tetano
Editor, Senior Moderator
Nat Commun
. 2022 Jun 25;13(1):3645.
doi: 10.1038/s41467-022-31247-x.
Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City
Joel O Wertheim[SUP] #[/SUP][SUP] 1 [/SUP], Jade C Wang[SUP] #[/SUP][SUP] 2 [/SUP], Mindy Leelawong[SUP] 3 [/SUP], Darren P Martin[SUP] 4 [/SUP], Jennifer L Havens[SUP] 5 [/SUP], Moinuddin A Chowdhury[SUP] 3 [/SUP], Jonathan E Pekar[SUP] 5 [/SUP], Helly Amin[SUP] 3 [/SUP], Anthony Arroyo[SUP] 3 [/SUP], Gordon A Awandare[SUP] 6 [/SUP], Hoi Yan Chow[SUP] 3 [/SUP], Edimarlyn Gonzalez[SUP] 3 [/SUP], Elizabeth Luoma[SUP] 7 [/SUP], Collins M Morang'a[SUP] 6 [/SUP], Anton Nekrutenko[SUP] 8 [/SUP], Stephen D Shank[SUP] 9 [/SUP], Stefan Silver[SUP] 3 [/SUP], Peter K Quashie[SUP] 6 [/SUP], Jennifer L Rakeman[SUP] 3 [/SUP], Victoria Ruiz[SUP] 3 [/SUP], Lucia V Torian[SUP] 3 [/SUP], Tetyana I Vasylyeva[SUP] 10 [/SUP], Sergei L Kosakovsky Pond[SUP] 9 [/SUP], Scott Hughes[SUP] 3 [/SUP]
Affiliations
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.
. 2022 Jun 25;13(1):3645.
doi: 10.1038/s41467-022-31247-x.
Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City
Joel O Wertheim[SUP] #[/SUP][SUP] 1 [/SUP], Jade C Wang[SUP] #[/SUP][SUP] 2 [/SUP], Mindy Leelawong[SUP] 3 [/SUP], Darren P Martin[SUP] 4 [/SUP], Jennifer L Havens[SUP] 5 [/SUP], Moinuddin A Chowdhury[SUP] 3 [/SUP], Jonathan E Pekar[SUP] 5 [/SUP], Helly Amin[SUP] 3 [/SUP], Anthony Arroyo[SUP] 3 [/SUP], Gordon A Awandare[SUP] 6 [/SUP], Hoi Yan Chow[SUP] 3 [/SUP], Edimarlyn Gonzalez[SUP] 3 [/SUP], Elizabeth Luoma[SUP] 7 [/SUP], Collins M Morang'a[SUP] 6 [/SUP], Anton Nekrutenko[SUP] 8 [/SUP], Stephen D Shank[SUP] 9 [/SUP], Stefan Silver[SUP] 3 [/SUP], Peter K Quashie[SUP] 6 [/SUP], Jennifer L Rakeman[SUP] 3 [/SUP], Victoria Ruiz[SUP] 3 [/SUP], Lucia V Torian[SUP] 3 [/SUP], Tetyana I Vasylyeva[SUP] 10 [/SUP], Sergei L Kosakovsky Pond[SUP] 9 [/SUP], Scott Hughes[SUP] 3 [/SUP]
Affiliations
- PMID: 35752633
- DOI: 10.1038/s41467-022-31247-x
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.