The appearance of viruses in mammals and plants is provoked by environmental factors - xenobiotics, formed mainly due to unreasonable human activity and resulting from the formation of an ecological (epidemiological) niche filled with molecular motifs of the microbiota - the intestines of mammals and the root system of plants. To do this, bacteria and archaea use retrovirus-like “cut and paste” mechanisms, including, for example, the CRISPR/Cas system, when the molecular motifs of the microbiota try to adapt the immune and hormonal systems. It all depends on how much xenobiotics damage the immune and hormonal systems. Therefore, viruses are not the cause, but the consequence of the disease. The fight against viruses with the help of vaccines prepared on their basis has been violating and restraining the natural mechanisms of regulation of biological processes in plants and mammals. Thus, molecular motifs arising from microbiota bacteria become either apaptogens (viruses) or adaptogens. In the first and second cases, genetic information is released into the environment. In the latter case, there is an adaptation or a kind of vaccination of others by a natural mechanism. This mechanism is also applicable to somatic diseases, such as cardiovascular, autoimmune, oncological, etc. As for the original properties of coronaviruses, it is their ability to suppress innate and acquired nonspecific viral immunity in the respiratory tract. This leads to the reactivation of chronic, mainly bacterial, respiratory infections - pneumococci, staphylococci, hemophiluses, however, fungal infections can also be observed – mucormycosis, aspergillosis, etc. This feature of the virus prompted doctors at the beginning of the epidemic (2020) to use a pneumococcal vaccine, which, as it turned out, similarly to the coronavirus vaccine reduces the severity of the disease and mortality. As for the diagnosis of coronavirus infection and its treatment, as practice has shown, everything depends on the stage of the disease, starting with a viral and ending with a bacterial infection. Similar and identical antigenic determinants in coronavirus and respiratory group bacteria often caused confusion when analyzing the results of serological and molecular biological diagnostic tests in patients with COVID-19. Moreover, the justified use of antibiotics in the post-viral, that is, in bacterial periods, made it possible to successfully treat patients with a positive PCR test for coronavirus on an outpatient basis.