Variant PCR Assays

To provide rapid results for public health, tribal health, and clinical samples, TGen has developed SARS-CoV-2 variant PCR assays. These assays allow TGen to report probable detection of Variants of Concern (VOC).

These assays target six mutations in the Spike protein that are present in currently circulating VOCs, including Omicron. Using these targets, we can also call Alpha, Beta, Delta, Epsilon, Gamma, and Mu lineages (see table below). We then rely on sequencing to confirm presumptive variant PCR results. These assays are providing >90% concordance with confirmatory sequencing results.

Lineage

T19R

69-70
del

L452R

E484K

N501Y

D950N

Alpha (B.1.1.7)

-

+

-

-

+

-

Beta (B.1.351) or Gamma (P.1)

-

-

-

+

+

-

Delta (B.1.617.2)

+

-

+

-

-

+

Mu (B.1.621)

-

-

-

+

+

+

Omicron (B.1.1.529)

-

+

-

-

+

-

Non-VOC

-

-

-

-

-

-

Note: T19R, 69-70del, L452R, E484K, N501Y, and D950N denote mutations occurring in the Spike protein of SARS-CoV-2. The structure of a mutation that is caused by an amino acid change (e.g., T19R) is as follows: the first letter (T) corresponds to the “wild-type” amino acid (in this case, Threonine), the number (19) corresponds to where the amino acid resides in the protein (in this case, 19 corresponds to the 19th amino acid), and the second letter (R) corresponds to the amino acid present in the variant (in this case, Arginine). 69-70del indicates that amino acids at the 69th and 70th positions along the Spike protein are deleted.

Variants in Arizona by PCR

Given the dominance of Delta in Arizona, new variant PCR assay targets are being developed. Stay tuned!