Diversity In sub-Saharan Africa Research Articles

Nile Tilapia Farming and Diversity in Sub-saharan Africa: A Review

Nile Tilapia Farming and Diversity in Sub-saharan Africa: A Review

Comprehensive Analysis of HIV-1 Integrase Resistance-Related Mutations in African Countries.

The growing emergence of non-nucleoside reverse transcriptase inhibitor (NNRTI) HIV drug resistance in sub-Saharan Africa (SSA) led to the World Health Organization (WHO) recommending, in 2018, a transition to dolutegravir (DTG) as a first-line antiretroviral therapy (ART) in SSA. The broad HIV-1 genetic diversity in SSA could shape DTG effectiveness and the pattern of drug resistance mutations (DRMs) in this region. This study evaluated HIV-1 integrase (IN) DRMs and conserved regions among published groups M, N, O, and P HIV-1 sequences spanning forty years of the HIV epidemic during the transition of DTG-based ART. Overall, we found low levels of integrase strand transfer inhibitor (INSTI)-DRMs (<1%) across HIV groups between the years 1983 and 2023; however, it was unexpected to detect DRMs at statistically significantly higher frequencies in pre-INSTI (1983-2007) than in the INSTI (2008-2023) era. The variability of accessory INSTI-DRMs depended on the HIV subtypes, with implications for susceptibility to DTG. Our findings provide new perspectives on the molecular epidemiology and drug resistance profiles of INSTIs in SSA, emphasizing the need for ongoing surveillance and customized treatment approaches to address the continent's varied HIV subtypes and changing resistance patterns.

Dolutegravir resistance in sub-Saharan Africa: should resource-limited settings be concerned for future treatment?

In sub-Saharan Africa (SSA) the burden of non-nucleoside reverse transcriptase inhibitor (NNRTI) HIV drug resistance (HIVDR) has been high over the years. Therefore, in 2018 the World Health Organization (WHO) recommended a regimen based on a integrase strand transfer inhibitor (INSTI), dolutegravir, as the default first-line antiretroviral therapy (ART) in countries in SSA. The scale-up of DTG-based regimens in SSA has gained significant momentum since 2018 and has continued to expand across multiple countries in recent years. However, whether or not the DTG robustness experienced in the developed world will also be achieved in SSA settings is still an important question. Evidence generated from in vitro and in vivo studies suggests that the emergence of DTG HIVDR is HIV-1 subtype dependent. These findings demonstrate that the extensive HIV-1 diversity in SSA can influence DTG effectiveness and the emergence of drug resistance. In addition, the programmatic approach to the transition to DTG adopted by many countries in the SSA region potentially exposes individuals to DTG functional monotherapy, which is associated with the emergence of DTG resistance. In this mini review, we describe the current trends of the effectiveness of DTG as reflected by viral suppression and DTG resistance. Furthermore, we explore how HIV-1 diversity and the programmatic approach in SSA could shape DTG effectiveness and DTG HIVDR in the region.

Trust Institutions, Perceptions of Economic Performance, and the Mitigating Role of Political Diversity in Sub-Saharan Africa

Several previous studies have explored the relationship between trust and socio-economic conditions but do not attempt to examine channels through which the relation operates. In this paper, we examine how political fractionalization mitigates the positive relationship between trust institutions and national economic performance in Sub-Saharan Africa. Using Round 7 data of Afrobarometer in over 1000 districts in 34 countries, we find that trust institutions positively and significantly affect economic performance. Nevertheless, the positive effect is attenuated in districts with a high level of political diversity. More specifically, a higher level of trust is associated with lower economic performance at a higher level of political fractionalization and vice versa, with a steady linear decrease of the estimated coefficients. Policy implications are discussed.

Vegetation ecotones are rich in unique and endemic woody species and can be a focus of community-based conservation areas

ABSTRACT Biodiversity is heterogeneously distributed across terrestrial landscapes. Although the impacts of habitat fragmentation on biodiversity were well studied, whether ecotones support biodiversity conservation or not is less understood, particularly in Sub-Saharan region. Hence, we compared woody species composition between ecotones and the adjoining vegetation types in Ethiopia. For this, firstly, four vegetation types, which are adjacent to each other at different sites, were selected from the vegetation map of Ethiopia. Secondly, a line transect (620 m in length) was laid out on ecotones at 50 m from the edges of the adjacent vegetation types on both sides. Moreover, transects that are equal in length to the ecotone transects were laid out on the adjoining vegetation types perpendicular to ecotone transects. Plots (size: 20 × 20 m each) were arranged on transects with 100 m interval. In total, from nine sites, 27 transect and 162 plots were used to collect data. The dissimilarity in woody species composition, differences in species richness and indicator species between ecotones and adjacent vegetation types were statistically analyzed. The results showed that woody species composition was dissimilar between ecotones and adjoining vegetation types. The species richness was significantly higher in ecotones when compared with the adjacent vegetation types. Moreover, the number of unique and endemic woody species was higher in ecotones than in adjoining vegetation types. The overall results suggest that ecotones promote plant diversity in Sub-Saharan Africa, as well as heterogeneity, and could be the focus of conservation in the face of continuing habitat fragmentation.

The Enduring Factors of HIV: Exploring the Role of Genetic Diversity in Sub-Saharan Africa's HIV Epidemic

The Enduring Factors of HIV: Exploring the Role of Genetic Diversity in Sub-Saharan Africa's HIV Epidemic

Trust Institutions, Perceptions of Economic Performance and the Mitigating role of Political Diversity in Sub-Saharan Africa

Trust Institutions, Perceptions of Economic Performance and the Mitigating role of Political Diversity in Sub-Saharan Africa

Plasmodium malariae structure and genetic diversity in sub-Saharan Africa determined from microsatellite variants and linked SNPs in orthologues of antimalarial resistance genes

Plasmodium malariae, a neglected human malaria parasite, contributes up to 10% of malaria infections in sub-Saharan Africa (sSA). Though P. malariae infection is considered clinically benign, it presents mostly as coinfections with the dominant P. falciparum. Completion of its reference genome has paved the way to further understand its biology and interactions with the human host, including responses to antimalarial interventions. We characterized 75 P. malariae isolates from seven endemic countries in sSA using highly divergent microsatellites. The P. malariae infections were highly diverse and five subpopulations from three ancestries (independent of origin of isolates) were determined. Sequences of 11 orthologous antimalarial resistance genes, identified low frequency single nucleotide polymorphisms (SNPs), strong linkage disequilibrium between loci that may be due to antimalarial drug selection. At least three sub-populations were detectable from a subset of denoised SNP data from mostly the mitochondrial cytochrome b coding region. This evidence of diversity and selection calls for including P. malariae in malaria genomic surveillance towards improved tools and strategies for malaria elimination.

Genetic Diversity of Schistosoma haematobium in Sub-Saharan Africa: A Systematic Review

Urogenital schistosomiasis caused by the parasite Schistosoma haematobium is the most common form of schistosomiasis. This parasite has a high potential for genetic exchange within parasite populations giving rise to the genetic diversity that is important for its survival. Genetic differences may lead to some parasite strains being more immunogenic which may have a negative impact on management and control of schistosomiasis. Therefore, understanding these genetic differences in the parasite may lead to better management of the disease. The aim of this review was to systematically review scientific literature on the genetic diversity and population structuring of S. haematobium and the methods used across sub-Saharan African countries. A literature search was done on PubMed, African Journals online and Google scholar using predefined search terms such as urinary schistosomiasis, S. haematobium, genetic diversity in sub-Saharan Africa in combination with Boolean operators (AND, OR). The search included studies published from 2000-2020 that emphasised on genetic diversity of S. haematobium in sub-Saharan Africa. A country in sub-Saharan Africa was included if had a study that determined the genetic diversity of S. haematobium Sixteen study articles from 18 sub-Saharan African countries met the inclusion criteria The genetic diversity of S. haematobium varied from low to high using different methods. Most studies conducted in these countries showed a high genetic diversity of S. haematobium 18/36 (50%) studies. Four methods namely, restriction fragment length polymorphism, randomly amplified polymorphic DNA, DNA barcoding and Microsatellite markers were used to determine diversity In these studies, measures of genetic diversity such as number of alleles per minute or allelic richness, heterozygosity, number of genotypes and unique haplotypes were used. Microsatellites were the most commonly used method and the studies reported number of alleles per locus ranging from 2-19 alleles per locus and heterozygosity of 6 to 71% in some studies. . The highest number of studies were conducted in West Africa Nigeria and Zimbabwe , 4/36(11%) each. Results show the need for continued monitoring of genetic variations in S. haematobium in sub- Saharan Africa. This will aid in understanding the epidemiology of disease, advancing novel treatment and vaccine strategies.

New insights into Human Pegivirus-1 (HPgV-1) genotypes diversity in sub-Saharan Africa.

In the framework of a viral discovery research program using metagenomics, Human Pegivirus-1 reads (HPgV-1, formerly known as GBV-C) were detected in plasma pools of healthy blood donors from seven sub-Saharan African countries. For five of these countries, Mauritania, Mali, Niger, Burundi and Madagascar, no data about HPgV-1 genotypes was reported to date. To confirm our metagenomic findings and further investigate the genotype diversity and distribution of HPgV-1 in Africa, 400 blood donations from these five localities as well as from Cameroon, the Democratic Republic of Congo (DRC) and the Burkina Faso were screened with a RT-nested PCR targeting the viral 5'NCR region. Amplified products were sequenced, and the virus was genotyped by phylogenetic analysis. Out of the 400 plasma samples tested, 65 were positive for HPgV-1 RNA and 61 were successfully genotyped. Among these, 54 strains (88.5%) clustered with genotype 1, six (9.8%) with genotype 2 and one (1.6%) with genotype 5. Genotype 1 was observed in all countries studied, except in Madagascar, genotype 2 was detected in Mauritania and Madagascar, and genotype 5 in DRC. Overall, our results extend the geographic distribution of HPgV-1 in Africa and provide six additional nearly complete genomes. Considering that some HPgV-1 genotypes have been reported as potential predictive indicators of lower disease progression in HIV-1 infected subjects, further investigations should be conducted to better understand the positive impact, if any, of this virus.

Vertical and Horizontal Decentralization and Ethnic Diversity in Sub-Saharan Africa

Vertical decentralization, either at the deconcentration, delegation or, more rarely, the devolution level, has been instituted in most countries of Sub-Saharan Africa. It usually has the effect of increasing the quantity as well as the quality, in terms of health and education, of public goods. More neglected in the literature is the issue of horizontal decentralization, shifting the decision-making power from the central ministry of finance to the ministries of education and health, as well as strengthening the legislative and judicial branches of government. We examine the relationship between horizontal decentralization with its important ethnic dimension and vertical decentralization. Local governments are accountable to the center under vertical and to democratic forces and civil society under horizontal decentralization. Smaller local units are more likely to be more homogeneous ethnically, leading to a larger quantity and higher quality of public goods.

Measuring Regional Ethnolinguistic Diversity in Sub-Saharan Africa: Surveys vs. GIS

Abstract This paper compares two approaches to measuring subnational ethnolinguistic diversity in Sub-Saharan Africa, one based on censuses and large-scale population surveys and the other relying on the use of geographic information systems (GIS). The two approaches yield sets of regional fractionalization indices that show a moderately positive correlation, with a stronger association across rural areas. These differences matter for empirical analysis: in a common sample of regions, survey-based indices of deep-rooted diversity show a more strongly negative association with a range of development indicators relative to their highest-quality GIS-based counterparts.

Measuring Regional Ethnolinguistic Diversity in Sub-Saharan Africa: Surveys vs. GIS

This paper compares two approaches to measuring subnational ethnolinguistic diversity in Sub-Saharan Africa, one based on censuses and large-scale population surveys and the other relying on the use of geographic information systems (GIS). The two approaches yield sets of regional fractionalization indices that are moderately positively correlated, with a stronger association across rural areas. These differences matter for empirical analysis: in a common sample of regions, survey-based indices of deep-rooted diversity are much more strongly negatively associated with a range of development indicators relative to their highest-quality GIS-based counterparts.

Mediterranean Ant Nest Beetles (Carabidae: Paussus): Out of Africa and Asia

Endemic to the Palaeotropic and southern Palaearctic regions, ant nest beetles (Carabidae: Paussus) are specialized predators that depend on ants for their survival. This obligate relationship has driven extreme morphological adaptations that obscured our understanding of Paussus species relationships and subgeneric clades for centuries. Molecular phylogenetics has revealed patterns of relationship with high levels of convergence, and as a general rule, areas of endemism are better predictors of monophyly than overall morphology. For example, the species rich fauna of Madagascar is the product of one dispersal event from Africa approximately 2.6 million years ago, after which Malagasy ant nest beetles undertook one of the fastest species radiations ever documented within animals. With their center of diversity in sub-Saharan Africa, the Paussus fauna of the Mediterranean is relatively depauperate with only seven species described from north of the Sahara. Pre-molecular subgeneric classifications, which were based on overall morphology, suggest that these seven species represent five species group lineages. Here, we use molecular sequence data from five genes and a taxon-sampling strategy aimed at investigating the biogeographic origins of five Mediterranean species. We find that the present-day Mediterranean fauna, unlike that of Madagascar, is the result of five separate dispersal events, four from the Afrotropical Region and one from the Indomalayan Region. Implications of associated host ant shifts are also explored.

Subnational diversity in Sub-Saharan Africa: Insights from a new dataset

This paper presents a new dataset on subnational ethnolinguistic and religious diversity in Sub-Saharan Africa covering 36 countries and almost 400 first-level administrative units. We use population censuses and large-scale household surveys to compile detailed data on the ethnolinguistic composition of each region and match all reported ethnicities to Ethnologue, a comprehensive catalog of world languages. This matching allows us to standardize the notion of an ethnolinguistic group and account for relatedness between language pairs, a correlate of shared history and culture, when calculating diversity indices. Exploiting within-country variation provided by our new dataset, we find that local public goods provision, as reflected in metrics of education, health, and electricity access, is negatively related to ethnolinguistic diversity, but only if the underlying basic languages are first aggregated into larger families or if linguistic distances between groups are taken into consideration. In other words, only deep-rooted diversity, based on cleavages formed in the distant past, is strongly inversely associated with a range of regional development indicators. Furthermore, we show that subnational diversity has been remarkably persistent over the past two-three decades implying that population sorting in the short to medium run is unlikely to bias our main findings.

English

HIV-1 genetic diversity in sub-Saharan Africa is broad and the AIDS epidemic is driven predominantly by recombinants in Central and West Africa. The classification of HIV-1 strains is therefore necessary to understand diagnostic efficiency, individual treatment responses as well as options for designing vaccines and antiretroviral (ARV) treatment guidelines. More so, accurate subtyping of a partial or full genome would represent the population dynamics of HIV and provide evidence for designing surveillance strategies within a geographic region. Evaluating the performance of rapid subtyping tools with options that incorporate phylogeny could be fast, more user-friendly and of high performance. A total of 570 HIV-1 partial sequences from Cameroon, Angola, Democratic Republic of Congo, Gabon and Senegal were obtained from the Los Alamos National Library (LANL) HIV Sequence Database. Phylogeny was performed using MEGA v6 and the results were used to evaluate the performance of eleven different rapid HIV-1 subtyping tools: REGA v2, REGA v3, NCBI, Stanford HIVDB, SUDI, Geno2Pheno, Euresist, STAR, jpHMM, COMET and SCUEAL. The performance of these subtyping tools differed among HIV-1 clades and across different viral genes. NCBI and SUDI showed the highest performance in subtyping. The discordance observed between the rapid subtyping tools and phylogeny implies that phylogenetic analysis is still the more suitable method for HIV-1 classification. However, the need to update the reference datasets of the subtyping tools, and validate algorithms for rapid subtyping and quality control is imperative as this information is relevant for clinical use and policy-making to the AIDS response. &nbsp; Key words: HIV, phylogeny, performance, subtyping tools, algorithm.

Subnational Diversity in Sub-Saharan Africa: Insights from a New Dataset

This paper presents a new dataset on subnational ethnolinguistic diversity in Sub-Saharan Africa covering 36 countries and almost 400 first-level administrative units. We compile detailed data on the ethnolinguistic composition of each region using population censuses and large-scale household surveys and match all reported ethnicities to Ethnologue, the most complete classifier of world languages. This matching allows to standardize the notion of an ethnolinguistic group and account for the relatedness between language pairs when calculating diversity indices. We exploit this high-quality dataset to investigate the connection between diversity, as captured by fractionalization and polarization indices, and development indicators at the subnational level. Educational and health outcomes, electricity access, and nighttime luminosity are all negatively related to diversity, even after controlling for country fixed effects and a rich set of regional characteristics, but only if the underlying ethnolinguistic groups are sufficiently aggregated into more basic language families or if linguistic similarities between them are taken into account. In other words, only deep-rooted diversity based on cleavages formed in the distant past is strongly inversely associated with regional development. Furthermore, we show that subnational diversity is remarkably persistent over time implying that reverse causality is unlikely to bias our main findings.

Genetic identification of cytomegaloviruses in a rural population of Côte d'Ivoire.

BackgroundCytomegaloviruses (CMVs) are herpesviruses that infect many mammalian species, including humans. Infection generally passes undetected, but the virus can cause serious disease in individuals with impaired immune function. Human CMV (HCMV) is circulating with high seroprevalence (60–100 %) on all continents. However, little information is available on HCMV genoprevalence and genetic diversity in subsaharan Africa, especially in rural areas of West Africa that are at high risk of human-to-human HCMV transmission. In addition, there is a potential for zoonotic spillover of pathogens through bushmeat hunting and handling in these areas as shown for various retroviruses. Although HCMV and nonhuman CMVs are regarded as species-specific, potential human infection with CMVs of non-human primate (NHP) origin, shown to circulate in the local NHP population, has not been studied.FindingsAnalysis of 657 human oral swabs and fecal samples collected from 518 individuals living in 8 villages of Côte d’Ivoire with generic PCR for identification of human and NHP CMVs revealed shedding of HCMV in 2.5 % of the individuals. Determination of glycoprotein B sequences showed identity with strains Towne, AD169 and Toledo, respectively. NHP CMV sequences were not detected.ConclusionsHCMV is actively circulating in a proportion of the rural Côte d’Ivoire human population with circulating strains being closely related to those previously identified in non-African countries. The lack of NHP CMVs in human populations in an environment conducive to cross-species infection supports zoonotic transmission of CMVs to humans being at most a rare event.

Do Religious Factors Impact Armed Conflict? Empirical Evidence From Sub-Saharan Africa

Theoretically, the “mobilization hypothesis” establishes a link between religion and conflict by arguing that particular religious structures are prone to mobilization; once politicized, escalation to violent conflict becomes more likely. Yet, despite the religious diversity in sub-Saharan Africa and the religious overtones in a number of African conflicts, this assumption has not yet been backed by systematic empirical research on the religion–conflict nexus in the region. The following questions thus remain: Do religious factors significantly impact the onset of (religious) armed conflict? If so, do they follow the logic of the mobilization hypothesis and, if so, in which way? To answer these questions, this article draws on a unique data inventory of all sub-Saharan countries for the period 1990–2008, particularly including data on mobilization-prone religious structures (e.g., demographic changes, parallel ethno-religious identities) as well as religious factors indicating actual politicization of religion (e.g., inter-religious tensions, religious discrimination, incitement by religious leaders). Logit regressions suggest that religion indeed plays a significant role in African armed conflicts. These findings are compatible with the mobilization hypothesis, and stress the impact of conflict-prone religious structures, and particularly, the fact that overlaps of religious and ethnic identities are conflict-prone. Future research should investigate the religion-ethnicity-nexus in more detail.

HLA Class-I Diversity in Cameroon: Evidence for a North-South Structure of Genetic Variation and Relationships with African Populations

HLA class I diversity (loci A, B and C) was analysed in four populations, two from North Cameroon (Podokwo and Uldeme) and two from South Cameroon (Ewondo and Bamileke). Northern and southern Cameroon populations show a substantial genetic diversity in terms of haplotype sharing and genetic distances, even despite the low percentage of variance due to differences among populations evidenced by analysis of molecular variance. The signals of differentiation among populations are consistent with their linguistic affiliation, and support previous evidence, based on autosomal microsatellites and protein loci, which has shown that the complex pattern of genetic variation of Cameroon can in part be described by contrasting the northern and southern part of the country. Looking at our results in the more general framework of HLA diversity in sub-Saharan Africa, it turns out that the Podokwo and Uldeme show some genetic links to populations of the southern western branch of the Sahel corridor, while their high frequency of A*02 and C*04 alleles is congruent with previously hypothesised introgression of non-sub-Saharan alleles. On the other hand, signals of shared ancestry between the Bamileke and Ewondo and the Bantu speakers from central and southern Africa were detected.