Extended Data Table 1.
Primer list used for SARS-CoV-2 infectious clones construction, RT-PCR and sequencing.
| Construction of Alpha full length and Alpha-backbone infectious clone | Forward primer | Reverse primer |
|---|---|---|
| C241T | atctaggtttTgtccgggtgtgaccgaaag | ctttcggtcacacccggacAaaacctagat |
| C913T | tgcactttgtcTgaacaactggactt | aagtccagttgttcAgacaaagtgca |
| C3037T | gtattgttctttTtaccctccagatgagg | cctcatctggagggtaAaaagaacaatac |
| C3177T | ctgctcttcaacTtgaagaagagcaa | ttgctcttcttcaAgttgaagagcag |
| C3267T | cagacaactaTtattcaaacaattgttgagg | cctcaacaattgtttgaataAtagttgtctg |
| C5388A | ggctggtgaagctgAtaacttttgtgc | gcacaaaagttaTcagcttcaccagcc |
| C5986T | attcttatttTacagagcaaccaattg | caattggttgctctgtAaaataagaat |
| T6954C | gataaatattaCaatttggtttttac | gtaaaaaccaaattGtaatatttatc |
| 11288–11296del | gatactagtttgaagctaaaagactgtgt | acacagtcttttagcttcaaactagtatc |
| C14408T | tacagtgttcccacTtacaagttttggacc | ggtccaaaacttgtaAgtgggaacactgta |
| C14676T | gtcaaaccTggtaattttaacaaag | ctttgttaaaattaccAggtttgac |
| C15279T | gaaaaccctcaTcttatgggttgggat | atcccaacccataagAtgagggttttc |
| T16176C | ctaatgataacacCtcaaggtattggga | tcccaataccttgaGgtgttatcattag |
| C27972T/G28048T | cttaacatcaaccatatgtagttgatgacccgtgtcctattcacttcta | ttatagctcctactctaatataccatttagaatagaagtgaata ggaca |
| A28111G/C28144T | cagtgcatcgatatcggtaattatacagtttcctgtttaccttttac | gtaaaaggtaaacaggaaactgtataattaccgatatcgatgcactg |
| A28271del/28280–28282GAT-CTA | caaactaaatgtctctaaatggaccccaaaatcagcg | cgctgattttggggtccatttagagacatttagtttg |
| 28881–28883GGG-AAC | caactccaggcagcagtaaacgaacttctcctgc | gcaggagaagttcgtttactgctgcctggagttg |
| C28977T | tgagagcaaaatgtttggtaaaggccaaca | tgttggcctttaccaaacattttgctctca |
| Alpha-F123-F1 | cattatacgaagttatattcgatgcggccgctaatacgactcactatagattaaag | gggccgacaacatgaagacagtg |
| Alpha-F123-F2 | acactgtcttcatgttgtcggcccaaatgttaacaaag | ctattacgtttgtaacacatcatacaTgtAgatgaattac |
| Alpha-F123-F3 | gtatgatgtgttacaaacgtaatagagcaacaagag | aggtcgactctagaggatcccacATCGAtggtctcaaaggcttcagtagtatctttagc |
| Alpha-F4 | tgtagaaaacccagatatatt | caaaacactctacacgagcac |
| Alpha-F567-F1 | tatacgaagttatattcgatgcggccgcgtctcagagtgctttggtttatgataataag | cttttgttgtataaacccacaaatg |
| Alpha-F567-F2 | catttgtgggtttatacaacaaaag | caatcaagccagctataaaacc |
| Alpha-F567-F3 | ggttttatagctggcttgattg | cgaggcttcttagaagcctca |
| Alpha-backbone-F567-F1 | tatacgaagttatattcgatgcggccgcgtctcagagtgctttggtttatgataataag | cttttgttgtataaacccacaaatg |
| Alpha-backbone-F567-F2 | catttgtgggtttatacaacaaaag | caatcaagccagctataaaacc |
| Alpha-backbone-F567-F3 | ggttttatagctggcttgattg | cgaggcttcttagaagcctca |
| C210T | GTTTCGTCCGTTTTGCAGCCGATCATC | GATGATCGGCTGCAAAACGGACGAAAC |
| C241T | ATCTAGGTTTTGTCCGGGTGTGACCGAAAG | CTTTCGGTCACACCCGGACAAAACCTAGAT |
| C1191T | CCAGTTGCGTCACTAAATGAATGCAACC | GGTTGCATTCATTTAGTGACGCAACTGG |
| C1267T | GGCAGACGGGTGATTTTGTTAAAGCC | GGCTTTAACAAAATCACCCGTCTGCC |
| C3037T | GTATTGTTCTTTTTACCCTCCAGATGAGG | CCTCATCTGGAGGGTAAAAAGAACAATAC |
| C5184T | ACACAACTGATCTTAGTTTTCTGGGTAG | CTACCCAGAAAACTAAGATCAGTTGTGT |
| C6539T | GAGGTTGGCTACACAGATCTAATGGC | GCCATTAGATCTGTGTAGCCAACCTC |
| T8782C | ACACATGGTTTAGCCAGCGTGGTGGTAG | CTACCACCACGCTGGCTAAACCATGTGT |
| C9891T | GATACTTAGTTCTTTATAATAAGTACAAG | CTTGTACTTATTATAAAGAACTAAGTATC |
| T11418C | CTTGACACTCGCTTATAAAGTTTATTATGG | CCATAATAAACTTTATAAGCGAGTGTCAAG |
| T12946C | GGTCCTAAAGTGAAGTACTTATACTTTATT | AATAAAGTATAAGTACTTCACTTTAGGACC |
| C14408T | TACAGTGTTCCCACTTACAAGTTTTGGACC | GGTCCAAAACTTGTAAGTGGGAACACTGTA |
| T14444C | GTGAGAAAAATATTTGCTGATGGTGTTCCA | TGGAACACCATCAGCAAATATTTTTCTCAC |
| G15451A | GGTCATGTGTGGCAGTTCACTATATGTT | AACATATAGTGAACTGCCACACATGACC |
| C16466T | GTAAATCACATAAACTACCCATTAGTTTTCC | GGAAAACTAATGGGTAGTTTATGTGATTTAC |
| A20262G | GGAAATTGATTTCTTGGAATTAGCTATGG | CCATAGCTAATTCCAAGAAATCAATTTCC |
| C20320T | GCTATGCCTTCGAATATATCGTTTATGG | CCATAAACGATATATTCGAAGGCATAGC |
| C21618G | GTGTGTTAATCTTAGAACCAGAACTC | GAGTTCTGGTTCTAAGATTAACACAC |
| G21987A | GATCCATTTTTGGATGTTTATTACCAC | GTGGTAATAAACATCCAAAAATGGATC |
| 22029–22034 deletion | GAAAGTGGAGTTTATTCTAGTGCGAATAATTGC | ATAAACTCCACTTTCCATCCAACTTTTGTTGTT |
| T22917G | GGTGGTAATTATAATTACCGGTATAGATTGTTTAGG | CCTAAACAATCTATACCGGTAATTATAATTACCACC |
| C22995A | GGCCGGTAGCAAACCTTGTAATGGTG | CACCATTACAAGGTTTGCTACCGGCC |
| A23604G | GACTAATTCTCGTCGGCGGGCACGTAGTGT | ACACTACGTGCCCGCCGACGAGAATTAGTC |
| G24410A | GGAAAACTTCAAAATGTGGTCAACC | GGTTGACCACATTTTGAAGTTTTCC |
| C24745T | CTCATGGTGTAGTTTTCTTGCATGTGAC | GTCACATGCAAGAAAACTACACCATGAG |
| C25469T | GATGCTACTCCTTTAGATTTTGTTCGCG | CGCGAACAAAATCTAAAGGAGTAGCATC |
| T26767C | CCGGTGGAATTGCTACCGCAATGGCTTG | CAAGCCATTGCGGTAGCAATTCCACCGG |
| T27638C | CGTGCCAGATCAGCTTCACCTAAACTGT | ACAGTTTAGGTGAAGCTGATCTGGCACG |
| C27739T/C27752T | TCAAAAGAAAGATAGAATGATTGAACTTTCA | CATTCTATCTTTCTTTTGAATGTGAAGCAAAGTG |
| C28144T | TCGGTAATTATACAGTTTCCTGTTTACCTTTTAC | GTAAAAGGTAAACAGGAAACTGTATAATTACCGA |
| 28248–28253 deletion | GACGTTCGTGTTGTTTTAATCTAAACGAACAAACT | AGTTTGTTCGTTTAGATTAAAACAACACG AACGTC |
| 28271 deletion | GAACAAACTAAATGTCTGATAATGGACCCC | GGGGTCCATTATCAGACATTTAGTTTGTTC |
| A28461G | CATGGCAAGGAAGGCCTTAAATTCCCTC | GAGGGAATTTAAGGCCTTCCTTGCCATG |
| G28881T | TCCAGGCAGCAGTATGGGAACTTCTCCTGC | GCAGGAGAAGTTCCCATACTGCTGCCTGGA |
| G29402T/G29427A | GCTTATGAAACTCAAGCCTTACCGCAGAAACAGAAGAAAC | GTTTCTGCGGTAAGGCTTGAGTTTCATAAGCCTTCTTCTT |
| G29742T/C29762T | CACTCGGAGTACGATCGAGTGTATAGTGAACAAT | ACTATACACTCGATCGTACTCCGAGTGGCCTCGG |
| Delta-F123-F1 | cattatacgaagttatattcgatgcggccgctaatacgactcactatagattaaag | gggccgacaacatgaagacagtg |
| Delta-F123-F2 | acactgtcttcatgttgtcggcccaaatgttaacaaag | aggtcgactctagaggatcccacATCGAtggtctcaaaggcttcagtagtatctttagc |
| Delta-F4 | cctcttacaacagcagccaaact | caaaacactctacacgagcac |
| Delta-F567 | tatacgaagttatattcgatgcggccgcgtctcagagtgct ttggtttatgataataag | caaacatgagaattggtcgacggccc |
| Delta-backbone-F567-F1 | tatacgaagttatattcgatgcggccgcgtctcagagtgctttggtttatgataataag | cttttgttgtataaacccacaaatg |
| Delta-backbone-F567-F2 | catttgtgggtttatacaacaaaag | caatcaagccagctataaaacc |
| Delta-backbone-F567-F3 | ggttttatagctggcttgattg | cgaggcttcttagaagcctca |
| RT-PCR for Sanger sequencing | Forward primer | Reverse primer |
|
| ||
| Delta vs Delta-P681 | tccacttttaagtgttatggag | gttaaagcacggtttaattgtg |
| Delta-P681 vs Alpha | tccacttttaagtgttatggag | gttaaagcacggtttaattgtg |
| Delta vs Alpha | tccacttttaagtgttatggag | gttaaagcacggtttaattgtg |
| Alpha vs Alpha-spike/Delta-backbone | tgtagaaaacccagatatatt | tggaaaaccagctgatttgtc |
| Delta vs Alpha-spike/Delta-backbone | tccacttttaagtgttatggag | gttaaagcacggtttaattgtg |
| RT-PCR for NGS | Forward primer | Reverse primer |
|
| ||
| Delta vs Alpha | ggttttaattgttactttcctttaca | aagaacacctgtgcctgtt |
| Alpha vs Alpha-spike/Delta-backbone | acagtgttcccacctacaagt | ccagaagcagcgtgcatagc |
| Delta vs Alpha-spike/Delta-backbone | ggttttaattgttactttcctttaca | aagaacacctgtgcctgtt |
| Sanger sequencing | Forward primer | |
|
| ||
| Delta vs Delta-P681 | aggatgttaactgcacaga | |
| Delta-P681 vs Alpha | aggatgttaactgcacaga | |
| Delta vs Alpha | gattgctgattataattata | |
| Alpha vs Alpha-spike/Delta-backbone | gttgacactgacttaacaaagcc | |
| Delta vs Alpha-spike/Delta-backbone | gattgctgattataattata | |