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Suggested assays to detect currently circulating SARS-CoV-2 variants of interest and variants of concern

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 20 Jun 2022 || By Manoj Gandhi Shares: Versions of this article Original article. Tags COVID-19, Mutations, Surveillance, Variants

This blog represents the most up-to-date information about the circulating SARS-CoV-2 variants based on available data from outbreak.info accessed on June 21, 2022.

As per the World Health Organization (WHO), the currently circulating variants of concern (VOCs) of SARS-CoV-2 is the Omicron variant which GISAID has reclassified to “BA.” lineages. The Omicron variant also includes sublineages and recombinants. Using the Lineage Comparison tool available on outbreak.info, it is possible to use the following suggested assays to detect these currently circulating VOCs:

 

Variant S.delH69V70 ORF1a.A2710T.GCT.ACT S.L452R.CTG.CGG ORF7b.L11F.TTG.TTT M.D3N.GAT.AAT
Assay ID / SKU A51808 CVZTDZ7 A51819 CVCE3VH CVAAAAK
Omicron BA.1 FAM FAM VIC VIC Low FAM from M:D3G mutation
Omicron BA.2 VIC VIC VIC VIC VIC
Omicron BA.4 FAM VIC FAM FAM VIC
Omicron BA.5 FAM VIC FAM VIC FAM
XE Omicron recombinant VIC FAM VIC VIC VIC

In addition, either of the following assays may be used to identify the Omicron BA.2.12.1 sublineage:

Mutation Assay ID Note
T15009C CVFVKKA Silent mutation in BA.2.12.1 as per Github, accessed June 10, 2022
S.L452Q.CTG.CAG CVKA3AV Present in BA.2.12.1 and not in other currently circulating VOC or variant of interest (VOI) in significant abundance as of June 10, 2022

Please note that L452Q and L452R are independent mutations that are located at the same position in the SARS-CoV-2 virus genome. This can complicate genotype analysis as the probes of an assay to one mutation will fail to bind to viral sequences that contain the other. It is recommended that both L452Q and L452R mutation assays are run on the same samples, and that the results of both assays are compared, to facilitate accurate genotype analysis.

Genotype Associated Variant
L452 (CTG) Wild type Omicron: BA.1 & BA.2 [1]
L452Q (CAG) Omicron: BA.2.12.1
Lambda [2]
L452R (CGG) Delta: All lineages (a low frequency variant)
Epsilon: B.1.429 [2]
Omicron: BA.4, BA.5

[1] Includes all sublineages of BA.1 and BA.2 except BA.2.12.1
[2] No longer VOI due to decline in frequency