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

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Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
Nature Medicine ( IF 58.7 ) Pub Date : 2022-06-27 , DOI: 10.1038/s41591-022-01911-2
Houriiyah Tegally _{1,

2} , Monika Moir ₁ , Josie Everatt ₃ , Marta Giovanetti _{4,

5,

6} , Cathrine Scheepers _{3,

7} , Eduan Wilkinson ₁ , Kathleen Subramoney _{8,

9} , Zinhle Makatini _{8,

9} , Sikhulile Moyo _{10,

11,

12} , Daniel G Amoako ₃ , Cheryl Baxter ₁ , Christian L Althaus ₁₃ , Ugochukwu J Anyaneji ₂ , Dikeledi Kekana ₃ , Raquel Viana ₁₄ , Jennifer Giandhari ₂ , Richard J Lessells ₂ , Tongai Maponga ₁₅ , Dorcas Maruapula ₁₀ , Wonderful Choga ₁₀ , Mogomotsi Matshaba ₁₂ , Mpaphi B Mbulawa ₁₆ , Nokukhanya Msomi ₁₇ , , Yeshnee Naidoo ₁ , Sureshnee Pillay ₂ , Tomasz Janusz Sanko ₁ , James E San ₂ , Lesley Scott ₁₈ , Lavanya Singh ₂ , Nonkululeko A Magini ₂ , Pamela Smith-Lawrence ₁₉ , Wendy Stevens _{18,

20} , Graeme Dor ₂₀ , Derek Tshiabuila ₂ , Nicole Wolter _{3,

9} , Wolfgang Preiser ₁₅ , Florette K Treurnicht _{8,

9} , Marietjie Venter ₂₁ , Georginah Chiloane ₂₁ , Caitlyn McIntyre ₂₁ , Aine O'Toole ₂₂ , Christopher Ruis ₂₃ , Thomas P Peacock ₂₄ , Cornelius Roemer ₂₅ , Sergei L Kosakovsky Pond ₂₆ , Carolyn Williamson _{27,

28,

29,

30} , Oliver G Pybus ₃₁ , Jinal N Bhiman _{3,

7} , Allison Glass _{9,

14} , Darren P Martin _{29,

30} , Ben Jackson ₂₂ , Andrew Rambaut ₂₂ , Oluwakemi Laguda-Akingba _{32,

33} , Simani Gaseitsiwe _{10,

11} , Anne von Gottberg _{3,

9,

34} , Tulio de Oliveira _{1,

2,

35}

Affiliation

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.
National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
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.
South African Medical Research Council Antibody Immunity Research Unit, 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.
Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
Lancet Laboratories, Johannesburg, South Africa.
Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
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.
Department of Molecular Medicine and Haematology, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.
Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana.
National Priority Program of the National Health Laboratory Service, Johannesburg, 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.
NHLS Port Elizabeth Laboratory, Port Elizabeth, South Africa.
Faculty of Health Sciences, Walter Sisulu University, Eastern Cape, South Africa.
Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
Department of Global Health, University of Washington, Seattle, WA, USA.

Three lineages (BA.1, BA.2 and BA.3) of the SARS-CoV-2 Omicron variant of concern predominantly drove South Africa’s fourth 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 comparable to BA.2 except for the addition of 69-70del (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 only differ 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 estimate growth advantages for BA.4 and BA.5 of 0.08 (95% 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.

中文翻译：

SARS-CoV-2 Omicron 谱系 BA.4 和 BA.5 在南非的出现

受关注的 SARS-CoV-2 Omicron 变体的三个谱系（BA.1、BA.2 和 BA.3）主要推动了南非的第四次 COVID-19 浪潮。我们现在已经确定了导致第五波感染的两个新谱系 BA.4 和 BA.5。BA.4 和 BA.5 的刺突蛋白是相同的，并且与 BA.2 相当，除了添加了 69-70del（存在于 Alpha 变体和 BA.1 谱系中）、L452R（存在于 Delta 变体中） , F486V 和 Q493 上的野生型氨基酸。这两个谱系仅在尖峰区域之外有所不同。穗中的 69-70 缺失允许这些谱系通过 S 基因靶标失败的代理标记来识别，在不具备此特征的变体的背景下。BA.4 和 BA.5 已迅速取代 BA.2，到 2022 年 4 月的第一周达到南非超过 50% 的测序病例。使用多项逻辑回归模型，我们估计南部地区 BA.4 和 BA.5 每天的增长优势分别为 0.08（95% CI：0.08 - 0.09）和 0.10（95% CI：0.09 - 0.11）。非洲。对遗传多样性 Omicron 谱系的持续发现表明，诸如人类慢性感染和/或动物宿主等离散宿主可能有助于病毒的进一步进化和传播。

更新日期：2022-06-28

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