Nucleotide sequence of the fusion and phosphoprotein genes of human respiratory syncytial (RS) virus Long strain: evidence of subtype genetic heterogeneity.

The nucleotide and deduced amino acid sequences of the fusion (F) and phosphoprotein (P) genes of the Long strain of human respiratory syncytial (RS) virus have been determined from cDNA copies cloned into pBSV9 shuttle vector. Comparison of these sequences with their counterparts of other strains reveals genetic heterogeneity within the same subtype. The percentage of nucleotide and amino acid changes occurring in both proteins is similar. Thus, the Long F and P proteins share 97.9% and 98.3% amino acid identity, respectively, with their homologs of the A2 strain. Nevertheless the F2 subunit of the fusion protein accumulates 3.1 times more amino acid changes than the F1 subunit. In addition, the percentage of nucleotide changes in the 3' extracistronic sequences is 6 times higher in the P than in the F gene. These results are discussed in terms of selective pressures operating in the evolution of RS virus in nature.