False Negative Mitigation in Group Testing for COVID-19 Screening

Amir Reza Alizad-Rahvar; Safar Vafadar; Mehdi Totonchi; Mehdi Sadeghi

doi:10.3389/fmed.2021.661277

False Negative Mitigation in Group Testing for COVID-19 Screening

Front Med (Lausanne). 2021 May 10:8:661277. doi: 10.3389/fmed.2021.661277. eCollection 2021.

Authors

Amir Reza Alizad-Rahvar¹, Safar Vafadar², Mehdi Totonchi³, Mehdi Sadeghi⁴

Affiliations

¹ School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran.
² Laboratory of Biological Complex Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
³ Department of Genetics, Royan Institute for Reproductive Biomedicine, The Academic Center for Education, Culture, and Research (ACECR), Tehran, Iran.
⁴ Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran.

Abstract

After lifting the COVID-19 lockdown restrictions and opening businesses, screening is essential to prevent the spread of the virus. Group testing could be a promising candidate for screening to save time and resources. However, due to the high false-negative rate (FNR) of the RT-PCR diagnostic test, we should be cautious about using group testing because a group's false-negative result identifies all the individuals in a group as uninfected. Repeating the test is the best solution to reduce the FNR, and repeats should be integrated with the group-testing method to increase the sensitivity of the test. The simplest way is to replicate the test twice for each group (the 2Rgt method). In this paper, we present a new method for group testing (the groupMix method), which integrates two repeats in the test. Then we introduce the 2-stage sequential version of both the groupMix and the 2Rgt methods. We compare these methods analytically regarding the sensitivity and the average number of tests. The tradeoff between the sensitivity and the average number of tests should be considered when choosing the best method for the screening strategy. We applied the groupMix method to screening 263 people and identified 2 infected individuals by performing 98 tests. This method achieved a 63% saving in the number of tests compared to individual testing. Our experimental results show that in COVID-19 screening, the viral load can be low, and the group size should not be more than 6; otherwise, the FNR increases significantly. A web interface of the groupMix method is publicly available for laboratories to implement this method.

Keywords: COVID-19 screening; RT-PCR; SARS-CoV-2; false-negative mitigation; group testing; groupMix; pool testing; sensitivity.