Fig. 1: Patients, samples, and study workflow.
From: Enhanced inflammation and suppressed adaptive immunity in COVID-19 with prolonged RNA shedding
a An overview timeline of our study cohort. The y-axis shows the patient ID, and the x-axis displays the length of RNA shedding measured from the onset. The 38 patients included 19 with short and 19 with long shedding courses (SC and LC, respectively). Other important information, including the virus nucleic acid test results (sputum or throat swab positive/negative result), gender, severity, comorbidities, etc., are shown in the right panel of the figure. The sputum swab was marked as positive from the first to the last continuously positive test during our observation; a persistent negative swab was negative until the end of our observation. The black dots indicate the sampling time for both omics data, while the blue or orange dots represent only the proteomics or metabolomics data, respectively. More details are provided in Supplementary Table S1. b Multi-omics overview involving virological detection based on RT-PCR, an immunological assay based on ELISA and flow cytometry, proteomics and metabolomics analyses for 38 COVID-19 patients and 35 control patients. A total of 298 sputum swab samples (from the 38 COVID-19 patients) and 70 sputum swab samples (from the 35 control patients) were used for the SARS-CoV-2 RNA assay across 16 weeks. Immunological measurements were comprised of 190 serum samples for antibodies-mediated detection over nine weeks and 43 whole blood samples for immune cell counting over three weeks. 217 serum samples and 251 peptide samples, including 34 technical replicates, were analyzed by TMT 16-plex-based quantitative proteomics. 193 serum samples and additional 29 quality control samples for metabolomics analysis were acquired with four different methods including three types of RP-UPLC and one of HILIC-UPLC. A total of 945 metabolites were identified.
