Phylodynamic profile of HIV-1 subtype B, CRF01-AE and the recently emerging CRF51-01B among men who have sex with men (MSM) in Singapore

Kim Tien Ng, Kah Ying Ng, Wei Xin Khong, Kuan Kiat Chew, Palvinder Kaur Singh, Joe Kwan Yap, Mei Ting Tan, Yee Sin Leo, Oliver B. Laeyendecker, Thomas C Quinn, Adeeba Kamarulzaman, Kok Keng Tee, Oon Tek Ng

Research output: Contribution to journalArticle

Abstract

HIV-1 subtype B and CRF01-AE are the predominant infecting subtypes among men who have sex with men (MSM) in Singapore. The genetic history, population dynamics and pattern of transmission networks of these genotypes remain largely unknown. We delineated the phylodynamic profiles of HIV-1 subtype B, CRF01-AE and the recently characterized CRF51-01B strains circulating among the MSM population in Singapore. A total of 105 (49.5%) newly-diagnosed treatmentnaïve MSM were recruited between February 2008 and August 2009. Phylogenetic reconstructions of the protease gene (HXB2: 2239 - 2629), gp120 (HXB2: 6942 - 7577) and gp41 (HXB2: 7803 - 8276) of the env gene uncovered five monophyletic transmission networks (two each within subtype B and CRF01-AE and one within CRF51-01B lineages) of different sizes (involving 3 - 23 MSM subjects, supported by posterior probability measure of 1.0). Bayesian coalescent analysis estimated that the emergence and dissemination of multiple sub-epidemic networks occurred between 1995 and 2005, driven largely by subtype B and later followed by CRF01-AE. Exponential increase in effective population size for both subtype B and CRF01-AE occurred between 2002 to 2007 and 2005 to 2007, respectively. Genealogical estimates suggested that the novel CRF51-01B lineages were probably generated through series of recombination events involving CRF01-AE and multiple subtype B ancestors. Our study provides the first insight on the phylodynamic profiles of HIV-1 subtype B, CRF01-AE and CRF51-01B viral strains circulating among MSM in Singapore. Copyright:

Original languageEnglish (US)
Article numbere80884
JournalPLoS One
Volume8
Issue number12
DOIs
StatePublished - Dec 2 2013

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Singapore
Electric power transmission networks
Human immunodeficiency virus 1
HIV-1
Genes
Population dynamics
gender
env Genes
Peptide Hydrolases
Bayes Theorem
History
Population Dynamics
Bayesian theory
Population Density
Genetic Recombination
ancestry
population size
proteinases
population dynamics
genes

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

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Phylodynamic profile of HIV-1 subtype B, CRF01-AE and the recently emerging CRF51-01B among men who have sex with men (MSM) in Singapore. / Ng, Kim Tien; Ng, Kah Ying; Khong, Wei Xin; Chew, Kuan Kiat; Singh, Palvinder Kaur; Yap, Joe Kwan; Tan, Mei Ting; Leo, Yee Sin; Laeyendecker, Oliver B.; Quinn, Thomas C; Kamarulzaman, Adeeba; Tee, Kok Keng; Ng, Oon Tek.

In: PLoS One, Vol. 8, No. 12, e80884, 02.12.2013.

Research output: Contribution to journalArticle

Ng, KT, Ng, KY, Khong, WX, Chew, KK, Singh, PK, Yap, JK, Tan, MT, Leo, YS, Laeyendecker, OB, Quinn, TC, Kamarulzaman, A, Tee, KK & Ng, OT 2013, 'Phylodynamic profile of HIV-1 subtype B, CRF01-AE and the recently emerging CRF51-01B among men who have sex with men (MSM) in Singapore', PLoS One, vol. 8, no. 12, e80884. https://doi.org/10.1371/journal.pone.0080884
Ng, Kim Tien ; Ng, Kah Ying ; Khong, Wei Xin ; Chew, Kuan Kiat ; Singh, Palvinder Kaur ; Yap, Joe Kwan ; Tan, Mei Ting ; Leo, Yee Sin ; Laeyendecker, Oliver B. ; Quinn, Thomas C ; Kamarulzaman, Adeeba ; Tee, Kok Keng ; Ng, Oon Tek. / Phylodynamic profile of HIV-1 subtype B, CRF01-AE and the recently emerging CRF51-01B among men who have sex with men (MSM) in Singapore. In: PLoS One. 2013 ; Vol. 8, No. 12.
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abstract = "HIV-1 subtype B and CRF01-AE are the predominant infecting subtypes among men who have sex with men (MSM) in Singapore. The genetic history, population dynamics and pattern of transmission networks of these genotypes remain largely unknown. We delineated the phylodynamic profiles of HIV-1 subtype B, CRF01-AE and the recently characterized CRF51-01B strains circulating among the MSM population in Singapore. A total of 105 (49.5{\%}) newly-diagnosed treatmentna{\"i}ve MSM were recruited between February 2008 and August 2009. Phylogenetic reconstructions of the protease gene (HXB2: 2239 - 2629), gp120 (HXB2: 6942 - 7577) and gp41 (HXB2: 7803 - 8276) of the env gene uncovered five monophyletic transmission networks (two each within subtype B and CRF01-AE and one within CRF51-01B lineages) of different sizes (involving 3 - 23 MSM subjects, supported by posterior probability measure of 1.0). Bayesian coalescent analysis estimated that the emergence and dissemination of multiple sub-epidemic networks occurred between 1995 and 2005, driven largely by subtype B and later followed by CRF01-AE. Exponential increase in effective population size for both subtype B and CRF01-AE occurred between 2002 to 2007 and 2005 to 2007, respectively. Genealogical estimates suggested that the novel CRF51-01B lineages were probably generated through series of recombination events involving CRF01-AE and multiple subtype B ancestors. Our study provides the first insight on the phylodynamic profiles of HIV-1 subtype B, CRF01-AE and CRF51-01B viral strains circulating among MSM in Singapore. Copyright:",
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