Genomic epidemiology of SARS-CoV-2 in Senegal in 2020-2021.

INTRODUCTION: In Senegal, molecular diagnosis was widely used for the detection and management of COVID-19 patients. However, genomic surveillance was very limited in the public sector. This study aimed to share the experience of a Senegalese public sector laboratory in response to the COVID-19 pandemic, and to describe the distribution of variants circulating in 2020 and 2021. METHODOLOGY: From July 2020 to December 2021, SARS-CoV-2 qRT-PCR was performed on nasopharyngeal samples from travelers and symptomatic patients at the Bacteriology and Virology Laboratory (LBV) of the Aristide le Dantec University Teaching Hospital. Samples with a cycle threshold (Ct) ≤ 30 were selected for whole-genome sequencing (WGS) using the Nanopore technology. In-house scripts were developed to study the spatial and temporal distribution of SARS-CoV-2 variants in Senegal, using our sequences and those retrieved from the GISAID database. RESULTS: Of 8,207 patients or travelers screened for SARS-CoV-2, 970 (11.8%) were positive and 386 had a Ct ≤ 30. WGS was performed on 133 samples. Concomitantly with high-quality sequences deposited in the GISAID database covering nine cities in Senegal in 2020 and 2021 (n = 1,539), we observed a high circulation of the 20A (B.1, B.1.416 and B.1.620) and 20B (B.1.1.420) lineages in 2020, while most of the samples belonged to Delta variants (AY34 and AY.34.1, 22%) in 2021. CONCLUSIONS: Despite its late involvement, COVID-19 diagnosis was routinely performed in LBV, but genomic characterization remained challenging. The genomic diversity of SARS-CoV-2 strains in Senegal reflected that observed worldwide during the first waves of the pandemic.

Health transformation toward universal healthcare coverage amidst conflict: examining the impact of international cooperation in Niger.

Background: Approximately 70% of Sub-Saharan African countries have experienced armed conflicts with significant battle-related fatalities in the past two decades. Niger has witnessed a substantial rise in conflict-affected populations in recent years. In response, international cooperation has aimed to support health transformation in Niger's conflict zones and other conflict-affected areas in Sub-Saharan Africa. This study seeks to review the available evidence on health interventions facilitated by international cooperation in conflict zones, with a focus on Niger. Methods: We conducted a systematic literature review (SLR) adhering to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The search was conducted from 2000 to 4 September 2022 using MeSH terms and keywords to identify relevant studies and reports in Sub-Saharan Africa and specifically in Niger. Databases such as PubMed (Medline), Google Scholar, Google, and gray literature were utilized. The findings were presented both narratively and through tables and a conceptual framework. Results: Overall, 24 records (10 studies and 14 reports) that highlighted the significant role of international cooperation in promoting health transformation in conflict zones across Sub-Saharan Africa, including Niger, were identified. Major multilateral donors identified were the World Health Organization (WHO), United Nations Children's Fund (UNICEF), United Nations Fund for Population Activities (UNFPA), World Bank, United States Agency for International Development (USAID), European Union, European Commission Humanitarian Aid (ECHO), Global Fund, and Global Alliance for Vaccines and Immunization (GAVI). Most supports targeted maternal, newborn, child, adolescent, and youth health, nutrition, and psycho-social services. Furthermore, interventions were in the form of public health initiatives, mobile clinic implementation, data management, human resource capacity building, health information systems, health logistics, and research funding in conflict zones. Conclusion: This literature review underscores the significant engagement of international cooperation in strengthening and transforming health services in conflict-affected areas across Sub-Saharan Africa, with a particular focus on Niger. However, to optimize the effectiveness of healthcare activities from short- and long-term perspectives, international partners and the Ministry of Public Health need to re-evaluate and reshape their approach to health intervention in conflict zones.

Specificity of serological screening tests and reference laboratory tests to diagnose gambiense human African trypanosomiasis: a prospective clinical performance study.

BACKGROUND: Serological screening tests play a crucial role to diagnose gambiense human African trypanosomiasis (gHAT). Presently, they preselect individuals for microscopic confirmation, but in future "screen and treat" strategies they will identify individuals for treatment. Variability in reported specificities, the development of new rapid diagnostic tests (RDT) and the hypothesis that malaria infection may decrease RDT specificity led us to evaluate the specificity of 5 gHAT screening tests. METHODS: During active screening, venous blood samples from 1095 individuals from Côte d'Ivoire and Guinea were tested consecutively with commercial (CATT, HAT Sero-K-SeT, Abbott Bioline HAT 2.0) and prototype (DCN HAT RDT, HAT Sero-K-SeT 2.0) gHAT screening tests and with a malaria RDT. Individuals with ≥ 1 positive gHAT screening test underwent microscopy and further immunological (trypanolysis with T.b. gambiense LiTat 1.3, 1.5 and 1.6; indirect ELISA/T.b. gambiense; T.b. gambiense inhibition ELISA with T.b. gambiense LiTat 1.3 and 1.5 VSG) and molecular reference laboratory tests (PCR TBRN3, 18S and TgsGP; SHERLOCK 18S Tids, 7SL Zoon, and TgsGP; Trypanozoon S2-RT-qPCR 18S2, 177T, GPI-PLC and TgsGP in multiplex; RT-qPCR DT8, DT9 and TgsGP in multiplex). Microscopic trypanosome detection confirmed gHAT, while other individuals were considered gHAT free. Differences in fractions between groups were assessed by Chi square and differences in specificity between 2 tests on the same individuals by McNemar. RESULTS: One gHAT case was diagnosed. Overall test specificities (n = 1094) were: CATT 98.9% (95% CI: 98.1-99.4%); HAT Sero-K-SeT 86.7% (95% CI: 84.5-88.5%); Bioline HAT 2.0 82.1% (95% CI: 79.7-84.2%); DCN HAT RDT 78.2% (95% CI: 75.7-80.6%); and HAT Sero-K-SeT 2.0 78.4% (95% CI: 75.9-80.8%). In malaria positives, gHAT screening tests appeared less specific, but the difference was significant only in Guinea for Abbott Bioline HAT 2.0 (P = 0.03) and HAT Sero-K-Set 2.0 (P = 0.0006). The specificities of immunological and molecular laboratory tests in gHAT seropositives were 98.7-100% (n = 399) and 93.0-100% (n = 302), respectively. Among 44 reference laboratory test positives, only the confirmed gHAT patient and one screening test seropositive combined immunological and molecular reference laboratory test positivity. CONCLUSIONS: Although a minor effect of malaria cannot be excluded, gHAT RDT specificities are far below the 95% minimal specificity stipulated by the WHO target product profile for a simple diagnostic tool to identify individuals eligible for treatment. Unless specificity is improved, an RDT-based "screen and treat" strategy would result in massive overtreatment. In view of their inconsistent results, additional comparative evaluations of the diagnostic performance of reference laboratory tests are indicated for better identifying, among screening test positives, those at increased suspicion for gHAT. TRIAL REGISTRATION: The trial was retrospectively registered under NCT05466630 in clinicaltrials.gov on July 15 2022.

New data on settlement and environment at the Pleistocene/Holocene boundary in Sudano-Sahelian West Africa: Interdisciplinary investigation at Fatandi V, Eastern Senegal.

The end of the Palaeolithic represents one of the least-known periods in the history of western Africa, both in terms of its chronology and the identification of cultural assemblages entities based on the typo-technical analyses of its industries. In this context, the site of Fatandi V offers new data to discuss the cultural pattern during the Late Stone Age in western Africa. Stratigraphic, taphonomical and sedimentological analyses show the succession of three sedimentary units. Several concentrations with rich lithic material were recognized. An in situ occupation, composed of bladelets, segments, and bladelet and flake cores, is confirmed while others concentrations of lithic materials have been more or less disturbed by erosion and pedogenic post-depositional processes. The sequence is well-dated from 12 convergent OSL dates. Thanks to the dating of the stratigraphic units and an OSL date from the layer (11,300-9,200 BCE [13.3-11.2 ka at 68%, 14.3-10.3 ka at 95%]), the artefacts are dated to the end of Pleistocene or Early Holocene. Palaeoenvironmental data suggest that the settlement took place within a mosaic environment and more precisely at the transition between the open landscape of savanna on the glacis and the plateau, and the increasingly densely-wooded alluvial corridor. These humid areas must have been particularly attractive during the dry season by virtue of their rich resources (raw materials, water, trees, and bushes). The Fatandi V site constitutes the first stratified site of the Pleistocene/Holocene boundary in Senegal with both precise geochronological and palaeoenvironmental data. It complements perfectly the data already obtained in Mali and in the rest of western Africa, and thus constitutes a reference point for this period. In any case, the assemblage of Fatandi V, with its bladelets and segments and in the absence of ceramics and grinding material, fits with a cultural group using exclusively geometric armatures which strongly differs from another group characterized by the production of bifacial armatures, accompanied in its initial phase by ceramics (or stoneware) and grinding material.