COVID-19 genomic recombination is uncommon but disproportionately occurs in spike protein region, study shows

An analysis of millions of SARS-CoV-2 genomes finds that recombination of the virus is uncommon, but when it occurs, it is most often in the spike protein region, the area which allows the virus to attach to and infect host cells.

The study, led by scientists at UC Santa Cruz, was published August 11 in the journal Nature. It details a new software created by the researchers to search the COVID-19 phylogenetic tree, a diagram of the virus’s evolutionary history, for instances of recombination. This software is open source, allowing public health officials to use it to track instances of recombination within their communities.

Recombination occurs when two genetically distinct forms of the virus hybridize. This study focused on detectable recombination, when the hybridization results in a sequence that is genetically new, and not on instances where two sequences combine to form a sequence identical to an already existing one.

“It’s really important for reconstructing the virus’s evolutionary history,” said Russell Corbett-Detig, senior author on the study and an associate professor of biomolecular engineering at the Baskin School of Engineering. “When there’s recombination it’s not one tree, it’s many trees, and being able to trace that accurately is really crucial for understanding evolution of the virus.”

Findings on recombination

The researchers analyzed 1.6 million samples of COVID-19 and found 589 recombination events, which indicates that only about 2.7% of sequenced genomes result from recombination. These sequences were sourced from the UC Santa Cruz SARS-CoV-2 Browser, a repository for COVID-19 genomic data, which is now the largest collection of genomic sequences of a single species ever assembled, currently at nearly 12 million sequences.

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