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

Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City. Wertheim, J. O, Wang, J. C, Leelawong, M., Martin, D. P, Havens, J. L, Chowdhury, M. A, Pekar, J. E, Amin, H., Arroyo, A., Awandare, G. A, Chow, H. Y., Gonzalez, E., Luoma, E., Morang'a, C. M, Nekrutenko, A., Shank, S. D, Silver, S., Quashie, P. K, Rakeman, J. L, Ruiz, V., Torian, L. V, Vasylyeva, T. I, Kosakovsky Pond, S. L, & Hughes, S. Nature Communications, 13:3645, Nature Publishing Group, jun, 2022.

Paper doi abstract bibtex

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. Here, the authors characterize a case of SARS-CoV-2 superinfection with Alpha and Epsilon variants, in which, via full genome sequencing analyses, they identify recombinant haplotypes in the spike, nucleocapsid, and ORF 8 coding regions, suggesting recombination could play a role in SARS-CoV-2 genetic diversity.

@article{Wertheim2022b,
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. Here, the authors characterize a case of SARS-CoV-2 superinfection with Alpha and Epsilon variants, in which, via full genome sequencing analyses, they identify recombinant haplotypes in the spike, nucleocapsid, and ORF 8 coding regions, suggesting recombination could play a role in SARS-CoV-2 genetic diversity.},
author = {Wertheim, Joel O and Wang, Jade C and Leelawong, Mindy and Martin, Darren P and Havens, Jennifer L and Chowdhury, Moinuddin A and Pekar, Jonathan E and Amin, Helly and Arroyo, Anthony and Awandare, Gordon A and Chow, Hoi Yan and Gonzalez, Edimarlyn and Luoma, Elizabeth and Morang'a, Collins M and Nekrutenko, Anton and Shank, Stephen D and Silver, Stefan and Quashie, Peter K and Rakeman, Jennifer L and Ruiz, Victoria and Torian, Lucia V and Vasylyeva, Tetyana I and {Kosakovsky Pond}, Sergei L and Hughes, Scott},
doi = {10.1038/s41467-022-31247-x},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Wertheim et al. - 2022 - Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New Y.pdf:pdf},
issn = {2041-1723},
journal = {Nature Communications},
keywords = {2,CoV,Molecular evolution,OA,Phylogenetics,SARS,genomics{\_}fund{\_}ack,original},
mendeley-tags = {OA,genomics{\_}fund{\_}ack,original},
month = {jun},
pages = {3645},
pmid = {35752633},
publisher = {Nature Publishing Group},
title = {{Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City}},
url = {https://www.nature.com/articles/s41467-022-31247-x},
volume = {13},
year = {2022}
}

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