Comparison of Copan ESwab and FLOQSwab for COVID-19 Diagnosis: Working around a Supply Shortage

Abstract

O n 16 March 2020, the WHO Director-General stated, "You cannot fight a fire blindfolded.And we cannot stop this pandemic if we don't know who is infected.We have a simple message for all countries: test, test, test.Test every suspected case" (https://www.who.int/dg/speeches/detail/who-director-general-s-opening-remarks-at-the-media-briefing-on-covid-19---16-march-2020).This strategy hinges on the availability of appropriate, validated collection and transport systems to ensure preservation of nucleic acids and compatibility with downstream molecular testing-an acute challenge in the current pandemic.We present direct comparison of COVID-19 specimens collected with FLOQSwab nasopharyngeal swab preserved in universal transport medium (Copan UTM system; Copan, Italy; catalog no.305C), optimized for viral specimens, and flocked regular nylon tip swab preserved in liquid Amies (ESwab collection system; Copan, Italy; catalog no.480C), optimized for bacterial specimens.COVID-19 symptomatic inpatients, outpatients, and emergency department patients across five hospitals were sampled with both collection systems.Nasopharyngeal sampling technique was used for the UTM collection system, and mid-turbinate sampling was used for the ESwab collection system.Paired specimens were sent to a centralized microbiology laboratory and processed using two distinct extraction/realtime reverse transcription-PCR (rRT-PCR) amplification platforms.In the first, nucleic acid extraction/amplification was performed on the BD Max System (Becton, Dickinson, USA), using the ExK TNA-2 extraction strip and detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 5= untranslated region (UTR).Alternatively, specimens were extracted on the NucliSENS EasyMAG (bioMérieux, France) and detection of SARS-CoV-2 5= UTR and envelope (1) was performed on the Rotor-gene Q (Qiagen, Germany).Both assays have been validated to detect 10 RNA copies/reaction (unpublished data).Paired specimens from 94 patients were analyzed.On the BD Max, 35 were concordantly positive and 59 were concordantly negative.There were no discrepant results.On the Rotor-gene, 1 pair of swabs could not be analyzed (disqualified), 33 were concordantly positive, 59 were concordantly negative, and 1 was only FLOQSwab positive.Positive and negative results were concordant between the 2 assays.Comparing swabs, positive percent agreement, negative percent agreement, and Cohen's kappa values were 100% (95% confidence interval [CI], 0.900 to 1.000), 100% (95% CI,

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