Utility of Extraction-Free SARS-CoV-2 Detection by RT–qPCR for COVID-19 Testing in a Resource-Limited Setting
Abstract
:1. Introduction
2. Materials and Methods
2.1. Samples
2.2. Solutions and Swabs
2.3. Viral RNA Extraction
2.4. Heat Inactivation
2.5. One-Step RT–qPCR
2.6. Biosafety Conditions
2.7. Data Analysis
3. Results
3.1. Evaluating Extraction-Free RT–qPCR Using Samples in Different Media with and without Heat Inactivation
3.2. Evaluating Degradation of Targets in Extraction-Free RT–qPCR Using Samples in Different Media after Freezing and Thawing
3.3. Evaluating the Impact of Plastic Shaft and Wooden Shaft Swabs in Extraction-Free COVID-19 RT–qPCR Assay after ≤6 h Incubation in Selected Media
3.4. Evaluating Plastic Shaft Versus Wooden Shaft Swabs in Extraction-Free COVID-19 RT–qPCR Assay after 2-Day Incubation in Selected Media
3.5. Effect of Freeze–Thawing on Extraction-Free COVID-19 RT–qPCR after Heating Samples at 95 °C
3.6. Extraction-Free COVID-19 RT–qPCR Compared to RT–qPCR Following Standard Extraction of Archived Samples across a Range of Ct Values
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
SARS-CoV-2 | severe acute respiratory syndrome coronavirus 2 |
RT–qPCR | reverse-transcription quantitative polymerase chain reaction |
rRT-PCR | real-time reverse-transcription-PCR |
Cq | quantification cycle |
COVID-19 | coronavirus disease 2019 |
WHO | World Health Organization |
PCR | polymerase chain reaction |
qPCR | quantitative real-time PCR |
RT | reverse-transcription |
cDNA | complementary DNA |
Pos ctrl | positive control |
Neg ctrl | Negative control |
MIC | magnetic induction cycler |
GITC | Guanidinium isothiocyanate |
Ext ctrl | extracted control |
0.9% Sal ht | unextracted samples in 0.9% normal saline, heated at 95 °C for 5 min |
1× PBS ht | unextracted samples in 1× PBS heated for 5 min at 95 °C |
0.1× PBS ht | unextracted samples in 0.1× PBS, heated for 5 min at 95 °C |
H2O ht | unextracted samples in nuclease-free water, heated for 5 min at 95 °C |
0.1× PBS rt | unextracted samples in 0.1× PBS at room temperature |
H2O rt | unextracted samples in nuclease-free water at room temperature |
Frz | Freeze |
Ext | Extracted |
HeFRA | Health Facilities Regulatory Agency |
PPE | personal protective equipment |
BSL-2 | Biosafety Level 2 |
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Yalley, A.K.; Ahiatrogah, S.; Moro, I.I.; Gmagna, P.; Yankson, I.K.; Kafintu-Kwashie, A.A.; Nii-Trebi, N.I. Utility of Extraction-Free SARS-CoV-2 Detection by RT–qPCR for COVID-19 Testing in a Resource-Limited Setting. Diseases 2024, 12, 198. https://doi.org/10.3390/diseases12090198
Yalley AK, Ahiatrogah S, Moro II, Gmagna P, Yankson IK, Kafintu-Kwashie AA, Nii-Trebi NI. Utility of Extraction-Free SARS-CoV-2 Detection by RT–qPCR for COVID-19 Testing in a Resource-Limited Setting. Diseases. 2024; 12(9):198. https://doi.org/10.3390/diseases12090198
Chicago/Turabian StyleYalley, Akua K., Selasie Ahiatrogah, Iddrisu I. Moro, Peter Gmagna, Isaac K. Yankson, Anna A. Kafintu-Kwashie, and Nicholas I. Nii-Trebi. 2024. "Utility of Extraction-Free SARS-CoV-2 Detection by RT–qPCR for COVID-19 Testing in a Resource-Limited Setting" Diseases 12, no. 9: 198. https://doi.org/10.3390/diseases12090198
APA StyleYalley, A. K., Ahiatrogah, S., Moro, I. I., Gmagna, P., Yankson, I. K., Kafintu-Kwashie, A. A., & Nii-Trebi, N. I. (2024). Utility of Extraction-Free SARS-CoV-2 Detection by RT–qPCR for COVID-19 Testing in a Resource-Limited Setting. Diseases, 12(9), 198. https://doi.org/10.3390/diseases12090198