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C. B. D. F. A. G. E. Figure S1 A. 473 patients assessed for eligibility 1 patient COVID-19+ excluded • Decline to participate 472 patients eligible in ONCOVID Trial 378 patients excluded • Negative RT-qPCR • Controls unmatched (age, 95 patients selected for translational gender) with cases research analysis Cancer_FR1_Translational Research (TR) 43 allocated to Control group (TR) 52 allocated to COVID-19 group (TR) No detection of SARS-CoV-2 by: Detection of SARS-CoV-2 by: • RT-qPCR • RT-qPCR (n=50) • Serology • Serology (n=45) • CT-Scan • CT-Scan (n=2) 43 analyzed 35 Cancer_FR1 analyzed for viral shedding (see Figure S2) 34 Cancer_FR1 analyzed for Ct and ALC at diagnosis • Excluded for absence of positive RT-qPCR (n=2) • Excluded for absence ofALC and Ct (n=16) B. C. Mild Moderate Severe S H S 5(12) 21(50) 16(38) (n=42) COVID--19 10(20) * (n=52) 42(80) H (n=10) 5(50) 3(30) 2(20) Patients (%) Patients (%) D. E. S H Sym Asym Sym 32(78) 9(22) (n=41) COVID--19 (n=52) 41(79) 11(21) Asym 10(90) 1(10) (n=11) Patients (%) Patients (%) F. G. L LA M Mild Moderate Severe L 5(30) 6(35) 6(35) (n=17) COVID--19 LA 1(9) 4(36) 6(55) (n=52) 24(46) 11(21) 17(33) (n=11) M (n=24) 4(17) 14(58) 6(25) Patients (%) Patients (%) Figure S1 A. 52 cancer patients COVI D-19 + 2 cancer pati ents diagnosed by CT-Scan 50 cancer pati ents with at least 2 RT-qPCR (n=210 assa ys) 14 cancer pati ents with time lapse bet ween last positi ve RT-qPCR and first negati ve RT-qPCR > 40 days (n=38 assa ys) 36 cancer patients (n=172 assays) Median durati on of viral sh edding (range) : 35.5 (6-137) 1 canc er pati ent with no ne gati ve RT-qPCR (n=4 assays) 35 cancer pati ents with reli able viral shed ding monitori ng (n=168 assa ys) Median durati on of viral sh edding (range) : 40 days (7-13 7) (see Fi gure 1A-B) B. 100 HCW COVI D-19 + (n=200 assa ys) 43 HCW with only one RT–qPCR (n=43 assays) 57 HCW with at l east 2 R T-qPCR (n=155 assa ys) 7 HCW with ti me lapse bet ween last positi ve RT-qPCR and first negati ve RT- qPCR > 40 da ys (n=15 assa ys) 50 HCW (n=140 assays) Median durati on of viral sh edding (range) : 21 days (7- 117) 5 HCW with no ne gati ve RT-qPCR (n=22 assays) 45 HCW with R T-qPCR stu dy desi gn identit cal as canc er pati ents (n=118 assays) Median durati on of viral sh edding (range) : 21 days (7-90) ) (see Fi gure 1A -B) Fig ure S2 A. 178 patients included 63 patients excluded • Enrolled in Cancer_FR1 (n=59) • Absence of cancer status (n=4) 115 patients selected for analysis 35 patients excluded • Absence of Ct and ALC at diagnosis and/or reliable viral shedding 80 allocated to Cancer_FR1_CR Detection of SARS-CoV-2 by: • RT-qPCR (n=80) 46 Cancer_FR1_CR analyzed for viral shedding 50 Cancer_FR1_CR analyzed for Ct and ALC at diagnosis B. C. S H Mild Moderate Severe S (n=68) 10(15) 42(62) 16(23) COVID-19 68(85) 12(15) (n=80) H 3(25) 9(75) (n=12) D. E. S H Sym Asym Sym (n=66) 55(83) 11(17) COVID-19 (n=80) 66(82)66(82) 14(18)14(18) Asym 1 (n=14) 13(93) (7) F. G. L LA M Mild Moderate Severe L (n=10) 6(60) 4(40) 10 LA COVID-19 56(70) 14(18) (n=14) 3(21) 6(43) 5(36) (n=80) (12) M (n=56) 10(18) 39(70) 7(12) Figure S3 A. * * * * ** ** * * * * **** **** 40 **** **** 100 ** **** + *** 30 in cMo 30 + 75 non-cMo o l 20 50 20 HLADR CD14 − + 10 25 10 % Monocytes in CD45 % CD16 0 % CD169 0 0 Ctls Asy m ≤ 20d > 20d Reco very Ctls Asy m ≤ 20d > 20d Reco very Ctls Asy m ≤ 20d > 20d Reco very C. B. ** s ** ) 100 * hi *** * *** + * 10.00 10.00 CD38 75 + + in Neutrophil 1.00 − 1.00 50 in CD19 CD10 0.10 − 0.10 25 ransitional (CD24 % Neutrophils in CD45 0.01 0 0.01 T Ctls Asy m ≤ 20d > 20d Reco very Ctls Asy m ≤ 20d > 20d Reco very % Ctls Asy m ≤ 20d > 20d Reco very % CD101 D. E. * 0,95 * * * 0,96 * * **** * 0,053 * ** 100. 0 r) 100. 0 100 e it T 10. 0 10. 0 50 Ctls Ctls 1. 0 Asy m Asy m 1. 0 IL-4 (pg/mL) anti−RBD ( ≤ 20 d ≤ 20 d 30 > 20 d IgM anti−RBD (Titer) > 20 d IgA 0. 1 Rec overy 0. 1 Rec overy Ctls SVS LVS Ctls SVS LVS Ctls Asym ≤ 20d > 20d Reco very F. G. * * *** ** ** * *** 1e+07 ** * ** 300 * ** 1000 3e+06 100 ) 30 100 1e+06 10 IL-6 (pg/mL) 10 Calprotectin (pg/mL) 3e+05 CXCL8 (pg/mL 3 1 Ctls Asym ≤ 20d > 20d Reco very Ctls Asym ≤ 20d > 20d Reco very Ctls Asym ≤ 20d > 20d Reco very H. * * 50 * * 30 1000 10 100 Legend: IFNγ (pg/mL) 5 Contro l CXCL10 (pg/mL) 10 Ctls Asym ≤ 20d > 20d Reco very Ctls Asym ≤ 20d > 20d Reco very Asymptomat ic SVS I. LVS * **** ** ** Rec ov ery **** **** *** *** **** ****** * ** **** o **** ** 1e+02 io 3.00 ** t 1.00 2a ra α 1e+00 FN 0.30 I / 1 /0.10 CXCL10 rati 1 1e −02 IFNγ 0.03 CCL Ctls Asym ≤ 20d > 20d Reco very Ctls Asym ≤ 20d > 20d Reco very Figu re S 4 1 2 3 Ct D0 Symptoms Sev eri ty Age Vir us sh edd ing Gender Cancer status classical monocyt es (CD14 +CD16 low )(cM o) in Mon ocytes Neutrophils in CD45 + CC L11/ CXC L11 CXCL5 CD1 01+CD10 + in Ne utr ophi ls Non-Switched Memory in CD19 + IgD -CD27 - in CD19 + Ig D+CD 27- (Na ive) in CD 19+ Scaled log valu e 4 + + CD19 in CD45 2 no n−c Mo (CD14 lowCD16 +)in Mo nocytes 0 CCL 11/C XCL1 0 −2 IF Nγ/ INFα2a −4 CD16 9-HLA -DR + in cMo Ct_D0 CD 24-IgD+CD 27- (Nai ve) in CD19 + <25 CD24 +IgD -CD27 - in CD19 + >25 Gran zym e B-CD9 5−L - in non-n aiv e CD8 +CD3+ Control na CD2 4high CD 38high (Tra nsi tion al) in CD1 9+ ND CD4 +/CD 8+ in C D3+ Symptoms CD4 + in CD3 + Control Symptomatic PD−1 + in Eom eshigh TCF7 high non- naiv e CD8 +CD3+ Asymptomatic Gr anz yme B+PD−1+ in Eome shigh TC F7high non-na ive CD8 +CD 3+ Seve rity PD −1+ in non−naiv e CD8 +CD 3+ Control Mild + + EM2 in CD8 CD 3 Modera te IgM anti-NC Severe CXCL 11 Age < 65 IFNγ >= 65 CXCL8 Virus shedding CCL 11 Control SVS CCL22 LVS CCL7 na CCL19 Gender TNF α F M CCL26 Cancer status GM-CSF Local Local ly adv anced CCL21 Metastatic Calprotectin CX3CL1 IgG anti-RBD/IgG anti-NC Eomes high TCF7 high in non−n aiv e CD8 +CD3 + Gran zyme B+CD95− L+ in no n-nai ve CD8 +CD3+ Gr anz yme B+ in non-n aiv e CD8 +CD3 + Granzyme B+ in Eomes high TCF7 high non-n aiv e CD8 +CD3+ CD 101 +- CD10+- CD16 - in Ne utr oph ils PD− 1high CXC R5+ in non- naiv e CD4 +CD3+ PD−1 +Granzyme B+ in non−naiv e CD8 +CD3+ CD19 lowCD38 high CD27 + (P lasmab last) in CD 19+ CD3 8+HLA −DR + in non −nai ve CD8 +CD 3+ CD 38+ICOS + in PD −1high CXCR 5+ no n-n aiv e CD4 +CD3 + CD16 9+HLA DR+ in c Mo IFNα2a CXCL10 NK cells in CD45 + CD3 + in CD45 + Lymphocytes in CD45 + Non−naiv e in CD8 + CD3 + CD8 + in CD3 + Non−naiv e in CD4 +CD3 + 7 8 6 3 12 19 58 57 34 29 22 26 31 53 37 32 54 15 38 18 25 50 17 41 55 20 21 14 10 33 36 35 49 91 83 13 47 39 70 40 27 413 201 202 255 193 203 142 258 177 173 106 252 172 Figu re S5 1 2 3 Ct D0 Symptoms Severity Age Virus shedding Gender Cancer status classical Monocytes (CD14+CD16low)(cMo) in Monocytes Neutrophils in CD45+ Calprotectin CD4+ in CD3+ CD4+/CD8+ inCD3+ Granzyme B-CD95−L- in non-naive CD8+CD3+ CCL11/CXCL10 IgG anti-RBD/IgG anti-NC Scaled log value CD101-+CD10-+ CD16- in Neutrophils 4 IgM anti-NC 2 EM2 in CD8+CD3+ 0 −2 + + CD169 HLA-DR in cMo −4 CXCL10 Ct_D0 CX3CL1 <25 IFNγ/INFα2a >25 CXCL8 Control na TNFα ND GM-CSF Symptoms CCL26 Control Symptomatic IFNγ Asymptomatic CXCL11 Severity CCL11 Control Mild CCL22 Moderate CCL19 Severe CCL7 Age < 65 CCL21 >= 65 CD19lowCD38highCD27+ (Plasmablast) in CD19+ Virus shedding CD38+ICOS+ in PD−1highCXCR5+ non−naive CD4+CD3+ Control + + + + RecoveryS VS CD38 HLA−DR in non−naive CD8 CD3 Re covery LVS PD−1+ in EomeshighTCF7high non−naive CD8+CD3+ na PD−1+ in non−naive CD8+CD3+ Gender Granzyme B+PD−1+ in EomeshighTCF7highnon−naive CD8+CD3+ Female Male + + + + PD−1 Granzyme B in non−naive CD8 CD3 Cancer status CD8+ in CD3+ Local + + Locally advanced Non−naive in CD8 CD3 Metastatic Non−naive in CD8+CD3+ NK cells in CD45+ Lymphocytes in CD45+ CD3+ in CD45+ non−cMo (CD14lowCD16+)in Monocytes EomeshighTCF7high in non−naive CD8+CD3+ Granzyme B+ in non−naive CD8+CD3+ Granzyme B+CD95−L+ in non−naive CD8+CD3+ Granzyme B+ in EomeshighTCF7high non−naive CD8+CD3+ PD−1highCXCR5+ in non-naive CD4+CD3+ B cells in CD45+ Non-Switched Memory in CD19+ CD24-IgD+CD27- (Naive) in CD19+ IgD+CD27+ (Naive) in CD19+ CD24-IgD-CD27- in CD19+ CD24highCD38high (Transitional) in CD19+ CD169+HLA-DR+ in cMo IgD-CD27- in CD19+ CD101+CD10+ in Neutrophils CCL11/CXCL11 CXCL5 IFNα2a 6 6 8 3 7 27 70 39 38 54 32 15 41 35 49 37 91 3 33 13 67 50 79 14 30 31 53 55 17 26 25 12 57 19 58 10 29 34 18 83 95 472 443 278 471 202 467 172 462 151 3 193 465 137 201 442 413 423 419 446 473 425 252 427 133 173 Figure S6 A.
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