Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 Nov 11;11(11):e0166145.
doi: 10.1371/journal.pone.0166145. eCollection 2016.

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

Anwar Ahmed  1   2 , Shakir H Haider  3 , Shama Parveen  3 , Mohammed Arshad  1 , Hytham A Alsenaidy  4 , Alawi Omar Baaboud  5 , Khalid Fahad Mobaireek  5 , Muslim Mohammed AlSaadi  6 , Abdulrahman M Alsenaidy  1 , Wayne Sullender  7
Affiliations

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

Anwar Ahmed et al. PLoS One. .

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.

PubMed Disclaimer

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Phylogenetic trees for hRSV group A (A) and group B (B).
The nucleotide sequences from the second variable region of the G protein gene of the study RSVA strains are indicated by solid circles and RSVB by solid triangles. The nucleotide sequences were aligned with the CLUSTAL W program, and phylogenetic trees were constructed by Maximum Likelihood method using MEGA6 software. Bootstrap values greater than 70% are shown at the branch nodes.
Fig 2
Fig 2
(A) Deduced amino acid alignment and mutations in the second hyper-variable region of G protein of the NA1 genotype. The figure includes alignment of Saudi NA1 strains with the prototype strain from Japan (AB470478). The amino acids sequence alignment corresponds to 227–297 amino acids of the prototype strain. Identical residues are indicated by dashes. Stop codons are indicated by asterisks. Potential N-glycosylation sites (NXT, where X is not proline) are indicated by grey shading. The potential sites for extensive O-glycosylation KPX - - - TTKX motifs are underlined. (B) The amino acid sequence of NA1 genotype showing mutations in the Saudi strains. The sequence corresponds to the 227–297 amino acids of the NA1 prototype strain. Changes at amino acid positions in Saudi strains are shown by arrows.
Fig 3
Fig 3
(A) Deduced amino acid alignment and mutations in the second variable region of G protein of the ON1 genotype. The figure includes alignment of study ON1 strains with the prototype strain from Canada (JN257694). The amino acids sequence alignment corresponds to 227–321 amino acids of the prototype strain. Identical residues are indicated by dashes. The two copies of the duplicated 24-amino-acid region in group ON1 strains are indicated by rectangular boxes. Stop codons are indicated by asterisks. Potential N-glycosylation sites (NXT, where X is not proline) are indicated by grey shading. The potential sites for extensive O-glycosylation KPX - - - TTKX motifs are underlined. (B) The amino acid sequence of ON1 genotype showing mutations in the study strains. The sequence corresponds to the 227–321 amino acids of the ON1 prototype strain. The rectangular boxes represent the analogous 24 amino acid region followed by duplicated 24 amino acid region in ON1 strains. Changes at amino acid positions in study strains are shown by arrows.
Fig 4
Fig 4
(A) Deduced amino acid alignment and mutations in the second variable region of G protein of the BA genotype. The figure includes alignment of Saudi BA strains with the prototype BA strain from Argentina (AY333364). The amino acids sequence alignment corresponds to 213–315 amino acids of the prototype strain. Identical residues are indicated by dashes. The two copies of the duplicated 20-amino-acid region in group BA strains are indicated by rectangular boxes. Stop codons are indicated by asterisks. Potential N-glycosylation sites (NXT, where X is not proline) are indicated by grey shading. (B) The amino acid sequence of the BA genotype showing mutations in the Saudi strains. The sequence corresponds to the 227–297 amino acids of the BA prototype strain. The rectangular boxes represent the analogous 20 amino acid region followed by duplicated 20 amino acid region in BA RSV strains. Changes at amino acid positions in Saudi strains are shown by arrows.
Fig 5
Fig 5. Shannon entropy plots of deduced amino acid sequences of the second hypervariable region of the G protein.
The data set includes (A) RSV-A: NA1 genotype, n = 26 (B) ON1 genotype, n = 05 and (C) RSV-B: BA genotype, n = 11 of Saudi strains with their respective prototype strains. The entropy plots show the amino acid variability in the second hypervariable region of the G protein gene determined by BioEdit software. The threshold value was set at 0.2. Amino acid sites with entropy values <0.2 are considered conserved and values >0.2 are considered variable.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Nair H, Nokes DJ, Gessner BD, Dherani M, Madhi SA, Singleton RJ, et al. (2010) Global burden of acute lower respiratory infections due to respiratory syncytial virus in young children: a systematic review and meta-analysis. Lancet 375: 1545–1555. 10.1016/S0140-6736(10)60206-1 - DOI - PMC - PubMed
    1. Gimferrer L, Campins M, Codina MG, Martin Mdel C, Fuentes F, Esperalba J, et al. (2015) Molecular epidemiology and molecular characterization of respiratory syncytial viruses at a tertiary care university hospital in Catalonia (Spain) during the 2013–2014 season. J Clin Virol 66: 27–32. 10.1016/j.jcv.2015.02.018 - DOI - PubMed
    1. Malasao R, Okamoto M, Chaimongkol N, Imamura T, Tohma K, Dapat I, et al. (2015) Molecular Characterization of Human Respiratory Syncytial Virus in the Philippines, 2012–2013. PLOS ONE 10: e0142192 10.1371/journal.pone.0142192 - DOI - PMC - PubMed
    1. Esposito S, Piralla A, Zampiero A, Bianchini S, Di Pietro G, Scala A, et al. (2015) Characteristics and Their Clinical Relevance of Respiratory Syncytial Virus Types and Genotypes Circulating in Northern Italy in Five Consecutive Winter Seasons. PLOS ONE 10: e0129369 10.1371/journal.pone.0129369 - DOI - PMC - PubMed
    1. Eshaghi A, Duvvuri VR, Lai R, Nadarajah JT, Li A, Patel SN, et al. (2012) Genetic variability of human respiratory syncytial virus A strains circulating in Ontario: a novel genotype with a 72 nucleotide G gene duplication. PLOS ONE 7: e32807 10.1371/journal.pone.0032807 - DOI - PMC - PubMed

MeSH terms

Grants and funding

The project was funded by the National Plan for Science, Technology and Innovation (MAARIFA), King Abdulaziz City for Science and Technology, Kingdom of Saudi Arabia, URL: http://maarifah.kacst.edu.sa/NSTIPWCPortal/faces/NSTIPHomePage; Award Number 12MED-2886-02, to AA.