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DETECTION OF A SARS-COV-2 VARIANT OF CONCERN IN SOUTH AFRICA
Autor
Tegally, Houriiyiah
Wilkinson, Eduan
Giovanetti, Marta
Iranzadeh, Arash
Fonseca, Vagner
Giandhari, Jennifer
Doolabh, Deelan
Pillay, Sureshnee
San, Emmanuel James
Msomi, Nokukhanya
Mlisana, Koleka
von Gottberg, Anne
Walaza, Sibongile
Allam, Mushal
Ismail9, Arshad
Mohale, Thabo
Glass, Allison J. G
Engelbrecht, Susan
Van Zyl, Gert
Preiser, Wolgang
Petruccione, Francesco
Sigal, Alex
Hardie, Diana
Marais, Gert
Hsiao, Nei-yuan
Korsman, Stephen
Davies, Mary-Ann
Tyers, Lynn
Mudau, Innocent
York, Denis
Maslo, Caroline
Goedhals, Dominique
Abrahams, Shareef
Laguda-Akingba, Oluwakemi
Alisoltani-Dehkord, Arghavan
Godzik, Adam
Wibmer, Constantinos Kurt
Sewell, Bryan Trevor
Lourenço, José
Alcantara, Luiz Carlos Junior
Pond, Sergei L. Kosakovsky
Weaver, Steven
Martin, Dareen
Lessells, Richard J.
Bhiman, JInal N.
Williamson, Carolyn
Oliveira, Tulio de
Wilkinson, Eduan
Giovanetti, Marta
Iranzadeh, Arash
Fonseca, Vagner
Giandhari, Jennifer
Doolabh, Deelan
Pillay, Sureshnee
San, Emmanuel James
Msomi, Nokukhanya
Mlisana, Koleka
von Gottberg, Anne
Walaza, Sibongile
Allam, Mushal
Ismail9, Arshad
Mohale, Thabo
Glass, Allison J. G
Engelbrecht, Susan
Van Zyl, Gert
Preiser, Wolgang
Petruccione, Francesco
Sigal, Alex
Hardie, Diana
Marais, Gert
Hsiao, Nei-yuan
Korsman, Stephen
Davies, Mary-Ann
Tyers, Lynn
Mudau, Innocent
York, Denis
Maslo, Caroline
Goedhals, Dominique
Abrahams, Shareef
Laguda-Akingba, Oluwakemi
Alisoltani-Dehkord, Arghavan
Godzik, Adam
Wibmer, Constantinos Kurt
Sewell, Bryan Trevor
Lourenço, José
Alcantara, Luiz Carlos Junior
Pond, Sergei L. Kosakovsky
Weaver, Steven
Martin, Dareen
Lessells, Richard J.
Bhiman, JInal N.
Williamson, Carolyn
Oliveira, Tulio de
Afiliación
KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences. University of KwaZulu–Natal. Durban, South Africa.
KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences. University of KwaZulu–Natal. Durban, South Africa.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil / Universidade Federal de Minas Gerais. Laboratório de Genética Celular e Molecular. BeloHorizonte, MG, Brasil. r
Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town. Cape Town, South Africa.
KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences. University of KwaZulu–Natal. Durban, South Africa / Universidade Federal de Minas Gerais. Laboratório de Genética Celular e Molecular. BeloHorizonte, MG, Brasil.
Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town. Cape Town, South Africa.
Division of Medical Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town. Cape Town, South Africa.
Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town. Cape Town, South Africa.
Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town. Cape Town, South Africa.
Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town. Cape Town, South Africa..
NHLS. Johannesburg, South Africa / Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.
National Institute for Communicable Diseases, NHLS. Johannesburg, South Africa / School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
National Institute for Communicable Diseases, NHLS. Johannesburg, South Africa / School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
National Institute for Communicable Diseases, NHLS. Johannesburg, South Africa.
National Institute for Communicable Diseases, NHLS. Johannesburg, South Africa
National Institute for Communicable Diseases, NHLS. Johannesburg, South Africa
School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa / Department of Molecular Pathology, Lancet Laboratories, Johannesburg, South Africa.
Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University and NHLS Tygerberg Hospital, Cape Town, South Africa.
Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University and NHLS Tygerberg Hospital, Cape Town, South Africa.
Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University and NHLS Tygerberg Hospital, Cape Town, South Africa.
Centre for Quantum Technology, University of KwaZulu–Natal, Durban, South Africa / National Institute for Theoretical Physics (NITheP), University of KwaZulu–Natal, Durban, South Africa.
Africa Health Research Institute, Durban, South Africa / School of Laboratory Medicine and Medical Sciences, University of KwaZulu– Natal, Durban, South Africa / Max Planck Institute for Infection Biology, Berlin, Germany.
Division of Medical Virology, NHLS Groote Schuur Hospital, University of Cape Town.Cape Town, South Africa.
Division of Medical Virology, NHLS Groote Schuur Hospital, University of Cape Town.Cape Town, South Africa.
Division of Medical Virology, NHLS Groote Schuur Hospital, University of Cape Town.Cape Town, South Africa.
Division of Medical Virology, NHLS Groote Schuur Hospital, University of Cape Town.Cape Town, South Africa.
Centre for Infectious Disease Epidemiology and Research, University of Cape Town. Cape Town, South Africa / Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa..
Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa.
Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa.
Molecular Diagnostics Services, Durban, South Africa.
Molecular Diagnostics Services, Durban, South Africa.
Division of Virology, NHLS Universitas Academic Laboratories, University of The Free State, Bloemfontein, South Africa.
NHLS, Port Elizabeth, South Africa.
NHLS, Port Elizabeth, South Africa / Department of Laboratory Medicine and Pathology, Faculty of Health Sciences, Walter Sisulu University, Mthatha, South Africa.
Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa./ Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA.
Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA.
National Institute for Communicable Diseases, NHLS, Johannesburg, South Africa.
National Institute for Communicable Diseases, NHLS, Johannesburg, South Africa.
Department of Zoology, University of Oxford, Oxford, UK.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil / Universidade Federal de Minas Gerais. Laboratório de Genética Celular e Molecular. BeloHorizonte, MG, Brasil.
Institute for Genomics and Evolutionary Medicine. Temple University, Philadelphia, PA, USA.
Institute for Genomics and Evolutionary Medicine. Temple University, Philadelphia, PA, USA.
Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa / Division of Medical Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa / KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa.
National Institute for Communicable Diseases, NHLS, Johannesburg, South Africa / School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Division of Medical Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa / Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa / Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.
KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences. University of KwaZulu–Natal. Durban, South Africa / Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa / Department of Global Health, University of Washington, Seattle, WA, USA.
KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences. University of KwaZulu–Natal. Durban, South Africa.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil / Universidade Federal de Minas Gerais. Laboratório de Genética Celular e Molecular. BeloHorizonte, MG, Brasil. r
Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town. Cape Town, South Africa.
KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences. University of KwaZulu–Natal. Durban, South Africa / Universidade Federal de Minas Gerais. Laboratório de Genética Celular e Molecular. BeloHorizonte, MG, Brasil.
Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town. Cape Town, South Africa.
Division of Medical Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town. Cape Town, South Africa.
Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town. Cape Town, South Africa.
Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town. Cape Town, South Africa.
Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town. Cape Town, South Africa..
NHLS. Johannesburg, South Africa / Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.
National Institute for Communicable Diseases, NHLS. Johannesburg, South Africa / School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
National Institute for Communicable Diseases, NHLS. Johannesburg, South Africa / School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
National Institute for Communicable Diseases, NHLS. Johannesburg, South Africa.
National Institute for Communicable Diseases, NHLS. Johannesburg, South Africa
National Institute for Communicable Diseases, NHLS. Johannesburg, South Africa
School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa / Department of Molecular Pathology, Lancet Laboratories, Johannesburg, South Africa.
Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University and NHLS Tygerberg Hospital, Cape Town, South Africa.
Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University and NHLS Tygerberg Hospital, Cape Town, South Africa.
Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University and NHLS Tygerberg Hospital, Cape Town, South Africa.
Centre for Quantum Technology, University of KwaZulu–Natal, Durban, South Africa / National Institute for Theoretical Physics (NITheP), University of KwaZulu–Natal, Durban, South Africa.
Africa Health Research Institute, Durban, South Africa / School of Laboratory Medicine and Medical Sciences, University of KwaZulu– Natal, Durban, South Africa / Max Planck Institute for Infection Biology, Berlin, Germany.
Division of Medical Virology, NHLS Groote Schuur Hospital, University of Cape Town.Cape Town, South Africa.
Division of Medical Virology, NHLS Groote Schuur Hospital, University of Cape Town.Cape Town, South Africa.
Division of Medical Virology, NHLS Groote Schuur Hospital, University of Cape Town.Cape Town, South Africa.
Division of Medical Virology, NHLS Groote Schuur Hospital, University of Cape Town.Cape Town, South Africa.
Centre for Infectious Disease Epidemiology and Research, University of Cape Town. Cape Town, South Africa / Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa..
Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa.
Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa.
Molecular Diagnostics Services, Durban, South Africa.
Molecular Diagnostics Services, Durban, South Africa.
Division of Virology, NHLS Universitas Academic Laboratories, University of The Free State, Bloemfontein, South Africa.
NHLS, Port Elizabeth, South Africa.
NHLS, Port Elizabeth, South Africa / Department of Laboratory Medicine and Pathology, Faculty of Health Sciences, Walter Sisulu University, Mthatha, South Africa.
Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa./ Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA.
Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA.
National Institute for Communicable Diseases, NHLS, Johannesburg, South Africa.
National Institute for Communicable Diseases, NHLS, Johannesburg, South Africa.
Department of Zoology, University of Oxford, Oxford, UK.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil / Universidade Federal de Minas Gerais. Laboratório de Genética Celular e Molecular. BeloHorizonte, MG, Brasil.
Institute for Genomics and Evolutionary Medicine. Temple University, Philadelphia, PA, USA.
Institute for Genomics and Evolutionary Medicine. Temple University, Philadelphia, PA, USA.
Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa / Division of Medical Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa / KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa.
National Institute for Communicable Diseases, NHLS, Johannesburg, South Africa / School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Division of Medical Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa / Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa / Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.
KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences. University of KwaZulu–Natal. Durban, South Africa / Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa / Department of Global Health, University of Washington, Seattle, WA, USA.
Resumen en ingles
Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus1,2. 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 importance3,4,5. 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.
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