Abstract summary 

Recombination is an evolutionary process by which many pathogens generate diversity and acquire novel functions. Although a common occurrence during coronavirus replication, detection of recombination is only feasible when genetically distinct viruses contemporaneously infect the same host. Here, we identify an instance of SARS-CoV-2 superinfection, whereby an individual was infected with two distinct viral variants: Alpha (B.1.1.7) and Epsilon (B.1.429). This superinfection was first noted when an Alpha genome sequence failed to exhibit the classic S gene target failure behavior used to track this variant. Full genome sequencing from four independent extracts reveals that Alpha variant alleles comprise around 75% of the genomes, whereas the Epsilon variant alleles comprise around 20% of the sample. Further investigation reveals the presence of numerous recombinant haplotypes spanning the genome, specifically in the spike, nucleocapsid, and ORF 8 coding regions. These findings support the potential for recombination to reshape SARS-CoV-2 genetic diversity.

Authors & Co-authors:  Wertheim Joel O JO Wang Jade C JC Leelawong Mindy M Martin Darren P DP Havens Jennifer L JL Chowdhury Moinuddin A MA Pekar Jonathan E JE Amin Helly H Arroyo Anthony A Awandare Gordon A GA Chow Hoi Yan HY Gonzalez Edimarlyn E Luoma Elizabeth E Morang'a Collins M CM Nekrutenko Anton A Shank Stephen D SD Silver Stefan S Quashie Peter K PK Rakeman Jennifer L JL Ruiz Victoria V Torian Lucia V LV Vasylyeva Tetyana I TI Kosakovsky Pond Sergei L SL Hughes Scott S

Study Outcome 

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