key: cord-321076-kont2sff
authors: Yeo, Wee Song; Ng, Qin Xiang; Tan, Kuan Yang
title: Cohort PCR Testing: A Strategic Method for Rapid SARS-CoV-2 Screening
date: 2020-05-30
journal: Am J Clin Pathol
DOI: 10.1093/ajcp/aqaa092
sha: 
doc_id: 321076
cord_uid: kont2sff

nan

The world is currently facing an unprecedented outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes viral pneumonias and the coronavirus disease 2019 (COVID-19) in humans. 1 More than 3 million persons have been infected with the virus, and there are more than 240,000 recorded COVID-related deaths, as of May 5, 2020. Many countries have implemented strict containment measures in response to this global pandemic, including active detection and quarantine of suspected or confirmed cases, social distancing, and closure of public spaces. Until a vaccine is available, screening has to be done regularly, as we now know that a significant proportion of COVID-19 cases remain relatively asymptomatic and the virus has been shown to be highly contagious. 2, 3 Various diagnostic methods have been utilized in the detection of SARS-CoV-2, among which real time reverse transcription polymerase chain reaction (RT-PCR) assay is the most established and commonly utilized test method. 4 In RT-PCR testing, upper respiratory specimens, consisting of nasopharyngeal or oropharyngeal aspirates, are collected using swabs made of synthetic fiber with plastic applicators. Once the specimens are collected, the swabs are placed in 2 to 3 mL of viral transport media, and the samples subsequently undergo RNA extraction followed by qualitative RT-PCR for target detection. Though highly sensitive and specific, some of the limitations prohibiting the widespread use of RT-PCR include cost, availability of specialized technical expertise, and reagents to run the tests.

We read with great interest the article by Abdalhamid et al 5 and view their results as most encouraging. Pooling strategies have historically also been used for the detection of other infectious pathogens, including the human immunodeficiency virus (HIV), hepatitis B (hep B) and C (hep C) viruses, Chlamydia trachomatis, and Neisseria gonorrhoeae. [6] [7] [8] In order to overcome some of the above-mentioned limitations of RT-PCR, we further propose the utilization of a novel "cohort PCR" approach. Cohort PCR is an expansion of existing pooling strategies and would involve the following steps. First is to identify individuals who live in close proximity to one another (eg, in the same room/household/ building). Second is to combine part of the RNA collected from each of the individuals in one single tube followed by addition of the master mix/reagents for the RT-PCR reaction. Last, any cohort PCR reaction tubes that are positive for SARS-CoV-2 will be followed up by running RT-PCR on each of the individual RNA samples to identify the infected individual(s). Cohort reaction tubes negative for SARS-CoV-2 would suggest the absence of SARS-CoV-2 in all the individuals in the cohort. This avoids the need of having to run individual RT-PCR on each of the individuals in the cohort, hence saving significant time and reagents.

Cohort PCR is applicable for rapid screening of family/living units in the community who are likely to be negative for SARS-CoV-2. If cohort PCR is used to test a family or living unit where one member has confirmed SARS-CoV-2 infection, then there would be a very high likelihood that the pool would be positive (increasing probability with pool size). In these cases, the cohort testing approach may not be useful. Conversely, if the goal is mass testing of family/living units without known exposure, then this approach would be particularly beneficial.

As many countries are now contemplating a mass testing strategy before they safely reopen for business as usual, we hope that the above proposed screening method would enable rapid population screening for SARS-CoV-2, especially in resource-limited settings. Even in developed countries, testing reagents are expected to become in short supply, hence a pooled strategy is both feasible and necessary. Time is of the essence in the fight against a pandemic. 

Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia

Estimating the asymptomatic proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond Princess cruise ship

High contagiousness and rapid spread of severe acute respiratory syndrome coronavirus 2. Emerg Infect Dis

The laboratory diagnosis of COVID-19 infection: current issues and challenges

Assessment of specimen pooling to conserve SARS CoV-2 testing resources

Evaluation of a pooling method for routine anti-HCV screening of blood donors to lower the cost burden on blood banks in countries under development

Mini-pool screening by nucleic acid testing for hepatitis B virus, hepatitis C virus, and HIV: preliminary results

Use of pooled urine samples and automated DNA isolation to achieve improved sensitivity and cost-effectiveness of large-scale testing for Chlamydia trachomatis in pregnant women