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The Central African Republic (CAR) is characterized by widespread HIV epidemic with notable prevalence and genetic diversity. We herein analysed the genetic diversity of atypical non-M HIV-1 strains. In-house serotyping assays for variants of HIV-1 (M, N, O, P) and HIV-2 were used to test a biological collection of 6092 HIV-seropositive blood samples collected between 2003 and 2014 at the Institut Pasteur de Bangui. Samples indicative of recombinant M/O groups, HIV-2, or those that yield doubtful/negative results underwent further PCR tests and sequencing. We found six atypical HIV strains: specifically, three (0.05%) HIV-1 group O strains (subtype H) detected in samples from 2005, 2008 and 2009, alongside three (0.05%) HIV-2 strains (two group A and one group B) identified in samples from 2007 and 2009. HIV-1/O strains showed a genetic link to Cameroon and Gabon strains. This study highlights the dominance of HIV-1/M in the CAR's HIV epidemic over time and underscores the infrequent occurrence of HIV-1 group O and HIV-2 strains. These findings validate the efficacy of WHO-recommended HIV testing protocols and emphasize the need for adaptive surveillance and management strategies to confront the complexities introduced by the genetic diversity of HIV strains., (© 2024 Scandinavian Societies for Pathology, Medical Microbiology and Immunology.)

Background: Sub-Saharan African countries have a high burden of viral hepatitis and poor access to screening and care. The aim of this study was to evaluate the feasibility and acceptability of using the plasma separation card (PSC) for viral hepatitis B and C screening among people living with HIV (PLHIV) in Cameroon and Uganda., Methods: This is a cross-sectional study carried out between 05/2021 and 03/2023 including 192 PLHIV in Cameroon (n = 104) and Uganda (n = 88). Basic sociodemographic variables and whole blood samples were collected. Adequate filling with blood of PSCs was used to determine feasibility together with participant responses to questions on acceptability. A logistic regression model was carried out to assess the relationship between PSC acceptability and factors of interest., Results: 70% of participants reported PSC as an acceptable viral hepatitis screening tool, and it was significantly more accepted in Uganda than Cameroon (100% vs. 43.2%, p < 0.001). Similarly, 75% of PSCs had at least one spot sample filled and were viable for analysis, 99% were correctly filled in Uganda and 53.4% in Cameroon. Reported ease of method performance (aOR: 24.77 95% CI 2.97-206.42, p = 0.003) and reduced collection time (aOR: 3.73 95% CI 1.26-11.04, p = 0.017) were associated with greater odds of PSC acceptance. HBsAg + and anti-HCV + prevalence were 11.1% and 1.0%, respectively., Conclusions: In spite of country differences, overall, the PSC was reported as a feasible and acceptable viral hepatitis testing method. Acceptability and feasibility of the method must be explored in heterogeneous target communities and qualitative research to better understand country-specific barriers and facilitators should be carried out., (© 2024. The Author(s).)

Introduction: Due to their common routes of transmission, human immunodeficiency virus (HIV) coinfection with hepatitis B virus (HBV) and/or hepatitis C virus (HCV) has become a major public health problem worldwide, particularly in Africa, where these viruses are endemic. Few systematic reviews report the epidemiological data of HBV and/or HCV coinfection with HIV in Africa, and none provided data on the case fatality rate (CFR) associated with this coinfection. This study was conducted to investigate the prevalence and case fatality rate of HBV and/or HCV infections among people living with human immunodeficiency virus (PLHIV) in Africa., Methods: We conducted a systematic review of published articles in PubMed, Web of Science, African Journal Online, and African Index Medicus up to January 2022. Manual searches of references from retrieved articles and grey literature were also performed. The meta-analysis was performed using a random-effects model. Sources of heterogeneity were investigated using subgroup analysis, while funnel plots and Egger tests were performed to assess publication bias., Results: Of the 4388 articles retrieved from the databases, 314 studies met all the inclusion criteria. The overall HBV case fatality rate estimate was 4.4% (95% CI; 0.7-10.3). The overall seroprevalences of HBV infection, HCV infection, and HBV/HCV coinfection in PLHIV were 10.5% [95% CI = 9.6-11.3], 5.4% [95% CI = 4.6-6.2], and 0.7% [95% CI = 0.3-1.0], respectively. The pooled seroprevalences of current HBsAg, current HBeAg, and acute HBV infection among PLHIV were 10.7% [95% CI = 9.8-11.6], 7.0% [95% CI = 4.7-9.7], and 3.6% [95% CI = 0.0-11.0], respectively. Based on HBV-DNA and HCV-RNA detection, the seroprevalences of HBV and HCV infection in PLHIV were 17.1% [95% CI = 11.5-23.7] and 2.5% [95% CI = 0.9-4.6], respectively. Subgroup analysis showed substantial heterogeneity., Conclusions: In Africa, the prevalence of hepatotropic viruses, particularly HBV and HCV, is high in PLHIV, which increases the case fatality rate. African public health programs should emphasize the need to apply and comply with WHO guidelines on viral hepatitis screening and treatment in HIV-coinfected patients., Review Registration: PROSPERO, CRD42021237795., Competing Interests: The authors have declared that no competing interests exist.

Hepatitis E virus (HEV) is a major cause of acute hepatitis worldwide. HEV infection is self-limiting, but fulminant hepatitis may occur with higher mortality rates. The aim of this study was to determine the seroprevalence of the HEV in three different populations in Cameroon and to assess alimentary risk factors of infection. A total of 903 individuals including 450 elderly people, 183 pregnant women, and 270 HIV-infected patients were enrolled during 2009-2015. All sera obtained were tested for the presence of anti-HEV antibodies with commercial enzyme-linked immunosorbent assay kits. The association between initial anti-HEV status and potential risk factors was assessed. Out of the 903 samples, 22.0% (199/903) were positives for anti-HEV immunoglobulin M (IgM), 5.8% (52/903) for anti-HEV IgG, and 3.5% (32/903) for both. The seropositivity for IgM was 7.0%, 13.1%, and 34.7%; meanwhile, the seropositivity for immunoglobulin G was 8.5%, 3.3%, and 5.1%, in HIV-infected patients, pregnant women, and the elderly population, respectively. Both antibodies were detected simultaneously in 2.2%, 1.6%, and 5.1% in HIV-infected patients, pregnant women, and the elderly population, respectively. No risk factors were significantly associated with HEV infection in these populations. This study showed a high prevalence of anti-HEV antibodies in three different populations in Cameroon., (© 2019 Wiley Periodicals, Inc.)

Background: To set priorities for efficient control of acute respiratory tract infection (ARTI) in Africa, it is necessary to have accurate estimate of its burden, especially among HIV-infected populations., Objectives: To compare case fatality rate (CFR) and viral aetiologies of ARTI between HIV-positive and HIV-negative populations in Africa., Study Design: We searched PubMed, EMBASE, Web of Knowledge, Africa Journal Online, and Global Index Medicus to identify studies published from January 2000 to April 2018. Random-effect meta-analysis method was used to assess association (pooled weighted odds ratios (OR) with 95% confidence interval (CI))., Results: A total of 36 studies (126,526 participants) were included. CFR was significantly higher in patients with HIV than in HIV-negative controls (OR 4.10, 95%CI: 2.63-6.27, I²: 93.7%). The risk was significantly higher among children ≤5 years (OR 5.51, 95%CI 2.83-10.74) compared to people aged >5 years (OR 1.48, 95%CI 1.17-1.89); p = 0.0002. There was no difference between children (15 years) and adults and between regions of Africa. There was no difference for viral respiratory aetiologies (Enterovirus, Adenovirus, Bocavirus, Coronavirus, Metapneumovirus, Parainfluenza, Influenza, and Respiratory Syncytial Virus) of ARTI between HIV-positive and HIV-negative people, except for Rhinovirus where being HIV-negative was associated with Rhinovirus (OR 0.70; 95%CI 0.51-0.97, I²: 63.4%)., Conclusions: This study shows an increased risk of deaths among HIV-infected individuals with ARTI, however with no difference in viral aetiologies compared to HIV-negative individuals in Africa. ARTI deserves more attention from HIV health-care providers for efficient control. Specific strategies are needed for HIV-positive children under 5., (Copyright © 2019 Elsevier B.V. All rights reserved.)

HIV-1 group N (HIV-1/N) remains rare and mainly restricted to Cameroon. In this study, we report a new HIV-1/N infected case identified during routine HIV screening activities in Yaounde. The genetic characterization of the near full-length genome of this virus strain revealed that it is genetically distinct to all HIV-1/N described to date. However, the Vpu protein responsible for tetherin antagonism displayed the same amino acid substitutions (E15A, V19A, I25L, and V26L) as other HIV-1/N from Cameroon.

Objective: This study was performed in order to fill the gap of knowledge regarding sero-epidemiology of hepatitis B virus (HBV) amongst Human Immunodeficiency virus (HIV)-infected patients and to assess the risk factors associated with HBV co-infection in a rural locality of Cameroon. A retrospective and cross-sectional study was carried out from January 2008 to April 2014 within the Mfou District Hospital. Naive HIV-infected patients were enrolled in the study and tested for hepatitis B surface antigen (HBsAg). Preliminary pre-therapeutic data essential for follow-up was collected from the participants., Results: Overall, the sample size was constituted of 712 HIV-infected patients. The prevalence of HBsAg was 8.99%. A significant difference was observed in the proportion of HBsAg positive subjects with respect to the year of inclusion; higher proportions were observed between 2011 and 2014 (P-value = 0.007). Majority of HBV co-infected participants had severe immuno-suppression with CD4 counts lower than 100 cells/µL as compared to HIV mono-infected population but the difference was not statistically significant. Our results confirm the high prevalence for HBV infection among HIV-infected patients in the Mfou District Hospital. These findings will enable stake holders to be better armed in the elimination of viral hepatitis as a public health problem.

In Gabon, a central African country, human immunodeficiency virus (HIV) and hepatitis B virus (HBV) are endemic. In a recent study, conducted in a semi-urban area (Franceville, Gabon), HBV infection was found to be more prevalent among HIV infected individuals. This study aims to investigate the prevalence and genetic diversity of hepatitis B virus infection among HIV infected individuals, predominantly under antiretroviral therapy, living in fully urbanized area: Libreville, capital of Gabon. Serological and molecular tests were performed to detect HBV infection among patients living with HIV/AIDS (PLHA). We used Monolisa HBsAg ULTRA, Anti-HBc Plus and Anti-HBs Plus EIA kits for serological analyses. HBV DNA viral load (HBV DNA VL) was determined by real time PCR and molecular characterization of HBV strains was performed by sequencing and phylogenetic analysis of partial HBV surface and core genes. At all, 70.2% of patients were under antiretroviral therapy. The prevalence of HBsAg was 8.8% (43/487). Detectable HBV DNA was found in 69.7% (30/43) of HBsAg positive patients and in 17.5% (24/137) HBsAg negative patients. HBV DNA VL was significantly higher among patient with CD4 cell counts less than 200 cells/mm3 than those with CD4 cell counts greater than 500 cells/mm3 (p = 0.008). We confirmed the presence of HBV sub-genotypes QS-A3 (40%), and A4 (20%) and HBV-E genotype (40%). The percentage of resistance to Lamivudine was high (40%) and varied according to the M204V/I motif. Occult hepatitis B infection (OBI) was found in patients with isolated HBcAb and among patients who had completed their HBsAg seroconversion. We detected HBV DNA for one patient without any HBV serological marker. This study provides a new landmark for the comprehension of HBV infection in PLHA in urban areas. OBI enhances HBV DNA prevalence and should be investigated in all HBsAg negative individuals.

Background: HIV infection in Cameroon is characterized by a great viral diversity with all HIV-1 groups (M, N, O, and P) and HIV-2 in circulation. HIV group determination is very important if tailored viral load analysis and treatments are to be applied. In our laboratory, HIV viral load is carried out using two platforms; Biocentric and Abbott depending on the HIV group identified. Biocentric which quantifies HIV-1 group M is a cheap and open system useful in resource limited settings. The objective of this study was to compare the viral load analyses of serologically group-indeterminate HIV samples using the two platforms with the view of reducing cost., Methods: Consecutive samples received between March and May 2014, and between August and September 2014 in our laboratory for HIV viral load analysis were included. All these samples were analyzed for their HIV groups using an in-house ELISA serotyping test. All HIV-1 group M samples were quantified using the Biocentric test while all other known atypical samples (HIV-1 groups N, O and P) were analyzed using the Abbott technique. HIV group-indeterminate samples (by serotyping) were quantified with both techniques., Results: Among the 6355 plasma samples received, HIV-1 group M was identified in 6026 (94.82%) cases; HIV-1 group O, in 20 (0.31%); HIV-1 group M + O, in 3 (0.05%) and HIV-2, in 3 (0.05%) case. HIV-group indeterminate samples represented about 4.76% (303/6355) and only 231 of them were available for analysis by Abbott Real-Time HIV-1 and Generic HIV Viral Load techniques. Results showed that 188 (81.39%) samples had undetectable viral load in both techniques. All the detectable samples showed high viral load, with a mean of 4.5 log copies/ml (range 2.1-6.5) for Abbott Real-Time and 4.5 log copies/ml (range 2-6.4) for Generic HIV Viral Load. The mean viral load difference between the two techniques was 0.03 log 10 copies/ml and a good correlation was obtained (r 2  = 0.89; P < 0.001)., Conclusion: Our results suggest that cheaper and open techniques such as Biocentric could be useful alternatives for HIV viral load follow-up quantification in resource limited settings like Cameroon; even with its high viral diversity.

Access to antiretrovirals has increased the life expectancy of patients living with HIV. However, HIV-viral hepatitis coinfections in countries endemic for these infections make management more difficult. To determine the extent of these coinfections in Gabon, we investigated markers of hepatitis B, C, and E viruses in 762 adults infected with HIV-1 by ELISA. We used real-time PCR to quantify plasma HBV DNA (HBV VL) and amplified HCV and HEV RNA by nested RT-PCR and PCR.The seroprevalence of chronic hepatitis B infection was 9.3 %. Among patients with isolated HBcAc profiles, the prevalence of occult hepatitis B infection was 26.7 %, for a real prevalence (detectable CV-HBV) of 17.3 % of the total population. HCV seroprevalence was 8.8 %. Of the 67 HIV-positive patients, 76.1 % had replicative profiles (detectable HCV RNA), that is, 6.7 % of the total population. For hepatitis E, seroprevalence was 3.5 %. No case of chronic HEV infection was found. In conclusion, this study highlights a high rate of HIV-Hepatitis B, C and E coinfections in Gabon. In addition, we show the interest of looking for chronic infections (replicative profiles) in HIV-infected patients in Gabon. The establishment of technical platforms for this type of research, accessible to middle-income countries, is necessary.

Introduction: The diagnostic procedure for chronic hepatitis C infection (CHC) usually combines anti-HCV antibody (HCV- Ab ) and HCV-RNA measurement. Quantifying HCV core antigen (cAg) as a one-step procedure could shorten the diagnostic process. We aimed to assess the performance of cAg quantification in diagnosing CHC and how it is influenced by concomitant HIV or HBV infections., Methods: The cAg was quantified by an automated assay (Abbott Diagnostics) in 465 HCV- Ab negative serum samples and 544 HCV-RNA positive serum samples ( n  = 1009) collected in patients from the Pasteur Center in Cameroon, some of whom were infected by HBV or HIV. Its performance was evaluated in comparison to the gold standard (ELISA or PCR) by estimating its sensitivity (Se) and specificity (Sp), and by comparing the area under ROC (AUROC) curves in each patient population: HCV mono-infected, HCV-HBV and HIV-HCV co-infected., Results: Among the 465 HCV- Ab negative patients, 51 and 79 were HIV- and HBV-infected, respectively, whereas among the 544 patients with CHC, 27 and 28 were HIV- and HBV-infected, respectively. The Spearman ρ correlation coefficient between cAg and HCV-RNA was 0.75 ( p  < 0.00001). The assay had a sensitivity of 95.7% (95% CI: 93.2-97.5) and a specificity of 99.7% (95% CI: 98.1-10) in diagnosing CHC, corresponding to an AUROC of 0.99 (95% CI: 0.98-1.0). Being HIV- or HBV-infected did not impact the performance of cAg (Se = 96.4%, Sp = 96.2% and AUROC = 0.98 (95% CI: 0.95-1.0) in the HBV group, Se = 100%, Sp = 88.2% and AUROC = 0.99 (95% CI: 0.97-1.0) in the HIV group, p between AUROC = 0.69)., Conclusions: The cAg quantification displayed a high specificity and sensitivity for the diagnosis of CHC in Cameroon, and its performance was not significantly modified by a concomitant HIV or HBV infection. In the context of CHC elimination on a global scale, using cAg quantification as a screening tool to directly identify CHC could be a reliable tool in a "test and treat" strategy., Competing Interests: The authors have no competing interests to declare.

According to the WHO/UNAIDS recommendations, an acceptable HIV rapid diagnostic tests (RDTs) has to perform a sensitivity≥99% and a specificity≥98%. Given the constant release of new RDTs for HIV testing in the market and the high HIV genetic diversity in Cameroon, it is interesting to monitor their performances in that setting. A total of 240 HIV positive (including 219 HIV-1 M, 15 HIV-1 O, 1 HIV-1 N, 1 HIV-1 M/O recombinant and 4 HIV-2) and 240 HIV negative plasma samples were used to evaluate twelve routinely used RDTs in Cameroon. A reference algorithm combining Enzyme Immunoassays and nucleic acid testing was used as gold standard. The sensitivity, specificity, positive predictive value, and negative predictive value of the twelve RDTs evaluated varied between 93.7 and 100%; 95.8 and 100%; 96.0 and 100%, and 94.1 and 100%, respectively. Five out of the twelve RDTs could not detect some HIV-1 O variants, one of them failed to detect an HIV-2 variant while all them efficiently detected HIV-1 N and HIV M/O recombinant. Our findings underscore the need to monitor the performances of RDTs to be used for HIV testing in Cameroon using locally obtained well-characterized samples panels., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Background: First line antiretroviral therapy in a resource-limited setting consists of nucleotide and non-nucleotide reverse transcriptase inhibitors. Protease inhibitors are the hub of second line therapy. The decision to change antiretroviral therapy for a patient is frequently presumptive because of the lack of genotypic resistance tests in routine follow-up. We describe here the resistance profiles observed in patients with varying terms of antiretroviral therapy in Cameroon after implementation of HIV genotypic resistance testing in routine practice., Methods: HIV genotypic resistance testing was carried out on consecutive samples received between August 2013 and November 2015. Protease (Prot) and reverse transcriptase (Rt) genes of the HIV genome were amplified, sequenced and analyzed for drug resistance mutations following the algorithm set up by the French National Agency for research on HIV/AIDS and viral hepatitis., Results: Specimens from a total of 167 patients infected with non-B HIV subtypes were received during the study period. Overall 61.7% patients had viral loads of more than 3log copies/ml, suggesting treatment failure. Among the 72 patients on first line, 56 (77.8%) were resistant to Lamivudine, 57 (79.1%) to Efavirenz and 58 (80.6%) to Nevirapine. Overall, more patients (75.0%) on first line antiretroviral therapy harbored multi-drug resistance compared to their counterparts on second line (25.8%)., Conclusion: This study revealed that a group of patients with antiretroviral therapy failure harbored multi-drug resistance mutations related to the majority of drugs in the first line regimen. Therefore, HIV resistance testing could be a useful tool to improve HIV care in resource limited settings like Cameroon where treatment options are limited., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.)

Integrated data on hepatitis B virus (HBV) patterns, HBV genotypes and mutations are lacking in human immunodeficiency virus type 1 (HIV-1) co-infected patients from Africa. This survey was conducted in 2010-2013 among 762 HIV-1-positive adults from Gabon who were predominantly treated with 3TC-based antiretroviral treatment. HBV patterns were identified using immunoassays detecting total antibody to hepatitis B core antigen (HBcAb), hepatitis B surface antigen (HBsAg), IgM HBcAb, hepatitis B e antigen (HBeAg), antibody to HBsAg (HBsAb) and an in-house real-time PCR test for HBV DNA quantification. Occult hepatitis B (OBI) was defined by the presence of isolated anti-HBc with detectable serum HBV DNA. HBV genotypes and HBV mutations were analyzed by PCR-direct sequencing method. Seventy-one (9.3%) patients tested positive for HBsAg, including one with acute hepatitis B (0.1%; 95% CI, 0.0%-0.2%), nine with HBeAg-positive chronic hepatitis B (CHB) (1.2%; 95% CI, 0.6%-2.2%), 16 with HBeAg-negative CHB (2.1%; 95% CI, 1.2%-3.3%) and 45 inactive HBV carriers (5.9%; 95% CI, 4.4%-7.8%). Sixty-one (8.0%; 95% CI, 6.2%-10.1%) patients showed OBI. Treated patients showed similar HBV DNA levels to those obtained in untreated patients, regardless of HBV patterns. Around 15.0% of OBI patients showed high (>1,000 UI/mL) viremia. The mutation M204V/I conferring resistance to 3TC was more common in HBV/A (47.4%) than in HBV/E isolates (0%) (P = .04). Our findings encouraged clinicians to promote HBV vaccination in patients with no exposure to HBV and to switch 3TC to universal TDF in those with CHB.

Objective: Despite the genetic divergence between HIV-1 groups M and O, HIV-1  M/O intergroup recombinants were reported. Actually, there is no data on the transmissibility of such recombinant forms. During a surveillance of HIV genetic diversity in Cameroon, we investigated the possible direct transmission of an HIV-1  M/O recombinant virus in an HIV-infected couple., Methods: Consecutive samples obtained from the couple were analysed for detection of dual HIV-1 groups M and O infections, and HIV-1  M/O recombinant forms. Analyses were performed using a serological and molecular algorithm based on HIV serotyping and group-specific PCRs targeting the polymerase and envelope genes. Pattern characterization of the strains found in both patients was based on complete genome sequencing. Phylogenetic and similarity profile analyses were performed to investigate the genetic relationship between viruses from both spouses and the previously described recombinant forms., Results: The sero-molecular algorithm data showed a group O serotype confirmed by molecular analysis in the envelope regions, whereas molecular tests identified HIV-1 group M in the polymerase. Phylogenetic analyses and similarity profiles of the full-length genome sequences showed that both spouses were infected with a unique recombinant virus having two recombination breakpoints in the vpr gene and LTR region. No phylogenetic link was found with the previous M/O recombinants., Conclusion: We provide, for the first time, molecular evidence of direct transmission of an HIV-1  M/O recombinant, highlighting the potential spread of these divergent viruses. The importance of HIV-1 recombination on genetic evolution and public health when implying divergent strains as group O has to be carefully considered.

Background: Fourth generation assays for HIV diagnosis are progressively being introduced into routine services, due to their improvement of diagnosis. In spite of this, HIV diagnosis remains a challenge in sub-Saharan Africa, due to false positive reactivity. There is a continuous need for field evaluations and routine validations of fourth generation HIV tests in African populations., Objectives: Evaluate the performances of the ARCHITECT HIV Ag/Ab kit (Abbott) in a population living in an African setting-Cameroon compared to a population living in a European setting-France., Study Design: 645 HIV samples from both France and Cameroon were evaluated. The positive panel (378 samples) included a diverse series of HIV-1 variants (groups M, N, O, and P) as well as HIV-2 samples. Results were compared to original diagnosis done with other 4th generation assays (AxSYM HIV Ag/Ab (Abbott) and Vidas HIV DUO QUICK) (bioMérieux)., Results: Sensitivity of the ARCHITECT was 100% in both sites. It diagnosed all variants of the panel with different reactivity profiles following strain diversity. A wider range of reactivity was observed for group O. Specificity was slightly lower (97.6%) in Cameroon than in France (98.6%), probably due to a higher rate of false positive reactivity. ARCHITECT HIV Ag/Ab assay had high performances in clinical sensitivity and specificity and is adapted to the wide genetic diversity of viruses circulating in West Central Africa., Conclusion: Our results further highlight the need to evaluate HIV diagnostic tests before introduction into routine diagnostic services both in the North and in the South., (Copyright © 2013 Elsevier B.V. All rights reserved.)

HIV-1 pol gene sequencing is now used routinely in France to identify mutations associated with resistance to reverse transcriptase (RT) or protease (PR) inhibitors. These sequences may also provide other information, such as the HIV-1 subtype. HIV-1 subtyping was compared using the RT and PR gene sequences to heteroduplex mobility assay (HMA) of the envelope gene. The RT and PR genes of 51 samples that had been subtyped earlier by HMA were sequenced. Sequences were aligned and subtypes were determined by phylogenetic analysis with reference HIV sequences. HMA gave the following subtypes: A (20), B (19), C (1), D (3), F (1), G (3) and CRF01-AE (4). Phylogenetic analysis of the RT gene gave: A (5), B (19), C (2), D (3), F (1), G (6), J (2), CRF01&#95;AE (4), CFR02&#95;AG (7) and undetermined (2). PR gene analysis did not infer subtypes with sufficient confidence. HMA and RT subtyping was not in agreement in nine cases. RT subtyping can identify CFR02&#95;AG and CRF01&#95;AE variants from A subtype RT. It was shown that phylogenetic analysis of the RT gene could provide a useful method for HIV-1 subtyping. The length of the amplicon and the relative performance of each primer pair used in this study favoured RT sequences as a subtyping tool. One potential advantage over env subtyping HMA is the ability to identify some circulating recombinant forms (CRFs).