TY - JOUR
T1 - Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City
AU - Wertheim, Joel O.
AU - Wang, Jade C.
AU - Leelawong, Mindy
AU - Martin, Darren P.
AU - Havens, Jennifer L.
AU - Chowdhury, Moinuddin A.
AU - Pekar, Jonathan E.
AU - Amin, Helly
AU - Arroyo, Anthony
AU - Awandare, Gordon A.
AU - Chow, Hoi Yan
AU - Gonzalez, Edimarlyn
AU - Luoma, Elizabeth
AU - Morang’a, Collins M.
AU - Nekrutenko, Anton
AU - Shank, Stephen D.
AU - Silver, Stefan
AU - Quashie, Peter K.
AU - Rakeman, Jennifer L.
AU - Ruiz, Victoria
AU - Torian, Lucia V.
AU - Vasylyeva, Tetyana I.
AU - Kosakovsky Pond, Sergei L.
AU - Hughes, Scott
N1 - Publisher Copyright:
© 2022, The Author(s).
PY - 2022/12
Y1 - 2022/12
N2 - 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.
AB - 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.
UR - https://www.scopus.com/pages/publications/85132998375
UR - https://www.scopus.com/pages/publications/85132998375#tab=citedBy
U2 - 10.1038/s41467-022-31247-x
DO - 10.1038/s41467-022-31247-x
M3 - Article
C2 - 35752633
AN - SCOPUS:85132998375
SN - 2041-1723
VL - 13
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 3645
ER -