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

Frequently Encountered Artifacts in the Application of Dual-Energy Computed Tomography to Cardiovascular Imaging for Urate Crystals in Gout: A Matched-Control Study.

There is surging interest in using dual-energy computed tomography (DECT) to identify cardiovascular monosodium urate (MSU) deposits in patients with gout. We sought to examine the prevalence and characterization of cardiovascular DECT artifacts using non-electrocardiogram (EKG)-gated DECT pulmonary angiograms. We retrospectively reviewed non-EKG-gated DECT pulmonary angiograms performed on patients with and without gout at a single academic center. We noted the presence and locations of vascular green colorization using the default postprocessing two-material decomposition algorithm for MSU. The high- and low-energy grayscale images and advanced DECT measurements were used to determine whether they were true findings or artifacts. We classified artifacts into five categories: streak, contrast medium mixing, misregistration due to motion, foreign body, and noise. Our study included CT scans from 48 patients with gout and 48 age- and sex-matched controls. The majority of patients were male with a mean age of 67 years. Two independent observers attributed all areas of vascular green colorization to artifacts. The most common types of artifacts were streak (56% vs 57% between patients and controls, respectively) and contrast medium mixing (51% vs 65%, respectively). Whereas some of the default DECT measurements of cardiovascular green colorization were consistent with values reported for subcutaneous tophi, advanced DECT measurements were not consistent with that of tophi. Artifacts that could be misconstrued as cardiovascular MSU deposits were commonly identified in patients with and without gout on non-EKG-gated DECT pulmonary angiograms. These artifacts can inform future vascular DECT studies on patients with gout to minimize false-positive findings