Background/Objectives: The coronavirus disease 2019 (COVID-19) has more severe symptoms and increased mortality among men than women. To address the prognostic impact of vaccination, comorbidities, and inflammatory biomarkers on classified clinical outcomes in hospitalized COVID-19 patients, we compared common and sex differences. Methods: Besides laboratory and clinical parameters at hospital admission, we performed a common and sex-based comparative analysis for the clinical outcomes, RT-qPCR analyses, and measured severe acute respiratory syndrome coronavirus (SARS-CoV-2)-specific IgM and IgG antibody levels of 702 COVID-19 patients in a single centre from June 2020 to April 2022. Results: Pro-inflammatory biomarkers (C-reactive protein (CRP), interleukin-6 (IL-6), fibrinogen, lactate dehydrogenase (LDH), D-dimer, ferritin), and liver enzymes (AST, ALT, GGT) were significantly more increased in COVID-19 male patients and generally elevated with the severity of clinical outcome, regardless of the SARS-CoV-2 variant. Cycle threshold (Ct) values of RT-qPCR testing were in negative correlation with IL-6 in COVID-19 male patients, indicating that higher viral load largely increased IL-6 levels in parallel with the severity of clinical outcome and regardless of vaccination. IgG levels were higher in early post-COVID-19 male patients. Comorbidities were more frequent in COVID-19 female patients and generally more common in the severe clinical outcomes. Vaccination was negatively correlated with the severity of clinical outcome, liver enzymes, LDH, and inflammatory parameters in hospitalized COVID-19 patients, while the risk of pneumonia was reduced. Vaccination reduced the need for corticosteroid and anti-inflammatory therapies, but increased the need for antiviral drug treatment. Conclusions: In addition to confirming inflammatory biomarkers and the importance of anti-inflammatory therapy in vaccinated patients, this study showed that vaccination reduces, but does not prevent, mortality in patients with COVID-19
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