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Up to now, all known env subtype E viruses (CRF01-AE) have had the same mosaic structure with subtype A, and no other env subtype E HIV-1 viruses with non-A subtypes in their genomes have been described. In this report we describe the full-length genome sequence of an env subtype E isolate with a recombinant genome different from the prototype CRF01-AE strains. The 97CD-KTB49 strain, obtained from a tuberculosis patient in Kinshasa, has a complex mosaic genome involving subtypes A, E, G, H, J, K, and several unknown fragments. The U sequences formed well-separated clusters together with previously described unknown fragments from CRF04-cpx (subtype I), and from Z321, the oldest intersubtype recombinant isolated in 1976 in the Democratic Republic of Congo. The complex recombinant virus from our study is not an isolated strain; partial sequencing of a second strain, 97CD-KFE45, confirmed the breakpoints observed in the 97CD-KTB49 strain in the regions sequenced. The complexity of these recombinant strains suggests a longstanding presence of subtype E in Central Africa.

Most human immunodeficiency virus (HIV) drug susceptibility studies have involved subtype B strains. Little information on the impact of viral diversity on natural susceptibility to antiretroviral drugs has been reported. However, the prevalence of non-subtype-B (non-B) HIV type 1 (HIV-1) strains continues to increase in industrialized countries, and antiretroviral treatments have recently become available in certain developing countries where non-B subtypes predominate. We sequenced the protease and reverse transcriptase (RT) genes of 142 HIV-1 isolates from antiretroviral-naive patients: 4 belonged to group O and 138 belonged to group M (9 subtype A, 13 subtype B, 2 subtype C, 5 subtype D, 2 subtype F1, 9 subtype F2, 4 subtype G, 5 subtype J, 2 subtype K, 3 subtype CRF01-AE, 67 subtype CRF02-AG, and 17 unclassified isolates). No major mutations associated with resistance to nucleoside reverse transcriptase inhibitors (NRTIs) or protease inhibitors were detected. Major mutations linked to resistance to non-NRTI agents were detected in all group O isolates (A98G and Y181C) and in one subtype J virus (V108I). In contrast, many accessory mutations were found, especially in the protease gene. Only 5.6% of the 142 strains, all belonging to subtype B or D, had no mutations in the protease gene. Sixty percent had one mutation, 22.5% had two mutations, 9.8% had three mutations, and 2.1% (all group O strains) had four mutations. In order of decreasing frequency, the following mutations were identified in the protease gene: M36I (86.6%), L10I/V (26%), L63P (12.6%), K20M/R (11.2%), V77I (5.6%), A71V (2.8%), L33F (0.7%), and M46I (0.7%). R211K, an accessory mutation associated with NRTI resistance, was also observed in 43.6% of the samples. Phenotypic and clinical studies are now required to determine whether multidrug-resistant viruses emerge more rapidly during antiretroviral therapy when minor resistance-conferring mutations are present before treatment initiation.

The purpose of this study was to document the genetic diversity of human immunodeficiency virus type 1 (HIV-1) in the Democratic Republic of Congo (DRC; formerly Zaire). A total of 247 HIV-1-positive samples, collected during an epidemiologic survey conducted in 1997 in three regions (Kinshasa [the capital], Bwamanda [in the north], and Mbuyi-Maya [in the south]), were genetically characterized in the env V3-V5 region. All known subtypes were found to cocirculate, and for 6% of the samples the subtype could not be identified. Subtype A is predominant, with prevalences decreasing from north to south (69% in the north, 53% in the capital city, and 46% in the south). Subtype C, D, G, and H prevalences range from 7 to 9%, whereas subtype F, J, K, and CRF01-AE strains represent 2 to 4% of the samples; only one subtype B strain was identified. The highest prevalence (25%) of subtype C was in the south, and CRF01-AE was seen mainly in the north. The high intersubtype variability among the V3-V5 sequences is the most probable reason for the low (45%) efficiency of subtype A-specific PCR and HMA (heteroduplex mobility assay). Eighteen (29%) of 62 samples had discordant subtype designations between env and gag. Sequence analysis of the entire envelope from 13 samples confirmed the high degree of diversity and complexity of HIV-1 strains in the DRC; 9 had a complex recombinant structure in gp160, involving fragments of known and unknown subtypes. Interestingly, the unknown fragments from the different strains did not cluster together. Overall, the high number of HIV-1 subtypes cocirculating, the high intrasubtype diversity, and the high numbers of possible recombinant viruses as well as different unclassified strains are all in agreement with an old and mature epidemic in the DRC, suggesting that this region is the epicenter of HIV-1 group M.

The purpose of this study was to generate data on the relative prevalences of the HIV-1 subtypes circulating in Nigeria. A total of 252 HIV-1-positive samples collected during an epidemiologic survey conducted in April 1996 were genetically characterized by HMA (heteroduplex mobility assay) and/or sequencing. Samples were collected in Lagos, Calabar, Kano, and Maiduguri. Overall, the predominant env subtypes were A (61.3%) and G (37.5%). Subtype A is more prevalent in the south (p < 0.001), about 70% in Lagos and Calabar, whereas a quarter of the samples was classified as subtype G in these states. In contrast, subtype G is predominant in the north ( < 0.001), representing 58% of the samples in Kano. In the northeastern region, Maiduguri, almost similar proportions of subtype A and G were seen, 49 and 47.4%, respectively. A total of 37 samples was also sequenced in the p24 region from the gag gene; 13 (35%) had discordant subtype designations between env and gag. The majority of the gag (12 of 17) and env (14 of 22) subtype A sequences clustered with the A/G-IBNG strain. Within subtype G, three different subclusters were seen among the envelope sequences. These different subclusters are observed among samples obtained from asymptomatic individuals and AIDS patients from the four Nigerian states studied. In conclusion, we observed a limited number of HIV-1 subtypes circulating in Nigeria, with subtypes A and G being the major env subtypes responsible for the HIV-1 epidemic. Nevertheless, the high rate of recombinant viruses (A/G) and the different A/G recombinant structures indicate a complex pattern of HIV-1 viruses circulating in this country.

Objective: To determine current data on HIV infection and to document changes and trends of HIV seroprevalence in selected populations over time in the Democratic Republic of the Congo (DRC; former Zaïre)., Methods: In February 1997, a large serosurvey was conducted on selected population groups from Kinshasa (capital city), Mbuji-May (southeast) and Bwamanda (northwest). Samples obtained from pregnant women, tuberculosis patients, commercial sex workers, blood donors and sexually transmitted disease patients were screened for the presence of HIV antibodies by a rapid assay and a commercial enzyme-linked immunosorbent assay. All reactive specimens were confirmed and discriminated by a line immunoassay, and were further tested for the presence of HIV-1 group O antibodies. Our results were compared to data reported in previous studies in Kinshasa., Results: Of a total 1970 samples collected, 219 (11.1%) were HIV-1-reactive and seven (0.3%) were dually reactive to HIV-1 and HIV-2. No case of HIV-1 group O or HIV-2 infection was diagnosed. HIV seroprevalence in pregnant women was 3.1% (16 out of 511), 6.3% (19 out of 300) and 1.5% (one out of 65) in Kinshasa, Mbuji-Mayi, and Bwamanda, respectively. HIV seroprevalence in tuberculosis patients was 26% (52 out of 200), 28% (17 out of 60), and 35.3% (29 out of 83), respectively. HIV seroprevalence among blood donors was 3.1% in Kinshasa and 2.8% in Mbuji-Mayi. Compared with data from previous studies performed in Kinshasa, no substantial change in HIV infection rates was observed among the selected population groups., Conclusions: Our results show that HIV prevalence rates have remained relatively unchanged in selected populations despite the political instability and poor environment observed since 1991 in DRC. It also shows the presence, still at very low rate, of dual HIV-1/HIV-2 seropositivity and a growing problem of HIV infection in rural areas. In contrast to other Central African countries, no HIV-1 group O infections were detected in DRC.

To determine current data on HIV infection and to further confirm the presence of HIV-1 group O infection in Nigeria, 2300 samples from five states were tested for the presence of HIV antibody. A convenience sampling was obtained from pregnant women, tuberculosis (TB) patients, commercial sex workers (CSWs), blood donors, patients with sexually transmitted diseases (STDs), patients with skin diseases, male clients of CSWs, outpatients suspected to have AIDS, truck drivers, and community dwellers. With the exception of pregnant women, the HIV prevalences in all these groups were high: 60.6% in CSWs, 16.2% in TB patients, 7.7% in blood donors in some states, and 16% in the rural area of Kano State. Male clients of CSWs, truck drivers, and STD patients had prevalences of 7.8%, 8.6%, and 21.2%, respectively. Regional differences in relation to HIV prevalences were observed; HIV-2 and most of the HIV-1/2 infections were found in the southern states of Nigeria. Higher HIV prevalences were observed in the north-northeast in pregnant women, TB patients, and CSWs, but for blood donors, higher rates were seen in the southeast-southwest. One asymptomatic 50-year-old woman, a community dweller in Kano, was identified to be HIV-1 group O-positive. Compared with data from national surveillance studies in 1991/1992 and 1993/1994, a substantial increase in HIV infection was observed. Our results show a growing incidence of HIV infection in Nigeria and suggest the presence of a rural HIV epidemic. The identification of HIV-1 group O in Kano shows that this virus strain is geographically widespread in Nigeria.