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

On atmospheric optical communications

This paper investigates, more rigorously, the diffraction of a powerful optical carrier propagating in an unguided communication channel (dry atmosphere). Four main relevant topics are considered i) the radial temperature distribution, ii) the average beamwidth parameter, iii) a dimensionless optical distortion figure of merit, and iv) the irradiance tailoring technique as a method to reduce the diffraction caused by refractive effects

On atmospheric optical communications

This paper investigates, more rigorously, the diffraction of a powerful optical carrier propagating in an unguided communication channel (dry atmosphere). Four main relevant topics are considered i) the radial temperature distribution, ii) the average beamwidth parameter, iii) a dimensionless optical distortion figure of merit, and iv) the irradiance tailoring technique as a method to reduce the diffraction caused by refractive effects.La diffraction d'une porteuse puissante qui se propage dans une chaine de communication non guidée (atmosphère sèche) est plus rigoureusement étudiée. Quatre points pertinents sont examinés i) distribution radiale de la température, ii) paramètre « largeur moyenne du faisceau », iii) facteur de mérite normalisé de distortion optique, et iv) mise en forme d'un champ optique pour réduire la diffraction créée par les effets réfractifs

New Architecture of Optical Interconnect for High-Speed Optical Computerized Data Networks (Nonlinear Response)

Although research into the use of optics in computers has increased in the last and current decades, the fact remains that electronics is still superior to optics in almost every way. Research into the use of optics at this stage mirrors the research into electronics after the 2nd World War. The advantages of using fiber optics over wiring are the same as the argument for using optics over electronics in computers. Even through totally optical computers are now a reality, computers that combine both electronics and optics, electro-optic hybrids, have been in use for some time. In the present paper, architecture of optical interconnect is built up on the bases of four Vertical-Cavity Surface- Emitting Laser Diodes (VCSELD) and two optical links where thermal effects of both the diodes and the links are included. Nonlinear relations are correlated to investigate the power-current and the voltage-current dependences of the four devices. The good performance (high speed) of the interconnect is deeply and parametrically investigated under wide ranges of the affecting parameters. The high speed performance is processed through three different effects, namely the device 3-dB bandwidth, the link dispersion characteristics, and the transmitted bit rate (soliton). Eight combinations are investigated; each possesses its own characteristics. The best architecture is the one composed of VCSELD that operates at 850 nm and the silica fiber whatever the operating set of causes. This combination possesses the largest device 3-dB bandwidth, the largest link bandwidth and the largest soliton transmitted bit rate. The increase of the ambient temperature reduces the high-speed performance of the interconnec