The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

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

utomated 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

A Multi-factor Approach for Flaky Test Detection and Automated Root Cause Analysis

Developers often spend time to determine whether test case failures are real failures or flaky. The flaky tests, also known as non-deterministic tests, switch their outcomes without any modification in the codebase, hence reducing the confidence of developers during maintenance as well as in the quality of a product. Re-running test cases to reveal flakiness is resource-consuming, unreliable and does not reveal the root causes of test flakiness. Our paper evaluates a multi-factor approach to identify flaky test executions implemented in a tool named MDF laker. The four factors are: trace-back coverage, flaky frequency, number of test smells, and test size. Based on the extracted factors, MDFlaker uses k-Nearest Neighbor (KNN) to determine whether failed test executions are flaky. We investigate MDFlaker in a case study with 2166 test executions from different open-source repositories. We evaluate the effectiveness of our flaky detection tool. We illustrate how the multi-factor approach can be used to reveal root causes for flakiness, and we conduct a qualitative comparison between MDF laker and other tools proposed in literature. Our results show that the combination of different factors can be used to identify flaky tests. Each factor has its own trade-off, e.g., trace-back leads to many true positives, while flaky frequency yields more true negatives. Therefore, specific combinations of factors enable classification for testers with limited information (e.g., not enough test history information)

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

An Industrial Study on the Challenges and Effects of Diversity-Based Testing in Continuous Integration

Many test prioritisation techniques have been proposed in order to improve test effectiveness of Continuous Integration (CI) pipelines. Particularly, diversity-based testing (DBT) has shown promising and competitive results to improve test effectiveness. However, the technical and practical challenges of introducing test prioritisation in CI pipelines are rarely discussed, thus hindering the applicability and adoption of those proposed techniques. This research builds on our prior work in which we evaluated diversity-based techniques in an industrial setting. This work investigates the factors that influence the adoption of DBT both in connection to improvements in test cost-effectiveness, as well as the process and human related challenges to transfer and use DBT prioritisation in CI pipelines. We report on a case study considering the CI pipeline of Axis Communications in Sweden. We performed a thematic analysis of a focus group interview with senior practitioners at the company to identify the challenges and perceived benefits of using test prioritisation in their test process. Our thematic analysis reveals a list of ten challenges and seven perceived effects of introducing test prioritisation in CI cycles. For instance, our participants emphasized the importance of introducing comprehensible and transparent techniques that instill trust in its users. Moreover, practitioners prefer techniques compatible with their current test infrastructure (e.g., test framework and environments) in order to reduce instrumentation efforts and avoid disrupting their current setup. In conclusion, we have identified tradeoffs between different test prioritisation techniques pertaining to the technical, process and human aspects of regression testing in CI. We summarize those findings in a list of seven advantages that refer to specific stakeholder interests and describe the effects of adopting DBT in CI pipelines.</p

The Comparative Evaluation of Test Prioritization Approaches in an Industrial Study

Many test prioritisation techniques have been proposed in order to improve test effectiveness of Continuous Integration (CI) pipelines. Particularly, diversity-based testing (DBT) has shown promising and competitive results to improve test effectiveness. We report on a case study considering the CI pipeline of Axis Communications in Sweden. We compared three different prioritisation approaches (i.e., diversity, failure history and time) in terms of their impact on coverage, failure detection rates and reduction on test execution time. Our results reveal that DBT is the best candidate to provide feature coverage, whereas failure rate prioritisation yields better failure coverage. Time-based prioritisation is not a reliable approach to provide cost-effective testing. Moreover, DBT would allow stakeholders to receive quick feedback on many combinations of integrated features to verify their code changes. Our participants report that developers are mainly interested in: (i) receiving quick feedback on a high combination of integrated features to verify their code changes, and (ii) associate their test suites to confidence scores representing the risk of missing failures given that fewer tests are executed

Activated carbon from pumpkin seeds: Production by simultaneous carbonization activation for occupational respiratory protection

Activated carbon materials are derived from carbonaceous sources and used as a technological element for various industrial purposes. These materials are present in most filters (cartridges) in personal respiratory protective equipment. Due to this context and to enhance sustainability concepts and human health in the production of materials, this study aimed to produce activated carbon from an abundant agricultural waste in the northeast Brazil through a route that not only favors its simultaneous carbonization and activation but also its thermal neutralization. The precursor biomass was characterized by particle size analysis, a standard testing method for moisture and ash content which were characterized by FRX, CHN, and thermal analysis. The produced activated carbon was characterized by potential of hydrogen (pH), XRD, BET, SEM, TPD by ammonia and UV-Vis analysis. The activated carbons showed yields�between 73 and 78%. The morphology varied in function of the biomass interaction with the type and concentration of acid used. The produced samples showed adsorption capacity and selectivity to ammonia gas.</jats:p

Activated carbon from pumpkin seeds: Production by simultaneous carbonization activation for occupational respiratory protection

Activated carbon materials are derived from carbonaceous sources and used as a technological element for various industrial purposes. These materials are present in most filters (cartridges) in personal respiratory protective equipment. Due to this context and to enhance sustainability concepts and human health in the production of materials, this study aimed to produce activated carbon from an abundant agricultural waste in the northeast Brazil through a route that not only favors its simultaneous carbonization and activation but also its thermal neutralization. The precursor biomass was characterized by particle size analysis, a standard testing method for moisture and ash content which were characterized by FRX, CHN, and thermal analysis. The produced activated carbon was characterized by potential of hydrogen (pH), XRD, BET, SEM, TPD by ammonia and UV-Vis analysis. The activated carbons showed yields�between 73 and 78%. The morphology varied in function of the biomass interaction with the type and concentration of acid used. The produced samples showed adsorption capacity and selectivity to ammonia gas.</jats:p

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