Retrospective phylogenetic analysis of circulating BA genotype of human respiratory syncytial virus with 60 bp duplication from New Delhi, India during 2007–2010

S, Vln Raghuram; Khan, Wajihul Hasan; Deeba, Farah; Sullender, Wayne M.; Broor, Shobha; Parveen, Shama

doi:10.1007/s13337-015-0283-7

Cited by 17 publications

(17 citation statements)

References 25 publications

(40 reference statements)

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“…Two additional mutations were identified in the duplicated region of both BA and ON1 genotypes which indicates gradual accumulation of mutations over time in the duplicated regions of these genotypes as described earlier [76]. Therefore, it is obvious that evolutionary pressure exists on the duplicated regions suggesting more such genetic variations in the BA and ON1 genotypes in future.…”

Section: Discussionsupporting

confidence: 55%

“…N- and O-linked glycosylation of the G protein are an important landmark of antigenicity of the virus because it may affect the expression of epitopes by either masking or facilitating the antibody recognition resulting in immune evasion [76]. Ten additional O-linked sites in the 24 amino acid duplicated region in ON1 and 2 additional O-linked sites in the 20 amino acid region in BA genotype were identified in the present study.…”

Section: Discussionmentioning

confidence: 61%

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Co-Circulation of 72bp Duplication Group A and 60bp Duplication Group B Respiratory Syncytial Virus (RSV) Strains in Riyadh, Saudi Arabia during 2014

et al. 2016

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Respiratory syncytial virus (RSV) is an important viral pathogen of acute respiratory tract infection (ARI). Limited data are available on molecular epidemiology of RSV from Saudi Arabia. A total of 130 nasopharyngeal aspirates were collected from children less than 5 years of age with ARI symptoms attending the Emergency Department at King Khalid University Hospital and King Fahad Medical City, Riyadh, Saudi Arabia between October and December, 2014. RSV was identified in the 26% of the hospitalized children by reverse transcriptase PCR. Group A RSV (77%) predominated during the study as compared to group B RSV (23%). The phylogenetic analysis of 28 study strains clustered group A RSV in NA1 and ON1 genotypes and group B viruses in BA (BA9) genotype. Interestingly, 26% of the positive samples clustered in genotypes with duplication in the G protein gene (ON1 for group A and BA for group B). Both the genotypes showed enhanced O-linked glycosylation in the duplicated region, with 10 and 2 additional sites in ON1 and BA respectively. Selection pressure analysis revealed purifying selection in both the ON1 and BA genotypes. One codon each in the ON1 (position 274) and BA genotypes (position 219) were positively selected and had high entropy values indicating variations at these amino acid positions. This is the first report describing the presence of ON1 genotype and the first report on co-circulation of two different genotypes of RSV with duplication in the G protein gene from Saudi Arabia. The clinical implications of the simultaneous occurrence of genotypes with duplication in G protein gene in a given population especially in the concurrent infections should be investigated in future. Further, the ongoing surveillance of RSV in this region will reveal the evolutionary trajectory of these two genotypes with duplication in G protein gene from largest country in the Middle East.

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Section: Discussionsupporting

confidence: 55%

Section: Discussionmentioning

confidence: 61%

Co-Circulation of 72bp Duplication Group A and 60bp Duplication Group B Respiratory Syncytial Virus (RSV) Strains in Riyadh, Saudi Arabia during 2014

et al. 2016

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“…We analysed the BA9 lineage of BA genotype in detail since it was the predominant lineage. This analysis revealed global distribution of the BA9 genotype that was reflected across different geographical regions including India, Spain, Philippines, Thailand, South Africa, Japan, China, Vietnam, Ireland, Italy, Israel, Argentina, Iran, Germany, Cambodia and Malaysia [ 8 , 10 , 13 – 15 , 17 , 21 , 23 , 24 , 26 , 28 , 51 , 55 , 57 , 64 – 81 ]. Further, the studied SAB4 strains clustered with sequences from Cambodia [ 13 ].…”

Section: Discussionmentioning

confidence: 99%

“…It was found that the BA genotype dominated in Pune, Maharashtra during the years 2009–12 [ 23 ]. Consequently, the BA viruses from New Delhi attracted our attention during the years 2007–10 [ 28 ] and we continued our work on BA genotype throughout the years 2011–15. Interestingly, BA9 was the dominant lineage of the BA genotype identified in our study.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2018

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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.

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“…It has been postulated that N-and O-linked glycosylation of the G protein contribute to the antigenic variation in RSV thus assisting the virus in host immune evasion [63]. At least two N-linked glycosylation sites have been predicted for all the Saudi RSV strains belonging to each of the three genotypes that are reported from this region i.e.…”

Section: Glycosylation Site Analysismentioning

confidence: 99%

An overview of respiratory syncytial virus infections in Saudi Arabia

Ahmed

Parveen

Alhassinah

et al. 2018

J Infect Dev Ctries

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Respiratory syncytial virus (RSV) is a major pathogen of acute respiratory tract infection (ARI) in different geographical regions including Saudi Arabia. Numerous hospital-based investigations have revealed the RSV prevalence between 0.2-54% in the paediatric population with ARI/ALRI from Saudi Arabia during 1991-2015. Maximum RSV infections occurred in children less than 1 year of age (51-97%) and male children (51-69%) were more commonly affected than females (31-49%). RSV infections are reported mostly during winter season suggesting seasonal distribution of the virus. Other respiratory viruses reported from this region are adenovirus, influenza, parainfluenza, human metapneumovirus and rhinovirus including many mixed infections. A few studies have reported the phylogenetic analysis of the circulating strains of RSV. These studies have revealed that circulating group A-RSV Saudi strains belonged to NA1 and ON1 genotypes and group B-RSV viruses clustered in the BA genotype. Molecular characterization of the Saudi strains was further carried out by mutational, selection pressure and glycosylation site analyses. We have compiled all the eighteen studies of RSV infection from Saudi Arabia in the form of this review and concluded that detailed comprehensive surveillance of RSV and other viruses in community and hospital settings is required. Information on the molecular characterization of currently circulating strains of RSV will contribute towards better understanding of the epidemiology and evolutionary dynamics of this viral pathogen. Moreover, the determination of the genetic composition of circulating RSV strains will be important during evaluation of initial vaccine trials.

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Retrospective phylogenetic analysis of circulating BA genotype of human respiratory syncytial virus with 60 bp duplication from New Delhi, India during 2007–2010

Cited by 17 publications

References 25 publications

Co-Circulation of 72bp Duplication Group A and 60bp Duplication Group B Respiratory Syncytial Virus (RSV) Strains in Riyadh, Saudi Arabia during 2014

Co-Circulation of 72bp Duplication Group A and 60bp Duplication Group B Respiratory Syncytial Virus (RSV) Strains in Riyadh, Saudi Arabia during 2014

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

An overview of respiratory syncytial virus infections in Saudi Arabia

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