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

Autonomous Soil Water Content Sensors Based on Bipolar Transistors Encapsulated in Porous Ceramic Blocks

We present an autonomous sensor to measure soil water content that uses a single heat pulse probe based on a transistor encapsulated in a porous block. The sensor uses a bipolar junction transistor, which performs as both a heating and temperature-sensing element. Since the sensor depends on a porous block to measure the matric potential of the soil, it does not suffer from accuracy problems if the contact between the probe and the soil is not perfect. A prototype of the sensor showed a temperature variation of Δ T = 2.9   ∘ C when the porous ceramic was saturated with water. The sensor presented an almost linear behavior for small changes in the matric potential of a red latosol when tested in the 1-kPa and 35-kPa pressure range, showing a sensitivity of S = 0.015   ∘ C/kPa. The ultra-low power signal conditioning circuit can read the sensor’s temperature with a resolution of approximately 0.02   ∘ C, so the matric potential can be read in increments of at least 1.33 kPa. When powered only by a 2-F supercapacitor from the energy-harvesting system, the interrogation circuit is able to take one soil water content measurement per day, for eleven days

A Web-Based Agent-Oriented Approach to Address Heterogeneity in Cooperative Embedded Systems

International audienceThis paper presents a MAS-oriented approach to enable emergence and execution of complex functionality among a fleet of heterogeneous connected objects. It relies on the Web of Things paradigm, in which such objects communicate using Web standards. In order to homogenize the objects and extend their capabilities, our approach is based on agents that can be deployed either on objects or in the cloud. Such agents can embody the object behaviors and perform negotiation to achieve collaborative functionalities