A survey of SARS-CoV-2 genome sequences from the UK has detected a number of variants that had been assigned to the B.1.1.7 lineage but which do not contain the full set of B.1.1.7 ‘lineage defining’ mutations. Examination of these sequences revealed that some genome sections carry mutations characteristic of B.1.1.7, whilst other sections carry mutations specific to another lineage. Long runs of mutations along the SARS-CoV-2 that match different lineages are strongly indicative of virus recombination*.
In four instances (recombinant groups A-D) the same mosaic genome structure is observed in multiple closely-related genomes sampled from different infected people (Figure S1). These sequences are therefore highly unlikely to be artefactual (see discussion below). Additionally, we detected a further four mosaic virus genomes, each represented by only one genome sequence (Figure S2). These are also likely to be recombinants, but with a lower level of confidence
* Recombination involves the exchange of genetic material between two related viruses during coinfection of a host cell.