SARS-CoV-2 Amino Acid Mutations Detection in Greek Patients Infected in the First Wave of the Pandemic
Abstract
:1. Introduction
2. Materials and Methods
2.1. SARS-CoV-2 Isolates
2.2. NGS and Data Analysis
2.3. SARS-CoV-2 RNA Quantification by Reverse Transcription-Quantitative PCR (RT-qPCR)
2.4. Detection of SARS-CoV-2 Mutations in Sequences Submitted to Online Databases
2.5. Bioinformatics Analysis for Prediction of Protein Structure and Stability
3. Results
3.1. SARS-CoV-2 Genomes Used in This Study
3.2. Mutation Sites in SARS-CoV-2 Genome
3.3. Most Common Mutations among the Genotypes Studied
3.4. Empirical Analysis of Changes in Structure and Stability Parameters
4. Discussion
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sample Name | Accession Number | Age | Gender # | Viral Load Log (−ΔΔCt) | Lineage | Amino Acid (Nucleotide) Mutations |
---|---|---|---|---|---|---|
1851-S45 | SRR19213734 | 23 | M | 3.89 | A | S_D614G (A23403G) |
4405-S34 | SRR19215536 | 42 | M | 1.70 | A | S_D614G (A23403G), ORF7a_X122Lext * (G27758T) |
2384-S29 | SRR19215599 | 45 | F | 4.13 | A | S_D614G (A23403G) |
3125-S32 | SRR19215604 | 40 | M | 2.12 | B.39 | ORF1ab_H417R or Nsp2_H237R (A1515G), ORF1ab_H2986H or Nsp4_H223H (C9223T), ORF1ab_L3606F or Nsp6_L37F (G11083T), ORF1ab_D4661N or Nsp12_D269N (G14245A), ORF1ab_Y4847Y or Nsp12_Y455Y (C14805T), ORF1ab_V5845V or Nsp13_V521V (A17799G), ORF3a_G251V (G26144T) |
3396-S31 | SRR19215602 | 59 | M | 3.81 | B.40 | ORF1ab_I739V or Nsp2_I559V (A2480G), ORF1ab_P765S or Nsp2_P585S (C2558T), ORF1ab_Y4847Y or Nsp12_Y455Y (C14805T), ORF1ab_S6713L or Nsp15_S261L (C20402T), ORF3a_G251V (G26144T) |
9096-S37 | SRR19215566 | 42 | M | −0.69 | A | ORF1ab_A1670V or Nsp3_A852V (C3064T), S_F342fs # (GTT22583G), S_D614G (A23403G), M_L54F (C26682T), M_F100F (C26822T) |
9097-S38 | SRR19215601 | 37 | F | −0.35 | B.40 | ORF1ab_I739V or Nsp2_I559V (A2480G), ORF1ab_P765S or Nsp2_P585S (C2558T), ORF1ab_L3606F or Nsp6_L37F (G11083T), ORF1ab_Y4847Y or Nsp12_Y455Y (C14805T), ORF3a_T271del (G26199-ACT) |
0524-S39 | SRR19215600 | 39 | F | −1.22 | A | ORF1ab_L3606F or Nsp6_L37F (G11083T), ORF1ab_Y4847Y or Nsp12_Y455Y (C14805T), ORF1ab_V5680V or Nsp13_V356V (C17304A), S_D614G (A23403G) |
2098-S40 | SRR19215598 | 26 | M | −1.37 | B.39 | ORF1ab_H417R or Nsp2_H237R (A1515G), ORF1ab_H2986H or Nsp4_H223H (C9223T), ORF1ab_L3606F or Nsp6_L37F (G11083T), ORF1ab_D4661N or Nsp12_D269N (G14245A), ORF1ab_Y4847Y or Nsp12_Y455Y (C14805T), ORF1ab_V5845V or Nsp13_V521V (A17799G) |
6642-S30 | SRR19215603 | 59 | M | 4.56 | B.40 | ORF1ab_I739V or Nsp2_I559V (A2480G), ORF1ab_P765S or Nsp2_P585S (C2558T), ORF1ab_Y4847Y or Nsp12_Y455Y (C14805T), ORF1ab_S6713L or Nsp15_S261L (C20402T), ORF3a_G251V (G26144T) |
Mutations | ORF1ab Mutations | MutType | C1 | C2 | C3 | Ref-Codon | Mut-Codon | Count | Proportion |
---|---|---|---|---|---|---|---|---|---|
Nsp2_H237R | H417R | nonsyn | 1514 | 1515 | 1516 | cAt | cGt | 1219 | 0.000233 |
Nsp2_I559V | I739V | nonsyn | 2480 | 2481 | 2482 | Att | Gtt | 3029 | 0.000579 |
Nsp2_P585S | P765S | nonsyn | 2558 | 2559 | 2560 | Cca | Tca | 3215 | 0.000615 |
Nsp3_A852V | A1670V | nonsyn | 5273 | 5274 | 5275 | gCa | gTa | 1428 | 0.000273 |
Nsp4_H223H | H2986H | syn | 9221 | 9222 | 9223 | caC | caT | 7684 | 0.00147 |
Nsp6_L37F | L3606F | nonsyn | 11,081 | 11,082 | 11,083 | ttG | ttT | 133,400 | 0.025514 |
Nsp12_D269N | D4661N | nonsyn | 14,245 | 14,246 | 14,247 | Gat | Aat | 1456 | 0.000278 |
Nsp12_Y455Y | Y4847Y | syn | 14,803 | 14,804 | 14,805 | taC | taT | 76,696 | 0.014669 |
Nsp13_V356V | V5680V | syn | 17,302 | 17,303 | 17,304 | gtC | gtA | 136 | 0.000026 |
Nsp13_V521V | V5845V | syn | 17,797 | 17,798 | 17,799 | gtA | gtG | 3079 | 0.000589 |
Nsp15_S261L | S6713L | nonsyn | 20,401 | 20,402 | 20,403 | tCa | tTa | 5484 | 0.001049 |
S_V341del | del | 22,583 | 22,584 | 22,585 | gTT | g-- | 13 | 0.000002 | |
S_D614G | nonsyn | 23,402 | 23,403 | 23,404 | gAt | gGt | 5,182,511 | 0.991216 | |
ORF3a_G251V | nonsyn | 26,143 | 26,144 | 26,145 | gGt | gTt | 8069 | 0.001543 | |
M_F100F | syn | 26,820 | 26,821 | 26,822 | ttC | ttT | 8300 | 0.001587 | |
ORF7a_X122L | nonsyn | 27,757 | 27,758 | 27,759 | tGa | tTa | 2104 | 0.000402 |
Protein | Mutation | Protein Structure | Dynamut2 (ΔΔGStability) | SDM (ΔΔGpred.) | MAESTROweb (ΔΔGpred.) |
---|---|---|---|---|---|
Nsp2 | H417R (H237R) # | 7MSW | −0.16 | +0.07 | −0.020 (0.902) |
Nsp2 | I739V & P765S (I559V & P585S) | 7MSW | −0.28 | −2.13 & 0.46 | +0.035 (0.902) |
Nsp3 | A1670V (A852V) | 7QCM | −0.58 | +1.16 | +0.010 (0.923) |
Nsp12 | D4661N (D269N) | 7C2K | −0.21 | −0.11 | +0.095 (0.862) |
Nsp15 | S6713L (S261L) | 7N06 | +0.28 | −0.3 | +0.006 (0.877) |
ORF3a | G251V | D-I-Tasser model | −1.53 | +0.31 | +0.473 (0.845) |
M protein | L54F | D-I-Tasser model | −0.78 | −1.31 | +2.230 (0.825) |
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Vassilaki, N.; Papadimitriou, K.; Ioannidis, A.; Papandreou, N.C.; Milona, R.S.; Iconomidou, V.A.; Chatzipanagiotou, S. SARS-CoV-2 Amino Acid Mutations Detection in Greek Patients Infected in the First Wave of the Pandemic. Microorganisms 2022, 10, 1430. https://doi.org/10.3390/microorganisms10071430
Vassilaki N, Papadimitriou K, Ioannidis A, Papandreou NC, Milona RS, Iconomidou VA, Chatzipanagiotou S. SARS-CoV-2 Amino Acid Mutations Detection in Greek Patients Infected in the First Wave of the Pandemic. Microorganisms. 2022; 10(7):1430. https://doi.org/10.3390/microorganisms10071430
Chicago/Turabian StyleVassilaki, Niki, Konstantinos Papadimitriou, Anastasios Ioannidis, Nikos C. Papandreou, Raphaela S. Milona, Vassiliki A. Iconomidou, and Stylianos Chatzipanagiotou. 2022. "SARS-CoV-2 Amino Acid Mutations Detection in Greek Patients Infected in the First Wave of the Pandemic" Microorganisms 10, no. 7: 1430. https://doi.org/10.3390/microorganisms10071430
APA StyleVassilaki, N., Papadimitriou, K., Ioannidis, A., Papandreou, N. C., Milona, R. S., Iconomidou, V. A., & Chatzipanagiotou, S. (2022). SARS-CoV-2 Amino Acid Mutations Detection in Greek Patients Infected in the First Wave of the Pandemic. Microorganisms, 10(7), 1430. https://doi.org/10.3390/microorganisms10071430