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SARS-CoV-2 evolution in the Omicron era

Nature Microbiology volume 8, pages 1952–1959 (2023)Cite this article

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Abstract

Since SARS-CoV-2 BA.5 (Omicron) emerged and spread in 2022, Omicron lineages have markedly diversified. Here we review the evolutionary trajectories and processes that underpin the emergence of these lineages, and identify the most prevalent sublineages. We discuss the potential origins of second-generation BA.2 lineages. Simple and complex recombination, antigenic drift and convergent evolution have enabled SARS-CoV-2 to accumulate mutations that alter its antigenicity. We also discuss the potential evolutionary trajectories of SARS-CoV-2 in the future.

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Fig. 1: Phylogenetic relatedness and convergent evolution in contemporary (as of July 2023) Omicron descendent lineages.
Fig. 2: Relative growth rates and variant proportions as of 22 May 2023.
Fig. 3: Genome schematics of the contemporary recombinant lineages.

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Acknowledgements

We gratefully acknowledge all data contributors—the authors, their originating laboratories that were responsible for obtaining the specimens, and their submitting laboratories for generating the genetic sequences and metadata and sharing through the GISAID initiative56, on which this research is based. The growth competition analysis from https://github.com/MurrellGroup/lineages (ref. 57) was performed on all available GISAID sequences, downloaded as a package on 22 May 2023. We thank the Pango lineage designation committee and wider contributors for identifying and naming lineages; the teams behind Pangolin, Nextstrain, covSPECTRUM and UShER (particularly A. Hinrichs) for developing tools that are used to identify and survey lineages; and S. Fleishon for his valuable feedback and discussions. T.P.P. is funded by the MRC-funded G2P-UK National Virology Consortium (MR/W005611/1); O.G.P. and C. Ruis are supported by the Oxford Martin School; O.G.P. acknowledges assistance from S. Attwood, funded by the Horizon Europe Research and Innovation programme under grant agreement no. 871075 (ELIXIR-CONVERGE); and D.J.S., K.S. and B.M. were supported by funding from SciLifeLab’s Pandemic Laboratory Preparedness programme (VC-2022-0028 and VC-2021-0033) and from the Erling Persson Foundation (ID: 2021 0125).

Author information

Authors and Affiliations

  1. Biozentrum, University of Basel, Basel, Switzerland

    Cornelius Roemer

  2. Swiss Institute of Bioinformatics, Lausanne, Switzerland

    Cornelius Roemer

  3. Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden

    Daniel J. Sheward, Kenta Sato & Ben Murrell

  4. University of Cape Town, Rondebosch, South Africa

    Ryan Hisner

  5. Independent researcher, Como, Italy

    Federico Gueli

  6. Independent researcher, Yotsukaido City, Japan

    Hitoshi Sakaguchi

  7. Independent researcher, Madison, WI, USA

    Nicholas Frohberg

  8. Independent researcher, Haarlem, The Netherlands

    Josette Schoenmakers

  9. Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK

    Áine O’Toole & Andrew Rambaut

  10. Department of Biology, University of Oxford, Oxford, UK

    Oliver G. Pybus

  11. Department of Pathobiology and Population Science, Royal Veterinary College, London, UK

    Oliver G. Pybus

  12. Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK

    Christopher Ruis

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

    Christopher Ruis

  14. Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK

    Christopher Ruis

  15. Department of Infectious Disease, Imperial College London, London, UK

    Thomas P. Peacock

  16. The Pirbright Institute, Woking, UK

    Thomas P. Peacock

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  1. Cornelius Roemer
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Contributions

C. Roemer, D.J.S., R.H., F.G., H.S., N.F., J.S., B.M. and T.P.P. researched data. C. Roemer, D.J.S., R.H., F.G., H.S., N.F., J.S., A.O., A.R., O.G.P. and C. Ruis substantially contributed to discussion of content. K.S., B.M. and T.P.P. performed updated analyses. D.J.S. and T.P.P. wrote the first draft. All authors reviewed and edited the paper before submission.

Corresponding author

Correspondence to Thomas P. Peacock.

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Competing interests

A.O., A.R. and O.G.P. have undertaken consulting for AstraZeneca AB relating to the genetic diversity and classification of SARS-COV-2 lineages. D.J.S. also consults for AstraZeneca AB on matters related to monoclonal antibody therapeutics for COVID-19. At the time of final submission of this manuscript, F.G. was a contractor for Invivyd, a company that develops monoclonal antibodies to treat COVID-19. The other authors declare no competing interests.

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Roemer, C., Sheward, D.J., Hisner, R. et al. SARS-CoV-2 evolution in the Omicron era. Nat Microbiol 8, 1952–1959 (2023). https://doi.org/10.1038/s41564-023-01504-w

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