Comparison of Simple RNA Extraction Methods for Molecular Diagnosis of Hepatitis C Virus in Plasma
Abstract
:1. Introduction
2. Materials and Methods
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Plasma HCV RNA Level (IU/mL) | Extraction Methods | ||||
---|---|---|---|---|---|
Silica-Membrane Based | Magnetic Beads-Based | Boiling with DEPC-Treated Distilled Water | Boiling with a Commercial Lysis Buffer | ||
106 | Concentration (ng/µL) | 345.80 ± 11.44 | 6.87 ± 4.03 | 125.63 ± 16.91 | 695.37 ± 13.62 |
Purity (260/280) | 3.45 ± 0.04 | 1.57 ± 0.12 | 0.87 ± 0.02 | 1.01 ± 0.04 | |
Real time RT-PCR, Ct a (mean ± SD) | 24.91 ± 0.29 | 24.11 ± 1.17 | 29.86 ± 0.77 | Undetectable | |
RT-LAMP, no. of detectable samples (%) | 3/3 (100) | 3/3 (100) | 2/3 (67) | Uninterpreted | |
105 | Concentration (ng/µL) | 347.73 ± 9.20 | 1.97 ± 0.83 | 28.30 ± 34.75 | 636.37 ± 1.19 |
Purity (260/280) | 3.44 ± 0.01 | 1.78 ± 0.90 | 0.99 ± 0.28 | 1.07 ± 0.04 | |
Real time RT-PCR, Ct (mean ± SD) | 28.27 ± 1.25 | 27.42 ± 0.78 | 32.48 ± 0.98 | Undetectable | |
RT-LAMP, no. of detectable samples (%) | 1/3 (33) | 1/3 (33) | 0/3 (0) | Uninterpreted | |
104 | Concentration (ng/µL) | 326.90 ± 47.56 | 2.80 ± 0.87 | 0.20 ± 0.14 | 620.47 ± 10.98 |
Purity (260/280) | 3.43 ± 0.04 | 1.97 ± 0.45 | 1.85 ± 2.06 | 1.08 ± 0.01 | |
Real time RT-PCR, Ct (mean ± SD) | 32.84 ± 0.42 | 32.80 ± 1.18 | 34.87 ± 1.01 | Undetectable | |
RT-LAMP, no. of detectable samples (%) | 0/3 (0) | 0/3 (0) | 0/3 (0) | Uninterpreted | |
103 | Concentration (ng/µL) | 318.33 ± 26.13 | 2.57 ± 0.72 | 0 ± 0.10 | 551.37 ± 126.27 |
Purity (260/280) | 3.46 ± 0.01 | 2.48 ± 0.73 | 0.14 ± 0.90 | 1.10 ± 0.01 | |
Real time RT-PCR, Ct (mean ± SD) | Undetectable | Undetectable | Undetectable | Undetectable | |
RT-LAMP, no. of detectable samples (%) | 0/3 (0) | 0/3 (0) | 0/3 (0) | Uninterpreted |
HCV Viral Load (log10 IU/mL) | Extraction Methods | |||||
---|---|---|---|---|---|---|
Silica-Membrane Based | Magnetic Beads-Based | Boiling with DEPC-Treated Distilled Water | ||||
Real Time RT-PCR, Ct (Mean ± SD) | RT-LAMP, No. of Detectable Samples (%) | Real Time RT-PCR, Ct (Mean ± SD) | RT-LAMP, No. of Detectable Samples (%) | Real Time RT-PCR, Ct (Mean ± SD) | RT-LAMP, No. of Detectable Samples (%) | |
6.01–7.00 (N = 10) | 24.95 ± 1.64 | 10/10 (100) | 23.19 ± 1.35 | 10/10 (100) | 29.50 ± 1.27 | 3/10 (30) |
5.01–6.00 (N = 14) | 26.76 ± 1.13 | 13/14 (93) | 24.59 ± 0.90 | 12/14 (86) | 30.86 ± 0.93 | 4/14 (29) |
4.01–5.00 (N = 14) | 29.89 ± 1.37 | 9/14 (64) | 27.89 ± 1.03 | 9/14 (64) | 33.83 ± 1.07 | 0/14 (0) |
3.01–4.00 (N = 12) | 32.60 ± 1.44 | 1/12 (8) | 31.21 ± 1.23 | 0/12 (0) | 34.11 ± 0.72 | 0/12 (0) |
Total (N = 50) | 50 (100) | 33 (66) | 50 (100) | 31 (62) | 38 (76) | 7 (14) |
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Hongjaisee, S.; Jabjainai, Y.; Sakset, S.; Preechasuth, K.; Ngo-Giang-Huong, N.; Khamduang, W. Comparison of Simple RNA Extraction Methods for Molecular Diagnosis of Hepatitis C Virus in Plasma. Diagnostics 2022, 12, 1599. https://doi.org/10.3390/diagnostics12071599
Hongjaisee S, Jabjainai Y, Sakset S, Preechasuth K, Ngo-Giang-Huong N, Khamduang W. Comparison of Simple RNA Extraction Methods for Molecular Diagnosis of Hepatitis C Virus in Plasma. Diagnostics. 2022; 12(7):1599. https://doi.org/10.3390/diagnostics12071599
Chicago/Turabian StyleHongjaisee, Sayamon, Yosita Jabjainai, Suthasinee Sakset, Kanya Preechasuth, Nicole Ngo-Giang-Huong, and Woottichai Khamduang. 2022. "Comparison of Simple RNA Extraction Methods for Molecular Diagnosis of Hepatitis C Virus in Plasma" Diagnostics 12, no. 7: 1599. https://doi.org/10.3390/diagnostics12071599