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Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City.

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posted on 2022-06-29, 08:41 authored by Joel O Wertheim, Jade C Wang, Mindy Leelawong, Darren P Martin, Jennifer L Havens, Moinuddin A Chowdhury, Jonathan E Pekar, Helly Amin, Anthony Arroyo, Gordon A Awandare, Hoi Yan Chow, Edimarlyn Gonzalez, Elizabeth Luoma, Collins M Morang'a, Anton Nekrutenko, Stephen D Shank, Stefan Silver, Peter K Quashie, Jennifer L Rakeman, Victoria Ruiz, Lucia V Torian, Tetyana I Vasylyeva, Sergei L Kosakovsky Pond, Scott Hughes
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.

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Medical Research Council (Grant ID: MR/P028071/1, Grant title: GCRF-Crick African Network)

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