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

被引:22
作者
Wertheim, Joel O. [1 ]
Wang, Jade C. [2 ]
Leelawong, Mindy [2 ]
Martin, Darren P. [3 ]
Havens, Jennifer L. [4 ]
Chowdhury, Moinuddin A. [2 ]
Pekar, Jonathan E. [4 ]
Amin, Helly [2 ]
Arroyo, Anthony [2 ]
Awandare, Gordon A. [5 ]
Chow, Hoi Yan [2 ]
Gonzalez, Edimarlyn [2 ]
Luoma, Elizabeth [6 ]
Morang'a, Collins M. [5 ]
Nekrutenko, Anton [7 ]
Shank, Stephen D. [8 ]
Silver, Stefan [2 ]
Quashie, Peter K. [5 ]
Rakeman, Jennifer L. [2 ]
Ruiz, Victoria [2 ]
Torian, Lucia, V [2 ]
Vasylyeva, Tetyana, I [1 ]
Pond, Sergei L. Kosakovsky [8 ]
Hughes, Scott [2 ]
机构
[1] Univ Calif San Diego, Dept Med, La Jolla, CA 92093 USA
[2] New York City Dept Hlth & Mental Hyg, New York City Publ Hlth Lab, New York, NY 10013 USA
[3] Univ Cape Town, Inst Infect Dis & Mol Med, Cape Town, South Africa
[4] Univ Calif San Diego, Bioinformat & Syst Biol Grad Program, La Jolla, CA 92093 USA
[5] Univ Ghana, West African Ctr Cell Biol Infect Pathogens WACCB, Accra, Ghana
[6] New York City Dept Hlth & Mental Hyg, Bur Communicable Dis, Long Isl City, NY USA
[7] Penn State Univ, Dept Biochem & Mol Biol, State Coll, PA USA
[8] Temple Univ, Dept Biol, Philadelphia, PA 19122 USA
基金
英国惠康基金; 美国国家卫生研究院;
关键词
CORONAVIRUS; TRANSMISSION; EMERGENCE; SEQUENCE; A/H3N2; RNA;
D O I
10.1038/s41467-022-31247-x
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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.
引用
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页数:11
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