# Back to the wildtype: SARS-CoV-2 evolution in critically ill patients with severe lung failure

## TL;DR

This study examines how SARS-CoV-2 evolves within critically ill patients with severe lung failure, finding that disease severity and prolonged replication drive mutations, often reverting to the original virus.

## Contribution

The study identifies factors driving intra-host SARS-CoV-2 evolution and highlights frequent reversion to the ancestral Wuhan-1 sequence in severe cases.

## Key findings

- 17 out of 41 patients developed amino acid substitutions in viral proteins, with 74.1% being reversion to the ancestral Wuhan-1 sequence.
- Mutation occurrence was significantly linked to younger age, prolonged ICU stay, and Delta variant infection.
- Remdesivir therapy was associated with a reduced likelihood of intra-host viral evolution.

## Abstract

To investigate intra-host evolution of SARS-CoV-2 in critically ill patients with severe lung failure.

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.

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.

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.

The online version contains supplementary material available at 10.1007/s15010-025-02650-5.