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

Transient photocyclization in ruthenium(II) polypyridine complexes of indolamines

Ruthenium polypyridine complexes have proved to be useful caging groups for visible-light photodelivery of biomolecules. In most photoreactions, one ligand is expelled upon irradiation, yielding ruthenium mono-aqua complexes and no other photoproduct. In this work we show that a long-lived transient photoproduct is generated when the ruthenium complexes involve indolamines. The spatial conformation of this species is compatible with a cyclic structure that contains both the amine and the normally non-coordinating aromatic ring coordinated to the ruthenium center.Fil: Carrone, Guillermo Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; ArgentinaFil: Zayat, Leonardo Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; ArgentinaFil: Slep, Leonardo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; ArgentinaFil: Etchenique, Roberto Argentino. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentin

Ruthenium polypyridyl phototriggers: from beginnings to perspectives

Octahedral Ru(II) polypyridyl complexes constitute a superb platform to devise photoactive triggers capable of delivering entire molecules in a reliable, fast, efficient and clean way. Ruthenium coordination chemistry opens the way to caging a wide range of molecules, such as amino acids, nucleotides, neurotransmitters, fluorescent probes and genetic inducers. Contrary to other phototriggers, these Ru- based caged compounds are active with visible light, and can be photolysed even at 532nm (green), enabling the use of simple and inexpensive equipment. These compounds are also active in the two-photon regime, a property that extends their scope to systems where IR light must be used to achieve high precision and penetrability. The state of the art and the future of ruthenium polypyridyl phototriggers are discussed, and several new applications are presented.Fil: Zayat, Leonardo Martin. Consejo Nacional de Investigaciones Científico Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Químico Física de los Materiales Medioambiente y Energía; Argentina;Fil: Filevich, Oscar. Consejo Nacional de Investigaciones Científico Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Químico Física de los Materiales Medioambiente y Energía; Argentina;Fil: Baraldo Victorica, Luis Mario. Consejo Nacional de Investigaciones Científico Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Químico Física de los Materiales Medioambiente y Energía; Argentina;Fil: Etchenique, Roberto Argentino. Consejo Nacional de Investigaciones Científico Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Químico Física de los Materiales Medioambiente y Energía; Argentina

A new inorganic photolabile protecting group for highly efficient visible light GABA uncaging

Inhibiting with visible light. An inorganic‐based caged compound of the inhibitory neurotransmitter, γ‐amino butyric acid (GABA), was prepared and photolysed by light at 450 nm with the highest uncaging quantum yield reported to date. GABA ion channels were activated by irradiation in a biological preparation by using this caged compound. (Image courtesy of the CNS Forum http://www.cnsforum.com)Fil: Zayat, Leonardo Martin. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Inorgánica, Analítica y Química Física; ArgentinaFil: Noval, María Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Inorgánica, Analítica y Química Física; ArgentinaFil: Campi, Julieta. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Inorgánica, Analítica y Química Física; ArgentinaFil: Calero, Cecilia Ines. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Calvo, Daniel Juan. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Etchenique, Roberto Argentino. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Inorgánica, Analítica y Química Física; Argentin