1. Table S4. List of genes significantly changed in late acute phase vs convalescent phase (HG-focus platform) Probeset IDGene SymbolGene Titlep-valueFold-Change 202411_atIFI27interferon, alpha-inducible protein 27046.6463 209773_s_atRRM2ribonucleotide reductase M24.66E-4212.1533 202589_atTYMSthymidylate synthetase8.37E-438.21124 206641_atTNFRSF17 tumor necrosis factor receptor superfamily, member 171.51E-236.90624 205692_s_atCD38CD38 molecule2.24E-396.38218 204026_s_atZWINTZW10 interactor1.70E-385.89996 218039_atNUSAP1nucleolar and spindle associated protein 11.33E-384.98383 209714_s_atCDKN3cyclin-dependent kinase inhibitor 32.47E-344.79591 209642_atBUB1 budding uninhibited by benzimidazoles 1 homolog (yeast)2.91E-354.70794 218350_s_atGMNNgeminin, DNA replication inhibitor5.05E-394.65378 202870_s_atCDC20cell division cycle 20 homolog (S. cerevisiae)3.34E-384.4008 202345_s_atFABP5fatty acid binding protein 5 (psoriasis-associated)1.77E-354.28958 204170_s_atCKS2CDC28 protein kinase regulatory subunit 26.20E-354.27096 203560_atGGH gamma-glutamyl hydrolase (conjugase, folylpolygammaglutamyl hydrolase)2.65E-264.22619 203418_atCCNA2cyclin A23.63E-354.05763 202705_atCCNB2cyclin B21.48E-343.91231 206632_s_atAPOBEC3B apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B1.74E-163.90992 201202_atPCNAproliferating cell nuclear antigen1.00E-363.8445 203554_x_atPTTG1pituitary tumor-transforming 11.78E-343.80797 203213_atCDK1cyclin-dependent kinase 13.50E-333.72729 201292_atTOP2Atopoisomerase (DNA) II alpha 170kDa4.16E-353.6958 219148_atPBKPDZ binding kinase4.33E-293.66208 204444_atKIF11kinesin family member 111.04E-273.63297 202095_s_atBIRC5baculoviral IAP repeat-containing 56.14E-363.51073 218662_s_atNCAPGnon-SMC condensin I complex, subunit G5.81E-343.46753 210052_s_atTPX2 TPX2, microtubule-associated, homolog (Xenopus laevis)1.81E-363.32847 212592_atIGJ immunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptid2.28E-213.32143 219117_s_atFKBP11FK506 binding protein 11, 19 kDa6.97E-273.28381 209340_atUAP1UDP-N-acteylglucosamine pyrophosphorylase 12.45E-253.25402 201930_atMCM6minichromosome maintenance complex component 61.37E-333.20054 221521_s_atGINS2GINS complex subunit 2 (Psf2 homolog)6.75E-363.2005 214446_atELL2elongation factor, RNA polymerase II, 21.62E-192.98713 203362_s_atMAD2L1MAD2 mitotic arrest deficient-like 1 (yeast)4.59E-252.96509 204162_atNDC80 NDC80 homolog, kinetochore complex component (S. cerevisiae)9.55E-332.90765 222077_s_atRACGAP1Rac GTPase activating protein 11.52E-312.88742 202954_atUBE2Cubiquitin-conjugating enzyme E2C8.74E-372.88309 209709_s_atHMMRhyaluronan-mediated motility receptor (RHAMM)5.76E-332.86716 200670_atXBP1X-box binding protein 11.57E-242.82083 208079_s_atAURKAaurora kinase A1.33E-302.80977 204962_s_atCENPAcentromere protein A1.39E-292.80204 204439_atIFI44Linterferon-induced protein 44-like5.48E-162.78656 203358_s_atEZH2enhancer of zeste homolog 2 (Drosophila)1.09E-322.7748 204767_s_atFEN1flap structure-specific endonuclease 18.11E-342.74142 218009_s_atPRC1protein regulator of cytokinesis 11.45E-282.73517 204023_atRFC4replication factor C (activator 1) 4, 37kDa5.64E-302.71296 201923_atPRDX4peroxiredoxin 44.57E-242.70944 200599_s_atHSP90B1heat shock protein 90kDa beta (Grp94), member 16.61E-262.671 203755_atBUB1B budding uninhibited by benzimidazoles 1 homolog beta (yeast)4.14E-302.66926 221760_atMAN1A1mannosidase, alpha, class 1A, member 11.79E-292.66329

2. Table S4 continued 218254_s_atSAR1BSAR1 homolog B (S. cerevisiae)1.91E-312.64868 202107_s_atMCM2minichromosome maintenance complex component 21.31E-332.63995 210164_atGZMB granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)1.93E-272.62008 204822_atTTKTTK protein kinase2.86E-262.5884 219159_s_atSLAMF7SLAM family member 74.92E-262.56478 205483_s_atISG15ISG15 ubiquitin-like modifier1.56E-182.55293 202655_atMANFmesencephalic astrocyte-derived neurotrophic factor6.68E-292.50904 200986_atSERPING1serpin peptidase inhibitor, clade G (C1 inhibitor), member 11.87E-122.5085 221004_s_atITM2Cintegral membrane protein 2C6.02E-192.50261 202086_atMX1 myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse)8.38E-252.50172 200783_s_atSTMN1stathmin 17.58E-332.46624 205393_s_atCHEK1CHK1 checkpoint homolog (S. pombe)2.55E-272.45848 205267_atPOU2AF1POU class 2 associating factor 11.45E-132.41956 218681_s_atSDF2L1stromal cell-derived factor 2-like 14.24E-202.37996 202270_atGBP1guanylate binding protein 1, interferon-inducible, 67kDa1.34E-142.36355 219306_atKIF15kinesin family member 151.31E-272.36262 213226_atCCNA2cyclin A29.68E-292.35029 200968_s_atPPIBpeptidylprolyl isomerase B (cyclophilin B)3.18E-212.33083 209610_s_atSLC1A4 solute carrier family 1 (glutamate/neutral amino acid transporter), member 41.15E-232.31721 201664_atSMC4structural maintenance of chromosomes 41.82E-282.31235 203153_atIFIT1interferon-induced protein with tetratricopeptide repeats 19.89E-092.30327 214512_s_atSUB1SUB1 homolog (S. cerevisiae)1.66E-272.27455 202338_atTK1thymidine kinase 1, soluble1.94E-312.2583 201477_s_atRRM1ribonucleotide reductase M15.73E-252.25801 205967_atHIST1H4Chistone cluster 1, H4c1.14E-162.24663 205909_atPOLE2polymerase (DNA directed), epsilon 2 (p59 subunit)5.24E-322.24138 219211_atUSP18ubiquitin specific peptidase 181.46E-222.23566 209398_atHIST1H1Chistone cluster 1, H1c2.86E-292.23171 218875_s_atFBXO5F-box protein 56.76E-272.23013 204033_atTRIP13thyroid hormone receptor interactor 133.25E-292.23002 212020_s_atMKI67antigen identified by monoclonal antibody Ki-675.89E-322.21218 210046_s_atIDH2isocitrate dehydrogenase 2 (NADP+), mitochondrial4.82E-282.19873 202763_atCASP3caspase 3, apoptosis-related cysteine peptidase7.13E-292.19736 209464_atAURKBaurora kinase B6.41E-292.19497 201577_atNME1non-metastatic cells 1, protein (NM23A) expressed in5.37E-272.18965 204126_s_atCDC45cell division cycle 45 homolog (S. cerevisiae)9.65E-322.18492 201897_s_atCKS1BCDC28 protein kinase regulatory subunit 1B6.18E-312.17519 209457_atDUSP5dual specificity phosphatase 52.65E-162.167 214453_s_atIFI44interferon-induced protein 445.79E-172.12358 202760_s_at AKAP2 /// PALM2- AKAP2A kinase (PRKA) anchor protein 2 /// PALM2-AKAP2 readthrough1.05E-162.12255 217933_s_atLAP3leucine aminopeptidase 35.62E-222.1091 218755_atKIF20Akinesin family member 20A5.81E-292.09876 204092_s_atAURKAaurora kinase A2.05E-282.09105 218355_atKIF4Akinesin family member 4A6.91E-292.09053 205046_atCENPEcentromere protein E, 312kDa2.56E-262.08747 203968_s_atCDC6cell division cycle 6 homolog (S. cerevisiae)9.43E-282.08655 204415_atIFI6interferon, alpha-inducible protein 65.04E-162.08142 204173_atMYL6Bmyosin, light chain 6B, alkali, smooth muscle and non-muscle2.57E-302.07988 216237_s_atMCM5minichromosome maintenance complex component 55.53E-252.07618 203605_atSRP54signal recognition particle 54kDa9.43E-302.07488 208002_s_atACOT7acyl-CoA thioesterase 71.22E-272.07373 202468_s_atCTNNAL1catenin (cadherin-associated protein), alpha-like 15.55E-252.07303 201714_atTUBG1tubulin, gamma 16.68E-292.06807 33304_atISG20interferon stimulated exonuclease gene 20kDa4.65E-282.06759 202433_atSLC35B1solute carrier family 35, member B12.40E-262.05143 201088_atKPNA2karyopherin alpha 2 (RAG cohort 1, importin alpha 1)8.63E-302.03115 203857_s_atPDIA5protein disulfide isomerase family A, member 56.07E-192.02804

3. Table S4 continued 201761_atMTHFD2 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate c1.35E-302.0255 202779_s_atUBE2Subiquitin-conjugating enzyme E2S6.79E-272.02355 206978_atCCR2chemokine (C-C motif) receptor 27.05E-132.02089 201013_s_atPAICS phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxami2.24E-212.01802 208546_x_atHIST1H2BHhistone cluster 1, H2bh8.15E-182.01469 203344_s_atRBBP8retinoblastoma binding protein 85.57E-302.01257 201690_s_atTPD52tumor protein D523.08E-112.00359 208658_atPDIA4protein disulfide isomerase family A, member 47.73E-222.00123 204146_atRAD51AP1RAD51 associated protein 12.36E-232.00047 201506_atTGFBItransforming growth factor, beta-induced, 68kDa1.88E-22-2.00974 37028_atPPP1R15Aprotein phosphatase 1, regulatory (inhibitor) subunit 15A1.33E-11-2.02589 39318_atTCL1AT-cell leukemia/lymphoma 1A2.78E-18-2.03062 207113_s_atTNFtumor necrosis factor5.43E-05-2.03205 201887_atIL13RA1interleukin 13 receptor, alpha 12.25E-24-2.05197 219434_atTREM1triggering receptor expressed on myeloid cells 11.51E-13-2.1145 205987_atCD1CCD1c molecule8.66E-40-2.13861 204440_atCD83CD83 molecule4.04E-09-2.19082 219947_atCLEC4AC-type lectin domain family 4, member A1.36E-20-2.19971 205114_s_at CCL3 /// CCL3L1 /// CCL3L3 chemokine (C-C motif) ligand 3 /// chemokine (C-C motif) ligand 3-like 1 /// chemokine8.76E-06-2.20679 208146_s_atCPVLcarboxypeptidase, vitellogenic-like3.65E-24-2.25026 203413_atNELL2NEL-like 2 (chicken)3.76E-28-2.275 201631_s_atIER3immediate early response 31.18E-08-2.40363 210356_x_atMS4A1membrane-spanning 4-domains, subfamily A, member 16.95E-23-2.48645 213524_s_atG0S2G0/G1switch 27.36E-06-2.4945 208450_atLGALS2lectin, galactoside-binding, soluble, 23.02E-23-2.5018 39402_atIL1Binterleukin 1, beta9.15E-07-2.67247 219714_s_atCACNA2D3calcium channel, voltage-dependent, alpha 2/delta subunit 31.37E-38-2.72636 213348_atCDKN1Ccyclin-dependent kinase inhibitor 1C (p57, Kip2)2.34E-17-2.7351 203485_atRTN1reticulon 16.96E-36-2.78108 204748_atPTGS2 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)2.79E-08-2.82777 214414_x_atHBA1 /// HBA2hemoglobin, alpha 1 /// hemoglobin, alpha 23.00E-09-2.95615 211506_s_atIL8interleukin 89.14E-08-3.10191 209458_x_atHBA1 /// HBA2hemoglobin, alpha 1 /// hemoglobin, alpha 21.87E-10-3.41108 217232_x_atHBBhemoglobin, beta3.24E-11-3.6272