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.
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Data availability
All data needed to evaluate the conclusions in this manuscript have been included. The whole-genome sequencing data for the SARS-CoV-2 mutants analyzed in this study are available at the GISAID (https://gisaid.org) under the accession number: EPI_ISL_18454580. EPI_ISL_18454581. EPI_ISL_18454582. EPI_ISL_18454583. EPI_ISL_18454584. EPI_ISL_18454585. EPI_ISL_18454586. EPI_ISL_18454587. EPI_ISL_18454588. EPI_ISL_18454589. EPI_ISL_18454590. EPI_ISL_18454591. EPI_ISL_18454592. EPI_ISL_18454593. EPI_ISL_18454683. EPI_ISL_18454777. EPI_ISL_18454826. EPI_ISL_18454855. EPI_ISL_18454857. EPI_ISL_18454858. EPI_ISL_18454859. EPI_ISL_18454860. EPI_ISL_18454862. EPI_ISL_18454863. EPI_ISL_18454864. EPI_ISL_18454866. EPI_ISL_18454867.
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Acknowledgements
We extend our gratitude to the National Culture Collection for Pathogens in Osong, Korea, for providing the SARS-CoV-2 Omicron.
Funding
This research was supported by a grant from the National Research Foundation (grant number: NRF-2022M3A9I2082292) funded by the Ministry of Science and ICT in the Republic of Korea and by a grant of the Korea Health Technology R&D Project (grant number: HV23C0052) through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare in the Republic of Korea.
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MSP, YL and HJK conceived the study and contributed to conceptualization and fund acquisition. DK, JK, MSP, YL and HJK designed experiments. KB, DK, JK, BMK, MK and SK performed experiments in BSL-3 and ABSL-3 facility including cell culture, viral cultivation and animal experiments. KB, DK, JK, SP, HES and MHL contributed to sample processing for DNA sequencing. KB, DK, JK, HP and BMK performed viral RNA extraction, analyzed whole-genome sequences data and prepared figures. KB, DK, JK and SP performed qRT-PCR. KB and BMK carried out H&E staining and immunohistochemistry. KB, DK, JK, HP, BMK, SP, HES, MHL, MK and SK contributed to methodology and formal analysis. JK, SM, YL and HJK contributed to Writing-original draft. YL and HJK contributed to Writing – review & editing. All authors contributed to editing of the manuscript and approved the final manuscript.
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All animal research was performed following the guidelines provided by the Guide for the Care and Use of Laboratory Animals from the National Veterinary Research & Quarantine Service of Korea. The Institutional Animal Care and Use Committee of Hallym University (Permit no. Hallym2022-52) approved the animal experiments in this study.
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Baek, K., Kim, D., Kim, J. et al. Analysis of SARS-CoV-2 omicron mutations that emerged during long-term replication in a lung cancer xenograft mouse model. Virus Genes (2024). https://doi.org/10.1007/s11262-024-02067-6
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DOI: https://doi.org/10.1007/s11262-024-02067-6