Table 1.
Primers and probes used: for RT-PCR, for N501Y detection and for sequencing.
| Use | Position | Name | Sequence (5’-3’) | Gen |
|---|---|---|---|---|
| Sense primer | CoV-2-OVI-S | ATCAAGTTAATGGTTACCCTAACATGT | SARS-CoV-2 ORF1ab |
|
| Antisense primer | CoV-2-OVI-A | AACCTAGCTGTAAAGGTAAATTGGTACC | ||
| Probe MGB FAM | CoV-2-OVI-FAM | CCGCGAAGAAGCTA | ||
| SARS-CoV-2 | Sense primer1 | 2019-nCoV_N1-F | GACCCCAAAATCAGCGAAAT | SARS-CoV-2 Gen N |
| detection | Antisense primer1 | 2019-nCoV_N1-R | TCTGGTTACTGCCAGTTGAATCTG | |
| Probe MGB VIC1 | 2019-nCoV_N1-P-VIC | CCGCATTACGTTTGGT2 | ||
| Sense primer | Beta-TR-S | ACACAACTGTGTTCACTAGC | Human β-globin gene |
|
| Antisense primer | Beta-TR-A | CCAACTTCATCCACGTTCACC | ||
| Probe Cy5.0 | Beta-Cy5.0 | TGCATCTGACTCCTGAGGA | ||
| Sense primer | CoV-N501Y-Fwd2 | AATCTATCAGGCCGGTAGCACA | SARS-CoV-2 Gen S |
|
| N501Y | Antisense primer | CoV-N501Y-Rev | ACAGTTGCTGGTGCATGTAGA | |
| detection | Probe MGB FAM | CoV-WT-N501-FAM | CCACTAATGGTGTTGGT3 | |
| Probe MGB VIC | CoV-Mut-Y501-VIC | CCACTTATGGTGTTGGT3 | ||
| N501Y | Sense primer | CoV-N501Y-Fwd2 | AATCTATCAGGCCGGTAGCACA | SARS-CoV-2 Gen S |
| Sequencing | Antisense primer | N501-Seq-R2 | CAGGGACTTCTGTGCAGTTAACA |
1
US Centers for Disease Control and Prevention (2020) 2019-Novel coronavirus (2019-nCoV) real-time rRT-PCR panel primers and probes. Available in: https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html.
2
Probe sequence has been shortened as it is a MGB probe.
3
The AAT (Asn) and TAT (Tyr) codons are underlined.