Table 2. The molecular targets used in this study as well as the primer and probe sequences.
The N, S, and ORF1a genes are located within SARS-CoV-2 genome. The BCoV target is for bovine coronavirus, a process control spiked into the sample during processing. PMMoV is for the internal endogenous control which is naturally present in high concentrations in the samples. Additional details of these assays can be found in Huisman et al. (2021).
| Target | Primer/Probe | Sequence |
|---|---|---|
| N Gene | Forward | CATTACGTTTGGTGGACCCT |
| Reverse | CCTTGCCATGTTGAGTGAGA | |
| Probe | CGCGATCAAAACAACGTCGG (5′FAM/ZEN/3′IBFQ) | |
| S Gene | Forward | CAGACTAATTCTCCTCGGCG |
| Reverse | TGCACCAAGTGACATAGTGT | |
| Probe | AGCTAGTCAATCCATCATTGCCT (5′HEX/ZEN/3′IBFQ) | |
| ORF1a | Forward | CAGAACTGGAACCACCTTGT |
| Reverse | TACAGTTGAATTGGCAGGCA | |
| Probe | TGCCACAGTACGTCTACAAGC (5′ FAM or HEX/ZEN/3′ IBFQ) | |
| BCoV | Forward | CTGGAAGTTGGTGGAGTT |
| Reverse | ATTATCGGCCTAACATACATC | |
| Probe | CCTTCATATCTATACACATCAAGTTGTT (5′ FAM/ZEN/3′ IBFQ) | |
| PMMoV | Forward | GAGTGGTTTGACCTTAACGTTTGA |
| Reverse | TTGTCGGTTGCAATGCAAGT | |
| Probe | CCTACCGAAGCAAATG (5′ HEX/ZEN/3′ IBFQ) |