Abstract
Background Our understanding of SARS-CoV-2 evolution and mutation rate is limited. The rate of SARS-CoV-2 evolution is minimized through a proofreading function encoded by NSP-14 and may be affected by patient comorbidity. Current understanding of SARS-CoV-2 mutational rate is through population based analysis while intra-host mutation rate remains poorly studied.
Methods Viral genome analysis was performed between paired samples and mutations quantified at allele frequencies (AF) ≥0.25, ≥0.5 and ≥0.75. Mutation rate was determined employing F81 and JC69 evolution models and compared between isolates with (ΔNSP-14) and without (wtNSP-14) non-synonymous mutations in NSP-14 and by patient comorbidity.
Results Forty paired samples with median interval of 13 days [IQR 8.5-20] were analyzed. The estimated mutation rate by F81 modeling was 93.6 (95%CI:90.8-96.4], 40.7 (95%CI:38.9-42.6) and 34.7 (95%CI:33.0-36.4) substitutions/genome/year at AF ≥0.25, ≥0.5, ≥0.75 respectively. Mutation rate in ΔNSP-14 were significantly elevated at AF>0.25 vs wtNSP-14. Patients with immune comorbidities had higher mutation rate at all allele frequencies.
Discussion Intra-host SARS-CoV-2 mutation rates are substantially higher than those reported through population analysis. Virus strains with altered NSP-14 have accelerated mutation rate at low AF. Immunosuppressed patients have elevated mutation rate at all AF. Understanding intra-host virus evolution will aid in current and future pandemic modeling.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Conflicts of interest DDR performs collaborative research that is sponsored by industry collaborators: BD, bioMerieux, Cepheid, Cleveland Diagnostics, Hologic, Luminex, Q-Linea, Qiagen, Roche, Specific Diagnostics, Thermo Fisher, and Vela. DDR is or has been on advisory boards for Luminex, Talis Biomedical, and Thermo Fisher. FE has served as a consultant to Proctor & Gamble. The remaining authors have or do not have an association that might pose a conflict of interest.
Funding This research was supported through the Ellen and Steven Ross Fellowship Research Award, Cleveland Clinic Children’s. This project was supported in part by NSF IIS-2027667 and NSF CCF-2200255 (JL and FE), NSF CCF-2006780 (JL), NSF CCF-1815139 (JL), and through unrestricted funds from the Robert J. Tomsich Pathology and Laboratory Medicine Institute.