Rapid cloning-free mutagenesis of new SARS-CoV-2 variants using a novel reverse genetics platform.
Kipfer ET, Hauser D, Lett MJ, Otte F, Urda L, Zhang Y, Lang CMR, Chami M, Mittelholzer C, Klimkait T
Elife. 2023 Nov 21;12:RP89035. doi: 10.7554/eLife.89035.
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Article
Plasmids from Article
| ID | Plasmid | Purpose |
|---|---|---|
| 211731 | pUC19_CoV-2_linker | Linker fragment for direct rescue of SARS-CoV-2, including 5' Promoter and 3' Termination signals and 100bp SARS-CoV-2 homology regions |
| 253115 | pUC19_CoV-2_frD1 | Encodes SARS-CoV-2 Wuhan spike |
| 253116 | pUC19_CoV-2_frD_S Omicron BA.1 | For recombinant virus rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), Wuhan backbone with Omicron BA.1 spike; chimeric |
| 253117 | pUC19_CoV-2_frD_S Omicron BA.2 | For recombinant virus rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), Wuhan backbone with Omicron BA.2 spike; chimeric |
| 253119 | pUC19_CoV-2_frD1_XBB.1.5 S | For recombinant virus rescue; encodes fragment D1 of SARS-CoV-2 (nt20950-25522), Omicron isolate XBB.1.5 Spike |
| 253121 | pUC19_CoV-2_frD_ΔE/GFP Δ68 | For recombinant virus rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), with deletion of envelope (residual AA) , orf6, orf8. GFP is inserted in the locus of envelope |
| 253122 | pUC19_CoV-2_frD2_XBB_ΔE67 3* | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of envelope, orf6, orf7a, premature stop codon in orf3a at AA213. GFP is inserted in the locus of env |
| 253124 | pUC19_CoV-2_frD_ΔORF3a | For recombinant virus rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), with deletion of orf3a |
| 253125 | pUC19_CoV-2_frD2_ΔORF6 | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), deletion of orf6 |
| 253126 | pUC19_CoV-2_frD2_ΔORF7a | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), deletion of orf7a |
| 253127 | pUC19_CoV-2_frD2_ΔORF7b | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), deletion of orf7b |
| 253128 | pUC19_CoV-2_frD2_ΔORF8 | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), deletion of orf8 |
| 253129 | pUC19_CoV-2_frD2_ΔORF68 | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), deletion of orf6 and orf8 |
| 253130 | pUC19_CoV-2_frD2_ΔORF67a8 | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), deletion of orf6, orf7a and orf8 |
| 253132 | pUC19_CoV-2_frD_ORF6-BirA | For recombinant virus rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), BirA fused to orf6, C-terminal |
| 253144 | pUC19_CoV-2_frD ΔS/GFP | For recombinant virus rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), with deletion of spike, GFP is inserted at the locus of Spike |
| 253146 | pUC19_CoV-2_frD2 ΔE7 3* Δ6/H1 WSN | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of envelope, orf6, orf7a;stop codon at AA213 in orf3a; Influenza H1 (WSN) replaces orf6 |
| 253147 | pUC19_CoV-2_frD2 ΔE7 3* Δ6/H1 PR8 | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of envelope, orf6, orf7a;stop codon at AA213 in orf3a; Influenza H1 (PR8) replaces orf6 |
| 253150 | pUC19_CoV-2_frD2_ΔrE/N1 PR8 Δ67 3* | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of envelope (residual AA), orf6, orf7a;stop codon at AA213 in orf3a; Influenza N1 (PR8) replaces env |
| 253151 | pUC19_CoV-2_frD2 ΔE6 3* Δr7a/H1 PR8 | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of envelope, orf6, orf7a (residual AA); stop codon at AA213 in orf3a; Influenza H1 (PR8) replaces orf7a |
| 253152 | pUC19_CoV-2_frD2_ΔrE/N1 Δ6 3* Δ7a/H1 PR8 | Virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), deletion of env (residual AA), orf6, orf7a;stop codon at AA213 in orf3a; Influenza N1 (PR8) replaces envelope; H1 (PR8) replaces orf7a |
| 253153 | pUC19_CoV-2_frD2 ΔE6 3* Δr7a/H1 WSN | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), deletion of env, orf6, orf7a (residual AA);stop codon at AA213 in orf3a; Influenza H1 (WSN) replaces orf7a |
| 253154 | pUC19_CoV-2_frD2_ΔrE/N1 WSN Δ67 3* | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of env (residual AA), orf6, orf7a; stop codon at AA213 in orf3a; Influenza N1 (WSN) replaces envelope |
| 253155 | pUC19_CoV-2_frD2_ΔrE/N1 Δ6 3* Δ7a/H1 WSN | Virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of env (residual AA), orf6, orf7a; stop codon at AA213 in orf3a;Influenza N1 (WSN) replaces env;H1 (WSN) replaces orf7a |
| 253157 | pUC19_CoV-2_frD_ΔE/F DS-Cav1 ΔCT ΔS67 3* | For recombinant virus rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), with deletion of spike, envelope, orf6, orf7a;stop codon at AA213 in orf3a; stabilized RSV F replaces envelope |
| 253160 | pUC19_CoV-2_frD_ΔrE/H1 WSN ΔTM ΔS67 3* | For recombinant virus rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), with deletion of spike, env (residual AA), orf6, orf7a;stop codon at AA213 in orf3a; Influenza H1 (WSN) ΔTM replaces env |
| 253161 | pUC19_CoV-2_frD2 ΔE6 3* Δ7a/H1 WSN ΔTM | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of envelope, orf6, orf7a;stop codon at AA213 in orf3a; Influenza H1 (WSN) ΔTM replaces orf7a |
| 253162 | pUC19_CoV-2_ frD2_ΔE67 3* NA-P2A-N PR8 | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of envelope, orf6, orf7a;stop codon at AA213 in orf3a; Influenza N1 (WSN)-P2A-N |
| 253165 | pUC19_CoV-2_ frD2 ΔE6 3* Δr7a/H1 PR8 ΔTM | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of envelope, orf6, orf7a;stop codon at AA213 in orf3a; Influenza H1 (PR8) ΔTM replaces orf7a |
| 253166 | pUC19_CoV-2_ frD2 ΔE6 3* Δr7a/N1 PR8 | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of envelope, orf6, orf7a (residual AA);stop codon at AA213 in orf3a; Influenza N1 (PR8) replaces orf7a |
| 253168 | pUC19_CoV-2_ frD_Δ3E/H1 PR8 Δ67a | For recombinant virus rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), with deletion of orf3a, envelope, orf6, orf7a; Influenza H1 (PR8) replaces orf3a and envelope |
| 253169 | pUC19_CoV-2_ frD_Δ3E/N1 PR8 Δ67a | For recombinant virus rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), with deletion of orf3a, envelope, orf6, orf7a; Influenza N1 (PR8) replaces orf3a and envelope |
| 253170 | pUC19_CoV-2_ frD2_ΔE67 3* VSVG-P2A-N | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of envelope, orf6, orf7a;stop codon at AA213 in orf3a; VSV glycoprotein fused to N, P2A |
| 253171 | pUC19_CoV-2_ frD2 ΔE6 3* Δr7a/VSVG | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of envelope, orf6, orf7a (residual AA);stop codon at AA213 in orf3a; VSV glycoprotein replaces orf7a |
| 253172 | pUC19_CoV-2_ frD_Δ3E/VSVG Δ67a | For recombinant virus rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), with deletion of envelope, orf6, orf7a;stop codon at AA213 in orf3a; VSV glycoprotein replaces orf3a and envelope |
| 253176 | pUC19_CoV-2_frD ΔS_RABVG CT CoV-2 ΔE67 3* | For recombinant virus rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), with deletion of spike, env, orf6, orf7a;stop codon at AA213 in orf3a; rabies glycoprotein (CT SARS-2) replaces spike |
| 253177 | pUC19_CoV-2_frD_Δ3E_RABVG Δ67a | For recombinant virus rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), with deletion of orf3a, envelope, orf6, orf7a; rabies glycoprotein replaces orf3a and envelope |
| 253178 | pUC19_CoV-2_frD ΔrS_GP LCMV ΔE67 3* | For recombinant virus rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), with deletion of spike (partial), envelope, orf6, orf7a;stop codon at AA213 in orf3a; LCMV glycoprotein replaces spike |
| 253179 | pUC19_CoV-2_frD_Δ3E_GP LCMV Δ67a | For recombinant virus rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), with deletion of orf3a, envelope, orf6, orf7a; LCMV glycoprotein replaces orf3a and envelope |
| 253180 | pUC19_CoV-2_frD2_ΔrE/esxA Δ67 3* | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of envelope, orf6, orf7a;stop codon at AA213 in orf3a; Mycobacterium tuberculosis esxA replaces envelope |
| 253183 | pUC19_CoV-2_frB | For recombinant virus rescue; encodes fragment B of SARS-CoV-2 (nt8590-15107) |
| 253184 | pUC19_CoV-2_frC | For recombinant virus rescue; encodes fragment C of SARS-CoV-2 (nt15100-20958) |
| 253185 | pUC19_CoV-2_frD_SV40 | For recombinant virus rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867) |
| 253186 | pUC19_CoV-2_frD2_ΔE67 3* | For recombinant virus rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of envelope, orf6, orf7a;stop codon at AA213 in orf3a |