Proposal for a unified norovirus nomenclature and genotyping

Abstract

Noroviruses belong to a genus of genetically diverse viruses within the family Caliciviridae and cause acute gastroenteritis in humans and animals. They are subdivided into genogroups, each of which further segregates into genotypes. Until recently, a new genotype was based on a defined pairwise distance cutoff of complete VP1 sequences, but with the increasing number of available norovirus sequences, this cutoff is no longer accurate, and sequences in the public database have been misclassified. In this paper, we demonstrate that the pairwise distance cutoff method can no longer be used and outline a phylogenetic approach to classify noroviruses. Furthermore, we propose a dual nomenclature using both ORF1 and VP1 sequences, as recombination is common and recognizing recombinant viruses may be relevant. With the continuing emergence of new norovirus lineages, we propose to coordinate nomenclature of new norovirus genotypes through an international norovirus working group.

Fig. 1

Phylogenetic trees (MrBayes) of complete capsid aa sequences of norovirus GI (a) and GII (b), showing all genotype clusters as defined in Fields Virology [16] and one new GI cluster GI.9 and three new GII clusters GII.20 – GII.22 (grey italic). The ML trees and the trees based on nucleotides are very similar (data not shown)

Fig. 2

Average within-genotype (GI.8, GII.4, GII.13, GII.1. GII.12, GII.16) distances and between-genotype (GI.8/ GI.9 and GII.4/GII.20, GII.13/ GII.21, GII.1/GII.22, GII.12/ G.II.22, GII.12/GII.22) distances of proposed new genotypes and the genotype clusters that are closest to them in the phylogenetic trees, calculated using Baysian and maximum-likelihood methods, and using nt and aa sequence alignments of complete norovirus capsid sequences. Error bars are + 2×SD and – 2×SD

Fig. 3

Maximum-likelihood tree of partial ORF1 nt sequences (1300 nt) of a set of 166 sequences with 12 clusters of more than sequences – GII.1=5, GII.3=3.G II.4=82, GII.6=2, GII.7=11,G II.12=28, GII.19=2, GII.21=8 (previously GII.b) [4], GII.22=2 (previously GII.d [6]) – and 7 separate single sequences. For nine clusters and six single sequences, the corresponding VP1 genotype is indicated. Two clusters correspond to two VP1 types each, as viruses of the two VP1 types have similar pORF1 sequences. The bracketed