Norovirus Deep sequencing.

Norovirus (NoV) is the most common cause of non-bacterial gastroenteritis and is a major agent associated with foodborne and hospital outbreaks of gastroenteritis.. Therefore, fast and reliable identification of transmission routes is necessary to initiate appropriate intervention strategies in order to prevent further spread. Conventional molecular analysis of NoV transmission routes relies mainly on standard typing methods (STM) based on Sanger-sequencing from only a limited part of the NoV genome, which could lead to wrong conclusions. Here, we combined a NoV capture method with next generation sequencing (NGS) which increased the proportion of norovirus reads by ?40 fold. This approach allowed for the identification of 14 complete and one partial genotypes compared with 10 and five for the STM from 15 samples from 6 outbreaks with a single NoV genotype and allowed for the detection of one additional genotype in two mixed genotype outbreaks. In addition, the NGS approach also generated complete or partial sequences from the P2 hypervariable region from 6 of 8 outbreaks and allowed for the identificationof a new NoV recombinant. This approach could therefore strengthen outbreak investigations and could be applied to other.important viruses in stool samples such as hepatitis A and enterovirus.