Abstract <p>The pathological processes contributing to local (at the site of invasion) and systemic (thrombotic and fibrotic manifestations) complications of the new coronavirus infection are assessed. The features of virus internalization into cells and S-protein-dependent biochemical processes that form inflammatory and barrier reactions are analyzed. When studying the options for the virus evading the immune control systems, attention is paid to the uncoupling of phagocytosis from lytic processes compartmentalized in lysosomes during the penetration of SARS-CoV-2 into cells, as well as to the multilevel suppression of the interferon response. COVID-19 is a powerful stress factor and is associated with an increase in cortisol, catecholamines, and lactate in the blood. Under hypoxic conditions, deviations in the course of metabolic processes and the reception of signaling molecules are traced. The redistribution of ionized iron in the progression of the viral process and the formation of its complications is traced. An important role in the formation of cellular damage and tissue structure reorganization is played by the systemic inflammatory response and immunothrombosis, associated with the formation of extracellular neutrophil traps, as a form of apoptotic cell death. The significance of DNA methylation, the appearance of mobile genetic elements and noncoding RNA is estimated. The formation of structural changes is largely associated with fibrosis, realized, in particular, through the virus-activated epithelial-mesenchymal transition, local and systemic correction of which will reduce the risk of complications of the infectious process.</p>