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:
|Assay ID / SKU||A51808||CVZTDZ7||A51819||CVCE3VH||CVAAAAK|
|Omicron BA.1||FAM||FAM||VIC||VIC||Low FAM from M:D3G mutation|
|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:
|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.
|L452 (CTG) Wild type||Omicron: BA.1 & BA.2 |
|L452Q (CAG)||Omicron: BA.2.12.1
|L452R (CGG)||Delta: All lineages (a low frequency variant)
Epsilon: B.1.429 
Omicron: BA.4, BA.5
 Includes all sublineages of BA.1 and BA.2 except BA.2.12.1
 No longer VOI due to decline in frequency