TABLE 1.
Primers used for amplification of the SARS-CoV-2 genome
| Primer | Nucleotide sequence | Pool | Length (no. of nucleotides) | Starta | Enda |
|---|---|---|---|---|---|
| CoV-2_1_L | ACCAACCAACTTTCGATCTCTTGT | 1 | 24 | 30 | 54 |
| CoV-2_1_R | ATGCACTCAAGAGGGTAGCCAT | 1 | 22 | 867 | 845 |
| CoV-2_2_L | AGTGGTGTTACCCGTGAACTCA | 2 | 22 | 763 | 785 |
| CoV-2_2_R | ACCTTCGGAACCTTCTCCAACA | 2 | 22 | 1600 | 1578 |
| CoV-2_3_L_v2 | GGCTGTGTGTTCTCTTATGTTGGT | 1 | 24 | 1487 | 1510 |
| CoV-2_3_R | ACAATCCCTTTGAGTGCGTGAC | 1 | 22 | 2414 | 2392 |
| CoV-2_4_L | TTTGGCTTTGTGTGCTGACTCT | 2 | 22 | 2319 | 2341 |
| CoV-2_4_R | AGCAGAAGTGGCACCAAATTCC | 2 | 22 | 3166 | 3144 |
| CoV-2_5_L | GATTGTGAAGAAGAAGAGTTTGAGCC | 1 | 26 | 3067 | 3093 |
| CoV-2_5_R | CAGCGATCTTTTGTTCAACTTGCT | 1 | 24 | 3878 | 3854 |
| CoV-2_6_L | TCGCACAAATGTCTACTTAGCTGT | 2 | 24 | 3771 | 3795 |
| CoV-2_6_R | ACCGAGCAGCTTCTTCCAAATT | 2 | 22 | 4658 | 4636 |
| CoV-2_7_L | ACAACTGTAGCGTCACTTATCAACA | 1 | 25 | 4549 | 4574 |
| CoV-2_7_R | AGCATCTTGTAGAGCAGGTGGA | 1 | 22 | 5359 | 5337 |
| CoV-2_8_L | ACTTCTATTAAATGGGCAGATAACAACTG | 2 | 29 | 5257 | 5286 |
| CoV-2_8_R | AGCCACCACATCACCATTTAAGT | 2 | 23 | 6172 | 6149 |
| CoV-2_9_L | CCATATCCAAACGCAAGCTTCG | 1 | 22 | 6019 | 6041 |
| CoV-2_9_R | GCCTCTAGACAAAATTTACCGACACT | 1 | 26 | 6903 | 6877 |
| CoV-2_10_L | AAACCGTGTTTGTACTAATTATATGCCTT | 2 | 29 | 6747 | 6776 |
| CoV-2_10_R | ACTGTAGTGACAAGTCTCTCGCA | 2 | 23 | 7694 | 7671 |
| CoV-2_11_L | GCTTTTGCAAACTACACAATTGGAAT | 1 | 26 | 7592 | 7618 |
| CoV-2_11_R | GCAGCACTACGTATTTGTTTTCGT | 1 | 24 | 8463 | 8439 |
| CoV-2_12_L | GCGCAGGTAGCAAAAAGTCACA | 2 | 22 | 8365 | 8387 |
| CoV-2_12_R | TGATCTTTCACAAGTGCCGTGC | 2 | 22 | 9241 | 9219 |
| CoV-2_13_L | TGCTCATGGATGGCTCTATTATTCAA | 1 | 26 | 9128 | 9154 |
| CoV-2_13_R | GAGCCTTTGCGAGATGACAACA | 1 | 22 | 9977 | 9955 |
| CoV-2_14_L | GTGATGTGCTATTACCTCTTACGCA | 2 | 25 | 9848 | 9873 |
| CoV-2_14_R | CAGCAGCGTACAACCAAGCTAA | 2 | 22 | 10688 | 10666 |
| CoV-2_15_L | CAACTGGAGTTCATGCTGGCAC | 1 | 22 | 10556 | 10578 |
| CoV-2_15_R | GTCCACACTCTCCTAGCACCAT | 1 | 22 | 11394 | 11372 |
| CoV-2_16_L | TGTCTGGTTTTAAGCTAAAAGACTGTGT | 2 | 28 | 11285 | 11313 |
| CoV-2_16_R | ATCACCATTAGCAACAGCCTGC | 2 | 22 | 12181 | 12159 |
| CoV-2_17_L | GGCAACCTTACAAGCTATAGCCT | 1 | 23 | 12078 | 12101 |
| CoV-2_17_R | CCTACAAGGTGGTTCCAGTTCTG | 1 | 23 | 12907 | 12884 |
| CoV-2_18_L | GGAGGTAGGTTTGTACTTGCACTG | 2 | 24 | 12793 | 12817 |
| CoV-2_18_R | CGTCCTTTTCTTGGAAGCGACA | 2 | 22 | 13621 | 13599 |
| CoV-2_19_L | ACAGGCACTAGTACTGATGTCGT | 1 | 23 | 13509 | 13532 |
| CoV-2_19_R | TGGGTGGTATGTCTGATCCCAA | 1 | 22 | 14328 | 14306 |
| CoV-2_20_L | CAAAGCCTTACATTAAGTGGGATTTGT | 2 | 27 | 14224 | 14251 |
| CoV-2_20_R | GGTGCGAGCTCTATTCTTTGCA | 2 | 22 | 15108 | 15086 |
| CoV-2_21_L | AGGATCAAGATGCACTTTTCGCA | 1 | 23 | 15004 | 15027 |
| CoV-2_21_R | AGTAAGGTCAGTCTCAGTCCAACA | 1 | 24 | 15858 | 15834 |
| CoV-2_22_L | TGCATCTCAAGGTCTAGTGGCT | 2 | 22 | 15749 | 15771 |
| CoV-2_22_R | GCGTTTCTGCTGCAAAAAGCTT | 2 | 22 | 16648 | 16626 |
| CoV-2_23_L | CGATAATGTTACTGACTTTAATGCAATTGC | 1 | 30 | 16535 | 16565 |
| CoV-2_23_R | GTGCAGGTAATTGAGCAGGGTC | 1 | 22 | 17458 | 17436 |
| CoV-2_24_L | TCTTTGATGAAATTTCAATGGCCACA | 2 | 26 | 17350 | 17376 |
| CoV-2_24_R | GCTTCTTCGCGGGTGATAAACA | 2 | 22 | 18275 | 18253 |
| CoV-2_25_L | TGGCATACCTAAGGACATGACCT | 1 | 23 | 18167 | 18190 |
| CoV-2_25_R | ACCAATGTCGTGAAGAACTGGG | 1 | 22 | 19038 | 19016 |
| CoV-2_26_L | TGATGAACTGAAGATTAATGCGGCT | 2 | 25 | 18938 | 18963 |
| CoV-2_26_R | GCAGCAATGTCCACACCCAAAT | 2 | 22 | 19862 | 19840 |
| CoV-2_27_L | ACACAAAAGTTGATGGTGTTGATGT | 1 | 25 | 19714 | 19739 |
| CoV-2_27_R | GGTTGCCACGCTTGACTAGATT | 1 | 22 | 20678 | 20656 |
| CoV-2_28_L | TCTGTAGTTTCTAAGGTTGTCAAAGTGA | 2 | 28 | 20553 | 20581 |
| CoV-2_28_R | AAAGACATAACAGCAGTACCCCTTAA | 2 | 26 | 21443 | 21417 |
| CoV-2_29_L_v2 | CAAACCACGCGAACAAATAG | 1 | 20 | 21297 | 21316 |
| CoV-2_29_R_v2 | CGAAAAACCCTGAGGGAGAT | 1 | 20 | 22225 | 22206 |
| CoV-2_30_L | AAACAGGGTAATTTCAAAAATCTTAGGGAA | 2 | 30 | 22105 | 22135 |
| CoV-2_30_R | TGTGCTACCGGCCTGATAGATT | 2 | 22 | 22996 | 22974 |
| CoV-2_31_L | AACAATCTTGATTCTAAGGTTGGTGGT | 1 | 27 | 22876 | 22903 |
| CoV-2_31_R | TGCTGCATTCAGTTGAATCACCA | 1 | 23 | 23813 | 23790 |
| CoV-2_32_L | ACCCACAAATTTTACTATTAGTGTTACCAC | 2 | 30 | 23703 | 23733 |
| CoV-2_32_R | TGCACTTCAGCCTCAACTTTGT | 2 | 22 | 24537 | 24515 |
| CoV-2_33_L | TGCACAAGCTTTAAACACGCTT | 1 | 22 | 24426 | 24448 |
| CoV-2_33_R | GCAGCAGGATCCACAAGAACAA | 1 | 22 | 25324 | 25302 |
| CoV-2_34_L | CTAGGTTTTATAGCTGGCTTGATTGC | 2 | 26 | 25213 | 25239 |
| CoV-2_34_R | ACATGTTCAACACCAGTGTCTGT | 2 | 23 | 26075 | 26052 |
| CoV-2_35_L | GGGAATCTGGAGTAAAAGACTGTGT | 1 | 25 | 25969 | 25994 |
| CoV-2_35_R | AATGACCACATGGAACGCGTAC | 1 | 22 | 26857 | 26835 |
| CoV-2_36_L | TGGATCACCGGTGGAATTGCTA | 2 | 22 | 26744 | 26766 |
| CoV-2_36_R | GTGTTTTACGCCGTCAGGACAA | 2 | 22 | 27612 | 27590 |
| CoV-2_37_L | ACGAGGGCAATTCACCATTTCA | 1 | 22 | 27511 | 27533 |
| CoV-2_37_R | ACTGCCAGTTGAATCTGAGGGT | 1 | 22 | 28351 | 28329 |
| CoV-2_38_L | AGAGTATCATGACGTTCGTGTTGT | 2 | 24 | 28219 | 28243 |
| CoV-2_38_R | GCTTCTTAGAAGCCTCAGCAGC | 2 | 22 | 29045 | 29023 |
| CoV-2_39_L | TGCTTGACAGATTGAACCAGCT | 1 | 22 | 28940 | 28962 |
| CoV-2_39_R | TTCTCCTAAGAAGCTATTAAAATCACATGG | 1 | 30 | 29866 | 29836 |
a
Nucleotide positions relative to the Wuhan Hu-1 reference genome.