Quantitative Genomic RNA from Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) strain USA/COR-22-063113/2022 (Omicron variant, BA.5)
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Quantitative genomic RNA isolated from a preparation of Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) strain USA/COR-22-063113/2022 (Omicron variant).
Genomic RNA from SARS-CoV-2 must be handled at BSL-2 containment
Innocuity testing was performed on the extracted RNA and results reported on the Certificate of Analysis.
This isolate is lineage BA.5.5 (Pango v.4.1.3 PLEARN-v1.17), Omicron (BA.5-like) (Scorpio), and GISIAD clade GRA using the Phylogenetic Assignment of Named Global Outbreak lineages (PANGO) tool. Due to the dynamic nature of lineage determination using PANGO, discrepancies may exist between vial labels and the current lineage assignment. Previous iterations of PANGO identified this isolate as lineage BA.5.
The complete genome of the clinical isolate of SARS-CoV-2, USA/COR-22-063113/2022 has been sequenced (GISAID: EPI_ISL_13512579). The following mutations are present in the clinical isolate: Spike A27S, Spike D405N, Spike D614G, Spike D796Y, Spike E484A, Spike F486V, Spike G142D, Spike G339D, Spike H69del, Spike H655Y, Spike K417N, Spike L24del, Spike L452R, Spike N440K, Spike N501Y, Spike N679K, Spike N764K, Spike N969K, Spike P25del, Spike P26del, Spike P681H, Spike Q498R, Spike Q954H, Spike R408S, Spike S371F, Spike S373P, Spike S375F, Spike S477N, Spike T19I, Spike T76I, Spike T376A, Spike T478K, Spike V70del, Spike V213G, Spike Y505H, E T9I, M A63T, M D3N, M Q19E, N E31del, N G204R, N P13L, N R32del, N R203K, N S33del, N S413R, NS3 T223I, NSP1 S135R, NSP3 G489S, NSP3 T24I, NSP4 L264F, NSP4 T327I, NSP4 T492I, NSP5 P132H, NSP5 P252L, NSP6 F108del, NSP6 G107del, NSP6 S106del, NSP12 P323L, NSP13 R392C, NSP14 I42V, NSP15 T112I. It was labelled as variant of concern (VOC) Omicron by the World Health Organization (WHO).
Acknowledgment for publications should read "The following reagent was deposited by the Centers for Disease Control and Prevention and obtained through BEI Resources, NIAID, NIH: Genomic RNA from SARS-Related Coronavirus 2, Isolate hCoV-19/USA/COR-22-063113/2022 (Lineage BA.5; Omicron Variant), NR-58496."
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Rambaut A, et al. A Dynamic Nomenclature Proposal for SARS-CoV-2 Lineages to Assist Genomic Epidemiology. Nat Microbiol 5: 1403-1407, 2020. PubMed: 32669681
Mercatelli D and Giorgi FM. Geographic and Genomic Distribution of SARS-CoV-2 Mutations. Front Microbiol: doi.org/10.3389/fmicb.2020.01800, 2020. PubMed: 32793182
Gralinski LE and Menachery VD. Return of the Coronavirus: 2019-nCoV. Viruses 12: 135, 2020. PubMed: 31991541