Emergence of a new norovirus genotype II.4 variant associated with global outbreaks of gastroenteritis

Abstract

Norovirus (NoV) is highly infectious and is the major cause of outbreak gastroenteritis in adults, with pandemic spread of the virus being reported in 1995 and 2002. The NoV genome is genetically diverse, which has hampered development of sensitive molecular biology-based methods. In this study we report on a nested reverse transcriptase PCR (nRT-PCR) that was designed to amplify the highly conserved 3' end of the polymerase region and the 5' end of the capsid gene of NoV genogroup II (GII). The nRT-PCR was validated with strains isolated from sporadic and outbreak cases between 1997 and 2004 in New South Wales, Australia. Phylogenetic analysis identified six genotypes circulating in New South Wales, GII.1, GII.3, GII.4, GII.6, GII.7, and GII.10, with GII.4 being the predominant genotype. In 2004, there was a marked increase in NoV GII activity in Australia, with a novel GII.4 variant being identified as the etiological agent in 18 outbreaks investigated. This novel GII.4 variant, termed Hunter virus, differed by more than 5% at the amino acid level across the capsid from any other NoV strain in the GenBank and EMBL databases. The Hunter virus was subsequently identified as the etiological agent in large epidemics of gastroenteritis in The Netherlands, Japan, and Taiwan in 2004 and 2005.

FIG. 1.

Phylogenetic analysis of a 266-bp region of the capsid region in NoV GII. Strains in boldface and italics were detected in this study by the new NoV GII nRT-PCR assay. The strain names indicate the suburb where the strain was isolated, their identification number, the year in which they were detected, and whether they were from an outbreak (O) or sporadic cases (S). The percent bootstrap values in which the major groupings were observed among 100 replicates are indicated. The branch lengths are proportional to the evolutionary distance between sequences, and the distance scale in nucleotide substitutions per position is shown. Phylogenetic analysis revealed that the nRT-PCR assay designed in this study was able to detect NoV GII strains from 6 of the 12 genetic clusters proposed by Vinje et al. (50).