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

A facility-based study of lipids, glucose levels and their correlates among pregnant women in public hospitals of northern Ethiopia

Background Lipids and glucose concentrations in the blood rise during pregnancy period. Poor control of these analytes results in cardio metabolic dysfunction. Despite this, there are no documented studies which investigate lipids and glucose among pregnant women in Tigrai, northern Ethiopia. Objective The objective of this study was to assess lipid and glucose levels and identify their correlates among pregnant women in Tigrai, northern Ethiopia. Method We conducted a facility-based cross sectional study comprising of systematically selected 200 pregnant women from July to October 2021. Those who were severely ill were excluded from the study. We used a structured questionnaire to collect socio-demographic and clinical characteristics of pregnant women. Lipids such as triglycerides, low density lipoprotein, cholesterol and blood glucose were also measured using Cobas C311 chemistry machine from plasma samples. The data were analyzed using SPSS version 25. Logistic regression was performed and statistical significance was declared at p-value Result Proportion of pregnant women with cholesterol, triglyceride, low density lipoprotein and blood glucose levels above the upper limit of the normal range used for clinical decision were 26.5%, 43%, 44.5% and 21%, respectively. Pregnant women’s income > = 10,000 ETB (AOR = 3.35; 95%CI: 1.46–7.66), age (AOR = 3.16; 95%CI: 1.03–9.68), gestational age 29–37 weeks (AOR = 8.02; 95%CI: 2.69–23.90) and having systolic blood pressure greater than 120 mmHg (AOR = 3.99; 95%CI: 1.64–9.75) demonstrated statistically significant association with raised levels of lipids. Conclusion and recommendation Proportion of pregnant women with out of normal range values of lipids, particularly triglycerides and low density lipoprotein, is high. Gestational age is a strong predictor of increase in blood levels for both lipids. Provision of life style related health education and dietary intake to pregnant mothers matters. Moreover, monitoring lipid profile and glucose level during antenatal care period is essential

A facility-based study of lipids, glucose levels and their correlates among pregnant women in public hospitals of northern Ethiopia.

BackgroundLipids and glucose concentrations in the blood rise during pregnancy period. Poor control of these analytes results in cardio metabolic dysfunction. Despite this, there are no documented studies which investigate lipids and glucose among pregnant women in Tigrai, northern Ethiopia.ObjectiveThe objective of this study was to assess lipid and glucose levels and identify their correlates among pregnant women in Tigrai, northern Ethiopia.MethodWe conducted a facility-based cross sectional study comprising of systematically selected 200 pregnant women from July to October 2021. Those who were severely ill were excluded from the study. We used a structured questionnaire to collect socio-demographic and clinical characteristics of pregnant women. Lipids such as triglycerides, low density lipoprotein, cholesterol and blood glucose were also measured using Cobas C311 chemistry machine from plasma samples. The data were analyzed using SPSS version 25. Logistic regression was performed and statistical significance was declared at p-value ResultProportion of pregnant women with cholesterol, triglyceride, low density lipoprotein and blood glucose levels above the upper limit of the normal range used for clinical decision were 26.5%, 43%, 44.5% and 21%, respectively. Pregnant women's income > = 10,000 ETB (AOR = 3.35; 95%CI: 1.46-7.66), age (AOR = 3.16; 95%CI: 1.03-9.68), gestational age 29-37 weeks (AOR = 8.02; 95%CI: 2.69-23.90) and having systolic blood pressure greater than 120 mmHg (AOR = 3.99; 95%CI: 1.64-9.75) demonstrated statistically significant association with raised levels of lipids.Conclusion and recommendationProportion of pregnant women with out of normal range values of lipids, particularly triglycerides and low density lipoprotein, is high. Gestational age is a strong predictor of increase in blood levels for both lipids. Provision of life style related health education and dietary intake to pregnant mothers matters. Moreover, monitoring lipid profile and glucose level during antenatal care period is essential