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Title: Direct whole-genome deep-sequencing of human respiratory syncytial virus A and B from Vietnamese children identifies distinct patterns of inter- and intra-host evolution
Authors: Ha Do, L.A
Wilm, A
Van Doorn, H.R
Lam, H.M
Sim, S
Sukumaran, R
Tran, A.T
Nguyen, B.H
Tran, T.T.L
Tran, Q.H
Vo, Q.B
Tran Dac, N.A
Trinh, H.N
Nguyen, T.T.H
Le Binh, B.T
Le, K
Nguyen, M.T
Thai, Q.T
Vo, T.V
Minh Ngo, N.Q
Dang, T.K.H
Cao, N.H
Van Tran, T
Ho, L.V
Farrar, J
De Jong, M
Chen, S 
Nagarajan, N 
Bryant, J.E
Hibberd, M.L 
Keywords: Article
consensus sequence
genetic variability
genome analysis
hospitalized child
Human respiratory syncytial virus
Human respiratory syncytial virus A
Human respiratory syncytial virus B
human tissue
major clinical study
priority journal
respiratory syncytial virus infection
Viet Nam
virus genome
amino acid sequence
gene expression regulation
genetic variation
Human respiratory syncytial virus
molecular evolution
molecular model
protein conformation
Respiratory Syncytial Virus Infections
virus genome
viral protein
Amino Acid Sequence
Evolution, Molecular
Gene Expression Regulation, Viral
Genetic Variation
Genome, Viral
Models, Molecular
Protein Conformation
Respiratory Syncytial Virus Infections
Respiratory Syncytial Virus, Human
Viral Proteins
Issue Date: 2015
Publisher: Microbiology Society
Citation: Ha Do, L.A, Wilm, A, Van Doorn, H.R, Lam, H.M, Sim, S, Sukumaran, R, Tran, A.T, Nguyen, B.H, Tran, T.T.L, Tran, Q.H, Vo, Q.B, Tran Dac, N.A, Trinh, H.N, Nguyen, T.T.H, Le Binh, B.T, Le, K, Nguyen, M.T, Thai, Q.T, Vo, T.V, Minh Ngo, N.Q, Dang, T.K.H, Cao, N.H, Van Tran, T, Ho, L.V, Farrar, J, De Jong, M, Chen, S, Nagarajan, N, Bryant, J.E, Hibberd, M.L (2015). Direct whole-genome deep-sequencing of human respiratory syncytial virus A and B from Vietnamese children identifies distinct patterns of inter- and intra-host evolution. Journal of General Virology 96 (12) : 3470-3483. ScholarBank@NUS Repository.
Rights: Attribution 4.0 International
Abstract: Human respiratory syncytial virus (RSV) is the major cause of lower respiratory tract infections in children, <2 years of age. Little is known about RSV intra-host genetic diversity over the course of infection or about the immune pressures that drive RSV molecular evolution. We performed whole-genome deep-sequencing on 53 RSV-positive samples (37 RSV subgroup A and 16 RSV subgroup B) collected from the upper airways of hospitalized children in southern Vietnam over two consecutive seasons. RSV A NA1 and RSV B BA9 were the predominant genotypes found in our samples, consistent with other reports on global RSV circulation during the same period. For both RSV A and B, the M gene was the most conserved, confirming its potential as a target for novel therapeutics. The G gene was the most variable and was the only gene under detectable positive selection. Further, positively selected sites in G were found in close proximity to and in some cases overlapped with predicted glycosylation motifs, suggesting that selection on amino acid glycosylation may drive viral genetic diversity. We further identified hotspots and coldspots of intra-host genetic diversity in the RSV genome, some of which may highlight previously unknown regions of functional importance. © 2015 The Authors.
Source Title: Journal of General Virology
ISSN: 0022-1317
DOI: 10.1099/jgv.0.000298
Rights: Attribution 4.0 International
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