PT  - JOURNAL ARTICLE
AU  - Yatish Turkahia
AU  - Bryan Thornlow
AU  - Angie Hinrichs
AU  - Jakob McBroome
AU  - Nicolas Ayala
AU  - Cheng Ye
AU  - Nicola De Maio
AU  - David Haussler
AU  - Robert Lanfear
AU  - Russell Corbett-Detig
TI  - Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region
AID  - 10.1101/2021.08.04.455157
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.08.04.455157
4099  - http://biorxiv.org/content/early/2021/08/05/2021.08.04.455157.short
4100  - http://biorxiv.org/content/early/2021/08/05/2021.08.04.455157.full
AB  - Accurate and timely detection of recombinant lineages is crucial for interpreting genetic variation, reconstructing epidemic spread, identifying selection and variants of interest, and accurately performing phylogenetic analyses. During the SARS-CoV-2 pandemic, genomic data generation has exceeded the capacities of existing analysis platforms, thereby crippling real-time analysis of viral recombination. Low SARS-CoV-2 mutation rates make detecting recombination difficult. Here, we develop and apply a novel phylogenomic method to exhaustively search a nearly comprehensive SARS-CoV-2 phylogeny for recombinant lineages. We investigate a 1.6M sample tree, and identify 606 recombination events. Approximately 2.7% of sequenced SARS-CoV-2 genomes have recombinant ancestry. Recombination breakpoints occur disproportionately in the Spike protein region. Our method empowers comprehensive real time tracking of viral recombination during the SARS-CoV-2 pandemic and beyond.Competing Interest StatementRL works as an advisor to GISAID. The remaining authors declare no competing interests.