Humanitarian crises-natural or human-made events that can threaten communities' health, safety, security, and well-being-may affect the HIV epidemic dynamics. Common aspects of humanitarian crises such as poverty, powerlessness, disruptions to the health systems, and social instability can contribute to a person's vulnerability to HIV infection through increased risk behaviors and limited access to health services. Guided by the Joanna Briggs Institute methodology for scoping reviews and the Preferred Reporting Items for Systematic Reviews and Meta-Analysis extension for Scoping Reviews (PRISMA-ScR) reporting guidelines, we conducted a scoping review of literature published in English between January 1990 and March 2022 to characterize the global evidence of modifiable and non-modifiable factors for HIV acquisition in the context of humanitarian crises. We systematically searched, screened, and synthesized literature from MEDLINE, Embase, Global Health (all accessed via Ovid), and Scopus, and also grey literature through websites of humanitarian agencies and relevant non-government organizations, the International AIDS Society's abstract databases, and Google Scholar. We considered studies presenting empirical data on HIV prevalence, incidence, or risk factors in humanitarian crises-affected populations, including refugees, asylum seekers, and internally displaced persons. Forty-nine studies met the inclusion criteria. The majority of studies were quantitative (n = 43, 87.8%) and cross-sectional (n = 37, 75.5%) in design. Most were single-country studies (n = 43, 87.8%) and conducted in Sub-Saharan Africa (n = 31, 63.3%). We identified 5 non-modifiable factors for HIV acquisition (i.e., age, gender, location, place of birth or origin, and ethnicity) and 60 modifiable factors that we further classified into five categories, namely 18 policy and structural, 9 sociocultural, 11 health and mental health, 16 sexual practice, and 6 humanitarian crisis-related traumatic event factors. Within the modifiable categories, factors that were most often investigated were education level, marital status, sexually transmitted infection diagnosis, condom use, and experience of rape or sexual trauma, respectively. Informed by the findings, we applied the social-ecological model to map the identified multidimensional factors associated with HIV acquisition at the levels of individual, social and sexual networks, community, public policy, and the context of humanitarian crises. The current review provides a comprehensive, global analysis of the available evidence on HIV prevalence, incidence, and risk factors in humanitarian crises and implications for potential programs and research. Future research is warranted to further understand the directionality of the non-modifiable and modifiable factors affecting HIV acquisition, and the multilevel barriers and facilitators to the uptake of HIV prevention strategies in the context of humanitarian crises. Such research can generate actionable evidence to inform the development of ethical, trauma-informed, and culturally appropriate HIV prevention interventions in humanitarian settings.

Human immunodeficiency virus (HIV) is a major public health concern, particularly in Africa where HIV rates remain substantial. Pregnant women are at an increased risk of acquiring HIV, which has a significant impact on both maternal and child health.

To review summarizes HIV seroprevalence among pregnant women in Africa. It also identifies regional and clinical characteristics that contribute to study-specific estimates variation.

The study included pregnant women from any African country or region, irrespective of their symptoms, and any study design conducted in any setting. Using electronic literature searches, articles published until February 2023 were reviewed. The quality of the included studies was evaluated. The DerSimonian and Laird random-effects model was applied to determine HIV pooled seroprevalence among pregnant women in Africa. Subgroup and sensitivity analyses were conducted to identify potential sources of heterogeneity. Heterogeneity was assessed with Cochran's Q test and I2 statistics, and publication bias was assessed with Egger's test.

A total of 248 studies conducted between 1984 and 2020 were included in the quantitative synthesis (meta-analysis). Out of the total studies, 146 (58.9%) had a low risk of bias and 102 (41.1%) had a moderate risk of bias. No HIV-positive pregnant women died in the included studies. The overall HIV seroprevalence in pregnant women was estimated to be 9.3% [95% confidence interval (CI): 8.3-10.3]. The subgroup analysis showed statistically significant heterogeneity across subgroups (P < 0.001), with the highest seroprevalence observed in Southern Africa (29.4%, 95%CI: 26.5-32.4) and the lowest seroprevalence observed in Northern Africa (0.7%, 95%CI: 0.3-1.3).

The review found that HIV seroprevalence among pregnant women in African countries remains significant, particularly in Southern African countries. This review can inform the development of targeted public health interventions to address high HIV seroprevalence in pregnant women in African countries.

The Democratic Republic of the Congo (DRC) has one of the lowest HIV prevalence in sub-Saharan Africa, estimated at 1.1% [0.9-1.3] of adults aged 15-49 in 2013 (UNAIDS). Within the 2 million km(2) country, however, there exists spatial variation in HIV prevalence, with the highest HIV prevalence observed in the large cities of Kinshasa and Lubumbashi. Globally, HIV is an increasingly rural disease, diffusing outwards from urban centers of high HIV prevalence to places where HIV was previously absent or present at very low levels. Utilizing data collected during Demographic and Health Surveillance (DHS) in 2007 and 2013 in the DRC, we sought to update the map of HIV prevalence in the DRC as well as to explore whether HIV in the DRC is an increasingly rural disease or remains confined to urban areas. Bayesian kriging and regression indicate that HIV prevalence in rural areas of the DRC is higher in 2013 than in 2007 and that increased distance to an urban area is no longer protective against HIV as it was in 2007. These findings suggest that HIV education, testing and prevention efforts need to diffuse from urban to rural areas just as HIV is doing.

Thirty years after the discovery of HIV-1, the early transmission, dissemination, and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa (in what is now the Democratic Republic of Congo) was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M and nonpandemic group O were similar until ~1960, after which group M underwent an epidemiological transition and outpaced regional population growth. Our results reconstruct the early dynamics of HIV-1 and emphasize the role of social changes and transport networks in the establishment of this virus in human populations.

West Central Africa has been implicated as the epicenter of the HIV-1 epidemic, and almost all group M subtypes can be found there. Previous analysis of early HIV-1 group M sequences from Kinshasa in the Democratic Republic of Congo, formerly Zaire, revealed that isolates from a number of individuals fall in different positions in phylogenetic trees constructed from sequences from opposite ends of the genome as a result of recombination between viruses of different subtypes. Here, we use discrete ancestral trait mapping to develop a procedure for quantifying HIV-1 group M intersubtype recombination across phylogenies, using individuals' gag (p17) and env (gp41) subtypes. The method was applied to previously described HIV-1 group M sequences from samples obtained in Kinshasa early in the global radiation of HIV. Nine different p17 and gp41 intersubtype recombinant combinations were present in the data set. The mean number of excess ancestral subtype transitions (NEST) required to map individuals' p17 subtypes onto the gp14 phylogeny samples, compared to the number required to map them onto the p17 phylogenies, and vice versa, indicated that excess subtype transitions occurred at a rate of approximately 7 × 10(-3) to 8 × 10(-3) per lineage per year as a result of intersubtype recombination. Our results imply that intersubtype recombination may have occurred in approximately 20% of lineages evolving over a period of 30 years and confirm intersubtype recombination as a substantial force in generating HIV-1 group M diversity.

The global spread of HIV-1 main group (group M) has resulted in differential distributions of subtypes and recombinants, with the greatest diversity being found in sub-Saharan Africa. The explanations for the current subtype distribution patterns are likely multifactorial, but the promotion of human migrations and movements through transportation link availability and quality, summarized through 'accessibility', have been consistently cited as strong drivers. We sought to address the question of whether accessibility has been a significant factor in HIV-1 spread across mainland Africa through spatial analyses of molecular epidemiology, transport network and land cover data.

The distribution of HIV-1 subtypes and recombinants in sub-Saharan Africa for the period 1998-2008 was mapped using molecular epidemiology data at a finer level of detail than ever before. Moreover, hypotheses on the role of distance, road network structure and accessibility in explaining the patterns seen were tested using spatial datasets representing African transport infrastructure, land cover and an accessibility model of landscape travel speed.

Coherent spatial patterns in HIV-1 subtype distributions across the continent exist, and a substantial proportion of the variance in the distribution and diversity pattern seen can be explained by variations in regional spatial accessibility.

The study confirms quantitatively the influence of transport infrastructure on HIV-1 spread within Africa, presents an approach for examining potential future impacts of road development projects and, more generally, highlights the importance of accessibility in the spread of communicable diseases.

This review examines the enormous progress that has been made in the past decade in understanding the origin of HIV, HIV genetic variability, and the impact of global HIV diversity on the pandemic. Multiple zoonotic transmissions of simian immunodeficiency virus (SIV) have resulted in different HIV lineages in humans. In addition, the high mutation and recombination rates during viral replication result in a great genetic variability of HIV within individuals, as well as within populations, upon which evolutionary selection pressures act. The global HIV pandemic is examined in the context of HIV evolution, and the global diversity of HIV subtypes and recombinants is discussed in detail. Finally, the impact of HIV diversity on pathogenesis, transmission, diagnosis, treatment, the immune response, and vaccine development is reviewed.

Blood transfusion safety in sub-Saharan Africa (SSA) is marred by the high prevalence of infectious agents, chronic blood shortage and lack of resources. However, considerable pressure is applied by richer countries and international transfusion bodies to establish voluntary, non-remunerated blood donors (VNRD) as the only source of blood, excluding the traditional family/replacement donors on the grounds of a higher level of safety. Such a policy increases the cost of a unit of blood by two to fivefold and exacerbates the pre-existing blood shortage. This review provides compelling evidence that first-time VNRD are no safer than family/replacement donors and that only repeat donation provides improved blood safety. In order to limit blood shortage and maintain affordability of the blood supply in SSA, both types of donors should be accepted and both should be encouraged to donate regularly.

We examined HIV prevalence trends over 4.5 years among women receiving antenatal care in Kinshasa, Democratic Republic of Congo, by geographic location, clinic management and urbanicity.

Quarterly proportions and 95% confidence intervals (CIs) of pregnant women with HIV positive results were determined using aggregate service provision and uptake data from 22 maternity units that provided vertical HIV prevention services from October 2004 to March 2009. Assuming linearity, proportions were assessed for trend via the Cochran-Armitage test. Multivariable binomial regression was used to describe detailed prevalence trends.

HIV testing was offered to 220,006 pregnant women; 210,348 (95.6%) agreed to be tested and 191,216 (90.9%) received their results. A total of 3999 women were found to be HIV positive, a prevalence of 1.90% (95% CI: 1.84-1.96%). The median quarterly proportion of women testing positive for HIV was 1.94% (range: 1.44-2.44%). Prevalence was heterogeneous in terms of maternity management, urbanicity and geographic location. Modeling suggested that the overall prevalence dropped from 2.04% (95% CI: 1.92-2.16%) to 1.77% (95% CI: 1.66-1.88%) over 4.5 years, a relative decrease of 13.2% (95% CI: 3.53-22.9%). Trend testing corroborated this decline (P < 0.01).

The decreasing HIV prevalence among Kinshasa antenatal care seekers is robust and encouraging. The relatively low prevalence and the weak existing healthcare system require prevention of mother-to-child transmission interventions that strengthen maternal and child healthcare service delivery. Complacency would be unwarranted: assuming a uniform national crude birth rate of 50/1000 and 1.8% antenatal HIV prevalence, approximately 7000 pregnant HIV infected women in Kinshasa, and 60,000 nationwide, are in need of care and prevention services yearly.

This study compares the sexual behavior and HIV prevalence of men and women at social venues where people meet new sexual partners in Eastern Kinshasa with that of sexually transmitted infection (STI) treatment and antenatal clinic (ANC) patients in the same area.

ANC patients, STI clinic patients, and social venue patrons were interviewed, asked to provide a blood sample on-site, and provided with information about obtaining test results. Every patron at identified social venues in the study area was invited to participate.

One thousand one hundred sixteen pregnant women; 66 male and 229 female STI clinic patients; and 952 male and 247 female patrons of social venues were interviewed and tested for HIV. HIV prevalence differed by group: ANC patients (4%); female venue patrons (12%); female STI patients (16%); male venue patrons (2%); and male STI patients (23%). HIV prevalence among sex workers at social venues (29%) was higher than HIV prevalence among other female patrons with new or multiple partnerships in the past four weeks (19%) and higher than HIV prevalence among female patrons denying sex work (6%). However, the absolute number of infected women was higher among women reporting recent new or multiple partnerships than among the smaller group of sex workers (23 vs. 18). Two-thirds of the infected female STI patients (24/36) reported no more than one and no new sexual partner in the past year.

Improving prevention programs in Kinshasa is essential. Prevention efforts should not neglect women at social venues who do not self-identify as sex workers but who have high rates of new sexual partnership formation.

We sought to investigate the evolutionary and historical reasons for the different epidemiological patterns of HIV-1 in the early epidemic. In order to characterize the demographic history of HIV-1 subtypes A and D in east Africa, we examined molecular epidemiology, geographical and historical data.

We employed high-resolution phylodynamics to investigate the introduction of HIV-1A and D into east Africa, the geographic trends of viral spread, and the demographic growth of each subtype. We also used geographic information system data to investigate human migration trends, population growth, and human mobility.

HIV-1A and D were introduced into east Africa after 1950 and spread exponentially during the 1970s, concurrent with eastward expansion. Spatiotemporal data failed to explain the establishment and spread of HIV based on urban population growth and migration. The low prevalence of the virus in the Democratic Republic of Congo before and after the emergence of the pandemic was, however, consistent with regional accessibility data, highlighting the difficulty in travel between major population centers in central Africa. In contrast, the strong interconnectivity between population centers across the east African region since colonial times has likely fostered the rapid growth of the epidemic in this locale.

This study illustrates how phylodynamic analysis of pathogens informed by geospatial data can provide a more holistic and evidence-based interpretation of past epidemics. We advocate that this 'landscape phylodynamics' approach has the potential to provide a framework both to understand epidemics' spread and to design optimal intervention strategies.

This study examined the prevalence of HIV and other sexually transmitted infections (STIs) in pregnant women in Kinshasa, the Democratic Republic of the Congo (DRC). Between April and July 2004, antenatal attendees at two of the largest maternity clinics in Kinshasa were tested to identify HIV status, syphilis, Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG). HIV seroprevalence was 1.9% in 2082 women. With PCR techniques, CT and NG infections were also uncommon in the first 529 women (1.7% and 0.4%, respectively). No active syphilis infection case was identified by Treponema pallidum haemagglutination assay (TPHA) and rapid plasma reagin test (RPR). A woman's risk of HIV infection was significantly associated with her reporting a male partner having had other female sexual partners (OR 2.7, 95% CI 1.2-6.2). The continuing low seroprevalence of HIV in pregnant women from Kinshasa was confirmed. Understanding factors associated with this phenomenon could help prevent a future HIV epidemic in low HIV transmission areas in Africa.

Violence and rape are believed to fuel the HIV epidemic in countries affected by conflict. We compared HIV prevalence in populations directly affected by conflict with that in those not directly affected and in refugees versus the nearest surrounding host communities in sub-Saharan African countries.

Seven countries affected by conflict (Democratic Republic of Congo, southern Sudan, Rwanda, Uganda, Sierra Leone, Somalia, and Burundi) were chosen since HIV prevalence surveys within the past 5 years had been done and data, including original antenatal-care sentinel surveillance data, were available. We did a systematic and comprehensive literature search using Medline and Embase. Only articles and reports that contained original data for prevalence of HIV infection were included. All survey reports were independently evaluated by two epidemiologists to assess internationally accepted guidelines for HIV sentinel surveillance and population-based surveys. Whenever possible, data from the nearest antenatal care and host country sentinel site of the neighbouring countries were presented. 95% CIs were provided when available.

Of the 295 articles that met our search criteria, 88 had original prevalence data and 65 had data from the seven selected countries. Data from these countries did not show an increase in prevalence of HIV infection during periods of conflict, irrespective of prevalence when conflict began. Prevalence in urban areas affected by conflict decreased in Burundi, Rwanda, and Uganda at similar rates to urban areas unaffected by conflict in their respective countries. Prevalence in conflict-affected rural areas remained low and fairly stable in these countries. Of the 12 sets of refugee camps, nine had a lower prevalence of HIV infection, two a similar prevalence, and one a higher prevalence than their respective host communities. Despite wide-scale rape in many countries, there are no data to show that rape increased prevalence of HIV infection at the population level.

We have shown that there is a need for mechanisms to provide time-sensitive information on the effect of conflict on incidence of HIV infection, since we found insufficient data to support the assertions that conflict, forced displacement, and wide-scale rape increase prevalence or that refugees spread HIV infection in host communities.

The objective of this study was to determine the prevalence and risk factors of HIV and other sexually transmitted infections (STIs) among female sex workers (FSWs) in Kinshasa, Democratic Republic of the Congo, in 2002.

A cross-sectional study was conducted among FSWs presenting for the first time at the STI clinic of Matonge, Kinshasa. The women were interviewed about sociodemographic characteristics, type of sex work, and sexual behavior. Blood was taken for HIV, syphilis, and herpes simplex virus type 2 serology. Vaginal secretions were collected on swabs for the diagnosis of gonorrhea, chlamydia, and trichomoniasis.

The overall HIV prevalence was 12.4% but varied within the different categories of FSWs: 11.8% in hotel-based, 24.0% in home-based, and 20.0% in street-based FSWs; 10.0% in homeless FSWs; and 6.6% in Masquées (clandestine sex workers). The overall herpes simplex virus type 2 seroprevalence was 58.5%.

The prevalence of HIV and other STIs seems to have stabilized since the beginning of the project in 1988.

This study assessed the extent and correlates of the practice of engaging in unprotected intercourse for extra money among commercial sex workers (CSWs) in Kinshasa, Democratic Republic of the Congo. We conducted a cross-sectional survey using a structured, interviewer-administered questionnaire among a convenience sample of 136 CSWs. More than one-quarter of CSWs (26.5%) engaged in unprotected intercourse for extra money. These CSWs charged about 3.5 times more for unprotected intercourse than for protected intercourse. Multivariate logistic regression showed that CSWs who engaged in unprotected intercourse for extra money were significantly more likely to live or work in non-downtown (lower socioeconomic) areas of Kinshasa (odds ratio [OR] = 3.07), to have at least one child less than six years of age (OR = 2.95), and to know other CSWs who engaged in the same practice (OR = 9.38). We hypothesize that desperate socioeconomic conditions combined with peer/social norms drive the practice of engaging in unprotected intercourse for extra money. Additional circumstances under which Kinshasa CSWs engaged in unprotected intercourse included intercourse with clients who tore their condoms to increase sexual pleasure (58.8% of CSWs), episodes of condom failure (56.8% of CSWs), and unprotected intercourse with regular noncommercial partners (only 5.3% of CSWs with noncommercial partners always used condoms with these partners).

The Democratic Republic of Congo (DRC) is characterized by low and stable HIV prevalences and high HIV-1 genetic diversity and is most probably the epicenter of HIV-1 group M. Our major goal was to study the distribution of HIV-1 variants over a 5-year period against a background of political instability and civil war. A total of 288 HIV-1-positive samples collected in 2002 from sentinel population groups in an HIV serosurveillance study performed in 4 cities (Kinshasa [capital city], Mbuji-Mayi [south], Lubumbashi [southeast], and Kisangani [northeast]) were genetically characterized by sequencing and phylogenetic analysis of the V3-V5 env region. The results were compared with those obtained in 1997. Similarly, as in 1997, an extremely high genetic diversity of HIV-1 strains overall and a heterogeneous geographic distribution were seen in 2002. All subtypes and several circulating recombinant forms were present, high intrasubtype diversity was observed, and 5.6% of the samples could not be classified. In each geographic region of the DRC, the genetic diversity was significantly higher than in neighboring countries. Comparison of subtype distribution in similar population groups in Kinshasa in 1997 and 2002 revealed an overall increase of subtype C in Kinshasa from 2.1% to 9.7% and, more precisely, from 0% to 18.9% in female sex workers (P = 0.013). Genetic characterization of HIV-positive samples from sentinel surveys adds significant additional information on new trends in the HIV epidemic. These changes could have implications regarding the spread of HIV infection in the DRC as well on vaccine and/or treatment strategies.

Central Africa was the epicenter of the HIV type 1 (HIV-1) pandemic. Understanding the early epidemic in the Democratic Republic of the Congo, formerly Zaire, could provide insight into how HIV evolved and assist vaccine design and intervention efforts. Using enzyme immunosorbent assays, we tested 3,988 serum samples collected in Kinshasa in the mid-1980s and confirmed seroreactivity by Western blot. Polymerase chain reaction of gag p17, env C2V3C3, and/or gp41; DNA sequencing; and genetic analyses were performed. Gene regions representing all the HIV-1 group M clades and unclassifiable sequences were found. From two or three short gene regions, 37% of the strains represented recombinant viruses, multiple infections, or both, which suggests that if whole genome sequences were available, most of these strains would have mosaic genomes. We propose that the HIV epidemic was well established in central Africa by the early 1980s and that some recombinant viruses most likely seeded the early global epidemic.

From the mid-1970s, seven countries in sub-Saharan Africa have experienced civil disorders and wars lasting for at least 10 years. In two-- Sierra Leone during 1991-2002, and Somalia from 1988 and continuing--adult HIV prevalence remained below 1%. In the Democratic Republic of the Congo, HIV prevalence appears to have stabilised during post-1991 civil disorder and war. Limited information from Angola (civil war 1975 -2002) and Liberia (civil disorder and war from 1989 and continuing) suggests low HIV prevalence. Mozambique's HIV prevalence was near 1% after its 1975 - 1992 civil war, but increased dramatically in the first post-war decade. Across African countries with long-term wars, HIV seems to have spread more slowly than in most neighbouring countries at peace. This evidence contributes to the ongoing debate about the factors that explain differential epidemic trajectories, a debate which is crucial to the design of HIV prevention programmes. One possible explanation for slow epidemic growth in wartime is that unsterile health care accounts for an important proportion of HIV transmission during peacetime, but much less when wars disrupt health services. However, other explanations are also possible. The roles of sex and blood exposures in HIV epidemics in war and peace await empirical determination.

To estimate the prevalence rates of HIV and other sexually transmitted infections (STI) among unregistered sex workers, and to describe their sociodemographic characteristics and sexual behaviours, and the reasons why they were not officially registered as sex workers, in order to design specific public health interventions.

A one-stage cluster-sample survey was conducted in Dakar in 2000. Unregistered sex workers were interviewed in randomly selected establishments (official and clandestine bars, brothels and nightclubs), and blood, endocervical and vaginal samples were collected for laboratory diagnosis.

A total of 390 women with a median age of 29 years were recruited. One-seventh of them were under the legal age for prostitution in Senegal (21 years). The median length of prostitution was 24 months and 73.5% of the women stated regular prostitution. Three-quarters of the women were found to have markers for at least one infection. The prevalence rates were as follows: HIV-1, 6.0%; HIV-2, 3.6%; HIV-1+2, 0.4%; syphilis, 23.8%; gonorrhea, 22.0%; chlamydial infection, 20.0%; trichomoniasis, 22.4%; candidiasis, 19.0%; and bacterial vaginosis, 28.8%. The main reported reason for non-registration was ignorance of the legal system and its procedures (19.4%); 18.9% of the women refused to register. One-third of the women reported that their clients used condoms inconsistently or never.

This survey suggests that a multidimensional public health response is needed in Senegal, comprising legal information, downwards revision of the legal age for prostitution, and specific medical follow-up based on education, condom promotion and management of STI for non-registered sex workers.

In earlier work, human immunodeficiency virus type 1 (HIV-1) sequences were analysed to estimate the timing of the ancestral sequence of the main group of HIV-1, the virus that is responsible for the acquired immune deficiency syndrome pandemic, yielding a best estimate of 1931 (95% confidence interval of 1915-1941). That work will be briefly reviewed, outlining how phylogenetic tools were extended to incorporate improved evolutionary models, how the molecular clock model was adapted to incorporate variable periods of latency, and how the approach was validated by correctly estimating the timing of two historically documented dates. The advantages, limitations, and assumptions of the approach will be summarized, with particular consideration of the implications of branch length uncertainty and recombination. We have recently undertaken new phylogenetic analysis of an extremely diverse set of human immunodeficiency virus envelope sequences from the Democratic Republic of the Congo (the DRC, formerly Zaire). This analysis both corroborates and extends the conclusions of our original study. Coalescent methods were used to infer the demographic history of the HIV-1 epidemic in the DRC, and the results suggest an increase in the exponential growth rate of the infected population through time.

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.

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.

We recently reported a high divergence among African subtype F strains. Three well-separated groups (F1, F2, and F3) have been shown based on the phylogenetic analysis of the p24 gag and envelope sequences with genetic distances similar to those observed for known subtypes. In this study, we characterized the near-full-length genomes of two strains from epidemiological unlinked individual belonging to each of the subgroups: F1 (96FR-MP411), F2 (95CM-MP255 and 95CM-MP257), and F3 (96CM-MP535 and 97ZR-EQTB11). Phylogenetic analysis of the near-full-length sequences and for each of the genes separately showed the same three groups, supported by high bootstrap values. Diversity plotting, BLAST subtyping, and bootstrap plotting confirmed that the divergent F strains correspond to nonrecombinant viruses. The divergence between F1 and F2 is consistently lower than that seen in any other intersubtype comparison, with the exception of subtypes B and D. Based on all the different analyses, we propose to divide subtype F into two subclades, with F1 gathering the known subtype F strains from Brazil and Finland, and our African strain (96FR-MP411), and F2 containing the 95CM-MP255 and 95CM-MP257 strains from Cameroon. The F3 strains, 97ZR-EQTB11 from the Democratic Republic of Congo and 96CM-MP535 from Cameroon, meet the criteria of a new subtype designated as K. The equidistance of subtype K to the other subtypes of HIV-1 suggests that this subtype existed as long as the others, the lower distance between B and D, and between F1 and F2 suggest a more recent subdivision for these latter strains.