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.