Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa.

Amino Acids Animals COVID-19 / epidemiology Humans SARS-CoV-2 / genetics South Africa / epidemiology Spike Glycoprotein, Coronavirus / genetics

Journal

Nature medicine
ISSN: 1546-170X
Titre abrégé: Nat Med
Pays: United States
ID NLM: 9502015

Informations de publication

Date de publication:
09 2022
Historique:
received: 28 04 2022
accepted: 21 06 2022
pubmed: 28 6 2022
medline: 28 9 2022
entrez: 27 6 2022
Statut: ppublish

Résumé

Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa's fourth Coronavirus Disease 2019 (COVID-19) wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. The spike proteins of BA.4 and BA.5 are identical, and similar to BA.2 except for the addition of 69-70 deletion (present in the Alpha variant and the BA.1 lineage), L452R (present in the Delta variant), F486V and the wild-type amino acid at Q493. The two lineages differ only outside of the spike region. The 69-70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure, on the background of variants not possessing this feature. BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa by the first week of April 2022. Using a multinomial logistic regression model, we estimated growth advantages for BA.4 and BA.5 of 0.08 (95% confidence interval (CI): 0.08-0.09) and 0.10 (95% CI: 0.09-0.11) per day, respectively, over BA.2 in South Africa. The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir, such as human chronic infections and/or animal hosts, is potentially contributing to further evolution and dispersal of the virus.

Identifiants

DOI: 10.1038/s41591-022-01911-2 PMID: 35760080 PMC: PMC9499863
pubmed: 35760080
doi: 10.1038/s41591-022-01911-2
pii: 10.1038/s41591-022-01911-2
pmc: PMC9499863
doi:

Substances chimiques

Amino Acids 0
Spike Glycoprotein, Coronavirus 0
spike protein, SARS-CoV-2 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. Research Support, N.I.H., Extramural

Langues

eng

Sous-ensembles de citation

IM

Pagination

1785-1790

Subventions

Organisme : Wellcome Trust
ID : 221003/Z/20/Z
Pays : United Kingdom
Organisme : Department of Health
Pays : United Kingdom
Organisme : NCIRD CDC HHS
ID : U01 IP001048
Pays : United States
Organisme : FIC NIH HHS
ID : U54 TW012041
Pays : United States
Organisme : FIC NIH HHS
ID : D43 TW009610
Pays : United States
Organisme : NIAID NIH HHS
ID : K24 AI131924
Pays : United States
Organisme : NIAID NIH HHS
ID : K24 AI131928
Pays : United States
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NIAID NIH HHS
ID : U01 AI151698
Pays : United States

Investigateurs

Armand Phillip Bester (AP)
Mathilda Claassen (M)
Deelan Doolabh (D)
Innocent Mudau (I)
Nokuzola Mbhele (N)
Susan Engelbrecht (S)
Dominique Goedhals (D)
Diana Hardie (D)
Nei-Yuan Hsiao (NY)
Arash Iranzadeh (A)
Arshad Ismail (A)
Rageema Joseph (R)
Arisha Maharaj (A)
Boitshoko Mahlangu (B)
Kamela Mahlakwane (K)
Ashlyn Davis (A)
Gert Marais (G)
Koleka Mlisana (K)
Anele Mnguni (A)
Thabo Mohale (T)
Gerald Motsatsi (G)
Peter Mwangi (P)
Noxolo Ntuli (N)
Martin Nyaga (M)
Luicer Olubayo (L)
Botshelo Radibe (B)
Yajna Ramphal (Y)
Upasana Ramphal (U)
Wilhelmina Strasheim (W)
Naume Tebeila (N)
Stephanie van Wyk (S)
Shannon Wilson (S)
Alexander G Lucaci (AG)
Steven Weaver (S)
Akhil Maharaj (A)
Yusasha Pillay (Y)
Michaela Davids (M)
Adriano Mendes (A)
Simnikiwe Mayaphi (S)

Informations de copyright

© 2022. The Author(s).

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Auteurs

Houriiyah Tegally (H)

Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.

Monika Moir (M)

Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.

Josie Everatt (J)

National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
ORCID: 0000-0002-0373-2093

Marta Giovanetti (M)

Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil.
Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy.
Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
ORCID: 0000-0002-5849-7326

Cathrine Scheepers (C)

National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
ORCID: 0000-0002-1683-0282

Eduan Wilkinson (E)

Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.

Kathleen Subramoney (K)

Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.

Zinhle Makatini (Z)

Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.

Sikhulile Moyo (S)

Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.
Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana.

Daniel G Amoako (DG)

National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
ORCID: 0000-0003-3551-3458

Cheryl Baxter (C)

Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
ORCID: 0000-0002-6033-7655

Christian L Althaus (CL)

Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
ORCID: 0000-0002-5230-6760

Ugochukwu J Anyaneji (UJ)

KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.

Dikeledi Kekana (D)

National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.

Raquel Viana (R)

Lancet Laboratories, Johannesburg, South Africa.

Jennifer Giandhari (J)

KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.

Richard J Lessells (RJ)

KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
ORCID: 0000-0003-0926-710X

Tongai Maponga (T)

Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
ORCID: 0000-0002-6876-3712

Dorcas Maruapula (D)

Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.

Wonderful Choga (W)

Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.

Mogomotsi Matshaba (M)

Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana.

Mpaphi B Mbulawa (MB)

National Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana.

Nokukhanya Msomi (N)

Discipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu-Natal, Durban, South Africa.

Yeshnee Naidoo (Y)

Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.

Sureshnee Pillay (S)

KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.

Tomasz Janusz Sanko (TJ)

Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
ORCID: 0000-0002-4154-7067

James E San (JE)

KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
ORCID: 0000-0002-5736-664X

Lesley Scott (L)

Department of Molecular Medicine and Haematology, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.

Lavanya Singh (L)

KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.

Nonkululeko A Magini (NA)

KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.

Pamela Smith-Lawrence (P)

Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana.

Wendy Stevens (W)

Department of Molecular Medicine and Haematology, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.
National Priority Program of the National Health Laboratory Service, Johannesburg, South Africa.

Graeme Dor (G)

National Priority Program of the National Health Laboratory Service, Johannesburg, South Africa.
ORCID: 0000-0001-9036-9933

Derek Tshiabuila (D)

KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.

Nicole Wolter (N)

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.

Wolfgang Preiser (W)

Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
ORCID: 0000-0002-0254-7910

Florette K Treurnicht (FK)

Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.

Marietjie Venter (M)

Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.
ORCID: 0000-0003-2696-824X

Georginah Chiloane (G)

Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.

Caitlyn McIntyre (C)

Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.

Aine O'Toole (A)

Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
ORCID: 0000-0001-8083-474X

Christopher Ruis (C)

Department of Medicine, University of Cambridge, Cambridge, UK.

Thomas P Peacock (TP)

Department of Infectious Disease, Imperial College London, London, UK.
ORCID: 0000-0001-7077-2928

Cornelius Roemer (C)

Biozentrum, University of Basel, Basel, Switzerland.
ORCID: 0000-0002-6138-6539

Sergei L Kosakovsky Pond (SL)

Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA.
ORCID: 0000-0003-4817-4029

Carolyn Williamson (C)

Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa.
Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa.
Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
ORCID: 0000-0003-0125-1226

Oliver G Pybus (OG)

Department of Zoology, University of Oxford, Oxford, UK.
ORCID: 0000-0002-8797-2667

Jinal N Bhiman (JN)

National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
ORCID: 0000-0001-6354-4003

Allison Glass (A)

School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Lancet Laboratories, Johannesburg, South Africa.
ORCID: 0000-0002-4275-3225

Darren P Martin (DP)

Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa.
Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.

Ben Jackson (B)

Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.

Andrew Rambaut (A)

Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
ORCID: 0000-0003-4337-3707

Oluwakemi Laguda-Akingba (O)

NHLS Port Elizabeth Laboratory, Port Elizabeth, South Africa.
Faculty of Health Sciences, Walter Sisulu University, Eastern Cape, South Africa.

Simani Gaseitsiwe (S)

Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.
Harvard T.H. Chan School of Public Health, Boston, MA, USA.

Anne von Gottberg (A)

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.
Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
ORCID: 0000-0002-0243-7455

Tulio de Oliveira (T)

Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa. tulio@sun.ac.za.
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa. tulio@sun.ac.za.
Department of Global Health, University of Washington, Seattle, WA, USA. tulio@sun.ac.za.
ORCID: 0000-0002-3027-5254

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Classifications MeSH

questionsmedicales.fr › Acides aminés, peptides et protéines › Acides aminés › Emergence of SARS-CoV-2 Omicron lineages BA.4...
questionsmedicales.fr › Eucaryotes › Animaux › Emergence of SARS-CoV-2 Omicron lineages BA.4...
questionsmedicales.fr › Maladies de l'appareil respiratoire › Infections de l'appareil respiratoire › Pneumopathie infectieuse › Pneumopathie virale › COVID-19 › Emergence of SARS-CoV-2 Omicron lineages BA.4...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Emergence of SARS-CoV-2 Omicron lineages BA.4...
questionsmedicales.fr › Virus › Virus à ARN › Virus à ARN à brin positif › Nidovirales › Coronaviridae › Coronavirus › Betacoronavirus › Virus du SRAS › SARS-CoV-2 › Emergence of SARS-CoV-2 Omicron lineages BA.4...
questionsmedicales.fr › Régions géographiques › Afrique › Afrique subsaharienne › Afrique australe › République d'Afrique du Sud › Emergence of SARS-CoV-2 Omicron lineages BA.4...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines virales › Protéines virales structurales › Protéines de l'enveloppe virale › Protéines de fusion virale › Glycoprotéine de spicule des coronavirus › Emergence of SARS-CoV-2 Omicron lineages BA.4...