Malaria remains a major public health challenge in Benin, where environmental conditions strongly influence its transmission dynamics. Understanding the spatial heterogeneity of malaria risk is essential for targeting interventions more effectively. This study applied high-resolution environmental covariates and a robust Stochastic Partial Differential Equation (SPDE) model to investigate the distribution of malaria prevalence across Benin. Remote sensing-derived variables, including temperature and vegetation indices, as well as information about soil, built-up areas, and bare surfaces, were integrated into the model. Malaria prevalence was estimated using rapid diagnostic test (RDT) data from national Demographic and Health Surveys (DHS), and model performance was assessed through receiver operating characteristic (ROC) analysis. The findings reveal pronounced spatial dependence in malaria prevalence, with transmission patterns strongly associated with temperature and vegetation cover. Distinct hotspots were identified in the northern and central regions of the country, indicating areas of elevated risk. The model demonstrated satisfactory predictive accuracy (with a sensitivity of 0.619 and a specificity of 1.000), underscoring the utility of environmental covariates in capturing the spatial variability of malaria transmission. Malaria in Benin exhibits marked spatial heterogeneity shaped by environmental factors. The identification of high-risk hotspots highlights priority areas for intensified intervention. Integrating spatial modelling with environmental data offers a powerful framework for refining malaria control strategies and accelerating progress towards elimination targets.

IntroductionMaize (Zea mays L.) is the most commonly grown cereal crop in Benin and is a staple for millions of people. However, its production is hampered by insect pests such as the fall armyworm (Spodoptera frugiperda J. E. Smith), which causes substantial yield losses. Chemical pest control has demonstrated several limitations, leading to the promotion of ecological approaches such as pushpull technology, which deters insect pests through strategic intercropping. Promoting this technology in Benin requires an understanding of the maize-based intercropping systems developed by Beninese farmers across different agroecological zones and ethnic groups, as well as their perception of crop associations. It is also crucial to identify the factors that have an impact on the adoption of a maize-based intercropping system.MethodsTo access this technology in Benin, 438 farmers from 60 villages located in seven agroecological zones, belonging to eight sociolinguistic groups, were interviewed using participatory methods.Results and DiscussionAccording to the findings, crop association was practiced by 70.56% of surveyed the farmers in their maize fields, and four distinct crop association types and systems were documented. Farmers listed six constraints that hinder the use of maize-based intercropping systems, with field maintenance difficulty (60.54% of responses) being the most important. Cultural prohibitions or taboos (21.67% of responses) regarding intercropping systems such as maize and common beans were recorded in the study area. The practices and types of crop associations vary according to ethnic groups and agroecological zones. The push-pull method should be implemented in Benin by targeting Yoa-Lokpa and Fon ethnic groups and agroecological zones 4 and 8. For mass adoption of the push-pull technology by Beninese farmers, it is necessary to implement participatory methods such as farmer field schools or field days and target farmers with extensive agricultural experience.

Abstract The recent MPXV epidemic across Africa revealed extensive viral diversity and complex transmission dynamics, prompting a continent-wide genomic investigation. We analysed 3,450 high-quality MPXV virus whole genomes from 24 African Union Member States, revealing the complex and concurrent circulation of Sub-clades Ia, Ib, IIa, and IIb. Subclade Ia showed high levels of virus diversity in reservoir hosts in Central Africa, detected through zoonotic transmission and some sustained human outbreak lastly detected. In contrast, Clade Ib exhibited signatures of sustained human-to-human transmission across Eastern and Southern Africa. Clade IIa remains largely zoonotic in West Africa. Like Ia, IIb shows continued zoonotic transmission, and sustained human outbreak linked to lineage G1 and G2 circulation. Phylogeographic analyses revealed frequent cross-border transmission and interconnectedness, which was aligned with both human mobility corridors and international boundaries. For instance, the Democratic Republic of the Congo or Sierra Leone seems to emerge as a source of regional exportation, while the Cameroon–Nigeria, CAR-Cameroon or CAR-DRC interfaces reflected ongoing cross-border zoonotic spillovers. These findings underscore the need for harmonised genomic surveillance, APOBEC3-aware triage, and integrated One Health strategies to prevent local outbreaks from escalating into regional epidemics and to inform vaccine deployment and public health preparedness.

The zoonotic Lassa virus (LASV), killing thousands of people annually, is maintained majorly by the multimammate mice Mastomys natalensis and M. erythroleucus; but other rodent reservoirs exist. Knowledge regarding LASV ecology remains limited in certain areas where Lassa fever continues to be incident and even recently emergent. Here, we assess community composition and LASV infection-status of small mammals in key localities across the Guinea savanna belt that spans the countries of Benin and Nigeria. Active LASV infection was determined by conventional (gel based)- and quantitative-PCR screening, while previous infection was determined by an immunofluorescent assay on IgG antibodies. Surprisingly, M. natalensis and M. erythroleucus, known to be sympatric across the Guinea savanna, co-occurred in only one locality and were PCR-negative for the virus; but showed IgG antibodies in localities endemic for Lassa fever within Nigeria. Viremia, alternately, was detected in Mus (Nannomys) baoulei and (a newly-discovered reservoir) Lemniscomys striatus, carrying relatively ancient LASV lineages, VIII & IX respectively, within Benin. Our results suggest non-Mastomys rodents assume an increased role in LASV ecology within the Guinea savanna belt of Benin and Nigeria; especially in central Benin, which turns out to be a long-overlooked hotbed of early evolution, host-switching and contemporary emergence.

BACKGROUND:SARS-CoV-2 (COVID-19) has emerged as a significant global public health challenge, revealing critical vulnerabilities within health systems worldwide. While extensive data on COVID-19 is available from high-income countries, information remains scarce in lower-income regions, particularly regarding its impact on pregnant women. This study aims to evaluate the burden of COVID-19 among pregnant women and its effects on maternal and birth outcomes during the third wave in Benin. METHODS:A cross-sectional, hospital-based survey was conducted from May 19 to September 19, 2022, at the Lagune Mother and Child Teaching Hospital. A standardized questionnaire was administered, and nasal swabs along with serological analysis were performed on 437 pregnant women. Multivariate logistic regression was used to assess risk factors and evaluate the impact of previous or current COVID-19 exposure on maternal and birth adverse outcomes. RESULTS:SARS-CoV-2 was detected in less than 1% of pregnant women through PCR testing of nasal swab samples. Among the study population, 14.4% of women were vaccinated against COVID-19. A total of 81.1% of women tested positive for antibodies, suggesting prior exposure or infection to SARS-CoV-2 or vaccination. Notably, 78.6% of unvaccinated women had detectable antibodies, which serves as a more accurate proxy for infection prevalence. No significant association was found between prior COVID-19 exposure and adverse maternal and birth outcomes (aOR: 0.48, 95% CI 0.15-1.51). CONCLUSIONS:Although PCR testing revealed a low incidence of active SARS-CoV-2 infection, the high prevalence of IgG antibodies among pregnant women suggests widespread prior exposure or infection. Vaccination was identified as a strong predictor of detectable IgG antibodies. Notably, despite the presence of antibodies, no significant association was found between prior COVID-19 exposure and adverse maternal or birth outcomes. These findings highlight the need for further research to explore the potential long-term effects of COVID-19 infection on pregnancy outcomes and to better understand the relationship between antibody presence and maternal and fetal health.

We screened 650 febrile patients from Benin for Rift Valley fever and Crimean-Congo hemorrhagic fever viruses during 2022-2023. None were positive by reverse transcription PCR; 1.1% and 0.3%, respectively, had virus-specific IgG. False-positive results from malaria-associated antibodies likely reacting with histidine-tagged viral antigens mandate careful validation of serologic tests in malaria-endemic regions.

Maternal and neonatal infections pose a significant public health challenge, particularly in developing countries like Benin. This retrospective study investigates the frequency and determinants of maternal and neonatal infections in Benin during 2022, utilizing data from six reference hospitals. The study includes 123 neonates suspected of infection, analyzing factors such as birth weight, breastfeeding practices, clinical delivery parameters, and laboratory-confirmed infection rates. Findings reveal that 32% of suspected cases were confirmed infections, with a higher prevalence among premature newborns and those born in specific hospitals. The study emphasizes the need for improved diagnostic facilities, infection control practices, and awareness among healthcare workers and pregnant women. Recommendations for future research include broader geographic coverage and enhanced training programs.

Background In mid-November, 2021, the SARS-CoV-2 omicron variant (B.1.1.529; BA.1 sublineage) was detected in southern Africa, prompting international travel restrictions. We aimed to investigate the spread of omicron BA.1 in Africa. Methods In this observational study, samples from patients infected with SARS-CoV-2 from 27 laboratories in 24 African countries, collected between June 1, 2021 and April 14, 2022, were tested for omicron BA.1 and delta (B.1.617.2) variants using real-time RT-PCR. Samples that tested positive for BA.1 by RT-PCR and were collected before estimated BA.1 emergence according to epidemiological properties were excluded from downstream analyses. The diagnostic precision of the assays was evaluated by high-throughput sequencing of samples from four countries. The observed spread of BA.1 was compared with mobility-based mathematical simulations and entries for SARS-CoV-2 in the Global Initiative on Sharing All Influenza Data (GISAID) genomic database. We estimated the effective reproduction number (R-t) at the country level considering the BA.1 fraction and the reported numbers of infections. Phylogeographical analyses were done in a Bayesian framework. Findings Through testing of 13 294 samples from patients infected with SARS-CoV-2, we established that, by November-December, 2021, omicron BA.1 had replaced the delta variant of SARS-CoV-2 in all African subregions, following a south-north gradient, with a median R-t of 2.60 (95% CI 2.46-2.71). This south-north spread, established on the basis of PCR data, was substantiated by phylogeographical reconstructions, ancestral state reconstructions, and GISAID data. PCR-based reconstructions of country-level BA.1 predominance and the availability of BA.1 genomic sequences in GISAID correlated significantly in time (p=0.0002, r=0.78). The first detections of BA.1 in high-income settings beyond Africa were predicted accurately in time by mobility-based mathematical simulations (p<0.0001). Comparing PCR-based reconstructions with mobility-based mathematical simulations suggested that SARS-CoV-2 infections in Africa were under-reported by approximately ten times. Inbound travellers infected with BA.1, departing from five continents, were identified in six African countries by early December, 2021. Interpretation Omicron BA.1 was widespread in Africa when travel bans were implemented, limiting their effectiveness. Combined with genomic surveillance and mobility-based mathematical modelling, PCR-based strategies can inform R-t and the geographical spread of emerging pathogens in a cost-effective and timely manner, and can guide evidence-based, non-pharmaceutical interventions such as travel restrictions or physical distancing. Copyright (c) 2025 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license.

In the context of the COVID-19 pandemic, Benin, like other regions in sub-Saharan Africa and around the world, has been grappling with a public health crisis since march 2020. The country responded to this crisis by implementing adaptive response measures. The STREESCO project is part of this dynamic effort, strengthening epidemiological surveillance at three sentinel sites. This study thoroughly examines the determinants of SARS-CoV-2 infection. This involved strategic support based in Cotonou, Allada, and Natitingou. Data collection took place from march 1 to november 30, with individuals voluntarily undergoing COVID-19 screening at dedicated health units. Before participation, free and informed consent was obtained. The collected data included sociodemographic information, clinical details, and the results of COVID-19 tests. A multivariate logistic regression model was used to identify factors associated with SARS-CoV-2 infection. Surveillance included 4178 participants, with a male/female ratio of 0.98 and a median age of 33 (IQR: 25-45). Across all sites, 13.12% of participants tested positive for SARS-CoV-2, and 85.40% of them had a SARS-CoV-2 infection.of participants were symptomatic at baseline. The proportion of positivity was 6%, 11% and 28% respectively during phases 1, 2 and 3 of the national strategy. Identified risk factors included the Allada site (aOR 2.04, 95%CI 1.59-2.62), phase 3 (aOR 3.16, 95%CI 2.34-4.27), phase 2 (aOR 1.67, 95%CI 1.12-2.51), secondary (aOR 1.67, 95%CI 1.12-2.51) and higher level of education (aOR 1.83, 95%CI 1.22-2.74), respiratory symptoms (aOR 1.88, 95%CI 1.40-2.53), and/or anosmia/ageusia (aOR 1.88, 95%CI 1.48-2.38). Conversely, the Natitingou site (aOR = 0.29, 95%CI: 0.20-0.42), group living (aOR = 0.75, 95%CI: 0.60-0.94), and digestive symptoms (aOR = 0.70, 95%CI: 0.54-0.91) were associated with a reduced risk of infection. These results underscore the importance of active surveillance during crisis situations, ensuring the acquisition of reliable and persuasive data to enhance individual care and guide health policies. Trial registration NCT06170320 (retrospectively registered on December 21, 2023).

BACKGROUND:Knowledge of epidemiology, pathogenesis, and public health burden is scarce for many arthropod-borne viruses (arboviruses). Insufficient knowledge is partly attributable to the lack of exhaustive laboratory diagnostics due to resource limitations. Among arboviruses, arthritogenic and encephalitogenic alphaviruses are globally widespread, can cause severe disease, and can co-occur regionally. OBJECTIVES:We developed and validated a multiplexed real-time reverse transcription-PCR assay for the detection of all alphaviruses commonly causing human disease except Barmah Forest virus. STUDY DESIGN:The assay combines five antigenic complex-specific assays and one Chikungunya virus (CHIKV)-specific assay in a single parallelized reaction. RESULTS:Comparisons with previously published PCR-based protocols for broad alphavirus detection using 20 different human-pathogenic alphaviruses revealed a significantly higher sensitivity of the new multiplexed assay (Fisher's exact test, p < 0.0001). Detection limits with the new assay ranged from 0.83 cps/μl of extracted O'nyong-nyong virus to 33.05 cps/μl of extracted Western equine encephalitis virus. Antigenic complexes could be clearly differentiated by reactivity, Ct values (t-test, p < 0.0025) and signal intensities (t-test, p < 0.0001), even when testing high alphavirus concentrations potentially capable of causing false-positive PCR results. Testing of high-titred cell culture supernatants of eight important non-alphaviral arboviruses, of 4308 serum samples collected from febrile patients in Benin and Peru, of seven CHIKV-positive diagnostic samples from Brazil, and of non-targeted alphaviruses confirmed excellent diagnostic performance by the new assay, including improved detection of CHIKV, Mayaro and Venezuelan equine encephalitis virus in clinical specimens. CONCLUSIONS:Short turn-around time, applicability in resource-limited settings, antigenic complex determination, and higher sensitivity compared to previously available tests make the new assay a useful tool for alphavirus surveillance and routine patient diagnostics.

Background: In mid-November 2021, the SARS-CoV-2 Omicron BA.1 variant was detected in Southern Africa, prompting international travel restrictions of unclear effectiveness that exacted a substantial economic toll. Methods: Amidst the BA.1 wave, we tested 13,294 COVID-19 patients in 24 African countries between mid-2021 to early 2022 for BA.1 and Delta variants using real-time reverse transcription-PCR tests. The diagnostic precision of the assays was evaluated by high-throughput sequencing in four countries. The observed BA.1 spread was compared to mobility-based mathematical simulations. Findings: By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a median Rt of 2.4 up to 30 days before BA.1 became predominant. PCR-based South-North spread was in agreement with phylogeographic reconstructions relying on 939 SARS-CoV-2 genomes from GISAID. PCR-based reconstructions of country-level BA.1 predominance correlated significantly in time with the emergence of BA.1 genomic sequences on GISAID (p=0.0035, cor=0.70). First BA.1 detections in affluent settings beyond Africa were predicted adequately in time by mobility-based mathematical simulations (p<0.0001). BA.1-infected inbound travelers departing from five continents were identified in five Western countries and one Northern African country by late November/early December 2021, highlighting fast global BA.1 spread aided by international travel. Interpretation: Unilateral travel bans were poorly effective because by the time they came into effect, BA.1 was already widespread in Africa and beyond. PCR-based variant typing combined with mobility-based mathematical modelling can inform rapidly and cost-efficiently on Rt, spread to inform non-pharmaceutical interventions. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement African Academy of Sciences grant SARSCov2-4-20-004 (IOD) AFROSCREEN project (grant agreement CZZ3209) through Agence Francaise de Developpement, coordinated by ANRS | Maladies infectieuses emergentes in partnership with Institut Pasteur and IRD (IPdG). We would additionally like to thank members from the AFROSCREEN Consortium (https://www.afroscreen.org/en/network/) for their work and support on genomic surveillance in Africa. Bill & Melinda Gates Foundation grant INV-005971 (JFD, CD); grant INV-024130 (IOD); The findings and conclusions contained within are those of the authors and do not necessarily reflect positions or policies of the Bill & Melinda Gates Foundation CIRMF is a member of CANTAM funding by EDCTP CSA2020NoE-3100 - CANTAM 3 and supported by the Gabonese Government and Total Gabon French Ministry of Europe and Foreign affairs (Bamako-Bordeaux decentralized cooperation in riposte to Covid-19) Horizon 2020, European and Developing Countries Clinical Trials Partnership (EDCTP2) programme, PANDORA-ID-NET Grant RIA2016E-1609 (AASy, ROP) Poliomyelitis Research Foundation grant 21/40 (KKP)Programa de Desenvolvimento de Ciencia e Tecnologia grant No11/MESCTI/PDCT/2020 (JFMdM) REPAIR Covid-19-Africa, coordinated by the Pasteur Network association and funded by French Ministry for Europe and Foreign Affairs (MEAE), funded COVID diagnosis and typing (IPdG). South African Department of Science and Innovation (sub-award via University of KwaZulu-Natal) grant S006872 (TGM) Stellenbosch University Postgraduate Scholarship Programme grant 25095676 (KKP) UKRI Global Challenges Research Fund, grant number NF118 (RB, RE, JMw) World Health Organization grant 2021/1113013-0 (IOD) ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethical approval for re-testing and scientific usage was provided by the institutional research ethics board (IRB) of Charite-Universitaetsmedizin Berlin (EA2/028/22) and by IRBs from Burkina Faso, Laboratoire National de Reference-Grippes (2020-7-126), Cameroon, Centre Pasteur du Cameroun (2020/05/1224/CE/CNERSH/SP), Ghana, Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), KNUST (CHRPE/AP/566/21), Kenya, Jomo Kenyatta University of Agriculture and Technology, Department of Biochemistry (JKU/2/4/896B), Uganda, Gulu University Multifunctional Laboratories (GUREC-093-20), Makerere University, College of Health Science, Kamala, Uganda (SBS-2022-130) and Zambia, Tropical Diseases Research Centre, Ndola Teaching Hospital (00003729). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Respiratory samples sent to laboratories for COVID-19 testing by attending physicians were re-tested in an anonymized fashion using the COVID-19 test developed in this study. Ethical approval for re-testing and scientific usage was provided by the institutional research ethics board (IRB) of Charite-Universitaetsmedizin Berlin (EA2/028/22) and by IRBs from Burkina Faso, Laboratoire National de Reference-Grippes (2020-7-126), Cameroon, Centre Pasteur du Cameroun (2020/05/1224/CE/CNERSH/SP), Ghana, Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), KNUST (CHRPE/AP/566/21), Kenya, Jomo Kenyatta University of Agriculture and Technology, Department of Biochemistry (JKU/2/4/896B), Uganda, Gulu University Multifunctional Laboratories (GUREC-093-20), Makerere University, College of Health Science, Kamala, Uganda (SBS-2022-130) and Zambia, Tropical Diseases Research Centre, Ndola Teaching Hospital (00003729). In all other countries, IRB approval for re-testing anonymized specimens was not required. Scripts for data analyses and data are available at GitHub (https://github.com/CarloFischer88/Analyse-the-BA.1-spread-in-Africa.git). Phylogenetic analyses of African BA.1 sequences (Fig. S6) and phylogeographic analyses (Fig. 3, Fig. S7) are based on 942 sequences available on GISAID, via 10.55876/gis8.230818aq. The performance of the used real-time RT-PCR assays was validated in this study against SARS-CoV-2 genomes generated by HTS (https://github.com/CarloFischer88/Analyse-the-BA.1-spread-in-Africa.git). Those genomes that were submitted to GISAID (Botswana, Guinea, South Africa) are available via 10.55876/gis8.240201eb. Mapped genomic reads for SARS-CoV-2 genomes generated from Beninese samples are available via the European Nucleotide Archive (ENA) (Project accession number PRJEB64297).

OBJECTIVE:Dengue is a widespread viral infection transmitted from mosquitoes to humans, mainly in tropical and subtropical climates. In Benin, only dengue virus (DENV) serotype 2 infection has been previously described in humans. This study aimed to investigate DENV infection and serotypes in suspected patients. METHODS:Plasma samples from 464 patients attending health centers in February 2023 with clinical symptoms and suspected for dengue infection were included, and analyzed for DENV by real time quantitative Polymerase Chain Reaction (Dengue Altona 3.0 kit). PCR positives samples were further characterized by whole genome sequencing and phylogenetic analysis to identify the circulating DENV serotype. RESULTS:The RT-qPCR results showed that four patients (D6, D23, D28, D44) were positive with the cycle threshold values less than 40 (31.3, 34.7, 14.7 and 14.3) respectively. Full-length DENV sequences were obtained for D6, D28 and D44. One patient (D6) was infected with DENV-1 serotype, and the two others (D28 and D44) were positive for DENV-3. Phylogenetic analysis shows that the new DENV-1 sequence is close to those obtained in Burkina Faso in 2022 and Nigeria in 2023, and the two DENV-3 sequences form a separate cluster with sequences obtained in Burkina Faso in 2022. CONCLUSION:We showed for the first time, the presence of dengue serotype 1 and serotype 3 infection in Benin. These results send a strong signal to health authorities and show that arbovirus surveillance efforts must be integrated into pathogen monitoring programs.

This study aimed to assess the specific diversity of Plasmodium infection in Anopheles mosquitoes in northern Benin. Anopheles mosquitoes were captured using human bait in four municipalities: Malanville, Cobly, Materi, and Boukoumbe. The mosquitoes were morphologically identified and characterized by polymerase chain reaction (PCR). Plasmodium species were detected using PCR. The sporozoite index (SI) was calculated, and the P-value test was employed. The kappa index (k) was also determined. A total of 3739 Anopheles mosquitoes were collected, of which 97.67% were Anopheles gambiae s.l., and 2.32% were Anopheles funestus. Two sibling species from the gambiae complex and one hybrid were identified. A. gambiae s.s. (74.38%), Anopheles coluzzii (24.79%), and A. gambiae/A. coluzzii (0.82%). Specifically, Plasmodium falciparum and Plasmodium vivax were detected in the municipalities of Malanville and Cobly, while only P. falciparum was detected in Materi and Boukoumbe using PCR. P. falciparum and P. vivax were detected in northern Benin, providing updated mapping of circulating Plasmodium species. These findings contribute to a better understanding of the epidemiology of infection and the dynamics of malaria transmission in Benin and West Africa.. KEYWORDS :Anopheles gambiae, Immunological analysis, Parasite diversity, Plasmodium falciparum, Plasmodium vivax, Vectors

The rapid detection and continuous surveillance of infectious diseases are important components of an effective public health response. However, establishing advanced molecular surveillance systems, crucial for monitoring and mitigating pandemics, poses significant challenges in resource-limited developing countries. In a collaborative effort, research institutions from Benin joined forces with Mali's National Institute of Public Health to implement a state-of-the-art molecular surveillance system in Mali. This approach was characterized by collaboration, multidisciplinarity, and tutoring. Key activities included a comprehensive assessment of infrastructure and human resources through document reviews, interviews, and laboratory visits; the development and validation of Standard Operating Procedures (SOPs) for advanced molecular surveillance following an inclusive approach; capacity-building initiatives for 25 biologists in Mali on sequencing techniques; and international tutoring sessions for eight Malian professionals held in Benin. These collective efforts enabled Mali to establish an advanced molecular surveillance system aligned with the WHO’s global strategy for genomic surveillance. This manuscript aims to share experiences, insights, and outcomes from this initiative, with the hope of contributing to the broader discussion on strengthening global health security through collaborative approaches and capacity-building efforts, particularly in developing countries.

Pregnant women are a vulnerable population to COVID-19 given an increased susceptibility to severe SARS-CoV-2 infection and pregnancy complications. However, few SARS-CoV-2 serological surveys have been performed among this population to assess the extent of the infection in sub-Saharan countries. The objectives of this study were to determine SARS-CoV-2 seroprevalence among Beninese pregnant women, to identify spatial seropositivity clusters and to analyse factors associated with the infection. A cross-sectional study including women in their third trimester of pregnancy attending the antenatal care (ANC) clinics at Allada (south Benin) and Natitingou (north Benin) was conducted. Rapid diagnostic tests (RDT) for detection of IgG/IgM against the SARS-CoV-2 spike protein were performed using capillary blood. Seroprevalence of SARS-CoV-2 antibodies and associations between SARS-CoV-2 serostatus and maternal characteristics were analyzed by multivariate logistic regression. Spatial analyses were performed using the spatial scan statistics to identify spatial clusters of SARS-CoV-2 infection. A total of 861 pregnant women were enrolled between May 4 and June 29, 2022. 58/861 (6.7

Background Lassa fever (LF), a haemorrhagic illness caused by the Lassa fever virus (LASV), is endemic in West Africa and causes 5000 fatalities every year. The true prevalence and incidence rates of LF are unknown as infections are often asymptomatic, clinical presentations are varied, and surveillance systems are not robust. The aim of the Enable Lassa research programme is to estimate the incidences of LASV infection and LF disease in five West African countries. The core protocol described here harmonises key study components, such as eligibility criteria, case definitions, outcome measures, and laboratory tests, which will maximise the comparability of data for between-country analyses. Method We are conducting a prospective cohort study in Benin, Guinea, Liberia, Nigeria (three sites), and Sierra Leone from 2020 to 2023, with 24 months of follow-up. Each site will assess the incidence of LASV infection, LF disease, or both. When both incidences are assessed the LASV cohort (nmin = 1000 per site) will be drawn from the LF cohort (nmin = 5000 per site). During recruitment participants will complete questionnaires on household composition, socioeconomic status, demographic characteristics, and LF history, and blood samples will be collected to determine IgG LASV serostatus. LF disease cohort participants will be contacted biweekly to identify acute febrile cases, from whom blood samples will be drawn to test for active LASV infection using RT-PCR. Symptom and treatment data will be abstracted from medical records of LF cases. LF survivors will be followed up after four months to assess sequelae, specifically sensorineural hearing loss. LASV infection cohort participants will be asked for a blood sample every six months to assess LASV serostatus (IgG and IgM). Discussion Data on LASV infection and LF disease incidence in West Africa from this research programme will determine the feasibility of future Phase IIb or III clinical trials for LF vaccine candidates.

Background The impact of the arbovirus vector Aedes aegypti is of major concern for global public health as the viruses that it transmits affect millions of people each year worldwide. Originating in Africa, Ae. aegypti has now spread throughout much of the world. While the genetic makeup of Ae. aegypti in the New World has been extensively studied, there is limited knowledge on its genetic diversity in Africa, particularly at a microgeographical level. Methods We investigated mitochondrial cytochrome oxidase I of four Ae. aegypti populations from Benin and employed wing morphometric analyses as a cost-effective and reliable tool to explore population structure. Our sampling encompassed various areas of Benin, from the southern to the northern borders of the country, and included urban, semi-urban, and sylvatic sites. Results We observed a notable level of genetic diversity (haplotype diversity of 0.8333) and nucleotide diversity (0.00421986), and identified seven distinct haplotypes. Sylvatic and semi-urban sites exhibited a greater number of haplotypes compared to urban sites. Utilizing 18 wing landmarks, we calculated the centroid size, which revealed significant variation among the three landscape types. However, principal component analysis, employed to assess wing shape variation, did not demonstrate significant differences between populations based on landscape type. Conclusions Our findings indicate substantial genetic and morphological diversity among Ae. aegypti populations in Benin, and provide insight into important biological characteristics of these populations with respect to their potential to transmit viruses. To the best of our knowledge, this is the first study undertaken in Africa to integrate genetics with morphology to analyse the population structure of the major arbovirus vector Ae. aegypti . Graphical Abstract

ABSTRACTBackgroundMany SARS-CoV-2 seroprevalence surveys since the end of 2020 have disqualified the first misconception that Africa had been spared by the pandemic. Through the analysis of three SARS-CoV-2 seroprevalence surveys carried out in Benin as part of the ARIACOV project, we argue that the integration of epidemiological serosurveillance of the SARS-COV2 infection in the national surveillance package would be of great use to refine the understanding of the COVID-19 pandemic in Africa.MethodsThree repeated cross-sectional surveys have been carried out in Benin, two in Cotonou, the economic capital in March and May 2021, and one in Natitingou, a semi-rural city in North in August 2021. The global and by age-groups weighted seroprevalences have been estimated and the risk factors of the infection by SARS-COV-2 have been assessed by using logistic regression.ResultsIn Cotonou, a slight increase in overall age-standardized SARS-CoV-2 seroprevalence from 29.77% (95% CI: 23.12-37.41%) at the first survey to 34.86% (95% CI: 31.57-38.30%) at the second survey was observed. In Natitingou the global adjusted seroprevalence was 33.34% (95% CI: 27.75-39.44%), much higher than expected. Adults over 40 seemed to be more at risk than the youngest during the first survey in Cotonou but no longer in the second survey, showing the persistence of the SARS-COV-2 virus circulation outside the epidemic waves.ConclusionsA routine serological surveillance on strategic sentinel sites and / or populations could constitute a cost / effective compromise to better anticipate the onset of new waves and define public health strategies.