#METABOLOMICS WORKBENCH gardinassi_20220908_111125 DATATRACK_ID:3450 STUDY_ID:ST002291 ANALYSIS_ID:AN003743 PROJECT_ID:PR001469 VERSION 1 CREATED_ON September 10, 2022, 12:44 pm #PROJECT PR:PROJECT_TITLE Integrated metabolic and inflammatory signatures associated with severity, PR:PROJECT_TITLE fatality, and recovery of COVID-19 PR:PROJECT_TYPE Research PR:PROJECT_SUMMARY Severe manifestations of coronavirus disease 2019 (COVID-19) and mortality have PR:PROJECT_SUMMARY been associated with physiological alterations that provide insights into the PR:PROJECT_SUMMARY pathogenesis of the disease. Moreover, factors that drive recovery from COVID-19 PR:PROJECT_SUMMARY can be explored to identify correlates of protection. The cellular metabolism PR:PROJECT_SUMMARY represents a potential target to improve survival upon severe disease, but the PR:PROJECT_SUMMARY associations between the metabolism and the inflammatory response during PR:PROJECT_SUMMARY COVID-19 are not well defined. We analyzed blood laboratorial parameters, PR:PROJECT_SUMMARY cytokines, and metabolomes of 150 individuals with mild to severe disease, of PR:PROJECT_SUMMARY which 33 progressed to a fatal outcome. A subset of 20 individuals was PR:PROJECT_SUMMARY followed-up after hospital discharge and recovery of acute disease. We used PR:PROJECT_SUMMARY hierarchical community networks to integrate metabolomics profiles with PR:PROJECT_SUMMARY cytokines and markers of inflammation, coagulation, and tissue damage. Infection PR:PROJECT_SUMMARY by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) promotes PR:PROJECT_SUMMARY significant alterations in the plasma metabolome, whose activity varies PR:PROJECT_SUMMARY according to disease severity and correlates with oxygen saturation. PR:PROJECT_SUMMARY Differential metabolism underlying death was marked by amino acids and related PR:PROJECT_SUMMARY metabolites, such as glutamate, tryptophan and oxoproline; and lipids, including PR:PROJECT_SUMMARY progesterone, phosphocholine and lysophosphatidylcholines (lysoPCs). Individuals PR:PROJECT_SUMMARY that recovered from severe disease displayed persistent alterations enriched for PR:PROJECT_SUMMARY metabolism of purines, phosphatidylinositol phosphate and glycolysis. Recovery PR:PROJECT_SUMMARY of mild disease was associated with vitamin E metabolism. Data integration shows PR:PROJECT_SUMMARY that the metabolic response is a hub connecting other biological features during PR:PROJECT_SUMMARY disease and recovery. Infection by SARS-CoV-2 induces concerted activity of PR:PROJECT_SUMMARY metabolic and inflammatory responses that depend on disease severity and PR:PROJECT_SUMMARY collectively predict clinical outcomes of COVID-19. PR:INSTITUTE Federal University of Goiás PR:LAST_NAME Gardinassi PR:FIRST_NAME Luiz Gustavo PR:ADDRESS R. 235 s/n - Institute of Tropical Pathology and Public Health - Federal PR:ADDRESS University of Goiás PR:EMAIL luizgardinassi@ufg.br PR:PHONE +55 62 3209-6530 #STUDY ST:STUDY_TITLE Integrated metabolic and inflammatory signatures associated with severity, ST:STUDY_TITLE fatality, and recovery of COVID-19 ST:STUDY_TYPE Research ST:STUDY_SUMMARY Severe manifestations of coronavirus disease 2019 (COVID-19) and mortality have ST:STUDY_SUMMARY been associated with physiological alterations that provide insights into the ST:STUDY_SUMMARY pathogenesis of the disease. Moreover, factors that drive recovery from COVID-19 ST:STUDY_SUMMARY can be explored to identify correlates of protection. The cellular metabolism ST:STUDY_SUMMARY represents a potential target to improve survival upon severe disease, but the ST:STUDY_SUMMARY associations between the metabolism and the inflammatory response during ST:STUDY_SUMMARY COVID-19 are not well defined. We analyzed blood laboratorial parameters, ST:STUDY_SUMMARY cytokines, and metabolomes of 150 individuals with mild to severe disease, of ST:STUDY_SUMMARY which 33 progressed to a fatal outcome. A subset of 20 individuals was ST:STUDY_SUMMARY followed-up after hospital discharge and recovery of acute disease. We used ST:STUDY_SUMMARY hierarchical community networks to integrate metabolomics profiles with ST:STUDY_SUMMARY cytokines and markers of inflammation, coagulation, and tissue damage. Infection ST:STUDY_SUMMARY by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) promotes ST:STUDY_SUMMARY significant alterations in the plasma metabolome, whose activity varies ST:STUDY_SUMMARY according to disease severity and correlates with oxygen saturation. ST:STUDY_SUMMARY Differential metabolism underlying death was marked by amino acids and related ST:STUDY_SUMMARY metabolites, such as glutamate, tryptophan and oxoproline; and lipids, including ST:STUDY_SUMMARY progesterone, phosphocholine and lysophosphatidylcholines (lysoPCs). Individuals ST:STUDY_SUMMARY that recovered from severe disease displayed persistent alterations enriched for ST:STUDY_SUMMARY metabolism of purines, phosphatidylinositol phosphate and glycolysis. Recovery ST:STUDY_SUMMARY of mild disease was associated with vitamin E metabolism. Data integration shows ST:STUDY_SUMMARY that the metabolic response is a hub connecting other biological features during ST:STUDY_SUMMARY disease and recovery. Infection by SARS-CoV-2 induces concerted activity of ST:STUDY_SUMMARY metabolic and inflammatory responses that depend on disease severity and ST:STUDY_SUMMARY collectively predict clinical outcomes of COVID-19. ST:INSTITUTE Institute of Tropical Pathology and Public Health - Federal University of Goiás ST:LAST_NAME Gardinassi ST:FIRST_NAME Luiz Gustavo ST:ADDRESS R. 235 s/n - Institute of Tropical Pathology and Public Health - Federal ST:ADDRESS University of Goiás ST:EMAIL luizgardinassi@ufg.br ST:PHONE +55 62 3209-6530 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS POOLED_PLASMA_1 ID_2 Group:pooled_plasma RAW_FILE_NAME=ID_2.RAW; RAW_FILE_NAME=ID_2.mzXML SUBJECT_SAMPLE_FACTORS POOLED_PLASMA_2 ID_3 Group:pooled_plasma RAW_FILE_NAME=ID_3.RAW; RAW_FILE_NAME=ID_3.mzXML SUBJECT_SAMPLE_FACTORS POOLED_PLASMA_1 ID_30 Group:pooled_plasma RAW_FILE_NAME=ID_30.RAW; RAW_FILE_NAME=ID_30.mzXML SUBJECT_SAMPLE_FACTORS POOLED_PLASMA_2 ID_31 Group:pooled_plasma RAW_FILE_NAME=ID_31.RAW; RAW_FILE_NAME=ID_31.mzXML SUBJECT_SAMPLE_FACTORS POOLED_PLASMA_1 ID_65 Group:pooled_plasma RAW_FILE_NAME=ID_65.RAW; 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RAW_FILE_NAME=ID_129.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.161 ID_130 Group:Fatal RAW_FILE_NAME=ID_130.RAW; RAW_FILE_NAME=ID_130.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.139 (S R C) ID_131 Group:Fatal RAW_FILE_NAME=ID_131.RAW; RAW_FILE_NAME=ID_131.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.246 ID_132 Group:Fatal RAW_FILE_NAME=ID_132.RAW; RAW_FILE_NAME=ID_132.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.205 ID_133 Group:Fatal RAW_FILE_NAME=ID_133.RAW; RAW_FILE_NAME=ID_133.mzXML SUBJECT_SAMPLE_FACTORS HC.CoV270 ID_134 Group:Fatal RAW_FILE_NAME=ID_134.RAW; RAW_FILE_NAME=ID_134.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.226 ID_138 Group:Mild RAW_FILE_NAME=ID_138.RAW; RAW_FILE_NAME=ID_138.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.171 ID_139 Group:Mild RAW_FILE_NAME=ID_139.RAW; RAW_FILE_NAME=ID_139.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.230 ID_140 Group:Mild RAW_FILE_NAME=ID_140.RAW; RAW_FILE_NAME=ID_140.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.243 ID_141 Group:Mild RAW_FILE_NAME=ID_141.RAW; RAW_FILE_NAME=ID_141.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.242 ID_142 Group:Mild RAW_FILE_NAME=ID_142.RAW; RAW_FILE_NAME=ID_142.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.203 ID_143 Group:Mild RAW_FILE_NAME=ID_143.RAW; RAW_FILE_NAME=ID_143.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.229 ID_144 Group:Mild RAW_FILE_NAME=ID_144.RAW; RAW_FILE_NAME=ID_144.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.233 ID_145 Group:Mild RAW_FILE_NAME=ID_145.RAW; RAW_FILE_NAME=ID_145.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.298 ID_146 Group:Mild RAW_FILE_NAME=ID_146.RAW; RAW_FILE_NAME=ID_146.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.300 ID_147 Group:Mild RAW_FILE_NAME=ID_147.RAW; RAW_FILE_NAME=ID_147.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.329 ID_148 Group:Mild RAW_FILE_NAME=ID_148.RAW; RAW_FILE_NAME=ID_148.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.305 ID_149 Group:Mild RAW_FILE_NAME=ID_149.RAW; RAW_FILE_NAME=ID_149.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.301 ID_150 Group:Mild RAW_FILE_NAME=ID_150.RAW; RAW_FILE_NAME=ID_150.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.231 ID_151 Group:Mild RAW_FILE_NAME=ID_151.RAW; RAW_FILE_NAME=ID_151.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.026 ID_152 Group:Mild RAW_FILE_NAME=ID_152.RAW; RAW_FILE_NAME=ID_152.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.308 ID_153 Group:Mild RAW_FILE_NAME=ID_153.RAW; RAW_FILE_NAME=ID_153.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.363 ID_154 Group:Mild RAW_FILE_NAME=ID_154.RAW; RAW_FILE_NAME=ID_154.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.332 ID_155 Group:Mild RAW_FILE_NAME=ID_155.RAW; RAW_FILE_NAME=ID_155.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.333 ID_156 Group:Mild RAW_FILE_NAME=ID_156.RAW; RAW_FILE_NAME=ID_156.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.022 ID_157 Group:Severe RAW_FILE_NAME=ID_157.RAW; RAW_FILE_NAME=ID_157.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.022 ID_158 Group:Severe RAW_FILE_NAME=ID_158.RAW; RAW_FILE_NAME=ID_158.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.022 ID_159 Group:Severe RAW_FILE_NAME=ID_159.RAW; RAW_FILE_NAME=ID_159.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.185 ID_163 Group:Moderated RAW_FILE_NAME=ID_163.RAW; RAW_FILE_NAME=ID_163.mzXML SUBJECT_SAMPLE_FACTORS NHc.CoV.008 ID_164 Group:Moderated RAW_FILE_NAME=ID_164.RAW; RAW_FILE_NAME=ID_164.mzXML SUBJECT_SAMPLE_FACTORS NHc.CoV.039 ID_165 Group:Moderated RAW_FILE_NAME=ID_165.RAW; RAW_FILE_NAME=ID_165.mzXML SUBJECT_SAMPLE_FACTORS NHc.CoV.040 ID_166 Group:Mild RAW_FILE_NAME=ID_166.RAW; RAW_FILE_NAME=ID_166.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.211 ID_167 Group:Mild RAW_FILE_NAME=ID_167.RAW; RAW_FILE_NAME=ID_167.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.129 (S R F) ID_168 Group:Mild RAW_FILE_NAME=ID_168.RAW; RAW_FILE_NAME=ID_168.mzXML SUBJECT_SAMPLE_FACTORS NHc.CoV.006 ID_169 Group:Moderated RAW_FILE_NAME=ID_169.RAW; RAW_FILE_NAME=ID_169.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.166 (N R S) ID_170 Group:Moderated RAW_FILE_NAME=ID_170.RAW; RAW_FILE_NAME=ID_170.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.240 ID_171 Group:Mild RAW_FILE_NAME=ID_171.RAW; RAW_FILE_NAME=ID_171.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.241 ID_172 Group:Mild RAW_FILE_NAME=ID_172.RAW; RAW_FILE_NAME=ID_172.mzXML SUBJECT_SAMPLE_FACTORS NHc.CoV.030 ID_173 Group:Moderated RAW_FILE_NAME=ID_173.RAW; RAW_FILE_NAME=ID_173.mzXML SUBJECT_SAMPLE_FACTORS NHc.CoV.023 ID_174 Group:Severe RAW_FILE_NAME=ID_174.RAW; RAW_FILE_NAME=ID_174.mzXML SUBJECT_SAMPLE_FACTORS NHc.CoV.031 ID_175 Group:Moderated RAW_FILE_NAME=ID_175.RAW; RAW_FILE_NAME=ID_175.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.237 ID_176 Group:Mild RAW_FILE_NAME=ID_176.RAW; RAW_FILE_NAME=ID_176.mzXML SUBJECT_SAMPLE_FACTORS NHc.CoV.005 ID_177 Group:Moderated RAW_FILE_NAME=ID_177.RAW; RAW_FILE_NAME=ID_177.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.235 ID_178 Group:Moderated RAW_FILE_NAME=ID_178.RAW; RAW_FILE_NAME=ID_178.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.328 ID_179 Group:Mild RAW_FILE_NAME=ID_179.RAW; RAW_FILE_NAME=ID_179.mzXML SUBJECT_SAMPLE_FACTORS NHc.CoV.033 ID_180 Group:Moderated RAW_FILE_NAME=ID_180.RAW; RAW_FILE_NAME=ID_180.mzXML SUBJECT_SAMPLE_FACTORS NHc.CoV.033 ID_181 Group:Mild RAW_FILE_NAME=ID_181.RAW; RAW_FILE_NAME=ID_181.mzXML SUBJECT_SAMPLE_FACTORS HC.CoV. 033 (D D ID_182 Group:Control donor RAW_FILE_NAME=ID_182.RAW; RAW_FILE_NAME=ID_182.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.306 ID_186 Group:Control donor RAW_FILE_NAME=ID_186.RAW; RAW_FILE_NAME=ID_186.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.349 ID_187 Group:Control donor RAW_FILE_NAME=ID_187.RAW; RAW_FILE_NAME=ID_187.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.304 ID_188 Group:Control donor RAW_FILE_NAME=ID_188.RAW; RAW_FILE_NAME=ID_188.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.261 ID_189 Group:Control donor RAW_FILE_NAME=ID_189.RAW; RAW_FILE_NAME=ID_189.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.350 ID_190 Group:Control donor RAW_FILE_NAME=ID_190.RAW; RAW_FILE_NAME=ID_190.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.076 ID_191 Group:Control donor RAW_FILE_NAME=ID_191.RAW; RAW_FILE_NAME=ID_191.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.040 ID_192 Group:Control donor RAW_FILE_NAME=ID_192.RAW; RAW_FILE_NAME=ID_192.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.346 ID_193 Group:Control donor RAW_FILE_NAME=ID_193.RAW; RAW_FILE_NAME=ID_193.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.326 ID_194 Group:Control donor RAW_FILE_NAME=ID_194.RAW; RAW_FILE_NAME=ID_194.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.348 ID_195 Group:Control donor RAW_FILE_NAME=ID_195.RAW; RAW_FILE_NAME=ID_195.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.338 ID_196 Group:Control donor RAW_FILE_NAME=ID_196.RAW; RAW_FILE_NAME=ID_196.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.344 ID_197 Group:Control donor RAW_FILE_NAME=ID_197.RAW; RAW_FILE_NAME=ID_197.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.340 ID_198 Group:Control donor RAW_FILE_NAME=ID_198.RAW; RAW_FILE_NAME=ID_198.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.353 ID_199 Group:Control donor RAW_FILE_NAME=ID_199.RAW; RAW_FILE_NAME=ID_199.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.351 ID_200 Group:Control donor RAW_FILE_NAME=ID_200.RAW; RAW_FILE_NAME=ID_200.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.356 ID_201 Group:Control donor RAW_FILE_NAME=ID_201.RAW; RAW_FILE_NAME=ID_201.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.342 ID_202 Group:Control donor RAW_FILE_NAME=ID_202.RAW; RAW_FILE_NAME=ID_202.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.343 ID_203 Group:Control donor RAW_FILE_NAME=ID_203.RAW; RAW_FILE_NAME=ID_203.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.355 ID_204 Group:Control donor RAW_FILE_NAME=ID_204.RAW; RAW_FILE_NAME=ID_204.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.051 ID_205 Group:Control donor RAW_FILE_NAME=ID_205.RAW; RAW_FILE_NAME=ID_205.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.085 ID_206 Group:Control donor RAW_FILE_NAME=ID_206.RAW; RAW_FILE_NAME=ID_206.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.052 ID_207 Group:Control donor RAW_FILE_NAME=ID_207.RAW; RAW_FILE_NAME=ID_207.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.082 ID_208 Group:Control donor RAW_FILE_NAME=ID_208.RAW; RAW_FILE_NAME=ID_208.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.345 ID_209 Group:Control donor RAW_FILE_NAME=ID_209.RAW; RAW_FILE_NAME=ID_209.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.345 ID_210 Group:Control donor RAW_FILE_NAME=ID_210.RAW; RAW_FILE_NAME=ID_210.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.345 ID_211 Group:Control donor RAW_FILE_NAME=ID_211.RAW; RAW_FILE_NAME=ID_211.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.347 ID_212 Group:Control donor RAW_FILE_NAME=ID_212.RAW; RAW_FILE_NAME=ID_212.mzXML SUBJECT_SAMPLE_FACTORS HC.CoV. 089 ID_213 Group:Control donor RAW_FILE_NAME=ID_213.RAW; RAW_FILE_NAME=ID_213.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.303 ID_214 Group:Control donor RAW_FILE_NAME=ID_214.RAW; RAW_FILE_NAME=ID_214.mzXML SUBJECT_SAMPLE_FACTORS HC.CoV. 093 ID_215 Group:Control donor RAW_FILE_NAME=ID_215.RAW; RAW_FILE_NAME=ID_215.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.129 (S R F) ID_218 Group:Recovered RAW_FILE_NAME=ID_218.RAW; RAW_FILE_NAME=ID_218.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.185 ID_219 Group:Recovered RAW_FILE_NAME=ID_219.RAW; RAW_FILE_NAME=ID_219.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.237 ID_220 Group:Recovered RAW_FILE_NAME=ID_220.RAW; RAW_FILE_NAME=ID_220.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.240 ID_221 Group:Recovered RAW_FILE_NAME=ID_221.RAW; RAW_FILE_NAME=ID_221.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.241 ID_222 Group:Recovered RAW_FILE_NAME=ID_222.RAW; RAW_FILE_NAME=ID_222.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.166 (N R S) ID_223 Group:Recovered RAW_FILE_NAME=ID_223.RAW; RAW_FILE_NAME=ID_223.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.154 (A C S) ID_224 Group:Recovered RAW_FILE_NAME=ID_224.RAW; RAW_FILE_NAME=ID_224.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.163 (N R S) ID_225 Group:Recovered RAW_FILE_NAME=ID_225.RAW; RAW_FILE_NAME=ID_225.mzXML SUBJECT_SAMPLE_FACTORS HC.CoV. 036 (J C L) ID_226 Group:Recovered RAW_FILE_NAME=ID_226.RAW; RAW_FILE_NAME=ID_226.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.105 (S G R) ID_227 Group:Recovered RAW_FILE_NAME=ID_227.RAW; RAW_FILE_NAME=ID_227.mzXML SUBJECT_SAMPLE_FACTORS HC.CoV. 065 (O C S) ID_228 Group:Recovered RAW_FILE_NAME=ID_228.RAW; RAW_FILE_NAME=ID_228.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.125(S N A) ID_229 Group:Recovered RAW_FILE_NAME=ID_229.RAW; RAW_FILE_NAME=ID_229.mzXML SUBJECT_SAMPLE_FACTORS HC.CoV. 050 (G E S) ID_230 Group:Recovered RAW_FILE_NAME=ID_230.RAW; RAW_FILE_NAME=ID_230.mzXML SUBJECT_SAMPLE_FACTORS HC.CoV.118 ID_231 Group:Recovered RAW_FILE_NAME=ID_231.RAW; RAW_FILE_NAME=ID_231.mzXML SUBJECT_SAMPLE_FACTORS HC.CoV. 064 (J M S) ID_232 Group:Recovered RAW_FILE_NAME=ID_232.RAW; RAW_FILE_NAME=ID_232.mzXML SUBJECT_SAMPLE_FACTORS HC.CoV. 008 (B A S) ID_233 Group:Recovered RAW_FILE_NAME=ID_233.RAW; RAW_FILE_NAME=ID_233.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.157 (N M) ID_234 Group:Recovered RAW_FILE_NAME=ID_234.RAW; RAW_FILE_NAME=ID_234.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.164 ID_235 Group:Recovered RAW_FILE_NAME=ID_235.RAW; RAW_FILE_NAME=ID_235.mzXML SUBJECT_SAMPLE_FACTORS Hc.CoV.127 ID_236 Group:Recovered RAW_FILE_NAME=ID_236.RAW; RAW_FILE_NAME=ID_236.mzXML SUBJECT_SAMPLE_FACTORS NHC.CoV.047 ID_237 Group:Recovered RAW_FILE_NAME=ID_237.RAW; RAW_FILE_NAME=ID_237.mzXML SUBJECT_SAMPLE_FACTORS NHC.CoV.047 ID_238 Group:Recovered RAW_FILE_NAME=ID_238.RAW; RAW_FILE_NAME=ID_238.mzXML SUBJECT_SAMPLE_FACTORS NHC.CoV.047 ID_239 Group:Recovered RAW_FILE_NAME=ID_239.RAW; RAW_FILE_NAME=ID_239.mzXML SUBJECT_SAMPLE_FACTORS HC.CoV. 045 ID_240 Group:Control donor RAW_FILE_NAME=ID_240.RAW; RAW_FILE_NAME=ID_240.mzXML #COLLECTION CO:COLLECTION_SUMMARY Individuals with COVID-19 were admitted to the Hospital das Clínicas and CO:COLLECTION_SUMMARY Hospital das Clínicas de Campanha or recruited at the Laboratório Profª CO:COLLECTION_SUMMARY Margarida Dobler Komma at the Federal University of Goiás, Goiânia, Brazil CO:COLLECTION_SUMMARY between June 2020 to February 2021, before vaccination rollout. Blood samples CO:COLLECTION_SUMMARY were collected in EDTA tubes from 150 individuals who had confirmed SARS-CoV-2 CO:COLLECTION_SUMMARY infection by RT-qPCR test from nasopharyngeal swabs or by serological assays to CO:COLLECTION_SUMMARY detect specific IgM/IgG antibodies (Eco diagnostics); and control donors (n=27), CO:COLLECTION_SUMMARY who were negative for SARS-CoV-2 infection confirmed by RT-qPCR from CO:COLLECTION_SUMMARY nasopharyngeal swabs and serological IgM/IgG tests. CO:SAMPLE_TYPE Blood (plasma) #TREATMENT TR:TREATMENT_SUMMARY The criteria defined on COVID-19 Treatment Guidelines (National Institute of TR:TREATMENT_SUMMARY Health, USA) and World Health Organization [21,22] were used to stratify TR:TREATMENT_SUMMARY individuals with COVID-19 into mild disease (individuals presenting various TR:TREATMENT_SUMMARY signs and symptoms without shortness of breath, dyspnea, or abnormal chest TR:TREATMENT_SUMMARY imaging), moderate disease (individuals presenting radiologically confirmed TR:TREATMENT_SUMMARY pneumonitis, hospitalization and oxygen therapy), severe disease (dyspnea, TR:TREATMENT_SUMMARY respiratory frequency ≥30 breaths/min, saturation of oxygen [SpO2] ≤ 93%, TR:TREATMENT_SUMMARY and/or lung infiltrates >50% within 24 to 48 hours, including individuals that TR:TREATMENT_SUMMARY required monitoring and treatment in Intensive Care Unit and mechanical TR:TREATMENT_SUMMARY ventilation), or fatal COVID-19. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY For metabolomics analyses, cold acetonitrile was added to plasma samples (2:1, SP:SAMPLEPREP_SUMMARY v/v) vortexed and centrifuged (10 min, 10000 rpm at 4 °C) for protein SP:SAMPLEPREP_SUMMARY precipitation. Stable isotopes caffeine-¹³C3, tyrosine-15N and progesterone-d9 SP:SAMPLEPREP_SUMMARY were used as internal standards. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY The binary mobile phases were water 0.5% formic acid with 5 mM of ammonium CH:CHROMATOGRAPHY_SUMMARY formate (A), and acetonitrile (B). Their gradient elution started with 20% (B) CH:CHROMATOGRAPHY_SUMMARY for 5 min, then linearly increased to 100% (B) in 30 min and kept constant for 8 CH:CHROMATOGRAPHY_SUMMARY min in 100% (B). The eluent was restored to the initial conditions in 4 minutes CH:CHROMATOGRAPHY_SUMMARY to re-equilibrate the column and held for the remaining 8 minutes. The flow rate CH:CHROMATOGRAPHY_SUMMARY was kept at 0.5 mL min-1. The injection volume for analysis was 3 μL, and the CH:CHROMATOGRAPHY_SUMMARY column temperature was set at 35 °C. CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Agilent 1220 Infinity CH:COLUMN_NAME Agilent Zorbax Eclipse Plus C18 column 4.6 x 150 mm 3.5 μm #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS The electrospray ionization was operating with the following settings: spray MS:MS_COMMENTS voltage 3.5 kV; capillary temperature: 269 °C; S-lens RF level 50 V; sheath gas MS:MS_COMMENTS flow rate at 53 L min-1; aux gas flow rate at 14 L min-1; sweep gas flow rate 3 MS:MS_COMMENTS L min-1. The high-resolution mass-spectrometry was obtained under full MS/dd-MS2 MS:MS_COMMENTS mode. The mass range in the full MS scanning experiments was m/z 80-1200. The MS:MS_COMMENTS max IT was set at 200 ms, and AGC target was set at 1 x 106. For fragmentation MS:MS_COMMENTS acquisition, the top 5 (TopN, 5, loop count 5) most abundant precursors were MS:MS_COMMENTS sequentially transferred into the C-Trap (AGC target 1 x 105; max IT 50 ms) for MS:MS_COMMENTS collision. The collision energy for target analytes was 20, 30 and 35 eV. MS:MS_COMMENTS Resolving power was set at 140,000 and 70,000 for full MS and dd-MS2 MS:MS_COMMENTS acquisitions, respectively. Proteowizard software was used to convert .raw files MS:MS_COMMENTS into mzXML format and apLCMS software was used to perform peak deconvolution and MS:MS_COMMENTS detection, to filter noise, to align mass-to-charge ratio (m/z) and retention MS:MS_COMMENTS time and to quantify metabolite features, which are defined by a specific m/z, MS:MS_COMMENTS retention time and intensity values for each sample. MS:MS_RESULTS_FILE ST002291_AN003743_Results.txt UNITS:peak area Has m/z:Yes Has RT:Yes RT units:Seconds #END