Sequence analysis of the NSP4 gene from human rotavirus strains isolated in the United States

Two major and one minor genotype of the rotavirus NSP4 gene have been descr ibed. The sequences of 29 NSP4 genes from rotavirus isolates obtained in th e United States during the 1996-1997 rotavirus season (types P[8]G1, P[8]G9 , P[4]G2 and P[6]G9) and 10 strains isolated during previous rotavirus seas ons (types P[8]G1 and P[4]G2) were determined. All NSP4 genes from strains with short E types (6 P[4]G2, 4 P[6]G9) belonged to genotype NSP4A, whereas all 19 strains with long E types (16 P[8]G1, 3 P[8]G9) had NSP4 genes of g enotype NSP4B. Genetic variation within genotypes was low (less than or equ al to 2.3% for both NSP4A and NSP4B), confirming that the NSP4 genes are hi ghly conserved. Nonetheless, at least two distinct sub-lineages could be de tected within each genotype: strains isolated in the same year, regardless of geographic location, were more closely related or even identical at the deduced amino acid level; strains isolated in different years were more dis tinct. Thus, geographic distance did not affect genetic distance. Northern hybridization analysis with NSP4A and NSP4B total gene probes failed to det ect any unusual combinations of the VP6 and NSP4 genes in 31 additional iso lates from the 1996-1997 rotavirus season.