Fig. 1

Overview of data collection and analysis for hospitalized COVID-19 patients. This comprehensive data collection framework aims to provide a holistic understanding of the COVID-19 symptoms and somatic, neuropsychiatric, and microbiological aspects of COVID-19 in hospitalized patients. (a) Clinical and Demographic Data. COVID patients (n = 124) are categorized into three severity groups based on a scoring index: low (0–2), moderate (3–7), and critical (> 8). This score is based on age, gender, heart failure, chronic obstructive pulmonary disease (COPD), diabetes mellitus, heart rate, respiratory rate, systolic blood pressure, temperature, oxygen saturation, including in patients with COPD, D-dimer levels, lymphocyte and platelet counts, dyspnea, chest X-ray alterations, and the need for supplemental oxygen. (b) Somatic and Neuropsychiatric Assessments: Patient Health Questionnaire-15 (PHQ-15) is used to assess somatic symptoms, including stomach pain, back pain, pain in arms, legs, and joints, menstrual cramps, headaches, chest pain, dizziness, fainting spells, heart palpitations, shortness of breath, pain during sexual intercourse, constipation, nausea, indigestion, fatigue, and trouble sleeping. Additional neuropsychiatric assessments include the Perceived Stress Scale (PSS), Hospital Anxiety and Depression Scale-Anxiety (HADS-A), and Hospital Anxiety and Depression Scale-Depression (HADS-D). (c) Laboratory Tests. Various serological assays are conducted to analyze hematological, coagulation, and biochemical parameters, as well as serum inflammatory cytokines. (d) Microbiome Analysis. Stool samples are collected for microbiome analysis. Full-length 16 S sequencing is performed using Oxford Nanopore Technologies, followed by microbial composition analysis using Emu. Data analysis uses tools such as phyloseq, ANCOMBC2, and SpiecEasi to understand the microbial landscape and its association with disease severity and patient outcomes