Sixteen novel lineages of SARS-CoV-2 in South Africa

Tegally, Houriiyah; Wilkinson, Eduan; Lessells, Richard; Giandhari, Jennifer; Pillay, Sureshnee; Msomi, Nokukhanya; Mlisana, Koleka; Bhiman, Jinal N.; von Gottberg, Anne; Walaza, Sibongile; Fonseca, Vagner; Allam, Mushal; Ismail, Arshad; Glass, Allison J.; Engelbrecht, Susan; Van Zy, Gert; Preiser, Wolfgang; Williamson, Carolyn; Petruccione, Francesco; Sigal, Alex; Gazy, Inbal; Hardie, Diana; Hsiao, Nei-yuan; Martin, Darren; York, Denis; Goedhals, Dominique; San, Emmanuel James; Giovanetti, Marta; Lourenço, José; Alcantara, Luiz Carlos Junior; Oliveira, Tulio de

Sixteen novel lineages of SARS-CoV-2 in South Africa

Detalhes bibliográficos
Autor(a) principal:	Tegally, Houriiyah
Data de Publicação:	2021
Outros Autores:	Wilkinson, Eduan, Lessells, Richard, Giandhari, Jennifer, Pillay, Sureshnee, Msomi, Nokukhanya, Mlisana, Koleka, Bhiman, Jinal N., von Gottberg, Anne, Walaza, Sibongile, Fonseca, Vagner, Allam, Mushal, Ismail, Arshad, Glass, Allison J., Engelbrecht, Susan, Van Zy, Gert, Preiser, Wolfgang, Williamson, Carolyn, Petruccione, Francesco, Sigal, Alex, Gazy, Inbal, Hardie, Diana, Hsiao, Nei-yuan, Martin, Darren, York, Denis, Goedhals, Dominique, San, Emmanuel James, Giovanetti, Marta, Lourenço, José, Alcantara, Luiz Carlos Junior, Oliveira, Tulio de
Tipo de documento:	Artigo
Idioma:	eng
Título da fonte:	Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo:	https://www.arca.fiocruz.br/handle/icict/46586
Resumo:	KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.

Metadados do item

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spelling	Tegally, HouriiyahWilkinson, EduanLessells, RichardGiandhari, JenniferPillay, SureshneeMsomi, NokukhanyaMlisana, KolekaBhiman, Jinal N.von Gottberg, AnneWalaza, SibongileFonseca, VagnerAllam, MushalIsmail, ArshadGlass, Allison J.Engelbrecht, SusanVan Zy, GertPreiser, WolfgangWilliamson, CarolynPetruccione, FrancescoSigal, AlexGazy, InbalHardie, DianaHsiao, Nei-yuanMartin, DarrenYork, DenisGoedhals, DominiqueSan, Emmanuel JamesGiovanetti, MartaLourenço, JoséAlcantara, Luiz Carlos JuniorOliveira, Tulio de2021-04-08T20:30:01Z2021-04-08T20:30:01Z2021TEGALLY, Houriiyah et al. Sixteen novel lineages of SARS-CoV-2 in South Africa. Nature Medicine, v. 27, n. 3, p. 440-446, Mar. 2021.1078-8956https://www.arca.fiocruz.br/handle/icict/4658610.1038/s41591-021-01255-3engNature Publishing GroupSARS-CoV-2Dezesseis novas linhagensÁfrica do SulVariantesSARS-CoV-2VariantsSouth AfricaSixteen novel lineagesSixteen novel lineages of SARS-CoV-2 in South Africainfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.Discipline of Virology, University of KwaZulu-Natal, Durban, South Africa.National Health Laboratory Service, Springbok, South Africa.National Institute For Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.National Institute For Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa / National Institute For Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.National Institute For Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa / School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.National Institute For Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.National Institute For Communicable Diseases (NICD) of the National Health Laboratory Service (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 at NHLS Tygerberg Hospital, Stellenbosch University, Stellenbosch, South Africa.Division of Medical Virology at NHLS Tygerberg Hospital, Stellenbosch University, Stellenbosch, South Africa.Division of Medical Virology at NHLS Tygerberg Hospital, Stellenbosch University, Stellenbosch, South Africa.Division of Medical Virology at NHLS Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.Centre for Quantum Technology, University of KwaZulu-Natal, Durban, South Africa / National Institute for Theoretical Physics (NITheP), KwaZulu-Natal, 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.KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.Division of Medical Virology at NHLS Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.Division of Medical Virology at NHLS Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.Division of Computational Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular medicine, The University of Cape Town, Cape Town, South Africa.Molecular Diagnostics Services, Durban, South Africa.Division of Virology at NHLS Universitas Academic Laboratories, University of The Free State, Bloemfontein, South Africa.KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil.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. Instituto de Ciências Biológicas. Laboratorio de Genetica Celular e Molecular. Belo Horizonte,., MG, Brasil.KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa / Department of Global Health, University of Washington, Seattle, WA, USA / Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.The first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in South Africa was identified on 5 March 2020, and by 26 March the country was in full lockdown (Oxford stringency index of 90)1. Despite the early response, by November 2020, over 785,000 people in South Africa were infected, which accounted for approximately 50% of all known African infections2. In this study, we analyzed 1,365 near whole genomes and report the identification of 16 new lineages of SARS-CoV-2 isolated between 6 March and 26 August 2020. Most of these lineages have unique mutations that have not been identified elsewhere. We also show that three lineages (B.1.1.54, B.1.1.56 and C.1) spread widely in South Africa during the first wave, comprising ~42% of all infections in the country at the time. The newly identified C lineage of SARS-CoV-2, C.1, which has 16 nucleotide mutations as compared with the original Wuhan sequence, including one amino acid change on the spike protein, D614G (ref. 3), was the most geographically widespread lineage in South Africa by the end of August 2020. An early South African-specific lineage, B.1.106, which was identified in April 2020 (ref. 4), became extinct after nosocomial outbreaks were controlled in KwaZulu-Natal Province. Our findings show that genomic surveillance can be implemented on a large scale in Africa to identify new lineages and inform measures to control the spread of SARS-CoV-2. Such genomic surveillance presented in this study has been shown to be crucial in the identification of the 501Y.V2 variant in South Africa in December 2020.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/46586/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALMartaGiovanettti_LuizCAlcantara_etal_IOC_2021.pdf.pdfMartaGiovanettti_LuizCAlcantara_etal_IOC_2021.pdf.pdfapplication/pdf12394983https://www.arca.fiocruz.br/bitstream/icict/46586/2/MartaGiovanettti_LuizCAlcantara_etal_IOC_2021.pdf.pdfa3fea24109644a7a4c6a0a7879b3bf52MD52TEXTMartaGiovanettti_LuizCAlcantara_etal_IOC_2021.pdf.pdf.txtMartaGiovanettti_LuizCAlcantara_etal_IOC_2021.pdf.pdf.txtExtracted 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dc.title.pt_BR.fl_str_mv	Sixteen novel lineages of SARS-CoV-2 in South Africa
title	Sixteen novel lineages of SARS-CoV-2 in South Africa
spellingShingle	Sixteen novel lineages of SARS-CoV-2 in South Africa Tegally, Houriiyah SARS-CoV-2 Dezesseis novas linhagens África do Sul Variantes SARS-CoV-2 Variants South Africa Sixteen novel lineages
title_short	Sixteen novel lineages of SARS-CoV-2 in South Africa
title_full	Sixteen novel lineages of SARS-CoV-2 in South Africa
title_fullStr	Sixteen novel lineages of SARS-CoV-2 in South Africa
title_full_unstemmed	Sixteen novel lineages of SARS-CoV-2 in South Africa
title_sort	Sixteen novel lineages of SARS-CoV-2 in South Africa
author	Tegally, Houriiyah
author_facet	Tegally, Houriiyah Wilkinson, Eduan Lessells, Richard Giandhari, Jennifer Pillay, Sureshnee Msomi, Nokukhanya Mlisana, Koleka Bhiman, Jinal N. von Gottberg, Anne Walaza, Sibongile Fonseca, Vagner Allam, Mushal Ismail, Arshad Glass, Allison J. Engelbrecht, Susan Van Zy, Gert Preiser, Wolfgang Williamson, Carolyn Petruccione, Francesco Sigal, Alex Gazy, Inbal Hardie, Diana Hsiao, Nei-yuan Martin, Darren York, Denis Goedhals, Dominique San, Emmanuel James Giovanetti, Marta Lourenço, José Alcantara, Luiz Carlos Junior Oliveira, Tulio de
author_role	author
author2	Wilkinson, Eduan Lessells, Richard Giandhari, Jennifer Pillay, Sureshnee Msomi, Nokukhanya Mlisana, Koleka Bhiman, Jinal N. von Gottberg, Anne Walaza, Sibongile Fonseca, Vagner Allam, Mushal Ismail, Arshad Glass, Allison J. Engelbrecht, Susan Van Zy, Gert Preiser, Wolfgang Williamson, Carolyn Petruccione, Francesco Sigal, Alex Gazy, Inbal Hardie, Diana Hsiao, Nei-yuan Martin, Darren York, Denis Goedhals, Dominique San, Emmanuel James Giovanetti, Marta Lourenço, José Alcantara, Luiz Carlos Junior Oliveira, Tulio de
author2_role	author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author
dc.contributor.author.fl_str_mv	Tegally, Houriiyah Wilkinson, Eduan Lessells, Richard Giandhari, Jennifer Pillay, Sureshnee Msomi, Nokukhanya Mlisana, Koleka Bhiman, Jinal N. von Gottberg, Anne Walaza, Sibongile Fonseca, Vagner Allam, Mushal Ismail, Arshad Glass, Allison J. Engelbrecht, Susan Van Zy, Gert Preiser, Wolfgang Williamson, Carolyn Petruccione, Francesco Sigal, Alex Gazy, Inbal Hardie, Diana Hsiao, Nei-yuan Martin, Darren York, Denis Goedhals, Dominique San, Emmanuel James Giovanetti, Marta Lourenço, José Alcantara, Luiz Carlos Junior Oliveira, Tulio de
dc.subject.other.pt_BR.fl_str_mv	SARS-CoV-2 Dezesseis novas linhagens África do Sul Variantes
topic	SARS-CoV-2 Dezesseis novas linhagens África do Sul Variantes SARS-CoV-2 Variants South Africa Sixteen novel lineages
dc.subject.en.pt_BR.fl_str_mv	SARS-CoV-2 Variants South Africa Sixteen novel lineages
description	KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
publishDate	2021
dc.date.accessioned.fl_str_mv	2021-04-08T20:30:01Z
dc.date.available.fl_str_mv	2021-04-08T20:30:01Z
dc.date.issued.fl_str_mv	2021
dc.type.status.fl_str_mv	info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv	info:eu-repo/semantics/article
format	article
status_str	publishedVersion
dc.identifier.citation.fl_str_mv	TEGALLY, Houriiyah et al. Sixteen novel lineages of SARS-CoV-2 in South Africa. Nature Medicine, v. 27, n. 3, p. 440-446, Mar. 2021.
dc.identifier.uri.fl_str_mv	https://www.arca.fiocruz.br/handle/icict/46586
dc.identifier.issn.pt_BR.fl_str_mv	1078-8956
dc.identifier.doi.none.fl_str_mv	10.1038/s41591-021-01255-3
identifier_str_mv	TEGALLY, Houriiyah et al. Sixteen novel lineages of SARS-CoV-2 in South Africa. Nature Medicine, v. 27, n. 3, p. 440-446, Mar. 2021. 1078-8956 10.1038/s41591-021-01255-3
url	https://www.arca.fiocruz.br/handle/icict/46586
dc.language.iso.fl_str_mv	eng
language	eng
dc.rights.driver.fl_str_mv	info:eu-repo/semantics/openAccess
eu_rights_str_mv	openAccess
dc.publisher.none.fl_str_mv	Nature Publishing Group
publisher.none.fl_str_mv	Nature Publishing Group
dc.source.none.fl_str_mv	reponame:Repositório Institucional da FIOCRUZ (ARCA) instname:Fundação Oswaldo Cruz (FIOCRUZ) instacron:FIOCRUZ
instname_str	Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str	FIOCRUZ
institution	FIOCRUZ
reponame_str	Repositório Institucional da FIOCRUZ (ARCA)
collection	Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv	https://www.arca.fiocruz.br/bitstream/icict/46586/1/license.txt https://www.arca.fiocruz.br/bitstream/icict/46586/2/MartaGiovanettti_LuizCAlcantara_etal_IOC_2021.pdf.pdf https://www.arca.fiocruz.br/bitstream/icict/46586/3/MartaGiovanettti_LuizCAlcantara_etal_IOC_2021.pdf.pdf.txt
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repository.name.fl_str_mv	Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
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Sixteen novel lineages of SARS-CoV-2 in South Africa

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