Prevalence and genetic characterization of caliciviruses among children hospitalized for acute gastroenteritis in the United States.

Human calicivirus was the first recognized viral agent causing gastroenteritis in humans. Norovirus (NV) and Sapovirus (SV), two genera within the Caliciviridae family, cause epidemic and endemic acute gastroenteritis in children and adults. The role of these viruses as a cause of sporadic acute gastroenteritis in young children requiring hospitalization is not well established. The aim of this study was to assess the prevalence and genetic diversity of caliciviruses among children hospitalized with symptoms of acute gastroenteritis. Stool samples were collected over 2 years from symptomatic children (N=1840) up to 5 years of age at three pediatric hospitals in the US. Overall, 156 (8.5%) samples were CV-positive, 131 (7.1%) confirmed by sequencing to be NV and 25 (1.4%) confirmed to be SV. Sequences of RT-PCR-amplified polymerase gene segments were analyzed using distance, maximum likelihood and parsimony algorithms. Phylogenetic analysis of 97 NV sequences showed that seven strains were in genogroup I, 86 strains were in genogroup II and four strains were not in genogroup I, II, or III, likely representing three new NV genogroups IV, VI and VII. Genogroup I and genogroup II strains were in 12 new genetic clusters, three in genogroup I and nine in genogroup II. Within genogroups I and II, most (98%) NV strains were in genetic clusters with no known prototype in GenBank. Phylogenetic analysis of 24 SV strains showed that half grouped with the London/92 strain in one genogroup and the remainder in three other proposed genogroups, one novel. In conclusion, NV and SV were frequent causes of hospitalization for acute gastroenteritis in young children and infecting strains were highly diverse, including newly recognized genogroups and genetic clusters within known genogroups.