Impact of Vaccination on Intra-Host Genetic Diversity of Patients Infected with SARS-CoV-2 Gamma Lineage
Abstract
:1. Introduction
2. Materials and Methods
2.1. Samples
2.2. Ethics
2.3. Molecular Investigation
2.4. Whole-Genome Sequencing
2.5. Genome Assembling and Variant Analyses
2.6. Evolutionary Analyses
2.7. Statistics
3. Results
3.1. Distribution of iSNVs across SARS-CoV-2 Genomes
3.2. Characterization of the iSNVs Detected in the SARS-CoV-2 Genomes
3.3. Allele Composition of the SARS-CoV-2 Genomes
3.4. Selection Pressures Detected in the SARS-CoV-2 Genomes
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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Unvaccinated | Vaccinated | |||
---|---|---|---|---|
Region | NS (%) | S (%) | NS (%) | S (%) |
ORF1ab | 79 (58.5) | 74 (71.8) | 92 (54.8) | 96 (73.3) |
S | 20 (14.8%) | 12 (11.7) | 27 (16.1) | 6 (4.6) |
ORF3a | 9 (6.7) | 0 (0.0) | 13 (7.7) | 3 (2.3) |
E | 0 (0.0) | 2 (1.9) | 0 (0.0) | 3 (2.3) |
M | 0 (0.0) | 2 (1.9) | 3 (1.8) | 7 (5.3) |
ORF6 | 3 (2.2) | 1 (1.0) | 3 (1.8) | 2 (1.5) |
ORF7a | 2 (1.5) | 2 (1.9) | 4 (2.4) | 3 (2.3) |
ORF7b | 0 (0.0) | 0 (0.0) | 0 (0.0) | 0 (0.0) |
ORF8 | 6 (4.4) | 0 (0.0) | 5 (3.0) | 1 (0.8) |
N | 16 (11.9) | 10 (9.8) | 20 (11.9) | 10 (7.6) |
ORF10 | 0 (0.0) | 0 (0.0) | 1 (0.5) | 0 (0.0) |
TOTAL | 135 (100) | 103 (100) | 168 (100) | 131 (100) |
Unvaccinated | Vaccinated | |||
---|---|---|---|---|
Locus | Positive Selection | Negative Selection | Positive Selection | Negative Selection |
ORF1ab | NSP6 (106) | NSP3 (106, 681), NSP10 (82), NSP13 (495) | NSP3 (1303), NSP6 (107) | NSP2 (91,443), NSP3 (236, 394, 447, 662, 1092, 1121, 1742), NSP6 (76, 138), NSP10 (16), NSP13 (237, 356), NSP14 (302, 373), NSP15 (278), NSP16 (178) |
S | 0 | 554, 995, 1065 | 0 | 0 |
ORF3a | 0 | 0 | 0 | 43 |
E | 0 | 0 | 0 | 8, 23 |
M | 0 | 53 | 0 | 0 |
ORF6 | 0 | 49 | 0 | 61 |
ORF7a | 0 | 88 | 0 | 11 |
ORF8 | 0 | 0 | 0 | 75 |
N | 0 | 0 | 200 | 194, 363 |
ORF10 | 0 | 0 | 0 | 0 |
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Marques, B.d.C.; Banho, C.A.; Sacchetto, L.; Negri, A.; Vasilakis, N.; Nogueira, M.L. Impact of Vaccination on Intra-Host Genetic Diversity of Patients Infected with SARS-CoV-2 Gamma Lineage. Viruses 2024, 16, 1524. https://doi.org/10.3390/v16101524
Marques BdC, Banho CA, Sacchetto L, Negri A, Vasilakis N, Nogueira ML. Impact of Vaccination on Intra-Host Genetic Diversity of Patients Infected with SARS-CoV-2 Gamma Lineage. Viruses. 2024; 16(10):1524. https://doi.org/10.3390/v16101524
Chicago/Turabian StyleMarques, Beatriz de Carvalho, Cecília Artico Banho, Lívia Sacchetto, Andreia Negri, Nikos Vasilakis, and Maurício Lacerda Nogueira. 2024. "Impact of Vaccination on Intra-Host Genetic Diversity of Patients Infected with SARS-CoV-2 Gamma Lineage" Viruses 16, no. 10: 1524. https://doi.org/10.3390/v16101524