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• Article libreArticleEn anglais

  Genital warts and infection with human immunodeficiency virus in high-risk women in Burkina Faso: a longitudinal study

  Andrea J Low, Tim Clayton, Issouf Konate, Nicolas Nagot, Abdoulaye Ouedraogo, Charlotte Huet, Marie-Noelle Didelot-Rousseau, Michel Segondy, Philippe Van de Perre, Philippe Mayaud

  BackgroundHuman papillomaviruses are the most common sexually transmitted infections, and genital warts, caused by HPV-6 and 11, entail considerable morbidity and cost. The natural history of genital warts in relation to HIV-1 infection has not been described in African women. We examined risk factors for genital warts in a cohort of high-risk women in Burkina Faso, in order to further describe their epidemiology.MethodsA prospective study of 765 high-risk women who were followed at 4-monthly intervals for 27 months in Burkina Faso. Logistic and Cox regression were used to identify factors associated with prevalent, incident and persistent genital warts, including HIV-1 serostatus, CD4+ count, and concurrent sexually transmitted infections. In a subset of 306 women, cervical HPV DNA was tested at enrolment.ResultsGenital wart prevalence at baseline was 1.6% (8/492) among HIV-uninfected and 7.0% (19/273) among HIV-1 seropositive women. Forty women (5.2%) experienced at least one incident GW episode. Incidence was 1.1 per 100 person-years among HIV-uninfected women, 7.4 per 100 person-years among HIV-1 seropositive women with a nadir CD4+ count >200 cells/μL and 14.6 per 100 person-years among HIV-1 seropositive women with a nadir CD4+ count ≤200 cells/μL. Incident genital warts were also associated with concurrent bacterial vaginosis, and genital ulceration. Antiretroviral therapy was not protective against incident or persistent genital warts. Detection of HPV-6 DNA and abnormal cervical cytology were strongly associated with incident genital warts.ConclusionsGenital warts occur much more frequently among HIV-1 infected women in Africa, particularly among those with low CD4+ counts. Antiretroviral therapy did not reduce the incidence or persistence of genital warts in this population.

  Biostatistiques et épidémiologieImmunologieMaladies infectieuses et tropicalesLicence : http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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• Article libreArticleEn anglais

  Genome analysis of Salmonella enterica serovar enteritis strains isolated from poultry and humans in Burkina Faso

  ABSTRACTWhole-genome sequencing (WGS) was used to characterize four Salmonella enterica Enteritidis isolates from poultry (n=2) and human (n=2) from Ouagadougou, Burkina Faso. Antimicrobial resistance genes, chromosomal mutations, and mobile genetic elements were identified by analysis of WGS data using sequence homology.

  Biologie cellulaire et moléculaireGénétiqueMicrobiologie (bactériologie, virologie)Licence : Creative Commons Attribution 4.0 International license This is an open-access article distributed under the terms of the.

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• Article libreArticleEn anglais

  Genome Wide Association Study of Fetal Hemoglobin in Sickle Cell Anemia in Tanzania

  BackgroundFetal hemoglobin (HbF) is an important modulator of sickle cell disease (SCD). HbF has previously been shown to be affected by variants at three loci on chromosomes 2, 6 and 11, but it is likely that additional loci remain to be discovered.Methods and FindingsWe conducted a genome-wide association study (GWAS) in 1,213 SCA (HbSS/HbSβ0) patients in Tanzania. Genotyping was done with Illumina Omni2.5 array and imputation using 1000 Genomes Phase I release data. Association with HbF was analysed using a linear mixed model to control for complex population structure within our study. We successfully replicated known associations for HbF near BCL11A and the HBS1L-MYB intergenic polymorphisms (HMIP), including multiple independent effects near BCL11A, consistent with previous reports. We observed eight additional associations with P<10−6. These associations could not be replicated in a SCA population in the UK.ConclusionsThis is the largest GWAS study in SCA in Africa. We have confirmed known associations and identified new genetic associations with HbF that require further replication in SCA populations in Africa.

  Biologie cellulaire et moléculaireGénétiqueHématologieLicence : This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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• Article libreArticleEn anglais

  Genome-Wide Analysis of Selection on the Malaria Parasite Plasmodium falciparum in West African Populations of Differing Infection Endemicity

  Victor A. Mobegi, Craig W. Duffy, Alfred Amambua-Ngwa, Kovana M. Loua, Eugene Laman, Davis C. Nwakanma, Bronwyn MacInnis, Harvey Aspeling-Jones, Lee Murray, Taane G. Clark, Dominic P. Kwiatkowski, David J. Conway

  Locally varying selection on pathogens may be due to differences in drug pressure, host immunity, transmission opportunities between hosts, or the intensity of between-genotype competition within hosts. Highly recombining populations of the human malaria parasite Plasmodium falciparum throughout West Africa are closely related, as gene flow is relatively unrestricted in this endemic region, but markedly varying ecology and transmission intensity should cause distinct local selective pressures. Genome-wide analysis of sequence variation was undertaken on a sample of 100 P. falciparum clinical isolates from a highly endemic region of the Republic of Guinea where transmission occurs for most of each year and compared with data from 52 clinical isolates from a previously sampled population from The Gambia, where there is relatively limited seasonal malaria transmission. Paired-end short-read sequences were mapped against the 3D7 P. falciparum reference genome sequence, and data on 136,144 single nucleotide polymorphisms (SNPs) were obtained. Within-population analyses identifying loci showing evidence of recent positive directional selection and balancing selection confirm that antimalarial drugs and host immunity have been major selective agents. Many of the signatures of recent directional selection reflected by standardized integrated haplotype scores were population specific, including differences at drug resistance loci due to historically different antimalarial use between the countries. In contrast, both populations showed a similar set of loci likely to be under balancing selection as indicated by very high Tajima’s D values, including a significant overrepresentation of genes expressed at the merozoite stage that invades erythrocytes and several previously validated targets of acquired immunity. Between-population FST analysis identified exceptional differentiation of allele frequencies at a small number of loci, most markedly for five SNPs covering a 15-kb reg

  Biologie cellulaire et moléculaireGénétiqueMicrobiologie (bactériologie, virologie)Licence : http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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• Article libreArticleEn anglais

  Genome-wide association analyses of agronomic traits and Striga hermonthica resistance in pearl millet

  Armel Rouamba, Hussein Shimelis, Inoussa Drabo, Emmanuel Mrema, Christopher Ochieng Ojiewo, Learnmore Mwadzingeni, Abhishek Rathore

  Pearl millet (Pennisetum glaucum [L.] R. Br.) is a nutrient-dense, relatively drought-tolerant cereal crop cultivated in dry regions worldwide. The crop is under-researched, and its grain yield is low (< 0.8 tons ha−1) and stagnant in the major production regions, including Burkina Faso. The low productivity of pearl millet is mainly attributable to a lack of improved varieties, Striga hermonthica [Sh] infestation, downy mildew infection, and recurrent heat and drought stress. Developing high-yielding and Striga-resistant pearl millet varieties that satisfy the farmers’ and market needs requires the identification of yield-promoting genes linked to economic traits to facilitate marker-assisted selection and gene pyramiding. The objective of this study was to undertake genome-wide association analyses of agronomic traits and Sh resistance among 150 pearl millet genotypes to identify genetic markers for marker-assisted breeding and trait introgression. The pearl millet genotypes were phenotyped in Sh hotspot fields and screen house conditions. Twenty-nine million single nucleotide polymorphisms (SNPs) initially generated from 345 pearl millet genotypes were filtered, and 256 K SNPs were selected and used in the present study. Phenotypic data were collected on days to flowering, plant height, number of tillers, panicle length, panicle weight, thousand-grain weight, grain weight, number of emerged Striga and area under the Striga number progress curve (ASNPC). Agronomic and Sh parameters were subjected to combined analysis of variance, while genome-wide association analysis was performed on phenotypic and SNPs data. Significant differences (P < 0.001) were detected among the assessed pearl millet genotypes for Sh parameters and agronomic traits. Further, there were significant genotype by Sh interaction for the number of Sh and ASNPC. Twenty-eight SNPs were significantly associated with a low number of emerged Sh located on chromosomes 1, 2, 3, 4, 6, and 7. Four SNPs we

  Biologie cellulaire et moléculaireGénétiqueMicrobiologie (bactériologie, virologie)Licence : Open Access http://creativecommons.org/licenses/by/4.0/ This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original autho

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• Article libreArticleEn anglais

  Genome-wide association study identifying novel risk variants associated with glycaemic traits in the continental African AWI-Gen cohort

  Vivien J. Chebii, Alisha N. Wade, Nigel J. Crowther, Engelbert A. Nonterah, Godfred Agongo, Z. Simayi, Palwende R. Boua, Isaac Kisiangani, Michèle Ramsay, Ananyo Choudhury, Dhriti Sengupta

  Aims/hypothesisGlycaemic traits such as high fasting glucose levels and insulin resistance are positively associated with the risk of type 2 diabetes and other cardiometabolic diseases. Genetic association studies have identified hundreds of associations for each glycaemic trait, yet very few studies have involved continental African populations. We report the results of genome-wide association studies (GWASs) in a pan-African cohort for four glycaemic traits, namely fasting glucose, fasting insulin, insulin resistance (HOMA-IR) and beta cell function (HOMA-B), which are quantitative variables that affect the risk of developing type 2 diabetes.MethodsGWASs for the four traits were conducted in approximately 10,000 individuals from the Africa Wits-INDEPTH Partnership for Genomics Studies (AWI-Gen) cohort, with participants from Burkina Faso, Ghana, Kenya and South Africa. Association testing was performed using linear mixed models implemented in BOLT-LMM, with age, sex, BMI and principal components as covariates. Replication, fine mapping and functional annotation were performed using standard approaches.ResultsWe identified a novel signal (rs574173815) in the intron of the ankyrin repeat domain 33B (ANKRD33B) gene associated with fasting glucose, and a novel signal (rs114029796) in the intronic region of the WD repeat domain 7 (WDR7) gene associated with fasting insulin. SNPs in WDR7 have been shown to be associated with type 2 diabetes. A variant (rs74806991) in the intron of ADAM metallopeptidase with thrombospondin type 1 motif 16 (ADAMTS16) and another variant (rs6506934) in the β-1,4-galactosyltransferase 6 gene (B4GALT6) are associated with HOMA-IR. Both ADAMTS16 and B4GALT6 are implicated in the development of type 2 diabetes. In addition, our study replicated several well-established fasting glucose signals in the GCK-YTK6, SLC2A2 and THORLNC gene regions.Conclusions/interpretationOur findings highlight the importance of performing GWASs for glycaemic traits

  Biologie cellulaire et moléculaireGénétiqueBiostatistiques et épidémiologieLicence : Open Access http://creativecommons.org/licenses/by/4.0/ This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original autho

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• Article libreArticleEn anglais

  Genome-wide association study of trypanosome prevalence and morphometric traits in purebred and crossbred Baoulé cattle of Burkina Faso

  In this study, single-SNP GWAS analyses were conducted to find regions affecting tolerance against trypanosomosis and morphometrics traits in purebred and crossbred Baoulé cattle of Burkina Faso. The trypanosomosis status (positive and negative) and a wide set of morphological traits were recorded for purebred Baoulé and crossbred Zebu x Baoulé cattle, and genotyped with the Illumina Bovine SNP50 BeadChip. After quality control, 36,203 SNPs and 619 animals including 343 purebred Baoulé and 279 crossbreds were used for the GWAS analyses. Several important genes were found that can influence morphological parameters. Although there were no genes identified with a reported strong connection to size traits, many of them were previously identified in various growth-related studies. A re-occurring theme for the genes residing in the regions identified by the most significant SNPs was pleiotropic effect on growth of the body and the cardiovascular system. Regarding trypanosomosis tolerance, two potentially important regions were identified in purebred Baoulé on chromosomes 16 and 24, containing the CFH, CRBN, TRNT1 and, IL5RA genes, and one additional genomic region in Baoulé, x Zebu crossbreds on chromosome 5, containing MGAT4C and NTS. Almost all of these regions and genes were previously related to the trait of interest, while the CRBN gene was to our knowledge presented in the context of trypanosomiasis tolerance for the first time.

  Biologie cellulaire et moléculaireGénétiqueBiostatistiques et épidémiologieLicence : Creative Commons Attribution License This is an open access article distributed under the terms of the, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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• Article libreArticleEn anglais

  Genome-Wide Linkage Analysis of Malaria Infection Intensity and Mild Disease

  Although balancing selection with the sickle-cell trait and other red blood cell disorders has emphasized the interaction between malaria and human genetics, no systematic approach has so far been undertaken towards a comprehensive search for human genome variants influencing malaria. By screening 2,551 families in rural Ghana, West Africa, 108 nuclear families were identified who were exposed to hyperendemic malaria transmission and were homozygous wild-type for the established malaria resistance factors of hemoglobin (Hb)S, HbC, alpha+ thalassemia, and glucose-6-phosphate-dehydrogenase deficiency. Of these families, 392 siblings aged 0.5–11 y were characterized for malaria susceptibility by closely monitoring parasite counts, malaria fever episodes, and anemia over 8 mo. An autosome-wide linkage analysis based on 10,000 single-nucleotide polymorphisms was conducted in 68 selected families including 241 siblings forming 330 sib pairs. Several regions were identified which showed evidence for linkage to the parasitological and clinical phenotypes studied, among them a prominent signal on Chromosome 10p15 obtained with malaria fever episodes (asymptotic z score = 4.37, empirical p-value = 4.0 × 10−5, locus-specific heritability of 37.7%; 95% confidence interval, 15.7%–59.7%). The identification of genetic variants underlying the linkage signals may reveal as yet unrecognized pathways influencing human resistance to malaria. Author SummaryIn tropical Africa, virtually all children become infected with malaria parasites. Most of them experience several malaria attacks per year, and over a million die from disease complications. Sickle-cell anemia, thalassemias, and other inherited red blood cell disorders indicate that malaria has selected for human genetic variants, but no attempts have so far been reported to systematically screen the human genome for malaria-resistance factors. We describe a genome-wide linkage analysis performed in children living in rural Ghana, W

  Biologie cellulaire et moléculaireGénétiqueBiostatistiques et épidémiologieLicence : This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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• Article libreArticleEn anglais

  Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes

  Licia Colli, Marco Milanesi, Andrea Talenti, Francesca Bertolini, Minhui Chen, Alessandra Crisà, Kevin Gerard Daly, Marcello Del Corvo, Bernt Guldbrandtsen, Johannes A. Lenstra, Benjamin D. Rosen, Elia Vajana, Gennaro Catillo, Stéphane Joost, Ezequiel Luis Nicolazzi, Estelle Rochat, Max F. Rothschild, Bertrand Servin, Tad S. Sonstegard, Roberto Steri, Curtis P. Van Tassell, Paolo Ajmone-Marsan, Paola Crepaldi, Alessandra Stella

  BackgroundGoat populations that are characterized within the AdaptMap project cover a large part of the worldwide distribution of this species and provide the opportunity to assess their diversity at a global scale. We analysed genome-wide 50 K single nucleotide polymorphism (SNP) data from 144 populations to describe the global patterns of molecular variation, compare them to those observed in other livestock species, and identify the drivers that led to the current distribution of goats.ResultsA high degree of genetic variability exists among the goat populations studied. Our results highlight a strong partitioning of molecular diversity between and within continents. Three major gene pools correspond to goats from Europe, Africa and West Asia. Dissection of sub-structures disclosed regional gene pools, which reflect the main post-domestication migration routes. We also identified several exchanges, mainly in African populations, and which often involve admixed and cosmopolitan breeds. Extensive gene flow has taken place within specific areas (e.g., south Europe, Morocco and Mali-Burkina Faso-Nigeria), whereas elsewhere isolation due to geographical barriers (e.g., seas or mountains) or human management has decreased local gene flows.ConclusionsAfter domestication in the Fertile Crescent in the early Neolithic era (ca. 12,000 YBP), domestic goats that already carried differentiated gene pools spread to Europe, Africa and Asia. The spread of these populations determined the major genomic background of the continental populations, which currently have a more marked subdivision than that observed in other ruminant livestock species. Subsequently, further diversification occurred at the regional level due to geographical and reproductive isolation, which was accompanied by additional migrations and/or importations, the traces of which are still detectable today. The effects of breed formation were clearly detected, particularly in Central and North Europe. Overall, ou

  Biologie cellulaire et moléculaireGénétiqueSanté publiqueLicence : Open Access http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/publicdomain/zero/1.0/ This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (), which permits unrestricted use, distribution, and reproduction in any medium, provid

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• Article libreArticleEn anglais

  Genome-Wide Transcription and Functional Analyses Reveal Heterogeneous Molecular Mechanisms Driving Pyrethroids Resistance in the Major Malaria Vector Anopheles funestus Across Africa

  Jacob M. Riveron, Sulaiman S. Ibrahim, Charles Mulamba, Rousseau Djouaka, Helen Irving, Murielle J. Wondji, Intan H. Ishak, Charles S. Wondji

  Pyrethroid resistance in malaria vector, An. funestus is increasingly reported across Africa, threatening the sustainability of pyrethroid-based control interventions, including long lasting insecticidal nets (LLINs). Managing this problem requires understanding of the molecular basis of the resistance from different regions of the continent, to establish whether it is being driven by a single or independent selective events. Here, using a genome-wide transcription profiling of pyrethroid resistant populations from southern (Malawi), East (Uganda), and West Africa (Benin), we investigated the molecular basis of resistance, revealing strong differences between the different African regions. The duplicated cytochrome P450 genes (CYP6P9a and CYP6P9b) which were highly overexpressed in southern Africa are not the most upregulated in other regions, where other genes are more overexpressed, including GSTe2 in West (Benin) and CYP9K1 in East (Uganda). The lack of directional selection on both CYP6P9a and CYP6P9b in Uganda in contrast to southern Africa further supports the limited role of these genes outside southern Africa. However, other genes such as the P450 CYP9J11 are commonly overexpressed in all countries across Africa. Here, CYP9J11 is functionally characterized and shown to confer resistance to pyrethroids and moderate cross-resistance to carbamates (bendiocarb). The consistent overexpression of GSTe2 in Benin is coupled with a role of allelic variation at this gene as GAL4-UAS transgenic expression in Drosophila flies showed that the resistant 119F allele is highly efficient in conferring both DDT and permethrin resistance than the L119. The heterogeneity in the molecular basis of resistance and cross-resistance to insecticides in An. funestus populations throughout sub-Saharan African should be taken into account in designing resistance management strategies.

  Biologie cellulaire et moléculaireGénétiqueMicrobiologie (bactériologie, virologie)Licence : http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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  Genomic analyses revealed low genetic variation in the intron-exon boundary of the doublesex gene within the natural populations of An. gambiae s.l. in Burkina Faso

  Mahamadi Kientega, Ioanna Morianou, Nouhoun Traoré, Nace Kranjc, Honorine Kaboré, Odette N Zongo, Abdoul-Azize Millogo, Patric Stephane Epopa, Franck A. Yao, Adrien M G Belem, Austin Burt, Abdoulaye Diabaté

  BackgroundThe recent success of a population control gene drive targeting the doublesex gene in Anopheles gambiae paved the way for developing self-sustaining and self-limiting genetic control strategies targeting the sex determination pathway to reduce and/or distort the reproductive capacity of insect vectors. However, targeting these genes for genetic control requires a better understanding of their genetic variation in natural populations to ensure effective gene drive spread. Using whole genome sequencing (WGS) data from the Ag1000G project (Ag3.0, 3.4 and 3.8), and Illumina pooled amplicon sequencing, we investigated the genetic polymorphism of the intron-4–exon-5 boundary of the doublesex gene in the natural populations of An. gambiae sensu lato (s.l.).ResultsThe analyses showed a very low variant density at the gRNA target sequence of the Ag(QFS)1 gene drive (previously called dsxFCRISPRh) within the populations of West and East Africa. However, populations from the forest area in Central Africa exhibited four SNP at frequencies ranging from 0.011 to 0.26. The SNP (2R:48714641[C > T]) at high frequencies, i.e. 0.26 is identified within the An. coluzzii population from Angola. The analyses also identified 90 low frequency (1 − 5%) SNPs in the genomic region around the gRNA target sequence (intron-4–exon-5 boundary). Three of these SNPs (2R:48714472 A > T; 2R:48714486 C > A; 2R:48714516 C > T) were observed at frequencies higher than 5% in the UTR region of the doublesex gene. The results also showed a very low variant density and constant nucleotide diversity over a five-year survey in natural An. gambiae s.l. populations of Burkina Faso.ConclusionThese findings will guide the implementation of doublesex-targeted gene drives to support the current control tools in malaria elimination efforts. Our methods can be applied to efficiently monitor the evolution of any sequence of interest in a natural population via pooled amplicon sequencing, surpassing the need f

  Biologie cellulaire et moléculaireGénétiqueBiostatistiques et épidémiologieLicence : Open Access http://creativecommons.org/licenses/by/4.0/ This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original autho

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  Genomic Analysis of Selected Maize Landraces from Sahel and Coastal West Africa Reveals Their Variability and Potential for Genetic Enhancement

  Charles Nelimor, Baffour Badu-Apraku, Ana Luísa Garcia-Oliveira, Antonia Tetteh, Agre Paterne, Assanvo Simon-Pierre N’guetta, Melaku Gedil

  Genetic adaptation of maize to the increasingly unpredictable climatic conditions is an essential prerequisite for achievement of food security and sustainable development goals in sub-Saharan Africa. The landraces of maize; which have not served as sources of improved germplasm; are invaluable sources of novel genetic variability crucial for achieving this objective. The overall goal of this study was to assess the genetic diversity and population structure of a maize panel of 208 accessions; comprising landrace gene pools from Burkina Faso (58), Ghana (43), and Togo (89), together with reference populations (18) from the maize improvement program of the International Institute of Tropical Agriculture (IITA). Genotyping the maize panel with 5974 DArTseq-SNP markers revealed immense genetic diversity indicated by average expected heterozygosity (0.36), observed heterozygosity (0.5), and polymorphic information content (0.29). Model-based population structure; neighbor-joining tree; discriminant analysis of principal component; and principal coordinate analyses all separated the maize panel into three major sub-populations; each capable of providing a wide range of allelic variation. Analysis of molecular variance (AMOVA) showed that 86% of the variation was within individuals; while 14% was attributable to differences among gene pools. The Burkinabe gene pool was strongly differentiated from all the others (genetic differentiation values >0.20), with no gene flow (Nm) to the reference populations (Nm = 0.98). Thus; this gene pool could be a target for novel genetic variation for maize improvement. The results of the present study confirmed the potential of this maize panel as an invaluable genetic resource for future design of association mapping studies to speed-up the introgression of this novel variation into the existing breeding pipelines.

  Biologie cellulaire et moléculaireGénétiqueSanté publiqueLicence : http://creativecommons.org/licenses/by/4.0/ Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ().

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  Genomic and environmental risk factors for cardiometabolic diseases in Africa: methods used for Phase 1 of the AWI-Gen population cross-sectional study

  Stuart A. Ali, Cassandra Soo, Godfred Agongo, Marianne Alberts, Lucas Amenga-Etego, Romuald P. Boua, Ananyo Choudhury, Nigel J. Crowther, Cornelius Depuur, F. Xavier Gómez-Olivé, Issa Guiraud, Tilahun N. Haregu, Scott Hazelhurst, Kathleen Kahn, Christopher Khayeka-Wandabwa, Catherine Kyobutungi, Zané Lombard, Felistas Mashinya, Lisa Micklesfield, Shukri F. Mohamed, Freedom Mukomana, Seydou Nakanabo-Diallo, Hamtandi M. Natama, Nicholas Ngomi, Engelbert A. Nonterah, Shane A. Norris, Abraham R. Oduro, Athanase M. Somé, Hermann Sorgho, Paulina Tindana, Halidou Tinto, Stephen Tollman, Rhian Twine, Alisha Wade, Osman Sankoh, Michèle Ramsay

  ABSTRACTThere is an alarming tide of cardiovascular and metabolic disease (CMD) sweeping across Africa. This may be a result of an increasingly urbanized lifestyle characterized by the growing consumption of processed and calorie-dense food, combined with physical inactivity and more sedentary behaviour. While the link between lifestyle and public health has been extensively studied in Caucasian and African American populations, few studies have been conducted in Africa. This paper describes the detailed methods for Phase 1 of the AWI-Gen study that were used to capture phenotype data and assess the associated risk factors and end points for CMD in persons over the age of 40 years in sub-Saharan Africa (SSA). We developed a population-based cross-sectional study of disease burden and phenotype in Africans, across six centres in SSA. These centres are in West Africa (Nanoro, Burkina Faso, and Navrongo, Ghana), in East Africa (Nairobi, Kenya) and in South Africa (Agincourt, Dikgale and Soweto). A total of 10,702 individuals between the ages of 40 and 60 years were recruited into the study across the six centres, plus an additional 1021 participants over the age of 60 years from the Agincourt centre. We collected socio-demographic, anthropometric, medical history, diet, physical activity, fat distribution and alcohol/tobacco consumption data from participants. Blood samples were collected for disease-related biomarker assays, and genomic DNA extraction for genome-wide association studies. Urine samples were collected to assess kidney function. The study provides base-line data for the development of a series of cohorts with a second wave of data collection in Phase 2 of the study. These data will provide valuable insights into the genetic and environmental influences on CMD on the African continent.

  Biologie cellulaire et moléculaireGénétiqueBiostatistiques et épidémiologieLicence : http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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  Genomic architecture of sickle cell disease in West African children

  Jacklyn Quinlan, Youssef Idaghdour, Jean-Philippe Goulet, Elias Gbeha, Thibault de Malliard, Vanessa Bruat, Jean-Christophe Grenier, Selma Gomez, Ambaliou Sanni, Mohamed C. Rahimy, Philip Awadalla

  Sickle cell disease (SCD) is a congenital blood disease, affecting predominantly children from sub-Saharan Africa, but also populations world-wide. Although the causal mutation of SCD is known, the sources of clinical variability of SCD remain poorly understood, with only a few highly heritable traits associated with SCD having been identified. Phenotypic heterogeneity in the clinical expression of SCD is problematic for follow-up (FU), management, and treatment of patients. Here we used the joint analysis of gene expression and whole genome genotyping data to identify the genetic regulatory effects contributing to gene expression variation among groups of patients exhibiting clinical variability, as well as unaffected siblings, in Benin, West Africa. We characterized and replicated patterns of whole blood gene expression variation within and between SCD patients at entry to clinic, as well as in follow-up programs. We present a global map of genes involved in the disease through analysis of whole blood sampled from the cohort. Genome-wide association mapping of gene expression revealed 390 peak genome-wide significant expression SNPs (eSNPs) and 6 significant eSNP-by-clinical status interaction effects. The strong modulation of the transcriptome implicates pathways affecting core circulating cell functions and shows how genotypic regulatory variation likely contributes to the clinical variation observed in SCD.

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  Genomic Epidemiology of SARS-CoV-2 in Western Burkina Faso, West Africa

  Background: After its initial detection in Wuhan, China, in December 2019, SARS-CoV-2 has spread rapidly, causing successive epidemic waves worldwide. This study aims to provide a genomic epidemiology of SARS-CoV-2 in Burkina Faso. Methods: Three hundred and seventy-seven SARS-CoV-2 genomes obtained from PCR-positive nasopharyngeal samples (PCR cycle threshold score < 35) collected between 5 May 2020, and 31 January 2022 were analyzed. Genomic sequences were assigned to phylogenetic clades using NextClade and to Pango lineages using pangolin. Phylogenetic and phylogeographic analyses were performed to determine the geographical sources and time of virus introduction in Burkina Faso. Results: The analyzed SARS-CoV-2 genomes can be assigned to 10 phylogenetic clades and 27 Pango lineages already described worldwide. Our analyses revealed the important role of cross-border human mobility in the successive SARS-CoV-2 introductions in Burkina Faso from neighboring countries. Conclusions: This study provides additional insights into the genomic epidemiology of SARS-CoV-2 in West Africa. It highlights the importance of land travel in the spread of the virus and the need to rapidly implement preventive policies. Regional cross-border collaborations and the adherence of the general population to government policies are key to prevent new epidemic waves.

  Biologie cellulaire et moléculaireGénétiqueBiostatistiques et épidémiologieLicence : https://creativecommons.org/licenses/by/4.0/ Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ().

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  Genomic insights into the spread and evolution of insecticide resistance in Anopheles gambiae s.l. from Burkina Faso

  Mahamadi Kientega, Honorine Kaboré, Grégoire Sawadogo, Tin-Yu J. Hui, Nouhoun Traoré, Abdoul-Azize Millogo, Hamidou Maiga, Alistair Miles, Chris S. Clarkson, Abdoulaye Diabaté

  BackgroundThe intensive use of insecticide-based control tools has led to the rapid evolution of resistant phenotypes in malaria vector populations. Understanding the evolutionary processes underlying these resistances is essential to inform the development and deployment of effective control interventions. This study investigated the geographical spread and the genetic background of insecticide resistance variants in Burkina Faso.ResultsThe study identified five pyrethroid-resistant mutations (995F, 995S, 402L(g > t,c), 1527T and 1570Y) at high frequencies. Six diplotype groups were identified, including novel combinations of the resistance-associated alleles (995F, V402L(g > t,c) and 1527T), which formed new genotypes within An. coluzzii populations. These results suggest the emergence of new resistance genotypes in An. coluzzii that are not associated with 995F, probably due to recombination and gene flow events. Interestingly, strong linkage disequilibrium (r2 = 0.821) was observed between 1527T and 402L(g > t) compared to 1527T and 402L(g > c). The PCA revealed three clusters of An. coluzzii populations, driven by 995F, 402L(g > t,c) and 1527T. Other insecticide resistance associated variants such as copy number variations and SNPs in the Ace1 gene (Ace1-G280S), cytochrome P450s, esterases and glutathione S-transferases were identified at high frequencies in the same mosquito populations, indicating the intensity and diversity of resistance mechanisms in the country.ConclusionThe study underscores the extent and spreads of insecticide resistance variants in Burkina Faso. It highlights the importance of genomic surveillance of malaria vectors to monitor and detect new resistance variants and to understand the evolutionary processes in vector populations.

  Biologie cellulaire et moléculaireGénétiqueMicrobiologie (bactériologie, virologie)Licence : Creative Commons Attribution 4.0 International License This work is licensed under a, which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.

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  Genomic insights into the spread and evolution of insecticide resistance variants in Anopheles gambiae s.l. from Burkina Faso

  Mahamadi Kientega, Honorine Kaboré, Grégoire Sawadogo, Tin-Yu J. Hui, Nouhoun Traoré, Abdoul-Azize A. Millogo, Hamidou Maiga, Alistair Miles, Chris S. Clarkson, Abdoulaye Diabaté

  The intensive use of insecticide-based control tools has led to the rapid evolution of resistant phenotypes in malaria vector populations. Understanding the evolutionary processes underlying these resistances is essential to inform the development and deployment of effective control interventions. This study investigated the geographical spread and the genetic background of insecticide resistance variants in Anopheles gambiae s.l. in Burkina Faso. The study identified five pyrethroid-resistant mutations (995F, 995S, 402L(g > t,c), 1527T and 1570Y) at high frequencies. Six diplotype groups were identified, including novel combinations of the resistance-associated alleles (995F, 402L(g > t,c) and 1527T), which formed new genotypes within An. coluzzii populations. These results suggest the emergence of new resistance genotypes in An. coluzzii that are not associated with 995F, probably due to recombination and gene flow events. Interestingly, strong linkage disequilibrium (r2 = 0.821) was observed between 1527T and 402L(g > t) compared to 1527T and 402L(g > c). The PCA revealed three clusters of An. coluzzii populations, driven by 995F, 402L(g > t,c) and 1527T. Other insecticide resistance associated variants such as copy number variations and SNPs in the Ace1 gene (ace1-G280S), cytochrome P450s, esterases and glutathione S-transferases were identified at high frequencies in the same mosquito populations, indicating the intensity and diversity of resistance mechanisms in the country. The study underscores the extent and spreads of insecticide resistance variants in Burkina Faso. It highlights the importance of genomic surveillance of malaria vectors to monitor and detect new resistance variants and to understand the evolutionary processes in vector populations.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-026-45950-y.

  Biologie cellulaire et moléculaireGénétiqueMicrobiologie (bactériologie, virologie)Licence : Open Access http://creativecommons.org/licenses/by/4.0/ This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original autho

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  Genomic population structure and insecticide resistance mechanisms in the malaria vector An. coluzzii across contrasting bioclimatic zones in West Africa

  Enock K. Amoako, Kelly L. Bennett, Anastasia Hernandez-Koutoucheva, Isaiah Debrah, Collins M. Morang’a, Stephen Binaansim, Victor A. Asoala, Cristina Ariana, Keziah L. Malm, Gordon Awandare, Alistair Miles, Chris S. Clarkson, Lucas N. Amenga-Etego

  Environmental barriers influencing the movement of insect vectors can govern adaptive gene flow, including the dispersal of insecticide resistance mechanisms that compromise population control. We sought to understand population connectivity of the major malaria vector, An. coluzzii, across the different bioclimatic zones of West Africa using SNPs from whole genomes and inversion karyotypes previously associated with environmental adaptation. We identified restricted gene flow between populations from northern savannah and southern forested regions. Using Ghana as a case study, we found marked differences in insecticide resistance profiles across the different bioclimatic zones suggesting that population connectivity impacts on adaptive allele sharing. Greater evidence for target site pyrethroid and metabolic cross-resistance in the North reflects differences in insecticide use across the country. We also observed distinct resistance mechanisms in the coastal region of Greater Accra which may result from intense urban agricultural activity. Overall, findings suggest that environmental conditions restrict An. coluzzii gene flow to impact the geographical distribution of molecular insecticide resistance.

  Biologie cellulaire et moléculaireGénétiqueMicrobiologie (bactériologie, virologie)Licence : Creative Commons Attribution 4.0 International License This work is licensed under a, which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.

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  Genomic profiles of Pyricularia oryzae in Sub-Saharan Africa: exploring population differences and their evolutionary implications in the region

  Geoffrey Onaga, Worrawit Suktrakul, Margaret Wanjiku, Ian Lorenzo Quibod, Jean-Baka Domelevo Entfellner, Joseph Bigirimana, Georges Habarugira, Rosemary Murori, Godfrey Asea, Hamidatou Euridice Tella, Gbenakpon Aubin G. Y. Amagnide, Negussie Zenna, Chatchawan Jantasuriyarat, Abdelbagi M. Ismail, Ricardo Oliva

  BackgroundRice blast, caused by Pyricularia oryzae (teleomorph: Magnaporthe oryzae), is one of the most economically damaging diseases affecting rice worldwide. While the evolutionary origins and genetic structures of Asian and European P. oryzae populations are relatively well characterized, African isolates remain underexplored. This knowledge gap impedes the development of informed management strategies for rice blast in the region. The present study was conducted to characterize the genetic origins, population structure, admixture, demographic history, and effector gene diversity of P. oryzae isolates in SSA, and to elucidate their evolutionary trajectories and implications for disease management.MethodsA total of 180 genome sequences (45 from SSA, 135 from other regions) were analyzed using population genomic approaches. Phylogeographic reconstructions, demographic modeling, and genome-wide association studies were performed to trace migration events, quantify genetic diversity, and identify candidate adaptation genes. Effector gene repertoires were also examined for diversity and selection signatures. ResultsOur findings provide new dates for the divergence of SSA populations from Asian populations. The introduction of P. oryzae into Africa occurred mainly from China in the late 19th century, initially in West Africa (WA; Mali and Burkina Faso), and subsequently in Uganda and Madagascar during the early 20th century, before extending to the wider African region, with subsequent repeated introductions. Tajima’s D and demographic modeling suggested complex population dynamics shaped by migration and asymmetric founder events, highlighting considerably shared genetic ancestry between Asia and East Africa (EA), in contrast with that between Asia and WA. Genome-wide association analysis identified a specific set of single nucleotide polymorphism markers, along with several candidate genes linked to adaptation. Effector analysis revealed that SSA isolates harbor few

  Biologie cellulaire et moléculaireGénétiqueSanté publiqueLicence : This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journa

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  Genomic Surveillance and Phylogenetic Analysis of Influenza A(H1N1) pdm09 and A(H3N2) Viruses in Burkina Faso, 2024

  BackgroundInfluenza is a major cause of acute respiratory infections worldwide. In tropical regions such as Sub‐Saharan Africa, influenza circulates year‐round with irregular peaks, yet genomic data guiding prevention strategies remain limited. This study characterized the genetic diversity and seasonal dynamics of influenza A(H1N1)pdm09 and A(H3N2) viruses circulating in Burkina Faso in 2024.MethodsA cross‐sectional study was conducted from January to December 2024, including seven sentinel surveillance sites. Patients presenting with influenza‐like illness or severe acute respiratory illness were enrolled. Respiratory specimens were tested by real‐time RT‐PCR. Influenza‐positive samples with a cycle threshold ≤ 30 underwent whole‐genome sequencing using Oxford Nanopore and Illumina platforms. Phylogenetic analyses and clade assignment were performed using MEGA Version 12.ResultsOut of 2951 samples tested, 6.74% were positive for influenza viruses. Females had higher odds of influenza positivity than males (OR = 1.48; 95% CI: 1.11–1.98). A significantly higher risk of positivity was observed in the age groups of 5–15 years (OR = 1.67; 95% CI: 1.07–2.52; p = 0.02) and 25–50 years (OR = 2.54; 95% CI: 1.53–4.03; p < 0.001). Influenza A(H3N2) peaked in July, while A(H1N1)pdm09 peaked in October. Phylogenetic analysis of 43 genomes revealed co‐circulation of multiple clades within both subtypes.ConclusionInfluenza A viruses circulating in Burkina Faso in 2024 showed substantial genetic diversity, underscoring the need for continuous genomic surveillance to inform vaccine strain selection and public health strategies in tropical Africa.

  Biologie cellulaire et moléculaireGénétiqueImmunologieLicence : https://creativecommons.org/licenses/by/4.0/ This is an open access article under the terms of theLicense, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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  GENOPARFUM : Création de ressources et d'outils moléculaires pour la mise en place d'une stratégie de sélection sur la lavande.

  Berline Fopa Fomeju, D. Brunel, A. Bérard, Jean-Baptiste Rivoal, P. Gallois, Marie-Christine Le Paslier, J.P. Bouverat-Bernier

  La lavande fine (Lavandula angustifolia) et le lavandin (Lavandula x intermedia) sont des espèces emblématiques de la France et présentent un fort intérêt économique. Grâce à la réduction des coûts des technologies de séquençage et au développement d’outils de bio-informatique adaptés, l’iteipmai, avec l’aide de ses partenaires (INRAE, CRIEPPAM et CNPMAI), a pu mettre en place un projet de développement d’outils moléculaires sur la lavande et le lavandin afin d’améliorer l’efficacité des programmes de sélection. Ainsi, le projet GenoParfum a été mis en place pour créer des ressources génomiques nécessaires au développement de ces nouvelles stratégies en utilisant les dernières technologies de séquençage haut débit. Cet objectif général se décline en trois axes : (i) développer un catalogue de gènes de référence de lavande, (ii) identifier du polymorphisme de type SNP (Single Nucleotide Polymorphism) pour la lavande et le lavandin et (iii) tester la validité de ce polymorphisme dans le cadre d’une analyse de diversité génétique (variétés clonales et populations naturelles de lavande). Cet article présente les travaux conduits dans l’axe 3 (les résultats des axes 1 et 2 sont présentés dans un article associé : Fopa Fomeju et al., 2018). Une approche de séquençage en mélange a été utilisée pour étudier le polymorphisme de type SNP dans 21 populations naturelles issues de 6 régions géographiques du sud-est de la France et nordouest de l’Italie. Ces populations ont été prélevées à des altitudes allant de 200m à 1500m. A ces populations, 3 variétés populations sélectionnées (Rapido, Carla et Saralia) ont été ajoutées. Les résultats ont indiqué une structuration de la diversité génétique selon l’origine géographique des populations et non selon l’altitude dans le panel étudié. Le taux de polymorphisme dans les populations améliorées était similaire à celui observé dans les populations naturelles. Cette approche a également permis de mettre en évidence la pertinence des out

  Biologie cellulaire et moléculaireGénétiqueLicence : https://creativecommons.org/licenses/by/4.0/

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  Génotypage par pcr-rflp de pfcrt et pfmdr1 sur des isolats de plasmodium falciparum collectés chez des enfants de Vatomandry, Madagascar

  Élisabeth RAVAOARISOA, Voahangy Hanitriniaina Isabelle ANDRIANARANJAKA, Aina David RAMANANTSAHALA, Tovonahary Angelo RAKOTOMANGA, Fanomezantsoa RALINORO, Rianasoambolanoro RAKOTOSAONA, Ranjàna Hanitra RANDRIANARIVO, Danielle Aurore Doll RAKOTO, Victor JEANNODA, Arsène RATSIMBASOA

  RésuméContexteLa surveillance de l'efficacité thérapeutique et des marqueurs génétiques de la résistance aux antipaludiques est primordiale afin de détecter le plus tôt possible l’émergence des parasites potentiellement résistants. Dans ce contexte, notre étude a pour objectif de réaliser le typage du gène Plasmodium falciparum chloroquine resistance transporter ou Pfcrt et Plasmodium falciparum multidrug resistant gene 1 ou Pfmdr1 sur des isolats provenant des enfants du district de Vatomandry.MéthodologiesAu total, 142 isolats de P. falciparum collectés lors d'un dépistage actif du paludisme chez des enfants âgés de moins de 15 ans, entre février et mars des années 2016 et 2017 à Vatomandry, ont été analysés. Le typage du codon K76T du gène Pfcrt et du codon N86Y du gène Pfmdr1 a été ensuite effectué par la technique de polymérisation en chaîne suivie de digestion enzymatique (restriction fragment length polymorphism) ou PCR-RFLP.RésultatsLe taux de succès d'amplification des gènes Pfcrt et Pfmdr1 était faible, de l'ordre de 27 % et 39 % respectivement. La prévalence des isolats mutants pour le codon K76T de Pfcrt était de 2,6 % [intervalle de confiance à 95 % (IC95%) : 0,1 - 15,0 %] et de 36 % [IC95% : 23,7 - 49,7 %] pour le codon N86Y du gène Pfmdr1.ConclusionNotre étude a mis en évidence la présence d'isolats portant à la fois la mutation au niveau du codon K76T de Pfcrt et N86Y de Pfmdr1. Bien que le taux de mutation que nous avons observé soit faible, d'autres études méritent d’être effectuées afin de suivre l’évolution de ces marqueurs dans le temps et dans l'espace à Madagascar.

  Biologie cellulaire et moléculaireGénétiqueBiostatistiques et épidémiologieLicence : https://creativecommons.org/licenses/by/4.0/ Cet article en libre accès est distribué selon les termes de la licence Creative Commons CC BY 4.0 ().

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  Genotype characterization of human papillomavirus in women infected and uninfected with HIV in Ouagadougou, Burkina Faso

  Florencia W Dkigma, Djeneba Ouermi, Tani Sagna, Charlemagne Ouedraogo, Cyrille Bisseye, Moctar Zeba, Simplice D Karou, Virginio Pietra, Jean-Baptiste Nikiema, Jacques Simpore

  ImmunologieMaladies infectieuses et tropicalesSanté publiqueLicence : http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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  Genotype-by-Environment Interaction Analysis of Metabolites in Pearl Millet Genotypes with High Concentrations of Slowly Digestible and Resistant Starch in Their Grains

  Genotype × environment interactions (GEIs) should play an important role in the selection of suitable germplasm in breeding programmes. We here assessed GEI effects on pearl millet (Pennisetum glaucum L.) genotypes, selected to possess a high concentration of slowly digestible starch (SDS) and resistant starch (RS) in their grains. Entries were grown in a randomized complete block design with three replications at locations in Bawku-Ghana, Sadore-Niger, Bamako-Mali, Konni-Nigeria, and Gampella-Burkina Faso across West Africa. Harvested grains from these locations were metabolomically profiled using flow injection ionization-high-resolution mass spectrometry (FIE-HRMS). A total of 3144 mass features (m/z) (1560 negative ion mode and 1584 positive ion mode) were detected, of which, 475 m/z were linked to metabolites be involved in starch, antioxidant and lipid biosynthesis, and vitamin metabolism. Combined ANOVA revealed that the GEI was significantly evident for 54 health-benefiting metabolites, many associated with sugar, especially galactose, metabolism. Additive main effects and multiplicative interaction (AMMI) analysis examined genotype variation and GEI effects, which, when combined with principal component analysis (PCA), found that m/z 171.14864 (positive ionisation, propenyl heptanoate) accounted for 89% of the GEI variation along PC1. The AMMI-based stability parameter (ASTAB), modified AMMI stability value (MASV), and modified AMMI stability index (MASI) were then applied to identify stable and high-performing genotypes for all the health-benefiting metabolites. Similarly, the best-linear-unbiased-prediction (BLUP)-based stability estimation was also performed using the harmonic mean of genotypic values (HMGV), relative performance of genotypic values (RPGV), and harmonic mean of relative performance of genotypic values (HMRPGV), to identify genotype rankings across multiple environments. The multi-trait stability index (MTSI) was calculated and found that

  Santé publiqueLicence : https://creativecommons.org/licenses/by/4.0/ Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ().

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