihood analyses revealed a lack of clock-like signals for the genotypes with ≥3 variants: GI.3 GII.6 and GII.17. Notably the evolutionary pattern of non-GII.4 viruses showed clock-like signals when each variant was analysed separately. A minimal impact on the long-term clock-like evolution of VP1 was detected due to the exchange (recombination) of the polymerase types. The linear evolution without replacement among variants is explained by minimal changes at the protein level due to the higher ratio of synonymous compared to non-synonymous substitutions in their evolution. Taken together these data indicate that (i) the variants of non-GII.4 noroviruses evolve and persist in the population independently probably due to strong evolutionary constraints on VP1 and (ii) variant-specific analyses with robust sequence databases that cover long periods of surveillance are needed to limit the potential for misinterpretation of the evolutionary dynamics of non-GII.4 noroviruses.
Genetic linkage of capsid protein-encoding RNA segments in group A equine rotaviruses
Rotavirus virions are formed by three concentric protein layers that enclose the 11 dsRNA genome segments and the viral proteins VP1 and VP3. Interactions amongst the capsid proteins (VP2 VP6 VP7 and VP4) have been described to play a major role in viral fitness whilst restricting the reassortment of the genomic segments during co-infection with different rotavirus strains. In this work we describe and characterize the linkage between VP6 and VP7 proteins based on structural and genomic analyses of group A rotavirus strains circulating in Argentinean horses. Strains with the VP7 genotype G3 showed a strong association with the VP6 genotype I6 whilst strains with G14 were associated with the I2 genotype. Most of the differences on the VP6 and VP7 proteins were observed in interactive regions between the two proteins suggesting that VP6 : VP7 interactions may drive the co-evolution and co-segregation of their respective gene segments.
Evidence of rotavirus intragenic recombination between two sublineages of the same genotype
Rotavirus G4 prevalence increased during the past decade with one of the highest prevalences reported during rotavirus surveillance in Argentina. Intragenotype diversity analysis has led to its subdivision into lineages (I and II) and sublineages (Ia–Id). On analysis of Argentine and G4 VP7 sequences from other locations one Argentine strain (ArgRes1723) appeared to be an intermediate between G4 sublineages Ib and Ic. Similarity and bootscanning analyses and Sawyer's test were carried out to demonstrate the recombinant nature of this strain. It was concluded that intragenic recombination occurred between sequences of sublineages Ib and Ic with a crossover point between nucleotide positions 336 and 387. This study constitutes the first report of a mechanism of evolution in rotaviruses that is currently considered unusual – a recombination event between two strains of the same rotavirus genotype. These results will help increase current knowledge about rotavirus evolution and divergence improving our understanding of the adaptation mechanisms used by these viruses.