title: Complex patterns of the HIV-1 epidemic in Kuala Lumpur, Malaysia: evidence for expansion of circulating recombinant form CRF33_01B and detection of multiple other recombinants.
abstract: The HIV protease-reverse transcriptase (PR-RT) (1047 bp), gp120-env (891 bp) and gp41-env (547 bp) regions from the plasma of 115 HIV-1-infected patients in Kuala Lumpur (KL), Malaysia were sequenced. Detailed phylogenetic and bootscanning analyses were performed to determine the mosaic structure of the HIV-1 strains and their recombination breakpoint(s). Among the 50 patient samples in which all three regions could be amplified, the HIV-1 CRF01_AE subtype (46%) was predominant followed by subtypes B (10%) and B' (6%). A total of 9/50 (18%) patients were infected with a CRF01_AE/B inter-subtype recombinant, displaying a recombinant form (RF)(PR-RT), CRF01_AE(gp120-env) and CRF01_AE(gp41-env). This RF was derived from the Thai variants of CRF01_AE and B' subtype, with two distinct B' subtype segments in the backbone of CRF01_AE, similar to the newly identified CRF33_01B. In addition, one sample demonstrated a close structural relationship with the new CRF33_01B in the PR-RT region but displayed B' segment in part of the env region (RF(PR-RT), CRF01_AE/B'(gp120-env) and B'(gp41-env)) indicating continuing evolution of CRF33_01B. The remaining 18% of samples were identified as unique recombinant forms (URFs).
authors.affiliation: Retroviral Genetics Division, Center for Virus Research, Westmead Millennium Institute, Westmead Hospital, The University of Sydney, Westmead NSW, Sydney, Australia.
authors.forename: Bin
authors.initials: B
authors.lastname: Wang
authors.forename: Katherine A
authors.initials: KA
authors.lastname: Lau
authors.forename: Lai-Yee
authors.initials: LY
authors.lastname: Ong
authors.forename: Meet
authors.initials: M
authors.lastname: Shah
authors.forename: Megan C
authors.initials: MC
authors.lastname: Steain
authors.forename: Brian
authors.initials: B
authors.lastname: Foley
authors.forename: Dominic E
authors.initials: DE
authors.lastname: Dwyer
authors.forename: Choo Beng
authors.initials: CB
authors.lastname: Chew
authors.forename: Adeeba
authors.initials: A
authors.lastname: Kamarulzaman
authors.forename: Kee Peng
authors.initials: KP
authors.lastname: Ng
authors.forename: Nitin K
authors.initials: NK
authors.lastname: Saksena
mesh_terms: D015752:Genes, env / Q000235:genetics; D005838:Genotype; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology*; D054303:HIV Reverse Transcriptase / Q000235:genetics*; D006679:HIV Seropositivity / Q000453:epidemiology / Q000235:genetics; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008296:Malaysia / Q000453:epidemiology; D017720:Molecular Epidemiology; D016865:Reassortant Viruses / Q000235:genetics*
chemical_list: D054303:HIV Reverse Transcriptase