Genetic analysis and pathogenetic aspects of emerging and re-emerging respiratory viral infections

Respiratory viruses are one of the leading causes of morbidity and mortality worldwide especially for children, immunocompromised subjects and older people. Flu, hRSV, hRVs, EVs, hAdVs, MPV, PIVs, seasonal hCoVs, and SARS-CoV-2 are the main viruses as etiologic agents of respiratory syndromes. Clinical syndromes of viral respiratory infections may range from mild to severe and are characterized by common symptoms such as fever, cough, pharyngitis or laryngitis. However, with few exceptions, there are no therapeutic options and therapy is mainly supportive. This research project aimed to perform genetic analysis and investigate the pathogenetic aspects of emerging and re-emerging respiratory viral infections. The analysis focused on SARS-CoV-2, Rhinoviruses, Echovirus 11, Influenza and Adenovirus-related infections. Multi-lineage circulation was demonstrated for SARS-CoV-2 and molecular signature associated with the viral progression from the upper to lower respiratory tract. Multiple genotypes were identified when investigating the epidemiology of Adenoviruses and Rhinoviruses; moreover, the ability of Rhinoviruses to cause prolonged and severe infections was assessed. Following the circulation of Echovirus 11 among newborns and infants, molecular analysis on the recombinant origin of the novel strain allowed the identification of Echovirus 6 as a parental strain for the partial P3 region of the viral genome. Lastly, Influenza A(H3N2) circulation during the 2021-2022 season was analyzed. Sequencing of hemagglutinin protein revealed the presence of 65 mutations in 59 amino acid sites, suggesting the circulation of drifted strains in comparison to the one included in the vaccine.