TABLE 4.
qPCR assays developed for SARS-CoV-2 variantsa
| Reference | Application | Target variant | Lineages | Target VSM |
|---|---|---|---|---|
| 49 | Clinical | Alpha | B.1.1.7 | 69-70DEL |
| Alpha/Beta/Gamma/Omicron/Mu | B.1.1.7; B.1.351; P1; B.1.617.2; BA.1-2; BA.4-5; BA.2.12.1; B.1.621 | N501Y | ||
| 50 | Clinical | Alpha | B.1.1.7 | 69-70DEL |
| 59 | Clinical | Alpha | B.1.1.7 | D3Lb |
| Beta | B.1.351 | 242-244DEL | ||
| 53 | Clinical | Alpha | B.1.1.7 | 69-70DEL; 144DEL |
| 60 | Clinical | Omicron | BA.1 | 211-214INSDEL |
| 54 | Clinical | Alpha | B.1.1.7 | 69-70DEL |
| Alpha/Beta/Gamma/Omicron/Mu | B.1.1.7; B.1.351; P1; B.1.617.2; BA.1-2; BA.4-5; BA.2.12.1; B.1.621 | N501Y | ||
| Beta/Gamma/Eta/Iota/Mu | B.1.351; P1; B.1.525; B.1.526; B.1.621 | E484K | ||
| 52 | Clinical | Alpha | B.1.1.7 | 69-70DEL |
| Alpha/Beta/Gamma/Omicron/Mu | B.1.1.7; B.1.351; P1; B.1.617.2; BA.1-2; BA.4-5; BA.2.12.1; B.1.621 | N501Y | ||
| Beta/Gamma/Eta/Iota/Mu | B.1.351; P1; B.1.525; B.1.526; B.1.621 | E484K | ||
| Beta | B.1.351 | K417N | ||
| 55 | Clinical | Alpha | B.1.1.7 | 69-70DEL |
| Alpha/Beta/Gamma/Omicron/Mu | B.1.1.7; B.1.351; P1; B.1.617.2; BA.1-2; BA.4-5; BA.2.12.1; B.1.621 | N501Y | ||
| Beta/Gamma/Eta/Iota/Mu | B.1.351; P1; B.1.525; B.1.526; B.1.621 | E484K | ||
| Beta | B.1.351 | K417N | ||
| Kappa/Delta | B.1.617.1; B.1.617.2 | L452R | ||
| Delta/Omicron | B.1.617.2; BA.1-2; BA.4-5; BA.2.12.1 | T478K | ||
| 57 | Clinical | Alpha/Beta/Gamma/Omicron/Mu | B.1.1.7; B.1.351; P1; B.1.617.2; BA.1-2; BA.4-5; BA.2.12.1; B.1.621 | N501Y |
| 58 | Clinical | Alpha/Beta/Gamma/ Omicron/Mu |
B.1.1.7; B.1.351; P1; B.1.617.2; BA.1-2; BA.4-5; BA.2.12.1; B.1.621 | N501Y |
| 61 | Clinical | Omicron | BA.1-2; BA.4-5; BA.2.12.1 | S477N |
| 51 | Wastewater | Alpha | B.1.1.7 | 69-70DEL |
| Beta | B.1.351 | 241-243DEL | ||
| 31 | Wastewater | Delta | B.1.617.2 | 157-158DEL |
| Gamma | P1 | 28269-28273INSc | ||
| 34 | Wastewater | Alpha | B.1.1.7 | 69-70DEL; D3Lb |
| Alpha/Beta/Gamma/ Omicron/Mu |
B.1.1.7; B.1.351; P1; B.1.617.2; BA.1-2; BA.4-5; BA.2.12.1; B.1.621 | N501Y | ||
| 56 | Wastewater | Alpha | B.1.1.7 | 69-70DEL; 144DEL; A570D |
a
Variant and lineage information were adopted from https://covariants.org/, as accessed on the May 31, 2022. VSM indicate point mutations, insertions (INS), and deletions (DEL) in the amino acids of the S protein gene, unless stated otherwise.
b
Mutation in N gene.
c
Four-nucleotide insertion in ORF8.