title: Emergence of HIV-1 CRF01_AE/B unique recombinant forms in Kuala Lumpur, Malaysia.
abstract: OBJECTIVE
  To investigate the molecular epidemiology of HIV-1 and to screen for the emergence of intersubtype recombinants in Kuala Lumpur, Malaysia.
  
  
  METHODS
  A molecular epidemiology study was conducted among HIV-1 seropositive patients attending the University Malaya Medical Center (UMMC) from July 2003 to June 2004.
  
  
  METHODS
  Protease (PR) and reverse transcriptase (RT) gene sequences were derived from drug resistance genotyping assay of 100 newly diagnosed or antiretroviral-naive patients. These were phylogenetically analysed to determine the subtypes and recombination breakpoint analyses were performed on intersubtype recombinants to estimate the recombination breakpoint(s).
  
  
  RESULTS
  CRF01_AE predominated in Kuala Lumpur with 65% in both PR and RT genes. B subtype was detected at 14% and 12% in PR and RT genes, respectively. C subtype was present at 1% in both genes. Overall, the concordance of PR and RT genes in discriminating subtypes/circulating recombinant forms (CRF) was high at 96%. In this study, novel CRF01_AE/B intersubtype recombinants were detected at high prevalence (22%), including those isolates with subtype discordance. Thai variants of CRF01_AE and B subtype were involved in the genesis of these unique recombinant forms (URF). Interestingly, 19 CRF01_AE/B intersubtype recombinant isolates shared similar recombination breakpoints in both PR and RT genes. Several distinct URF were also identified.
  
  
  CONCLUSIONS
  PR and RT genes can be utilized for subtype/CRF assessment with high degree of agreement, allowing concurrent surveillance of circulating HIV-1 subtypes with antiretroviral drug resistance genotyping tests. The emergence of highly identical CRF01_AE/B intersubtype recombinants suggests the possibility of the appearance of a new circulating recombinant form in Kuala Lumpur.
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Kok Keng
authors.initials: KK
authors.lastname: Tee
authors.forename: Chee Keong
authors.initials: CK
authors.lastname: Pon
authors.forename: Adeeba
authors.initials: A
authors.lastname: Kamarulzaman
authors.forename: Kee Peng
authors.initials: KP
authors.lastname: Ng
mesh_terms: D000328:Adult; D001483:Base Sequence; D005240:Feasibility Studies; D005260:Female; D005838:Genotype; D054303:HIV Reverse Transcriptase / Q000235:genetics; D006679:HIV Seropositivity / Q000453:epidemiology / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008296:Malaysia / Q000453:epidemiology; D008297:Male; D008875:Middle Aged; D010447:Peptide Hydrolases / Q000235:genetics; D010802:Phylogeny; D015995:Prevalence; D012367:RNA, Viral / Q000235:genetics; D011995:Recombination, Genetic / Q000235:genetics*
chemical_list: D012367:RNA, Viral; D054303:HIV Reverse Transcriptase; D010447:Peptide Hydrolases