No data on HIV-1 genetic subtypes in Burkina Faso have yet been reported. Among 70 samples obtained in 2001, the predominantenvsubtype was CRF06-cpx, followed by CRF02-AG, subtypes A and G. Nineteen of the 70 samples from 2001 had discordant subtype or circulation recombinant form (CRF) designations betweenenvandgag. In contrast to surrounding countries, CRF06 is predominant in Burkina Faso. This virus was probably introduced early in the HIV epidemic because of its high representation in strains tested in 1996.
Phylogenetic analysis of numerous strains of HIV-1, isolated from diverse geographical origins, have revealed that they can be further subdivided into groups (M, N, and O) subtypes (A–D, F–J and K), sub-subtypes and circulating recombinant forms (CRF; CRF01–CRF14) [1]. Subtype designations have been powerful molecular epidemiological markers to track the course of the HIV-1 pandemic. The global subtype distribution is very heterogeneous and the greatest genetic diversity of HIV-1 has been found in Africa, especially central Africa, where all groups and subtypes are found. Also within Africa, important differences are observed according to the regions studied, from country to country, and even within a country [2,3].
Since the emergence of the AIDS epidemic, no data on HIV-1 genetic subtypes in Burkina Faso, a sahelian country in West Africa (bordered by Ivory Coast, Mali, Niger, Togo, Benin and Ghana), have been reported. The only HIV-1 strain genetically characterized was from a patient originating from Burkina Faso, but residing in Australia [4]. The characterization of this virus led to the description of a novel complex circulating recombinant, CRF06-cpx, which involves recombination events between at least four different subtypes, A, G, J and K [5,6]. In the present study, we have examined the HIV-1 genetic subtype distribution among HIV-1-positive patients attending the ambulatory treatment centre in Ouagadougou in 1996 and 2001.
A total of 89 HIV-1-positive samples were genetically characterized in part of the env or gag regions, 19 samples were collected in 1996 and 70 were collected in 2001. All of them were from natives of Burkina Faso. Fifty-four per cent of the patients were women, and their mean age was sligthly lower than that of the men, 34.1 versus 37.8 years, respectively. The samples from 1996 were collected as dried blood spots on filter paper. For the samples from 2001, whole blood was collected on ethylenediamine tetraacetic acid tubes. Plasma and cell pellets were stored at −20°C. DNA was extracted from the dry cell pellets or dried blood spots using the IsoQuick isolation kit (Microprobe Corp., Garden Cove, CA, USA), or the Qiagen DNA extraction kit (Quiagen SA, Courtabeauf, France). Genetic subtypes were determined in the V3–V5 env region or the p24 gag region by sequencing followed by phylogenetic analysis as previously described [7]. The newly determined HIV-1 env and gag sequences were aligned with known HIV-1 sequences representing the different genetic subtypes and the CRFs documented in west and west central Africa (CRF01-AE, CRF02-AG, CRF06-cpx and CRF11-cpx) using clustal W [8]. Phylogenetic trees using the neighbour joining method [9] and the reliability of the branching orders using the bootstrap approach were implemented by using clustal W. In order to identify clearly whether a sequence belonged to a subgroup representing a CRF within a certain subtype or not, phylogenetic analysis was performed for each sequence individually.
All the samples from 2001 were sequenced in env and gag, those from 1996 were only sequenced in env. In 2001, the predominant env subtype was CRF06-cpx (50.0%), followed by CRF02-AG (30.0%), subtype A (10.0%), and G (7.1%). Although the sample size was very small in 1996, a closely related subtype distribution was observed: CRF06-cpx (47.4%), CRF02-AG (36.8%), subtype A (10.5%), and one strain (5.2%) could not be classified.
Nineteen (27.1%) of the 70 samples from 2001 had discordant subtype or CRF designations between env and gag, and in all the 19 samples a CRF was involved in the recombination event. Approximately 10% of the total number of samples from 2001 were recombinants between the predominant viral variants, CRF02 and CRF06; i.e. 5.7% (n = 4) were CRF06 in env but CRF02 in gag, and for three samples (4.3%) the opposite was seen. Other subtypes, F1 and H were also observed in gag and env, respectively, but both were recombinants, CRF11/F1 and H/CRF06.
In Burkina Faso, env subtype G strains predominate (57% in 2001), and more detailed phylogenetic analysis showed that more than 85% of these strains are in fact representatives of the complex CRF06-cpx variant. Apparently only a few HIV-1 variants circulate in Burkina Faso; however, the situation is more complex than just co-circulating subtypes A and G. The two predominant variants are complex recombinants, especially CRF06-cpx, which is a mosaic virus of at least four subtypes, A, G, K and J and some small unclassified fragments [6]. In addition, the situation becomes even more complex, because the CRF02 and CRF06 strains seem to recombine with each other and with other circulating subtypes. In west and west central Africa, env subtype A and more precisely CRF02-AG variants are predominant, together representing 70–80% of the circulating strains [10,11]. Env subtype G is the next predominant variant in this region of Africa, and can reach up to 30% of the circulating strains, with the majority of them being representatives of CRF06-cpx [12]. In contrast to surrounding countries, CRF06 is predominant in Burkina Faso, and this virus was most probably introduced early in the HIV epidemic in the country because of its high representation among strains from 1996. These data show clearly that subtype distibution is very heterogeneous and probably the result of different founder effects in different west African countries. Whether significant differences exist in pathogenesis, transmissibility or vaccine efficiency among HIV-1 variants has still to be determined, but there is well established evidence that differences related to the efficiency of diagnostic assays and antiretroviral drugs exist among the various HIV-1 variants. Therefore, it remains important to track the molecular epidemiology of HIV-1 and to characterize the prevalent HIV-1 strains genetically.
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