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Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City.
Wertheim, Joel O; Wang, Jade C; Leelawong, Mindy; Martin, Darren P; Havens, Jennifer L; Chowdhury, Moinuddin A; Pekar, Jonathan E; Amin, Helly; Arroyo, Anthony; Awandare, Gordon A; Chow, Hoi Yan; Gonzalez, Edimarlyn; Luoma, Elizabeth; Morang'a, Collins M; Nekrutenko, Anton; Shank, Stephen D; Silver, Stefan; Quashie, Peter K; Rakeman, Jennifer L; Ruiz, Victoria; Torian, Lucia V; Vasylyeva, Tetyana I; Kosakovsky Pond, Sergei L; Hughes, Scott.
  • Wertheim JO; Department of Medicine, University of California San Diego, La Jolla, CA, USA. jwertheim@health.ucsd.edu.
  • Wang JC; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA. jwang7@health.nyc.gov.
  • Leelawong M; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
  • Martin DP; Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
  • Havens JL; Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA.
  • Chowdhury MA; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
  • Pekar JE; Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA.
  • Amin H; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
  • Arroyo A; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
  • Awandare GA; West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana.
  • Chow HY; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
  • Gonzalez E; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
  • Luoma E; Bureau of the Communicable Diseases, New York City Department of Health and Mental Hygiene, Long Island City, NY, USA.
  • Morang'a CM; West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana.
  • Nekrutenko A; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA, USA.
  • Shank SD; Department of Biology, Temple University, Philadelphia, PA, USA.
  • Silver S; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
  • Quashie PK; West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana.
  • Rakeman JL; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
  • Ruiz V; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
  • Torian LV; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
  • Vasylyeva TI; Department of Medicine, University of California San Diego, La Jolla, CA, USA.
  • Kosakovsky Pond SL; Department of Biology, Temple University, Philadelphia, PA, USA.
  • Hughes S; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
Nat Commun ; 13(1): 3645, 2022 Jun 25.
Article in English | MEDLINE | ID: covidwho-1908172
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Superinfection / COVID-19 Type of study: Observational study Topics: Variants Limits: Humans Country/Region as subject: North America Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2022 Document Type: Article Affiliation country: S41467-022-31247-x

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Superinfection / COVID-19 Type of study: Observational study Topics: Variants Limits: Humans Country/Region as subject: North America Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2022 Document Type: Article Affiliation country: S41467-022-31247-x