Objective
To investigate intra-host evolution of SARS-CoV-2 in critically ill patients with severe lung failure.
Methods
Between November 2020 to December 2022, respiratory samples were collected from 41 mechanically ventilated patients at the intensive care unit of University Hospital Regensburg, Germany, including 16 on extracorporeal membrane oxygenation (ECMO). Paired initial and follow-up samples were obtained at a median interval of 15 days (range: 6–42) and analyzed using next-generation sequencing. Amino acid substitutions in the viral genome were correlated with clinical, virological, immunological, and therapeutic markers using binary logistic regression.
Results
Seventeen of 41 patients (41%) developed amino acid substitutions in non-structural proteins (nsp2, 3, 4, 10, 12, 14, and 15), ORF3a, ORF8, and structural proteins (spike and nucleocapsid). Among 27 identified mutations, 21 were single nucleotide polymorphisms, and 6 were nucleotide deletions (3 single, 3 multiple). Notably, 20 mutations (74.1%) represented reversions to the ancestral Wuhan-1 sequence, including eight at position 323 in nsp12. Mutation occurrence was significantly associated with younger age, prolonged ICU stay, ECMO therapy, catecholamine use, thrombotic events, extended viral replication, and Delta variant infection (p < 0.05), whereas Remdesivir therapy showed a negative association. Multivariate analysis confirmed younger age, prolonged replication, and ECMO as independent predictors of intra-host viral evolution.
Conclusions
Intra-host SARS-CoV-2 evolution in critically ill patients is driven by disease severity and prolonged viral replication. Frequent reversions to the ancestral sequence suggest selective pressure favoring wildtype variants in inflamed and hypoxic lung areas – a process attenuated by the administration of Remdesivir.