Human norovirus (NoV) has been studied extensively as the cause of gastroenteritis outbreaks worldwide, but only a fraction of NoV studies have examined the virus distribution in the estuarine environment: including NoV presence in oyster, water, and plankton samples. Here we evaluated two silica-based viral RNA extraction protocols and two norovirus realtime TaqMan RT-PCR assays for the detection of norovirus in shellfish and plankton. The optimized method, a combination of a rapid RNA extraction followed by a TaqMan RT-PCR assay, assisted in detecting 21 NoV-positive samples from the 225 environmental samples analyzed. Twenty-four percent, 28.6%, 31.0%, and 9.5% were from oyster, water, the small plankton fraction, and the large plankton fraction samples and the majority of these samples (90.5%) were from genogroup I. The quantities of NoV found in plankton, water, and oysters provides clues about the presence and distribution of human NoV in the estuarine environment.
