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

Abstract

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.

Analysis of genetic variability of respiratory syncytial virus groups A and B in Kuwait

“…A total of 305 samples from ARTI patients, including infants, children and adults, were collected, and 77 (25.2%) of the patients were found to be positive for RSV by multiplex real-time PCR. Our results, which demonstrated the predominance of the RSV-A group over the RSV-B group in the clinical samples, are in agreement with the findings of the majority of the studies on the epidemiology of RSV genotypes [23,[25][26][27][28][29][30]. We found that most of the patients had RSV single infections, while 17 (22%) had mixed infections of RSV and other respiratory viruses.…”

“…Also, the AN1 genotype was a dominated genotype in India among children < 6 years old during the period 2009-2012 [28] and in Italy among children < 3 years old during 2006-2012 [63]. Moreover, between October and December 2014, NA1 and ON1 genotypes of group A RSV dominated in Riyadh, Saudi Arabia, among children less than five years of age with ARI symptoms [30].…”

“…3A) were more closely related to the new RSV-A/ON1 genotype than the rest of the Kuwaiti strains according to the percentage of differences in the nucleotide sequences. RSV-A/ON1 is novel genotype that was first described by Eshaghi et al in Ontario, Canada [57], and this strain later emerged and became the dominant genotype in different countries, including northern Italy, Germany, Thailand, Turkey, and Saudi Arabia [16,19,30,47,54,[58][59][60][61]. A further significant result is that the two Kuwaiti strains (KW-1411 and KW-827) were more closely related to the RSV-A/NA1 strain than other Kuwaiti strains based on pairwise nucleotide distances.…”

Genomic Loads and Genotypes of Respiratory Syncytial Virus: Viral Factors during Lower Respiratory Tract Infection in Chilean Hospitalized Infants

“…Further genetic analysis of the nucleotide sequence of the second hypervariable region on the G gene allowed for the classification into genotypes within antigenic groups RSV-A and B [9,10]. Many studies have reported the molecular epidemiology and genetic variability of RSV worldwide [10,11,12,13,14,15,16,17,18,19,20], revealing the emergence and spread of new genotypes with duplication of ~60 to 70 nucleotides in this G hypervariable region for RSV-A (RSV Ontario) and RSV-B (RSV Buenos Aires) [15,19,21,22]. Although none of the variants or genotypes has been consistently associated with greater virulence or pathogenicity [13,18,22,23], some recent reports describing clinical aspects of contemporary genotypes (NA1 and ON1) have shown higher frequencies of LRTI and hospitalizations rates [24,25,26].…”

Evolution and Emergence of Pathogenic Viruses: Past, Present, and Future

“…Two such remarkable events were the 60-bp duplication in group B RSV in Argentina in 1999 and the 72-bp duplication in group A RSV in Canada in 2011 [45,46] . These new genotypes of RSV with their duplications, known as BA and ON1, respectively, spread to different geographical regions across the globe due to immunologically naive travellers [47][48][49][50] . The mathematics of these spreading events is well known today, and a sophisticated array of computational and mathematical models can be used to accurately back-predict such events.…”