Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.
Large-scale, population-based genomic studies have provided a context for modern medical genetics. Among such studies, however, African populations have remained relatively underrepresented. The breadth of genetic diversity across the African continent argues for an exploration of local genomic context to facilitate burgeoning disease mapping studies in Africa. We sought to characterize genetic variation and to assess population substructure within a cohort of HIV-positive children from Botswana-a Southern African country that is regionally underrepresented in genomic databases. Using whole-exome sequencing data from 164 Batswana and comparisons with 150 similarly sequenced HIV-positive Ugandan children, we found that 13%-25% of variation observed among Batswana was not captured by public databases. Uncaptured variants were significantly enriched (p = 2.2 × 10) for coding variants with minor allele frequencies between 1% and 5% and included predicted-damaging non-synonymous variants. Among variants found in public databases, corresponding allele frequencies varied widely, with Botswana having significantly higher allele frequencies among rare (<1%) pathogenic and damaging variants. Batswana clustered with other Southern African populations, but distinctly from 1000 Genomes African populations, and had limited evidence for admixture with extra-continental ancestries. We also observed a surprising lack of genetic substructure in Botswana, despite multiple tribal ethnicities and language groups, alongside a higher degree of relatedness than purported founder populations from the 1000 Genomes project. Our observations reveal a complex, but distinct, ancestral history and genomic architecture among Batswana and suggest that disease mapping within similar Southern African populations will require a deeper repository of genetic variation and allelic dependencies than presently exists.
Background Antimicrobial resistance (AMR) is a major global health concern with increasing reports of microorganisms resistant to most of the available antibiotics. There are limited data on antibiotic practices, perceptions and self-medication among Ugandans, necessitating this study. Methods A cross-sectional study was conducted among patients at Kiruddu National Referral Hospital, Kampala, Uganda. A pre-tested interviewer administered a questionnaire that was used to collect data after an informed consent. Chi-square tests and logistic regression were used to assess associations between outcome and exposure variables. A P<0.05 was statistically significant. Results A total of 279 patients (response rate=71%) with a median age of 32 years participated in the study. The majority were females (55.6%, n=155) and from the outpatient department (74.9%, n=209). Overall, 212 (76%) participants had taken an antibiotic in the past 6 months, and some 22.2% (n=47) of the participants had practiced self-medication. Male participants (adjusted odds ratio (aOR)=2.13, 95% confidence intervals (CI): 1.01 to 4.50, P=0.046) and Muslims (aOR=4.37, 96% CI:1.54 to 12.44, P=0.006) were more likely to self-medicate. Employees (aOR=0.06, 95% CI:0.01 to 0.51, P=0.010) and patients with tertiary education (aOR=0.14, 95% CI: 0.02 to 0.81, P=0.028) were less likely to practice self-medication. About 33% (n=70) of the participants had not completed treatment dosage during their last course of antibiotic treatment because of feeling better (60%, n=42), lack of money to purchase the medication (15.7%, n=11) and side effects (10%, n=7). Whereas 169 participants (79.7%) believed that not completing treatment would have an impact on their personal health, only 96 participants (45.3%) believed that this behaviour could affect the health of others. Conclusion Antibiotic misuse is significant among patients in Uganda. Continuous health education programs aimed at informing the public on antimicrobial resistance, and its dangers are recommended to curtail this challenge.
Here, we describe how the Collaborative African Genomics Background Network ( of the Human Heredity and Health in Africa (H3Africa) CAfGEN) consortium is using genomics to probe host genetic factors important to the progression of HIV and HIV-tuberculosis (TB) coinfection in sub-Saharan Africa. The H3Africa was conceived to facilitate the application of genomics technologies to improve health across Africa.. :is an H3Africa collaborative centre comprising expertise Methods CAfGEN : The project has focused on utilizing whole-exome sequencing to Results identify genetic variants contributing to extreme HIV disease progression phenotypes in children, as well as RNA sequencing and integrated genomics to identify host genetic factors associated with TB disease progression among HIV-positive children. These cohorts, developed using the COEs' electronic medical records, are exceptionally well-phenotyped and present an unprecedented opportunity to assess genetic factors in individuals whose HIV was acquired by a different route than their adult counterparts in the context of a unique clinical course and disease pathophysiology.: Our approach offers the prospect of developing a critical mass Conclusions of well-trained, highly-skilled, continent-based African genomic scientists. To ensure long term genomics research sustainability in Africa, CAfGEN contributes to a wide range of genomics capacity and infrastructure development on the continent, has laid a foundation for genomics graduate programs at its institutions, and continues to actively promote genomics research through innovative forms of community engagement brokered by partnerships with governments and academia to support genomics policy formulation.
Background: The Human Heredity and Health in Africa consortium (H3Africa) was conceived to facilitate the application of genomics technologies to improve health across Africa. Here, we describe how the Collaborative African Genomics Network (CAfGEN) of the H3Africa consortium is using genomics to probe host genetic factors important to the progression of HIV and HIV-tuberculosis (TB) coinfection in sub-Saharan Africa. Methods: CAfGEN is an H3Africa collaborative centre comprising expertise from the University of Botswana; Makerere University; Baylor College of Medicine Children’s Clinical Centers of Excellence (COEs) in Botswana, Uganda, and Swaziland; as well as Baylor College of Medicine, Texas. The COEs provide clinical expertise for community engagement, participant recruitment and sample collection while the three University settings facilitate processing and management of genomic samples and provide infrastructure and training opportunities to sustain genomics research. Results: The project has focused on utilizing whole-exome sequencing to identify genetic variants contributing to extreme HIV disease progression phenotypes in children, as well as RNA sequencing and integrated genomics to identify host genetic factors associated with TB disease progression among HIV-positive children. These cohorts, developed using the COEs’ electronic medical records, are exceptionally well-phenotyped and present an unprecedented opportunity to assess genetic factors in individuals whose HIV was acquired by a different route than their adult counterparts in the context of a unique clinical course and disease pathophysiology. Conclusions: Our approach offers the prospect of developing a critical mass of well-trained, highly-skilled, continent-based African genomic scientists. To ensure long term genomics research sustainability in Africa, CAfGEN contributes to a wide range of genomics capacity and infrastructure development on the continent, has laid a foundation for genomics graduate programs at its institutions, and continues to actively promote genomics research through innovative forms of community engagement brokered by partnerships with governments and academia to support genomics policy formulation.
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