The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Quality of Chronic Disease (Diabetes & Hypertension) Care in Health Care Facilities in High Disease Burden Areas in Sidama Region: Cross-Sectional Study

Bedilu Deribe Derese,1 Fikru Tadesse,1 Gezahegn Bekele Dadi,1 Mohammed Ayalew,1 Yacob Abraham Borie,1 Tinbete Samuel Alemayehu,1 Amdehiwot Aynalem,1 Ephrem Geja Gechere,1 Martha Girma Gebrekidan,1 Alemu Tamiso Debiso,2 Akalewold Alemayehu,2 Meskerem Jisso Ebido,2 Kindalem Worku Mihrete,3 Rekiku Fikre,4 Amanuel Ejeso,5 Wondwossen Abera6 1School of Nursing; Hawassa University College of Medicine and Health Science, Hawassa, Sidama Regional State, Ethiopia; 2School of Public Health; Hawassa University College of Medicine and Health Sciences, Hawassa, Sidama Regional State, Ethiopia; 3School of Medicine; Hawassa University College of Medicine and Health Sciences, Hawassa, Sidama Regional State, Ethiopia; 4Department of Midwifery; Hawassa University College of Medicine and Health Sciences, Hawassa, Sidama Regional State, Ethiopia; 5Department of Environmental; Hawassa University College of Medicine and Health Sciences Health, Hawassa, Sidama Regional State, Ethiopia; 6School of Medical Laboratory; Hawassa University College of Medicine and Health Sciences, Hawassa, Sidama Regional State, EthiopiaCorrespondence: Bedilu Deribe Derese, Email [email protected]; [email protected]: Diabetes and hypertension are major synergistic risk factors for microvasculopathy, microangiopathy, and neuropathy problems among patients with chronic disorder. Control of hypertension and diabetes have significant value in delaying these complications. The key for delaying complications in diabetes and hypertension is the quality of care.Objective: This study explored the quality of diabetes-hypertension care in health care facilities with high disease burden in Sidama region.Methodology: An institution-based cross-sectional study was carried out. Patients with diabetes and hypertension were included in the study. In this study, we included 844 patients were included in the study. For data collection, the application software Kobo Collect was utilized. For data analysis, SPSS version 25 was used. Logistic regression was used to identify factors associated with quality of care. To measure quality, we employed patient outcome indicators focusing on long-term complications of the eye, heart, fasting blood pressure, and neuropathic complications. Ethical approval clearance was obtained from Hawassa University, College of Medicine and Health Sciences ethical review board.Results: The mean age of patients was 47.99 ± 15.26 years, with a range of 18– 90 years, while men make up 62% of the overall number of respondents. In terms of marital status, 700 (82.9%) were married. Concerning place of residence; 433 (51.3%) were from rural area. The primary diagnosis is diabetes for 419 (49.6%) patients, and nearly 23% of patients have both diabetes and hypertension. In terms of blood pressure, the average systolic pressure was 129.6 mmHg and the average diastolic pressure was 82.6 mmHg. Among the study participants, 391 (46.33%) patients received poor quality of chronic disease care. Patients living alone, patients who have professional work, fasting blood glucose in normal range, patients with higher education, and patients with serum creatinine receive relatively good chronic illness care.Keywords: high blood glucose, high blood pressure, diabetes-hypertension, Sidama, Ethiopi