Circulation of human respiratory syncytial virus strains among hospitalized children with acute lower respiratory infection in malaysia

Abstract

Human respiratory syncytial virus (RSV) is a major viral pathogen associated with acute lower respiratory tract infections (ALRTIs) among hospitalized children. In this study, the genetic diversity of the RSV strains was investigated among nasopharyngeal aspirates (NPA) taken from children less than 5 years of age hospitalized with ALRTIs in Hospital Serdang, Malaysia. A total of 165 NPA samples were tested for the presence of RSV and other respiratory viruses from June until December 2009. RSV was found positive in 83 (50%) of the samples using reverse transcription polymerase chain reaction (RT-PCR). Further classification of 67 RSV strains showed that subgroups A and B comprised 11/67 (16.4%) and 56/67 (83.6%) of the strains, respectively. The second hypervariable region at the carboxyl-terminal of the G gene was amplified and sequenced in order to do phylogenetic study. The phylogenetic relationships of the samples were determined separately for subgroups A and B using neighbor joining (NJ), maximum parsimony (MP), and Bayesian inference (BI). Phylogenetic analysis of the 32 sequenced samples showed that all 9 RSV-A strains were clustered within NA1 genotype while the remaining 23 strains of the RSV-B subgroup could be grouped into a clade consisted of strains with 60-nucleotide duplication region. They were further classified into newly discovered BA10 and BA9 genotypes. The present finding suggests the emergence of RSV genotypes of NA1 and BA. This is the first documentation of the phylogenetic relationship and genetic diversity of RSV strains among hospitalized children diagnosed with ALRTI in Serdang, Malaysia.

Keywords: Malaysia; acute lower respiratory tract infections (ALRTIs); human respiratory syncthial virus (RSV).

Figure 1

Phylogenetic tree for RSV group A nucleotide sequences based on the second variable region of the G protein (270 bp) constructed by the Bayesian analysis method using MrBayes 3.0 software. Notes: Nodes represent posterior probability/maximum parimony/neighbor-joining bootsratpe values. Numbers at the branches are bootstrap values determined for 1000 replicates. A bootstrap value of more than 50% was depicted in the tree. The representative sequences for each genotype (GA1-7, SAA1, and NA1) were retrieved from GenBank and included in the tree. UPM strains are indicated in dark triangles. Strain Long was used as the outgroup sequences. The asterisks represent bootstrap value equal 100%. The genotypes are shown on the right.

Figure 2

Phylogenetic tree for RSV group B nucleotide sequences based on the second variable region of the G protein (270 and 330 bp) constructed by the Bayesian analysis method using MrBayes 3.0 software. Notes: Nodes represent posterior probability/maximum parimony/neighbor-joining bootstrap values. Numbers at the branches are bootstrap values determined for 1000 replicates. A bootstrap value of more than 50% was depicted in the tree. The representative sequences for each genotype (GB1-4, SAB1-3, and BA1-10) were retrieved from GenBank and included in the tree. UPM strains are indicated in dark triangles. Strain CH18537 was used as the outgroup sequences. The asterisks represent bootstrap value equal 100%. Strain CH18537 was used as the outgroup sequences. The genotypes are shown on the right.

Figure 3

Deduced AA alignment of the second hypervariable region of the G protein gene of RSV A for 9 UPM detected strains and 5 retrieved GeneBank sequences. Notes: The amino acids shown correspond to the second variable region of the G protein strain Long for the subgroup A. Identical residues are shown by dots. Stop codons are indicated by asterisks. Length numbers indicate the position of resides relative to positions 222 to 298 of the Long strain.

Figure 4

Deduced AA alignment of the second hypervariable region of the G protein gene of RSV B for 7 representative UPM strains and 5 retrieved GeneBank sequences. Notes: The amino acids shown correspond to the second variable region of the G protein strain BA prototype strain JN119966 for the group B. Identical residues are shown by dots. Stop codons are indicated by asterisks. Length numbers indicate the position of resides relative to positions 213 to 315 of the BA prototype strain JN119966. Box denotes the 60 nt duplication in BA strains.