title: Continuous crossover(s) events of HIV-1 CRF01_AE and B subtype strains in Malaysia: evidence of rapid and extensive HIV-1 evolution in the region.
abstract: The Asian HIV epidemic appears to be complex, characterized by the prevalence of multiple subtypes and circulating recombinant forms with gradual replacement of pure HIV-1 subtypes in several geographical regions. The main objectives of the present study are to identify and analyse the full-length viral genomes of three unique recombinant forms (URFs); the HIV-1 isolates 07MYKLD47, 07MYKLD48 and 07MYKLD49 from Malaysia. Long-range polymerase chain reaction (PCR) amplification of seven overlapping reading frames was used to derive near full-length HIV-1 genomes. Detailed phylogenetic and bootscanning analyses were performed to determine phylogenetic associations and subtypic assignments. We further confirmed the mosaic composition of these CRF01_AE/B inter-subtype recombinant forms, which are composed of B-subtype fragment(s) in the backbone of CRF01_AE. Both 07MYKLD47 and 07MYKLD48 have an insertion of B subtype (880 bp and 532 bp) in the gag-pol and gp41-env gene regions, respectively. Whereas the isolate 07MYKLD49 has three B-subtype fragments inserted in different gene region along the genome; one each in the gag-pol (1862 bp) and pol-vif (1935 bp) regions, and a short B-subtype insertion (541 bp) in the 5' LTR-gag region. This highlights the public health relevance of newly emerging second generation HIV-1 recombinant forms and their dispersal, along with their rapid and continuous evolution in the region.
authors.affiliation: Retroviral Genetics Division, Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital, The University of Sydney, Westmead, Sydney, Australia.
authors.forename: Katherine A
authors.initials: KA
authors.lastname: Lau
authors.forename: Bin
authors.initials: B
authors.lastname: Wang
authors.forename: Adeeba
authors.initials: A
authors.lastname: Kamarulzaman
authors.forename: Kee-Peng
authors.initials: KP
authors.lastname: Ngb
authors.forename: Nitin K
authors.initials: NK
authors.lastname: Saksena
mesh_terms: D016000:Cluster Analysis; D019143:Evolution, Molecular; D016679:Genome, Viral; D005838:Genotype; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008296:Malaysia / Q000453:epidemiology; D017720:Molecular Epidemiology; D016254:Mutagenesis, Insertional; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D017385:Sequence Homology