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

被引：460

作者：

Tegally, Houriiyah ^{[1
,2
]}

Moir, Monika ^{[1
]}

Everatt, Josie ^{[3
]}

Giovanetti, Marta ^{[4
,5
,6
]}

Scheepers, Cathrine ^{[3
,7
]}

Wilkinson, Eduan ^{[1
]}

Subramoney, Kathleen ^{[8
,9
]}

Makatini, Zinhle ^{[8
,9
]}

Moyo, Sikhulile ^{[10
,11
,12
]}

Amoako, Daniel G. ^{[3
]}

Baxter, Cheryl ^{[1
]}

Althaus, Christian L. ^{[13
]}

Anyaneji, Ugochukwu J. ^{[2
]}

Kekana, Dikeledi ^{[3
]}

Viana, Raquel ^{[14
]}

Giandhari, Jennifer ^{[2
]}

Lessells, Richard J. ^{[2
]}

Maponga, Tongai ^{[15
]}

Maruapula, Dorcas ^{[10
]}

Choga, Wonderful ^{[10
]}

Matshaba, Mogomotsi ^{[12
]}

Mbulawa, Mpaphi B. ^{[16
]}

Msomi, Nokukhanya ^{[17
]}

Naidoo, Yeshnee ^{[1
]}

Pillay, Sureshnee ^{[2
]}

Sanko, Tomasz Janusz ^{[1
]}

San, James E. ^{[2
]}

Scott, Lesley ^{[18
]}

Singh, Lavanya ^{[2
]}

Magini, Nonkululeko A. ^{[2
]}

Smith-Lawrence, Pamela ^{[19
]}

Stevens, Wendy ^{[18
,20
]}

Dor, Graeme ^{[20
]}

Tshiabuila, Derek ^{[2
]}

Wolter, Nicole ^{[3
,9
]}

Preiser, Wolfgang ^{[15
]}

Treurnicht, Florette K. ^{[8
,9
]}

Venter, Marietjie ^{[21
]}

Chiloane, Georginah ^{[21
]}

McIntyre, Caitlyn ^{[21
]}

O'Toole, Aine ^{[22
]}

Ruis, Christopher ^{[23
]}

Peacock, Thomas P. ^{[24
]}

Roemer, Cornelius ^{[25
]}

Kosakovsky Pond, Sergei L. ^{[26
]}

Williamson, Carolyn ^{[27
,28
,29
,30
]}

Pybus, Oliver G. ^{[31
]}

Bhiman, Jinal N. ^{[3
,7
]}

Glass, Allison ^{[9
,14
]}

Martin, Darren P. ^{[29
,30
]}

机构：

[1] Stellenbosch Univ, Ctr Epidem Response & Innovat CERI, Sch Data Sci & Computat Thinking, Stellenbosch, South Africa

[2] Univ KwaZulu, KwaZulu Natal Res Innovat & Sequencing Platform K, Nelson R Mandela Sch Med, Durban, South Africa

[3] Natl Hlth Lab Serv NHLS, Natl Inst Communicable Dis NICD, Johannesburg, South Africa

[4] Fundacao Oswaldo Cruz, Lab Flavivirus, Rio De Janeiro, Brazil

[5] Univ Campus Biomed Roma, Dept Sci & Technol Humans & Environm, Rome, Italy

[6] Univ Fed Minas Gerais, Lab Genet Celular Mol, Belo Horizonte, MG, Brazil

[7] Univ Witwatersrand, Fac Hlth Sci, Sch Pathol, South African Med Res Council Antibody Immun Res, Johannesburg, South Africa

[8] Charlotte Maxeke Johannesburg Acad Hosp, Dept Virol, Johannesburg, South Africa

[9] Univ Witwatersrand, Fac Hlth Sci, Sch Pathol, Johannesburg, South Africa

[10] Botswana Harvard AIDS Inst Partnership, Botswana Harvard HIV Reference Lab, Gaborone, Botswana

[11] Harvard TH Chan Sch Publ Hlth, Boston, MA USA

[12] Botswana Presidential COVID 19 Taskforce, Gaborone, Botswana

[13] Univ Bern, Inst Social & Prevent Med, Bern, Switzerland

[14] Lancet Labs, Johannesburg, South Africa

[15] Stellenbosch Univ, Fac Med & Hlth Sci, Div Med Virol, Cape Town, South Africa

[16] Minist Hlth & Wellness, Natl Hlth Lab, Hlth Serv Management, Gaborone, Botswana

[17] Univ KwaZulu, Discipline Virol, Sch Lab Med & Med Sci, Natl Hlth Lab Serv NHLS, Durban, South Africa

[18] Univ Witwatersrand, Fac Hlth Sci, Sch Pathol, Dept Mol Med & Haematol, Johannesburg, South Africa

[19] Minist Hlth & Wellness, Hlth Serv Management, Gaborone, Botswana

[20] Natl Prior Program Natl Hlth Lab Serv, Johannesburg, South Africa

[21] Univ Pretoria, Ctr Viral Zoonoses, Dept Med Virol, Zoonot Arbo & Resp Virus Program, Pretoria, South Africa

[22] Univ Edinburgh, Inst Evolutionary Biol, Edinburgh, Scotland

[23] Univ Cambridge, Dept Med, Cambridge, England

[24] Imperial Coll London, Dept Infect Dis, London, England

[25] Univ Basel, Biozentrum, Basel, Switzerland

[26] Temple Univ, Inst Gen & Evolutionary Med, Dept Biol, Philadelphia, PA USA

[27] Univ Cape Town, Fac Hlth Sci, Div Med Virol, Cape Town, South Africa

[28] NHLS Groote Schuur Lab, Div Virol, Cape Town, South Africa

[29] Wellcome Ctr Infect Dis Res Africa CIDRI, Cape Town, South Africa

[30] Univ Cape Town, Inst Infect Dis & Mol Med, Cape Town, South Africa

[31] Univ Oxford, Dept Zool, Oxford, England

[32] NHLS Port Elizabeth Lab, Port Elizabeth, South Africa

[33] Walter Sisulu Univ, Fac Hlth Sci, Eastern Cape, South Africa

[34] Univ Cape Town, Fac Hlth Sci, Dept Pathol, Div Med MicroBiol, Cape Town, South Africa

[35] Univ Washington, Dept Global Hlth, Seattle, WA 98195 USA

[36] Natl Hlth Lab Serv, Div Virol, Bloemfontein, South Africa

[37] Univ Free State, Div Virol, Bloemfontein, South Africa

[38] PathCare Vermaak, Pretoria, South Africa

[39] Univ Cape Town, Fac Hlth Sci, Div Computat Biol, Cape Town, South Africa

[40] NHLS Tygerberg Lab, Cape Town, South Africa

[41] Natl Hlth Lab Serv NHLS, Johannesburg, South Africa

[42] Ctr AIDS Programme Res South Africa CAPRISA, Durban, South Africa

[43] Univ Free State, Fac Hlth Sci, Div Virol, Next Generat Sequencing Unit, Bloemfontein, South Africa

[44] Univ Pretoria, Dept Med Virol, Pretoria, South Africa

来源：

NATURE MEDICINE | 2022年 / 28卷 / 09期

基金：

美国国家卫生研究院; 英国医学研究理事会;

关键词：

RECEPTOR-BINDING DOMAIN; MUTATIONS; IMMUNITY;

D O I：

10.1038/s41591-022-01911-2

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Genomic characterization of the SARS-CoV-2 Omicron lineages BA.4 and BA.5, responsible for the fifth COVID-19 pandemic wave in South Africa, shows continued viral diversification and provides insights into the potential mechanisms underlying the ability of the new lineages to outcompete their predecessors. 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.

引用

页码：1785 / +

页数：18

共 41 条

[1] Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021 [J].

Campbell, Finlay ;

Archer, Brett ;

Laurenson-Schafer, Henry ;

Jinnai, Yuka ;

Konings, Franck ;

Batra, Neale ;

Pavlin, Boris ;

Vandemaele, Katelijn ;

Van Kerkhove, Maria D. ;

Jombart, Thibaut ;

Morgan, Oliver ;

de Waroux, Olivier le Polain .

EUROSURVEILLANCE, 2021, 26 (24) :1-6

[2]

CDC, 2020, Centers for disease control and prevention, vaccines and immunization

[3]

Chen LL, 2022, NAT COMMUN, V13, DOI [10.1038/s41467-022-31395-0, 10.1038/s41467-022-33675-1]

[4]

cran.r-project, PACKAGE EMMEANS ESTI

[5] Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England [J].

Davies, Nicholas G. ;

Abbott, Sam ;

Barnard, Rosanna C. ;

Jarvis, Christopher, I ;

Kucharski, Adam J. ;

Munday, James D. ;

Pearson, Carl A. B. ;

Russell, Timothy W. ;

Tully, Damien C. ;

Washburne, Alex D. ;

Wenseleers, Tom ;

Gimma, Amy ;

Waites, William ;

Wong, Kerry L. M. ;

van Zandvoort, Kevin ;

Silverman, Justin D. ;

Diaz-Ordaz, Karla ;

Keogh, Ruth ;

Eggo, Rosalind M. ;

Funk, Sebastian ;

Jit, Mark ;

Atkins, Katherine E. ;

Edmunds, W. John .

SCIENCE, 2021, 372 (6538) :149-+

[6] SERAPHIM: studying environmental rasters and phylogenetically informed movements [J].

Dellicour, Simon ;

Rose, Rebecca ;

Faria, Nuno R. ;

Lemey, Philippe ;

Pybus, Oliver G. .

BIOINFORMATICS, 2016, 32 (20) :3204-3206

[7] Molecular epidemiology of the SARS-CoV-2 variant Omicron BA.2 sub-lineage in Denmark, 29 November 2021 to 2 January 2022 [J].

Fonager, Jannik ;

Bennedbaek, Marc ;

Bager, Peter ;

Wohlfahrt, Jan ;

Ellegaard, Kirsten Maren ;

Ingham, Anna Cacilia ;

Edslev, Sofie Marie ;

Stegger, Marc ;

Sieber, Raphael Niklaus ;

Lassauniere, Ria ;

Fomsgaard, Anders ;

Lillebaek, Troels ;

Svarrer, Christina Wiid ;

Moller, Frederik Trier ;

Moller, Camilla Holten ;

Legarth, Rebecca ;

Sydenham, Thomas Vognbjerg ;

Steinke, Kat ;

Paulsen, Sarah Juel ;

Castruita, Jose Alfredo Samaniego ;

Schneider, Uffe Vest ;

Schouw, Christian Hojte ;

Nielsen, Xiaohui Chen ;

Overvad, Maria ;

Nielsen, Rikke Thoft ;

Marvig, Rasmus L. ;

Pedersen, Martin Schou ;

Nielsen, Lene ;

Nilsson, Line Lynge ;

Bybjerg-Grauholm, Jonas ;

Tarpgaard, Irene Harder ;

Ebsen, Tine Snejbjerg ;

Lam, Janni Uyen Hoa ;

Gunalan, Vithiagaran ;

Rasmussen, Morten .

EUROSURVEILLANCE, 2022, 27 (10)

[8]

github, NEHERLAB NEXTALIGN

[9] An antibody-escape estimator for mutations to the SARS-CoV-2 receptor-binding domain [J].

Greaney, Allison J. ;

Starr, Tyler N. ;

Bloom, Jesse D. .

VIRUS EVOLUTION, 2022, 8 (01)

[10] Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies [J].

Greaney, Allison J. ;

Loes, Andrea N. ;

Crawford, Katharine H. D. ;

Starr, Tyler N. ;

Malone, Keara D. ;

Chu, Helen Y. ;

Bloom, Jesse D. .

CELL HOST & MICROBE, 2021, 29 (03) :463-+

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