Table 1.
Summary of the five RT-PCR assays targeting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
| Country (Institute) | Target | Oligonucleotide | Sequence | Amplicon Size a | Polymerase | Thermocycler Used in the Reference Publication | Volume of RNA Extract |
|---|---|---|---|---|---|---|---|
| Charité (Germany) [5,6] | RdRp b | Charité_RdRp_F | GTGARATGGTCATGTGTGGCGG | 100 bp | SuperScript™ III Platinum® One-Step Quantitative RT-PCR System | Light Cycler ® 480II (Roche) or Applied Biosystems ViiA™7 (Therom Fisher) | 5 µL |
| Charité_S_RdRp_P c | FAM-CAGGTGGAACCTCATCAGGAGATGC-BBQ | ||||||
| Charité_NS_RdRp_P d | FAM-CCAGGTGGWACRTCATCMGGTGATGC-BBQ | ||||||
| Charité_RdRp_R | CARATGTTAAASACACTATTAGCATA | ||||||
| E e | Charité_E_F | ACAGGTACGTTAATAGTTAATAGCGT | 113 bp | ||||
| Charité_E_P | FAM-ACACTAGCCATCCTTACTGCGCTTCG-BBQ | ||||||
| Charité_E_R | ATATTGCAGCAGTACGCACACA | ||||||
| N | Charité_N_F | CACATTGGCACCCGCAATC | 128 bp | ||||
| Charité_N_P | FAM-ACTTCCTCAAGGAACAACATTGCCA-BBQ | ||||||
| Charité_N_R | GAGGAACGAGAAGAGGCTTG | ||||||
| HKU (Hong Kong) [10,11] | ORF1b-nsp14 f | HKU_ORF_F | TGGGGYTTTACRGGTAACCT | 132 bp | TaqMan Fast Virus Master mix | Applied Biosystems ViiA™7 (Therom Fisher) | 4 µL |
| HKU_ORF_P | FAM-TAGTTGTGATGCWATCATGACTAG-TAMRA | ||||||
| HKU_ORF_R | AACRCGCTTAACAAAGCACTC | ||||||
| N e | HKU_N_F | TAATCAGACAAGGAACTGATTA | 110 bp | ||||
| HKU_N_P | FAM-GCAAATTGTGCAATTTGCGG-TAMRA | ||||||
| HKU_N_R | CGAAGGTGTGACTTCCATG | ||||||
| China CDC (China) [12] | N | ChinaCDC_N_F | GGGGAACTTCTCCTGCTAGAAT | 99 bp | Unspecified | Unspecified | Unspecified |
| ChinaCDC_N_P | FAM-TTGCTGCTGCTTGACAGATT-TAMRA | ||||||
| ChinaCDC_N_R | CAGACATTTTGCTCTCAAGCTG | ||||||
| ORF1ab-nsp10 | ChinaCDC_ORF_F | CCCTGTGGGTTTTACACTTAA | 119 bp | ||||
| ChinaCDC_ORF_P | FAM-CCGTCTGCGGTATGTGGAAAGGTTATGG-BHQ1 | ||||||
| ChinaCDC_ORF_R | ACGATTGTGCATCAGCTGA | ||||||
| US CDC (United States) [13] | N1 c | USCDC_N1_F | GACCCCAAAATCAGCGAAAT | 72 bp | TaqPath™ 1-Step RT-qPCR Master Mix, CG (Thermo Fisher) | Applied Biosystems™ 7500 Fast (Thermo Fisher) | 5 µL |
| USCDC_N1_P | FAM-ACCCCGCATTACGTTTGGTGGACC-BHQ1 | ||||||
| USCDC_N1_R | TCTGGTTACTGCCAGTTGAATCTG | ||||||
| N2 c | USCDC_N2_F | TTACAAACATTGGCCGCAAA | 67 bp | ||||
| USCDC_N2_P | FAM-ACAATTTGCCCCCAGCGCTTCAG-BHQ1 | ||||||
| USCDC_N2_R | GCGCGACATTCCGAAGAA | ||||||
| N3 d | USCDC_N3_F | GGGAGCCTTGAATACACCAAAA | 72 bp | ||||
| USCDC_N3_P | FAM-AYCACATTGGCACCCGCAATCCTG-BHQ1 | ||||||
| USCDC_N3_R | TGTAGCACGATTGCAGCATTG | ||||||
| Institut Pasteur, Paris (France) [14] | RdRp IP2 (Flo2) | Pasteur_IP2_F | ATGAGCTTAGTCCTGTTG | 108 bp | SuperScript™ III Platinum® One-Step Quantitative RT-PCR System | LightCycler ® 480 (Roche) | 5 µL |
| Pasteur_IP2_P | HEX-AGATGTCTTGTGCTGCCGGTA-BHQ1 | ||||||
| Pasteur_IP2_R | CTCCCTTTGTTGTGTTGT | ||||||
| RdRp IP4 (Flo4) | Pasteur_IP4_F | GGTAACTGGTATGATTTCG | 107 bp | ||||
| Pasteur_IP4_P | FAM-TCATACAAACCACGCCAGG-BHQ1 | ||||||
| Pasteur_IP4_R | CTGGTCAAGGTTAATATAGG |
a Amplicon size in base-pairs (bp) deduced from BetaCoV/Wuhan-Hu-1/2019 sequence (GISAID |EPI ISL 402125). b Target used for confirmation and discrimination of SARS-CoV-2 and SARS-CoV. c Probe specific for SARS-CoV-2. d Probe detecting SARS-CoV-2, SARS-CoV, and bat-SARS-related CoVs. e Target used for screening. f Target used for confirmation.