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Tandel K, Ghedia M, Namaji MAA, Rai P, Anand KB, Singh SP. Evaluation of a commercial Real Time PCR for clinical samples without RNA extraction for detection of SARS-CoV-2. Diagn Microbiol Infect Dis 2024; 110:116441. [PMID: 39128205 DOI: 10.1016/j.diagmicrobio.2024.116441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 08/13/2024]
Abstract
RT-PCR is the gold standard for diagnosis of COVID-19. All RT-PCR kits are based on RNA extraction from the clinical sample. There was a sudden increase in demand of these kits, both RNA extraction and COVID-19 RT-PCR kits during the pandemic. This sudden spurt in global demand created a situation of shortage of consumables, especially the RNA extraction kits. Hence, this study was carried out to evaluate and compare COVID-19 RT-PCR without RNA extraction step using buffer R3. Sensitivity, specificity and accuracy of RT-PCR kit without RNA extraction were 89.16 %, 100% and 89.6% respectively. This approach saved more than 50 % time compared to the RT-PCR kit with RNA extraction approach allowing enhanced daily sample processing capability. RT-PCR kit without RNA extraction help in managing a greater number of samples, reduces cost and turnaround time.
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Affiliation(s)
- Kundan Tandel
- Department of Microbiology, Armed Forces Medical College Pune, 411040, India.
| | - Mayank Ghedia
- Department of Microbiology, Armed Forces Medical College Pune, 411040, India.
| | | | - Preeti Rai
- Department of Microbiology, Armed Forces Medical College Pune, 411040, India.
| | - Kavita Bala Anand
- Department of Microbiology, Armed Forces Medical College Pune, 411040, India.
| | - Sanjay Pratap Singh
- Department of Microbiology, Armed Forces Medical College Pune, 411040, India.
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Ramírez-Córdova C, Morales-Jadán D, Alarcón-Salem S, Sarmiento-Alvarado A, Proaño MB, Camposano I, Sarmiento-Alvarado B, Bravo-Castro M, Hidalgo-Jiménez JF, Coello D, Rodríguez ÁS, Viteri-Dávila C, Vallejo-Janeta AP, Arcos-Suárez D, Garcia-Bereguiain MA. Fast, cheap and sensitive: Homogenizer-based RNA extraction free method for SARS-CoV-2 detection by RT-qPCR. Front Cell Infect Microbiol 2023; 13:1074953. [PMID: 36968109 PMCID: PMC10035754 DOI: 10.3389/fcimb.2023.1074953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/01/2023] [Indexed: 03/11/2023] Open
Abstract
BackgroundThe SARS-CoV-2 gold standard detection method is an RT-qPCR with a previous step of viral RNA extraction from the patient sample either by using commercial automatized or manual extraction kits. This RNA extraction step is expensive and time demanding.ObjectiveThe aim of our study was to evaluate the clinical performance of a simple SARS-CoV-2 detection protocol based on a fast and intense sample homogenization followed by direct RT-qPCR.Results388 nasopharyngeal swabs were analyzed in this study. 222 of them tested positive for SARS-CoV-2 by the gold standard RNA extraction and RT-qPCR method, while 166 tested negative. 197 of those 222 positive samples were also positive for the homogenization protocol, yielding a sensitivity of 88.74% (95% IC; 83.83 – 92.58). 166 of those negative samples were also negative for the homogenization protocol, so the specificity obtained was 97% (95% IC; 93.11 – 99.01). For Ct values below 30, meaning a viral load of 103 copies/uL, only 4 SARS-CoV-2 positive samples failed for the RNA extraction free method; for that limit of detection, the homogenizer-based method had a sensitivity of 97.92% (95% CI; 96.01 – 99.83).ConclusionsOur results show that this fast and cheap homogenization method for the SARS-CoV-2 detection by RT-qPCR is a reliable alternative of high sensitivity for potentially infectious SARS-CoV-2 positive patients. This RNA extraction free protocol would help to reduce diagnosis time and cost, and to overcome the RNA extraction kits shortage experienced during COVID-19 pandemic.
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Affiliation(s)
- Cristina Ramírez-Córdova
- Laboratorio Clínico Segurilab, Quito, Ecuador
- Carrera de Ingeniería en Biotecnología, Universidad de las Américas, Quito, Ecuador
| | | | | | - Alisson Sarmiento-Alvarado
- Laboratorio Clínico Segurilab, Quito, Ecuador
- Carrera de Ingeniería en Biotecnología, Universidad de las Américas, Quito, Ecuador
| | | | | | | | | | | | - Dayana Coello
- Laboratorio de Investigación, Dirección General de Investigación, Universidad de Las Américas, Quito, Ecuador
| | - Ángel S. Rodríguez
- Laboratorio de Investigación, Dirección General de Investigación, Universidad de Las Américas, Quito, Ecuador
| | | | | | - Daniela Arcos-Suárez
- Laboratorio Clínico Segurilab, Quito, Ecuador
- *Correspondence: Daniela Arcos-Suárez, ; Miguel Angel Garcia-Bereguiain,
| | - Miguel Angel Garcia-Bereguiain
- One Health Research Group, Universidad de Las Américas, Quito, Ecuador
- *Correspondence: Daniela Arcos-Suárez, ; Miguel Angel Garcia-Bereguiain,
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Morehouse ZP, Proctor CM, Ryan GL, Nash RJ. A Novel PCR-Based Methodology for Viral Detection Utilizing Mechanical Homogenization. Bio Protoc 2022; 12:e4349. [PMID: 35592597 PMCID: PMC8918218 DOI: 10.21769/bioprotoc.4349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 11/14/2021] [Accepted: 01/14/2022] [Indexed: 12/29/2022] Open
Abstract
The impact of viral diseases on human health is becoming increasingly prevalent globally with the burden of disease being shared between resource-rich and poor areas. As seen in the global pandemic caused by SARS-CoV-2, there is a need to establish viral detection techniques applicable to resource-limited areas that provide sensitive and specific testing with a logistically conscious mindset. Herein, we describe a direct-to-PCR technology utilizing mechanical homogenization prior to viral PCR detection, which allows the user to bypass traditional RNA extraction techniques for accurate detection of human coronavirus. This methodology was validated in vitro, utilizing human coronavirus 229E (HCoV-229E), and then clinically, utilizing patient samples to test for SARS-CoV-2 infection. In this manuscript, we describe in detail the protocol utilized to determine the limit of detection for this methodology with in vitro testing of HCoV-229E.
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Affiliation(s)
- Zachary P. Morehouse
- Michigan State University College of Osteopathic Medicine, East Lansing, MI, USA
,Omni International Inc, A PerkinElmer Company, Kennesaw, GA, USA
,Jeevan Biosciences LLC, Tucker, GA, USA
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*For correspondence:
| | - Caleb M. Proctor
- Omni International Inc, A PerkinElmer Company, Kennesaw, GA, USA
| | | | - Rodney J. Nash
- Jeevan Biosciences LLC, Tucker, GA, USA
,Department of Biology, Georgia State University, Atlanta, GA, USA
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Capacitive biosensor based on vertically paired electrodes for the detection of SARS-CoV-2. Biosens Bioelectron 2022; 202:113975. [PMID: 35042131 PMCID: PMC8741629 DOI: 10.1016/j.bios.2022.113975] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/31/2021] [Accepted: 01/06/2022] [Indexed: 12/21/2022]
Abstract
Vertically paired electrodes (VPEs) with multiple electrode pairs were developed for the enhancement of capacitive measurements by optimizing the electrode gap and number of electrode pairs. The electrode was fabricated using a conductive polymer layer of PEDOT:PSS instead of Ag and Pt metal electrodes to increase the VPE fabrication yield because the PEDOT:PSS layer could be effectively etched using a reactive dry etching process. In this study, sensitivity enhancement was realized by decreasing the electrode gap and increasing the number of VPE electrode pairs. Such an increase in sensitivity according to the electrode gap and the number of electrode pairs was estimated using a model analyte for an immunoassay. Additionally, a computer simulation was performed using VPEs with different electrode gaps and numbers of VPE electrode pairs. Finally, VPEs with multiple electrode pairs were applied for SARS-CoV-2 nucleoprotein (NP) detection. The capacitive biosensor based on the VPE with immobilized anti-SARS-CoV-2 NP was applied for the specific detection of SARS-CoV-2 in viral cultures. Using viral cultures of SARS-CoV-2, SARS-CoV, MERS-CoV, and CoV-strain 229E, the limit of detection (LOD) was estimated to satisfy the cutoff value (dilution factor of 1/800) for the medical diagnosis of COVID-19, and the assay results from the capacitive biosensor were compared with commercial rapid kit based on a lateral flow immunoassay.
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