Population interconnectivity over the past 120,000 years explains distribution and diversity of Central African hunter-gatherers.

The evolutionary history of African hunter-gatherers holds key insights into modern human diversity. Here, we combine ethnographic and genetic data on Central African hunter-gatherers (CAHG) to show that their current distribution and density are explained by ecology rather than by a displacement to marginal habitats due to recent farming expansions, as commonly assumed. We also estimate the range of hunter-gatherer presence across Central Africa over the past 120,000 years using paleoclimatic reconstructions, which were statistically validated by our newly compiled dataset of dated archaeological sites. Finally, we show that genomic estimates of divergence times between CAHG groups match our ecological estimates of periods favoring population splits, and that recoveries of connectivity would have facilitated subsequent gene flow. Our results reveal that CAHG stem from a deep history of partially connected populations. This form of sociality allowed the coexistence of relatively large effective population sizes and local differentiation, with important implications for the evolution of genetic and cultural diversity in Homo sapiens.

High seroreactivities to orthoebolaviruses in rural Cameroon: a case-control study on non-human primate bites and a cross-sectional survey in rural population.

BACKGROUND: Ebola (EBOV) and Sudan (SUDV) orthoebolaviruses are responsible for lethal haemorrhagic fever outbreaks in humans in Central and West Africa, and in apes that can be at the source of human outbreaks for EBOV. METHODS: To assess the risk of exposure to orthoebolaviruses through contact with non-human primates (NHP), we tested the presence of antibodies against different viral proteins with a microsphere-based multiplex immunoassay in a case-control study on bites from NHPs in forest areas from Cameroon (n=795), and in cross-sectional surveys from other rural populations (n=622) of the same country. RESULTS: Seroreactivities against at least two viral proteins were detected in 13% and 12% of the samples for EBOV and SUDV, respectively. Probability of seroreactivity was not associated with history of NHP bites, but was three times higher in Pygmies compared to Bantus. Although no neutralizing antibodies to EBOV and SUDV were detected in a selected series of highly reactive samples, avidity results indicate strong affinity to SUDV antigens. CONCLUSION: The detection of high level of seroreactivities against orthoebolaviruses in rural Cameroon where no outbreaks have been reported, raises the possibilities of silent circulation of orthoebolavirus, or of other not yet documented filoviruses, in these forested regions.

Concurrent Clade I and Clade II Monkeypox Virus Circulation, Cameroon, 1979-2022.

During 1979-2022, Cameroon recorded 32 laboratory-confirmed mpox cases among 137 suspected mpox cases identified by the national surveillance network. The highest positivity rate occurred in 2022, indicating potential mpox re-emergence in Cameroon. Both clade I (n = 12) and clade II (n = 18) monkeypox virus (MPXV) were reported, a unique feature of mpox in Cameroon. The overall case-fatality ratio of 2.2% was associated with clade II. We found mpox occurred only in the forested southern part of the country, and MPXV phylogeographic structure revealed a clear geographic separation among concurrent circulating clades. Clade I originated from eastern regions close to neighboring mpox-endemic countries in Central Africa; clade II was prevalent in western regions close to West Africa. Our findings suggest that MPXV re-emerged after a 30-year lapse and might arise from different viral reservoirs unique to ecosystems in eastern and western rainforests of Cameroon.

Newly Identified Mycobacterium africanum Lineage 10, Central Africa.

Analysis of genome sequencing data from >100,000 genomes of Mycobacterium tuberculosis complex using TB-Annotator software revealed a previously unknown lineage, proposed name L10, in central Africa. Phylogenetic reconstruction suggests L10 could represent a missing link in the evolutionary and geographic migration histories of M. africanum.

Protecting an artificial savanna as a nature-based solution to restore carbon and biodiversity in the Democratic Republic of the Congo.

A large share of the global forest restoration potential is situated in artificial 'unstable' mesic African savannas, which could be restored to higher carbon and biodiversity states if protected from human-induced burning. However, uncertainty on recovery rates in protected unstable savannas impedes science-informed forest restoration initiatives. Here, we quantify the forest restoration success of anthropogenic fire exclusion within an 88-ha mesic artificial savanna patch in the Kongo Central province of the Democratic Republic of the Congo (DR Congo). We found that aboveground carbon recovery after 17 years was on average 11.40 ± 0.85 Mg C ha-1 . Using a statistical model, we found that aboveground carbon stocks take 112 ± 3 years to recover to 90% of aboveground carbon stocks in old-growth forests. Assuming that this recovery trajectory would be representative for all unstable savannas, we estimate that they could have a total carbon uptake potential of 12.13 ± 2.25 Gt C by 2100 across DR Congo, Congo and Angola. Species richness recovered to 33.17% after 17 years, and we predicted a 90% recovery at 54 ± 2 years. In contrast, we predicted that species composition would recover to 90% of old-growth forest composition only after 124 ± 3 years. We conclude that the relatively simple and cost-efficient measure of fire exclusion in artificial savannas is an effective nature-based solution to climate change and biodiversity loss. However, more long-term and in situ monitoring efforts are needed to quantify variation in long-term carbon and diversity recovery pathways. Particular uncertainties are spatial variability in socio-economics and growing conditions as well as the effects of projected climate change.

Genomic insights into Plasmodium vivax population structure and diversity in central Africa.

BACKGROUND: Though Plasmodium vivax is the second most common malaria species to infect humans, it has not traditionally been considered a major human health concern in central Africa given the high prevalence of the human Duffy-negative phenotype that is believed to prevent infection. Increasing reports of asymptomatic and symptomatic infections in Duffy-negative individuals throughout Africa raise the possibility that P. vivax is evolving to evade host resistance, but there are few parasite samples with genomic data available from this part of the world. METHODS: Whole genome sequencing of one new P. vivax isolate from the Democratic Republic of the Congo (DRC) was performed and used in population genomics analyses to assess how this central African isolate fits into the global context of this species. RESULTS: Plasmodium vivax from DRC is similar to other African populations and is not closely related to the non-human primate parasite P. vivax-like. Evidence is found for a duplication of the gene PvDBP and a single copy of PvDBP2. CONCLUSION: These results suggest an endemic P. vivax population is present in central Africa. Intentional sampling of P. vivax across Africa would further contextualize this sample within African P. vivax diversity and shed light on the mechanisms of infection in Duffy negative individuals. These results are limited by the uncertainty of how representative this single sample is of the larger population of P. vivax in central Africa.

An overview of artemisinin-resistant malaria and associated Pfk13 gene mutations in Central Africa.

Malaria caused by Plasmodium falciparum is one of the deadliest and most common tropical infectious diseases. However, the emergence of artemisinin drug resistance associated with the parasite's Pfk13 gene, threatens the public health of individual countries as well as current efforts to reduce malaria burdens globally. It is of concern that artemisinin-resistant parasites may be selected or have already emerged in Africa. This narrative review aims to evaluate the published evidence concerning validated, candidate, and novel Pfk13 polymorphisms in ten Central African countries. Results show that four validated non-synonymous polymorphisms (M476I, R539T, P553L, and P574L), directly associated with a delayed therapy response, have been reported in the region. Also, two Pfk13 polymorphisms associated to artemisinin resistance but not validated (C469F and P527H) have been reported. Furthermore, several non-validated mutations have been observed in Central Africa, and one allele A578S, is commonly found in different countries, although additional molecular and biochemical studies are needed to investigate whether those mutations alter artemisinin effects. This information is discussed in the context of biochemical and genetic aspects of Pfk13, and related to the regional malaria epidemiology of Central African countries.

Availability of the current and future water resources in Equatorial Central Africa: case of the Nyong forest catchment in Cameroon.

To anticipate disasters (drought, floods, etc.) caused by environmental forcing and reduce their impacts on its fragile economy, sub-Saharan Africa needs a good knowledge of the availability of current water resources and reliable hydroclimatic forecasts. This study has an objective to quantify the availability of water resources in the Nyong basin and predict its future evolution (2024-2050). For this, the SWAT (Soil and Water Assessment Tool) model was used. The performance of this model is satisfactory in calibration (2001-2005) and validation (2006-2010), with R2, NSE, and KGE greater than 0.64. Biases of - 11.8% and - 13.9% in calibration and validation also attest to this good performance. In the investigated basin, infiltration (GW_RCH), evapotranspiration (ETP), surface runoff (SURQ), and water yield (WYLD) are greater in the East, probably due to more abundant rainfall in this part. The flows and sediment load (SED) are greater in the middle zone and in the Southwest of the basin, certainly because of the flat topography of this part, which corresponds to the valley floor. Two climate models (CCCma and REMO) predict a decline in water resources in this basin, and two others (HIRHAM5 and RCA4) are the opposite. However, based on a statistical study carried out over the historical period (2001-2005), the CCCma model seems the most reliable. It forecasts a drop in precipitation and runoff, which do not exceed - 19% and - 18%, respectively, whatever the emission scenario (RCP4.5 or RCP8.5). Climate variability (CV) is the only forcing whose impact is visible in the dynamics of current and future flows, due to the modest current (increase of + 102 km2 in builds and roads) and future (increase of + 114 km2 in builds and roads) changes observed in the evolution of land use and land cover (LULC). The results of this study could contribute to improving water resource management in the basin studied and the region.

Epidemiological Evidence of Nosocomial and Zoonotic Transmission of Human T-Cell Leukemia Virus-1 in a Large Survey in a Rural Population of Central Africa.

BACKGROUND: Central Africa is one of the largest areas of high endemicity for human T-cell leukemia virus-1 (HTLV-1). However, no preventive measures are yet implemented to reduce its transmission, which can be sexual, from mother-to-child, or through contaminated blood products. Rare zoonotic transmissions from nonhuman primates (NHPs) have also been reported in this region. Here we investigated the HTLV-1 prevalence and associated risk factors in a rural population in Cameroon. METHODS: From 2019 to 2021, we performed a cross-sectional survey in the eastern region of Cameroon. HTLV-1 infection was first screened by ELISA, then tested by western blot and envelope gene targeted polymerase chain reaction. Risk factors associated with HTLV-1 infection were identified by logistic regression in univariable and multivariable analyses. RESULTS: Among 3400 participants, HTLV-1 prevalence was 1.1% (95% confidence interval [CI], .7-1.5). Factors independently associated with HTLV-1 infection were Pygmy ethnicity (adjusted odd ratio [aOR], 2.9; 95% CI, 1.3-6.2), history of surgery (aOR, 6.3; 95% CI, 2.2-17.8), and NHP bite (aOR, 6.6; 95% CI, 2.2-19.8). CONCLUSIONS: These results suggest both iatrogenic and zoonotic transmission of HTLV-1 in Cameroon. Further studies are needed to assess the risk of nosocomial transmission of HTLV-1, to guide public health authorities in implementing preventive measures to control HTLV-1 transmission.

"I take it and give it to my partners who will give it to their partners": Secondary distribution of HIV self-tests by key populations in Côte d'Ivoire, Mali, and Senegal.

INTRODUCTION: HIV epidemics in Western and Central Africa (WCA) remain concentrated among key populations, who are often unaware of their status. HIV self-testing (HIVST) and its secondary distribution among key populations, and their partners and relatives, could reduce gaps in diagnosis coverage. We aimed to document and understand secondary HIVST distribution practices by men who have sex with men (MSM), female sex workers (FSW), people who use drugs (PWUD); and the use of HIVST by their networks in Côte d'Ivoire, Mali, and Senegal. METHODS: A qualitative study was conducted in 2021 involving (a) face-to-face interviews with MSM, FSW, and PWUD who received HIVST kits from peer educators (primary users) and (b) telephone interviews with people who received kits from primary contacts (secondary users). These individual interviews were audio-recorded, transcribed, and coded using Dedoose software. Thematic analysis was performed. RESULTS: A total of 89 participants, including 65 primary users and 24 secondary users were interviewed. Results showed that HIVST were effectively redistributed through peers and key populations networks. The main reported motivations for HIVST distribution included allowing others to access testing and protecting oneself by verifying the status of partners/clients. The main barrier to distribution was the fear of sexual partners' reactions. Findings suggest that members of key populations raised awareness of HIVST and referred those in need of HIVST to peer educators. One FSW reported physical abuse. Secondary users generally completed HIVST within two days of receiving the kit. The test was used half the times in the physical presence of another person, partly for psychological support need. Users who reported a reactive test sought confirmatory testing and were linked to care. Some participants mentioned difficulties in collecting the biological sample (2 participants) and interpreting the result (4 participants). CONCLUSION: The redistribution of HIVST was common among key populations, with minor negative attitudes. Users encountered few difficulties using the kits. Reactive test cases were generally confirmed. These secondary distribution practices support the deployment of HIVST to key populations, their partners, and other relatives. In similar WCA countries, members of key populations can assist in the distribution of HIVST, contributing to closing HIV diagnosis gaps.

A 43-year of human thermal comfort in Central Africa.

In this study, the human thermal stress was quantified across Central Africa (C.A.) using the Universal Thermal Climate Index (UTCI). Although many of the documented studies on the use of UTCI in relation to human health are currently restricted to countries in the northern hemisphere, this contribution constitutes a prerequisite of information for future research in the region. To mitigate the problem of lack of field data in the Central African sub-region, we downloaded UTCI data via the ERA5 reanalysis portal. Based on this data source, we have explored the spatiotemporal characteristics and the resulting behaviour at annual, seasonal and monthly scales in Central Africa over the period 1982 to 2022. On these different scales, 4 of the 10 UTCI thermal stress categories were experienced, ranging from mild cold stress to strong heat stress. Spatially, cases of moderate heat stress were the most widespread, with cases of strong intensity occurring in a few isolated areas in the centre, east and west. Slight cold stress is confined to the south-east domain, particularly in autumn and winter. From 1982 to 2022, heat stress has increased significantly in the region, with peaks observed in January and October; very few areas have been spared the phenomenon of thermal stress. However, a slight decreasing trend was noticed along coastal regions and the south of C.A. Thereafter, the trend values showed the degree of C.A. vulnerability to global warming, and thus appropriate measures should be taken in relation to outdoor occupations and its impacts on the population of this region.

Socio-Ecological Approach to a Forest-Swamp-Savannah Mosaic Landscape Using Remote Sensing and Local Knowledge: a Case Study in the Bas-Ogooué Ramsar Site, Gabon.

Studies of landscape dynamics in protected areas often rely exclusively on remotely-sensed data, leading to bias by neglecting how local inhabitants, who often have a long history of interaction with their environment, perceive and structure the landscape over time. Using a socio-ecological system (SES) approach in a forest-swamp-savannah mosaic within the Bas-Ogooué Ramsar site in Gabon, we assess how human populations participate in landscape dynamics over time. We first conducted a remote sensing analysis to produce a land-cover map representing the biophysical dimension of the SES. This map is based on pixel-oriented classifications, using a 2017 Sentinel-2 satellite image and 610 GPS points, that categorized the landscape in 11 ecological classes. To study the landscape's social dimension, we collected data on local knowledge to understand how local people perceive and use the landscape. These data were collected through 19 semi-structured individual interviews, three focus groups and 3 months of participant observation during an immersive field mission. We developed a systemic approach by combining data on biophysical and social dimensions of the landscape. Our analysis shows that in the absence of continued anthropic interventions, both savannahs and swamps dominated by herbaceous vegetation will experience closure by encroaching woody vegetation, leading to eventual biodiversity loss. Our methodology based on an SES approach to landscapes could improve the conservation programs developed by Ramsar site managers. Designing actions at the local scale, rather than applying one set of actions to the entire protected area, allows the integration of human perceptions, practices and expectations, a challenge that is more than essential in the context of global change.

National Monkeypox Surveillance, Central African Republic, 2001-2021.

We analyzed monkeypox disease surveillance in Central African Republic (CAR) during 2001-2021. Surveillance data show 95 suspected outbreaks, 40 of which were confirmed as monkeypox, comprising 99 confirmed and 61 suspected monkeypox cases. After 2018, CAR's annual rate of confirmed outbreaks increased, and 65% of outbreaks occurred in 2 forested regions bordering the Democratic Republic of the Congo. The median patient age for confirmed cases was 15.5 years. The overall case-fatality ratio was 7.5% (12/160) for confirmed and suspected cases, 9.6% (8/83) for children <16 years of age. Decreasing cross-protective immunity from smallpox vaccination and recent ecologic alterations likely contribute to increased monkeypox outbreaks in Central Africa. High fatality rates associated with monkeypox virus clade I also are a local and international concern. Ongoing investigations of zoonotic sources and environmental changes that increase human exposure could inform practices to prevent monkeypox expansion into local communities and beyond endemic areas.

Early Circulation of SARS-CoV-2, Congo, 2020.

To determine when severe acute respiratory syndrome coronavirus 2 arrived in Congo, we retrospectively antibody tested 937 blood samples collected during September 2019-February 2020. Seropositivity significantly increased from 1% in December 2019 to 5.3% in February 2020, before the first officially reported case in March 2020, suggesting unexpected early virus circulation.

PERCHING syndrome: Clinical presentation in the first African patient confirmed by clinical whole genome sequencing.

PERCHING syndrome is a rare multisystem developmental disorder caused by autosomal recessive (AR) variants (truncating and missense) in the Kelch-like family member 7 gene (KLHL7). We report the first phenotypic and molecular description of PERCHING syndrome in a patient from Central Africa. The patient presented multiple dysmorphic features in addition to neurological, respiratory, gastroenteric, and dysautonomic disorders. Clinical Whole Genome Sequencing in the proband and his mother identified two novel heterozygous variants in the KLHL7 gene, including a maternally inherited intronic variant (NM_001031710.2:c.793 + 5G > C) classified as Variant of Uncertain Significance and a frameshift stop gain variant (NM_001031710.2:c.944delG; p.Ser315ThrfsTer23) of unknown inheritance classified as likely pathogenic. Although the diagnosis was only evoked after genomic testing, the review of published patients suggests that this disease could be clinically recognizable and maybe considered as an encephalopathy. Our report will allow expanding the phenotypic and molecular spectrum of Perching syndrome.

Infestation rates, seasonal distribution, and genetic diversity of ixodid ticks from livestock of various origins in two markets of Yaoundé, Cameroon.

Little is known about the impact of ticks on livestock and humans in Cameroon. This study aimed to determine the prevalence, seasonal variation, and genetic diversity of hard ticks in the country. Ticks were collected during a cross-sectional survey on domestic livestock in two markets of Yaoundé in 2019 and 2020 and identified using morphological keys, 16S ribosomal DNA, (16S rDNA), and the cytochrome c oxidase subunit 1 (Cox1) genes. The infestation rates were 39.18%, 11.53%, and 2.74% in cattle, sheep, and goats respectively. Three genera of ticks were identified, Rhipicephalus, Amblyomma, and Hyalomma comprising eleven tick species. The main species were Rhipicephalus decoloratus (30.25%), R. microplus (24.43%), and Amblyomma variegatum (12.96%). Rhipicephalus spp. (81.31%) and Amblyomma variegatum (51.54%) were abundant during the rainy season, while Hyalomma spp. (83.86%) during the dry season (p-value <0.00001). Cox1 and 16S rDNA analysis showed a high level of genetic diversity among tick species with sequences close to those observed across Africa. Phylogenetic analysis revealed that our R. microplus belong to clade A and we identified R. sanguineus s.l. as R. linnea. This study shows a high tick infestation rate in cattle, while low in small ruminants with an extensive diversity of tick species, including several known vectors of important tick-borne diseases.

Value of DNA testing in the diagnosis of sickle-cell anemia in childhood in an environment with a high prevalence of other causes of anemia.

BACKGROUND: Sickle-cell anemia (SCA) is the most common genetic disease worldwide caused by a single mutation in the gene HBB. DNA testing can help to clarify the diagnosis when Hb electrophoresis is inconclusive. We evaluated the usefulness and feasibility of DNA-based diagnosis of SCA in rural Central Africa. METHODS: This is a cross-sectional study conducted from November 2016 to end October 2017 in the Hôpital Saint Luc de Kisantu, located 120 km from Kinshasa. This hospital offers the management of SCA patients, mainly identified using the Sickling test (Emmel test) combined with clinical features. We included patients aged 6 months to 18 years locally diagnosed as SCA, and we collected clinical and hematological data. All patients were offered Hb electrophoresis and DNA testing at the Center for Human Genetics of the University of Kinshasa. RESULTS: This study included 160 patients. Hemoglobin capillary electrophoresis suggested that 136 (85%) were homozygote SS, 13 (8.1%) were heterozygote (AS), and 11 (6.9%) were homozygote normal (AA). DNA testing confirmed these electrophoresis findings, with the exception of four patients, two AS in electrophoresis were found SS due to recent transfusion, and two SS in electrophoresis were found AS because they have compound heterozygous form S/ß°-thalassemia. The diagnosis of SCA was therefore wrongly ascertained with Emmel test in 15% of patients. CONCLUSION: This study reveals a high proportion of false-positive SCA diagnoses in a rural environment in Central Africa. This underlines the importance of DNA testing in conjunction with Hb electrophoresis.

Yaws in Pygmy and Bantu children inhabiting the rural zones of Central Africa.

Introduction: Yaws, an infectious dermatosis is one of 17 neglected tropical diseases still present in the world despite the efforts aiming at the eradication of the disease undertaken in 2020. It is mainly found in populations living in poor hygiene conditions with a limited access to water and health care facilities. BaAka Pygmies and Bantu people inhabiting the rural areas of the Central African Republic (CAR) are still affected by yaws on a large scale. Aim: To assess the prevalence of yaws in Central Africa, treatment accessibility, and the need for implementing future health programs. Material and methods: Primary school BaAka Pygmy and Bantu children from the Dzanga Sangha region (CAR) were assessed in the context of yaws prevalence in years 2019-2020. The diagnosis was based on the clinical picture of the typical skin lesions and their location. Serologic tests were not performed. Results: Four hundred and ninety-four Pygmies and 235 Bantu children were examined, of whom 38.7% and 43.0%, respectively, presented primary yaws lesions. The mean age of Pygmy and Bantu children with lesions was 9.1 and 9.7 years old, respectively. In both ethnic groups boys predominated. The most common location of yaws lesions were lower legs, ankles, knees and feet. Conclusions: Yaws, like all other neglected tropical diseases, might become a cosmopolitan skin disease transferred from Africa to Europe and North America by tourists travelling to sub-Saharan destinations in Africa and migrants. The knowledge of tropical skin diseases and ability to make a differential diagnosis might become necessary for each dermatologist in the next 10-20 years.

Prevalence of human leukocyte antigen HLA-B*57:01 in individuals with HIV in West and Central Africa.

BACKGROUND: The presence of the human leukocyte antigen HLA-B*57:01 is associated with the development of a hypersensitivity reaction to abacavir (ABC). Limited data exist on HLA-B*57:01 prevalence in individuals with HIV-1 in Africa. This study aimed to estimate HLA-B*57:01 prevalence in individuals with HIV-1 in West and Central Africa. METHODS: A cross-sectional study was conducted in four countries in West and central Africa (Burkina-Faso, Côte d'Ivoire, Gabon, and Togo) from January 2016 to February 2020 to determine the status of HLA-B*57:01 in adults with HIV-1. The presence of HLA-B*57:01 was determined by using Single Specific Primer-Polymerase Chain Reaction (SSP-PCR) in blood samples. Prevalence rates were stratified based on country. RESULTS: A total of 4016 (69.8% women) individuals with HIV were enrolled. Their median age was 45, and the interquartile range was 38-52. We included 500 (12.4%) patients in Burkina-Faso, 1453 (36.2%) in Côte d'Ivoire, 951 (23.7%) in Gabon, and 1112 (27.7%) in Togo. The overall HLA-B*57:01 prevalence was 0.1% [95% CI: 0.0-0.2%]. The prevalence of HLA-B*57:01 was similar according to the four countries. Only one case was reported in each country except Togo, with no cases. CONCLUSIONS: HLA-B*57:01 prevalence is low in individuals with HIV in West and central Africa, and there is no difference among countries. This study does not confirm the utility of HLA-B*57:01 allele testing for abacavir use in this region.

Parallel diversification of the African tree toad genus Nectophryne (Bufonidae).

African amphibian diversity remains underestimated with many cryptic lineages awaiting formal description. An important hotspot of amphibian diversification is the Guineo-Congolian rainforest in Central Africa, its richness attributable to present day and ancestral range fragmentation through geological barriers, habitat expansion and contraction, and the presence of steep ecological gradients. The charismatic Nectophryne tree toads present an interesting case study for diversification in this region. The two formally described species comprising this genus show nearly identical geographic distributions extending across most of the Guineo-Congolian rainforest, but show little morphological disparity. Both species harbour extensive genetic diversity warranting taxonomic revisions, and interestingly, when comparing the subclades within each, the two species show remarkably parallel diversification histories, both in terms of timing of phylogenetic splits and their geographic distributions. This indicates that common processes may have shaped the evolutionary history of these lineages.