ABSTRACT
In response to the ongoing SARS-CoV-2 pandemic in the UK, the COVID-19 Genomics UK (COG-UK) consortium was formed to rapidly sequence SARS-CoV-2 genomes as part of a national-scale genomic surveillance strategy. The network consists of universities, academic institutes, regional sequencing centres and the four UK Public Health Agencies. We describe the development and deployment of CLIMB-COVID, an encompassing digital infrastructure to address the challenge of collecting and integrating both genomic sequencing data and sample-associated metadata produced across the COG-UK network.
Subject(s)
Cloud Computing , Genomics/organization & administration , SARS-CoV-2/genetics , COVID-19/epidemiology , Epidemiological Monitoring , Genome, Viral , Humans , Sequence Analysis, DNA , United Kingdom , User-Computer Interface , Whole Genome SequencingABSTRACT
This letter is the Human Genome Organisation's summary reaction to the 2020 COVID-19 pandemic. It identifies key areas for genomics research, and areas in which genomic scientists can contribute to a global response to the pandemic. The letter has been reviewed and endorsed by the HUGO Committee on Ethics, Law and Society (CELS) and the HUGO Council.
Subject(s)
COVID-19 , SARS-CoV-2/genetics , Societies, Scientific , COVID-19/epidemiology , Genomics/organization & administration , Human Genome Project , Humans , Information Dissemination , Organizations, Nonprofit , PandemicsABSTRACT
The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a suite of database resources to support worldwide research activities in both academia and industry. With the explosive growth of multi-omics data, CNCB-NGDC is continually expanding, updating and enriching its core database resources through big data deposition, integration and translation. In the past year, considerable efforts have been devoted to 2019nCoVR, a newly established resource providing a global landscape of SARS-CoV-2 genomic sequences, variants, and haplotypes, as well as Aging Atlas, BrainBase, GTDB (Glycosyltransferases Database), LncExpDB, and TransCirc (Translation potential for circular RNAs). Meanwhile, a series of resources have been updated and improved, including BioProject, BioSample, GWH (Genome Warehouse), GVM (Genome Variation Map), GEN (Gene Expression Nebulas) as well as several biodiversity and plant resources. Particularly, BIG Search, a scalable, one-stop, cross-database search engine, has been significantly updated by providing easy access to a large number of internal and external biological resources from CNCB-NGDC, our partners, EBI and NCBI. All of these resources along with their services are publicly accessible at https://bigd.big.ac.cn.
Subject(s)
Big Data , Computational Biology/standards , Databases, Genetic , Genomics/statistics & numerical data , SARS-CoV-2/genetics , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/virology , China , Computational Biology/methods , Computational Biology/organization & administration , Computational Biology/trends , Data Mining/methods , Data Mining/statistics & numerical data , Epidemics , Genetic Variation , Genome, Viral/genetics , Genomics/methods , Genomics/organization & administration , Humans , Internet , Search Engine/methods , Search Engine/statistics & numerical dataABSTRACT
This opinion commentary on the coronavirus disease 2019 (COVID-19) pandemic brings together observations from Zimbabwe specifically, and Africa broadly, drawing from the fields of pharmacogenomics, precision herbal medicine, and responsible innovation so as to respond to the pandemic in ways that are efficient, critically informed, principled, and responsive to needs in rural and urban communities across Africa. With new findings suggesting that COVID-19 is a systemic disease, impacting the respiratory system and beyond in some individuals, we need new molecular targets for therapeutics innovation more than ever. We argue that the current pandemic will likely strip the limited resources from other diseases such as malaria, human immunodeficiency virus (HIV) infection, and among others affecting the African continent. Hence, we need to address not only COVID-19 but also its broader health care and societal impacts in Africa. Extensive diagnostic testing to trace and isolate the COVID-19 cases as well as basic income and economic support for those who are unable to work will be needed. A critically informed and democratic governance that builds on transparency and trust for the elected leaders is crucial. Finally, the pandemic offers a silver lining for Africa: the prospects to integrate omics research with long-standing expertise in herbal medicine in Africa, thus accelerating the advances toward novel molecular therapeutic targets for COVID-19 and precision herbal medicine worldwide.