This paper advances our understanding of the relationship between climate change and ideal fertility in Sahelian West Africa by exploring sources of variation in that relationship. Using an integrated dataset of Demographic and Health Surveys with monthly rainfall and temperature data, the analyses model dimensions of prospective ideal fertility for young, childless men and women in Senegal, Mali, Burkina Faso and Nigeria. Temperature, particularly in the arid climate zone, is shown to have a positive effect on ideal fertility. Landowning insulates individuals from adjusting their fertility ideals in response to change. Gender-stratified models reveal that under hotter conditions, women have a higher ideal number of children but their ideal gender composition remains relatively balanced, while men do not change their ideal number of children but show a preference for more sons. The increase in ideal fertility in response to weather change may be understood as an increasing need to generate human capital to meet the increased labour demands that climate change brings over both the short and the long term.
Biostatistiques et épidémiologiePédiatrieSanté publiqueLicence : Open Access https://creativecommons.org/licenses/by/4.0/ This article is published under the terms of the Creative Commons Attribution 4.0 International License () that allows the sharing, use and adaptation in any medium, provided that the user gives appropriate credit, provides a link to the licen
The World Health Organisation rotavirus surveillance networks have documented and shown eclectic geographic and temporal diversity in circulating G- and P- genotypes identified in children <5 years of age. To effectively monitor vaccine performance and effectiveness, robust molecular and phylogenetic techniques are essential to detect novel strain variants that might emerge due to vaccine pressure. This study inferred the phylogenetic history of the VP7 and VP4 genes of previously non-typeable strains and provided insight into the diversity of P[8] VP4 sequences which impacted the outcome of our routine VP4 genotyping method. Near-full-length VP7 gene and the VP8 fragment of the VP4 gene were obtained by Sanger sequencing and genotypes were determined using RotaC v2.0 web-based genotyping tool. The genotypes of the 57 rotavirus-positive samples with sufficient stool was determined. Forty-eight of the 57 (84.2%) had the P[8] specificity, of which 43 (89.6%) were characterized as P[8]a subtype and 5 (10.4%) as the rare OP354-like subtype. The VP7 gene of 27 samples were successfully sequenced and their G-genotypes confirmed as G1 (18/27) and G9 (9/27). Phylogenetic analysis of the P[8]a sequences placed them in subcluster IIIc within lineage III together with contemporary G1P[8], G3P[8], G8P[8], and G9P[8] strains detected globally from 2006–2016. The G1 VP7 sequences of the study strains formed a monophyletic cluster with African G1P[8] strains, previously detected in Ghana and Mali during the RotaTeq vaccine trial as well as Togo. The G9 VP7 sequences of the study strains formed a monophyletic cluster with contemporary African G9 sequences from neighbouring Burkina Faso within the major sub-cluster of lineage III. Mutations identified in the primer binding region of the VP8 sequence of the Ghanaian P[8]a strains may have resulted in the genotyping failure since the newly designed primer successfully genotyped the previously non-typeable P[8] strains. In summary, t
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The stay-green phenomenon is a key plant trait with wide usage in managing crop production under limited water conditions. This trait enhances delayed senescence, biomass, and grain yield under drought stress. In this study we sought to identify QTLs in cowpea (Vigna unguiculata) consistent across experiments conducted in Burkina Faso, Nigeria, Senegal, and the United States of America under limited water conditions. A panel of 383 diverse cowpea accessions and a recombinant inbred line population (RIL) were SNP genotyped using an Illumina 1536 GoldenGate assay. Phenotypic data from thirteen experiments conducted across the four countries were used to identify SNP-trait associations based on linkage disequilibrium association mapping, with bi-parental QTL mapping as a complementary strategy. We identified seven loci, five of which exhibited evidence suggesting pleiotropic effects (stay-green) between delayed senescence, biomass, and grain yield. Further, we provide evidence suggesting the existence of positive pleiotropy in cowpea based on positively correlated mean phenotypic values (0.34< r <0.87) and allele effects (0.07< r <0.86) for delayed senescence and grain yield across three African environments. Three of the five putative stay-green QTLs, Dro-1, 3, and 7 were identified in both RILs and diverse germplasm with resolutions of 3.2 cM or less for each of the three loci, suggesting that these may be valuable targets for marker-assisted breeding in cowpea. Also, the co-location of early vegetative delayed senescence with biomass and grain yield QTLs suggests the possibility of using delayed senescence at the seedling stage as a rapid screening tool for post-flowering drought tolerance in cowpea breeding. BLAST analysis using EST sequences harboring SNPs with the highest associations provided a genomic context for loci identified in this study in closely related common bean (Phaseolus vulgaris) and soybean (Glycine max) reference genomes.
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Mariette F. Ducatez, Zekiba Tarnagda, Marc C. Tahita, Adama Sow, Sebastien de Landtsheer, Brandon Z. Londt, Ian H. Brown, Albert D.M.E. Osterhaus, Ron A.M. Fouchier, Jean-Bosco B. Ouedraogo, Claude P. Muller
Genetic analysis of highly pathogenic avian influenza (H5N1) viruses from poultry and hooded vultures in Burkina Faso shows that these viruses belong to 1 of 3 sublineages initially found in Nigeria and later in other African countries. Hooded vultures could potentially be vectors or sentinels of influenza subtype H5N1, as are cats and swans elsewhere.
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Jennifer M G Shelton, Patrick Corran, Paul Risley, Nilupa Silva, Christina Hubbart, Anna Jeffreys, Kate Rowlands, Rachel Craik, Victoria Cornelius, Meike Hensmann, Sile Molloy, Nuno Sepulveda, Taane G Clark, Gavin Band, Geraldine M Clarke, Christopher C A Spencer, Angeliki Kerasidou, Susana Campino, Sarah Auburn, Adama Tall, Alioune Badara Ly, Odile Mercereau-Puijalon, Anavaj Sakuntabhai, Abdoulaye Djimdé, Boubacar Maiga, Ousmane Touré, Ogobara K Doumbo, Amagana Dolo, Marita Troye-Blomberg, Valentina D Mangano, Frederica Verra, David Modiano, Edith Bougouma, Sodiomon B Sirima, Muntaser Ibrahim, Ayman Hussain, Nahid Eid, Abier Elzein, Hiba Mohammed, Ahmed Elhassan, Ibrahim Elhassan, Thomas N Williams, Carolyne Ndila, Alexander Macharia, Kevin Marsh, Alphaxard Manjurano, Hugh Reyburn, Martha Lemnge, Deus Ishengoma, Richard Carter, Nadira Karunaweera, Deepika Fernando, Rajika Dewasurendra, Christopher J Drakeley, Eleanor M Riley, Dominic P Kwiatkowski, Kirk A Rockett
BackgroundMany studies report associations between human genetic factors and immunity to malaria but few have been reliably replicated. These studies are usually country-specific, use small sample sizes and are not directly comparable due to differences in methodologies. This study brings together samples and data collected from multiple sites across Africa and Asia to use standardized methods to look for consistent genetic effects on anti-malarial antibody levels.MethodsSera, DNA samples and clinical data were collected from 13,299 individuals from ten sites in Senegal, Mali, Burkina Faso, Sudan, Kenya, Tanzania, and Sri Lanka using standardized methods. DNA was extracted and typed for 202 Single Nucleotide Polymorphisms with known associations to malaria or antibody production, and antibody levels to four clinical grade malarial antigens [AMA1, MSP1, MSP2, and (NANP)4] plus total IgE were measured by ELISA techniques. Regression models were used to investigate the associations of clinical and genetic factors with antibody levels.ResultsMalaria infection increased levels of antibodies to malaria antigens and, as expected, stable predictors of anti-malarial antibody levels included age, seasonality, location, and ethnicity. Correlations between antibodies to blood-stage antigens AMA1, MSP1 and MSP2 were higher between themselves than with antibodies to the (NANP)4 epitope of the pre-erythrocytic circumsporozoite protein, while there was little or no correlation with total IgE levels. Individuals with sickle cell trait had significantly lower antibody levels to all blood-stage antigens, and recessive homozygotes for CD36 (rs321198) had significantly lower anti-malarial antibody levels to MSP2.ConclusionAlthough the most significant finding with a consistent effect across sites was for sickle cell trait, its effect is likely to be via reducing a microscopically positive parasitaemia rather than directly on antibody levels. However, this study does demonstrate a framew
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Ocimum americanum is a wild, aromatic species belonging to the Lamiaceae family. It holds significant socioeconomic importance as it is widely utilized in agriculture, medicine, and food by the local population in Burkina Faso. Previous works revealed that O. americanum is one of the candidate species for domestication in Burkina Faso. Such a perspective requires a good understanding of its genetic diversity. This study was carried out to assess the genetic diversity of O. americanum based on simple sequence repeat (SSR) markers, also known as microsatellites. To achieve this goal, 79 accessions of O. americanum collected in three phytogeographic sectors (sub‐Sahelian, North Sudanian, and South Sudanian) were genotyped using 13 SSR markers. Nine SSR markers out of 13 revealed polymorphism within the accessions with PIC values ranging between 0.047 and 0.443. In all, 36 alleles were identified and the expected heterozygosity ranged from 0.047 to 0.449. Significant differences were observed between the accessions based on the phytogeographic sectors of origin. The analysis of the organization of the genetic diversity using the STRUCTURE approach led to two genetic groups, while the discriminant analysis of principal components (DAPC) revealed six groups. This study is the first report on the genetic diversity of O. americanum in Burkina Faso. The results of this study could help in developing a strategy for the sustainable management and utilization of the genetic resources of hoary basil.
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The objective of this study was to investigate the genetic diversity and population structure of local chicken ecotypes from Burkina Faso using microsatellite markers. A total of 71 individuals representing local chicken populations from the Centre-East (18), Centre-North (17), Sahel (18) and South-West (18) were used to estimate genetic diversity indices, population structure and phylogenetic relationships using 20 selected polymorphic microsatellite markers. The number of alleles, mean number of alleles, mean of observed and expected heterozygosity and polymorphic information content were 127, 6.35, 0.391, 0.521, 0.539 and 0.541, respectively. The estimated overall fixation index between loci (F), among populations (FIS) and inbreeding coefficient within chicken ecotypes were 0.239, 0.267 and 0.243, respectively. Analysis of the molecular variance revealed that 77% of the total genetic diversity was attributed to within-population variation and the remaining 1% and 22% were attributed to among-regions differentiation (FST) and among-individual differentiation (FIT), respectively. The highest pairwise genetic distance (0.026) was found between the local Konde ecotype and those from the Centre-North region while the lowest distance was observed between local chickens from the Sahel and the Centre-North regions (0.003). Neighbour-joining phylogenetic tree and principal component discriminant analyses confirmed the observed genetic distances between populations. The results show that local chickens in Burkina Faso have a rich genetic diversity with little differentiation between the studied populations. This study provides important information on measures of genetic diversity that could help in the design and implementation of future genetic improvement and conservation programs for local chickens in Burkina Faso.
Biologie cellulaire et moléculaireGénétiqueSanté 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 ().
Simple SummaryBactrocera dorsalis is a highly invasive fruit fly that is of major economic importance worldwide. In Burkina Faso, it is one of the main problems associated with mango production, and it is often responsible for the loss of the whole harvest in the most affected areas. Innovative strategies are being developed to improve the current means of controlling this pest. The aim of this study was to understand the distribution, diversity, and genetic structure of B. dorsalis in Burkina Faso. Male B. dorsalis were collected transversally in Burkina Faso in July 2021. The results showed that the abundance of B. dorsalis varied from 87 to 2986 flies per trap per day at the different sampling sites. The genetic variability was high at all sites, with an average Shannon diversity index of 0.72 per site. The migration rates were high between the study populations and ranged from 10.62 to 27.53 migrants. A genetic structural analysis identified three weakly separated genetic groups in the population of B. dorsalis in Burkina Faso. The results of this study will help to better guide control interventions against this pest.AbstractBactrocera dorsalis Hendel is a highly invasive horticultural pest that is of major economic importance worldwide. In Burkina Faso, it is one of the main insect pests that affects the production and exportation of mangos. Understanding the biology and the genetic dynamics of this insect pest provides crucial information for the development of effective control measures. The aim of this study was to understand the distribution, diversity, and genetic structure of B. dorsalis in Burkina Faso. Male flies were collected transversally in Burkina Faso and analyzed by PCR using 10 microsatellite markers. The results showed an abundance of B. dorsalis varying from 87 to 2986 flies per trap per day at the different sampling sites. The genetic diversity was high at all sites, with an average Shannon’s Information Index (I) of 0.72 per site. The gene
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In recent years, Brown spot disease of rice (BSR) has been observed on leaves and seeds of rice in all rice-growing areas of Burkina Faso. Bipolaris oryzae and Exserohilum rostratum are the main fungal species isolated from BSR infected tissues and they are frequently observed in the same field. However, we are lacking information on the genetic diversity and population structure of these fungi in Burkina Faso. The mode of reproduction is also unknown. The genetic diversity of isolates of B. oryzae (n=61) and E. rostratum (n=151), collected from major rice-growing areas of Burkina Faso, was estimated using genotyping-by-sequencing (GBS). The mean values for nucleotide diversity (π) were 1.9 x10-4 for B. oryzae and 4.8 x10-4 for E. rostratum. There is no genetic differentiation between the geographical populations of each species. The analysis of molecular variance revealed that 89% and 94% of the genetic variances were within the populations of B. oryzae and E. rostratum, respectively. For each species, four genetic clusters were identified by two clustering methods (DAPC and sNMF). The distribution of these genetic groups was independent of the geographical origin of the isolates. Evidence of recombination was detected in the populations of B. oryzae and E. rostratum. For B. oryzae balanced mating type ratios were supporting sexual reproduction. For E. rostratum overrepresentation of MAT1-2 isolates (79%) suggested a predominant asexual reproduction. This study provides important information on the biology and genetics of the two major fungi causing brown spot disease of rice in Burkina Faso.
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BackgroundViral gastrointestinal infections remain a major public health concern in developing countries. In Burkina Faso, there are very limited updated data on the circulating viruses and their genetic diversity.ObjectivesThis study investigates the detection rates and characteristics of rotavirus A (RVA), norovirus (NoV), sapovirus (SaV) and human astrovirus (HAstV) in patients of all ages with acute gastrointestinal infection in urban and rural areas.Study design & MethodsFrom 2018 to 2021, stool samples from 1,295 patients with acute gastroenteritis were collected and screened for RVA, NoV, SaV and HAstV. Genotyping and phylogenetic analyses were performed on a subset of samples.ResultsAt least one virus was detected in 34.1% of samples. NoV and SaV were predominant with detection rates of respectively 10.5 and 8.8%. We identified rare genotypes of NoV GII, RVA and HAstV, recombinant HAstV strains and a potential zoonotic RVA transmission event.ConclusionsWe give an up-to-date epidemiological picture of enteric viruses in Burkina Faso, showing a decrease in prevalence but a high diversity of circulating strains. However, viral gastroenteritis remains a public health burden, particularly in pediatric settings. Our data advocate for the implementation of routine viral surveillance and updated management algorithms for diarrheal disease. Author summaryDiseases of the gastrointestinal tract can be caused by a variety of pathogens, such as bacteria, viruses, fungi or parasites. Viruses play a particularly important role, especially in low-income countries, where viral gastroenteritis leads to high morbidity and mortality, particularly among children and the elderly. As part of the African Network for Improved Diagnostics, Epidemiology and Management of Common Infectious Agents (ANDEMIA), patients of all ages from four African countries with symptoms of acute gastroenteritis were tested for the most common viral, bacterial and parasitic pathogens. Samples from Burkin
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.
Curtis E. Lind, Seth K. Agyakwah, Felix Y. Attipoe, Christopher Nugent, Richard P. M. A. Crooijmans, Aboubacar Toguyeni
Nile tilapia (Oreochromis niloticus) is a globally significant aquaculture species rapidly gaining status as a farmed commodity. In West Africa, wild Nile tilapia genetic resources are abundant yet knowledge of fine-scale population structure and patterns of natural genetic variation are limited. Coinciding with this is a burgeoning growth in tilapia aquaculture in Ghana and other countries within the region underpinned by locally available genetic resources. Using 192 single nucleotide polymorphism (SNP) markers this study conducted a genetic survey of Nile tilapia throughout West Africa, sampling 23 wild populations across eight countries (Benin, Burkina Faso, Côte d’Ivoire, Ghana, Togo, Mali, Gambia and Senegal), representing the major catchments of the Volta, Niger, Senegal and Gambia River basins. A pattern of isolation-by-distance and significant spatial genetic structure was identified throughout West Africa (Global FST = 0.144), which largely corresponds to major river basins and, to a lesser extent, sub-basins. Two populations from the Gambia River (Kudang and Walekounda), one from the western Niger River (Lake Sélingué) and one from the upper Red Volta River (Kongoussi) showed markedly lower levels of diversity and high genetic differentiation compared to all other populations, suggesting genetically isolated populations occurring across the region. Genetic structure within the Volta Basin did not always follow the pattern expected for sub-river basins. This study identifies clear genetic structuring and differentiation amongst West African Nile tilapia populations, which concur with broad patterns found in previous studies. In addition, we provide new evidence for fine-scale genetic structuring within the Volta Basin and previously unidentified genetic differences of populations in Gambia. The 192 SNP marker suite used in this study is a useful tool for differentiating tilapia populations and we recommend incorporating this marker suite into future popula
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Issiaka Soulama, Jude D. Bigoga, Magatte Ndiaye, Edith C. Bougouma, Josephine Quagraine, Prisca N. Casimiro, Timothy T. Stedman, Sodiomon B. Sirima
The malaria vaccine candidate antigens erythrocyte binding antigen 175 (EBA-175), merozoite surface protein 3 (MSP-3), and apical membrane antigen (AMA-1) from Plasmodium falciparum isolates from countries in central and west Africa were assessed for allelic diversity. Samples were collected on filter paper from 600 P. falciparum-infected symptomatic patients in Cameroon, Republic of Congo, Burkina Faso, Ghana, and Senegal and screened for class-specific amplification fragments. Genetic diversity, assessed by mean heterozygosity, was comparable among countries. We detected a clinical increase in eba 175 F-allele frequency from west to east across the study region. No statistical difference in msp-3 allele distribution between countries was observed. The ama-1 3D7 alleles were present at a lower frequency in central Africa than in West Africa. We also detected little to no genetic differentiation among sampling locations. This finding indicates that, at least at the level of resolution offered by restriction fragment length polymorphism analysis, these antigens showed remarkable genetic homogeneity throughout the region sampled, perhaps caused by balancing selection to maintain a diverse array of antigen haplotyes.
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Idrissa Nonmon Sanogo, Claire Guinat, Simon Dellicour, Mohamed Adama Diakité, Mamadou Niang, Ousmane A Koita, Christelle Camus, Mariette Ducatez
AbstractAvian influenza viruses (AIVs) of the H9N2 subtype have become widespread in Western Africa since their first detection in 2017 in Burkina Faso. However, the genetic characteristics and diffusion patterns of the H9N2 virus remain poorly understood in Western Africa, mainly due to limited surveillance activities. In addition, Mali, a country considered to play an important role in the epidemiology of AIVs in the region, lacks more comprehensive data on the genetic characteristics of these viruses, especially the H9N2 subtype. To better understand the genetic characteristics and spatio-temporal dynamics of H9N2 virus within this region, we carried out a comprehensive genetic characterization of H9N2 viruses collected through active surveillance in live bird markets in Mali between 2021 and 2022. We also performed a continuous phylogeographic analysis to unravel the dispersal history of H9N2 lineages between Northern and Western Africa. The identified Malian H9N2 virus belonged to the G1 lineage, similar to viruses circulating in both Western and Northern Africa, and possessed multiple molecular markers associated with an increased potential for zoonotic transmission and virulence. Notably, some Malian strains carried the R-S-N-R motif at their cleavage site, mainly observed in H9N2 strains in Asia. Our continuous phylogeographic analysis revealed a single and significant long-distance lineage dispersal event of the H9N2 virus to Western Africa, likely to have originated from Morocco in 2015, shaping the westward diffusion of the H9N2 virus. Our study highlights the need for long-term surveillance of H9N2 viruses in poultry populations in Western Africa, which is crucial for a better understanding of virus evolution and effective management against potential zoonotic AIV strain emergence.
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Ambroise Wonkam, Emile R. Chimusa, Khuthala Mnika, Gift Dineo Pule, Valentina Josiane Ngo Bitoungui, Nicola Mulder, Daniel Shriner, Charles N. Rotimi, Adebowale Adeyemo
AbstractBackgroundSickle cell anemia (SCA) is a clinically heterogeneous, monogenic disorder. Medical care has less‐than‐optimal impact on clinical outcomes in SCA in Africa due to several factors, including patient accessibility, poor access to resources, and non‐availability of specific effective interventions for SCA.MethodsAgainst this background, we investigated 192 African participants who underwent whole exome sequencing. Participants included 105 SCA patients spanning variable clinical expression: a “long survivor” group (age over 40 years), a “stroke” group (at least one episode of overt stroke), and a “random” group (patients younger than 40 years without overt cerebrovascular disease). Fifty‐eight ethnically matched homozygous hemoglobin A controls were also studied. Findings were validated in an independently recruited sample of 29 SCA patients. Statistical significance of the mutational burden of deleterious and loss‐of‐function variants per gene against a null model was estimated for each group, and gene‐set association tests were conducted to test differences between groups.ResultsIn the “long survivor” group, deleterious/loss‐of‐function variants were enriched in genes including CLCN6 (a voltage‐dependent chloride channel for which rare deleterious variants have been associated with lower blood pressure) and OGHDL (important in arginine metabolism, which is a therapeutic target in SCA). In the “stroke” group, significant genes implicated were associated with increased activity of the blood coagulation cascade and increased complement activation, for example, SERPINC1, which encodes antithrombin. Oxidative stress and glutamate biosynthesis pathways were enriched in “long survivors” group. Published transcriptomic evidence provides functional support for the role of the identified pathways.ConclusionsThis study provides new gene sets that contribute to variability in clinical expression of SCA. Identified genes and pathways suggest new avenues for othe
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Shailesh Yadav, Vimal Kumar Semwal, Gbènakpon Aubin Y. G. Amagnide, Esther Pegalepo, Kora Orou Kobi, Kossi Lorimpo Adjah, Nana Kofi Abaka Amoah, Raafat El-Namaky, Negussie Zenna, Epa N’da Ghislain Noumouha, Faye Omar Ndaw, Muhammad Liman Muhammad, Laho Mamadou Barry, Medoune Khouma, Dolo Menidiou, Dule Zhao, Baboucarr Manneh
Rice is a vital staple crop in sub-Saharan Africa (SSA), where improving grain yield is critical for food security and economic growth. Assessing genetic gain over time is essential for measuring breeding effectiveness and guiding future strategies and evaluating the return on investment in rice improvement programs. This study aimed to estimate baseline genetic gains in grain yield from AfricaRice-bred released and pre-released varieties between 1986 and 2020 using multilocation data from ERA trials. “ERA trials” are designed to estimate historic rates of genetic gain for grain yield by testing a series of varieties released over different years or different breeding periods or “eras.” Three sets of trials representing irrigated lowland, rainfed lowland, and rainfed upland ecologies were conducted in 2021 and 2022 at AfricaRice breeding stations in Côte d’Ivoire, Nigeria, and Senegal as well as National Agricultural Research and Evaluation Systems (NARES) sites in Burkina Faso, Guinea Conakry, and Mali. The trials were conducted using an alpha- lattice design with three replications, and data were collected on grain yield, plant height, and days to flowering. A two-stage analysis was implemented, where genotype-by-environment (G × E) means from the first stage were used in the second stage to model G × E interaction with a second-order factor analytic model, thereby accommodating genetic heteroscedasticity across environments and enabling estimation of genetic trends. Finlay–Wilkinson regression model identified high-performing and stable varieties in each ecology. Consistent positive genetic trends were estimated across all the ecologies, though gains remained low: 12 kg/ha/year (0.34%) in rainfed lowland, 10 kg/ha/year (0.27%) in rainfed upland, and 7 kg/ha/year (0.14%) in irrigated lowland. The top-performing varieties contributed maximum gains was ARICA 18 in rainfed lowland (16 kg/ha/year), FARO 59 (NERICA 8) in rainfed upland (11 kg/ha/year), and Yiriwamalo i
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A. Diallo, I. Wonni, A. Sicard, L. Blondin, L. Gagnevin, C. Vernière, B. Szurek, M. Hutin
Bacterial Leaf Blight of rice (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major threat for food security in many rice growing countries including Burkina Faso, where the disease was first reported in the 1980’s. In line with the intensification of rice cultivation in West-Africa, BLB incidence has been rising for the last 15 years. West-African strains of Xoo differ from their Asian counterparts as they (i) are genetically distant, (ii) belong to new races and, (iii) contain reduced repertoires of Transcription Activator Like (TAL) effector genes. In order to investigate the evolutionary dynamics of Xoo populations in Burkina Faso, 177 strains were collected from 2003 to 2018 in three regions where BLB is occurring. Multilocus VNTR Analysis (MLVA-14) targeting 10 polymorphic loci discriminated 24 haplotypes and showed that Xoo populations were structured according to their geographical localization and year of collection. Considering their major role in Xoo pathogenicity, we assessed the TAL effector repertoires of the 177 strains upon RFLP-based profiling. Surprisingly, an important diversity was revealed with up to eight different RFLP patterns. Finally, comparing neutral vs. tal effector gene diversity allowed to suggest scenarios underlying the evolutionary dynamics of Xoo populations in Burkina Faso, which is key to rationally guide the deployment of durably resistant rice varieties against BLB in the country.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12284-023-00648-x.
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Members of the Anopheles gambiae species complex are primary vectors of human malaria in Africa. Population heterogeneities for ecological and behavioral attributes expand and stabilize malaria transmission over space and time, and populations may change in response to vector control, urbanization and other factors. There is a need for approaches to comprehensively describe the structure and characteristics of a sympatric local mosquito population, because incomplete knowledge of vector population composition may hinder control efforts. To this end, we used a genome-wide custom SNP typing array to analyze a population collection from a single geographic region in West Africa. The combination of sample depth (n = 456) and marker density (n = 1536) unambiguously resolved population subgroups, which were also compared for their relative susceptibility to natural genotypes of Plasmodium falciparum malaria. The population subgroups display fluctuating patterns of differentiation or sharing across the genome. Analysis of linkage disequilibrium identified 19 new candidate genes for association with underlying population divergence between sister taxa, A. coluzzii (M-form) and A. gambiae (S-form).
Biologie cellulaire et moléculaireGénétiqueParasitologie et mycologieLicence : 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
Irina Matos, Brígida Santos, Elisângela Gonçalves, Pedro Lopes, Miguel Brito, Ana Paula Arez, Paula Faustino
BackgroundSickle cell anemia (SCA) is a genetic disease marked by abnormal hemoglobin S and sickle-shaped red blood cells. It is highly prevalent in sub-Saharan Africa, especially in Angola, where SCA and malaria are major causes of childhood mortality. This study aimed to explore whether genetic variants in genes associated with red blood cell adhesion to the vascular endothelium influence the manifestations of SCA in Angolan pediatric patients in the context of malaria.Methods and resultsThe study enrolled 65 pediatric SCA patients living in Luanda or Caxito. Their clinical, hematological, and biochemical profiles were monitored through longitudinal pediatric follow-up appointments. Fifteen polymorphic sites were genotyped in CD36 and ICAM-1 genes using PCR, Sanger sequencing, and fragment analysis by capillary electrophoresis. Malaria infection was evaluated by detecting Plasmodium species DNA through PCR analysis of blood spot samples. The CD36 variant rs3211891_C is revealed for the first time as a potential modulator of anemia severity in SCA. Additionally, the CD36 variant rs3211938_G, along with the ICAM-1 variants rs5491_T and rs5496_A, significantly impacted the severity of the hematological phenotype in SCA. Furthermore, SCA patients carrying the ICAM-1 rs5494_T variant showed a 5.63-fold increased risk of having malaria infection compared to those with the wild-type genotype.ConclusionsThis study enhances our understanding of genetic modifiers of red blood cell adhesion to the vascular endothelium and their influence on the severity of pediatric SCA in the context of frequent concomitant malaria infection in Angola.
Biologie cellulaire et moléculaireGénétiqueParasitologie et mycologieLicence : 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
Hamatandi Magloire Natama, Eduard Rovira-Vallbona, Meryam Krit, Pieter Guetens, Hermann Sorgho, M. Athanase Somé, Maminata Traoré-Coulibaly, Innocent Valéa, Petra F. Mens, Henk D. F. H. Schallig, Dirk Berkvens, Luc Kestens, Halidou Tinto, Anna Rosanas-Urgell
BackgroundGenetic polymorphisms in the human immune system modulate susceptibility to malaria. However, there is a paucity of data on the contribution of immunogenetic variants to malaria susceptibility in infants, who present differential biological features related to the immaturity of their adaptive immune system, the protective effect of maternal antibodies and fetal haemoglobin. This study investigated the association between genetic variation in innate immune response genes and malaria susceptibility during the first year of life in 656 infants from a birth cohort survey performed in Nanoro, Burkina Faso.MethodsSeventeen single nucleotide polymorphisms (SNPs) in 11 genes of the immune system previously associated with different malaria phenotypes were genotyped using TaqMan allelic hybridization assays in a Fluidigm platform. Plasmodium falciparum infection and clinical disease were documented by active and passive case detection. Case–control association analyses for both alleles and genotypes were carried out using univariate and multivariate logistic regression. For cytokines showing significant SNP associations in multivariate analyses, cord blood supernatant concentrations were measured by quantitative suspension array technology (Luminex).ResultsGenetic variants in IL-1β (rs1143634) and FcγRIIA/CD32 (rs1801274)—both in allelic, dominant and co-dominant models—were significantly associated with protection from both P. falciparum infection and clinical malaria. Furthermore, heterozygote individuals with rs1801274 SNP in FcγRIIA/CD32 showed higher IL-1RA levels compared to wild-type homozygotes (P = 0.024), a cytokine whose production is promoted by the binding of IgG immune complexes to Fcγ receptors on effector immune cells.ConclusionsThese findings indicate that genetic polymorphisms in genes driving innate immune responses are associated to malaria susceptibility during the first year of life, possibly by modulating production of inflammatory mediators.
Biologie cellulaire et moléculaireGénétiqueBiostatistiques et épidémiologieLicence : Open Access http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/publicdomain/zero/1.0/ 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
Alexandre Atkinson, Séverine Garnier, Sarwat Afridi, Francis Fumoux, Pascal Rihet
BackgroundThere is accumulating evidence that host heparan sulphate proteoglycans play an important role in the life cycle of Plasmodium through their heparan sulphate chains, suggesting that genetic variations in genes involved in heparan sulphate biosynthesis may influence parasitaemia. Interestingly, Hs3st3a1 and Hs3st3b1 encoding enzymes involved in the biosynthesis of heparan sulphate are located within a chromosomal region linked to Plasmodium chabaudi parasitaemia in mice. This suggests that HS3ST3A1 and HS3ST3B1 may influence P. falciparum parasitaemia in humans.MethodsPolymorphisms within HS3ST3A1 and HS3ST3B1 were identified in 270 individuals belonging to 44 pedigrees and living in Burkina Faso. Linkage and association between parasitaemia and the polymorphisms were assessed with MERLIN and FBAT. A genetic interaction analysis was also conducted based on the PGMDR approach.ResultsLinkage between P. falciparum parasitaemia and the chromosomal region containing HS3ST3A1 and HS3ST3B1 was detected on the basis of the 20 SNPs identified. In addition, rs28470223 located within the promoter of HS3ST3A1 was associated with P. falciparum parasitaemia, whereas the PGMDR analysis revealed a genetic interaction between HS3ST3A1 and HS3ST3B1. Seventy-three significant multi-locus models were identified after correcting for multiple tests; 37 significant multi-locus models included rs28470223, whereas 38 multi-locus models contained at least one mis-sense mutation within HS3ST3B1.ConclusionGenetic variants of HS3ST3A1 and HS3ST3B1 are associated with P. falciparum parasitaemia. This suggests that those variants alter both the function of heparan sulphate proteoglycans and P. falciparum parasitaemia.
Biologie cellulaire et moléculaireGénétiqueParasitologie et mycologieLicence : 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.
Paul Sondo, Karim Derra, Thierry Lefevre, Seydou Diallo-Nakanabo, Zekiba Tarnagda, Odile Zampa, Adama Kazienga, Innocent Valea, Hermann Sorgho, Jean-Bosco Ouedraogo, Tinga Robert Guiguemde, Halidou Tinto
There is a large genetic diversity of Plasmodium falciparum strains that infect people causing diverse malaria symptoms. This study was carried out to explore the effect of mixed-strain infections and the extent to which some specific P. falciparum variants are associated with particular malaria symptoms. P. falciparum isolates collected during pharmacovigilance study in Nanoro, Burkina Faso were used to determine allelic variation in two polymorphic antigens of the merozoite surface (msp1 and msp2). Overall, parasite density did not increase with additional strains, suggesting the existence of within-host competition. Parasite density was influenced by msp1 allelic families with highest parasitaemia observed in MAD20 allelic family. However, when in mixed infections with allelic family K1, MAD20 could not grow to the same levels as it would alone, suggesting competitive suppression in these mixed infections. Host age was associated with parasite density. Overall, older patients exhibited lower parasite densities than younger patients, but this effect varied with the genetic composition of the isolates for the msp1 gene. There was no effect of msp1 and msp2 allelic family variation on body temperature. Haemoglobin level was influenced by msp2 family with patients harboring the FC27 allele showing lower haemoglobin level than mono-infected individuals by the 3D7 allele. This study provides evidence that P. falciparum genetic diversity influenced the severity of particular malaria symptoms and supports the existence of within-host competition in genetically diverse P. falciparum.
Biologie cellulaire et moléculaireGénétiqueParasitologie et mycologieLicence : 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
Depuis quelques années, le monde agricole adopte une nouvelle perspective : celle de l’agroécologie. Cette approche représente un véritable changement de paradigme, essentiel pour assurer la durabilité de l’agriculture en Europe. En effet, les ressources en Europe sont limitées, et certaines comme l’énergie s’épuisent. L’agriculture évolue d’un paradigme du contrôle vers celui de l’adaptation. Les préoccupations de maximisation du potentiel génétique et de dépassement des limites des systèmes laissent place au respect de ces limites, à la variabilité des réponses et à la multi-performance. En termes génétiques, l’équation P=G+E où la valeur phénotypique P résulte d’effets génétiques G et d’effets de l’environnement E, doit dorénavant s’appliquer dans un contexte où l’on ne cherche plus à maximiser tous les termes de l’équation. Il faudra notamment composer avec des effets environnementaux plus contrastés et instables. Pour garantir la durabilité de l’élevage, il est essentiel de considérer et d’améliorer les capacités d’adaptation des animaux d’élevage. Pour améliorer ces capacités d’adaptation, j’ai développé 3 axes de recherches : 1.L’étude de la sensibilité environnementale 2.L’étude des compromis entre fonctions biologiques 3.L’étude de nouveaux critères et objectifs de sélection inhérents aux systèmes agroécologiques J’ai la chance de travailler sur deux modèles : les vaches laitières et les poules pondeuses. Les deux espèces présentent des différences importantes, qui sont la classe biologique (mammifère vs oiseau), la structure des filières (nationales et segmentées pour les bovins vs concentrées, multinationales et standardisées pour les volailles), les programmes de sélection (collectifs en bovin, avec autant de voies maternelles que d’éleveurs vs noyau de sélection et utilisation du croisement en volailles), les systèmes d’élevage, la taille des troupeaux… Malgré cela, elles ont aussi des points communs : ce sont des animaux pour lesquels les phénotypes d’
Biologie cellulaire et moléculaireGénétiqueGynécologie-obstétriqueLicence : https://creativecommons.org/licenses/by/4.0/
Gisèle Alexandre, Jean Pierre Bidanel, Didier Boichard, Coralie Danchin-Burge, Alain Ducos, Vincent Ducrocq, Jean-Michel Elsen, Aline Fugeray-Scarbel, Hervé Guyomard, Thomas Heams, Julie Labatut, Denis Laloë, Stéphane Lemarié, Grégoire Leroy, Nathalie Mandonnet, Denis Milan, Philippe Monget, Florence Phocas, Claire Rogel-Gaillard, Xavier Rognon, Michèle Tixier-Boichard, Michel Trommetter, Étienne Verrier, Alain Vignal, Emmanuelle Vila
Alors que le monde vit un changement global et une crise climatique, que de nombreux questionnements sociétaux apparaissent sur le rôle et la place de l’élevage, cet ouvrage dresse un panorama sur l’histoire, les méthodes et la dynamique de changement qui s’est opérée au cours de la dernière décennie pour dessiner les futurs de la sélection animale. La domestication des animaux et leur sélection sont fondées sur une longue histoire partagée entre les hommes, les animaux et les territoires. Elle s’est nourrie par l’accumulation continue de nouvelles connaissances et approches méthodologiques qui permettent de caractériser la diversité génétique et de progresser dans le choix des reproducteurs adaptés à des systèmes de production de plus en plus diversifiés en lien avec la transition agroécologique et la sécurité alimentaire mondiale. L’amélioration génétique contribue à façonner le vivant, ce qui pose des questions éthiques dont l’acuité est renforcée par les outils de la génomique et les « big data ».
Biologie cellulaire et moléculaireGénétiqueLicence : https://creativecommons.org/publicdomain/zero/1.0/
David Lupande, David Kaishusha, Carine Mihigo, Moise Itongwa, Gustave Yenga, Philippe Katchunga
IntroductionEn Afrique subsaharienne, les méthodes de diagnostic de la tuberculose sont insuffisantes et reposent essentiellement sur la microscopie. Elles constituent un réel frein pour le contrôle de la tuberculose. La présente étude voudrait évaluer les performances du GeneXpert MTB/RIF vis à vis de la microscopie classique de Ziehl-Neelsen à l’Hôpital Provincial Général de Référence de Bukavu, à l’Est de la République Démocratique du Congo après 10 mois d’utilisation.MéthodesLes résultats de la coloration au Ziehl-Neelsen et de la biologie moléculaire sur GeneXpert MTB/RIF de 452 patients suspects de tuberculose ont été colligés. La validité d’un test par rapport à l’autre dans la détection de la tuberculose a été étudiée.RésultatsDans le groupe entier, la fréquence de la tuberculose pulmonaire était de 16.3%. La positivité était significativement plus élevée pour le GeneXpert MTB/RIF que pour le Ziehl-Neelsen dans le groupe entier (15.9% vs 9.3%, p= 0.03) et chez les séropositifs pour le VIH (52.0% vs 24.0%; p = 0.007). Cependant, la sensibilité de GeneXpert MTB/RIF comparé au Ziehl-Neelsen n’était pas maximale (95.2%). Enfin, GeneXpert MTB/RIF a détecté 20.8% de résistance à la rifampicine.ConclusionLa présente étude confirme la supériorité de GeneXpert MTB/RIF sur la coloration de Ziehl-Neelsen dans la détection de la tuberculose et dans la prédiction de la multi résistance. Son utilisation systématique couplée au Ziehl-Neelsen permettrait de mieux contrôler la tuberculose en Afrique subSaharienne.
Microbiologie (bactériologie, virologie)ImmunologiePharmacologieLicence : The Pan African Medical Journal - ISSN 1937-8688. 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.