key: cord-0758658-r4c63zzh
authors: You, Huey-Ling; Lin, Meng-Chih; Lee, Chen-Hsiang
title: Comparison of the Roche cobas 6800 SARS-CoV-2 test and the Taiwan CDC protocol for the molecular diagnosis of COVID-19
date: 2020-12-29
journal: Biomed J
DOI: 10.1016/j.bj.2020.12.007
sha: acc2031f5de99482e6d7a7abe709fab831c6a138
doc_id: 758658
cord_uid: r4c63zzh

The current coronavirus disease 2019 (COVID-19) pandemic has caused significant challenges throughout the world and a rapid, reliable diagnostic test is in high demand. Real-time reverse transcriptase polymerase chain reaction (RT-PCR) was one of the most quickly established methods of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection and is considered to be the gold standard. In this report, we share our experience of using two different testing platforms: the cobas 6800 SARS-CoV-2 test, an automated system that was recently granted Emergency Use Authorization by the FDA, and a laboratory-developed test based on protocol from the Taiwan Centers for Disease Control (CDC). There was an overall 96.2% agreement between the two platforms. However, the positive agreement between the two platforms was only 80.0%. We found 3 instances of discordance between the two systems and this emphasized the need for timely diagnosis with a reliable testing platform.

In December 2019, a cluster of patients with atypical pneumonia of unknown etiology emerged in Wuhan, China [1] . A novel beta-coronavirus, defined as severe 22 acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the cause 23 of these cases [2] . According to the Johns Hopkins University COVID-19 Dashboard, 24 as of May 29 th 2020, there were over 5.8 million confirmed cases of COVID-19 and 25 more than 360,000 deaths worldwide [3] . Testing capabilities are absolutely essential 26 for managing a pandemic. Reverse transcription-polymerase chain reaction (RT-PCR) 27 was considered the primary mode of diagnosis for infection with SARS-CoV-2. Centers for Disease Control (CDC) organized COVID-19 testing and established a 32 protocol for clinical laboratories to follow [5] . 33

During the pandemic, timely and effective RT-PCR assay design was possible 34 because of the availability of significant SARS-CoV-2 sequence data [6] . However, 35 there is a need for a sensitive, accessible, and rapid diagnostic test for COVID-19 [7] . 36

The aim of this manufacturer-independent study, was to evaluate the clinical 37 performance of a laboratory-developed test based on the Taiwan CDC protocol and  38 the automated Roche cobas 6800 SARS-CoV-2 test (Roche, Pleasanton, CA, USA) that 39 Administration (FDA) for use as a detection assay. 41 J o u r n a l P r e -p r o o f A total of 79 respiratory samples (nasopharyngeal or throat swabs) were obtained 43 from 72 symptomatic patients or contact persons. After collection the swabs were 44 placed in 1 ml viral transport medium and then the specimen volume specified by 45 each assay was transferred as appropriate. All specimens were tested by both testing 46 platforms. The protocol recommended by the Taiwan CDC was as follows: viral RNA 47 was extracted from 300 µL of the sample using the LabTurbo automated purification test based on the modified USA CDC protocol has a lower input volume for the initial 116 specimen (120-140 µL) compared with our study (300 µL). In addition, most 117 commercially available viral (universal) transport mediums have a volume of 3.0 mL 118 but to enhance the sensitivity of the SARS-CoV-2 detection methods, we used 1.0 mL 119 viral transport medium to achieve a concentrated specimen. 120

There were three samples in which SARS-CoV-2 was "not-detected" by the 121 laboratory-developed test based on the Taiwan CDC protocol but was "detected" by 122 the automated system. This may have happened because the amount of virus in the 123 sample was below the detection limit for this method, thus leading to failure to 124 detect a positive result. Conventional molecular diagnostic methods include several 125 manual steps, such as nucleic acid extraction, master mix preparation and RT-PCR 126 setup, as well as the interpretation of results. These steps are labor intensive and 127 time consuming. A fully automated system allows for the handling/testing of large 128 numbers of samples and also significantly reduces the hands-on time required by up 129 to 50%. In addition, it is easier and quicker to train personnel who are not familiar 130 with molecular diagnostic assays to work with automated tests. However, a limitation 131 instrument; it must be pre-treated to avoid instruction malfunctions. 133

Taiwan successfully used big data analytics for efficient contact tracing 134 management, and surveillance of those who require quarantine and isolation [12] . 135 Therefore, the number of patients infected with COVID-19 in Taiwan J o u r n a l P r e -p r o o f

A Novel Coronavirus from Patients with Pneumonia in China

The species severe acute respiratory syndrome-related coronavirus: Classifying 2019-nCoV and naming it SARS-CoV-2

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-Novel Coronavirus (2019-nCoV) Real-Time rRT-PCR Panel Primers and Probes

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