Updated classification of norovirus genogroups and genotypes

Abstract

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 48 (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.

Keywords: 2xSD criteria; Norovirus; P-group; P-type; acute gastroenteritis; classification; genogroup; genotype.

Fig. 1.

Classification of noroviruses into genogroups, genotypes, variants, P-groups and P-types. Tentative genogroups, genotypes, P-groups and P-types are currently represented only by a single sequence or multiple non-identical sequences from a single geographic location and are therefore named as non-assigned (NA).

Fig. 2.

Phylogenetic classification of noroviruses based on VP1 amino acid sequences into ten norovirus genogroups and two non-assigned (NA) genogroups (a), GI genotypes (b) and GII genotypes (c). Phylogenetic analysis was performed using maximum likelihood (PhyML). Resulting trees were plotted and edited in FigTree (http://tree.bio.ed.ac.uk/software/figtree/). Newly identified genogroups and genotypes are labelled in red.

Fig. 3.

Phylogenetic trees of partial (762 nucleotides at 3′-end of ORF1) RdRp sequences of norovirus genogroups (a), GI P-types (b) and GII P-types (c). Tentative P-groups and P-types with only a single sequence or multiple non-identical sequences from a single geographic location are referred to as non-assigned (NA). Phylogenetic analysis was carried out using maximum likelihood (ML) with PhyML. The resulting trees were plotted and edited in FigTree (http://tree.bio.ed.ac.uk/software/figtree/). Newly identified genogroups and genotypes are labelled in red. In Fig 3c, only GII P-types with highly divergent clusters are shown with a gray circle for clarity.

Fig. 4.

Patristic and P-distance comparison of GI.P11 (previously GI.Pb) (a and b), GII.P33 viruses (c and d) and GII.P22 viruses (e and f) with their phylogenetically closest P-types. Error bars represent 2xsd for each P-type comparison. The red * and font indicate the overlap of 2×sd error bars for viruses within a cluster and its closest P-types (a, b and e). After re-assigning GI.P11 viruses into two clusters (GI.P11 and GI.PNA1) (c), GII.P33 into GII.P33 and GII.P41 (d) and GII.P22 into three clusters (GII.P22, GII.P40 and GII.PNA5) (f), no overlap of 2×sd error bars within or in-between P-types was present (blue * and font). Y-axis represents comparison of distances within and in-between P-types. Below the dotted line, distances within P-type are indicated and above the dotted line, distances between P-types are indicated. (2×sd criteria: phylogenetic distances of sequences within a P-type should not overlap with distances between different P-types.)

Fig. 5.

Updated norovirus classification scheme with the number of genogroups and genotypes based on complete VP1 amino acids and the number of P-groups and P-types based on a partial region (762 nucleotides) of the RNA-dependent RNA polymerase (RdRp) at the 5′-end of ORF1. P=P-group, T=tentative genotype/P-type (when only a single sequence or multiple non-identical sequences from a single geographic location as available, they are non-assigned (NA).