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Pandemic-Scale Phylogenomics Reveals The SARS-CoV-2 Recombination Landscape – Nature.com

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Nature (2022)
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We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.
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 1–4. During the SARS-CoV-2 pandemic, genomic data generation has exceeded the capacities of existing analysis platforms, thereby crippling real-time analysis of viral evolution 5. Here, we use a novel phylogenomic method to search a nearly comprehensive SARS-CoV-2 phylogeny for recombinant lineages. In a 1.6M sample tree from May 2021, we identify 589 recombination events, which indicate that approximately 2.7% of sequenced SARS-CoV-2 genomes have detectable recombinant ancestry. Recombination breakpoints are inferred to occur disproportionately in the 3’ portion of the genome that contains the spike protein. Our results highlight the need for timely analyses of recombination for pinpointing the emergence of recombinant lineages with the potential to increase transmissibility or virulence of the virus. We anticipate that this approach will empower comprehensive real time tracking of viral recombination during the SARS-CoV-2 pandemic and beyond.
These authors contributed equally: Yatish Turakhia and Bryan Thornlow
Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
Yatish Turakhia, Bryan Thornlow, Jakob McBroome, Nicolas Ayala, David Haussler & Russell Corbett-Detig
Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
Yatish Turakhia, Bryan Thornlow, Angie Hinrichs, Jakob McBroome, Nicolas Ayala, David Haussler & Russell Corbett-Detig
Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA, USA
Yatish Turakhia & Cheng Ye
Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
Kyle Smith
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
Nicola De Maio
Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
David Haussler
Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
Robert Lanfear
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Correspondence to Yatish Turakhia or Russell Corbett-Detig.
This file contains Supplementary Text S1-S18 referenced in the main text; legends for Supplementary Tables 1–4 and Supplementary References.
This file contains acknowledgments recognizing originating laboratories responsible for obtaining the specimens, as well as the submitting laboratories where the genome data were generated and shared via GISAID.
This file contains acknowledgments recognizing originating and submitting laboratories for data from the China National Center for Bioinformation.
This file contains acknowledgments recognizing originating and submitting laboratories for data from the COVID-19 Genomics UK (COG-UK) Consortium.
This file contains acknowledgments recognizing originating and submitting laboratories for data from the National Center for Biotechnology Information database.
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Turakhia, Y., Thornlow, B., Hinrichs, A. et al. Pandemic-Scale Phylogenomics Reveals The SARS-CoV-2 Recombination Landscape. Nature (2022). https://doi.org/10.1038/s41586-022-05189-9
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DOI: https://doi.org/10.1038/s41586-022-05189-9
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