Development of a simplified and cost effective norovirus capsid typing method using next generation sequencing

Abstract: Human noroviruses are a major cause of acute gastroenteritis worldwide and can betransmitted through consumption of contaminated raw food. Shellfish like oysters can becontaminated by human sewage during production and accumulate multiple Norovirus strainsin low concentrations. Here we developed a simplified and cost effective targetedmetagenomic approach by sequencing PCR amplicons with next generation sequencing(NGS) of the capsid (VP1) viral gene. New design of reverse primers using the codehopstrategy and direct addition of illumina adapter with one step RT-PCR and sequencing onnano chip reduced hand on time and cost of the analysis. A mix of faecal samples and oystersamples associated with outbreaks were used to evaluate the ability and limitations in theidentification of strains from Norovirus genogroup I (GI) and genogroup II (GII). Withsamples containing only one genotype the method was able to identify all strains. Usingartificially mixed samples the method was able to identify almost all strains except a few GIIat low concentrations. Oyster samples showed more limitations for the method and it waswere only able to identify the strain in some of the samples but did find multiple GI strains inmore than one sample. Despite some limitations, the simplified method for VP1-targetedmetagenomics is a sensitive approach allowing the study of norovirus diversity incontaminated oysters and the identification of norovirus strains implicated in outbreaks. Thisat a lower cost and hands on time compared to published methods.