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Volume 20, Number 6—June 2014

Research

Rapid Spread and Diversification of Respiratory Syncytial Virus Genotype ON1, Kenya

Charles N. AgotiComments to Author , James R. Otieno, Caroline W. Gitahi, Patricia A. Cane, and D. James Nokes
Author affiliations: Kenya Medical Research Institute–Wellcome Trust Research Programme, Kilifi, Kenya (C.N. Agoti, J.R. Otieno, C.W. Gitahi, D.J. Nokes); Public Health England, London, UK (P.A. Cane); University of Warwick and WIDER, Coventry, UK (D.J. Nokes)

Main Article

Table 2

Signature codon changes in circulating global RSV group A genotype ON1 viruses*

Signature change† First detected No. viruses with mutation No. viruses compared‡ Detection location(s) Comment(s)
P88S 2012 Nov 3 7 China Occur within the mucin-like first hypervariable region; potentially O-glycosylated (4)
L115P 2012 Aug 10 84 China, Kenya Defines Kenyan RSV lineage 3; occurs within the mucin-like first hypervariable region; potentially O-glycosylated (4)
S128F 2012 May 5 84 Kenya Defines Kenya RSV lineage 2
T136I 2012 Feb 54 111 Kenya Defines Kenyan RSV lineage 1
P172A 2012 Dec 9 150 Italy
P206Q 2011 5 162 India, Italy, Japan
T249N 2012 Jan 5 195 Italy
L274P 2011 131 195 India, Italy, Germany, Japan, Kenya Predicted to be positively selected; exhibits reversible amino acid substitutions (i.e., flip-flop pattern) (25); position N-glycosylated in some strains
H290Y 2012 Feb 5 195 Italy Predicted to be positively selected; exhibits flip-flop pattern(25)
G296S 2012 Dec 11 195 Italy Adjacent codon (i.e., 295) predicted to be positively selected (26)
L298P 2011 133 195 India, Italy, Germany, Japan, Kenya Duplicated epitope; concurrent substitution with L274P in many sequences
Y304H 2011 129 195 India, Italy, Germany, Japan, Kenya
E308K 2012 Feb 13 195 Italy, South Africa, China
L310P 2011 96 195 Italy, Kenya, Japan, India Equivalent to L286P in non-ON1 genotypes; change previously observed in certain monoclonal antibody escape mutants (27)

*RSV, respiratory syncytial virus.
†Only substitutions observed in >3 viruses are shown.
‡Numbers in this column indicate the number of sequences that span the given amino acid position; the number 195 implies that all the datasets we collated, including the sequences for viruses from Kilifi, Kenya. The numbers differ because the nucleotide sequences found in GenBank for these viruses were of variable lengths.

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