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Dhibika M, Madhusudhan NS, Malini A, Natarajan M. Comparison of Manual and Automated Nucleic Acid (RNA) Extraction Methods for the Detection of SARS-CoV-2 by qRT-PCR. Cureus 2023; 15:e36773. [PMID: 37123735 PMCID: PMC10133768 DOI: 10.7759/cureus.36773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2023] [Indexed: 03/30/2023] Open
Abstract
Objectives During the COVID-19 pandemic, several laboratories used different RNA extraction methods based on the resources available. Hence this study was done to compare the Ct values in qRT-PCR, time taken (sample processing-loading to PCR), manpower requirement, and cost of consumables between manual and automated methods. Materials and methods A cross-sectional study was done on 120 nasopharyngeal/oropharyngeal swabs received in VRDL for RT-PCR testing. Based on the results of automated RNA extraction (Genetix, HT 96 Purifier) and RT-PCR (Trivitron PCR Kit) detecting E gene (screening) and ORF gene (confirmatory), the division into Group- I (Ct 15-22), Group- II (Ct 23-29), Group-III (Ct 30-36) and Group-IV (Ct >36) was done. Manual RNA extraction was done using magnetic beads (Lab system, Trivitron). Statistical analysis Data were analyzed by SPSS 19.0 version software. Ct values obtained in the two methods were compared by paired t-test, GroupWise. Z test was used to compare the other parameters. Results The difference in Ct values for target genes was statistically significant (p<0.05) in Group-I to III; however, no variation in result interpretation. The difference in time, manpower, and cost were statistically significant (p<0.05). The manual method required twice more manpower; 40 minutes more time & automated method cost 3.5 times more for consumables. Conclusion The study showed that RNA yield was better with automated extraction in comparison to manual extraction. The samples extracted by the automated method detected the virus at a lower Ct range by PCR than the manual method. Automated method processed samples in less time and with less manpower. Considering the cost factor, manual extraction can be preferred in resource-limited settings as there was no difference in the results of the test. The manual method requires more hands-on time with potential chances of cross-contamination and technical errors.
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Wu TY, Liao YC, Fuh CS, Weng PW, Wang JY, Chen CY, Huang YM, Chen CP, Chu YL, Chen CK, Yeh KL, Yu CH, Wu HK, Lin WP, Liou TH, Wu MS, Liaw CK. An improvement of current hypercube pooling PCR tests for SARS-CoV-2 detection. Front Public Health 2022; 10:994712. [PMID: 36339215 PMCID: PMC9627488 DOI: 10.3389/fpubh.2022.994712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/20/2022] [Indexed: 01/26/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic can be effectively controlled by rapid and accurate identification of SARS-CoV-2-infected cases through large-scale screening. Hypercube pooling polymerase chain reaction (PCR) is frequently used as a pooling technique because of its high speed and efficiency. We attempted to implement the hypercube pooling strategy and found it had a large quantization effect. This raised two questions: is hypercube pooling with edge = 3 actually the optimal strategy? If not, what is the best edge and dimension? We used a C++ program to calculate the expected number of PCR tests per patient for different values of prevalence, edge, and dimension. The results showed that every edge had a best performance range. Then, using C++ again, we created a program to calculate the optimal edge and dimension required for pooling samples when entering prevalence into our program. Our program will be provided as freeware in the hope that it can help governments fight the SARS-CoV-2 pandemic.
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Affiliation(s)
- Tai-Yin Wu
- Department of Family Medicine, Zhongxing Branch, Taipei City Hospital, Taipei, Taiwan,Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan,General Education Center, University of Taipei, Taipei, Taiwan
| | - Yu-Ciao Liao
- Institute of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
| | - Chiou-Shann Fuh
- Institute of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
| | - Pei-Wei Weng
- Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan,Department of Orthopedics, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan,Graduate Institute of Biomedical Optomechatronics, College of Biomedical Engineering, Research Center of Biomedical Device, Taipei Medical University, Taipei, Taiwan
| | - Jr-Yi Wang
- Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan,Department of Orthopedics, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan
| | - Chih-Yu Chen
- Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan,Department of Orthopedics, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan,Graduate Institute of Biomedical Optomechatronics, College of Biomedical Engineering, Research Center of Biomedical Device, Taipei Medical University, Taipei, Taiwan,International Ph.D. Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, Taiwan
| | - Yu-Min Huang
- Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan,Department of Orthopedics, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan
| | - Chung-Pei Chen
- Department of Orthopedics, Cathay General Hospital, Taipei, Taiwan
| | - Yo-Lun Chu
- Department of Orthopedics, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan,School of Medicine, College of Medicine, Fu Jen Catholic University, Taipei, Taiwan,Department of Biomedical Engineering, National Taiwan University, Taipei, Taiwan
| | - Cheng-Kuang Chen
- Department of Orthopedics, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan,Department of Biomedical Engineering, National Taiwan University, Taipei, Taiwan
| | - Kuei-Lin Yeh
- Institute of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan,Department of Orthopaedics, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan,Department of Long-Term Care and Management, WuFeng University, Chiayi, Taiwan
| | - Ching-Hsiao Yu
- Department of Orthopaedic Surgery, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan,Department of Orthopaedic Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Hung-Kang Wu
- Department of Orthopaedic Surgery, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan,Department of Orthopaedic Surgery, National Taiwan University Hospital, Taipei, Taiwan,Department of Nursing, Yuanpei University of Medical Technology, Hsinchu, Taiwan
| | - Wei-Peng Lin
- Department of Orthopaedic Surgery, National Taiwan University Hospital, Taipei, Taiwan,Department of Orthopedics, Postal Hospital, Taipei, Taiwan
| | - Tsan-Hon Liou
- Department of Physical Medicine and Rehabilitation, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Mai-Szu Wu
- Division of Nephrology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chen-Kun Liaw
- Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan,Department of Orthopedics, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan,Graduate Institute of Biomedical Optomechatronics, College of Biomedical Engineering, Research Center of Biomedical Device, Taipei Medical University, Taipei, Taiwan,TMU Biodesign Center, Taipei Medical University, Taipei, Taiwan,*Correspondence: Chen-Kun Liaw ;
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