Pooled Specimen Testing Using Automated Cartridge-Based System for COVID-19: The Cost on Sensitivity

Reem Y Aljindan,Fatimah A Alturki,Ali J Al Haddad,Amani M Alnimr,Reem A Al Dossary,Nouf Mohammed Al-Romihi,Khaled R Alkharsah,Bashayer Hussain Aldossary

doi:10.21315/mjms2021.28.6.10

Abstract

BackgroundPooled specimen screening for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can improve laboratory testing capacity. This study assessed the impact of pooling and retesting individual swabs on the overall detection rate and reduction in the frequency of retesting.MethodsOne hundred respiratory swabs specimens were tested individually and in pools of three or five samples using the Cepheid’s Xpert® Xpress SARS-CoV-2 test kit. The optimum number of samples per pool was calculated using the application ‘A Shiny App for Pooled Testing’.ResultsTwenty-five pools were generated from 101 samples. Out of 13 pools that contained five samples each, three pools gave true positive results. While out of the 12 pools that contained three samples each, five pools gave true positive results. Four samples gave a false negative pool result. The overall sensitivity and specificity of the assay in the pools were 66.6% and 100%, respectively. The cycle threshold was reduced in most of the pools compared to individual sample tests.ConclusionThe overall pooled test had a remarkable impact on laboratory resources. Yet, caution is warranted when selecting the cases for pooled testing, since the reduction in sensitivity can significantly impact and increase the risk of exposure to infection.

Highlights

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic instigated a huge impact on clinical microbiology laboratories and contributed to major challenges in the laboratory diagnosis
Pooling strategy was introduced to laboratory testing long time ago and has been widely applied for human immunodeficiency virus (HIV) surveillance and blood donation, hepatitis C virus (HCV) and for some parasitic infections too [3]
We examined the effect of pooled specimen testing for COVID-19 using a fully automated nucleic acid amplification test

Summary

Introduction

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic instigated a huge impact on clinical microbiology laboratories and contributed to major challenges in the laboratory diagnosis. In order to conserve the resources and overcome their ongoing shortage, several diagnostic laboratories considered pooled testing strategy that was accepted later on by the US Food and Drug. Pooling strategy was introduced to laboratory testing long time ago and has been widely applied for human immunodeficiency virus (HIV) surveillance and blood donation, hepatitis C virus (HCV) and for some parasitic infections too [3]. Pooling test for SARS-CoV-2 means running single molecular test for a mixture of respiratory specimens collected from different patients. If the result of a pooled test is negative, it would imply that all specimens that were included in the test are negative. Individual testing is required for all specimens that were included in the positive pooled result. Pooled specimen screening for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can improve laboratory testing capacity. This study assessed the impact of pooling and retesting individual swabs on the overall detection rate and reduction in the frequency of retesting

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