An early warning system for emerging SARS-CoV-2 variants

Lorenzo Subissi¹, Anne von Gottberg^{2

3}, Lipi Thukral⁴, Nathalie Worp^{5

6}, Bas B Oude Munnink^{5

6}, Surabhi Rathore⁴, Laith J Abu-Raddad⁷, Ximena Aguilera⁸, Erik Alm⁹, Brett N Archer¹, Homa Attar Cohen¹, Amal Barakat¹⁰, Wendy S Barclay¹¹, Jinal N Bhiman^{2

3}, Leon Caly¹², Meera Chand¹³, Mark Chen¹⁴, Ann Cullinane¹⁵, Tulio de Oliveira¹⁶, Christian Drosten¹⁷, Julian Druce⁸, Paul Effler¹⁸, Ihab El Masry¹⁹, Adama Faye²⁰, Simani Gaseitsiwe^{21

22}, Elodie Ghedin²³, Rebecca Grant¹, Bart L Haagmans^{5

6}, Belinda L Herring²⁴, Shilpa S Iyer²⁵, Zyleen Kassamali¹, Manish Kakkar²⁶, Rebecca J Kondor²⁷, Juliana A Leite²⁸, Yee-Sin Leo¹⁴, Gabriel M Leung²⁹, Marco Marklewitz³⁰, Sikhulile Moyo^{21

22}, Jairo Mendez-Rico²⁸, Nada M Melhem³¹, Vincent Munster³², Karen Nahapetyan³⁰, Djin-Ye Oh³³, Boris I Pavlin¹, Thomas P Peacock^{11

13}, Malik Peiris²⁹, Zhibin Peng³⁴, Leo L M Poon²⁹, Andrew Rambaut³⁵, Jilian Sacks¹, Yinzhong Shen³⁶, Marilda M Siqueira³⁷, Sofonias K Tessema³⁸, Erik M Volz¹¹, Volker Thiel^{39

40}, Sylvie van der Werf⁴¹, Sylvie Briand¹, Mark D Perkins¹, Maria D Van Kerkhove⁴², Marion P G Koopmans^{5

6}, Anurag Agrawal⁴³

Affiliations

¹ World Health Organization, Geneva, Switzerland.
² National Institute for Communicable Diseases, Johannesburg, South Africa.
³ School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
⁴ CSIR Institute of Genomics and Integrative Biology, Delhi, India.
⁵ Erasmus Medical Centre, Rotterdam, the Netherlands.
⁶ Pandemic and Disaster Preparedness Research Centre, Rotterdam/Delft, the Netherlands.
⁷ Weill Cornell Medicine - Qatar of Cornell University, Doha, Qatar.
⁸ Epidemiology and Health Policy Centre, Universidad del Desarollo, Santiago, Chile.
⁹ European Centre for Disease Prevention and Control, Stockholm, Sweden.
¹⁰ World Health Organization Regional Office for the Eastern Mediterranean, Cairo, Egypt.
¹¹ Imperial College London, London, UK.
¹² Victorian Infectious Diseases Reference Laboratory, Melbourne, Victoria, Australia.
¹³ UK Health Security Agency, London, UK.
¹⁴ National Centre for Infectious Diseases, Singapore, Singapore.
¹⁵ World Organisation for Animal Health, Paris, France.
¹⁶ Centre for Epidemic Response and Innovation, Stellenbosch University, Stellenbosch, South Africa.
¹⁷ Charité Medical Center, Berlin, Germany.
¹⁸ University of Western Australia, Perth, Western Australia, Australia.
¹⁹ Food and Agriculture Organization, Rome, Italy.
²⁰ Institut de Santé et Développement, Université Cheikh Anta Diop, Dakar, Senegal.
²¹ Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.
²² Harvard T.H Chan School of Public Health, Department of Immunology & Infectious Diseases, Boston, MA, USA.
²³ National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
²⁴ World Health Organization Regional Office for Africa, Brazzaville, Republic of Congo.
²⁵ World Health Organization Regional Office for Western Pacific, Manila, The Philippines.
²⁶ World Health Organization Regional Office for South-East Asia, New Delhi, India.
²⁷ United States Centers for Disease Control and Prevention, Atlanta, GA, USA.
²⁸ World Health Organization Regional Office for the Americas, Washington, DC, USA.
²⁹ School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, The People's Republic of China.
³⁰ World Health Organization Regional Office for Europe, Copenhagen, Denmark.
³¹ American University of Beirut, Beirut, Lebanon.
³² National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT, USA.
³³ Robert Koch Institute, Berlin, Germany.
³⁴ Chinese Center for Disease Control and Prevention, Beijing, The People's Republic of China.
³⁵ University of Edinburgh, Edinburgh, UK.
³⁶ Shanghai Public Health Clinical Center, Fudan University, Shanghai, The People's Republic of China.
³⁷ Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil.
³⁸ Africa Centers for Disease Control and Prevention, Addis Ababa, Ethiopia.
³⁹ Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
⁴⁰ Institute of Virology and Immunology, Mittelhäusern and Bern, Switzerland.
⁴¹ Institut Pasteur, Université Paris Cité, Paris, France.
⁴² World Health Organization, Geneva, Switzerland. vankerkhovem@who.int.
⁴³ Trivedi School of Biosciences, Ashoka University, Sonipat, India.

PMID: 35637337
PMCID: PMC11346314
DOI: 10.1038/s41591-022-01836-w

An early warning system for emerging SARS-CoV-2 variants

Lorenzo Subissi et al. Nat Med. 2022 Jun.

. 2022 Jun;28(6):1110-1115.

doi: 10.1038/s41591-022-01836-w.

Authors

Affiliations

¹ World Health Organization, Geneva, Switzerland.
² National Institute for Communicable Diseases, Johannesburg, South Africa.
³ School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
⁴ CSIR Institute of Genomics and Integrative Biology, Delhi, India.
⁵ Erasmus Medical Centre, Rotterdam, the Netherlands.
⁶ Pandemic and Disaster Preparedness Research Centre, Rotterdam/Delft, the Netherlands.
⁷ Weill Cornell Medicine - Qatar of Cornell University, Doha, Qatar.
⁸ Epidemiology and Health Policy Centre, Universidad del Desarollo, Santiago, Chile.
⁹ European Centre for Disease Prevention and Control, Stockholm, Sweden.
¹⁰ World Health Organization Regional Office for the Eastern Mediterranean, Cairo, Egypt.
¹¹ Imperial College London, London, UK.
¹² Victorian Infectious Diseases Reference Laboratory, Melbourne, Victoria, Australia.
¹³ UK Health Security Agency, London, UK.
¹⁴ National Centre for Infectious Diseases, Singapore, Singapore.
¹⁵ World Organisation for Animal Health, Paris, France.
¹⁶ Centre for Epidemic Response and Innovation, Stellenbosch University, Stellenbosch, South Africa.
¹⁷ Charité Medical Center, Berlin, Germany.
¹⁸ University of Western Australia, Perth, Western Australia, Australia.
¹⁹ Food and Agriculture Organization, Rome, Italy.
²⁰ Institut de Santé et Développement, Université Cheikh Anta Diop, Dakar, Senegal.
²¹ Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.
²² Harvard T.H Chan School of Public Health, Department of Immunology & Infectious Diseases, Boston, MA, USA.
²³ National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
²⁴ World Health Organization Regional Office for Africa, Brazzaville, Republic of Congo.
²⁵ World Health Organization Regional Office for Western Pacific, Manila, The Philippines.
²⁶ World Health Organization Regional Office for South-East Asia, New Delhi, India.
²⁷ United States Centers for Disease Control and Prevention, Atlanta, GA, USA.
²⁸ World Health Organization Regional Office for the Americas, Washington, DC, USA.
²⁹ School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, The People's Republic of China.
³⁰ World Health Organization Regional Office for Europe, Copenhagen, Denmark.
³¹ American University of Beirut, Beirut, Lebanon.
³² National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT, USA.
³³ Robert Koch Institute, Berlin, Germany.
³⁴ Chinese Center for Disease Control and Prevention, Beijing, The People's Republic of China.
³⁵ University of Edinburgh, Edinburgh, UK.
³⁶ Shanghai Public Health Clinical Center, Fudan University, Shanghai, The People's Republic of China.
³⁷ Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil.
³⁸ Africa Centers for Disease Control and Prevention, Addis Ababa, Ethiopia.
³⁹ Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
⁴⁰ Institute of Virology and Immunology, Mittelhäusern and Bern, Switzerland.
⁴¹ Institut Pasteur, Université Paris Cité, Paris, France.
⁴² World Health Organization, Geneva, Switzerland. vankerkhovem@who.int.
⁴³ Trivedi School of Biosciences, Ashoka University, Sonipat, India.

PMID: 35637337
PMCID: PMC11346314
DOI: 10.1038/s41591-022-01836-w

Abstract

Global sequencing and surveillance capacity for SARS-CoV-2 must be strengthened and combined with multidisciplinary studies of infectivity, virulence, and immune escape, in order to track the unpredictable evolution of the ongoing COVID-19 pandemic.

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Conflict of interest statement

Competing interests

No financial and non-financial competing interests declared

Figures

**Figure 1.. Overview of VOCs and spike amino acid substitutions.**
The spike structure of the index virus is shown, together with key domains, including N-terminal domain (NTD), Receptor Binding Domain (RBD), the S1/S2 junction (including the polybasic cleavage site), and the heptapeptide repeat domains (HR1, HR2) highlighted in different colours. The five VOCs and the characterising amino acids are marked with blue lines, both on the spike protein schematic and protein structure. VOCs are plotted chronologically according to date of identification.

**Figure 2.. Schematic of spike amino acid substitutions with known impact.**
The circular plot shows key amino acid substitutions and their associated lineage, and presence in N-terminal domain, RBD, and S1/S2 polybasic cleavage site. The red are marked to emphasize mutations involved in immune evasion. The complete list of mutations is shown in Table 1.

See this image and copyright information in PMC

References

1. World Health Organization. Terms of Reference for the Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE).
1. World Health Organization. Tracking SARS-CoV-2 variants. https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/.
1. World Health Organization Best Practices for the Naming of New Human Infectious Diseases. https://apps.who.int/iris/bitstream/handle/10665/163636/WHO_HSE_FOS_15.1....
1. Konings F et al. Nat Microbiol 6, 821–823 (2021). - PubMed
1. World Health Organization. Weekly Epidemiological Updates. https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situatio....

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An early warning system for emerging SARS-CoV-2 variants

Affiliations

An early warning system for emerging SARS-CoV-2 variants

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

MeSH terms

Supplementary concepts

Grants and funding

LinkOut - more resources

Full Text Sources

Medical

Miscellaneous