Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link
Volume 28, Number 7—July 2022
Dispatch

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

Kristine A. Lacek, Benjamin L. Rambo-Martin, Dhwani Batra, Xiao-yu Zheng, Norman Hassell, Hitoshi Sakaguchi, Thomas Peacock, Natalie Groves, Matthew Keller, Malania M. Wilson, Mili Sheth, Morgan L. Davis, Mark Borroughs, Jonathan Gerhart, Samuel S. Shepard, Peter W. Cook, Justin Lee, David E. Wentworth, John R. Barnes, Rebecca Kondor, and Clinton R. PadenComments to Author 
Author affiliations: Centers for Disease Control and Prevention, Atlanta, Georgia, USA (K.A. Lacek, B.L. Rambo-Martin, D. Batra, X. Zheng, N. Hassell, M. Keller, M.M. Wilson, M. Sheth, M.L. Davis, M. Burroughs, J. Gerhart, S.S. Shepard, P.W. Cook, J. Lee, D.E. Wentworth, J.R. Barnes, R. Kondor, C.R. Paden); General Dynamics Information Technology, Inc., Atlanta (X. Zheng); Retired, Yotsukaido City, Japan (H. Sakaguchi); UK Health Security Agency, London, UK (T. Peacock, N. Groves); Imperial College London, London (T. Peacock); ASRT Incorporated, Smyrna, Georgia, USA (M.L. Davis, J. Gerhart)

Main Article

Table

Candidate recombinant samples, states, collection dates, and Bolotie outputs for the SARS-CoV-2 AY.119.2:BA.1.1 recombinant cluster, United States*

GISAID accession no. State GISAID virus name Collection date Bolotie results
EPI_ISL_8720194
 TN
 hCoV-19/USA/TN-CDC-ASC210559252/2021
 2021 Dec 31
 21J (Delta): 1-22032; 21K (Omicron): 22033-29903
EPI_ISL_9147438
 NJ
 hCoV-19/USA/NJ-CDC-IBX952397337138/2022
 2022 Jan 4
 21J (Delta): 1-22032; 21K (Omicron): 22033-29903
EPI_ISL_8981712
 PA
 hCoV-19/USA/PA-CDC-LC0473996/2022
 2022 Jan 4
 21J (Delta): 1-22032; 21K (Omicron): 22033-29903
EPI_ISL_8981824
 PA
 hCoV-19/USA/PA-CDC-LC0474055/2022
 2022 Jan 4
 21J (Delta): 1-22032; 21K (Omicron): 22033-29903
EPI_ISL_8981459
 PA
 hCoV-19/USA/PA-CDC-LC0474301/2022
 2022 Jan 4
 21J (Delta): 1-22032; 21K (Omicron): 22033-29903
EPI_ISL_9088187
 MA
 hCoV-19/USA/MA-CDC-STM-HZEBR92XC/2022
 2022 Jan 12
 21J (Delta): 1-22032; 21K (Omicron): 22033-29903
EPI_ISL_9147935
 NJ
 hCoV-19/USA/NJ-CDC-IBX640654818289/2022
 2022 Jan 12
 21J (Delta): 1-22032; 21K (Omicron): 22033-29903
EPI_ISL_10389336
 NJ
 hCoV-19/USA/NJ-CDC-ASC210553977/2022
 2022 Feb 12
 21J (Delta): 1-22032; 21K (Omicron): 22033-29903
EPI_ISL_10389339 NJ hCoV-19/USA/NJ-CDC-ASC210553978/2022 2022 Feb 12 21J (Delta): 1-22032; 21K (Omicron): 22033-29903

*These 9 candidate recombinant viruses were identified by an exhaustive search of publicly available SARS-CoV-2 viral genomes with orf1ab:2855V,4176N,6248S and S:95I,142D,157-,346K,501Y mutations. hCoV-19/USA/PA-CDC-LC0474055/2022 and hCoV-19/USA/PA-CDC-LC0474301/2022 underwent resequencing at the Centers for Disease Control and Prevention. Bolotie (3) identified all 9 as recombinant genomes between Delta (clade 21J) and Omicron (clade 21K). Bolotie cannot determine the true breakpoint because of high sequence homology, but the same region is identified for all 9 sequences (nt position 22032 as referenced to GenBank accession no. NC_045512.2).

Main Article

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/scientific-brief-emerging-variants.html
  2. 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. DOIPubMedGoogle Scholar
  3. Varabyou  A, Pockrandt  C, Salzberg  SL, Pertea  M. Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie. Genetics. 2021;218:iyab074.
  4. 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. DOIPubMedGoogle Scholar
  5. 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. DOIPubMedGoogle Scholar
  6. Escalera-Zamudio  M, Sánchez  HGC, Arredondo  LJD, Gutiérrez  BRE. Proposal to redesignate B.1.631 as recombinant lineage XB [cited 2022 Feb 18]. https://virological.org/t/re-proposal-to-redesignate-b-1-631-as-recombinant-lineage-xb/746
  7. Jackson  B, Rambaut  A, Pybus  OG, Robertson  DL, Connor  T, Loman  NJ, et al. Recombinant SARS-CoV-2 genomes involving lineage B.1.1.7 in the UK [cited 2022 Feb 18]. https://virological.org/t/recombinant-sars-cov-2-genomes-involving-lineage-b-1-1-7-in-the-uk/658.
  8. Liu  L, Iketani  S, Guo  Y, Chan  JF, Wang  M, Liu  L, et al. Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2. Nature. 2022;602:676–81. DOIPubMedGoogle Scholar
  9. Chakraborty  C, Bhattacharya  M, Sharma  AR. Emerging mutations in the SARS-CoV-2 variants and their role in antibody escape to small molecule-based therapeutic resistance. Curr Opin Pharmacol. 2022;62:64–73. DOIPubMedGoogle Scholar
  10. Kreier  F. Deltacron: the story of the variant that wasn’t. Nature. 2022;602:19. DOIPubMedGoogle Scholar
  11. Aksamentov  I, Roemer  C, Hodcroft  EB, Neher  RA. Nextclade: clade assignment, mutation calling and quality control for viral genomes. J Open Source Softw. 2021;6:3773. DOIGoogle Scholar
  12. Hadfield  J, Megill  C, Bell  SM, Huddleston  J, Potter  B, Callender  C, et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. 2018;34:4121–3. DOIPubMedGoogle Scholar

Main Article

Page created: May 04, 2022
Page updated: June 18, 2022
Page reviewed: June 18, 2022
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
file_external