TABLE 5.
Primers and oligonucleotides used in this study
| Pool for enrichment (method) or primera | Sequence (5′→3′)b |
|---|---|
| T7-P5-VSP pool (1) | TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTcactgctatgtttagtgttc |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTcaacataagagaacacacag | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTtgcttttcactcttcatttc | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTaaacctagatgtgctgatg | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTgtgtgaaggtattgtttgtt | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTtttttgtcctttttaggctc | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTctttaccagacattttgctc | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTatctttcattttaccgtcac | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTgttctccattctggttactg | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTgtgctatgtagttacgagaa | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTatagaagtgaataggacacg | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTtcaagtcctccctaatgtt | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTattggttgctcttcatctaa | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTgtctgaaagaagcaatgaag | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTagaggatgaaatggtgaatt | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTcaagtgagaaccaaaagataa | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTgagtaaacgtaaaaagaaggt | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTaagccaaagcctcattatta | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTaatctactgatgtcttggtc | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTcctttccacaaaaatcaact | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTtaatcagcaatctttccagt | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTacagaaagtagtgaaaccat | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTcaaaataggcatacaccatc | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTctttccatccaacttttgtt | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTttctgtgtaactccaatacc | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTaaacccacttctcttgttat | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTtgggtggtttatgtgattta | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTggtcaaggttaatataggca | |
| TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTtacgtccattcataccattt | |
| P7-N6 | GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNN |
| P7-VSP pool (2) | GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTgaacactaaacatagcagtg |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTctgtgtgttctcttatgttg | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTgaaatgaagagtgaaaagca | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTcatcagcacatctaggttt | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTaacaaacaataccttcacac | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTgagcctaaaaaggacaaaaa | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTgagcaaaatgtctggtaaag | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTgtgacggtaaaatgaaagat | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTcagtaaccagaatggagaac | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTtctcgtaactacatagcac | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTcgtgtcctattcacttctat | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTaacattagggaggacttga | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTttagatgaagagcaaccaat | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTcttcattgcttctttcagac | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTaattcaccatttcatcctct | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTttatcttttggttctcacttg | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTaccttctttttacgtttactc | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTtaataatgaggctttggctt | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTgaccaagacatcagtagatt | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTagttgatttttgtggaaagg | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTactggaaagattgctgatta | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTatggtttcactactttctgt | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTgatggtgtatgcctattttg | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTaacaaaagttggatggaaag | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTggtattggagttacacagaa | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTataacaagagaagtgggttt | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTtaaatcacataaaccaccca | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTtgcctatattaaccttgacc | |
| GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTaaatggtatgaatggacgta | |
| T7-P5-dT | TAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCTtttttttttttttttttt |
a
Oligonucleotides used in viral-fragment enrichment method 1 and 2, respectively. P7, Illumina primer; VSP, SARS-CoV-2-specific primer; P5, Illumina primer; T7, T7 promoter for in vitro transcription; N6, random hexamer; dT, oligo(dT).
b
Lowercase letters represent virus specific primers/regions.