Respiratory syncytial virus heterogeneity during an epidemic: analysis by limited nucleotide sequencing (SH gene) and restriction mapping (N gene).

The genes encoding the small hydrophobic (SH) proteins of a series of respiratory syncytial (RS) virus strains were amplified using the polymerase chain reaction, cloned and sequenced. Analysis of the SH gene sequences from 12 RS virus strains isolated between 1956 and 1989 confirmed the homogeneity of the two subgroups. A and B, previously defined serologically. Although there is only 76% deduced amino acid sequence identity of SH proteins between subgroups, there was little variation in deduced amino acid sequences within the subgroups; nucleotide homologies within the subgroups ranged between 93% and 99%. Forty-two isolates of RS virus from a single epidemic season (autumn/winter 1989) were also examined to determine their relatedness. For these isolates regions of both the SH and nucleocapsid protein genes of each isolate were amplified and these regions were further analysed by direct nucleotide sequencing or restriction mapping. It was possible to discriminate at least six different lineages (or substrains) of RS virus circulating at the same time and in the same locality.