SARS-CoV-2 evolution in the Omicron era

Cornelius Roemer^{1

2}, Daniel J Sheward³, Ryan Hisner⁴, Federico Gueli⁵, Hitoshi Sakaguchi⁶, Nicholas Frohberg⁷, Josette Schoenmakers⁸, Kenta Sato³, Áine O'Toole⁹, Andrew Rambaut⁹, Oliver G Pybus^{10

11}, Christopher Ruis^{12

13

14}, Ben Murrell³, Thomas P Peacock^{15

16}

Affiliations

¹ Biozentrum, University of Basel, Basel, Switzerland.
² Swiss Institute of Bioinformatics, Lausanne, Switzerland.
³ Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
⁴ University of Cape Town, Rondebosch, South Africa.
⁵ Independent researcher, Como, Italy.
⁶ Independent researcher, Yotsukaido City, Japan.
⁷ Independent researcher, Madison, WI, USA.
⁸ Independent researcher, Haarlem, The Netherlands.
⁹ Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.
¹⁰ Department of Biology, University of Oxford, Oxford, UK.
¹¹ Department of Pathobiology and Population Science, Royal Veterinary College, London, UK.
¹² Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK.
¹³ Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
¹⁴ Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK.
¹⁵ Department of Infectious Disease, Imperial College London, London, UK. tpp09@ic.ac.uk.
¹⁶ The Pirbright Institute, Woking, UK. tpp09@ic.ac.uk.

PMID: 37845314
DOI: 10.1038/s41564-023-01504-w

Review

SARS-CoV-2 evolution in the Omicron era

Cornelius Roemer et al. Nat Microbiol. 2023 Nov.

. 2023 Nov;8(11):1952-1959.

doi: 10.1038/s41564-023-01504-w. Epub 2023 Oct 16.

Authors

Affiliations

¹ Biozentrum, University of Basel, Basel, Switzerland.
² Swiss Institute of Bioinformatics, Lausanne, Switzerland.
³ Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
⁴ University of Cape Town, Rondebosch, South Africa.
⁵ Independent researcher, Como, Italy.
⁶ Independent researcher, Yotsukaido City, Japan.
⁷ Independent researcher, Madison, WI, USA.
⁸ Independent researcher, Haarlem, The Netherlands.
⁹ Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.
¹⁰ Department of Biology, University of Oxford, Oxford, UK.
¹¹ Department of Pathobiology and Population Science, Royal Veterinary College, London, UK.
¹² Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK.
¹³ Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
¹⁴ Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK.
¹⁵ Department of Infectious Disease, Imperial College London, London, UK. tpp09@ic.ac.uk.
¹⁶ The Pirbright Institute, Woking, UK. tpp09@ic.ac.uk.

PMID: 37845314
DOI: 10.1038/s41564-023-01504-w

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.

PubMed Disclaimer

References

1. Carabelli, A. M. et al. SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nat. Rev. Microbiol. 21, 162–177 (2023). - PubMed - PMC
1. Harvey, W. T. et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat. Rev. Microbiol. 19, 409–424 (2021). - PubMed - PMC - DOI
1. Markov, P. V. et al. The evolution of SARS-CoV-2. Nat. Rev. Microbiol. 21, 361–379 (2023). - PubMed - DOI
1. Schmidt, F. et al. High genetic barrier to SARS-CoV-2 polyclonal neutralizing antibody escape. Nature 600, 512–516 (2021). - PubMed - PMC - DOI
1. Greaney, A. J. et al. Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies. Cell Host Microbe 29, 463–476 (2021). - PubMed - PMC - DOI

Publication types

Actions

MeSH terms

Actions
Actions
Actions
Actions

Grants and funding

LinkOut - more resources

Full Text Sources
- Nature Publishing Group
Medical
- MedlinePlus Health Information
Miscellaneous
- NCI CPTAC Assay Portal

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

SARS-CoV-2 evolution in the Omicron era

Affiliations

SARS-CoV-2 evolution in the Omicron era

Authors

Affiliations

Abstract

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Medical

Miscellaneous