Volume 28, Number 7—July 2022
Dispatch
SARS-CoV-2 Delta–Omicron Recombinant Viruses, United States
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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