{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T20:48:56Z","timestamp":1791492536083,"version":"4.3.4"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,6,15]],"date-time":"2021-06-15T00:00:00Z","timestamp":1623715200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIAID Centers of Excellence for Influenza Research and Surveillance","award":["HHSN272201400004C"],"award-info":[{"award-number":["HHSN272201400004C"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Viral recombination can generate novel genotypes with unique phenotypic characteristics, including transmissibility and virulence. Although the capacity for recombination among betacoronaviruses is well documented, recombination between strains of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has not been characterized in detail. Here, we present a lightweight approach for detecting genomes that are potentially recombinant. This approach relies on identifying the mutations that primarily determine SARS-CoV-2 clade structure and then screening genomes for ones that contain multiple mutational markers from distinct clades. Among the over 537,000 genomes queried that were deposited on GISAID.org prior to 16 February 2021, we detected 1,175 potential recombinant sequences. Using a highly conservative criteria to exclude sequences that may have originated through de novo mutation, we find that at least 30\u2009per cent (n\u2009=\u2009358) are likely of recombinant origin. An analysis of deep-sequencing data for these putative recombinants, where available, indicated that the majority are high quality. Additional phylogenetic analysis and the observed co-circulation of predicted parent clades in the geographic regions of exposure further support the feasibility of recombination in this subset of potential recombinants. An analysis of these genomes did not reveal evidence for recombination hotspots in the SARS-CoV-2 genome. While most of the putative recombinant sequences we detected were genetic singletons, a small number of genetically identical or highly similar recombinant sequences were identified in the same geographic region, indicative of locally circulating lineages. Recombinant genomes were also found to have originated from parental lineages with substitutions of concern, including D614G, N501Y, E484K, and L452R. Adjusting for an unequal probability of detecting recombinants derived from different parent clades and for geographic variation in clade abundance, we estimate that at most 0.2\u20132.5\u2009per cent of circulating viruses in the USA and UK are recombinant. Our identification of a small number of putative recombinants within the first year of SARS-CoV-2 circulation underscores the need to sustain efforts to monitor the emergence of new genotypes generated through recombination.<\/jats:p>","DOI":"10.1093\/ve\/veab059","type":"journal-article","created":{"date-parts":[[2021,6,15]],"date-time":"2021-06-15T07:09:36Z","timestamp":1623740976000},"source":"Crossref","is-referenced-by-count":60,"title":["Recombinant SARS-CoV-2 genomes circulated at low levels over the first year of the pandemic"],"prefix":"10.1093","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1933-8103","authenticated-orcid":false,"given":"David","family":"VanInsberghe","sequence":"first","affiliation":[{"name":"Department of Biology, Emory University , Atlanta, 1510 Clifton Rd, Atlanta, GA, 30322 USA"},{"name":"Department of Microbiology and Immunology, Emory University School of Medicine , 100 Woodruff Circle, Atlanta, GA, 30322 USA"},{"name":"Department of Pathology, Emory University School of Medicine , 1364 Clifton Rd, Atlanta, GA, 30322 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew S","family":"Neish","sequence":"additional","affiliation":[{"name":"Department of Pathology, Emory University School of Medicine , 1364 Clifton Rd, Atlanta, GA, 30322 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anice C","family":"Lowen","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Emory University School of Medicine , 100 Woodruff Circle, Atlanta, GA, 30322 USA"},{"name":"Emory-UGA Center of Excellence for Influenza Research and Surveillance (CEIRS) , Atlanta, GA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0254-6141","authenticated-orcid":false,"given":"Katia","family":"Koelle","sequence":"additional","affiliation":[{"name":"Department of Biology, Emory University , Atlanta, 1510 Clifton Rd, Atlanta, GA, 30322 USA"},{"name":"Emory-UGA Center of Excellence for Influenza Research and Surveillance (CEIRS) , Atlanta, GA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,7,15]]},"reference":[{"key":"2023042112013823700_R1","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic Local Alignment Search Tool","volume":"215","author":"Altschul","year":"1990","journal-title":"Journal of Molecular Biology"},{"key":"2023042112013823700_R2","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1016\/0042-6822(91)90795-D","article-title":"Random Nature of Coronavirus RNA Recombination in the Absence of Selection Pressure","volume":"185","author":"Banner","year":"1991","journal-title":"Virology"},{"key":"2023042112013823700_R3","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1002\/gch2.1018","article-title":"Data, Disease and Diplomacy: GISAID\u2019s Innovative Contribution to Global Health","volume":"1","author":"Elbe","year":"2017","journal-title":"Global Challenges"},{"key":"2023042112013823700_R4","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2020.25.17.2000257","article-title":"Estimating the Generation Interval for Coronavirus Disease (COVID-19) Based on Symptom Onset Data, March 2020","volume":"25","author":"Ganyani","year":"2020","journal-title":"Eurosurveillance"},{"key":"2023042112013823700_R5","article-title":"Clade and Lineage Nomenclature Aids in Genomic Epidemiology Studies of Active hCoV-19 Viruses","author":"Global Initiative on Sharing All Influenza Data (GISAID)","year":"2021"},{"key":"2023042112013823700_R6","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1009226","article-title":"The Coronavirus Proofreading Exoribonuclease Mediates Extensive Viral Recombination","volume":"17","author":"Gribble","year":"2021","journal-title":"PLOS Pathogens"},{"key":"2023042112013823700_R7","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0","volume":"59","author":"Guindon","year":"2010","journal-title":"Systematic Biology"},{"key":"2023042112013823700_R8","doi-asserted-by":"publisher","first-page":"4121","DOI":"10.1093\/bioinformatics\/bty407","article-title":"Nextstrain: Real-time Tracking of Pathogen Evolution (J. 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