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

Relation of High Resolution Pulmonary CT Findings and Clinical Condition of COVID-19 Patients

Introduction: At present, chest computed tomography (CT) is accepted as a tool for assessment COVID-19 patients. However, there are few data about the relationship between initial imaging results at presentation and the presence of systemic inflammatory mediators and outcome in patients with COVID-19. The aim of study is to evaluate the relation of initial high resolution com-puted tomography (HRCT) chest findings to inflammatory indices and clinical course of COVID-19 patients during hospitalization. Material and Methods: This is a retrospective cohort study carried out on 108 confirmed COVID-19 patients. Demographic, laboratory and radiological data were recorded from patients medical records. Based on predominant HRCT density, patients were classified into either normal, ground glass opacity (GGO) and consolidation groups. By HRCT score, patients were classified into either no infilteration, ≤50% infilteration and >50% infilteration groups. Comparison between clinical and laboratory parameters were observed among the groups. Results: More hypoxemia, higher inflammatory indices (CRP, d-dimer, ferritin), more requirement of ventilatory support and more mortality rate were observed in consolidation group compared to GGO (p < 0.05) and in patients with HRCT score > 50% compared to ≤50% infilteration group (p < 0.05). Conclusions: Consolidation pattern and high CT chest quantitative score are associated with elevated inflammatory indices and poor outcome in COVID-19 patients. HRCT chest can be used for risk stratification of COVID-19 patients

Relation of high resolution pulmonary CT findings and clinical condition of COVID-19 patients

Introduction: At present, chest computed tomography (CT) is accepted as a tool for assessment COVID-19 patients. However, there are few data about the relationship between initial imaging results at presentation and the presence of systemic inflamma-tory mediators and outcome in patients with COVID-19. The aim of study is to evaluate the relation of initial high resolution com-puted tomography (HRCT) chest findings to inflammatory indices and clinical course of COVID-19 patients during hospitalization. Material and methods: This is a retrospective cohort study carried out on 108 confirmed COVID-19 patients. Demographic, lab-oratory and radiological data were recorded from patients medical records. Based on predominant HRCT density, patients were classified into either normal, ground glass opacity (GGO) and consolidation groups. By HRCT score, patients were classified into either no infilteration, ≤ 50% infilteration and > 50% infilteration groups. Comparison between clinical and laboratory parameters were observed among the groups.Results: More hypoxemia, higher inflammatory indices (CRP, d-dimer, ferritin), more requirement of ventilatory support and more mortality rate were observed in consolidation group compared to GGO (p < 0.05) and in patients with HRCT score > 50% compared to ≤ 50% infilteration group (p < 0.05). Conclusions: Consolidation pattern and high CT chest quantitative score are associated with elevated inflammatory indices and poor outcome in COVID-19 patients. HRCT chest can be used for risk stratification of COVID-19 patients

Correlation between severity of pulmonary embolism and obstructive sleep apnea using computed tomography pulmonary artery obstruction index and right ventricular to left ventricular diameter ratio as severity indices

Abstract Background Recent studies have shown a bidirectional association between pulmonary embolism (PE) and obstructive sleep apnea (OSA), and due to their morbidity and mortality, this contributes significantly to the global health-care burden, so this study aims to assess the relationship between PE and OSA severity using the obstruction index of the pulmonary artery and the ratio of right ventricular to left ventricular (RV/LV) diameter as severity indices. Results The study comprised 138 patients with a high clinical suspicion of PE that was verified by computed tomography pulmonary angiography. In addition to calculating the RV/LV diameter ratio and pulmonary artery obstruction index (PAOI), the pulmonary embolism severity index was also calculated, and the Epworth Sleepiness Scale and polysomnography (PSG) were used to assess all patients for OSA. Finally, three groups of patients ( 50%) were created based on the PAOI. Age, gender, neck, and waist circumference showed no significant difference between the three groups, but there were significant correlations between higher PAOI and increased BMI, provoked PE, increased rate of thrombolysis, increase in the recurrence of venous thrombosis, a longer length of hospital stay, and a higher ratio of RV/LV diameter (p value was  40%, and the ratio of RV/LV diameter > 1 being found to be predictors of severe sleep apnea. Conclusions We deduced from this study that there is a substantial relationship between the severity of PE and the severity of OSA, as patients with higher obstruction of the pulmonary artery had severe OSA, and both the obstruction index of the pulmonary artery > 40% and the ratio of RV/LV diameter > 1 were considered significant predictors for the severity of OSA among the acute PE patients