PMC:7068162 / 8120-12048 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7068162","sourcedb":"PMC","sourceid":"7068162","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7068162","text":"Discussion\nOutbreaks of novel pathogens, such as the ongoing SARS-CoV-2 situation, represent a challenge for molecular diagnostics. However, identification of the agent, sequencing and publication of specific PCR assays for general use, a process that took several weeks 15 years ago, can now be accomplished in a few days [8]. With this rapid pace in identification and sharing of information comes the responsibility of local laboratories to be able to implement available assays and provide tests for the outbreak strain in an equally short timeframe. Furthermore, demand can be unpredictable and may suddenly spike, even outside the primary endemic areas, putting testing capacity under strain and potentially causing delays. For example, in February 2020, an entire cruise ship carrying almost 4,000 passengers and crew was quarantined off the port of Yokohama, Japan, and hundreds of people had to be tested for the virus in a short period of time [9].\nAutomated solutions for molecular diagnostics can help handle large numbers of samples and can be scaled to keep pace with fluctuating demand [10-12]. The system used in this study fully automates nucleic acid extraction, purification, amplification and detection. We, among others, have previously demonstrated that laboratory-developed tests can be adapted for fully automated PCR platforms such as the cobas 6800 system [6,13]. After brief preparation, clinical samples can be loaded directly into the device; required hands-on time and manual steps are reduced by up to 60% (manual steps reduced from 33 to 14, hands-on time reduced from 74 min to 14 min) compared with conventional workflows which usually involve automated extraction and PCR performed as separate procedures [13]. The inclusion of a full-process control for each reaction further facilitates the handling of results, allowing interpretation by personnel not familiar with RT-PCR diagnostics.\nThe system has passed clinical evaluation for a variety of viral and bacterial targets [14-17] and is also used for blood safety testing, another diagnostic field in which large numbers of samples have to be cleared by PCR-based screening tests.\nIn this study, we demonstrated good analytical performance of an adapted SARS-CoV-2 assay on swab samples with an LoD of 689.3 copies/mL (e.g. 275.72 copies/process) at 95% detection probability, which is roughly in line with results published by Corman et al. [4]. They report an LoD for SARS-CoV-2 RNA of 5.2 copies per reaction at 95% detection probability, which corresponds to 208 copies/mL based on a 25 µL reaction volume. It has to be noted that manual determination of LoD usually involves adding purified target RNA directly into the reagent mix for amplification, whereas in our study, control material (purified RNA) was spiked into samples and underwent the full workflow of the cobas 6800 device, including extraction and purification. Therefore, differences in nominal analytical performance are to be expected. One important limitation of the study is that we had to rely on spiked-in material and could not validate the performance of the assay using clinical SARS-CoV-2-positive samples.\nHowever, we believe that our assay designed for high-throughput molecular testing could be useful in the ongoing outbreak situation. It demonstrates how commercial PCR platforms can enhance outbreak readiness for emerging pathogens, allowing for large numbers of patients to be screened in a reasonable timeframe, if necessary. It has to be noted that by its nature as a screening test targeting only a single viral gene, positive results should always be confirmed with an independent PCR as recommended [4]. Finally, we want to stress the importance of closely coordinating with local reference centres and public health authorities for determining clinical indications for testing, as well as the handling of confirmed cases and contact 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