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 August 31, 2022.
As per the World Health Organization (WHO), the currently circulating variant of concern (VOC) 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 | C12280T* | ORF7b.L11F.TTG.TTT | M.D3N.GAT.AAT |
| Assay ID / SKU | A51808 | CVZTDZ7 | CVEPRZD | CVCE3VH | CVAAAAK |
| Omicron BA.1 | FAM | FAM | VIC | VIC | No amp or low FAM from M:D3G mutation |
| Omicron BA.2 | VIC | VIC | FAM | VIC | VIC |
| Omicron BA.3 | FAM | VIC | FAM | VIC | VIC |
| Omicron BA.4 | FAM | VIC | FAM | FAM | VIC |
| Omicron BA.5 | FAM | VIC | FAM | VIC | FAM |
| XE Omicron recombinant | VIC | FAM | FAM | VIC | VIC |
In addition, the following assays may be used to identify VOC lineages under monitoring (VOC-LUM), which belong to currently circulating VOC, show signals of transmission advantage and have additional amino acid changes that are known or suspected to confer the observed change in epidemiology and fitness advantage:
| Variant | T15009C** | S.N460K.AAT.AAG | ORF7b.L11F.TTG.TTT | M.D3N.GAT.AAT |
| Assay ID / SKU | CVFVKKA | CV9HHWN | CVCE3VH | CVAAAAK |
| Omicron BA.2.12.1 | FAM | VIC | VIC | VIC |
| Omicron BA.2.75 | VIC | FAM | VIC | VIC |
| Omicron BA.4 | VIC | VIC | FAM | VIC |
| Omicron BA.5 | VIC | VIC | VIC | FAM |
Notes:
* Silent mutation in BA.2, BA.3, BA.4 and BA.5 as per GISAID data on covSPECTRUM, accessed August 31, 2022
** Silent mutation in BA.2.12.1 as per Github, accessed August 31, 2022
Please note that S:L452M, S:L452Q and S: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 L452M 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] |
| L452M (ATG) | Omicron: BA.2.9.1 & BA.2.13 |
| L452R (CGG) | Delta: All lineages [2] Epsilon: B.1.429 [2] Omicron: BA.4, BA.5, & BA.2.11 |
[1] Includes all sublineages of BA.1 and BA.2 except BA.2.12.1
[2] No longer VOC or VOI due to decline in frequency