Phylogenetic analysis of RSV
Among the confirmed RSV samples, only 48 were amplified during the heminested PCR targeting the 2nd HVR of the G protein. The remaining 74 samples (37 RSV-A, 35 RSV-B and 2 co-infection) that failed to amplify were not included for sequencing and phylogenetic analysis, and were classified as untypable. Failure in the amplification of viral genomic fragments during the conventional PCR may be due to the variation in primer binding sites.
Phylogenetic trees were constructed for 35 RSV-A and 14 RSV-B strains by including 45 (23 RSV-A and 20 RSV-B) Philippine strains from previous studies [11] and 97 ( 46 RSV-A and 51 RSV-B) from other countries by BLASTn search. Philippine RSV-A strains in this study were distributed into four clusters NA1, ON1, GA2 and GA5. Philippine NA1 and ON1 strains clustered with previously reported circulating strains in the Philippines and other countries. Philippine GA2 strains clustered with strains from Brazil and HongKong whereas,, the Philippine GA5 strain clustered with strains from Malaysia and USA. Majority of the Philippine RSV-A strains were identified as NA1 genotype (27/122, 22.1%). Respectively, the following RSV-A genotypes were identified: ON1 (5/122, 4.1%), GA2 (2/122, 1.6%) and GA5 (1/122, 0.8%).
All Philippine RSV-B strains in this study clustered under the BA strains with 60-nucleotide duplication. Most of the Philippine BA strains were identified as BA9 genotype (13/122, 10.6%) except for one (1/122, 0.8%) that was identified as BA2. Philippine BA2 strains clustered under strains from Japan, Thailand and Malaysia whereas Philippine BA9 strains under strains from Malaysia and Colombia.