Abstract
SummaryWe 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.
Highlights
Recombination, the transfer of genetic information between molecules derived from different organisms, is a fundamental process in evolution, because it can generate novel genetic variation upon which selection can act (Felsenstein, 1974)
The zoonotic transmission of an alphacoronavirus whose spike gene shows evidence of being the product of recombination between feline and canine coronaviruses has occurred in Malaysia, which demonstrates the potential for coronavirus recombination associated with host reservoirs (Vlasova et al, 2021)
Identification of putative recombinants We identified a total of 16 recombinant sequences from the whole United Kingdom (UK) dataset of 279,000 sequences up to March 7, 2021 using our bioinformatic and evolutionary analysis pipeline
Summary
Recombination, the transfer of genetic information between molecules derived from different organisms, is a fundamental process in evolution, because it can generate novel genetic variation upon which selection can act (Felsenstein, 1974). Recombination has the potential to be important in the context of pathogen evolution, because it can ‘‘rescue’’ genomes with otherwise deleterious mutations or provide the opportunity to create novel phenotypes by bringing genetic variation from different backgrounds onto a single genome. A concerning scenario from an epidemiological perspective is the potential for recombination to combine, in the same genome, mutations that may confer immune-escape properties with those that may enhance transmissibility. Enhanced transmissibility (Volz et al, 2021) and immune-escape (Planas et al, 2021) phenotypes have already been observed in SARS-CoV-2. The characterization of recombination in SARS-CoV-2 is important for surveillance purposes
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