Dataset Information

COVID-19 in 16 West African Countries: An Assessment of the Epidemiology and Genetic Diversity of SARS-CoV-2 after Four Epidemic Waves.

ABSTRACT: West Africa faced the COVID-19 pandemic in early March 2020 and, as of March 31, 2022, had more than 900,000 confirmed cases and more than 12,000 deaths. During this period, SARS-CoV-2 genomes evolved genetically, resulting in the emergence of distinct lineages. This review was conducted to provide the epidemiological profile of COVID-19, the mutational profile of SARS-CoV-2, and the dynamics of its lineages in the 16 west African countries by analyzing data from 33 studies and seven situation reports. For a more complete representation of the epidemiology and genetic diversity of SARS-CoV-2, we used reliable public data in addition to eligible studies. As of March 31, 2022, the 16 west African countries experienced four epidemic waves with variable intensities. Higher mortality was noted during the third wave with a case fatality rate (CFR) of 1.9%. After these four epidemic waves, Liberia recorded the highest CFR (4.0%), whereas Benin had the lowest CFR (0.6%). Through mutational analysis, a high genetic heterogeneity of the genomes was observed, with a predominance of mutations in the spike protein. From this high mutational rate, different lineages emerged. Our analysis of the evolutionary diversity allowed us to count 205 lineages circulating in west Africa. This study has provided a good representation of the mutational profile and the prevalence of SARS CoV-2 lineages beyond the knowledge of the global epidemiology of the 16 African countries.

SUBMITTER: Ndiaye AJS

PROVIDER: S-EPMC10551082 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

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COVID-19 in 16 West African Countries: An Assessment of the Epidemiology and Genetic Diversity of SARS-CoV-2 after Four Epidemic Waves.

Ndiaye Anna Julienne Selbé AJS Beye Mamadou M Sow Aissatou A Lo Gora G Padane Abdou A Sokhna Cheikh C Kane Coumba Touré CT Colson Philippe P Fenollar Florence F Mboup Souleymane S Fournier Pierre-Edouard PE

The American journal of tropical medicine and hygiene 20230828 4

West Africa faced the COVID-19 pandemic in early March 2020 and, as of March 31, 2022, had more than 900,000 confirmed cases and more than 12,000 deaths. During this period, SARS-CoV-2 genomes evolved genetically, resulting in the emergence of distinct lineages. This review was conducted to provide the epidemiological profile of COVID-19, the mutational profile of SARS-CoV-2, and the dynamics of its lineages in the 16 west African countries by analyzing data from 33 studies and seven situation r ...[more]

PMID: 37640294

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Project description:BackgroundAfrica contains the most genetically divergent group of continental populations and several studies have reported that African populations show a high degree of population stratification. In this regard, it is important to investigate the potential for population genetic structure or stratification in genetic epidemiology studies involving multiple African populations. The presences of genetic sub-structure, if not properly accounted for, have been reported to lead to spurious association between a putative risk allele and a disease. Within the context of the Africa America Diabetes Mellitus (AADM) Study (a genetic epidemiologic study of type 2 diabetes mellitus in West Africa), we have investigated population structure or stratification in four ethnic groups in two countries (Akan and Gaa-Adangbe from Ghana, Yoruba and Igbo from Nigeria) using data from 372 autosomal microsatellite loci typed in 493 unrelated persons (986 chromosomes).ResultsThere was no significant population genetic structure in the overall sample. The smallest probability is associated with an inferred cluster of 1 and little of the posterior probability is associated with a higher number of inferred clusters. The distribution of members of the sample to inferred clusters is consistent with this finding; roughly the same proportion of individuals from each group is assigned to each cluster with little variation between the ethnic groups. Analysis of molecular variance (AMOVA) showed that the between-population component of genetic variance is less than 0.1% in contrast to 99.91% for the within population component. Pair-wise genetic distances between the four ethnic groups were also very similar. Nonetheless, the small between-population genetic variance was sufficient to distinguish the two Ghanaian groups from the two Nigerian groups.ConclusionThere was little evidence for significant population substructure in the four major West African ethnic groups represented in the AADM study sample. Ethnicity apparently did not introduce differential allele frequencies that may affect analysis and interpretation of linkage and association studies. These findings, although not entirely surprising given the geographical proximity of these groups, provide important insights into the genetic relationships between the ethnic groups studied and confirm previous results that showed close genetic relationship between most studied West African groups.

Project description:Climate change strongly impacts the agricultural sector in West Africa, threatening food security and nutrition, particularly for populations with the least adaptive capacity. Little is known about national climate change policies in the region. This systematic review identifies and analyses climate change policy documents in all 16 West African countries: (1) What are the existing climate change adaptation policies publicly available? (2) Which topics are addressed? (3) How are agriculture and food security framed and addressed? Following PRISMA guidelines, PubMed and Google scholar as key databases were searched with an extensive grey literature search. Keywords for searches were combinations of "Africa", "Climate Change", and "National Policy/Plan/Strategy/Guideline". Fifteen countries have at least one national policy document on climate change in the frame of our study. Nineteen policy documents covered seven key sectors (energy, agriculture, water resources, health, forestry, infrastructure, and education), and eight thematic areas (community resilience, disaster risk management, institutional development, industry development, research and development, policy making, economic investment, and partnerships/collaboration). At the intersection of these sectors/areas, effects of changing climate on countries/populations were evaluated and described. Climate change adaptation strategies emerged including development of local risk/disaster plans, micro-financing and insurance schemes (public or private), green energy, and development of community groups/farmers organizations. No clear trend emerged when analysing the adaptation options, however, climate change adaptation in the agriculture sector was almost always included. Analysing agriculture, nutrition, and food security, seven agricultural challenges were identified: The small scale of West African farming, information gaps, missing infrastructure, poor financing, weak farmer/community organizations, a shifting agricultural calendar, and deteriorating environmental ecology. They reflect barriers to adaptation especially for small-scale subsistence farmers with increased climate change vulnerabilities. The study has shown that most West African countries have climate change policies. Nevertheless, key questions remain unanswered, and demand for further research, e.g., on evaluating the implementation in the respective countries, persists.

Dataset Information

COVID-19 in 16 West African Countries: An Assessment of the Epidemiology and Genetic Diversity of SARS-CoV-2 after Four Epidemic Waves.

Publications

COVID-19 in 16 West African Countries: An Assessment of the Epidemiology and Genetic Diversity of SARS-CoV-2 after Four Epidemic Waves.

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