Molecular Epidemiology of HIV Type 1 in Singapore and Identification of Novel CRF01_AE/B Recombinant Forms

Abstract

To investigate HIV-1 molecular epidemiology in Singapore, we sequenced portions of three regions of the HIV-1 genome (protease HXB2: 2163 to 2620, gp120 HXB2: 6904 to 7628, and gp41 HXB2: 7817 to 8264) from 212 plasma samples collected between February 2008 and August 2009. From these samples, 109 (51.4%) generated interpretable data in all regions. Sixty-one (56.0%) were identified as CRF01_AE, 26 (23.9%) as subtype B and 14 (12.8%) as possible novel recombinant forms. The main novel recombinant pattern, detected in 13 sequences, had subtype B in protease and gp41 and CRF01_AE in gp120. There was intermixing of subtypes within transmission risk groups. However, 85% of subjects infected with the novel recombinant forms self-identified as men who have sex with men or bisexuals compared with only 41% of individuals infected with CRF01_AE and 62% infected with subtype B ( p ¼ 0.001).

Identification of New CRF51_01B in Singapore Using Full Genome Analysis of Three HIV Type 1 Isolates

“…In our prior study, this CRF had a higher prevalence among homosexuals and bisexuals compared to subtype B and CRF01_AE. 5 Continual monitoring of the molecular epidemiology of HIV-1 in Singapore will provide vital insight concerning local and transnational transmission. The recombinant gene mosaic structure is shown at the bottom of the figure with nucleotide positions corresponding to the reference HXB2 sequence.…”

“…[1][2][3][4] A recent HIV-1 molecular epidemiology study in Singapore was performed to determine if there was any cross-border transmission of the newly identified CRFs. 5 Unexpectedly, a novel recombinant form, with subtype B in protease and gp41 and CRF01_AE in gp120, was identified in 13 (11.9%) of 109 individuals tested.…”

“…5 Demographic information (age, gender, and ethnicity) and transmission risk factor data were obtained from clinical chart review. The National Healthcare Group ethics committee approved this study.…”

HIV-1 subtype CRF01_AE and B differ in utilization of low levels of CCR5, Maraviroc susceptibility and potential N-glycosylation sites

“…We obtained a total of 89 (65=Subtype AE, 24=Subtype B) archival plasma samples from a cross-sectional cohort of HIV infected patients from Singapore (Ng et al, 2013; Ng et al, 2011b). From the available samples we were able to amplify and clone 37 (27=Subtype AE, 10=Subtype B) full length functional Envs.…”

“…Interestingly, certain strains/subtypes circulate in defined populations which emphasizes the relevance of host genetic makeup in governing the course of HIV disease (Kawashima et al, 2009). In this study, we cloned 37 full length Envs from a cohort from Singapore with documented differences in disease progression (Ng et al, 2013; Ng et al, 2011b) and determined the genotypic and phenotypic differences in the Env glycoproteins derived from AE and B subtype infected individuals. While genetic analysis alone is of value, its credibility can be further improved when combined with phenotypic analysis, which was the objective of this study.…”