Supplementary Information Whole transcriptome profiling reveals major cell types in the cellular immune response against acute and chronic active Epstein‐Barr virus infection Huaqing Zhong1, Xinran Hu2, Andrew B. Janowski2, Gregory A. Storch2, Liyun Su1, Lingfeng Cao1, Jinsheng Yu3, and Jin Xu1 Department of Clinical Laboratory1, Children's Hospital of Fudan University, Minhang District, Shanghai 201102, China; Departments of Pediatrics2 and Genetics3, Washington University School of Medicine, Saint Louis, Missouri 63110, United States. Supplementary information includes the following: 1. Supplementary Figure S1: Fold‐change and correlation data for hyperactive and hypoactive genes. 2. Supplementary Table S1: Clinical data and EBV lab results for 110 study subjects. 3. Supplementary Table S2: Differentially expressed genes between AIM vs. Healthy controls. 4. Supplementary Table S3: Differentially expressed genes between CAEBV vs. Healthy controls. 5. Supplementary Table S4: Fold‐change data for 303 immune mediators. 6. Supplementary Table S5: Primers used in qPCR assays. Supplementary Figure S1. Fold‐change (a) and Pearson correlation data (b) for 10 cell markers and 61 hypoactive and hyperactive genes identified in subjects with acute EBV infection (AIM) in the primary cohort. Note: 23 up‐regulated hyperactive genes were highly correlated positively with cytotoxic T cell (Tc) marker CD8A and NK cell marker CD94 (KLRD1), and 38 down‐regulated hypoactive genes were highly correlated positively with B cell, conventional dendritic cell (cDC), Treg and granulocyte markers. Supplementary Table S1 -Clinical data and EBV lab results EBV DNA load in EBV DNA load in Time at Days HTA2.0 qPCR Flow cytometry EBV VCA- EBV VCA- Patient ID Gender Age Group Cohort plasma (copies/ml white blood cells EBV-NA sampling from Symtoms hospitolized Days to recovery (outcome) microarray assay assay IgM IgG blood) (copies/ml blood) disease onset (total) 15VC1799 M 27 m AIM Primary Yes Yes 1.34E+04 n/a (+) (+) (-) 5 d fever, tonsil swelling, cervical lymphadenopathy 3 14 15VC1803 F 18 m AIM Primary Yes Yes undetectable 3.58E+03 (+) (+) (-) 3 d fever, cough, tonsil swelling, cervical lymphadenopathy 3 15 15VC2293 M 4 y AIM Primary Yes Yes undetectable 2.38E+03 (+) (+) (-) 2 d fever, cough, tonsil swelling, cervical lymphadenopathy, liver enlargement 3 15 fever, sore throat, tonsil swelling, cervical lymphadenopathy, liver 15VC2386 F 3 y AIM Primary Yes Yes 1.03E+04 n/a (+) (+) (-) 2 d 820 enlargement ED483 M 24 m AIM Primary Yes Yes undetectable 1.07E+05 (+) (+) (-) 2 d fever, tonsil swelling, enlargement of liver & spleen 3 15 fever, sore throat, tonsil swelling, cervical lymphadenopathy, enlargement ED490 M 12 m AIM Primary Yes Yes 3.68E+03 5.13E+05 (+) (+) (-) 7 d 520 of liver & spleen fever, jaundice, tonsil swelling, cervical lymphadenopathy, enlargement of 15VC2295 F 3 y CAEBV Primary Yes Yes 5.46E+05 n/a (-) (+) (+) 2 m 45 hemophagocytic syndrome liver & spleen, ALT & AST elevated fever, cervical lymphadenopathy, enlargement of liver & spleen, ALT & disease continued, with recurrence 15VC2407 M 9 y CAEBV Primary Yes Yes 1.46E+07 n/a (-) (+) (+) 3 m 17 AST elevated of 2 times disease continued, with recurrence 15VC2414 M 15 y CAEBV Primary Yes Yes 3.44E+03 n/a (-) (+) (+) 12 m fever, tonsil swelling, splenectomy 79 of 2 times disease continued, with recurrence 15VC2656 F 2 y CAEBV Primary Yes Yes 7.70E+03 n/a (-) (+) (+) 3 m fever, enlargement of liver & spleen, ALT & AST elevated 13 of 2 times disease continued, with recurrence 15VC3454 M 12 y CAEBV Primary Yes Yes 3.60E+05 n/a (-) (+) (+) 14 m fever, skin impetigo, cervical lymphadenopathy, liver enlargement 27 of 3 times C13 M 1 y CTRL Primary Yes Yes undetectable n/a (-) (+) (-) C15 F 3 y CTRL Primary Yes Yes undetectable n/a (-) (+) (+) C21 F 1 y CTRL Primary Yes Yes undetectable n/a (-) (+) (-) C22 M 3 y CTRL Primary Yes Yes undetectable n/a (-) (+) (+) C23 M 3 y CTRL Primary Yes Yes undetectable n/a (-) (+) (+) C24 F 4 y CTRL Primary Yes Yes undetectable n/a (-) (+) (+) fever, palpebral edema, sore throat, skin rash, tonsil swelling, cervical 16VC0100 F 4 y AIM Secondary Yes 1.80E+03 1.55E+06 (+) (+) (-) 6 d outpatient 23 lymphadenopathy fever, sore throat, tonsil swelling, cervical lymphadenopathy, ALT & AST 16VC9468 F 9 y AIM Secondary Yes 6.17E+03 n/a (+) (+) (-) 7 d 427 elevated 16VC9539 F 3 y AIM Secondary Yes undetectable 2.01E+06 (+) (+) (-) 3 d fever, palpebral edema, tonsil swelling, cervical lymphadenopathy outpatient 29 fever, sore throat, skin rash, palpebral edema, tonsil swelling, cervical 16VC9546 M 1 y AIM Secondary Yes 3.98E+03 n/a (+) (+) (-) 4 d outpatient 24 lymphadenopathy, enlargement of liver & spleen, ALT & AST elevated 16VC9677 F 2 y AIM Secondary Yes undetectable 1.46E+05 (+) (-) (-) 4 d fever, sore throat, tonsil swelling, cervical lymphadenopathy outpatient 22 16VC9724 F 1 y AIM Secondary Yes undetectable 1.63E+04 (+) (+) (-) 3 d fever, sore throat, skin rash, tonsil swelling, cervical lymphadenopathy, outpatient 19 16VC9731 M 2 y AIM Secondary Yes 2.88E+03 3.76E+06 (+) (+) (-) 4 d fever, sore throat, cough, tonsil swelling outpatient 19 fever, palpebral edema, tonsil swelling, cervical lymphadenopathy, 16VC9784 M 4 y AIM Secondary Yes undetectable 5.51E+04 (+) (+) (-) 4 d 323 enlargement of liver & spleen, ALT & AST elevated 16VC9799 M 12 y AIM Secondary Yes undetectable 2.80E+04 (+) (+) (-) 10 d fever, cough, sore throat, tonsil swelling, cervical lymphadenopathy outpatient 30 fever, palpebral edema, sore throat, tonsil swelling, cervical 16VC9842 M 3 y AIM Secondary Yes 1.02E+03 2.30E+05 (+) (+) (-) 3 d 313 lymphadenopathy fever, cough, tonsil swelling, cervical lymphadenopathy, enlargement of ED482 * F 5 y AIM Secondary Yes undetectable 1.07E+04 (+) (+) (-) 10 d 923 liver & spleen fever, palpebral edema, tonsil swelling, cervical lymphadenopathy, ALT & ED504 * F 12 y AIM Secondary Yes undetectable 2.17E+04 (+) (+) (-) 3 d 519 AST elevated IM-1(17ES171) M 3 y AIM Secondary cell surface 1.26E+03 3.53E+04 (+) (+) (-) 7 d fever, tonsil swelling, cervical lymphadenopathy, ALT & AST elevated outpatient 20 IM-10(17ES204) F 1 y AIM Secondary cell surface undetectable 1.87E+03 (+) (+) (-) 3 d fever, tonsil swelling, cervical lymphadenopathy, ALT & AST elevated 5 26 fever, cough, tonsil swelling, cervical lymphadenopathy, ALT & AST IM-11(17ES2247) M 9 y AIM Secondary intracellular undetectable 5.91E+03 (+) (+) (-) 4 d outpatient 23 elevated IM-12(17ES2279) M 3 y AIM Secondary intracellular 1.57E+03 3.01E+04 (+) (+) (-) 4 d fever, palpebral edema, tonsil swelling, cervical lymphadenopathy, outpatient 25 fever, palpebral edema, tonsil swelling, sore throat, cervical IM-13(17ES2281) M 7 y AIM Secondary intracellular 7.24E+03 3.40E+05 (+) (+) (-) 2 d 318 lymphadenopathy, fever, palpebral edema, tonsil swelling, cervical lymphadenopathy, IM-14(17ES3780) M 2 y AIM Secondary intracellular 2.39E+03 4.50E+05 (+) (+) (-) 3 d 317 palpebral edema fever, sore throat, cough, tonsil swelling, cervical lymphadenopathy, ALT & IM-15(17ES3929) F 3 y AIM Secondary intracellular 6.06E+03 1.60E+06 (+) (+) (-) 2 d outpatient 23 AST elevated IM-16(17ES3979) M 2 y AIM Secondary intracellular undetectable 1.30E+05 (+) (+) (-) 4 d fever, sore throat, tonsil swelling, cervical lymphadenopathy outpatient 24 IM-17(17ES3998) M 2 y AIM Secondary intracellular undetectable 3.64E+04 (+) (+) (-) 3 d fever, sore throat, tonsil swelling, cervical lymphadenopathy 3 27 fever, palpebral edema, cough, tonsil swelling, cervical lymphadenopathy, IM-18(17ES4051) M 3 y AIM Secondary intracellular undetectable 9.29E+03 (+) (+) (-) 4 d 422 enlargement of liver & spleen, ALT & AST elevated IM-2(17ES182) M 2 y AIM Secondary cell surface undetectable undetectable (+) (-) (-) 2 d fever, skin rash, cough, cervical lymphadenopathy 310 fever, palpebral edema, tonsil swelling, cervical lymphadenopathy, ALT & IM-3(17ES183) M 7 y AIM Secondary cell surface undetectable 3.39E+03 (+) (+) (-) 2 d 322 AST elevated IM-4(17ES310) M 10 y AIM Secondary cell surface undetectable 3.20E+04 (+) (+) (-) 3 d fever, palpebral edema, tonsil swelling, cervical lymphadenopathy 7 18 IM-5(17ES322) M 4 y AIM Secondary cell surface undetectable 1.20E+03 (+) (+) (-) 5 d fever, cough, tonsil swelling 6 34 IM-6(17ES509) M 2 y AIM Secondary cell surface undetectable 4.21E+05 (+) (-) (-) 6 d fever, cough, tonsil swelling outpatient 24 IM-7(17ES618) M 7 y AIM Secondary cell surface undetectable 1.19E+03 (+) (-) (-) 3 d fever, tonsil swelling, cervical lymphadenopathy, ALT & AST elevated 3 16 IM-8(17ES619) M 4 y AIM Secondary cell surface undetectable 2.01E+03 (+) (+) (-) 4 d fever, sore throat, cough 3 26 IM-9(17ES1904) M 1 y AIM Secondary cell surface 1.54E+04 9.62E+05 (+) (-) (-) 3 d fever, tonsil swelling, cervical lymphadenopathy 3 14 IM41 F 5Y AIM Secondary population undetectable 2.40E+03 (+) (-) (-) 3d fever, cough, tonsil swelling outpatient 10 IM42 F 2Y AIM Secondary population undetectable 1.65E+05 (+) (+) (-) 4 d fever, tonsil swelling, cervical lymphadenopathy，palpebral edema outpatient 15 IM43 M 2Y AIM Secondary population 4.70E+03 2.00E+05 (+) (+) (-) 5d fever, tonsil swelling, cervical lymphadenopathy，palpebral edema 3 18 Page 1 of 2 EBV DNA load in EBV DNA load in Time at Days HTA2.0 qPCR Flow cytometry EBV VCA- EBV VCA- Patient ID Gender Age Group Cohort plasma (copies/ml white blood cells EBV-NA sampling from Symtoms hospitolized Days to recovery (outcome) microarray assay assay IgM IgG blood) (copies/ml blood) disease onset