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Updated: Nov 11, 2025
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Live Imaging and Quantification of Viral Infection in K18 hACE2 Transgenic Mice Using Reporter-Expressing Recombinant SARS-CoV-2
Published on: November 5, 2021
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Recombinant SARS-CoV-2 genomes are currently circulating at low levels
David VanInsberghe1,2,3, Andrew S Neish1, Anice C Lowen3,4
1Department of Pathology, Emory University, Atlanta, GA, USA.
Biorxiv : the Preprint Server for Biology
|March 24, 2021
Summary
Viral recombination can create new SARS-CoV-2 genotypes. Researchers identified over 1100 potential recombinants, with some now widely transmitted and carrying concerning mutations.
Area of Science:
- Virology
- Genomics
- Epidemiology
Background:
- Betacoronaviruses are known to recombine, but evidence for SARS-CoV-2 recombination was limited.
- Understanding recombination is crucial for tracking viral evolution and public health.
- Novel genotypes can exhibit altered transmissibility and virulence.
Approach:
- Developed a lightweight method to detect SARS-CoV-2 recombinant genomes based on clade-defining mutations.
- Analyzed over 537,000 SARS-CoV-2 genomes.
- Utilized phylogenetic analysis and geographic co-circulation data to validate findings.
Key Points:
- Identified 1175 putative SARS-CoV-2 recombinants with markers from distinct clades.
- No evidence of recombination hotspots was found in the SARS-CoV-2 genome.
- At least two recombinant lineages are now widely transmitted, some carrying concerning mutations (e.g., D614G, N501Y, E484K, L452R).
- Estimated that at most 5% of circulating viruses in the USA and UK are recombinant.
Conclusions:
- Recombination is a feasible mechanism generating novel SARS-CoV-2 genotypes.
- Transmitted recombinants carry mutations associated with increased transmissibility and reduced vaccine efficacy.
- Continuous genomic surveillance is essential to monitor emerging recombinant SARS-CoV-2 strains.
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