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Table 2 List of ORFs searched for and the transcript frequency for each ORF

From: SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

  MRC-5 cells A549 cells 293 cells
Feature Count 24 h Percent of total at 24 h Count 48 h Percent of total at 48 h Count 72 h Percent of total at 72 h Count 24 h Percent of total at 24 h Count 48 h Percent of total at 48 h Count 72 h Percent of total at 72 h Count 24 h Percent of total at 24 h
Total of all reads 4443 100.00 9201 100.00 6849 100.00 2070 100.00 1937 100.00 1811 100.00 62,281 100.00
SARS_CoV_2_S_protein 4156 93.54 8570 93.14 6453 94.22 1536 74.20 1447 74.70 1645 90.83 10,586 17.00
None from list 148 3.33 278 3.02 214 3.12 92 4.44 112 5.78 53 2.93 4138 6.64
pIX 21 0.47 27 0.29 23 0.34 14 0.68 13 0.67 2 0.11 909 1.46
DBP(E2A) 1 0.02 3 0.03 0 0.00 205 9.90 95 4.90 13 0.72 5198 8.35
fibre(L5) 0 0.00 0 0.00 0 0.00 2 0.10 9 0.46 2 0.11 6011 9.65
hexon(L3) 0 0.00 0 0.00 0 0.00 16 0.77 20 1.03 3 0.17 3990 6.41
33K_full_length(L4) 0 0.00 0 0.00 0 0.00 10 0.48 20 1.03 7 0.39 3217 5.17
preVII(L2) 0 0.00 0 0.00 0 0.00 12 0.58 7 0.36 2 0.11 3212 5.16
100K(L4) 0 0.00 0 0.00 0 0.00 11 0.53 25 1.29 7 0.39 2212 3.55
i_leader_protein 0 0.00 0 0.00 0 0.00 18 0.87 46 2.37 11 0.61 1969 3.16
IVa2 0 0.00 0 0.00 0 0.00 6 0.29 14 0.72 3 0.17 1676 2.69
pV(L2) 0 0.00 0 0.00 0 0.00 4 0.19 3 0.15 0 0.00 1373 2.20
52/55K(L1) 0 0.00 0 0.00 0 0.00 20 0.97 28 1.45 6 0.33 1345 2.16
22K(L4) 0 0.00 0 0.00 0 0.00 9 0.43 9 0.46 2 0.11 1193 1.92
preX(L2) 0 0.00 0 0.00 0 0.00 6 0.29 8 0.41 4 0.22 1180 1.89
E4_orf2 0 0.00 2 0.02 0 0.00 0 0.00 1 0.05 2 0.11 1040 1.67
E4_orf3 0 0.00 1 0.01 0 0.00 13 0.63 8 0.41 3 0.17 1011 1.62
preVI(L3) 0 0.00 0 0.00 0 0.00 8 0.39 7 0.36 1 0.06 821 1.32
preVIII(L4) 0 0.00 0 0.00 0 0.00 1 0.05 2 0.10 1 0.06 821 1.32
penton_base(L2) 0 0.00 0 0.00 0 0.00 1 0.05 2 0.10 1 0.06 631 1.01
Ad5_E1b_19K 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 506 0.81
E4_orf1 0 0.00 0 0.00 0 0.00 1 0.05 0 0.00 0 0.00 286 0.46
preIIIa(L1) 0 0.00 0 0.00 0 0.00 5 0.24 3 0.15 0 0.00 239 0.38
E4_orf4 0 0.00 0 0.00 0 0.00 2 0.10 2 0.10 0 0.00 187 0.30
UXP 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 159 0.26
Ad5_E1a_13S 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 97 0.16
E4_orf6_7 0 0.00 0 0.00 0 0.00 1 0.05 0 0.00 1 0.06 79 0.13
23K_protease(L3) 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 70 0.11
Ad5_E1a_12S 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 26 0.04
preTP(E2B) 0 0.00 0 0.00 0 0.00 1 0.05 0 0.00 0 0.00 23 0.04
Ad5_pIX 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 10 0.02
pol(E2B) 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 4 0.01
Ad5_E1a_10S(171R) 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 3 0.00
E4_orf6 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 3 0.00
Ad5_E1b_13S(E1b-84R) 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 2 0.00
Ad5_E1b_22S(E1b 55 K) 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 2 0.00
Ad5_E1a_9S 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 1 0.00
Ad5_E1a_11S(217R) 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00
Ad5_E1b_14.5S(E1b-93R) 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00
Ad5_E1b_14S(E1b-156R) 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00
Ad5_E1b_novel-84R 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00
  1. This table details how many transcripts would code for each indicated ORF from the ChAdOx1 nCoV-19 genome or ORFs coded by the region of Ad5 integrated into the HEK293 cell line. The “total of all reads” row indicates how many transcripts map to either the ChAdOx nCoV-19 genome or the region of human Ad5 integrated into the HEK 293 genome. The “none from list” row indicates how many transcripts did map but the pipeline was unable to correlate the 5′ most ORF on that transcript with any of the known ORFs from the genomes under consideration