Genetic variability of respiratory syncytial viruses (RSV) prevalent in Southwestern China from 2006 to 2009: emergence of subgroup B and A RSV as dominant strains

Abstract

Respiratory syncytial virus (RSV) is the most commonly identified viral agent in young children with acute respiratory tract infections (ARIs) and often causes repeated infections throughout life. This study investigated the genetic variability of the attachment (G) protein gene among RSV strains prevalent in southwestern China. Reverse transcription-PCR (RT-PCR) for a fragment of the RSV G gene was performed with nasopharyngeal aspirates (NPAs) collected from children with ARIs hospitalized in Chongqing Children's Hospital, Chongqing, China. A total of 1,387 NPA specimens were collected from April 2006 to March 2009, and 439 (31.7%) were positive for RSV. During the study period, subgroup A and B viruses accounted for 79.5% (349/439) and 19.8% (87/439) of the total positive samples, respectively. Both subgroup A and B viruses were identified in three samples. Subgroup A viruses were predominant during two epidemic seasons (2006 to 2008), while subgroup B strains prevailed during the 2008-2009 epidemic season. Phylogenetic analyses showed that all 30 group A strains could be clustered into one genotype, genotype GA2, and 30 group B strains could be clustered into three genotypes, genotypes GB1, GB3, and BA, among which 17 genotype BA strains were detected from 23 group B strains selected during the 2008-2009 epidemic season. The G gene of genotype BA was predicted to encode proteins of five different lengths. These data suggest that group A RSV likely predominated in southwestern China and that a new genotype of subgroup B with a 60-nucleotide insertion, named BA-like virus, became the dominant genotype in the 2008-2009 epidemic season.

FIG. 1.

(A) Seasonal distribution of group A and B HRSV strains in infants and children with acute lower respiratory tract infection in Chongqing, China, between April 2006 and March 2009. (B) Monthly distribution of subgroup B genotypes of HRSV in Chongqing, China, between April 2006 and March 2009.

FIG. 2.

Phylogenetic trees of Chinese RSV group A (A) and group B (B) nucleotide sequences from the second variable region of the gene encoding the G protein. The numbers at the branch nodes represent the number of bootstrap probabilities. Reference sequences for each genotype (genotypes GA1 to GA7, SAA1, GB1 to GB4, SAB1, and SAB3) were obtained from GenBank. Additional sequences from around the world were included in the comparison by selecting representatives of distinct clusters found in previous studies and selecting isolate sequences from GenBank that gave the best hits in BLAST searches with each of the Chinese clusters. Prototype strains (strain A2 for group A and strain CH18537 for group B) were used as the outgroup sequences in the tree. The genotype assignment is indicated by the braces on the right.

FIG. 3.

Amino acid alignment of the G protein of Chinese group A (A) and group B (B) strains. Alignments relative to the sequences of prototype strains A2 and CH18537 are shown. The relative lengths (in number of amino acids [aa]) for these regions are indicated in parentheses on the right.