Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2022 Jun 7;14(6):1239.
doi: 10.3390/v14061239.

Recombination in Coronaviruses, with a Focus on SARS-CoV-2

Daniele Focosi  1 , Fabrizio Maggi  2
Affiliations
Review

Recombination in Coronaviruses, with a Focus on SARS-CoV-2

Daniele Focosi et al. Viruses. .

Abstract

Recombination is a common evolutionary tool for RNA viruses, and coronaviruses are no exception. We review here the evidence for recombination in SARS-CoV-2 and reconcile nomenclature for recombinants, discuss their origin and fitness, and speculate how recombinants could make a difference in the future of the COVID-19 pandemics.

Keywords: COVID-19; Coronaviridae; PANGOLIN; SARS-CoV-2; coinfection; recombination; superinfection.

PubMed Disclaimer

Conflict of interest statement

We declare we have no conflict of interest to disclose.

Figures

Figure 1
Figure 1
Summary of selected recombinant SARS-CoV-2 lineages of interest between VOC Delta and Omicron (upper panel) and within Omicron VOC sublineages (lower panel). Unlabeled private mutations are marked with *.
Figure 2
Figure 2
Basic reproductive number (R0) and estimated herd immunity threshold for SARS-CoV-2 variants of concern and the XE recombinant compared to other human pathogens. Please note herd immunity cannot be currently achieved with the current generation of systemically delivered vaccines [92].
See this image and copyright information in PMC

References

    1. Lai M.M. Genetic recombination in RNA viruses. Curr. Top. Microbiol. Immunol. 1992;176:21–32. doi: 10.1007/978-3-642-77011-1_2. - DOI - PubMed
    1. Bonnet J., Fraile A., Sacristán S., Malpica J.M., García-Arenal F. Role of recombination in the evolution of natural populations of Cucumber mosaic virus, a tripartite RNA plant virus. Virology. 2005;332:359–368. doi: 10.1016/j.virol.2004.11.017. - DOI - PubMed
    1. Varsani A., Lefeuvre P., Roumagnac P., Martin D. Notes on recombination and reassortment in multipartite/segmented viruses. Curr. Opin. Virol. 2018;33:156–166. doi: 10.1016/j.coviro.2018.08.013. - DOI - PubMed
    1. González-Candelas F., López-Labrador F.X., Bracho M.A. Recombination in hepatitis C virus. Viruses. 2011;3:2006–2024. doi: 10.3390/v3102006. - DOI - PMC - PubMed
    1. Yebra G., Frampton D., Gallo Cassarino T., Raffle J., Hubb J., Ferns R.B., Waters L., Tong C.Y.W., Kozlakidis Z., Hayward A., et al. A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project. PLoS ONE. 2018;13:e0192081. doi: 10.1371/journal.pone.0192081. - DOI - PMC - PubMed