Genetic analysis of G12P[8] rotaviruses detected in the largest U.S. G12 genotype outbreak on record

- Rochester outbreak G12P[8] strains resemble currently circulating G12P[8] strains.
- Unique nucleotide sequences were identified in the VP7 and VP4 genes.
- Nucleotide substitutions produced amino acid changes in the VP4 gene of 6 strains.
- Selection analyses indicated that positive section was occurring at one VP7 site.
- Purifying selection also appears to be operating in the VP7 and VP4 genes.

In 2006-07, 77 cases of gastroenteritis in Rochester, NY, USA were associated with rotavirus genotype G12P[8]. Sequence analysis identified a high degree of genetic relatedness among the VP7 and VP4 genes of the Rochester G12P[8] strains and between these strains and currently circulating human G12P[8] strains. Out of 77 samples, two and seven unique nucleotide sequences were identified for VP7 and VP4 genes, respectively. Rochester strain VP7 genes were found to occupy the G12-III lineage and VP4 genes clustered within the P[8]-3 lineage. Six strains contained non-synonymous nucleotide substitutions that produced amino acid changes at 6 sites in the VP8∗ region of the VP4 gene. Two sites (amino acids 242 and 246) were located in or near a described trypsin cleavage site. Selection analyses identified one positively selected VP7 site (107) and strong purifying selection at 58 sites within the VP7 gene as well as 2 of the 6 variant sites (79 and 218) in VP4.