The challenge of HIV-1 subtype diversity.

New England Journal of Medicine (Impact Factor: 54.42). 11/2008; 359(18):1965-6. DOI: 10.1056/NEJMc086373
Source: PubMed
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    ABSTRACT: There is continuous need to genetically characterize HIV strains in circulation in order to inform intervention and vaccine discovery. We partially sequenced the envelope C2V3 gene from a total of 59 Kenyan patients on highly active antiretroviral treatment (HAART) and determined HIV subtypes using both the JPHMM subtyping tool and the phylogenetic method. HIV-1 subtype A1 was the predominant strain in circulation, representing 65.5% and 74.5% of all isolates as determined by JPHMM and phylogenetic methods respectively. Subtypes C and D were the next most prevalent pure strains at 9.1% each by both methods. JPHMM identified 9.1% of the isolates as recombinant. Four isolates had short sequences not covering entire C2V3 region and were thus not subtyped. From this study, subtype A viruses are still the predominant HIV-1 strains in local circulation in the Kenya. Constant surveillance is needed to update molecular trends under continuing HAART scale-up.
    AIDS Research and Human Retroviruses 11/2014; 31(4). DOI:10.1089/AID.2014.0306 · 2.46 Impact Factor
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    ABSTRACT: Background: In Thailand, new HIV-1 infections are largely concentrated in certain risk groups such as men who have sex with men (MSM), where annual incidence may be as high as 12% per year. The paucity of information on the molecular epidemiology of HIV-1 in Thai MSM limits progress in understanding the epidemic and developing new prevention methods. We evaluated HIV-1 subtypes in seroincident and seroprevalent HIV-1 infected men enrolled in the Bangkok MSM Cohort Study (BMCS) between 2006 and 2011. Methods: We characterized HIV-1 subtype in 231 seroprevalent and 194 seroincident subjects using the multihybridization assay (MHA). Apparent dual infections, recombinant strains, and isolates found to be non-typeable by MHA were further characterized by targeted genomic sequencing. Results: Most subjects were infected with HIV-1 CRF01_AE (82%), followed by infections with recombinants (11%, primarily CRF01_AE/B recombinants), subtype B (5%), and dual infections (2%). More than 11 distinct chimeric patterns were observed among CRF01B_AE/B recombinants, most involving recombination within integrase. A significant increase in the proportion of non-typeable strains was observed among seroincident MSM between 2006 and 2011. Conclusion: CRF01_AE and subtype B were the most and least common infecting strains, respectively. The predominance of CRF01_AE among HIV-1 infections in Thai MSM participating in the BMCS parallels trends observed in Thai heterosexuals and injecting drug users. The presence of complex recombinants, and a significant rise in non-typeable strains suggest ongoing changes in the genetic makeup of the HIV-1 epidemic in Thailand, which may pose challenges for HIV-1 prevention efforts and vaccine development.
    AIDS Research and Human Retroviruses 11/2014; 31(4). DOI:10.1089/AID.2014.0139 · 2.46 Impact Factor