Identifying Darwinian selection acting on different human APOL1 variants among diverse African populations.

Disease susceptibility can arise as a consequence of adaptation to infectious disease. Recent findings have suggested that higher rates of chronic kidney disease (CKD) in individuals with recent African ancestry might be attributed to two risk alleles (G1 and G2) at the serum-resistance-associated (SRA)-interacting-domain-encoding region of APOL1. These two alleles appear to have arisen adaptively, possibly as a result of their protective effects against human African trypanosomiasis (HAT), or African sleeping sickness. In order to explore the distribution of potential functional variation at APOL1, we studied nucleotide variation in 187 individuals across ten geographically and genetically diverse African ethnic groups with exposure to two Trypanosoma brucei subspecies that cause HAT. We observed unusually high levels of nonsynonymous polymorphism in the regions encoding the functional domains that are required for lysing parasites. Whereas allele frequencies of G2 were similar across all populations (3%-8%), the G1 allele was only common in the Yoruba (39%). Additionally, we identified a haplotype (termed G3) that contains a nonsynonymous change at the membrane-addressing-domain-encoding region of APOL1 and is present in all populations except for the Yoruba. Analyses of long-range patterns of linkage disequilibrium indicate evidence of recent selection acting on the G3 haplotype in Fulani from Cameroon. Our results indicate that the G1 and G2 variants in APOL1 are geographically restricted and that there might be other functional variants that could play a role in HAT resistance and CKD risk in African populations.

Effects of natural selection and gene conversion on the evolution of human glycophorins coding for MNS blood polymorphisms in malaria-endemic African populations.

Malaria has been a very strong selection pressure in recent human evolution, particularly in Africa. Of the one million deaths per year due to malaria, more than 90% are in sub-Saharan Africa, a region with high levels of genetic variation and population substructure. However, there have been few studies of nucleotide variation at genetic loci that are relevant to malaria susceptibility across geographically and genetically diverse ethnic groups in Africa. Invasion of erythrocytes by Plasmodium falciparum parasites is central to the pathology of malaria. Glycophorin A (GYPA) and B (GYPB), which determine MN and Ss blood types, are two major receptors that are expressed on erythrocyte surfaces and interact with parasite ligands. We analyzed nucleotide diversity of the glycophorin gene family in 15 African populations with different levels of malaria exposure. High levels of nucleotide diversity and gene conversion were found at these genes. We observed divergent patterns of genetic variation between these duplicated genes and between different extracellular domains of GYPA. Specifically, we identified fixed adaptive changes at exons 3-4 of GYPA. By contrast, we observed an allele frequency spectrum skewed toward a significant excess of intermediate-frequency alleles at GYPA exon 2 in many populations; the degree of spectrum distortion is correlated with malaria exposure, possibly because of the joint effects of gene conversion and balancing selection. We also identified a haplotype causing three amino acid changes in the extracellular domain of glycophorin B. This haplotype might have evolved adaptively in five populations with high exposure to malaria.

Patterns of nucleotide and haplotype diversity at ICAM-1 across global human populations with varying levels of malaria exposure.

Malaria is one of the strongest selective pressures in recent human evolution. African populations have been and continue to be at risk for malarial infections. However, few studies have re-sequenced malaria susceptibility loci across geographically and genetically diverse groups in Africa. We examined nucleotide diversity at Intercellular adhesion molecule-1 (ICAM-1), a malaria susceptibility candidate locus, in a number of human populations with a specific focus on diverse African ethnic groups. We used tests of neutrality to assess whether natural selection has impacted this locus and tested whether SNP variation at ICAM-1 is correlated with malaria endemicity. We observe differing patterns of nucleotide and haplotype variation in global populations and higher levels of diversity in Africa. Although we do not observe a deviation from neutrality based on the allele frequency distribution, we do observe several alleles at ICAM-1, including the ICAM-1 (Kilifi) allele, that are correlated with malaria endemicity. We show that the ICAM-1 (Kilifi) allele, which is common in Africa and Asia, exists on distinct haplotype backgrounds and is likely to have arisen more recently in Asia. Our results suggest that correlation analyses of allele frequencies and malaria endemicity may be useful for identifying candidate functional variants that play a role in malaria resistance and susceptibility.

Genome-wide patterns of population structure and admixture in West Africans and African Americans.

Quantifying patterns of population structure in Africans and African Americans illuminates the history of human populations and is critical for undertaking medical genomic studies on a global scale. To obtain a fine-scale genome-wide perspective of ancestry, we analyze Affymetrix GeneChip 500K genotype data from African Americans (n = 365) and individuals with ancestry from West Africa (n = 203 from 12 populations) and Europe (n = 400 from 42 countries). We find that population structure within the West African sample reflects primarily language and secondarily geographical distance, echoing the Bantu expansion. Among African Americans, analysis of genomic admixture by a principal component-based approach indicates that the median proportion of European ancestry is 18.5% (25th-75th percentiles: 11.6-27.7%), with very large variation among individuals. In the African-American sample as a whole, few autosomal regions showed exceptionally high or low mean African ancestry, but the X chromosome showed elevated levels of African ancestry, consistent with a sex-biased pattern of gene flow with an excess of European male and African female ancestry. We also find that genomic profiles of individual African Americans afford personalized ancestry reconstructions differentiating ancient vs. recent European and African ancestry. Finally, patterns of genetic similarity among inferred African segments of African-American genomes and genomes of contemporary African populations included in this study suggest African ancestry is most similar to non-Bantu Niger-Kordofanian-speaking populations, consistent with historical documents of the African Diaspora and trans-Atlantic slave trade.

Experiences and challenges of African traditional medicine: lessons from COVID-19 pandemic.

Management of COVID-19 in Africa is challenging due to limited resources, including the high cost of vaccines, diagnostics, medical devices and routine pharmaceuticals. These challenges, in addition to wide acceptability, have resulted in increased use of herbal medicines based on African traditional medicines (ATMs) by patients in Africa. This is in spite of the often-significant gaps in evidence regarding these traditional medicines as to their efficacy and safety for COVID-19. African scientists, with some support from their governments, and guidance from WHO and other bodies, are addressing this evidence gap, developing and testing herbal medicines based on ATMs to manage mild-to-moderate cases of COVID-19. Such efforts need further support to meet public health needs.

Towards universal health coverage: advancing the development and use of traditional medicines in Africa.

African traditional medicine (ATM) and traditional health practitioners (THPs) could make significant contributions to the attainment of universal health coverage (UHC). Consequently, the WHO provided technical tools to assist African countries to develop ATM as a significant component of healthcare. Many African countries adopted the WHO tools after appropriate modifications to advance research and development (R&D) of ATM. An analysis of the extent of this development was undertaken through a survey of 47 countries in the WHO African region. Results show impressive advances in R&D of ATM, the collaboration between THP and conventional health practitioners, quality assurance as well as regulation, registration and THP integration into the national health systems. We highlight the various ways investment in the R&D of ATM can impact on policy, practice and the three themes of UHC. We underscore the need for frameworks for fair and equitable sharing of all benefits arising from the R&D of ATM products involving all the stakeholders. We argue for further investment in ATM as a complement to conventional medicine to promote attainment of the objectives of UHC.

Genotypic and phenotypic analyses of human immunodeficiency virus type 1 in antiretroviral drug-naive Nigerian patients.

We analyzed the subtypes and genotypic and phenotypic drug susceptibility profiles of 18 HIV-1 isolates from treatment-naive patients in Nigeria. A modified gp41-based heteroduplex mobility assay was used to determine the clade designation based on the envelope gene. The protease and most of the reverse transcriptase regions were cloned into a retroviral expression vector and sequenced. Samples were also analyzed phenotypically using a rapid phenotypic assay (PhenoSense HIV, ViroLogic, Inc.). According to the modified gp41-based heteroduplex mobility assay, the patients were infected with either clade G (17 specimens) or clade A (one specimen) isolates. From phylogenetic analyses of 1212 nucleotides of the polymerase gene, 14 of the 18 isolates were strongly grouped with subtype G reference strains. The remaining four isolates were grouped with the CRF_02_AG clade. Within the protease region, all 18 isolates had mutations/polymorphic substitutions at six locations compared to the HIV-1 NL4-3 reference sequence, two of which have been associated with resistance to protease inhibitors (K20I and M36I). At least half of the isolates had mutations/polymorphic substitutions at an additional five positions in the protease region. Within the reverse transcriptase (RT) region, all 18 isolates showed an E291D mutation/polymorphic substitution. Mutations/polymorphic substitutions were also found in at least half of the isolates at 21 positions. The phenotypic profiles of the viruses correlated well with the observed genotypes. Two isolates showed slightly reduced susceptibility to one or two of the five PIs assessed (ritonavir and ritonavir/nelfinavir) and all 18 viruses were susceptible to all NRTIs and NNRTIs analyzed.

Status of national health research systems in ten countries of the WHO African Region.

BACKGROUND: The World Health Organization (WHO) Regional Committee for Africa, in 1998, passed a resolution (AFR/RC48/R4) which urged its Member States in the Region to develop national research policies and strategies and to build national health research capacities, particularly through resource allocation, training of senior officials, strengthening of research institutions and establishment of coordination mechanisms. The purpose of this study was to take stock of some aspects of national resources for health research in the countries of the Region; identify current constraints facing national health research systems; and propose the way forward. METHODS: A questionnaire was prepared and sent by pouch to all the 46 Member States in the WHO African Region through the WHO Country Representatives for facilitation and follow up. The health research focal person in each of the countries Ministry of Health (in consultation with other relevant health research bodies in the country) bore the responsibility for completing the questionnaire. The data were entered and analysed in Excel spreadsheet. RESULTS: The key findings were as follows: the response rate was 21.7% (10/46); three countries had a health research policy; one country reported that it had a law relating to health research; two countries had a strategic health research plan; three countries reported that they had a functional national health research system (NHRS); two countries confirmed the existence of a functional national health research management forum (NHRMF); six countries had a functional ethical review committee (ERC); five countries had a scientific review committee (SRC); five countries reported the existence of health institutions with institutional review committees (IRC); two countries had a health research programme; and three countries had a national health research institute (NHRI) and a faculty of health sciences in the national university that conducted health research. Four out of the ten countries reported that they had a budget line for health research in the Ministry of Health budget document. CONCLUSION: Governments of countries of the African Region, with the support of development partners, private sector and civil society, urgently need to improve the research policy environment by developing health research policies, strategic plans, legislations, programmes and rolling plans with the involvement of all stakeholders, e.g., relevant sectors, research organizations, communities, industry and donors. In a nutshell, development of high-performing national health research systems in the countries of the WHO African Region, though optional, is an imperative. It may be the only way of breaking free from the current vicious cycle of ill-health and poverty.

Nigerian HIV type 2 subtype A and B from heterotypic HIV type 1 and HIV type 2 or monotypic HIV type 2 infections.

The presence of HIV-2 in Nigeria has been confirmed serologically, but not genetically. To determine the frequency of HIV-2 infections and the dynamics between HIV-1 and HIV-2 in 35 of 36 Nigerian states, 420 blood samples were collected in 1999. Antibodies to HIV-1 and HIV-2 were detected by EIA and seroreactivity was confirmed with the INNO-LIA HIV Line Assay. The frequency of HIV-2 was 4.3% (18 of 420), with 3.8% (16 of 420) HIV-1 and HIV-2 (HIV-1/2) heterotypic and 0.5% (2 of 420) HIV-2 homotypic infections. The presence of HIV-2 subtype B in the two monotypic HIV-2 infections and subtype A in 11 (68.8%) of 16 HIV-1/2 dually seropositive samples was established by sequencing and phylogenetic analysis. HIV-2 subtype B viruses were not found in any of the HIV-1/2 dual infections, and HIV-2 subtype A strains were not identified in either of the two monotypic HIV-2 infections. Since our sample size was small and represented only convenience samples, larger randomized studies will be needed to better understand the dynamics of infection between HIV-1 and different HIV-2 subtypes and to determine whether significant biological differences exist among the HIV- 2 subtypes.

Status of national research bioethics committees in the WHO African region.

BACKGROUND: The Regional Committee for Africa of the World Health Organization (WHO) in 2001 expressed concern that some health-related studies undertaken in the Region were not subjected to any form of ethics review. In 2003, the study reported in this paper was conducted to determine which Member country did not have a national research ethics committee (REC) with a view to guiding the WHO Regional Office in developing practical strategies for supporting those countries. METHODS: This is a descriptive study. The questionnaire was prepared and sent by diplomatic pouch to all the 46 Member States in the WHO African Region, through the WHO country representatives, for facilitation and follow up. The data were entered in Excel spreadsheet and subsequently exported to STATA for analysis. A Chi-Squared test (chi2) for independence was undertaken to test the relationship between presence/absence of Research Ethics Committee (REC) and selected individual socioeconomic and health variables. RESULTS: The main findings were as follows: the response rate was 61% (28/46); 64% (18/28) confirmed the existence of RECs; 36% (10/28) of the respondent countries did not have a REC (although 80% of them reported that they had in place an ad hoc ethical review mechanism); 85% (22/26) of the countries that responded to this question indicated that ethical approval of research proposals was, in principle, required; and although 59% of the countries that had a REC expected it to meet every month, only 44% of them reported that the REC actually met on a monthly basis. In the Chi-Squared test, only the average population in the group of countries with a REC was statistically different (at 5% level of significance) from that of the group of countries without a REC. CONCLUSION: In the current era of globalized biomedical research, good ethics stewardship demands that every country, irrespective of its level of economic development, should have in place a functional research ethics review system in order to protect the dignity, integrity and safety of its citizens who participate in research.

HIV-2 protease sequences of subtypes A and B harbor multiple mutations associated with protease inhibitor resistance in HIV-1.

BACKGROUND: HIV-1 protease inhibitors (PI) have been used for treating HIV-2-infected persons but little is known about amino acid mutations associated with PI resistance in HIV-2 and whether they are similar to those seen in HIV-1. OBJECTIVE: To determine the frequency of HIV-1 PI resistance-associated mutations in PI-naive HIV-2-infected individuals. DESIGN: Using PCR, protease genes were amplified from 76 individuals, directly sequenced, phylogenetically subtyped, and translated into amino acids to analyze PI-associated major and minor mutations. RESULTS: Of the 76 HIV-2 sequences, 68% belonged to subtype A and 32% to subtype B. All sequences contained at least four codon changes giving substitutions at 10, 30, 32, 36, 46, 47, 71 or 77. The frequency of these mutations was similar in subtype A and B viruses. Two major resistance-conferring mutations, 30N and 46I, were identified in one (1%) and 68 (89%) specimens, respectively. Minor mutations 10V/I, 32I, 36I, 47V, and 71V were predominant (89%-100%), followed by the rare mutation 77I (1%). Of the 76 strains, 89% harbored multiple PI resistance-associated substitutions comprising both the major 46I and minor mutations: 10V/I, 32I, 36I, 46I, 47V, 71V (76%); 10V, 32I, 36I, 46I, 47V (9%); and 10V, 32I, 36I, 46I, 47V 71V, 77I (1.3%), 10V, 32I, 46I, 47V, 71V (1.3%), and 10V, 30N, 32I, 36I, 46I, 47V, 71V (1.3%). The remaining 11% of the sequences had patterns with only minor mutations: 10V, 32I, 36I, 47V, 71V (9%) and 10V, 32I, 36I, 47V (1.3%). CONCLUSIONS: The high frequency of multiple PI-associated substitutions represent natural polymorphisms occurring in HIV-2 strains of subtypes A and B. Phenotypic and clinical studies are needed to determine the relevance of these substitutions.

Linkage disequilibrium and age estimates of a deletion polymorphism (1597DeltaC) in HLA-G suggest non-neutral evolution.

A single base deletion in HLA-G (1597DeltaC) that is a null allele for the full-length protein is found at frequencies of 6%-11% in populations of African descent. To test the null hypothesis that 1597DeltaC "drifted" to this frequency by neutral evolutionary processes, we compared the pattern of variation and linkage disequilibrium (LD) around this allele and around a conservative amino acid replacement polymorphism in HLA-G (T31S) in African-Americans and Nigerians. There was no significant LD between the 31S allele and flanking STRPs at 150-200 kb in either sample, but significant LD was observed between the 1597DeltaC allele and the same flanking STRPs (p < 0.001 in both samples). To further characterize the evolutionary history of these variants, age estimates were determined assuming evolutionary neutrality. If these alleles were neutral, their frequencies indicate that they arose approximately 9500 (95% CI = 1557, 17557) generations ago (200,000 years). However, using LD to estimate the allele age, the 1597DeltaC allele was estimated to have arisen only 744 (95% CI = 375,2713) generations ago (18,000 years ago), whereas the 31S allele has a much older estimate of 3241 (95% CI = 1680, 20500) generations ago (81,000 years ago). These data suggest that these two polymorphisms in the HLA-G gene have had different evolutionary histories. We propose that natural selection has acted on the 1597DeltaC allele.

Behavioural effect of Pavetta crassipes extract on rodents.

The effects of the ethanol extract of Pavetta crassipes on the central nervous system (CNS) and on actions of some selected centrally acting drugs were studied in mice and rats. These studies were carried out using the spontaneous motor activity (SMA), amphetamine-induced hyperactivity and stereotyped behaviour, pentobarbital-induced hypnosis and exploratory activity, apomorphine-induced climbing and haloperidol-induced catalepsy in rats. The results demonstrated that the extract of P. crassipes dose-dependently decreased SMA in mice and attenuated amphetamine-induced hyperactivity and the different episodes of stereotypic behavioural patterns induced by amphetamine. In addition, the extract decreased the number of head dips in the exploratory activity test and potentiated pentobarbital-induced sleeping time in rats. Furthermore, the extract inhibited apomorphine-induced climbing in mice and potentiated haloperidol-induced catalepsy in rats. Our results suggest that the extract of P. crassipes contains biologically active substance(s) that might be acting centrally through the inhibition of dopaminergic pathway or a system linked to this pathway to mediate the observed pharmacological effects.

The genetic structure and history of Africans and African Americans.

Africa is the source of all modern humans, but characterization of genetic variation and of relationships among populations across the continent has been enigmatic. We studied 121 African populations, four African American populations, and 60 non-African populations for patterns of variation at 1327 nuclear microsatellite and insertion/deletion markers. We identified 14 ancestral population clusters in Africa that correlate with self-described ethnicity and shared cultural and/or linguistic properties. We observed high levels of mixed ancestry in most populations, reflecting historical migration events across the continent. Our data also provide evidence for shared ancestry among geographically diverse hunter-gatherer populations (Khoesan speakers and Pygmies). The ancestry of African Americans is predominantly from Niger-Kordofanian (approximately 71%), European (approximately 13%), and other African (approximately 8%) populations, although admixture levels varied considerably among individuals. This study helps tease apart the complex evolutionary history of Africans and African Americans, aiding both anthropological and genetic epidemiologic studies.

An investigator-blind, single-center, controlled, parallel group study to confirm the suitability of sanitary pads for menstrual protection in an ethnic nigerian population.

This study assessed the suitability of a widely used brand of sanitary pad with a formed film top sheet (study pad) for comfort, protection from soiling, and fit to underwear in a local female Nigerian population compared to a leading nonwoven product (reference pad) marketed in Nigeria. Two hundred eighty-nine healthy Nigerian women 18-45 years of age were randomized to wear one of the brands over two menstrual cycles. Both groups reported comparable (yet few) sensations of itching, rubbing/chafing, redness/rash, and burning/stinging. Participants rated menstrual protection of the study pad statistically significantly better for 88% of questions on a rating form. The percentage of negative comments regarding leakage and pad slip was statistically significantly lower for the study pad than for the reference product. There were no pad-related adverse events. These results show that the study pad was preferred in terms of comfort, protection from soiling, and fit to underwear. Further, top sheet technologies do not differ from nonwoven products in terms of compatibility to skin during use.

Behavioural effects in rodents of methyl angolensate: a triterpenoid isolated from Entandrophragma angolense.

Behavioral effects of methyl angolensate were investigated in mice and rats. Spontaneous motor activity, pentobarbital sleeping time, amphetamine-stereotyped behaviour, exploratory activity and apomorphine-induced climbing studies in mice were evaluated. The results revealed that methyl angolensate reduced spontaneous motor activity in mice, prolonged the duration of pentobarbital sleeping time in rats and attenuated amphetamine-induced stereotype behaviour in rats. Methyl angolensate also decreased exploratory activity in mice and reduced the rate of apomorphine-induced climbing in mice at the doses tested. It is suggested that methyl angolensate possesses some biologically active principles that are sedative in nature.

Hypotensive activity of the ethanol extract of Pavetta crassipes leaves.

Pavetta crassipes leaf is routinely used locally in Nigeria for the management of respiratory disorders and hypertension. The hypotensive and other cardiovascular effects of Pavetta crassipes were investigated in cats and rats. The effects of the extract on rat and cat blood pressures, isolated rat atria, rat portal vein, isolated rat aorta and rat vas deferens were studied. Specific receptor antagonists (atropine, mepyramine, phentolamine, propranolol) were used to elucidate the underlying mechanism(s) involved in the cardiovascular changes induced by P. crassipes. The results revealed that the ethanolic extract of Pavetta crassipes lowered the blood pressures of cats and rats in a dose dependent manner. The extract also caused a concentration-dependent decrease in the force of contraction of the isolated rat atria and rat portal vein. The decreases in blood pressure values were attenuated in the presence of a beta-adrenoceptor antagonist, propranolol. The extract also attenuated isoprenaline-induced contraction of the rat atria. However, the extract did not affect contractions evoked by KCl, norepinephrine and 5-HT on the rat aorta. Pavetta crassipes contains biologically active substances that may be useful in the management of hypertension.

Development of vaccination strategies that elicit broadly neutralizing antibodies against human immunodeficiency virus type 1 in both the mucosal and systemic immune compartments.

The antigenic diversity, rapid genetic integration into host cell DNA, and immune evasion tactics of human immunodeficiency virus type 1 (HIV-1) create formidable obstacles to the development of an effective vaccine against it. In spite of this, the advent of conformationally constrained HIV-1 Env and gp120 immunogens has made it feasible to formulate HIV-1 vaccines that induce broadly cross-reactive neutralizing antibodies and afford protection through humoral mechanisms. This paper reviews recent advances made by the authors toward the development of an HIV-1 vaccine that elicits such antibodies in both the mucosal and systemic immune compartments.