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

Autor: 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.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2022 Jun 25; Vol. 13 (1), pp. 3645. Date of Electronic Publication: 2022 Jun 25.
DOI: 10.1038/s41467-022-31247-x
Abstrakt: 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. The Author(s).)
Databáze: MEDLINE
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