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Abstract
The SARS-CoV-2 pandemic prompts evaluation of recombination in human coronavirus (hCoV) evolution. We undertook recombination analyses of 158,118 public seasonal hCoV, SARS-CoV-1, SARS-CoV-2 and MERS-CoV genome sequences using the RDP4 software. We found moderate evidence for 8 SARS-CoV-2 recombination events, two of which involved the spike gene, and low evidence for one SARS-CoV-1 recombination event. Within MERS-CoV, 229E, OC43, NL63 and HKU1 datasets, we noted 7, 1, 9, 14, and 1 high-confidence recombination events, respectively. There was propensity for recombination breakpoints in the non-ORF1 region of the genome containing structural genes, and recombination severely skewed the temporal structure of these data, especially for NL63 and OC43. Bayesian time-scaled analyses on recombinant-free data indicated the sampled diversity of seasonal CoVs emerged in the last 70 years, with 229E displaying continuous lineage replacements. These findings emphasize the importance of genomic based surveillance to detect recombination in SARS-CoV-2, particularly if recombination may lead to immune evasion.
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1 Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, USA (GRID:grid.507680.c) (ISNI:0000 0001 2230 3166); Uniformed Services University of the Health Sciences, Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Bethesda, USA (GRID:grid.265436.0) (ISNI:0000 0001 0421 5525); Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, USA (GRID:grid.201075.1) (ISNI:0000 0004 0614 9826)
2 Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, USA (GRID:grid.507680.c) (ISNI:0000 0001 2230 3166)
3 Walter Reed Army Institute of Research, Emerging Infectious Diseases Branch, Silver Spring, USA (GRID:grid.507680.c) (ISNI:0000 0001 2230 3166)