SARS-CoV-2 variant natural evolution in K18-ACE2 mice increases virulence and produces treatment resistance-linked variant alleles

AbstractThe continuing COVID-19 pandemic is partially due to viral evolution reducing vaccine and treatment efficacy. Others have observed serial infections in mice with reference SARS-CoV-2 lineage IME-BJ05 produce adapted strains with significantly greater infectivity and mortality. We investigated the impact of long-term B.1.351 (Beta) and B.1.617.2 (Delta) lineage viral evolution in K18-ACE2 mice, which express human ACE2 receptor. We infected mice with these unmodified variants in a BSL-3 laboratory and studied viral evolution across 20 passages without selective pressure, sequencing virus at key points. Our IRB determined the research was not gain-of-function. We observed variant alleles with documented contributions towards evading vaccine-induced immunity arisede-novo, including Omicron-characteristic mutation S371F. Passage 20 (P20) viruses were more virulent, and P20 Delta was significantly more resistant to antibody neutralization. These developments occurred rapidly, emulating pandemic progression in non-immune mammals. Our model could be rapidly adapted to include selective pressures to study the evolution of viruses resistant to antivirals or vaccine-induced immunity.