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 (Spain)

Recombination is an evolutionary strategy to quickly acquire new viral properties inherited from the parental lineages. The systematic survey of the SARS-CoV-2 genome sequences of the Andalusian genomic surveillance strategy (PRJEB44396) has allowed the detection of an unexpectedly high number of co-infections, which constitute the ideal scenario for the emergence of new recombinants. Also, novel SARS-CoV-2 delta-omicron and omicron-omicron recombinant variants with two break points have been detected. Our observations document how the epidemiological scenario seems to be evolving towards one in which co-infection and, consequently, recombination is becoming more pervasive. And, actually, 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