Table 2.
Primers used for the molecular detection of SARS-CoV-2 RNA.
| Target Gene | Primer Name (orientation) | Nucleotide sequence 5′-3′ | Taa (°C) | Amplicon size | Positionb nucleotide (amino acid) | Mutation or Motifc | Reference |
|---|---|---|---|---|---|---|---|
| NsP3 | C3037T F1/2 (+) | TTGATTTAGATGAGTGGAGTATGGCTAC | 60 | 263 bp | 2949-3212 (76–164) | C3037T (F106F) | This study |
| C3037T R1 (−) | GTCTGAACAACTGGTGTAAGTTCC | ||||||
| C3037T R2 (−) | CATCATCTAACCAATCTTCTTCTTGCT | ||||||
| RdRp | C14408T F1/2 (+) | TTTGGATGACAGATGCATTCTGC | 58 | 335 bp | 14343-14678 (300–412) | C14408T (P323L) | This study |
| C14408T R1 (−) | GATAGTAGTCATAATCGCTGATAGCAG | ||||||
| C14408T R2 (−) | CCGGGTTTGACAGTTTGAAAAGC | ||||||
| Spike A | A23403G F1 (+) | TTCAACTTCAATGGTTTAACAGGCA | 60 | 421 bp | 23288-23709 (575–715) | A23403G (D614G) FCSd |
This study |
| A23403G F2 (+) | GTCCGTGATCCACAGACACTTG | ||||||
| A23403G R1/2 (−) | GTGGGTATGGCAATAGAGTTATTAGAGT | ||||||
| Spike B | OUT-F (+) | AGGCTGCGTTATAGCTTGGA | 55 | 470 bp | 22882-23352 (440–596) | T22917G (L452R), G23012A (E484K), G23012C (E484Q), A23063T (N501Y), C23271A (A570D) | Amendola et al. (2021) |
| MaSi_AR (−) | ACACTGACACCACCAAAAGAAC | ||||||
| SiMa_BF (+) | TCTTGATTCTAAGGTTGGTGGT |
a
Annealing temperature.
b
Referred to Wuhan-Hu-1 (NC_045512.2).
c
Amino acid mutations are indicated in parenthesis.
d
FCS: furin cleavage site (amino acids 680–689).