Abstract

    Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus. Here we describe a newly arisen lineage of SARS-CoV-2 (designated 501Y.V2; also known as B.1.351 or 20H) that is defined by eight mutations in the spike protein, including three substitutions (K417N, E484K and N501Y) at residues in its receptor-binding domain that may have functional importance. This lineage was identified in South Africa after the first wave of the epidemic in a severely affected metropolitan area (Nelson Mandela Bay) that is located on the coast of the Eastern Cape province. This lineage spread rapidly, and became dominant in Eastern Cape, Western Cape and KwaZulu–Natal provinces within weeks. Although the full import of the mutations is yet to be determined, the genomic data—which show rapid expansion and displacement of other lineages in several regions—suggest that this lineage is associated with a selection advantage that most plausibly results from increased transmissibility or immune escape. Read more!


    PHA4GE overview

    The Public Health Alliance for Genomic Epidemiology (PHA4GE) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatic tools and resources, and advocate for greater openness, interoperability, accessibility and reproducibility in public health microbial bioinformatics.

    In the face of the current SARS-CoV-2 pandemic, PHA4GE has identified a clear and present need for a fit-for-purpose, open source SARS-CoV-2 contextual data standard. As such, we have developed a SARS-CoV-2 contextual data specification based on harmonizable, publicly available, community standards.

    SARS-CoV-2 contextual data specification overview

    Public health genomics contextual data includes sample metadata, lab/clinical/epidemiological data, and analysis methods information. Contextual data enables the interpretation of the sequence data, informs decision making for public health responses, and facilitates scientific understanding of infectious disease. Structured and consistent contextual data can also be more easily processed, aggregated, and reused by both humans and computers for different types of analyses. Read more!


    Description

    The COVID-19 module can be used to collect essential phenotypes associated with COVID-19 and MISC-related research, including: COVID-19 Exposure History; Symptoms and Signs; Comorbidities; COVID-19 Diagnoses and Treatments. The module is subdivided into core phenotypes (phenotypes incorporated from the H3Africa Standard) and COVID-19 & MISC-specific phenotypes. Read more!


    Genomic analysis of SARS-CoV-2 has made a profound impact in support of the global response to the pandemic. The ability to carry out analysis on samples is increasingly being considered as a crucial functionality of public health labs. However, many labs are faced with the daunting task of starting an entire bioinformatics program and integrating the appropriate tools and software from the ground up. The benefits these technologies bring to public health are invaluable.
    In an effort to bridge the gap in integrating these technologies for SARS-CoV-2 (SC2) analysis, PHA4GE Pipelines and Visualization Working Group members collaborated on a guidance document to define the major challenges and to highlight various open source resources that have emerged from the public health community. Conceptualizing the challenges faced aided in identifying and accentuating the major open access and open source resources available in the public health space. Read more!


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