Cited by 1,179SARS-CoV-2 and COVID-19 ResearchEvolution and Genetic DynamicsAnimal Virus Infections Studies

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The evolution of SARS-CoV-2

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Markov, Peter V., Ghafari, Mahan, Beer, Martin, Lythgoe, Katrina, Simmonds, Peter, Stilianakis, Nikolaos I., Katzourakis, Aris·2023·Nature Reviews Microbiology

DOI 10.1038/s41579-023-00878-2

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Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths and substantial morbidity worldwide. Intense scientific effort to understand the biology of SARS-CoV-2 has resulted in daunting numbers of genomic sequences. We witnessed evolutionary events that could mostly be inferred indirectly before, such as the emergence of variants with distinct phenotypes, for example transmissibility, severity and immune evasion. This Review explores the mechanisms that generate genetic variation in SARS-CoV-2, underlying the within-host and population-level processes that underpin these events. We examine the selective forces that likely drove the evolution of higher transmissibility and, in some cases, higher severity during the first year of the pandemic and the role of antigenic evolution during the second and third years, together with the implications of immune escape and reinfections, and the increasing evidence for and potential relevance of recombination. In order to understand how major lineages, such as variants of concern (VOCs), are generated, we contrast the evidence for the chronic infection model underlying the emergence of VOCs with the possibility of an animal reservoir playing a role in SARS-CoV-2 evolution, and conclude that the former is more likely. We evaluate uncertainties and outline scenarios for the possible future evolutionary trajectories of SARS-CoV-2.

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Authors: Markov, P. V., Ghafari, M., Beer, M., Lythgoe, K., Simmonds, P., Stilianakis, N. I., & Katzourakis, A.
Affiliations: University of London (GB)
University of Oxford (GB)
Friedrich-Loeffler-Institut (DE)
Friedrich-Alexander-Universität Erlangen-Nürnberg (DE)
Corresponding author: Markov, Peter V.
Katzourakis, Aris
ORCID: Markov, Peter V.
Ghafari, Mahan
Beer, Martin
Lythgoe, Katrina
Stilianakis, Nikolaos I.
Katzourakis, Aris
Venue: Nature Reviews Microbiology
Publisher: Springer Science and Business Media LLC
Published: 2023-04-05
Volume: 21
Issue: 6
Pages: 361-379
ISSN: 1740-1526 (ISSN-L)
1740-1534
DOI: 10.1038/s41579-023-00878-2
OpenAlex: W4362609000
Semantic Scholar: b6c3324e790174aac7a7b28fcfe0bc22f5461418
Cited by: 1,179
References: 225
Citations by year: 2026: 204 · 2025: 390 · 2024: 441 · 2023: 130
FWCI: 55.63
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.springernature.com/gp/researchers/text-and-data-mining (tdm)
www.springernature.com/gp/researchers/text-and-data-mining (vor)
Locations: Nature Reviews Microbiology (publishedVersion)
PubMed (publishedVersion)
LSHTM Research Online (London School of Hygiene and Tropical Medicine) (acceptedVersion)
OpenAgrar (submittedVersion)
Funders: Wellcome Trust (107652/Z/15/Z)
H2020 European Research Council (101001623)
Topics: Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
Keywords: SARS-CoV-2, viral evolution, genetic variation, variants of concern, antigenic evolution, immune evasion, reinfection, recombination, chronic infection, reservoir hosts, transmissibility, disease severity, COVID-19 pandemic, evolutionary trajectories
MeSH terms: COVID-19, SARS-CoV-2, Animals, Genomics, Immune Evasion, Pandemics

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