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The systematic survey of the SARS-CoV-2 genome sequences of the Andalusian genomic surveillance strategy has allowed the detection of an unexpectedly high number of co-infections, which constitute the ideal scenario for the emergence of new recombinants. Whole genome sequence of SARS-CoV-2 has been carried out as part of the genomic surveillance programme. Sample sources included the main hospitals in the Andalusia region. In addition to the increase of co-infections and known recombinants, three novel SARS-CoV-2 delta-omicron and omicron-omicron recombinant variants with two break points have been detected. Our observations document an epidemiological scenario in which co-infection and recombination are detected more frequently. Finally, we describe a family case in which co-infection is followed by the detection of a recombinant made from the two co-infecting variants. This increased number of recombinants raises the risk of emergence of recombinant variants with increased transmissibility and pathogenicity.<\/jats:p>","DOI":"10.3390\/ijms24032419","type":"journal-article","created":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T01:58:59Z","timestamp":1674784739000},"page":"2419","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Detection of High Level of Co-Infection and the Emergence of Novel SARS CoV-2 Delta-Omicron and Omicron-Omicron Recombinants in the Epidemiological Surveillance of Andalusia"],"prefix":"10.3390","volume":"24","author":[{"given":"Javier","family":"Perez-Florido","sequence":"first","affiliation":[{"name":"Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain"},{"name":"Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Roc\u00edo\/CSIC\/University of Sevilla, 41013 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