Extraction Free Rapid Detection of SARS-CoV-2 from Oropharyngeal/Nasopharyngeal Swabs by Real Time PCR
Introduction: The emergence of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic has been troublesome particularly for developing countries that lack infrastructure and capacities to produce the kits locally. Simplification of the method can increase diagnostic efficiency whi...
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oai:doaj.org-article:83f2766fe6f443c0b054d7ef147385bc2021-11-07T08:43:12ZExtraction Free Rapid Detection of SARS-CoV-2 from Oropharyngeal/Nasopharyngeal Swabs by Real Time PCR10.7860/JCDR/2021/50193.154012249-782X0973-709Xhttps://doaj.org/article/83f2766fe6f443c0b054d7ef147385bc2021-09-01T00:00:00Zhttps://www.jcdr.net/articles/PDF/15401/50193_CE[Ra1]_F[SH]_PF1(AG_SHU_KM)_PN(KM).pdfhttps://doaj.org/toc/2249-782Xhttps://doaj.org/toc/0973-709XIntroduction: The emergence of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic has been troublesome particularly for developing countries that lack infrastructure and capacities to produce the kits locally. Simplification of the method can increase diagnostic efficiency which can benefit patients and help in infection control, consequently saving time and lives. Aim: To evaluate the diagnostic value of four methods (that omit extraction step) for detection of SARS-CoV-2 against the traditional extraction method. Materials and Methods: This was a cross-sectional analysis for evaluating diagnostic accuracy of four methods for detection of SARS-CoV-2 by real-time Reverse Transcriptase Polymerase Chain Reaction (rRT-PCR), conducted in the Department of Microbiology, SMS Medical College, Jaipur, Rajasthan, India, in October 2020. Ninety four SARS-CoV-2 RT-PCR positive samples and 20 negative samples were taken for this study. Automated extraction system was used for Ribonucleic Acid (RNA) extraction and four different approaches were compared to the traditional extraction method for detection of SARS-CoV-2 by RT-PCR. Data was entered and analysed using Statistical Package for the Social Sciences (SPSS) statistical software version 24.0. Results: The automated RNA extraction method was compared to the method of direct addition of samples with (Heat processed Direct Viral transport medium Sample (HDVS)) and without heating (Direct Viral transport medium Sample (DVS)), directs addition of diluted (1:5) sample with (Heat processed diluted VTM sample (HdVS)) and without heating (Diluted VTM sample (dVS)) as well as after addition of Proteinse K (PK) to the diluted samples that came either negative/invalid. Out of four methods, the HdVS method gave the best results, considering extraction with Perkin Elmer as standard, this method showed sensitivity of 96.74%, specificity of 100%. Conclusion: In current pandemic, molecular testing is critically challenged by the limited supplies of reagents of nucleic acid extraction alternative method like diluting and heating of Viral Transport Media (VTM) samples and using them directly as elutes serve as an easy, fast and inexpensive alternative.Parul SinhaSandeep GuptaMegha GuptaDinesh Kumar JainMalvika Sharma Kanika SharmaSaroj HoojaNitya VyasJCDR Research and Publications Private Limitedarticlecoronavirus disease-19molecular testingreverse transcriptase polymerase chain reactionviral transport mediaMedicineRENJournal of Clinical and Diagnostic Research, Vol 15, Iss 9, Pp DC11-DC15 (2021) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
coronavirus disease-19 molecular testing reverse transcriptase polymerase chain reaction viral transport media Medicine R |
| spellingShingle |
coronavirus disease-19 molecular testing reverse transcriptase polymerase chain reaction viral transport media Medicine R Parul Sinha Sandeep Gupta Megha Gupta Dinesh Kumar Jain Malvika Sharma Kanika Sharma Saroj Hooja Nitya Vyas Extraction Free Rapid Detection of SARS-CoV-2 from Oropharyngeal/Nasopharyngeal Swabs by Real Time PCR |
| description |
Introduction: The emergence of Severe Acute Respiratory Syndrome
Coronavirus-2 (SARS-CoV-2) pandemic has been troublesome
particularly for developing countries that lack infrastructure and
capacities to produce the kits locally. Simplification of the method
can increase diagnostic efficiency which can benefit patients and
help in infection control, consequently saving time and lives.
Aim: To evaluate the diagnostic value of four methods (that omit
extraction step) for detection of SARS-CoV-2 against the traditional
extraction method.
Materials and Methods: This was a cross-sectional analysis for
evaluating diagnostic accuracy of four methods for detection of
SARS-CoV-2 by real-time Reverse Transcriptase Polymerase Chain
Reaction (rRT-PCR), conducted in the Department of Microbiology,
SMS Medical College, Jaipur, Rajasthan, India, in October 2020.
Ninety four SARS-CoV-2 RT-PCR positive samples and 20 negative
samples were taken for this study. Automated extraction system
was used for Ribonucleic Acid (RNA) extraction and four different
approaches were compared to the traditional extraction method
for detection of SARS-CoV-2 by RT-PCR. Data was entered and
analysed using Statistical Package for the Social Sciences (SPSS)
statistical software version 24.0.
Results: The automated RNA extraction method was compared
to the method of direct addition of samples with (Heat processed
Direct Viral transport medium Sample (HDVS)) and without
heating (Direct Viral transport medium Sample (DVS)), directs
addition of diluted (1:5) sample with (Heat processed diluted
VTM sample (HdVS)) and without heating (Diluted VTM sample
(dVS)) as well as after addition of Proteinse K (PK) to the diluted
samples that came either negative/invalid. Out of four methods,
the HdVS method gave the best results, considering extraction
with Perkin Elmer as standard, this method showed sensitivity
of 96.74%, specificity of 100%.
Conclusion: In current pandemic, molecular testing is critically
challenged by the limited supplies of reagents of nucleic acid
extraction alternative method like diluting and heating of Viral
Transport Media (VTM) samples and using them directly as
elutes serve as an easy, fast and inexpensive alternative. |
| format |
article |
| author |
Parul Sinha Sandeep Gupta Megha Gupta Dinesh Kumar Jain Malvika Sharma Kanika Sharma Saroj Hooja Nitya Vyas |
| author_facet |
Parul Sinha Sandeep Gupta Megha Gupta Dinesh Kumar Jain Malvika Sharma Kanika Sharma Saroj Hooja Nitya Vyas |
| author_sort |
Parul Sinha |
| title |
Extraction Free Rapid Detection of SARS-CoV-2 from Oropharyngeal/Nasopharyngeal Swabs by Real Time PCR |
| title_short |
Extraction Free Rapid Detection of SARS-CoV-2 from Oropharyngeal/Nasopharyngeal Swabs by Real Time PCR |
| title_full |
Extraction Free Rapid Detection of SARS-CoV-2 from Oropharyngeal/Nasopharyngeal Swabs by Real Time PCR |
| title_fullStr |
Extraction Free Rapid Detection of SARS-CoV-2 from Oropharyngeal/Nasopharyngeal Swabs by Real Time PCR |
| title_full_unstemmed |
Extraction Free Rapid Detection of SARS-CoV-2 from Oropharyngeal/Nasopharyngeal Swabs by Real Time PCR |
| title_sort |
extraction free rapid detection of sars-cov-2 from oropharyngeal/nasopharyngeal swabs by real time pcr |
| publisher |
JCDR Research and Publications Private Limited |
| publishDate |
2021 |
| url |
https://doaj.org/article/83f2766fe6f443c0b054d7ef147385bc |
| work_keys_str_mv |
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