Coexistence of multiple genotypes, including newly identified genotypes, in outbreaks of gastroenteritis due to Norovirus in Japan

Abstract

Norovirus (NV) (formerly called Norwalk-like virus) is the most common cause of acute nonbacterial gastroenteritis in humans. Recently, we reported an NV genotyping scheme based on variability in the capsid N-terminal/shell (N/S) domain gene (Katayama et al., Virology 299:225-239, 2002). We found 19 genotypes, including nine of genogroup I and 10 of genogroup II. In the present study, we investigated the molecular epidemiology of NV from 66 outbreaks that occurred in Saitama Prefecture, Japan, from 1997 to 2002. We screened 416 stool specimens by a real-time reverse transcription (RT)-PCR method (Kageyama et al., J. Clin. Microbiol. 41:1548-1557, 2003) and detected 156 NV-positive specimens, from which we amplified the capsid N/S domain gene by RT-PCR and then cloned the PCR products. After sequencing these clones, we obtained 368 sequence variants (strains). By applying our classification scheme to the strains from Saitama and other published strains, we identified a total of 31 genotypes, including an additional five genotypes for genogroup I and seven for genogroup II. Of the 31 genotypes, 26 were present in the Saitama area during that time period. These results provide additional evidence for the great diversity of human NV genotypes. Specimens from all shellfish-related infections contained multiple genotypes, including several new genotypes. On the other hand, single genotypes were observed mostly in outbreaks that originated in semiclosed communities. Thus, the number of NV genotypes in each outbreak depended on the route of transmission.

FIG. 1.

Phylogenetic dendrograms based on the capsid N/S domain gene of NV. Phylogenetic dendrograms were generated separately for GI (A) and GII (B). The numbers on each branch indicate the bootstrap values for the clusters supported by that branch. Letters in italics designate the reference strains. Cryptograms indicating the location or strain name/(isolate)/year/country are given for key strains. Putative genotypes are indicated for each cluster. The numbering of genotypes GI/1 to GI/7 and GII/1 to GII/7 was changed from the previously published list (19) and is based on Fields Virology (8). GI/10 to GI/14, GII/9 to GII/11, and GII/13 to GII/16 (boxed) are genotypes newly identified in this study. Genotypes with an asterisk were present in the Saitama area in 1997 to 2002.

FIG. 1.

Phylogenetic dendrograms based on the capsid N/S domain gene of NV. Phylogenetic dendrograms were generated separately for GI (A) and GII (B). The numbers on each branch indicate the bootstrap values for the clusters supported by that branch. Letters in italics designate the reference strains. Cryptograms indicating the location or strain name/(isolate)/year/country are given for key strains. Putative genotypes are indicated for each cluster. The numbering of genotypes GI/1 to GI/7 and GII/1 to GII/7 was changed from the previously published list (19) and is based on Fields Virology (8). GI/10 to GI/14, GII/9 to GII/11, and GII/13 to GII/16 (boxed) are genotypes newly identified in this study. Genotypes with an asterisk were present in the Saitama area in 1997 to 2002.