We present evidence for multiple independent origins of recombinant SARS-CoV-2 viruses sampled from late 2020 and early 2021 in the United Kingdom. Their genomes carry single-nucleotide polymorphisms and deletions that are characteristic of the B.1.1.7 variant of concern but lack the full complement of lineage-defining mutations. Instead, the remainder of their genomes share contiguous genetic variation with non-B.1.1.7 viruses circulating in the same geographic area at the same time as the recombinants. In four instances, there was evidence for onward transmission of a recombinant-origin virus, including one transmission cluster of 45 sequenced cases over the course of 2 months. The inferred genomic locations of recombination breakpoints suggest that every community-transmitted recombinant virus inherited its spike region from a B.1.1.7 parental virus, consistent with a transmission advantage for B.1.1.7's set of mutations.

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Jackson, B., Boni, M., Bull, M., Colleran, A., Colquhoun, R., Darby, A., Haldenby, S., Hill, V., Lucaci, A., McCrone, J., Nicholls, S., O'Toole, Á., Pacchiarini, N., Poplawski, R., Scher, E., Todd, F., Webster, H., Whitehead, M., Wierzbicki, C., The COVID-19 Genomics UK (COG-UK) Consortium, Loman, N., Connor, T., Robertson, D., Pybus, O. & Rambaut, A. 2021, 'Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic', Cell, 184(20), pp. 5179-5188.e8. https://doi.org/10.1016/j.cell.2021.08.014

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Last updated: 16 June 2022
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