Detection of recombination amongst SARS-CoV-2 strains

Cameron Hosking0, Daniel Reti0, Brendan Hosking0, Suzanne Scott0, Aidan Tay0, Denis Bauer0, Laurence Wilson0
(0) CSIRO

Find me on Tues Nov 24th, 1:40-3pm AEDT in Remo, table 37

Abstract
The emergence and spread of the SARS-CoV-2 virus has been accompanied by a significant increase in the genetic diversity of the virus, with multiple phylogenetic clusters emerging. Contributing to this diversity is the potential for recombination events to occur between distinct viral strains. When two strains coinfect the same host, they may exchange genetic information during replication, creating new strains with characteristics of both parents. While a recombination event between zoonotic coronavirus strains has been postulated as the origin of the current pandemic virus, so far there has been little research into whether recombination is occurring among the human-specific SARS-CoV-2 strains currently circulating. We sought to undertake a thorough analysis of all viral genomes currently available (>100,000 strains) to investigate whether the virus is undergoing active recombination.

Examining existing phylogenetic trees, we find that many strains are poorly explained by just one parent. To examine whether these can be better explained be recombination events we developed an algorithm to find possible recombination events. We first used phylogenetic analysis to calculate the average mutation frequency distribution of the virus. Using this we simulated both natural evolution of the virus as well as recombination, varying the frequency and extent of the events. Based on these simulated datasets, we developed and benchmarked an algorithm for detecting recombination between SARS-CoV-2 strains which we then applied to viral sequences downloaded from GISAID. Using this approach, we identified a number of recombination events amongst circulating strains, characterizing their distribution in terms of both time and geography. Based on our analysis, we believe that there is evidence SARS-CoV-2 is undergoing recombination and that this is contributing to the genetic diversity being observed.