EVA

Template for recombinant SARS-CoV-2 rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), C-terminal tagging of orf6 with BirA, separated by a flexible linker (GGGGS). Full protocol for virus recovery using the CLEVER method in (10.7554/eLife.89035). Functionality of BirA in rescued virus not tested.

Template for recombinant SARS-CoV-2 rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), C-terminal tagging of orf8 with 3xFLAG, separated by a flexible linker (GGGGS). Use as fragment D2, S gene not sequence verified. Full protocol for virus recovery using the CLEVER method in (10.7554/eLife.89035).

Template for recombinant SARS-CoV-2 rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), C-terminal tagging of orf7b with 3xFLAG, separated by a flexible linker (GGGGS). Use as fragment D2, S gene not sequence verified. Full protocol for virus recovery using the CLEVER method in (10.7554/eLife.89035).

Template for recombinant SARS-CoV-2 rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), N-terminal tagging of orf7a with 3xFLAG, separated by a flexible linker (GGGGS). Use as fragment D2, S gene not sequence verified. Full protocol for virus recovery using the CLEVER method in (10.7554/eLife.89035).

Template for recombinant SARS-CoV-2 rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), C-terminal tagging of orf6 with 3xFLAG, separated by a flexible linker (GGGGS). Use as fragment D2, S gene not sequence verified. Full protocol for virus recovery using the CLEVER method in (10.7554/eLife.89035).

Template for recombinant SARS-CoV-2 rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), C-terminal tagging of orf3a with 3xFLAG, separated by a flexible linker (GGGGS). Use as fragment D2, S gene not sequence verified. Full protocol for virus recovery using the CLEVER method in (10.7554/eLife.89035).

Template for recombinant SARS-CoV-2 rescue; encodes fragment C of SARS-CoV-2 (nt15100-20958). Needed for recombinant virus rescue using the CLEVER method as described in (10.7554/eLife.89035).

Template for recombinant SARS-CoV-2 rescue; encodes fragment B of SARS-CoV-2 (nt8590-15107). Needed for recombinant virus rescue using the CLEVER method as described in (10.7554/eLife.89035).

Template for recombinant SARS-CoV-2 rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), with deletion of orf3a. Full protocol for virus recovery using the CLEVER method in (10.7554/eLife.89035).

Template for recombinant SARS-CoV-2 rescue; encodes fragment A of SARS-CoV-2 (nt1-8594). Needed for recombinant virus rescue using the CLEVER method as described in (10.7554/eLife.89035).

Template for recombinant SARS-CoV-2 rescue; Linker plasmid for the CLEVER method as described in (10.7554/eLife.89035). This plasmid encodes the 3' termination signals (poly A, HDV ribozyme, SV40 termination signal), followed by a spacer region and CMV promoter. The signal sequences are flanked by 100 bp of SARS-CoV-2 3' UTR and 5' UTR.

Template for recombinant SARS-CoV-2 rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), with deletion of orf3a, orf6, orf7a and orf8. Full protocol for virus recovery using the CLEVER method in (10.7554/eLife.89035). Only Fragment D2 sequence verified.

Template for recombinant SARS-CoV-2 rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of orf6, orf7a and orf8. Full protocol for virus recovery using the CLEVER method in (10.7554/eLife.89035).

Template for recombinant SARS-CoV-2 rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of orf6 and orf8. Full protocol for virus recovery using the CLEVER method in (10.7554/eLife.89035).

Recombinant SARS-CoV-2, orf7a endogenously tagged with 3xFLAG (N terminal), separated by a flexible linker GGGGS. Virus was produced using the CLEVER method as described in (doi: 10.7554/eLife.89035).

Recombinant SARS-CoV-2, orf7b endogenously tagged with 3xFLAG (C terminal), separated by a flexible linker GGGGS. Virus was produced using the CLEVER method as described in (doi: 10.7554/eLife.89035).

Infectious cell culture supernatant containing SARS-CoV-2 (strain hCoV-19/Slovenia/LP3/30/25; lineage Omicron, XFG). This strain is preserved in viral storage medium -80°C.

Template for recombinant SARS-CoV-2 rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of orf8. Full protocol for virus recovery using the CLEVER method in (10.7554/eLife.89035).

Template for recombinant SARS-CoV-2 rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of orf7b. Full protocol for virus recovery using the CLEVER method in (10.7554/eLife.89035).

Template for recombinant SARS-CoV-2 rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), Wuhan background with Omicron BA.1 S gene. Full protocol for virus recovery using the CLEVER method in (10.7554/eLife.89035).

Template for recombinant SARS-CoV-2 rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), Wuhan background with Omicron BA.2 S gene. Full protocol for virus recovery using the CLEVER method in (10.7554/eLife.89035).

Template for recombinant SARS-CoV-2 rescue; encodes fragment D of SARS-CoV-2 (nt20950-29867), Wuhan background with Omicron BA.4/ BA.5 S gene. Full protocol for virus recovery using the CLEVER method in (10.7554/eLife.89035).

Template for recombinant SARS-CoV-2 rescue; encodes fragment D1 of SARS-CoV-2 (nt20950-25522), encodes S of XBB.1.5 lineage. Full protocol for virus recovery using the CLEVER method in (10.7554/eLife.89035).

Template for recombinant SARS-CoV-2 rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), XBB.1.5 lineage. Full protocol for virus recovery using the CLEVER method in (10.7554/eLife.89035). E-expressing cells will be required to produce ∆E viruses.

Template for recombinant SARS-CoV-2 rescue; encodes fragment D2 of SARS-CoV-2 (nt25422-29867), with deletion of orf6. Full protocol for virus recovery using the CLEVER method in (10.7554/eLife.89035).