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Analysis of SARS-CoV-2 omicron mutations that emerged during long-term replication in a lung cancer xenograft mouse
Kyeongbin Baek1, Dongbum Kim2, Jinsoo Kim2
1Department of Microbiology, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea.
Abstract:
SARS-CoV-2 Omicron has the largest number of mutations among all the known SARS-CoV-2 variants. The presence of these mutations might explain why Omicron is more infectious and vaccines have lower efficacy to Omicron than other variants, despite lower virulence of Omicron. We recently established a long-term in vivo replication model by infecting Calu-3 xenograft tumors in immunodeficient mice with parental SARS-CoV-2 and found that various mutations occurred majorly in the spike protein during extended replication. To investigate whether there are differences in the spectrum and frequency of mutations between parental SARS-CoV-2 and Omicron, we here applied this model to Omicron. At 30 days after infection, we found that the virus was present at high titers in the tumor tissues and had developed several rare sporadic mutations, mainly in ORF1ab with additional minor spike protein mutations. Many of the mutant isolates had higher replicative activity in Calu-3 cells compared with the original SARS-CoV-2 Omicron virus, suggesting that the novel mutations contributed to increased viral replication. Serial propagation of SARS-CoV-2 Omicron in cultured Calu-3 cells resulted in several rare sporadic mutations in various viral proteins with no mutations in the spike protein. Therefore, the genome of SARS-CoV-2 Omicron seems largely stable compared with that of the parental SARS-CoV-2 during extended replication in Calu-3 cells and xenograft model. The sporadic mutations and modified growth properties observed in Omicron might explain the emergence of Omicron sublineages. However, we cannot exclude the possibility of some differences in natural infection.
Insights
The SARS-CoV-2 Omicron variant shows genome stability during extended replication in mice and cell cultures, unlike the parental strain. Novel mutations in Omicron may drive sublineage emergence and increased viral replication.
Area of Science:
- Virology
- Infectious Diseases
- Molecular Biology
Background:
- Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Omicron exhibits numerous mutations, potentially impacting infectivity and vaccine efficacy.
- Previous studies established a SARS-CoV-2 replication model in Calu-3 xenograft tumors, revealing spike protein mutations during extended replication.
Purpose of the Study:
- To compare mutation spectrum and frequency between parental SARS-CoV-2 and Omicron during extended in vivo and in vitro replication.
- To investigate the impact of novel mutations on viral replication and the potential role in Omicron sublineage emergence.
Main Methods:
- Application of a long-term in vivo replication model using Calu-3 xenograft tumors infected with SARS-CoV-2 Omicron in immunodeficient mice.
- Serial propagation of SARS-CoV-2 Omicron in cultured Calu-3 cells.
- Analysis of viral mutations, titers, and replicative activity in Calu-3 cells.
Main Results:
- Omicron developed rare sporadic mutations, primarily in ORF1ab and minor spike protein mutations, with high titers in tumor tissues after 30 days.
- Mutant Omicron isolates demonstrated increased replicative activity in Calu-3 cells compared to the original Omicron.
- Serial propagation in Calu-3 cells yielded rare mutations in various viral proteins but no spike protein mutations, indicating genome stability.
Conclusions:
- The SARS-CoV-2 Omicron genome appears largely stable during extended replication in the Calu-3 xenograft model and cell cultures compared to parental SARS-CoV-2.
- Sporadic mutations and altered growth properties in Omicron may contribute to the emergence of its sublineages.
- Differences in natural infection dynamics cannot be excluded.
