SARS-CoV-2 Evolution in Critically Ill Patients with Prolonged Infections Requiring Intubation or ECMO

The outbreak of SARS-CoV-2 in December 2019 and the ensuing global pandemic raised critical questions about the virus's capacity for rapid adaptation to environmental conditions. In this study, we investigated viral evolution in critically ill patients suffering from severe lung failure. From November 2020 to December 2022, respiratory samples were collected from a total of 41 patients upon admission to the intensive care unit at the University Hospital Regensburg, Germany, and during the course of treatment (median interval: 15 days; range: 6 to 42 days). The samples were analyzed for genomic alterations using next-generation sequencing. Detected changes were correlated with clinical, virological, immunological, and therapeutic parameters using both univariate and multivariate logistic regression analysis. Seventeen of 41 patients (41%) developed amino acid substitutions in non-structural proteins (nsp) 2, 3, 4, 10, 14, and 15, as well as in open reading frames 3a and 8, and within the spike and nucleocapsid proteins over the course of the study. Notably, 20 of 27 observed changes represented reversions to the Wuhan-1 wild-type genome, including eight at position 323 of the polymerase nsp12. Statistically significant factors associated with the occurrence of mutations included younger age, prolonged stay in the intensive care unit, ECMO and catecholamine treatment, development of thrombosis, extended virus replication period, and infection with the Delta variant (p<0.05). In contrast, treatment with remdesivir was negatively correlated with the emergence of mutations. Epitope mapping revealed that the humoral immune response was unlikely to be the main driver of viral evolution in vivo. Thus, the likelihood of genomic alterations in severely ill patients increases with both disease severity and duration of virus replication. The frequent observation of reversions to the wildtype genome suggests that the virus preferentially replicates in inflamed and poorly ventilated areas of the lungs – an effect that may be further amplified by the presence of pulmonary embolism. Furthermore, replication appears to be suppressed by the administration of remdesivir. These findings highlight that integrating antiviral strategies into the clinical management of severely ill patients may limit the emergence of potentially novel mutations.