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

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.
Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivirus. Rio de Janeiro, RJ, Brasil / Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy / Universidade Federal de Minas Gerais. Laboratório de Genética Celular e Molecular. Belo Horizonte, Brasil.
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.
Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
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.
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.
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.
National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
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.
Lancet Laboratories, Johannesburg, 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.
Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.
Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.
Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana.
National Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana.
Discipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu-Natal, Durban, South Africa.
NGSSA Consortium
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.
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.
Department of Molecular Medicine and Haematology, Faculty of Health Science, School of Pathology, 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.
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu- Natal, Durban, South Africa.
Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana.
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.
National Priority Program of the National Health Laboratory Service, 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 / School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
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.
Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.
Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.
Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
Department of Medicine, University of Cambridge, Cambridge, UK.
Department of Infectious Disease, Imperial College London, London, UK.
Biozentrum, University of Basel, Basel, Switzerland.
Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA.
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.
Department of Zoology, University of Oxford, Oxford, UK.
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.
School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa / Lancet Laboratories, Johannesburg, 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.
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
NHLS Port Elizabeth Laboratory, Port Elizabeth, South Africa / Faculty of Health Sciences, Walter Sisulu University, Eastern Cape, South Africa.
Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana / Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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.
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 / Department of Global Health, University of Washington, Seattle, WA, USA.

Resumen en ingles

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.

Palabras clave en portugues

SARS-CoV-2
Surgimento de linhagens
Omicron BA.4
BA.5
África do Sul

Palabras clave en ingles

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

Editor

Nature

Referencia

TEGALLY, Houriiyah et al. Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa. Nature Medicine, v. 28, p. 1785-1790, p. 1 - 18, Sept. 2022.

DOI

10.1038/s41591-022-01911-2

ISSN

1546-170X

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