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

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 and Scott Hughes
Additional contact information
Joel O. Wertheim: University of California San Diego
Jade C. Wang: New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene
Mindy Leelawong: New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene
Darren P. Martin: University of Cape Town
Jennifer L. Havens: University of California San Diego
Moinuddin A. Chowdhury: New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene
Jonathan E. Pekar: University of California San Diego
Helly Amin: New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene
Anthony Arroyo: New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene
Gordon A. Awandare: University of Ghana
Hoi Yan Chow: New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene
Edimarlyn Gonzalez: New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene
Elizabeth Luoma: Bureau of the Communicable Diseases, New York City Department of Health and Mental Hygiene
Collins M. Morang’a: University of Ghana
Anton Nekrutenko: The Pennsylvania State University
Stephen D. Shank: Temple University
Stefan Silver: New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene
Peter K. Quashie: University of Ghana
Jennifer L. Rakeman: New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene
Victoria Ruiz: New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene
Lucia V. Torian: New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene
Tetyana I. Vasylyeva: University of California San Diego
Sergei L. Kosakovsky Pond: Temple University
Scott Hughes: New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene

Nature Communications, 2022, vol. 13, issue 1, 1-11

Abstract: Abstract 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.

Date: 2022
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DOI: 10.1038/s41467-022-31247-x

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