The purpose of this study was to investigate polymorphic variants of the genes FGB (rs1800790), NOS3 (rs2070744) and TMPRSS2 (rs12329760) in patients with SARS-CoV-2 and to determine their role in the COVID-19 severity course against the background of antiviral therapy. Real-time polymerase chain reaction (RT-PCR) was used to genotype the polymorphism of the selected genes. GS-5734 (remdesivir) was prescribed as the basic antiviral drug. Binary logistic regression confirmed a low probability of COVID-19 developing in carriers of the A-allele of the FGB gene. The highest probability of moderate and severe COVID-19 clinical forms developing was found in G-allele carriers (especially the GG genotype) of the FGB gene (rs1800790) and the T-allele of the TMPRSS2 gene (rs12329760). Antiviral drug GS-5734 (remdesivir) administration with anti-inflammatory therapy reduces the TMPRSS2 blood level in moderate COVID-19, IL-6 in severe COVID-19 course, and fibrinogen A- and D-dimers in both groups. The proposed treatment does not significantly affect the concentration of endothelin-1, but a decrease in procalcitonin associated with additional antibacterial use was observed, especially in severe COVID-19.