SARS-CoV-2 evolution in the Omicron era

Cornelius Roemer; Daniel J Sheward; Ryan Hisner; Federico Gueli; Hitoshi Sakaguchi; Nicholas Frohberg; Josette Schoenmakers; Kenta Sato; Áine O'Toole; Andrew Rambaut; Oliver G Pybus; Christopher Ruis; Ben Murrell; Thomas P Peacock

doi:10.1038/s41564-023-01504-w

SARS-CoV-2 evolution in the Omicron era

Nat Microbiol. 2023 Nov;8(11):1952-1959. doi: 10.1038/s41564-023-01504-w. Epub 2023 Oct 16.

Authors

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. [email protected].
¹⁶ The Pirbright Institute, Woking, UK. [email protected].

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.

SARS-CoV-2 evolution in the Omicron era

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