Distribution of norovirus genotypes and subtypes in river water by ultra-deep sequencing-based analysis.

To determine the distribution of Norovirus (NoV) genotypes in natural river water in Thailand, we conducted a genome analysis using a next-generation sequencer. Twenty-five river water samples were collected at five different sites of the Khlong Klon River in the suburbs of Bangkok between August 2013 and December 2014. The partial genome of NoV was detected in 15 of the 25 samples (60·0%). Seven of these 15 samples (46·7%) contained multiple NoV GII genotypes: GII.4, GII.6, and GII.17. Our data showed that GII.17 had already emerged in August 2013 as a minor population, and it became a major genotype in December 2014. Our findings indicate that the virus was likely to have been circulating in the community before it appeared in the river water. SIGNIFICANCE AND IMPACT OF THE STUDY: Our study was to investigate the frequencies of multiple genogroups and genotypes of norovirus in the river water near Bangkok, Thailand, by ultra-deep sequencing-based analysis. This study revealed that the epidemic strain was likely to have been circulating in the community before it appeared in the river water. Monitoring of the Norovirus (NoV) genomes in the natural environment may contribute to an understanding of the emergence of new epidemic NoV strains in human populations.

Molecular detection and characterization of noroviruses in river water in Thailand.

UNLABELLED: Norovirus (NoV) generally exists as a mixture of multiple genotype variants in nature. However, there has been no published report monitoring NoV in natural settings in Thailand. To obtain information on mixed presence of the NoV RNA genome, we conducted viral genome analysis of 15 water specimens collected from five sites in a river near Bangkok between August 2013 and August 2014. The number of viral RNA copies per specimen declined progressively from the most upstream to the most downstream site. Following direct nucleotide sequencing of the PCR products, we obtained three partial genome sequences of the NoV GI strain and 13 partial genome sequences of the NoV GII strains. Phylogenetic analysis indicated the presence of four GII.4 variant groups pro-circulated after the Den Haag_2006b, New Orleans_2009 and Sydney_2012 outbreaks. On the other hand, only GI.4 was observed from the specimens collected on April, 2014. These results indicated that multiple genogroups and genotypes of noroviruses are present and are circulating in the natural environment in Thailand as in other countries. Our study provides comprehensive information on the occurrence of new variants. SIGNIFICANCE AND IMPACT OF THE STUDY: Our study is the first paper that multiple genogroups and genotypes of norovirus exist, and are circulating in the river water near Bangkok, Thailand. Phylogenetic analysis indicated the presence of four GII.4 variant groups pro-circulated after the Den Haag_2006b, New Orleans_2009 and Sydney_2012 that caused outbreaks in the world. Continued research will be essential for understanding the natural history of NoV and the control of future outbreaks.