An evaluation of pooling strategies for RT-qPCR testing for SARS-CoV-2 infection: A pragmatic multi-site parallel operational study
https://doi.org/10.21141/PJP.2020.12
- Author:
Raymundo Lo
1
;
Agnes Barrientos
2
;
Bernadette Espiritu
3
;
Farrah Kristine Santiago
4
;
Amado Tandoc III
5
;
Januario Veloso
6
;
Soccoro Yañez
7
Author Information
1. COVID-19 Testing Laboratory, Philippine Childrens Medical Center, Quezon City
2. Department of Pathology and Laboratory Services, University of Perpetual Help System DALTA Medical Center, Las Pinas, Philippines
3. Bulacan Medical Center, Philippines
4. Section of Hematology, Philippine Childrens Medical Center Pathology Division, Quezon City
5. Laboratory Research Division, Research Institute for Tropical Medicine, Alabang, Muntinlupa, Philippines
6. Medical Research Laboratory, University of the Philippines-Philippine General Hospital Medical Center, Ermita, Manila
7. Section of Anatomic Pathology, University of the East Ramon, Magsaysay Memorial Medical Center, Quezon City, Philippines
- Publication Type:Journal Article
- Keywords:
Pooled testing;
Specimen pooling;
RT-qPCR
- MeSH:
COVID-19;
SARS-CoV-2
- From:
Philippine Journal of Pathology
2020;5(2):12-33
- CountryPhilippines
- Language:English
-
Abstract:
Background and Objectives:Sample pooling of COViD-19 PCR tests has been recently proposed as a low-cost alternative to individual tests. This multi-site, laboratory-based, proof-of-concept study explores the feasibility of pooled SARS-CoV-2 RT-qPCR testing, by demonstrating the effect of pooling on sensitivity, specificity, accuracy, number of tests saved, and turnaround time.
Methodology:The research was conducted in two experiments. In Experiment 1, archival nasopharyngeal (NPS) and oropharyngeal (OPS) swab samples were diluted to simulate 5, 10, and 20 sized pools, and tested for SARS-CoV-2 RNA using RT-qPCR. In Experiment 2, actual nasopharyngeal and oropharyngeal swab samples were collected from asymptomatic low-risk volunteers. Aliquots of the samples were pooled following the 5, 10-5, and 20-10-5 multi-staged Dorfman pooling methods and tested. The sensitivity, specificity, accuracy, test savings, and turnaround time for each pooling method were documented.
Results and Conclusions:The study provided evidence that pooling of NP and OP samples for SARS-CoV-2 RNA detection using RT-qPCR is feasible and can be implemented in the Philippines. A 2-stage Dorfman 5 pooling strategy appears to be the best method, because it has the highest over-all accuracy, while still achieving acceptable test savings, and turnaround time. Pooling of nasopharyngeal and oropharyngeal swab samples prior to RT-qPCR testing may be considered by select molecular diagnostic laboratories to further increase testing capacity and at the same time reduce the cost of testing.
- Full text:58 pjp.pdf
