SARS-CoV-2: Genome, New Variant and Risk of Infection in Immunized Individuals
TL;DR: The presence of the new variant of SARS-CoV-2 described above affects the risk of infection in immunized individuals.
Abstract: The COVID-19 outbreak was caused by SARS-CoV-2. This situation is concerning because it has created uncertainty and has become a world problem. Regarding the COVID-19 outbreak, a genomic analysis of SARS-CoV-2 has been carried out. The genome of SARS-CoV-2 contains 29.903 nucleotides (nt). The SARS-CoV-2 genome consists of the: 5’ UTR, ORF 1ab gene, S gene, ORF 3a gene, E gene, M gene, ORF 6 gene, ORF 7a gene, ORF 7b gene, ORF 8 gene, N gene, ORF 10 gene and 3’ UTR. It has been reported about the discovery of a new variant namely B.1.1.7 (20I/501Y.V1), B.1.351 (20H/501Y.V2), B.1.429 (452R.V1), P.1-lineage (20J/501Y.V3). Consequently, the presence of the new variant of SARS-CoV-2 described above affects the risk of infection in immunized individuals.
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University of KwaZulu-Natal1, Universidade Federal de Minas Gerais2, Oswaldo Cruz Foundation3, University of Cape Town4, National Health Laboratory Service5, Centre for the AIDS Programme of Research in South Africa6, University of the Witwatersrand7, Stellenbosch University8, Max Planck Society9, University of the Free State10, Walter Sisulu University11, University of California, Riverside12, University of Oxford13, Temple University14, University of Washington15
TL;DR: In this paper, the authors describe a new SARS-CoV-2 lineage (501Y.V2) characterised by eight lineage-defining mutations in the spike protein, including three at important residues in the receptor-binding domain (K417N, E484K and N501Y).
Abstract: Summary Continued uncontrolled transmission of the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) in many parts of the world is creating the conditions for significant virus evolution. Here, we describe a new SARS-CoV-2 lineage (501Y.V2) characterised by eight lineage-defining mutations in the spike protein, including three at important residues in the receptor-binding domain (K417N, E484K and N501Y) that may have functional significance. This lineage emerged in South Africa after the first epidemic wave in a severely affected metropolitan area, Nelson Mandela Bay, located on the coast of the Eastern Cape Province. This lineage spread rapidly, becoming within weeks the dominant lineage in the Eastern Cape and Western Cape Provinces. Whilst the full significance of the mutations is yet to be determined, the genomic data, showing the rapid displacement of other lineages, suggest that this lineage may be associated with increased transmissibility.
980 citations
TL;DR: The genomic signature analysis demonstrates that a strong association between the time of sample collection, location of sample and accumulation of genetic diversity is found and heavily supports an intense requirement for additional prompt, inclusive investigations that combine genomic detail, epidemiological information and graph records of the clinical features of patients with COVID-19.
622 citations
University of Oxford1, Wellcome Trust Sanger Institute2, University of Cambridge3, Public Health England4, Liverpool School of Tropical Medicine5, University of Sheffield6, Newcastle University7, Newcastle upon Tyne Hospitals NHS Foundation Trust8, University Hospital Southampton NHS Foundation Trust9, University of Southampton10, University Hospitals Bristol NHS Foundation Trust11, St George's, University of London12, University College London13, Guy's and St Thomas' NHS Foundation Trust14, University Hospitals Birmingham NHS Foundation Trust15, University of Glasgow16, North Bristol NHS Trust17, University College Hospital18, University of Hull19, Northwest University (China)20, Glasgow Dental Hospital and School21, Western General Hospital22, University of Nottingham23, Nottingham University Hospitals NHS Trust24, AstraZeneca25, Cardiff University26, Aneurin Bevan University Health Board27
TL;DR: A post-hoc analysis of the efficacy of the adenoviral vector vaccine, ChAdOx1 nCoV-19 (AZD1222), against B.1.7, emerged as the dominant cause of COVID-19 disease in the UK from November, 2020 as discussed by the authors.
521 citations
TL;DR: England's health secretary has told parliament that a new variant of covid-19 has been identified and may be driving infections in the south east, leading to headlines about “mutant covid.”
Abstract: England’s health secretary, Matt Hancock, has told parliament that a new variant of covid-19 has been identified and may be driving infections in the south east, leading to headlines about “mutant covid.” Jacqui Wise answers some common questions
291 citations
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