Based on partial env and pol (protease and RT) subtyping, we recently documented that the majority (>80%) of the HIV-1 strains that circulate in Côte d'Ivoire were CRF02_AG and about 11% were recombinants or could not be clearly assigned to a known subtype or CRF. In order to determine in more detail the precise structure of these viruses we sequenced the full-length genomes for six such strains. Bootscan and phylogenetic tree analysis showed that four strains were complex and unique CRF02_AG/CRF09_cpx recombinants, one was a CRF02_AG/CRF06_cpx recombinant, and one was a pure CRF09_cpx. Reanalysis of the remaining recombinants asserted the predominance of CRF09_cpx within intersubtype recombinants and circulation of CRF09_cpx in Côte d'Ivoire. More detailed analysis of the CRF09_cpx strains revealed also that part of the pol gene belonged to subtype K. This is the first time that such recombinants are described.
"Group M can be further subdivided into subtypes (A-D, F-H, J-K) and sub-subtypes (A1-A4, F1-F2). In addition an increasing number of Circulating Recombinant Forms (CRFs, CRF01-CRF37) and many Unique Recombinants Forms (URFs) have also been described [4-6]. The geographic distribution of the different HIV-1 M variants is very heterogeneous and specific distributions of the various subtypes are seen among the different continents, even from country to country or within countries . "
[Show abstract][Hide abstract] ABSTRACT: Prevalence of HIV-1 non-B subtypes has increased overtime in patients diagnosed at the time of primary infection (PHI) in France. Our objective was to characterize in detail non-B strains which could not be genetically classified into the known subtypes/Circulating Recombinant Forms (CRFs).
Among 744 patients enrolled in the ANRS PRIMO Cohort since 1996, 176 (23.7%) were infected with HIV-1 non-B strains. The subtype/CRF could not be identified in RT for 15 (2%). The V3-V5 env region was sequenced and 3 strains (04FR-KZS, 06FR-CRN, 04FR-AUK) were full-length sequenced. Phylogenetic and bootscan analyses were used to characterize the mosaic structures.
Among V3-V5 sequences, 6 were divergent A, 2 distantly related to E or D, 2 C, 1 B and 2 remained unclassified. 04FR-KZS, isolated in a Congolese woman infected in France, clustered with 2 previously described viruses from the Democratic Republic of Congo. They represent CRF27_cpx involving A/E/G/H/J/K/U subtypes. 06FR-CRN, isolated in a homosexual Caucasian patient, was a B/C/U recombinant involving a Brazilian C strain. 04FR-AUK, isolated in a Congolese patient infected in France, was a A/K/CRF09/U recombinant clustering from gag to vif with HIV-1 MAL. Others PHI were further observed in 2006-2007 with 1 KZS and 5 CRN-like viruses, suggesting their spread in France.
This study illustrates the increasing HIV-1 diversity in France associating new (06FR-CRN) and old (CRF27_cpx and "MAL-like" 04FR-AUK) strains, which are rare in their region of origin but may have a possible founder effect in France. Our results strengthen the French guidelines recommending viro-epidemiological surveillance of HIV-1 diversity.
[Show abstract][Hide abstract] ABSTRACT: The picture of HIV-1 genetic diversity in the global pandemic continues to evolve. Identification of new variants, including circulating and unique recombinant forms, recognition of new outbreaks and of changes in established epidemics, and characterization of growing numbers of full-length genomes provide a view of high dynamism and increasing complexity. The pervasive role of recombination as a major driving force in the generation of diversity in the HIV-1 pandemic is becoming evident, and is particularly visible in areas in which different genetic forms meet, referred to as "geographic recombination hotspots". The importance of superinfection and its impact on HIV-1 diversification and propagation is surfacing, although restrictions to superinfection are also apparent. Genetic diversity within subtypes is increasing over time and new geographically localized lineages deriving from point introductions are being recognized. Characterization of such variants may be of relevance to vaccine development and may allow the detection of intrasubtype recombination and superinfection. Recent studies supporting the correlation of HIV-1 clades to immune responses and to drug resistance-associated mutations lend increasing relevance to the role of molecular epidemiology as an essential tool in combating the AIDS pandemic. However, knowledge on the global HIV-1 genetic diversity and its implications is still far from adequate and a major scaling up of efforts is needed.
AIDS reviews 11/2004; 7(4):210-24. · 3.79 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: As the HIV-1 pandemic becomes increasingly complex and as new countries acceed to antiretroviral drugs, the molecular characterization of HIV-1 strains circulating has important implications for vaccine research and for the efficacy of treatments. To follow the evolution of HIV-1 diversity in African countries, we have carried out a molecular analysis of HIV-1 strains collected from 150 HIV-1-positive pregnant women recruited in Bangui, Central African Republic (CAR). We have sequenced reverse transcriptase (RT) and protease (PROT) genes to (1) characterize the subtypes and CRFs, (2) describe the polymorphism of RT and PROT, particularly at the positions of drug resistance mutations in subtype B, and (3) observe potential drug resistance mutations and evaluate the prevalence of isolates bearing such mutations in this untreated population. The results showed that there is a very high and increasing diversity of HIV-1 strains circulating in CAR; out of 117 samples sequenced, we have observed 45 CRF11_cpx, 22 subtypes A1, 13 subtypes G, 7 subtypes CRF01_AE, 3 subtypes B, 3 subtypes CRF02_AG, 2 of each subtype F2 and CRF09_cpx, and one of each subtype D, J, C, H, CRF06_cpx, CRF13_cpx, and CRF19_cpx; the remaining 13 strains showed discordant genomic results suggesting multiple recombinations leading to mosaic viruses. The polymorphism of RT and PROT was high compared to subtype B, particularly at some positions that have been involved in antiretroviral resistance in subtype B, but we could not observe any major resistance mutation in this sample of untreated patients. The prevalence of drug resistance mutations in this population was therefore clearly under the WHO 5% threshold.
AIDS Research and Human Retroviruses 11/2006; 22(10):1036-44. DOI:10.1089/aid.2006.22.1036 · 2.33 Impact Factor
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