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

The hyperfine structure of mercury extracted from neutron irradiated gold

The hyperfine structure of mercury extracted from neutron irradiated gold has been investigated with the aid of a Fabry-Perot etalon. The theory and design of the interferometer are discussed in detail. The wavelengths of sixteen lines in the spectrum of Hg¹⁹⁸, and the hyperfine structure of many lines in the spectrum of Hg¹⁹⁹ have been evaluated and compared with former determinations, The ratio of Hg¹⁹⁹ to Hg¹⁹⁸ produced during the neutron bombardment of gold has been determined from intensity measurements of the hyperfine structure patterns. The result yields a value of (1.78± 0.10) X 10⁴ barns for the neutron capture cross section of Au¹⁹⁸ .Science, Faculty ofPhysics and Astronomy, Department ofGraduat

A study of the spark spectra of arsenic

The spectra of arsenic have been photographed from the infra-red to the vacuum ultraviolet with a 21 foot grating, a 2 metre vacuum grating, a Littrow prism spectrograph, and a constant deviation spectrograph using an elect-rodeless discharge source. The wave lengths of 1500 lines in the region 550 to 9300 A have been measured relative to Iron standards. Some 300 of these were previously classified, chiefly in As I and As II. Another 500 have now been assigned to the various spark spectra, leaving less than 10% of the observed intensity unaccounted for. The chief extension has been made in As II with more than 50 new energy levels being established. The resulting analyses have been critically examined in terms of the intermediate coupling relations proposed by M.H. Johnson* and the atomic energy relations due to Bacher and Goudsmit+. These relations permit the evaluation of important radial integrals of Slater, and the study for the first time of how these integrals changes both in the various spark spectra of an element and with the successive series members within a given spectrum For unperturbed configurations these theories are found to be satisfactory. *M.H. Johnson, Jr. Phys. Rev. 38, l628, 1931; 39, 197, 1932 + R.F. Bacher and S.A. Goudsmit, Phys. Rev. 46 948; 1934Science, Faculty ofPhysics and Astronomy, Department ofGraduat