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Objective: This study was aimed at examining the vulnerability of Central Africa to the COVID-19 pandemic. Methods: Demographic, health, and socio-economic indicators were used to describe the vulnerability. The study period was from December 31st, 2019 to May 31st, 2020 (i.e. 5 months after the start of the pandemic). Results: According to demographic indicators, African populations appear younger than in Europe, Asia, and North America, where evidence showed a higher lethality of COVID-19 and a higher frequency of hospitalization among the elderly. This highlights the protective effect of the age structure of Central African populations. Their populations face significant vulnerability from high morbidity and a considerable deficit in health care facilities and services. Poverty indicators are not in their favour for a sustainable implementation of effective pandemic control measures. Very low literacy rates in some countries, misinformation, and belief in conspiracy theories could affect the community involvement in the response. Several countries are weakened by other humanitarian crises, including conflicts and other epidemics. The early easing of lockdown restrictions in certain countries could worsen the situation. Conclusion: In this sub-region, where the largest proportion of the population lives in poverty, poor sanitary conditions, conflicts, and humanitarian crises, the question of standards of prevention could appear to be a luxurious idea relegated to the background. Central African countries need financial and logistical support for a sustainable and effective response. These observations could be easily extrapolated to other sub-Saharan sub-regions.

Although the first HIV circulating recombinant form (CRF01_AE) is the predominant strain in many Asian countries, it is uncommonly found in the Congo Basin from where it first originated. To fill the gap in the evolutionary history of this important strain, we sequenced near complete genomes from HIV samples with subgenomic CRF01_AE regions collected in Cameroon and the Democratic Republic of the Congo from 2001 to 2006. HIV genomes were generated from N = 13 plasma specimens by next-generation sequencing of metagenomic libraries prepared with spiked primers targeting HIV, followed by Sanger gap-filling. Genome sequences were aligned to reference strains, including Asian and African CRF01_AE sequences, and evaluated by phylogenetic and recombinant analysis to identify four CRF01_AE strains from Cameroon. We also identified two CRF02, one CRF27, and six unique recombinant form genomes (01|A1|G, 01|02|F|U, F|G|01, A1|D|01, F|G|01, and A1|G|01). Phylogenetic analysis, including the four new African CRF01_AE genomes, placed these samples as a bridge between basal Central African Republic CRF01_AE strains and all Asian, European, and American CRF01_AE strains. Molecular dating confirmed previous estimates indicating that the most recent common CRF01_AE ancestor emerged in the early 1970s (1968–1970) and spread beyond Africa around 1980 to Asia. The new sequences and analysis presented in this study expand the molecular history of the CRF01_AE clade, and are illustrated in an interactive Next Strain phylogenetic tree, map, and timeline at (https://nextstrain.org/community/EduanWilkinson/hiv-1_crf01).

Metagenomic next-generation sequencing (mNGS), the shotgun sequencing of RNA and DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and the genomic surveillance of viral outbreaks. An additional target enrichment step is generally needed for high-sensitivity pathogen identification in low-titre infections, yet available methods using PCR or capture probes can be limited by high cost, narrow scope of detection, lengthy protocols and/or cross-contamination. Here, we developed metagenomic sequencing with spiked primer enrichment (MSSPE), a method for enriching targeted RNA viral sequences while simultaneously retaining metagenomic sensitivity for other pathogens. We evaluated MSSPE for 14 different viruses, yielding a median tenfold enrichment and mean 47% (±16%) increase in the breadth of genome coverage over mNGS alone. Virus detection using MSSPE arboviral or haemorrhagic fever viral panels was comparable in sensitivity to specific PCR, demonstrating 95% accuracy for the detection of Zika, Ebola, dengue, chikungunya and yellow fever viruses in plasma samples from infected patients. Notably, sequences from re-emerging and/or co-infecting viruses that have not been specifically targeted a priori, including Powassan and Usutu, were successfully enriched using MSSPE. MSSPE is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making this method directly applicable for diagnostic laboratory and field use., This study describes a new method that improves the sensitivity of viral detection compared with next-generation sequencing and enables the detection of emerging flaviviruses not specifically targeted a priori. Metagenomic sequencing with spiked primer enrichment is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making it applicable for diagnostic laboratory and field use.

Early diagnosis of hepatitis C virus (HCV) infection is essential for prompt initiation of treatment and prevention of transmission, yet several logistical barriers continue to limit access to HCV testing. Dried blood spot (DBS) technology involves a simple fingerstick that eliminates the need for trained personnel, and DBS can be stored and transported at room temperature. We evaluated the use of DBS whole blood samples in the modified Abbott ARCHITECT anti-HCV assay, comparing assay performance against the standard assay run using DBS and venous plasma samples. 144 HCV positive and 104 HCV negative matched venous plasma and whole blood specimens were selected from a retrospective study with convenience sampling in Cameroon. Results obtained using a modified volume DBS assay were highly correlated to the results of the standard assay run with plasma on clinical samples and dilution series (R2 = 0.71 and 0.99 respectively). The ARCHITECT Anti-HCV assay with input volume modification more accurately detects HCV antibodies in DBS whole blood samples with 100% sensitivity and specificity, while the standard assay had 90.97% sensitivity. The use of DBS has the potential to expand access to HCV testing to underserved or marginalized populations with limited access to direct HCV care.

Defining genetic diversity of viral infections directly from patient specimens is the ultimate goal of surveillance. Simple tools that can provide full-length sequence information on blood borne viral hepatitis viruses: hepatitis C, hepatitis B and hepatitis D viruses (HCV, HBV and HDV) remain elusive. Here, an unbiased metagenomic next generation sequencing approach (mNGS) was used for molecular characterization of HCV infections (n = 99) from Israel which yielded full-length HCV sequences in 89% of samples, with 7 partial sequences sufficient for classification. HCV genotypes were primarily 1b (68%) and 1a (19%), with minor representation of genotypes 2c (1%) and 3a (8%). HBV/HDV coinfections were characterized by suppressed HBV viral loads, resulting in sparse mNGS coverage. A probe-based enrichment approach (xGen) aiming to increase HBV and HDV coverage was validated on a panel of diverse genotypes, geography and titers. The method extended HBV genome coverage a median 61% (range 8-84%) and provided orders of magnitude boosts in reads and sequence depth for both viruses. When HBV-xGen was applied to Israeli samples, coverage was improved by 28-73% in 4 samples and identified HBV genotype A1, A2, D1 specimens and a dual B/D infection. Abundant HDV reads in mNGS libraries yielded 18/26 (69%) full genomes and 8 partial sequences, with HDV-xGen only providing minimal extension (3-11%) of what were all genotype 1 genomes. Advanced molecular approaches coupled to virus-specific capture probes promise to enhance surveillance of viral infections and aid in monitoring the spread of local subtypes.

Periodic evaluation of the impact of viral diversity on diagnostic tests is critical to ensure current technologies are keeping pace with viral evolution. To determine whether HIV diversity impacts the ARCHITECT HIV Combo Ag/Ab (HIV Combo) or RealTime HIV-1 (RT) assays, a set of N = 199 HIV clinical specimens from Cameroon, Senegal, Saudi Arabia, and Thailand were sequenced and tested in both assays. The panel included historical groups N and P specimens and a newly identified group N specimen. These and specimens classified as H, U (unclassified)/URF (unique recombinant form), CRF (circulating recombinant form) 01, 02, 06, 09, 11, 13, 18, 22, 37, and 43 were detected by both the RT assay (1.75–6.84 log copies/ml) and the HIV Combo assay (3.26–1121.96 sample to cutoff ratios). Sequence alignment identified 3 or fewer mismatches to the RT assay oligos in 82.4% of samples. Altogether, these data demonstrate the HIV Combo and RT assays detect diverse strains of HIV in clinical specimens.

Surveillance of emerging viral variants is critical to ensuring that blood screening and diagnostic tests detect all infections regardless of strain or geographic location. In this study, we conducted serological and molecular surveillance to monitor the prevalence and diversity of HIV, HBV, and HTLV in South Cameroon. The prevalence of HIV was 8.53%, HBV was 10.45%, and HTLV was 1.04% amongst study participants. Molecular characterization of 555 HIV-1 specimens identified incredible diversity, including 7 subtypes, 12 CRFs, 6 unclassified, 24 Group O and 2 Group N infections. Amongst 401 HBV sequences were found a rare HBV AE recombinant and two emerging sub-genotype A strains. In addition to HTLV-1 and HTLV-2 strains, sequencing confirmed the fifth known HTLV-3 infection to date. Continued HIV/HBV/HTLV surveillance and vigilance for newly emerging strains in South Cameroon will be essential to ensure diagnostic tests and research stay a step ahead of these rapidly evolving viruses.

Background In-depth analysis of the HIV pandemic at its epicenter in the Congo basin has been hampered by 40 years of political unrest and lack of functional public health infrastructure. In recent surveillance studies (2017-18), we found that the prevalence of HIV in Kinshasa, Democratic Republic of Congo (11%) far exceeded previous estimates. Methods 10,457 participants were screened in Kinshasa with rapid tests from 2017-2019. Individuals confirmed as reactive by the Abbott ARCHITECT HIV Ag/Ab Combo assay (n=1968) were measured by the Abbott RealTime HIV-1 viral load assay. Follow up characterization of samples was performed with alternate manufacturer viral load assays, qPCR for additional blood borne viruses, unbiased next generation sequencing, and HIV Western blotting. Findings Our data suggested the existence of a significant cohort (n=429) of HIV antibody positive/viral load negative individuals. We systematically eliminated collection site bias, sample integrity, and viral genetic diversity as alternative explanations for undetectable viral loads. Mass spectroscopy unexpectedly detected the presence of 3TC antiviral medication in approximately 60% of those tested (209/354), and negative Western blot results indicated false positive serology in 12% (49/404). From the remaining Western blot positives (n=53) and indeterminates (n=31) with reactive Combo and rapid test results, we estimate 2.7-4.3% of infections in DRC to be potential elite controllers. We also analyzed samples from the DRC collected in 1987 and 2001-03, when antiretroviral drugs were not available, and found similarly elevated trends. Interpretation Viral suppression to undetectable viral loads without therapy occurs infrequently in HIV-1 infected patients around the world. Mining of global data suggests a unique ability to control HIV infection arose early in central Africa and occurs in

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Hepatitis delta virus (HDV), a satellite virus of hepatitis B virus (HBV), infects an estimated 15–20 million people worldwide and confers a greater risk for accelerated progression to liver disease. However, limited HDV surveillance data are available in sub-Saharan Africa where HDV diversity is high. To determine the prevalence and diversity of HDV in Cameroon, serological and molecular characterization was performed on 1928 HBsAg positive specimens selected from retrospective viral surveillance studies conducted in Cameroon from 2010–2016. Samples were screened for HDV antibodies on the Abbott ARCHITECT instrument and for HDV RNA on the Abbott m2000 instrument by research assays. HDV positive specimens with sufficient viral load were selected for genomic sequencing. The seroprevalence of HDV in HBsAg positive samples from Cameroon was 46.73% [95% CI; 44.51–48.96%], with prevalence of active HDV infection being 34.2% [95% CI; 32.09–36.41%]. HDV genotypes 1, 6, 7 and 8 were identified amongst N = 211 sequences, including N = 145 genomes. HDV prevalence is high within the study cohort, indicating that a large portion of HBV infected individuals in Cameroon are at elevated risk for severe hepatitis and death. Collectively, these results emphasize the need for HBV vaccination and HDV testing in HBsAg positive patients in Cameroon.

Immunoglobulin G specific responses againstPlasmodium falciparummerozoite antigens such as the merozoite surface protein 3 (MSP3) and UB05 are known to play critical roles in parasitemia control and protection from symptomatic illness. However when there is intense perennial malaria transmission coupled with concurrent infection with the human immunodeficiency virus type 1 (HIV), knowledge of IgG antibody response profiles is limited. In this study we assessed the impact of dual HIV-Malaria infections on IgG subclass responses to MSP3 (QβMSP3) and UB05 (QβUB05) in individuals living in two areas of Cameroon differing in transmission intensity. We observed differences in antigen specific IgG and IgG subclass responses which was dependent upon the antigen type, malaria transmission intensity, HIV infection, malaria infection and dual HIV-malaria infections. Individuals living in high malaria transmission areas irrespective of HIV or malaria status had significantly higher IgG responses to both antigens (P=0.0001 for QβMSP3, P=0.0001 for QβUB05) than their counterpart from low transmission areas. When dual HIV-Malaria infection is considered significantly higher QβMSP3 specific IgG1 (P=0.0001) and IgG3 (P=0.04) responses in double negative individuals was associated with protection against malaria in low transmission areas. Superior QβUBO5 specific IgG1 responses (P=0.0001) in double negative individuals were associated with protection in high transmission areas in contrast to significantly higher IgG3 responses to QβUB05 (P=0.0001) which were more relevant to protection in low malaria transmission areas in the same population. Thus, understanding immune responses to QβUB05 and QβMSP3 could facilitate the development of immunotherapeutic strategies suitable for areas differing in malaria transmission intensity.

Worldwide, an estimated 5% of hepatitis B virus (HBV) infected people are coinfected with hepatitis delta virus (HDV). HDV infection leads to increased mortality over HBV mono-infection, yet HDV diagnostics are not widely available. Prototype molecular (RNA) and serologic (IgG) assays were developed for high-throughput testing on the Abbott m2000 and ARCHITECT systems, respectively. RNA detection was achieved through amplification of a ribozyme region target, with a limit of detection of 5 IU/ml. The prototype serology assay (IgG) was developed using peptides derived from HDV large antigen (HDAg), and linear epitopes were further identified by peptide scan. Specificity of an HBV negative population was 100% for both assays. A panel of 145 HBsAg positive samples from Cameroon with unknown HDV status was tested using both assays: 16 (11.0%) had detectable HDV RNA, and 23 (15.7%) were sero-positive including the 16 HDV RNA positive samples. Additionally, an archival serial bleed panel from an HDV superinfected chimpanzee was tested with both prototypes; data was consistent with historic testing data using a commercial total anti-Delta test. Overall, the two prototype assays provide sensitive and specific methods for HDV detection using high throughput automated platforms, allowing opportunity for improved diagnosis of HDV infected patients.

Background Urogenital schistosomiasis is a parasitic infection of public health importance that affects over 112 million people worldwide. The study aimed at assessing the urogenital schistosomiasis prevalence and risk factors of transmission around Mape dam suburds in Malantouen district, West, Cameroon. Methods The study was conducted using semi-structured pretested questionnaires to collect socio-demographic and ecological data. Urine samples were also collected and used to confirm the prevalence of schistosomiasis in consented school-aged children in four primary schools between March – July 2014. Snails’ samples around the dam surburbs were also collected for taxonomy characterization and species identification. Data were compiled and quality control assessed and analysed using SPSS version 17 and Epiinfo data 3.1. P

BackgroundPrevious evaluation of the state of ethics regulation in Cameroon revealed: law regulating clinical research is lacking; existing committees lack infrastructure and financial support to sustainably review and effectively monitor approved protocols. The present Cameroon National Ethics Committee (CNEC)-EDCTP project aimed at implementing and evaluating active monitoring of clinical research in Cameroon.MethodsBetween 2011–2013, approved clinical trials and protocols involving transfer of biological materials abroad were consecutively monitored. The monitoring tool, a questionnaire on the conformity of key documents e.g. research protocols, ethical clearance, informed consent documents, investigator’s brochure, with a focus on GCP standards was sent to promoters/investigators ten days prior to the field visit. Teams of two-three monitors, made up of CNEC members and independent consultants, were mobilised per site (hospital/research institute/NGO). Reports with key recommendations were submitted to CNEC for review and approval, to different promoters/investigators, and the Regulatory Authority for action; the monitoring summary was submitted to EDCTP.ResultsUp to 22 site visits were done throughout the country, monitoring about 30 protocols within 11 hospitals, 9 research institutes, a National Programme and a non-governmental organisation. All sites had ethical clearance and administrative authorisation for research. From the registered number of research participants, less than half of the signed consent forms were available. Other issues were the lack of full involvement of local investigators, inexistence of material transfer and data sharing agreements with collaborative studies, non-implication of study communities/participants. As educators-consultants, monitors formulated recommendations to investigators, ethics committees and regulatory authority, insisting on the implication of local PI/collaborators with defined percentages of time to be devoted for research and good participatory practice among research communities/participants.ConclusionActive monitoring shows some formality in the application of ethical/administrative clearance in Cameroon. However, complex issues raised confirm the necessity of continuous monitoring to meet the high standards for clinical research ethics in Cameroon.

BackgroundImmunoglobulin G (IgG)-specific responses against Plasmodium falciparum merozoite antigens such as the merozoite surface protein 3 (MSP3) and UBO5 are known to play critical roles in parasitaemia control and protection from symptomatic illness. However, when there is intense perennial malaria transmission coupled with concurrent infection with the human immunodeficiency virus type 1 (HIV), knowledge of IgG antibody response profiles is limited.In this study we assessed the impact of dual HIV/malaria infections on IgG subclass responses to MSP3 (QβMSP3) and UBO5 (QβUB05) in individuals living in two areas of Cameroon differing in malaria transmission intensity.MethodsIgG and IgG subclass responses specific to either MSP3 or UBO5 were determined in plasma from study participant by ELISA. To improve reactivity with their respective antibodies the antigens were displayed upon the surface of the RNA coliphage Qβ.ResultsWe observed differences in antigen-specific IgG and IgG subclass responses which were dependent upon the antigen type, malaria transmission intensity, HIV infection, malaria infection and dual HIV/malaria infections. Individuals living in areas with high malaria transmission, had irrespective of HIV or malaria status significantly higher IgG responses to both antigens (p=0.0001 for QβMSP3, p=0.0001 for QβUB05) than their counterpart from areas with low transmission. When dual HIV/malaria infection is considered, significantly higher QβMSP3 specific IgG1 (p=0.0001) and IgG3 (p=0.04) responses in double-negative individuals was associated with protection against malaria in areas with low transmission. Superior QβUBO5 specific IgG1 responses (p=0.0001) in double-negative individuals were associated with protection in areas with high transmission in contrast to significantly higher IgG3 responses to QβUBO5 (p=0.0001) which were more relevant to protection in areas with low malaria transmission in the same population.ConclusionThus, understanding immune responses to QβUBO5 and QβMSP3 could facilitate the development of immunotherapeutic strategies suitable for areas differing in malaria transmission intensity.

We report the second human immunodeficiency virus (HIV) belonging to the new HIV type 1 (HIV-1) group P lineage that is closely related to the simian immunodeficiency virus found in gorillas. This virus was identified in an HIV-seropositive male hospital patient in Cameroon, confirming that the group P virus is circulating in humans. Results from screening 1,736 HIV-seropositive specimens collected in Cameroon indicate that HIV-1 group P infections are rare, accounting for only 0.06% of HIV infections. Despite its rarity, group P shows evidence of adaptation to humans.

Although Cameroon, in west central Africa, has a relatively low HIV prevalence of 5–6%, all HIV-1 groups (M, N, O, and P), nearly all HIV-1 group M subtypes, and numerous intersubtype recombinant forms have been identified in Cameroon. In this report, we describe the near full-length sequence of 04CMU11421, an HIV-1 group M subtype J strain collected in Cameroon in 2004. Phylogenetic analysis of the genome sequence shows high bootstrap support with three subtype J reference sequences in the HIV Sequence database. Therefore, 04CMU11421 represents a fourth pure subtype J isolate and the first reported in Cameroon.

Risk factors for HIV transmission within a hospital setting were assessed using pre-structured questionnaires and observations. Of 409 respondents, 66.3% corresponded to the nursing staff, 14.4% doctors and 8.3% laboratory staff. The irregular use of gloves and other protective clothing for risky tasks, and recapping of needles after use were some of the risk factors identified, especially amongst nurses. Preventive measures were not always implemented by health personnel. More emphasis should be placed not only on diffusing universal precautions and recommendations for hospital staff safety, but accompanying measures for monitoring and evaluation of implementation of these standards are also indispensable.

Objective: The HIV epidemic in Cameroon is characterized by a high level of strain diversity despite a relatively low prevalence of infection. In this study, HIV strains infecting blood donors in Cameroon were characterized to determine the prevalence of subtypes and intersubtype recombinants and if strain prevalence was changing over time. Methods: From 1996 through 2004, 676 HIV-infected blood donations were collected at blood banks in Douala and Yaounde, Cameroon. A subset of the HIV-1 group M strains (n = 574) were classified based on phylogenetic analysis of viral sequences from the gag p24, pol integrase, and env gp41 regions. Results: HIV-1 group M accounted for 97.3% (n = 658) of infections, whereas group O was present in 2.2% (n = 15) and HIV-2 in 0.4% (n = 3). Within the group M infections, 14 subtypes and circulating recombinant forms (CRFs) and unique recombinant forms (URFs) were identified. Overall, CRF02_AG accounted for 58.2% of infections, URFs 14.8%, and levels of subtypes, A, B, C, D, F2, and G, and CRFs, 01, 06, 09, 11, 13, 22, and 37, varied from 0.2% to 6.1%. Evaluation of HIV strains present in the donor population over this 9-year period showed no substantial changes in the proportion of infections caused by each subtype and CRF, the percentage of intersubtype recombinants, or the strain composition of the URFs. Conclusions: HIV-1 strain diversity in Cameroon did not significantly change, suggesting a mature and relatively stable epidemic.

Recombinant forms of HIV-1 contribute significantly to the ongoing epidemic. In the present study, we characterized the near full-length genome of one candidate HIV-1 CRF25_cpx strain originating in Cameroon, 06CM-BA-040. Viral RNA was extracted from plasma, and the genome was obtained using RT-PCR amplification to generate 10 overlapping fragments. Bootscanning, recombination breakpoint analysis, and phylogenetic trees confirmed that 06CM-BA-040 had a genomic structure consistent with two available CRF25_cpx reference sequences. The CRF25_cpx mosaic composition consisted of nine segments derived from subtypes A and G as well as unclassified (U) regions. Subtype G and CRF25_cpx clusters diverged from each other with long branch lengths but were distinct from other known subtypes with high bootstrap support (94%). The epidemiological significance of CRF25_cpx strains is unknown; however, the availability of additional genomic sequences will improve our understanding of the overall genetic diversity within this recombinant form of HIV-1.

Summary In 2002, compelling evidence highlighted human exposure to a plethora of primate lenti-viruses through hunting, handling of bushmeat and/or animals kept as pets in Cameroon. To determine SIV prevalence in pet animals, sera from 28 non-human primates (3 species), kept as household pets in southern Cameroon, was analyzed. Results showed there was no SIV infection among greater spot nosed monkeys (0/5) or chimpanzees (0/10). However, there was a prevalence rate of 23.1% (3/13) in mandrills. Phylogenetical analysis based on pol-integrase (IN) region and mitochondrial (mt) cytochrome b gene showed that the newly found SIVs from Mandrillus sphinx (SIVmndCM-202, SIVmndCM-211 and SIVmndCM-218) clustered significantly with SIVmnd-2. Questionnaire data were also collected to assess whether owners had experienced bites, scratches or exposure to blood and/or body fluid. Risk to human health from cross-species transmission of the newly identified SIVmnd-2 to infect humans remains unknown.

The Nef protein of human immunodeficiency virus type 1 (HIV-1) has multiple functional domains, is immunogenic, and contains several cytotoxic T lymphocyte (CTL)-targeted epitopes. Several defined subfunctions of Nef are important for the pathogenesis of HIV-1 infection. In this study, we present the genetic diversity of the nef gene of 55 newly derived HIV-1 sequences obtained from Cameroonian patients. Four genetic subtypes and three circulating recombinant forms (CRFs) were identified: subtypes A (11%), G (7.3%), D (5.4%), F1 (1.8%), F2 (5.4%), CRF01_AE (5.4%), CRF02_AG (58.2%), and CRF11_cpx (1.8%). Two isolates clustered distinctly from the known HIV-1 genetic subtypes in nef and were designated as unclassified. Interestingly, the majority of all functional domains including the myristoylation signal, CD4 binding motif, beta turn motif, and the phosphorylation sites were well conserved in our cohort. Putative CTL-epitopic domains of the central portion of Nef were also well conserved, whereas those at the C-term were not. Our study demonstrated that despite high genetic diversity observed in the nef gene, most described functional domains and CTL epitopes were well conserved among Cameroonian HIV-1 subtypes. These findings could be used for the development of antiretroviral-acting therapeutics and anti-HIV-1 vaccines.

The prevalence of antiretroviral therapy (ART) resistance-associated mutations among HIV-1 strains in western Cameroon was evaluated by genotypically analyzing strains isolated from drug-naive individuals. Proviral DNA was extracted from 54 blood samples and amplified by polymerase chain reaction of protease, reverse transcriptase, integrase, and envelope genes. At least 4 clones per sample were analyzed. Of 54 HIV-1 strains, 45 (83.3%) had a concordant subtype or circulating recombinant form (CRF) designation: 40 CRF02_AG, 2 subtype A1, 2 G, and 1 F2. The remaining 9 (16.7%) had a discordant subtype: 6 subtype A1/CRF02_AG, 2 D/CRF02, and 1 G/CRF02. Protease inhibitor-associated primary resistance mutations were found in 4 (7.4%) cases: M46L with full clones in 1 case, and M46I, M46L, and V82A as minor populations in 1 case each. Reverse transcriptase inhibitor-associated primary resistance mutations were found in 5 (9.8%) samples: Y188C in 2 cases, and L100I, M184V, and V75I in 1 case each, although all of these mutations were found as minor populations. This is one of the first reports of the emergence of primary ART resistance mutations among drug-naive, non-B subtype HIV-1-infected individuals in Cameroon. Follow-up studies should be conducted to assess whether these drug-resistant mutants found as minor populations might impact future ART.

HIV-1 is classified into three groups, M (major), N (non-M non-O), and O (outlier); each group arose from a separate transmission of SIVcpz into humans. HIV-1 group N was recently discovered and infections with this virus are rare with only eight documented cases. All group N infections have been found in Cameroon and there is no evidence of direct linkage between the infected patients. We report here the identification of HIV-1 group N infections in a husband and wife. The group N infection in the husband, 1131-03, was identified first based on seroreactivity in peptide EIAs and confirmed by PCR amplification of group N viral sequences. Subsequently the wife, 1015-04, was evaluated and confirmed to also be infected with a group N virus. Near full-length viral genomes were amplified and sequenced from each patient's specimen. The low level of diversity between the two viral sequences provides evidence of horizontal transmission of group N from one spouse to the other. Patient 1131-03 was receiving antiviral therapy consisting of reverse transcriptase inhibitors; the treatment appears effective for suppression of group N viral replication based on apparently low viral load in plasma specimens collected from the patient and the absence of drug resistance mutations in RT sequences amplified from 1131-03. This report brings to 10 the number of group N infections identified and to 5 the number of group N genomes sequenced. Although group N infections continue to be rare, group N is a pathogenic virus and its prevalence needs to be monitored.

Blood samples (n=544) from two different populations (Pygmies and Bantus) in Cameroon, West Africa, were analysed. Serological tests indicated that the anti-hepatitis C virus (HCV) prevalence in Bantus (20·3 %) was higher than that in Pygmies (2·3 %, P

To investigate the route of zoonotic transmission of HIV-1, we isolated three and seven HIV-1 strains from 449 Pygmy hunter gatherers and 169 neighboring Bantu, respectively, in southern Cameroon. Phylogenetic analysis based on pol-integrase and env-C2V3 sequences revealed that strains from Pygmies were 1 CRF02_AG/CRF02_AG, 1 subtype G/CRF02_AG (pol/env), and 1 CRF11_cpx/CRF11_cpx, and that those from Bantu were 2 CRF02_AG/CRF02_AG, 1 CRF02_AG/CRF01_AE/A, 1 CRF02_AG/subtype A, 1 G/A, 1 G/CRF02_AG, and 1 unclassified/H. CRF02_AG and CRF11_cpx have been identified in Cameroon. The results suggest that HIV-1 has been introduced into Pygmies through their neighboring Bantu rather than directly from nonhuman primates.

HIV-1 group O strains have a level of genetic diversity similar to that of strains in group M; however, group O has not been readily classified into genetic subtypes. Phylogenetic classification of group O has been hindered by the limited sequence information available. To facilitate phylogenetic analysis, we sequenced the gag p24 (693 nt), pol p32 (864 nt), and env gp160 (approximately 2700 nt) genes from 39 group O-infected specimens. These specimens include 32 plasma samples collected in Cameroon between 1996 and 1999, 2 specimens collected in the United States, and 5 infections previously isolated in Equatorial Guinea. Phylogenetic analysis of HIV-1 group O sequences resulted in the identification of five clusters that are maintained across gag, pol, and env, generally supported by high bootstrap values, and approximately equidistant from each other. In addition to the group O clusters, several isolates branch independently and are equidistant from the other group O isolates. Cluster I comprises greater than 50% of the group O isolates and is a diverse set of isolates that is subdivided into subclusters. The average intra-, sub-, and intercluster distances for group O are similar to the corresponding distances for group M subtypes. The five group O clusters have characteristics similar to those of group M subtypes. Thus the data presented may form the basis for classification of group O into subtypes. However, full-length genomes representing each group O cluster will be required to formalize a group O subtype classification.

In this study we report the molecular and biological characteristics of 19 HIV-1 primary isolates obtained in April 1999 from 47 HIV-1-infected individuals living mainly in western Cameroon. Discontinuous portions of gag, pol, and env were amplified by polymerase chain reaction and directly sequenced. Phylogenetic analysis of these sequences showed that all were of HIV-1 group M with the following genotypes: A(gag)/A(pol)/A(env) (n = 4), A(gag)/AG(pol)/AG(env) (n = 2), AG(gag)/A(pol)/AG(env) (n = 1), AG(gag)/U(pol)/AG(env) (n = 1), AG(gag)/AG(pol)/AG(env) (n = 6), G(gag)/G(pol)/G(env) (n = 3), F2(gag)/F2(pol)/F2(env) (n = 1), and a novel A(gag)/J(pro/rt)/A(int)/U(env) complex recombinant (n = 1). This A/J/U recombinant shared the same gag-pol cross-over point with known CRF02.AG viruses and 99CMBD6, an AG recombinant from our panel of isolates. The biological phenotype of most of the isolates correlated with the clinical status of the patient. Six isolates were syncytium inducing (SI) on MT-2 cells whereas 13 isolates were of the non-syncytium-inducing phenotype (NSI). Coreceptor usage by these isolates determined on GHOST cells correlated with their biological phenotype, as all SI isolates used CXCR4 and all NSI isolates used CCR5. Our results show a high predominance of subtype A (mainly CRF02.AG-like viruses) in western Cameroon and fewer HIV-1 subtypes compared with other parts of Cameroon. Genetic variability was, however, not reflected in the biological characteristics of the isolates. The presence of a novel A/J/U complex recombinant from this region further emphasizes the role of recombination in the global evolution of HIV.

Cette etude descriptive transversale de juillet a novembre 2012 a pour objectif de decrire la prise en charge de l’anemie chez les patients âges d’au moins 1 mois. Le traitement et l’analyse des donnees ont ete effectues par les logiciels CsPro et IBM SPSS 20.0. L’incidence de l’anemie sur 328 admissions est de 22,5 % (soit 74 cas) avec une frequence elevee dans la tranche de 1 a 5 ans (38,30 %) et 56,75 % des anemies etaient de sexe feminin. Parmi les causes d’anemies, le paludisme represente 68,90 % des cas suivi de l’infection a VIH/SIDA (17,60 % des cas). Entre temps, le CTA du VIH/SIDA de l’HRB a enregistre une file active moyenne mensuelle de 4796 patients dont 150 de moins de 15 ans (3,13 %). Le taux d’hemoglobine des patients anemies variait de 1,5 a 11 g/dl, avec une moyenne de 6,63 g/dL. L’anemie etait severe chez 47 patients (63,51 %) avec 44,6 % d’anemie microcytaire. A l’HRB, l’anemie severe constitue 4,1 % des principales causes de mise en observation aux urgences. Parmi les causes de ces anemies, la frequence de la drepanocytose etait de 32,43 % (soit 24 cas). L’automedication representait 41,90 % des cas. Le taux de reference des structures sanitaires peripheriques etant de 58,1 %. La frequence des dons de sang mensuels est de 98 par mois. Le taux de transfusion chez nos patients est de 71,6 % (53 patients) avec une moyenne de 2,5 poches de sang total par patients. Il ressort de cette etude, que malgre certaines insuffisances de prises en charge des anemies, l’issue de la prise en charge des patients a ete favorable dans 95,90 % des cas.

Here we describe, for the first time, recombinants between two highly divergent major groups of human immunodeficiency virus type 1 (HIV-1), M and O, within a Cameroonian woman infected with three different HIV-1 strains, a group O virus, a subtype D virus, and a recently reported IBNG (A/G)-like recombinant virus. Using nested extra-long PCR amplification, we sequenced from thepolregion to theenvregion including accessory genes of the viral genome obtained from the patient’s uncultured peripheral blood mononuclear cells and examined the phylogenetic position of each gene. Compared with sequential blood samples obtained in 1995 and 1996, there were multiple segmental exchanges between three HIV-1 strains (O, D, and IBNG) and all the recombinants appeared to be derived from a common M/O ancestor. Importantly, recombination between groups M and O occurred, even though the homology between these two groups is 69, 76, 68, and 55% in thegag,pol,vif-vpr, andenvregions, respectively. Recombination between strains with such distant lineages may contribute substantially to generating new HIV-1 variants.

Ninety-four GB virus C/hepatitis G virus (GBV-C/HGV) RNA-positive serum samples were obtained from all over the world. We found that all 15 GBV-C/HGV isolates from the Pygmies and the Bantu in the Central African region had a 12-amino acid indel (i.e. insertion or deletion) in the non-structural protein (NS) 5A region. Phylogenetic analyses of the NS5A region, using GBV-A as an outgroup, showed that these 15 isolates had diverged from the common ancestor much earlier than the remaining isolates, indicating an African origin of GBV-C/HGV.

Our previous analysis of an HTLV–I isolate (CMR229) from a Cameroonian Pygmy demonstrated that the isolate is distinct from typical HTLV–ls of the “Central African group,” which has a close similarity to HTLV–I–related simian viruses (STLV–I) in Africa. In this study, we analyzed six new HTLV–ls from Cameroon consisting of three isolates from the Pygmy and three from the Bantu to examine further the genetic features of HTLV–I in Cameroon, especially in the Pygmy. A phylogenetic tree based on the long terminal repeats (LTR) region showed that all the new HTLV–ls belong to the Central African group. On the other hand, an env–based analysis of CMR229 confirmed the previous finding derived from LTR–based analysis that CMR229 has a similarity to African STLV–Is, but is distinct from the typical Central African group of HTLV–I. This suggests that multiple interspecies transmissions from non–human primates to humans have occurred in Central Africa, resulting in the presence of two distinct HTLV–I strains in this area. In addition, it seems likely that the Pygmy harbors the heterogeneous HTLV–I strains from which the main HTLV–I population spread into the Bantu.

An alternative view of public health ethics characterizes the fundamental problematic of public health ethics differently: what lies at the moral foundation of public health is social justice [2]. While balancing individuals' liberties with promoting social goods is one area of concern, it is embedded within a broader commitment to secure a sufficient level of health for all and to narrow unjust inequalities [2, 3]. Another important area of concern is the balancing of this commitment with the injunction to maximize good aggregate or collective health outcomes. Public health ethics has therefore a strong moral connection to broader questions of social justice, poverty, and systematic disadvantage [3,4].

Given the dynamic changes in HIV-1 complexity and diversity, next-generation sequencing (NGS) has the potential to revolutionize strategies for effective HIV global surveillance. In this study, we explore the utility of metagenomic NGS to characterize divergent strains of HIV-1 and to simultaneously screen for other co-infecting viruses. Thirty-five HIV-1-infected Cameroonian blood donor specimens with viral loads of >4.4 log10 copies/ml were selected to include a diverse representation of group M strains. Random-primed NGS libraries, prepared from plasma specimens, resulted in greater than 90% genome coverage for 88% of specimens. Correct subtype designations based on NGS were concordant with sub-region PCR data in 31 of 35 (89%) cases. Complete genomes were assembled for 25 strains, including circulating recombinant forms with relatively limited data available (7 CRF11_cpx, 2 CRF13_cpx, 1 CRF18_cpx, and 1 CRF37_cpx), as well as 9 unique recombinant forms. HPgV (formerly designated GBV-C) co-infection was detected in 9 of 35 (25%) specimens, of which eight specimens yielded complete genomes. The recovered HPgV genomes formed a diverse cluster with genotype 1 sequences previously reported from Ghana, Uganda, and Japan. The extensive genome coverage obtained by NGS improved accuracy and confidence in phylogenetic classification of the HIV-1 strains present in the study population relative to conventional sub-region PCR. In addition, these data demonstrate the potential for metagenomic analysis to be used for routine characterization of HIV-1 and identification of other viral co-infections.