TABLE 6.
Test results using fourplex sets of primers/probes for the detection of SARS-CoV-2 variants in clinical specimens.
| SARS-CoV-2 mutations | Number of cases among clinical specimens* | Fourplex A | Number of positives** | Fourplex B | Number of positives** | Fourplex C | Number of positives** | Fourplex D | Number of positives** |
|---|---|---|---|---|---|---|---|---|---|
| Orf1ab L with 501Y with 614G | 49*** | E Sarbeco-FAM | 49 (100%) | N LSPQ-HEX | 49 (100%) | Orf1ab L LNA-TEX | 49 (100%) | Orf1ab S LNA-HEX | 0 (0%) |
| Spike 501Y LNA-HEX | 49 (100%) | Spike N501 LNA-FAM | 0 (0%) | Spike N501 LNA-FAM | 0 (0%) | Spike N501 LNA-FAM | 0 (0%) | ||
| Spike 614G LNA-TEX | 49 (100%) | Spike 614G LNA-TEX | 49 (100%) | Spike 614G LNA-HEX | 49 (100%) | Spike D614 LNA-TEX | 0 (0%) | ||
| B2M-Cy5 | 49 (100%) | B2M-Cy5 | 49 (100%) | B2M-Cy5 | 49 (100%) | B2M-Cy5 | 49 (100%) | ||
| Orf1ab L with N501 with 614G | 101**** | E Sarbeco-FAM | 101 (100%) | N LSPQ-HEX | 101 (100%) | Orf1ab L LNA-TEX | 101 (100%) | Orf1ab S LNA-HEX | 0 (0%) |
| Spike 501Y LNA-HEX | 0 (0%) | Spike N501 LNA-FAM | 100 (99%) | Spike N501 LNA-FAM | 100 (99%) | Spike N501 LNA-FAM | 100 (99%) | ||
| Spike 614G LNA-TEX | 101 (100%) | Spike 614G LNA-TEX | 101 (100%) | Spike 614G LNA-HEX | 101 (100%) | Spike D614 LNA-TEX | 0 (0%) | ||
| B2M-Cy5 | 101 (100%) | B2M-Cy5 | 101 (100%) | B2M-Cy5 | 101 (100%) | B2M-Cy5 | 101 (100%) | ||
| Orf1ab L with N501 with D614 | 5***** | E Sarbeco-FAM | 5 (100%) | N LSPQ-HEX | 5 (100%) | Orf1ab L LNA-TEX | 5 (100%) | Orf1ab S LNA-HEX | 0 (0%) |
| Spike 501Y LNA-HEX | 0 (0%) | Spike N501 LNA-FAM | 5 (100%) | Spike N501 LNA-FAM | 5 (100%) | Spike N501 LNA-FAM | 5 (100%) | ||
| Spike 614G LNA-TEX | 0 (0%) | Spike 614G LNA-TEX | 0 (0%) | Spike 614G LNA-HEX | 0 (0%) | Spike D614 LNA-TEX | 5 (100%) | ||
| B2M-Cy5 | 5 (100%) | B2M-Cy5 | 5 (100%) | B2M-Cy5 | 5 (100%) | B2M-Cy5 | 5 (100%) | ||
| Orf1ab S with N501 with D614 | 5***** | E Sarbeco-FAM | 5 (100%) | N LSPQ-HEX | 5 (100%) | Orf1ab L LNA-TEX | 0 (0%) | Orf1ab S LNA-HEX | 5 (100%) |
| Spike 501Y LNA-HEX | 0 (0%) | Spike N501 LNA-FAM | 5 (100%) | Spike N501 LNA-FAM | 5 (100%) | Spike N501 LNA-FAM | 5 (100%) | ||
| Spike 614G LNA-TEX | 0 (0%) | Spike 614G LNA-TEX | 0 (0%) | Spike 614G LNA-HEX | 0 (0%) | Spike D614 LNA-TEX | 5 (100%) | ||
| B2M-Cy5 | 5 (100%) | B2M-Cy5 | 5 (100%) | B2M-Cy5 | 5 (100%) | B2M-Cy5 | 5 (100%) | ||
| Negative clinical specimens | 100**** | E Sarbeco-FAM | 0 (0%) | N LSPQ-HEX | 0 (0%) | Orf1ab L LNA-TEX | 0 (0%) | Orf1ab S LNA-HEX | 0 (0%) |
| Spike 501Y LNA-HEX | 0 (0%) | Spike N501 LNA-FAM | 0 (0%) | Spike N501 LNA-FAM | 0 (0%) | Spike N501 LNA-FAM | 0 (0%) | ||
| Spike 614G LNA-TEX | 0 (0%) | Spike 614G LNA-TEX | 0 (0%) | Spike 614G LNA-HEX | 0 (0%) | Spike D614 LNA-TEX | 0 (0%) | ||
| B2M-Cy5 | 100 (100%) | B2M-Cy5 | 100 (100%) | B2M-Cy5 | 100 (100%) | B2M-Cy5 | 100 (100%) |
*
All positives have been confirmed by sequencing
**
Number of positive test results (% of detection).
***
Sampling period between February 21 and March 30, 2021.
****
Sampling periods between March 19 and March 25, 2020 and February 21 and March 30, 2021.
*****
Sampling period between March 19 and March 25, 2020.