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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] [MESH Headings] [Grants] [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
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Kästner A, Lücker P, Sombetzki M, Ehmke M, Koslowski N, Mittmann S, Hannich A, Schwarz A, Meinck K, Schmeyers L, Schmidt K, Reisinger EC, Hoffmann W. SARS-CoV-2 surveillance by RT-qPCR-based pool testing of saliva swabs (lollipop method) at primary and special schools—A pilot study on feasibility and acceptability. PLoS One 2022; 17:e0274545. [PMID: 36099277 PMCID: PMC9469960 DOI: 10.1371/journal.pone.0274545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 08/30/2022] [Indexed: 12/03/2022] Open
Abstract
Background Since the onset of the COVID-19 pandemic, children have been mentally and physically burdened, particularly due to school closures, with an associated loss of learning. Therefore, efficient testing strategies with high sensitivity are necessary to keep schools open. Apart from individual rapid antigen testing, various methods have been investigated, such as PCR-based pool-testing of nasopharyngeal swabs, gargle, or saliva samples. To date, previous validation studies have found the PCR-based saliva swab pool testing method to be an effective screening method, however, the acceptability and feasibility of a widespread implementation in the school-setting among stakeholders has not been comprehensively evaluated. Methods In this pilot study, SARS-CoV-2 saliva swab pool testing of up to 15 swabs per pool was conducted in ten primary and special schools in Mecklenburg-Western Pomerania, Germany, over a period of one month. Thereafter, parents, teachers and school principals of the participating schools as well as the participating laboratories were surveyed about the feasibility and acceptability of this method, its large-scale implementation and challenges. Data were analyzed quantitatively and qualitatively. Results During the study period, 1,630 saliva swab pools were analyzed, of which 22 tested SARS-CoV-2 positive (1.3%). A total of N = 315 participants took part in the survey. Across all groups, the saliva swab pool testing method was perceived as more child-friendly (>87%), convenient (>82%), and easier (>81%) compared to rapid antigen testing by an anterior nasal swab. Over 80% of all participants favored widespread, regular use of the saliva swab method. Conclusion In school settings in particular, a high acceptability of the test method is crucial for a successful SARS-CoV-2 surveillance strategy. All respondents clearly preferred the saliva swab method, which can be used safely without complications in children six years of age and older. Hurdles and suggestions for improvement of an area-wide implementation were outlined.
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Affiliation(s)
- Anika Kästner
- Institute for Community Medicine, Section Epidemiology of Health Care and Community Health, University Medicine Greifswald, Greifswald, Germany
- * E-mail:
| | - Petra Lücker
- Institute for Community Medicine, Section Epidemiology of Health Care and Community Health, University Medicine Greifswald, Greifswald, Germany
| | - Martina Sombetzki
- Department of Tropical Medicine and Infectious Diseases, University Medical Center Rostock, Rostock, Germany
| | - Manja Ehmke
- Department of Tropical Medicine and Infectious Diseases, University Medical Center Rostock, Rostock, Germany
| | - Nicole Koslowski
- Department of Tropical Medicine and Infectious Diseases, University Medical Center Rostock, Rostock, Germany
| | - Swantje Mittmann
- Department of Tropical Medicine and Infectious Diseases, University Medical Center Rostock, Rostock, Germany
| | - Arne Hannich
- Institute for Community Medicine, Section Epidemiology of Health Care and Community Health, University Medicine Greifswald, Greifswald, Germany
| | | | | | - Lena Schmeyers
- Institute for Community Medicine, Section Epidemiology of Health Care and Community Health, University Medicine Greifswald, Greifswald, Germany
| | - Katrin Schmidt
- Department of Tropical Medicine and Infectious Diseases, University Medical Center Rostock, Rostock, Germany
| | - Emil C. Reisinger
- Department of Tropical Medicine and Infectious Diseases, University Medical Center Rostock, Rostock, Germany
| | - Wolfgang Hoffmann
- Institute for Community Medicine, Section Epidemiology of Health Care and Community Health, University Medicine Greifswald, Greifswald, Germany
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