Table 5.
Main primers and probes used in molecular detection and quantification of SARS-CoV-2 in wastewater.
| Study | Oligonucleotide name | Oligonucleotide Sequencea (5′ to 3′) | Target genes | Reference |
|---|---|---|---|---|
|
Ahmed et al., 2020; April 18, 2020 |
N_Sarbeco_F | CACATTGGCACCCGCAATC | Nucleocapsid protein (N) | (Corman et al., 2020) |
| N_Sarbeco_R | GAGGAACGAGAAGAGGCTTG | |||
| N_Sarbeco_P | FAM-ACTTCCTCAAGGAACAACATTGCCA-BBQ | |||
| NIID_2019-nCOV_N_F2 | AAATTTTGGGGACCAGGAAC | Nucleocapsid protein (N) | (Shirato et al., 2020) | |
| NIID_2019-nCOV_N_R2 | TGGCAGCTGTGTAGGTCAAC | |||
| NIID_2019-nCOV_N_R2ver3 | TGGCACCTGTGTAGGTCAAC | |||
| NIID_2019-nCOV_N_P2 | FAM-ATGTCGCGCATTGGCATGGA-BHQ | |||
|
La Rosa et al., 2020; May 7, 2020 |
2274 - CO-FW1 | GTGCTAAACCACCGCCTG | ORF1ab | (La Rosa et al., 2020) |
| 2275 - CO-REV1 | CAGATCATGGTTGCTTTGTAGGT | |||
| 2276 - CO-FW2 | CGCCTGGAGATCAATTTAAACAC | |||
| 2277 - CO-REV2 | ACCTGTAAAACCCCATTGTTGA | |||
| WuhanCoV-spk1-f | TTGGCAAAATTCAAGACTCACTTT | Spike protein gene (S). | (Shirato et al., 2020) | |
| WuhanCoV-spk2-r | TGTGGTTCATAAAAATTCCTTTGTG | |||
| NIID_WH-1_F24381 | TCAAGACTCACTTTCTTCCAC | |||
| NIID_WH-1_R24873 | ATTTGAAACAAAGACACCTTCAC | |||
| RdRP_SARSr-F2 RdRP_SARSr-R1 RdRP_SARSr-P2 |
GTGARATGGTCATGTGTGGCGG CARATGTTAAASACACTATTAGCATA FAM-CAGGTGGAACCTCATCAGGAGATGCBHQ1 |
RdRP gene | (Corman et al., 2020) | |
|
Wurtzer et al., 2020; April 17, 2020 Alpaslan Kocamemi et al., 2020 May 16, 2020 |
RdRp_SARSr-F | GTGARATGGTCATGTGTGGCG | RNA-dependent RNA polymerase gene (RdRp) | (Corman et al., 2020) |
| RdRp_SARSr-R | CARATGTTAAASACACTATTAGCATA | |||
| RdRP_SARSr-P1 | FAM-CCAGGTGGWACRTCATCMGGTGATGC-BBQ | (Corman et al., 2020) | ||
| RdRp_SARSr-P2 | FAM-CAGGTGGAACCTCATCAGGAGATGC-BBQ | |||
|
Medema et al., 2020 March 30, 2020 Wu et al., 2020 April 7, 2020 Randazzo et al., 2020 April 28, 2020 Peccia et al., 2020a June 12, 2020 |
2019-nCoV_N1-F | GACCCCAAAATCAGCGAAAT | Nucleocapsid protein (N) | Centers for Disease Control and Prevention, CDC (US 2020) |
| 2019-nCoV_N1-R | TCTGGTTACTGCCAGTTGAATCTG | |||
| 2019-nCoV_N1-P | FAM-ACCCCGCATTACGTTTGGTGGACC-BHQ1 | |||
| 2019-nCoV_N2-F | TTACAAACATTGGCCGCAAA | |||
| 2019-nCoV_N2-F | GCGCGACATTCCGAAGAA | |||
| 2019-nCoV_N2-F | FAM-ACAATTTGCCCCCAGCGCTTCAG- BHQ1 | |||
| 2019-nCoV_N3-F | GGGAGCCTTGAATACACCAAAA | |||
| 2019-nCoV_N3-F | TGTAGCACGATTGCAGCATTG | |||
| 2019-nCoV_N3-F | FAM-AYCACATTGGCACCCGCAATCCTG- BHQ1 | |||
|
Medema et al., 2020 March 30, 2020 Wurtzer et al., 2020 April 17, 2020 |
E_Sarbeco_F | ACAGGTACGTTAATAGTTAATAGCGT | Envelope protein gene (E) | (Corman et al., 2020) |
| E_Sarbeco_R | ATATTGCAGCAGTACGCACACA | |||
| E_Sarbeco_P | FAM-ACACTAGCCATCCTTACTGCGCTTCG-BBQ | |||
| F. Wu et al., 2020 April 7, 2020 |
S-RPA-Forward_v1 | GAAATTAATACGACTCACTATAGGGAGGT TTCAAACTTTACTTGCTTTACATAGA |
Spike protein gene (S) | (Zhang et al., n.d.) |
| S-RPA-Reverse_v1 | TCCTAGGTTGAAGATAACCCACATAATAAG | |||
|
Nemudryi et al., 2020 April 20, 2020 |
N1 forward and reverse | sequences not available | Nucleocapsid protein (N) | 2019-nCoV CDC EUA Kit-IDT#10006606 |
| N2 forward and reverse | sequences not available | Nucleocapsid protein (N) | ||
|
Zhang et al., 2020 May 14,2020 |
CCDC-ORF1, forward primer Reverse primer Fluorescence probe |
CCCTGTGGGTTTTACACTTAA ACGATTGTGCATCAGCTGA FAM-CCGTCTGCGGTATGTGGAAAGGTTATGG-BHQ1 |
ORFlab | Not indicated |
| CCDC-N, forward primer Reverse primer Fluorescence probe |
GGGGAACTTCTCCTGCTAGAAT CAGACATTTTGCTCTCAAGCTG FAM-TTGCTGCTGCTTGACAGATT-TAMRA |
Nucleocapsid protein (N) | Not indicated | |
|
Haramoto et al., 2020 20 June 2020 |
N_Sarbeco_F1 | CACATTGGCACCCGCAATC | Nucleocapsid protein (N) | (Corman et al., 2020) |
| N_Sarbeco_R1 | GAGGAACGAGAAGAGGCTTG | |||
| N_Sarbeco_P1 | FAM-ACTTCCTCAAGGAACAACATTGCCA-BBQ | |||
| NIID_2019-nCOV_N_F2 | AAATTTTGGGGACCAGGAAC | Nucleocapsid protein (N) | (Shirato et al., 2020) | |
| NIID_2019-nCOV_N_R2ver3 | TGGCACCTGTGTAGGTCAAC | |||
| NIID_2019-nCOV_N_P2 | FAM-ATGTCGCGCATTGGCATGGA-BHQ1 | |||
| 2019-nCoV_N1-F | GACCCCAAAATCAGCGAAAT | Nucleocapsid protein (N) | Centers for Disease Control and Prevention, CDC (US 2020) | |
| 2019-nCoV_N1-R | TCTGGTTACTGCCAGTTGAATCTG | |||
| 2019-nCoV_N1-P | FAM-ACCCCGCATTACGTTTGGTGGACC-BHQ1 | |||
| 2019-nCoV_N2-F | TTACAAACATTGGCCGCAAA | |||
| 2019-nCoV_N2-F | GCGCGACATTCCGAAGAA |
Note: FAM: 6-carboxyfluorescein; BBQ: blackberry quencher; BHQ (and BHQ1): Black Hole Quencher 1
a
N1 and N2 primer sets only