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!

    The Africa CDC Pathogen Genomics Initiative NGS Academy aims to develop and deliver a comprehensive training framework for the implementation of next generation sequencing (NGS) for pathogen surveillance. This includes all aspects of NGS, from sample collection to sequencing and analysis to inform public health interventions.

    Pathogen genomics and epidemiology training survey.

    A landscaping exercise is being carried out to identify existing training courses and materials relevant to Pathogen Genomics and Epidemiology. Information about courses and training materials are being collated into a central resource that may be used in training the various role players in this area, most notably in the public health sector. Read more

    A SARS-CoV-2 protein interaction map reveals targets for drug repurposing
    By Nevan Krogan

    May 19, 2020 at 11:00 AM EDT!
    Efforts to develop antiviral drugs versus COVID-19 or vaccines for its prevention have been hampered by limited knowledge of the molecular details of SARS-CoV-2 infection. This webinar will describe our efforts to address this challenge by expressing 26 of the 29 SARS-CoV-2 proteins in human cells and identifying the human proteins physically associated with each using affinity-purification mass spectrometry. Among 332 high-confidence SARS-CoV-2-human protein-protein interactions, we identified 66 druggable human proteins or host factors targeted by 69 compounds (29 FDA-approved drugs, 12 drugs in clinical trials, and 28 preclinical compounds). Within a subset of these, multiple viral assays identified two sets of pharmacological agents that displayed antiviral activity.
      Registration is complimentary.

    The African Institute of Biomedical Science and Technology (AiBST) node is involved in the following activities:

    1. A technical partner of the Ministry of Health in the provision of rt-PCR tests. The research Lab has done thousands of such tests to assist in the national response. This is being coordinated Dr. Justen Manasa.
    2. The node got a grant from the Global Health Protection (GHP) program in German to determine the frequency of genetic variants that could affect some of the drugs that are being tested in the SOLIDARITY study. The Lab has genotyped 118 samples from their biobank and are preparing a short communication to that effect.
    3. The node is also part of a GATES Foundation and Cetara company funded multi-centre study to create a Healthcare Workers (HCW)  taking care of COVID-19 patient registry. They are currently working with the various COVID-19 treatment centres to establish this registry and collecting samples to test for the infection rates among the HCW.

    Since early this year, researchers have been racing to understand and characterize COVID-19, the illness caused by the SARS-CoV-2 coronavirus, before it becomes unmanageable. The virus, originating in Wuhan, China, was confirmed by Chinese officials and the World Health Organization (WHO) on 7 January and named by the WHO on 11 February.

    Comparisons have been made between the current crisis and 2003, when the Severe Acute Respiratory Syndrome (SARS) virus spread from the south of China to countries including Canada, Spain, and Russia, infecting 8,098 people and killing 774. SARS first appeared in November 2002 and was characterized as a coronavirus in late March 2003, in work that was fully published in Science at the end of May 2003. At the time, it was considered one of the fastest, most effective responses to a public health emergency ever. Read more.

    Source: Nature 2020.

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