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

Optimizing the Synthesis of Self-Immolative Poly(hexyl isocyanate)

An optimized synthesis is presented for the anionic polymerization of hexyl isocyanate that undergoes selective depolymerization. This self-immolative polymer contains a reactive detection unit at the terminus of the polymer, that is cleaved from the backbone when a specific stimulus is applied, and results in continuous depolymerization into small molecules. A key aspect of this research was using commercially available reagents to polymerize hexyl isocyanate that resulted in good yields, predictable lengths, and low PDI values. The control over the molecular weight of the polymer was achieved at various lengths, ranging from 200 repeating units to 1,000 repeating units long. Under these optimized conditions, selective depolymerization was accomplished with base responsive, and UV-light responsive poly(hexyl isocyanate)s

Synthesis of Aziridinomitosenes for Exploration as Potential Chemotherapeutics

Aziridinomitosenes (AZMs) are a group of potential chemotherapy compounds that are structurally and functionally similar to the anti-tumor agent Mitomycin C (MC). Both act by forming cross-links with the DNA of cancerous cells, thereby inhibiting cell replication and resulting in cell death. However, it is likely that AZMs do not require a reductive activation mechanism, which presumably contributes to some of MC’s adverse side effects. Additionally, past AZM investigations have shown that substituting a methyl group at the C7 electrophilic center creates the most potent analog. In order to enable further testing, C6-methyl and unsubstituted AZM analogs are being prepared using a 20 step sequence. Key structural features being incorporated into the compound include a quinone group, a carbamate at C10, and an aziridine ring at C1. Progress accomplished thus far includes the formation of the tetracyclic core that includes the aziridine ring, as well as installation of the C10 hydroxy group. These and other related results will be presented