Detection of norovirus epidemic genotypes in raw sewage using next generation sequencing

Tulio M Fumian; Julia M Fioretti; Jennifer H Lun; Ingrid A L Dos Santos; Peter A White; Marize P Miagostovich

doi:10.1016/j.envint.2018.11.054

Detection of norovirus epidemic genotypes in raw sewage using next generation sequencing

Environ Int. 2019 Feb:123:282-291. doi: 10.1016/j.envint.2018.11.054. Epub 2018 Dec 12.

Authors

Tulio M Fumian¹, Julia M Fioretti², Jennifer H Lun³, Ingrid A L Dos Santos², Peter A White³, Marize P Miagostovich²

Affiliations

¹ Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Rio de Janeiro, RJ, Brazil. Electronic address: tuliomf@ioc.fiocruz.br.
² Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Rio de Janeiro, RJ, Brazil.
³ Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.

PMID: 30553201
DOI: 10.1016/j.envint.2018.11.054

Abstract

Noroviruses are a leading cause of epidemic and pandemic acute gastroenteritis (AGE) worldwide, and contaminated food and water are important routes for its transmission. Raw sewage has been used for viral surveillance to monitor the emergence of new norovirus strains with the potential to cause epidemics. In this study, we investigated norovirus occurrence and norovirus RNA levels in 156 samples collected from May 2013 to May 2014, across three different stages (52 samples each) of a wastewater treatment plant (WWTP) in Rio de Janeiro, Brazil. We also explored norovirus GII diversity in raw sewage samples by next-sequencing generation (NGS). In addition, we examined norovirus prevalence and molecular epidemiology from acute gastroenteritis cases. Using RT-qPCR, norovirus GI and GII was detected in 38.5% and 96.1% of raw sewage samples, 40.4% and 96.1% of primary effluent samples and 1.9% and 5.8% of final effluent samples, respectively. Norovirus RNA levels varied from 4 to 6.2 log₁₀ genome copies per litre (gc L^-1) for GI and from 4.4 to 7.3 log₁₀ gc L^-1 for GII. Using MiSeq NGS, we identified 13 norovirus genotypes over the one-year period, with six dominant capsid genotypes, including GII.4, GII.17, GII.5, GII.2, GII.3 and GII.1. GII.4 noroviruses were the most prevalent in wastewater samples (68.5%), and a similar trend was observed in AGE cases (71%). The emergent GII.17 was the second most prevalent genotype (14.3%) identified in the raw sewage samples, however, it was not detected in clinical cases. Due to the high burden of norovirus outbreaks and the lack of vaccine and antiviral drugs, it is essential to understand the genotypic diversity of norovirus at the population level. Complementary data obtained from both clinical and environmental (sewage) samples proved to be an effective strategy to monitor the circulation and emergence of norovirus epidemic genotypes.

Keywords: Environmental surveillance; Next-generation sequencing; Noroviruses; Phylogenetic analysis; Wastewater.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Brazil
Caliciviridae Infections / epidemiology
Caliciviridae Infections / virology
Disease Outbreaks
Epidemics
Gastroenteritis / epidemiology
Gastroenteritis / virology
Genotype
High-Throughput Nucleotide Sequencing
Humans
Molecular Epidemiology
Norovirus / genetics
Norovirus / isolation & purification*
Phylogeny
RNA, Viral
Real-Time Polymerase Chain Reaction
Sewage / virology*
Wastewater / virology

Substances

RNA, Viral
Sewage
Waste Water