Generation of viral cDNA clones and recovery of recombinant SARS-CoV-2 and SARS-CoV-2-GFP.a, Schematic representation of SARS-CoV-2 (upper panel) and SARS-CoV-2-GFP (lower panel) genome organisation with 12 and 14 viral subgenomic overlapping cDNA fragments, respectively, used for TAR cloning. pT7, T7 RNA polymerase promoter; UTR, untranslated region; An, poly (A) tail; J represents assembly junction between two overlapping DNA fragments. b, Representation of predicted RNA stem-loop (SL) secondary structures formed in the 5'-UTR of SARS-CoV-2. The SARS-CoV-2 RNA secondary structures were manually adjusted based on RNA structure predictions by Chan et al.22. Black letters and numbering represents the SARS-CoV-2 5'-terminal sequence. Red letters depict nucleotides that are different within the SARS-CoV 5'-terminal sequence ("-" indicates nucleotide deletion in SARS-CoV versus SARS-CoV-2). N20 indicates 20 nucleotides. SL structures 1, 2, and 4 are shown according to Chan et al.22. Note that recombinant virus construct 1 (rSARS-CoV-2 clone 1) and construct 4 (rSARS-CoV-GFP clone 4) contain the SARS-CoV-2 5'-terminus with nucleotides 3-5 (UAA) exchanged by nucleotides 3-5 (AUU) of SARS-CoV; recombinant virus construct 2 (rSARS-CoV-2 clone 2) and construct 5 (rSARS-CoV-2-GFP clone 5) contain a 5'-terminus with the first 124 nucleotides from SARS-CoV; and recombinant virus construct 3 (rSARS-CoV-2 clone 3) and construct 6 (rSARS-CoV-GFP clone 6) contain the authentic SARS-CoV-2 5'-terminus. 