An improvement of current hypercube pooling PCR tests for SARS-CoV-2 detection

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...

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Published inFrontiers in public health Vol. 10; p. 994712
Main Authors Wu, Tai-Yin, Liao, Yu-Ciao, Fuh, Chiou-Shann, Weng, Pei-Wei, Wang, Jr-Yi, Chen, Chih-Yu, Huang, Yu-Min, Chen, Chung-Pei, Chu, Yo-Lun, Chen, Cheng-Kuang, Yeh, Kuei-Lin, Yu, Ching-Hsiao, Wu, Hung-Kang, Lin, Wei-Peng, Liou, Tsan-Hon, Wu, Mai-Szu, Liaw, Chen-Kun
Format Journal Article
LanguageEnglish
Published Switzerland Frontiers Media S.A 19.10.2022
Subjects
COVID-19
COVID-19 - diagnosis
COVID-19 Testing
Humans
hypercube pooling
one round pooling PCR
Pandemics
Polymerase Chain Reaction
pooling PCR
Public Health
SARS-CoV-2
SARS-CoV-2 - genetics
COVID-19
SARS-CoV-2
pooling PCR
one round pooling PCR
hypercube pooling
Online AccessGet full text
ISSN2296-2565
2296-2565
DOI10.3389/fpubh.2022.994712

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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.
AbstractList 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.
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.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.
Author Yeh, Kuei-Lin
Weng, Pei-Wei
Huang, Yu-Min
Wu, Hung-Kang
Liao, Yu-Ciao
Chu, Yo-Lun
Wu, Mai-Szu
Chen, Chung-Pei
Fuh, Chiou-Shann
Liou, Tsan-Hon
Yu, Ching-Hsiao
Lin, Wei-Peng
Chen, Cheng-Kuang
Liaw, Chen-Kun
Wu, Tai-Yin
Chen, Chih-Yu
Wang, Jr-Yi
AuthorAffiliation 14 Department of Long-Term Care and Management, WuFeng University , Chiayi , Taiwan
21 TMU Biodesign Center, Taipei Medical University , Taipei , Taiwan
1 Department of Family Medicine, Zhongxing Branch, Taipei City Hospital , Taipei , Taiwan
12 Department of Biomedical Engineering, National Taiwan University , Taipei , Taiwan
2 Institute of Epidemiology and Preventive Medicine, National Taiwan University , Taipei , Taiwan
4 Institute of Computer Science and Information Engineering, National Taiwan University , Taipei , Taiwan
18 Department of Orthopedics, Postal Hospital , Taipei , Taiwan
10 Department of Orthopedics, Shin Kong Wu Ho-Su Memorial Hospital , Taipei , Taiwan
11 School of Medicine, College of Medicine, Fu Jen Catholic University , Taipei , Taiwan
5 Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University , Taipei , Taiwan
3 General Education Center, University of Taipei , Taipei , Taiwan
17 Department of Nursing, Yuanpei University of Medical Tec
AuthorAffiliation_xml – name: 4 Institute of Computer Science and Information Engineering, National Taiwan University , Taipei , Taiwan
– name: 15 Department of Orthopaedic Surgery, Taoyuan General Hospital, Ministry of Health and Welfare , Taoyuan , Taiwan
– name: 5 Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University , Taipei , Taiwan
– name: 12 Department of Biomedical Engineering, National Taiwan University , Taipei , Taiwan
– name: 6 Department of Orthopedics, Shuang Ho Hospital, Taipei Medical University , New Taipei , Taiwan
– name: 10 Department of Orthopedics, Shin Kong Wu Ho-Su Memorial Hospital , Taipei , Taiwan
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– name: 8 International Ph.D. Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University , Taipei , Taiwan
– name: 9 Department of Orthopedics, Cathay General Hospital , Taipei , Taiwan
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Copyright Copyright © 2022 Wu, Liao, Fuh, Weng, Wang, Chen, Huang, Chen, Chu, Chen, Yeh, Yu, Wu, Lin, Liou, Wu and Liaw.
Copyright © 2022 Wu, Liao, Fuh, Weng, Wang, Chen, Huang, Chen, Chu, Chen, Yeh, Yu, Wu, Lin, Liou, Wu and Liaw. 2022 Wu, Liao, Fuh, Weng, Wang, Chen, Huang, Chen, Chu, Chen, Yeh, Yu, Wu, Lin, Liou, Wu and Liaw
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Keywords COVID-19
SARS-CoV-2
pooling PCR
one round pooling PCR
hypercube pooling
Language English
License Copyright © 2022 Wu, Liao, Fuh, Weng, Wang, Chen, Huang, Chen, Chu, Chen, Yeh, Yu, Wu, Lin, Liou, Wu and Liaw.
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This article was submitted to Infectious Diseases - Surveillance, Prevention and Treatment, a section of the journal Frontiers in Public Health
Edited by: Reza Lashgari, Shahid Beheshti University, Iran
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Snippet The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic can be effectively controlled by rapid and accurate identification of...
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SubjectTerms COVID-19
COVID-19 - diagnosis
COVID-19 Testing
Humans
hypercube pooling
one round pooling PCR
Pandemics
Polymerase Chain Reaction
pooling PCR
Public Health
SARS-CoV-2
SARS-CoV-2 - genetics
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Title An improvement of current hypercube pooling PCR tests for SARS-CoV-2 detection
URI https://www.ncbi.nlm.nih.gov/pubmed/36339215
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