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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)

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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).

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