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

Improving Continuous Integration with Similarity-based Test Case Selection

Automated testing is an essential component of Continuous Integration (CI) and Delivery (CD), such as scheduling automated test sessions on overnight builds. That allows stakeholders to execute entire test suites and achieve exhaustive test coverage, since running all tests is often infeasible during work hours, i.e., in parallel to development activities. On the other hand, developers also need test feedback from CI servers when pushing changes, even if not all test cases are executed. In this paper we evaluate similarity-based test case selection (SBTCS) on integration-level tests executed on continuous integration pipelines of two companies. We select test cases that maximise diversity of test coverage and reduce feedback time to developers. Our results confirm existing evidence that SBTCS is a strong candidate for test optimisation, by reducing feedback time (up to 92% faster in our case studies) while achieving full test coverage using only information from test artefacts themselves.Software Center: Aspects of Automated Testin

Interrelationship between some morphometric parameters and bodyweight of tank-based cultured African catfish (Clarias gariepinus Burchell, 1822)

Morphometrics and fish bodyweight studies have shown great importance in estimation of productivity and stock assessment for some fish species. Herein, the aim of this study was to identify the morphometric parameter(s) that has most direct correlation with bodyweight of African catfish (Clarias gariepinus). The experimental layouts were four groups of experimental units, each group was replicated twice. Morphometric parameters considered in this study were total length, standard length, head length, head width and snout length. Data collected were processed and subjected to analysis of variance (ANOVA) and correlation analyses at 5% significant level. Results revealed significantly high correlations between bodyweight and morphometric parameters, with values ranging from 0.834 to 0.977 (upper and lower limits for total and snout lengths respectively). The results further revealed that relationship between bodyweight and morphometric parameters followed third-degree polynomial, with R2 ranging from 0.700 to 0.969 (upper and lower limits for total and snout lengths respectively). Significant high correlations (>0.85) exist between morphometric parameters selected for this study. In conclusion, in sampling programs of African catfish where the aim is to select fishes with high bodyweights, emphasis should be given to fishes with highest total length

Scalable Set-Based Design Optimization and Remanufacturing for Meeting Changing Requirements

Engineering design problems often have open-ended requirements, especially in the early stages of development. Setbased design is a paradigm for exploring, and keeping under consideration, several alternatives so that commitment to a single design can be delayed until requirements are settled. In addition, requirements may change over the lifetime of a component or a system. Novel manufacturing technologies enable designs to be remanufactured to meet changed requirements. By considering this capability during the set-based design optimization process, solutions can be scaled to meet evolving requirements and customer specifications even after commitment. Such an ability can also support a circular economy paradigm based on the return of used or discarded components and systems to working condition. We propose a set-based design methodology to obtain scalable optimal solutions that can satisfy changing requirements through remanufacturing. We first use design optimization and surrogate modeling to obtain parametric optimal designs. This set of parametric optimal designs is then reduced to scalable optimal designs by observing a set of transition rules for the manufacturing process used (additive or subtractive). The methodology is demonstrated by means of a structural aeroengine component that is remanufactured by direct energy deposition of a stiffener to meet higher loading requirements