Application of whole-genome sequencing for norovirus outbreak tracking and surveillance efforts in Orange County, CA

Anthony J Silva; Zhihui Yang; Julia Wolfe; Kirsten A Hirneisen; Shannon B Ruelle; Angelica Torres; Donna Williams-Hill; Michael Kulka; Rosalee S Hellberg

doi:10.1016/j.fm.2021.103796

Application of whole-genome sequencing for norovirus outbreak tracking and surveillance efforts in Orange County, CA

Food Microbiol. 2021 Sep:98:103796. doi: 10.1016/j.fm.2021.103796. Epub 2021 Mar 26.

Authors

Anthony J Silva¹, Zhihui Yang², Julia Wolfe³, Kirsten A Hirneisen⁴, Shannon B Ruelle⁴, Angelica Torres³, Donna Williams-Hill⁴, Michael Kulka², Rosalee S Hellberg⁵

Affiliations

¹ Chapman University, Schmid College of Science and Technology, Food Science Program, One University Drive, Orange, CA, 92866, USA.
² US Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Division of Molecular Biology, 8301 Muirkirk Road, MOD 1, Laurel, MD, 20708, USA.
³ Orange County Health Care Agency, Public Health Laboratory, Santa Ana, CA, 92706, USA.
⁴ US Food and Drug Administration, Office of Regulatory Affairs, Office of Regulatory Science, Pacific Southwest Food and Feed Laboratory, 19701 Fairchild Rd, Irvine, CA, 92612, USA.
⁵ Chapman University, Schmid College of Science and Technology, Food Science Program, One University Drive, Orange, CA, 92866, USA. Electronic address: hellberg@chapman.edu.

PMID: 33875224
DOI: 10.1016/j.fm.2021.103796

Abstract

Noroviruses are the leading cause of acute gastroenteritis and foodborne illness in the United States. Traditional Sanger sequencing of short genomic regions (~300-600 bp) is the primary method for differentiation of this pathogen; however, whole-genome sequencing (WGS) offers a valuable approach to further characterize strains of this virus. The objective of this study was to investigate the ability of WGS compared to Sanger sequencing to differentiate norovirus strains and enhance outbreak investigation and surveillance efforts. WGS results for 41 norovirus-positive stool samples from 15 different outbreaks occurring from 2012 to 2019 in Orange County, CA, were analyzed for this study. All samples were genotyped with both WGS and Sanger sequencing based on the B-C region. WGS generated nearly full-length viral genome sequences (7029-7768 bp) with 4x to 35,378x coverage. Phylogenetic analysis of WGS data enabled differentiation of genotypically similar strains from separate outbreaks. Single nucleotide variation (SNV) analysis on a subset of strains revealed nucleotide variations (15-79 nt) among isolates from multiple outbreaks of GII.4 Sydney_2015[P31] and GII.17[P17]. Overall, the results demonstrated that coupling norovirus genotype identification with WGS enables enhanced genetic differentiation of strains and provides valuable information for outbreak investigation and surveillance efforts.

Keywords: Genotyping; Norovirus; Sanger sequencing; Surveillance; Whole-genome sequencing.

MeSH terms

Caliciviridae Infections / epidemiology
Caliciviridae Infections / virology*
California / epidemiology
Disease Outbreaks
Gastroenteritis / epidemiology
Gastroenteritis / virology*
Genome, Viral
Genotype
Humans
Norovirus / classification
Norovirus / genetics
Norovirus / isolation & purification*
Norovirus / physiology
Phylogeny
RNA, Viral / genetics
Whole Genome Sequencing

Substances

RNA, Viral