BA9 lineage of respiratory syncytial virus from across the globe and its evolutionary dynamics

Abstract

Respiratory syncytial virus (RSV) is an important pathogen of global significance. The BA9 is one of the most predominant lineages of the BA genotype of group B RSV that has acquired a 60bp duplication in its G protein gene. We describe the local and global evolutionary dynamics of the second hyper variable region in the C- terminal of the G protein gene of the BA9 lineage. A total of 418 sequences (including 31 study and 387 GenBank strains) from 29 different countries were used for phylogenetic analysis. This analysis showed that the study strains clustered with BA (BA9 and BA8) and SAB4 genotype of group B RSV. We performed time-scaled evolutionary clock analyses using Bayesian Markov chain Monte Carlo methods. We also carried out glycosylation, selection pressure, mutational, entropy and Network analyses of the BA9 lineage. The time to the most recent common ancestor (tMRCA) of the BA genotype and BA9 lineage were estimated to be the years 1995 (95% HPD; 1987–1997) and 2000 (95% HPD; 1998–2001), respectively. The nucleotide substitution rate of the BA genotype [(4.58×10−3 (95% HPD; 3.89–5.29×10−3) substitution/site/year] was slightly faster than the BA9 lineage [4.03×10−3 (95% HPD; 4.65–5.2492×10−3)]. The BA9 lineage was categorized into 3 sub lineages (I, II and III) based on the Bayesian and Network analyses. The local transmission pattern suggested that BA9 is the predominant lineage of BA viruses that has been circulating in India since 2002 though showing fluctuations in its effective population size. The BA9 lineage established its global distribution with report from 23 different countries over the past 16 years. The present study augments our understanding of RSV infection, its epidemiological dynamics warranting steps towards its overall global surveillance.

Epidemiology and genetic variability of respiratory syncytial virus in Portugal, 2014–2018

“…The alignment of the predicted amino acid sequences of strains from BA9, NA1 and ON1 genotypes confirmed the relatively high genetic variability associated with the HVR2. Strains from both of subtypes showed common changes, conserved N-glycosilation sites and subtitutions leading to loss or gain of these sites that had been previously reported [11,40,41,45,46,49,50,[54][55][56][57][58][59]. Within RSV-A strains, the number of substitutions among ON1 strains was higher compared with its NA1 counterparts.…”

“…In Portugal, ON1 genotype was detected during the 2011/12 season for the first time [27], and since then, it has predominated in the country as reported worldwide [48,49]. Regarding RSV-B genetic diversity, all belonged to BA genotype, which has already been detected in at least 23 countries [50]. BA9 genotype has predominated in Portugal since 2010 [27,42] as in other countries [10,45,49,51], being detected alongside with BA10 genotype until 2015/16, when BA9 remained the only genotype detected onwards.…”

Respiratory syncytial virus B sequence analysis reveals a novel early genotype

“…Reference sequences were selected through an extensive search of the literature. First, we identified 736 sequences included in 22 articles published between 2003 to 2018 as genotype references 5,6,10,[13][14][15][16][23][24][25][26]33,[43][44][45][46][47][48][49][50][51][52] ; subsequently, these were assessed to verify concordance in genotype assignment; some sequences could not be identified or traced due to assignment of IDs different from strain names or Gen-Bank accession numbers. A total of 691 of these 736 sequences were traceable.…”

A Contemporary View of Respiratory Syncytial Virus (RSV) Biology and Strain-Specific Differences

“…While nearly all studies evaluating recent clinical isolates have focused on genetic variations (rather than phenotypic differences), these viruses are known to differ appreciably in genetic sequence from current laboratory strains. Several studies have been performed to determine the relative mutation rates of RSV strains and have shown rates ranging from 10 -3 to 10 -4 nucleotide substitutions/site/year, depending upon the location and strain [49,50,113,114]. These data strongly suggest that evolutionary pressures are continuing to drive RSV evolution and potentially push modern circulating RSV strains further from the common laboratory strains isolated during 1950s and 1960s.…”