SARS-CoV-2 Mutant Spectra at Different Depth Levels Reveal an Overwhelming Abundance of Low Frequency Mutations
Abstract
1. Introduction
2. Materials and Methods
2.1. Origin of HCV from Chronically Infected Patients, and of HCV Populations Adapted to Human Hepatoma Cells in Culture
2.2. COVID-19 Patient Cohort, Stratification, and Amplification of SARS-CoV-2 RNA from Diagnostic Samples
2.3. Ultra-Deep Sequencing of SARS-CoV-2
2.4. Bioinformatics Analyses of SARS-CoV-2 Nucleotide Sequences
2.5. Statistics
3. Results
3.1. A Review of Implications of HCV Population Complexity and Dynamics for Antiviral Resistance and Vaccine Efficacy
3.2. Ultra-Deep Sequencing Analysis at 0.1% Cut-Off SARS-CoV-2 Mutant Spectra from Patients Progressing towards Different COVID-19 Severity
3.3. A Comparison of the SARS-CoV-2 Point Mutation and Deletion Repertoire at 0.5% and 0.1% Frequency Cut-Off
3.4. SARS-CoV-2 Mutation and Deletion Repertoires at Progressively Lower Detection Limit
3.5. Acceptability of the Low Frequency Amino Acid Substitutions
3.6. Comparison of HCV and SARS-CoV-2 Mutant Spectra
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Patient Category | ||||||
---|---|---|---|---|---|---|
Total | Mild | Moderate | Exitus | |||
nsp12 (polymerase) | Number of different mutations | Transitions (Ts) (%) | 578 (98.97%) | 544 (99.63%) | 344 (99.42%) | 416 (99.05%) |
Transversions (Tv) (%) | 6 (1.03%) | 2 (0.37%) | 2 (0.58%) | 4 (0.24%) | ||
Ratio (Ts/Tv) | 96.33 | 272 | 172 | 104 | ||
p-value | <0.001 | <0.001 | <0.001 | <0.001 | ||
Significance a | *** | *** | *** | *** | ||
Number of total mutations | Transitions (Ts) (%) | 7587 (99.82%) | 2883 (99.93%) | 2254 (99.65%) | 2451 (99.84%) | |
Transversions (Tv) (%) | 14 (0.18%) | 2 (0.07%) | 8 (0.35%) | 4 (0.16%) | ||
Ratio (Ts/Tv) | 541.93 | 1441.50 | 281.75 | 612.75 | ||
p-value | <0.001 | <0.001 | <0.001 | <0.001 | ||
Significance a | *** | *** | *** | *** | ||
spike | Number of different mutations | Transitions (Ts) (%) | 297 (99.33%) | 273 (100%) | 209 (99.52%) | 210 (99.53%) |
Transversions (Tv) (%) | 2 (0.67%) | 0 (0%) | 1 (0.48%) | 1 (0.47%) | ||
Ratio (Ts/Tv) | 148.50 | - | 209 | 210 | ||
p-value | <0.001 | <0.001 | <0.001 | <0.001 | ||
Significance a | *** | *** | *** | *** | ||
Number of total mutations | Transitions (%) | 3718 (99.95%) | 1343 (100%) | 1187 (99.92%) | 1188 (99.92%) | |
Transversions (%) | 2 (0.05%) | 0 (0%) | 1 (0.08%) | 1 (0.08%) | ||
Ratio (Ts/Tv) | 1859 | - | 1187 | 1188 | ||
p-value | <0.001 | <0.001 | <0.001 | <0.001 | ||
Significance a | *** | *** | *** | *** |
Patient Category | ||||||
---|---|---|---|---|---|---|
Total | Mild | Moderate | Exitus | |||
nsp12 (polymerase) | Number of different mutations | Synonymous (Syn) (%) | 238 (40.75%) | 218 (39.93%) | 146 (42.20%) | 175 (41.67%) |
Non-synonymous (Non-syn) (%) | 346 (59.25%) | 328 (60.07%) | 200 (57.80%) | 245 (58.33%) | ||
Ratio (Syn/Non-syn) | 0.69 | 0.66 | 0.73 | 0.71 | ||
p-value | <0.001 | <0.001 | <0.001 | <0.001 | ||
Significance a | *** | *** | *** | *** | ||
Number of total mutations | Synonymous (Syn) (%) | 2971 (39.08%) | 1130 (39.17%) | 877 (38.78%) | 964 (39.27%) | |
Non-synonymous (Non-syn) (%) | 4631 (60.92%) | 1755 (60.83%) | 1385 (61.23%) | 1491 (60.73%) | ||
Ratio (Syn/Non-syn) | 0.64 | 0.64 | 0.63 | 0.65 | ||
p-value | <0.001 | <0.001 | <0.001 | <0.001 | ||
Significance a | *** | *** | *** | *** | ||
spike | Number of different mutations | Synonymous (Syn) (%) | 125 (41.95%) | 115 (42.28%) | 90 (43.06%) | 89 (42.38%) |
Non-synonymous (Non-syn) (%) | 173 (58.05%) | 157 (57.72%) | 119 (56.94%) | 121 (57.62%) | ||
Ratio (Syn/Non-syn) | 0.72 | 0.73 | 0.76 | 0.74 | ||
p-value | <0.001 | <0.001 | 0.006 | 0.002 | ||
Significance a | *** | *** | *** | *** | ||
Number of total mutations | Synonymous (Syn) (%) | 1659 (44.60%) | 606 (45.12%) | 525 (44.19%) | 528 (44.41%) | |
Non-synonymous (Non-syn) (%) | 2061 (55.40%) | 737 (54.88%) | 663 (55.81%) | 661 (55.59%) | ||
Ratio (Syn/Non-syn) | 0.80 | 0.82 | 0.79 | 0.80 | ||
p-value | <0.001 | <0.001 | <0.001 | <0.001 | ||
Significance a | *** | *** | *** | *** |
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Martínez-González, B.; Soria, M.E.; Vázquez-Sirvent, L.; Ferrer-Orta, C.; Lobo-Vega, R.; Mínguez, P.; de la Fuente, L.; Llorens, C.; Soriano, B.; Ramos-Ruíz, R.; et al. SARS-CoV-2 Mutant Spectra at Different Depth Levels Reveal an Overwhelming Abundance of Low Frequency Mutations. Pathogens 2022, 11, 662. https://doi.org/10.3390/pathogens11060662
Martínez-González B, Soria ME, Vázquez-Sirvent L, Ferrer-Orta C, Lobo-Vega R, Mínguez P, de la Fuente L, Llorens C, Soriano B, Ramos-Ruíz R, et al. SARS-CoV-2 Mutant Spectra at Different Depth Levels Reveal an Overwhelming Abundance of Low Frequency Mutations. Pathogens. 2022; 11(6):662. https://doi.org/10.3390/pathogens11060662
Chicago/Turabian StyleMartínez-González, Brenda, María Eugenia Soria, Lucía Vázquez-Sirvent, Cristina Ferrer-Orta, Rebeca Lobo-Vega, Pablo Mínguez, Lorena de la Fuente, Carlos Llorens, Beatriz Soriano, Ricardo Ramos-Ruíz, and et al. 2022. "SARS-CoV-2 Mutant Spectra at Different Depth Levels Reveal an Overwhelming Abundance of Low Frequency Mutations" Pathogens 11, no. 6: 662. https://doi.org/10.3390/pathogens11060662
APA StyleMartínez-González, B., Soria, M. E., Vázquez-Sirvent, L., Ferrer-Orta, C., Lobo-Vega, R., Mínguez, P., de la Fuente, L., Llorens, C., Soriano, B., Ramos-Ruíz, R., Cortón, M., López-Rodríguez, R., García-Crespo, C., Somovilla, P., Durán-Pastor, A., Gallego, I., de Ávila, A. I., Delgado, S., Morán, F., ... Perales, C. (2022). SARS-CoV-2 Mutant Spectra at Different Depth Levels Reveal an Overwhelming Abundance of Low Frequency Mutations. Pathogens, 11(6), 662. https://doi.org/10.3390/pathogens11060662