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Capturing intrahost recombination of SARS-CoV-2 during superinfection with Alpha and Epsilon variants in New York City

Wertheim, Joel O.
; 
Wang, Jade C.
; 
Leelawong, Mindy
; 
Martin, Darren P.
; 
Havens, Jennifer L.
; 
Chowdhury, Moinuddin A.
; 
Pekar, Jonathan
; 
Amin, Helly
; 
Arroyo, Anthony
; 
Awandare, Gordon A.
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Pre-print
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2022-01-21
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Biology
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http://hdl.handle.net/20.500.12613/7567
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COVID-19 Research
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ShankPond-Preprint-2022.pdf
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https://doi.org/10.1101/2022.01.18.22269300
Abstract
Recombination is an evolutionary process by which many pathogens generate diversity and acquire novel functions. Although a common occurrence during coronavirus replication, recombination can only be detected when two genetically distinct viruses contemporaneously infect the same host. Here, we identify an instance of SARS-CoV-2 superinfection, whereby an individual was simultaneously 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 revealed that Alpha variant alleles comprised between 70-80% of the genomes, whereas the Epsilon variant alleles comprised between 20-30% of the sample. Further investigation revealed 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.
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