Ten Years of Global Evolution of the Human Respiratory Syncytial Virus BA Genotype with a 60-Nucleotide Duplication in the G Protein Gene

The emergence of natural isolates of human respiratory syncytial virus group B (HRSV-B) with a 60-nucleotide (nt) duplication in the G protein gene in Buenos Aires, Argentina, in 1999 (A. Trento et al., J. Gen. Virol. 84:3115-3120, 2003) and their dissemination worldwide allowed us to use the duplicated segment as a natural tag to examine in detail the evolution of HRSV during propagation in its natural host. Viruses with the duplicated segment were all clustered in a new genotype, named BA (A. Trento et al., J. Virol. 80:975-984, 2006). To obtain information about the prevalence of these viruses in Spain, we tested for the presence of the duplicated segment in positive HRSV-B clinical samples collected at the Severo Ochoa Hospital (Madrid) during 12 consecutive epidemics (1996-1997 to 2007-2008). Viruses with the 60-nt duplication were found in 61 samples, with a high prevalence relative to the rest of B genotypes in the most recent seasons. Global phylogenetic and demographic analysis of all G sequences containing the duplication, collected across five continents up until April 2009, revealed that the prevalence of the BA genotype increased gradually until 2004-2005, despite its rapid dissemination worldwide. After that date and coinciding with a bottleneck effect on the population size, a relatively new BA lineage (BA-IV) replaced all other group B viruses, suggesting further adaptation of the BA genotype to its natural host.Human respiratory syncytial virus (HRSV), a member of the Pneumovirus genus within the Paramyxoviridae family, is recognized as the leading agent responsible for severe respiratory infections in the pediatric population (31, 34, 35) and a pathogen of considerable importance in vulnerable adults (23, 24). The global respiratory syncytial virus (RSV) disease burden is estimated at 64 million cases and 160,000 deaths every year (70). This virus causes regular seasonal epidemics which take place during the winter months in temperate countries or during the rainy season in tropical areas (12). A peculiar aspect of HRSV is that the immune response produced by infection does not confer long-lasting protection, which is why reinfections are common throughout life (30).Neutralization tests performed with hyperimmune serum (16) and reactivity with specific monoclonal antibodies (4, 45) were used to classify HRSV isolates into two antigenic groups, A and B, which correlated with genetically distinct viruses (18). The main differences between these two groups are located in the major attachment G protein. This protein is a type II glycoprotein that shares neither sequence nor structural features with the attachment proteins (HN or H) of other paramyxoviruses (69), and it represents one of the targets of the immune response (27, 43). The full-length membrane-bound G protein (Gm) of 292 to 319 amino acids (depending on the viral strain) is also expressed in a secreted version (Gs) that lacks the transmembrane domain due to alternative initiation of translation at a second in-frame AUG codon in the G open reading frame (M48) (52). The G protein is the viral gene product with the highest degree of antigenic and genetic diversity among viral isolates (4, 18, 28, 45). Most changes are concentrated in two hypervariable regions that flank a highly conserved central region of the G protein ectodomain, which includes a cluster of four cysteines and the putative receptor binding site (43). It has been suggested that antigenic differences within this protein could facilitate repeated HRSV infections (37, 59). In addition, positive selection of amino acid changes was observed in the two hypervariable regions of the G protein ectodomain (7, 43, 71, 73, 74). One of the hypervariable regions, located in the C-terminal one-third of the G molecule, contains multiple epitopes recognized by monoclonal antibodies (43), suggesting that immune selection of new variants by antibodies may contribute to generation of HRSV diversity.Phylogenetic studies based on sequence analysis of the G protein have identified numerous genotypes in the antigenic groups A and B that show complex circulation patterns, since multiple genotypes of both antigenic groups may circulate within the same season and community, with one or two dominant genotypes being replaced in successive years (13, 14, 26, 27, 32, 49, 50). Each community shows a seasonal circulation pattern of genotypes, probably determined by local factors, such as the level of herd immunity to certain strains (3, 14, 49).The capacity of the G protein to accommodate drastic sequence changes was illustrated best by three antigenic group B viruses isolated in Buenos Aires, Argentina, in 1999 that contained a duplication of 60 nucleotides (nt) in the C-terminal third of the G protein gene (63). The global dissemination of these viruses allowed us to use the duplicated segment as a natural tag to reexamine the evolution of HRSV during propagation in its natural host. Phylogenetic analysis of G sequences revealed that all viruses with the duplicated segment clustered in a new genotype, named BA, and this finding supported the idea of a common ancestor for all viruses with the 60-nt duplication, dated about 1998 (64). The limited information about the molecular epidemiology of HRSV in Spain, together with an increase in G sequences with the duplicated segment reported worldwide, prompted us to conduct both a local search in Madrid for these viruses and a global phylogenetic analysis of HRSV with the 60-nt duplication from the time that these viruses were first detected, taking into account the geographic and temporal distribution of each isolate.