Molecular evolution of respiratory syncytial virus subgroup A genotype NA1 and ON1 attachment glycoprotein ( G ) gene in central Vietnam

Abstract

We performed molecular evolutionary analyses of the G gene C-terminal 3rd hypervariable region of RSV-A genotypes NA1 and ON1 strains from the paediatric acute respiratory infection patients in central Vietnam during the 2010-2012 study period. Time-scaled phylogenetic analyses were performed using Bayesian Markov Chain Monte Carlo (MCMC) method, and pairwise distances (p-distances) were calculated. Bayesian Skyline Plot (BSP) was constructed to analyze the time-trend relative genetic diversity of central Vietnam RSV-A strains. We also estimated the N-glycosylation sites within G gene hypervariable region. Amino acid substitutions under positive and negative selection pressure were examined using Conservative Single Likelihood Ancestor Counting (SLAC), Fixed Effects Likelihood (FEL), Internal Fixed Effects Likelihood (IFEL) and Mixed Effects Model for Episodic Diversifying Selection (MEME) models. The majority of central Vietnam ON1 strains detected in 2012 were classified into lineage 1 with few positively selected substitutions. As for the Vietnamese NA1 strains, four lineages were circulating during the study period with a few positive selection sites. Shifting patterns of the predominantly circulating NA1 lineage were observed in each year during the investigation period. Median p-distance of central Vietnam NA1 strains was wider (p-distance = 0.028) than that of ON1 (p-distance = 0.012). The molecular evolutionary rate of central Vietnam ON1 strains was estimated to be 2.55 × 10-2 (substitutions/site/year) and was faster than NA1 (7.12 × 10-3 (substitutions/site/year)). Interestingly, the evolutionary rates of both genotypes ON1 and NA1 strains from central Vietnam were faster than the global strains respectively. Furthermore, the shifts of N-glycosylation pattern within the G gene 3rd hypervariable region of Vietnamese NA1 strains were observed in each year. BSP analysis indicated the rapid growth of RSV-A effective population size in early 2012. These results suggested that the molecular evolution of RSV-A G gene detected in central Vietnam was fast with unique evolutionary dynamics.

Respiratory syncytial virus genotypes NA1, ON1, and BA9 are prevalent in Thailand, 2012–2015

“…More recently, ON1 has displaced NA1 to become the predominantly circulating RSV-A strain ( Eshaghi et al, 2012 ; Valley-Omar et al, 2013 ; Pierangeli et al, 2014 ; Kim et al, 2014 ), although it does not appear to cause more severe disease than other genotypes ( Panayiotou et al, 2014 ; Viegas, Goya & Mistchenko, 2016 ). Our study confirms findings of previous studies in that NA1 and ON1, but not NA3, are frequently identified in Southeast Asia ( Arnott et al, 2011 ; Yoshihara et al, 2016 ).…”

Analysis of phylogenetic diversity and in vitro adherence characteristics of respiratory syncytial virus and Streptococcus pneumoniae clinical isolates obtained during pediatric respiratory co-infections

“…The RSV strains and S. pneumoniae molecular serotypes identified within this cohort are consistent with global circulation patterns from around the time of the study period [43–45]. RSV genotype GA2 was the most highly prevalent strain, followed by BA and GA5.…”

Molecular epidemiology of human respiratory syncytial virus among children in Japan during three seasons and hospitalization risk of genotype ON1

“…The ON1, with a 72 nucleotide duplication in the C-terminal region of the G protein, was first detected in hospitalized children in Ontario, Canada in December 2010 [ 12 ]. Since then the genotype was detected various parts of the world and replaced NA1 [ 14 , 18 , 25 , 28 , 37 , 41 , 42 , 44 – 47 , 56 – 59 , 61 – 67 ]. In Japan, the ON1 strain was first detected in 2012 (this study and Tsukagoshi et al)[ 37 ] but it did not prevail until winter during 2014–2015 season as was shown in this study.…”

“…In neighboring China, ON1 was initially detected in February 2011 and became the dominant HRSV-A genotype in December 2013[ 42 ]. Other countries, such as Vietnam, the Philippines, Italy and Kenya, reported that the shift from NA1 to ON1 predominance occurred during the 2012–2013 season, almost one to two years earlier than in Japan and mainland China[ 22 , 44 , 56 , 67 ]. Evolutionary analysis of the ON1 strain suggests that this genotype might have emerged from the Americas, specifically in Panama around 2010 [ 45 ].…”