Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

SARS-CoV-2 Delta-Omicron Recombinant Viruses, United States

Kristine A Lacek et al. Emerg Infect Dis. 2022 Jul.

Abstract

To detect new and changing SARS-CoV-2 variants, we investigated candidate Delta-Omicron recombinant genomes from Centers for Disease Control and Prevention national genomic surveillance. Laboratory and bioinformatic investigations identified and validated 9 genetically related SARS-CoV-2 viruses with a hybrid Delta-Omicron spike protein.

Keywords: 2019 novel coronavirus disease; COVID-19; Delta; Omicron; SARS-CoV-2; United States; bioinformatics; coronavirus disease; next-generation sequencing; recombination; respiratory infections; severe acute respiratory syndrome coronavirus 2; viruses; zoonoses.

PubMed Disclaimer

Similar articles

  • Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination.
    Bolze A, Basler T, White S, Dei Rossi A, Wyman D, Dai H, Roychoudhury P, Greninger AL, Hayashibara K, Beatty M, Shah S, Stous S, McCrone JT, Kil E, Cassens T, Tsan K, Nguyen J, Ramirez J, Carter S, Cirulli ET, Schiabor Barrett K, Washington NL, Belda-Ferre P, Jacobs S, Sandoval E, Becker D, Lu JT, Isaksson M, Lee W, Luo S. Bolze A, et al. Med. 2022 Dec 9;3(12):848-859.e4. doi: 10.1016/j.medj.2022.10.002. Epub 2022 Oct 20. Med. 2022. PMID: 36332633 Free PMC article.
  • Genomic Surveillance for SARS-CoV-2 Variants: Predominance of the Delta (B.1.617.2) and Omicron (B.1.1.529) Variants - United States, June 2021-January 2022.
    Lambrou AS, Shirk P, Steele MK, Paul P, Paden CR, Cadwell B, Reese HE, Aoki Y, Hassell N, Zheng XY, Talarico S, Chen JC, Oberste MS, Batra D, McMullan LK, Halpin AL, Galloway SE, MacCannell DR, Kondor R, Barnes J, MacNeil A, Silk BJ, Dugan VG, Scobie HM, Wentworth DE, Caravas J, Kovacs NA, Gerhart JG, Jia Ng H, Beck A, Chau R, Cintron R, Cook PW, Gulvik CA, Howard D, Jang Y, Knipe K, Lacek KA, Moser KA, Paskey AC, Rambo-Martin BL, Nagilla RR, Retchless AC, Schmerer MW, Seby S, Shepard SS, Stanton RA, Stark TJ, Uehara A, Unoarumhi Y, Bentz ML, Burgin A, Burroughs M, Davis ML, Keller MW, Keong LM, Le SS, Lee JS, Madden Jr JC, Nobles S, Owuor DC, Padilla J, Sheth M, Wilson MM; Strain Surveillance and Emerging Variants Bioinformatic Working Group; Strain Surveillance and Emerging Variants NS3 Working Group. Lambrou AS, et al. MMWR Morb Mortal Wkly Rep. 2022 Feb 11;71(6):206-211. doi: 10.15585/mmwr.mm7106a4. MMWR Morb Mortal Wkly Rep. 2022. PMID: 35143464 Free PMC article.
  • Identification of Various Recombinants in a Patient Coinfected With the Different SARS-CoV-2 Variants.
    Sayama Y, Sakagami A, Okamoto M, Sakamoto M, Koizumi H, Kimura Y, Dapat C, Saito M, Suzuki Y, Sasaki M, Sugawara N, Oshitani H. Sayama Y, et al. Influenza Other Respir Viruses. 2024 Jun;18(6):e13340. doi: 10.1111/irv.13340. Influenza Other Respir Viruses. 2024. PMID: 38890805 Free PMC article.
  • The Deltacron conundrum: Its origin and potential health risks.
    Farheen S, Araf Y, Tang YD, Zheng C. Farheen S, et al. J Med Virol. 2022 Nov;94(11):5096-5102. doi: 10.1002/jmv.27990. Epub 2022 Jul 22. J Med Virol. 2022. PMID: 35815524 Review.
  • Incorporating COVID-19 into Acute Febrile Illness Surveillance Systems, Belize, Kenya, Ethiopia, Peru, and Liberia, 2020-2021.
    Shih DC, Silver R, Henao OL, Alemu A, Audi A, Bigogo G, Colston JM, Edu-Quansah EP, Erickson TA, Gashu A, Gbelee GB Jr, Gunter SM, Kosek MN, Logan GG, Mackey JM, Maliga A, Manzanero R, Morazan G, Morey F, Munoz FM, Murray KO, Nelson TV, Olortegui MP, Yori PP, Ronca SE, Schiaffino F, Tayachew A, Tedasse M, Wossen M, Allen DR, Angra P, Balish A, Farron M, Guerra M, Herman-Roloff A, Hicks VJ, Hunsperger E, Kazazian L, Mikoleit M, Munyua P, Munywoki PK, Namwase AS, Onyango CO, Park M, Peruski LF, Sugerman DE, Gutierrez EZ, Cohen AL. Shih DC, et al. Emerg Infect Dis. 2022 Dec;28(13):S34-S41. doi: 10.3201/eid2813.220898. Emerg Infect Dis. 2022. PMID: 36502419 Free PMC article. Review.
See all similar articles

Cited by

See all "Cited by" articles

References

    1. National Center for Immunization and Respiratory Diseases (NCIRD) DoVD. Science brief: emerging SARS-CoV-2 variants [cited 2022 Feb 17]. https://www.cdc.gov/coronavirus/2019-ncov/science/science-briefs/scienti...
    1. Lai MM, Baric RS, Makino S, Keck JG, Egbert J, Leibowitz JL, et al. Recombination between nonsegmented RNA genomes of murine coronaviruses. J Virol. 1985;56:449–56. 10.1128/jvi.56.2.449-456.1985 - DOI - PMC - PubMed
    1. Varabyou A, Pockrandt C, Salzberg SL, Pertea M. Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie. Genetics. 2021;218:iyab074. - PMC - PubMed
    1. Li X, Giorgi EE, Marichannegowda MH, Foley B, Xiao C, Kong X-P, et al. Emergence of SARS-CoV-2 through recombination and strong purifying selection. Sci Adv. 2020;6:eabb9153. 10.1126/sciadv.abb9153 - DOI - PMC - PubMed
    1. Sekizuka T, Itokawa K, Saito M, Shimatani M, Matsuyama S, Hasegawa H, et al. Genome recombination between Delta and Alpha variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Jpn J Infect Dis. 2022;JJID.2021.844; Epub ahead of print. 10.7883/yoken.JJID.2021.844 - DOI - PubMed

Publication types

Supplementary concepts