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

Line positions in the v6=1 band of methyl iodide: Validation of the C3v TDS package based on the tensorial formalism

International audienceA tensorial formalism adapted to the case of symmetric-top molecules has been recently developed in Dijon (El Hilali et al., J Quant Spectrosc Radiat Transf 2010;111, 1305–1315) [18]. It is based on the O(3)⊃C3v group chain and allows a systematic expansion of the Hamiltonian and dipole moment operators, including all possible interactions for a given rovibrational polyad system. This suite of programs is used to analyze and simulate the mid-infrared spectrum of methyl iodide in order to test its performance. The v6 fundamental band has been recorded using the FTIR Bruker HR125 at the AILES beamline of the SOLEIL Synchrotron facility with the Globar internal source. 3882 lines up to J=61 were assigned and fitted with only 16 tensorial parameters

eco-friendly organic compound effect on the corrosion inhibition behavior of tin in alkaline environment

L-Cysteine (L-Cyst) was tested as corrosion inhibitor of tin in Na2CO3 0.1M + NaCl 1M solution. The inhibition action of this inhibitor was studied by using electrochemical impedance spectroscopy (EIS) and potentiodynamic polarization (PDP) techniques.  Temperature effect on the inhibition efficiency was studied in the range from 298 to 328 K and the values of activation thermodynamic parameters were calculated and explained. Experiment results show that inhibition efficiency increases with increasing of L-Cysteine concentration and decreases slightly with elevation of temperature. L-Cyst is a good inhibitor and inhibition efficiency reach 88% at 10−3M. Analysis of the polarization curves revealed that L-Cyst is considered as a mixed inhibitor. The results from electrochemical measurements and theoretical calculations are in good agreement. The surface morphology of the metal surface was investigated by scanning electron microscopy (SEM)