Capturing intrahost recombination of SARS-CoV-2 during superinfection with Alpha and Epsilon variants in New York City
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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Preprint| Erscheinungsjahr: |
2024 |
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| Erschienen: |
2024 |
| Enthalten in: |
bioRxiv.org - (2024) vom: 23. Apr. Zur Gesamtaufnahme - year:2024 |
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| Sprache: |
Englisch |
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| Beteiligte Personen: |
Wertheim, Joel O. [VerfasserIn] |
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| doi: |
10.1101/2022.01.18.22269300 |
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| PPN (Katalog-ID): |
XBI035050861 |
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| 245 | 1 | 0 | |a Capturing intrahost recombination of SARS-CoV-2 during superinfection with Alpha and Epsilon variants in New York City |
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| 520 | |a 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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| 700 | 1 | |a Leelawong, Mindy |e verfasserin |4 aut | |
| 700 | 1 | |a Martin, Darren P. |e verfasserin |4 aut | |
| 700 | 1 | |a Havens, Jennifer L. |e verfasserin |4 aut | |
| 700 | 1 | |a Chowdhury, Moinuddin A. |e verfasserin |4 aut | |
| 700 | 1 | |a Pekar, Jonathan |e verfasserin |4 aut | |
| 700 | 1 | |a Amin, Helly |e verfasserin |4 aut | |
| 700 | 1 | |a Arroyo, Anthony |e verfasserin |4 aut | |
| 700 | 1 | |a Awandare, Gordon A. |e verfasserin |4 aut | |
| 700 | 1 | |a Chow, Hoi Yan |e verfasserin |4 aut | |
| 700 | 1 | |a Gonzalez, Edimarlyn |e verfasserin |4 aut | |
| 700 | 1 | |a Luoma, Elizabeth |e verfasserin |4 aut | |
| 700 | 1 | |a Morang’a, Collins M. |e verfasserin |4 aut | |
| 700 | 1 | |a Nekrutenko, Anton |e verfasserin |4 aut | |
| 700 | 1 | |a Shank, Stephen D. |e verfasserin |4 aut | |
| 700 | 1 | |a Quashie, Peter K. |e verfasserin |4 aut | |
| 700 | 1 | |a Rakeman, Jennifer L. |e verfasserin |4 aut | |
| 700 | 1 | |a Ruiz, Victoria |e verfasserin |4 aut | |
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| 700 | 1 | |a Vasylyeva, Tetyana I. |e verfasserin |4 aut | |
| 700 | 1 | |a Kosakovsky Pond, Sergei L. |e verfasserin |4 aut | |
| 700 | 1 | |a Hughes, Scott |e verfasserin |4 aut | |
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