Abstract:In order to explore the reason of RSV molecular variation and severer pathogenicity at the molecular level, we cloned the RNA3 and RNA4 cDNA fragments of RSV-SD-JN2 by reverse transcriptase-polymerase chain reaction (RT-PCR) and sequenced them. The results showed that the length of RNA3 and RNA4 of SD-JN2 were 2487bp and 2157bp respectively; the NS3 gene, IR and CP gene in RNA3 were 636bp, 725bp and 969bp, respectively; the SP gene, and IR and NSvc4 in RNA4 was 537bp, 654bp, 861bp, respectively. Compared with the c sequences of the RSV isolates that had been reported previously with different periods, different areas, different pathogenicity, we found that the highly conserved regions located in 5‘ and 3‘ untranslated regions, which had only few base difference; the coding regions was also very conserved, and the homology of the nucleotide sequence was more than 93%, while the amino acid sequence was more than 97%, and most of the mutations were nonsense mutation; however, the most variable regions located in the intergenic region (IR). The molecular variation of RSV has nearly relation to its geographical distribution. The variability of RNA4 IR leaded to heighten of RNA secondary structures-hairpin structures stability, which was an important reason of severer pathogenicity.