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

Assessment of left ventricular diastolic function: Comparison of Doppler echocardiography and gated blood pool scintigraphy

Although left ventricular diastolic filling patterns can be examined by both Doppler velocity recordings and gated blood pool scintigraphy, few data exist regarding a comparison of these techniques. Therefore, Doppler echocardiography and scintigraphy were compared in 25 patients. Pulsed Doppler echocardiography was performed using an apical four chamber view with the sample volume at the level of the mitral anulus. Doppler measurements included peak velocity of the early diastolic filling wave, time to peak early diastolic velocity from both end-systole and end-diastole, diastolic time period and diastolic integrated velocity (early, atrial and total). The cross-sectional area of the mitral anulus and the left ventricular end-diastolic volume were estimated from measurements made on the apical four chamber view. Scintigraphic measurements included normalized peak filling rate, time to normalized filling rate from both end-diastole and end-systole, diastolic time period and relative diastolic filling during early and atrial filling.Doppler echocardiography and scintigraphy com- pared favorably in assessment of fractional Ailing during early diastole (r = 0.84) and atrial systole (r = 0.85), ratio of early to atrial filling (r = 0.83), diastolic filling period (r = 0.94) and interval from end-diastole to peak early diastolic flow (r = 0.88). Normalized peak filling rate and time to normalized peak filling rate from end-systole did not correlate closely by these two techniques. The differences in normalized peak filling rate may be explained by difficulties in estimating mitral anulus cross-sectional area and left ventricular end-diastolic volume. The weak correlation for time from end-systole to peak flow was a result of the inclusion of isovolumic relaxation by scintigraphy, as opposed to its exclusion by Doppler echocardiography.Thus, both Doppler echocardiography and gated blood pool scintigraphy provide comparable information regarding left ventricular filling when identical variables are measured, and both methods may be of value in assessing left ventricular diastolic properties

Obesity dilemma in the global burden of cardiovascular diseases

Aim: Obesity is a well-known risk factor in the cardiovascular disease continuum. However, its clinical effects are multimodal, perplexed and non-unanimously understood. Our aim was to assess the prevalence and effects of obesity on the cardiometabolic risk factors and systolic function of left ventricle ejection fraction (LVEF) in patients scheduled for cardiovascular rehabilitation. Methods: A cohort of 302 consecutive patients recently treated for ischaemic or valvular heart disease was matched according to the existence of obesity, defined with body mass index (BMI ≥ 30 kg/m2;n = 90 vs. 212), and the advanced grade of obesity (BMI ≥ 35 kg/m2;n= 19 vs. 283). Nutritional risk screening was performed using the standardised NRS-2002 tool. Results: The mean age of patients was 62.4 11.2 (range 23–86) years; there were more men than women 244 (80.8%) : 58 (19.2%). Group of obese conveyed higher prevalence of ischaemic heart disease than non-obese (OR = 2.69; 95% CI: 1.01–7.20; p = 0.048); while the difference was insignificant for the advanced grade of obesity (n = 17; 89.5%) vs. controls (n = 233; 82.3%; p > 0.05). There was no significant difference in prevalence of other comorbidities (diabetes, glucose intolerance, hypercholesterolaemia, chronic renal and chronic obstructive pulmonary disease) between studied groups (p > 0.05). Utilisation of lipid-lowering drugs was of similar range between the studied groups (p > 0.05), respectively. LVEF (%) was 50.5 8.2 vs. 50.7 7.7 (p > 0.05) and 50.6 7.8 vs. 49.6 10.9 (p > 0.05; Rho = 0.001; p > 0.05), respectively. Conclusion: In studied set of patients, BMI positively correlated with left ventricle dimension and thickness. No significant connection of obesity was found with the prevalence of chronic comorbidities, increased nutritional risk, laboratory diagnostics or systolic function of left ventricle. Existence of obesity paradox in clinical practice was in part reaffirmed with our stud