Application of SARS-CoV-2 nucleic acid amplification test systems in our hospital during the COVID-19 epidemic

Abstract

In COVID-19 assay, the polymerase chain reaction (PCR) test is used for a definitive diagnosis. We have introduced the use of the Ampdirect^TM2019-nCoV detection kit (Ampdirect method) for regular examinations, GeneXpert Xpress SARS-CoV-2 “Cepheid” (GeneXpert method), and FilmArray Respiratory Panel 2.1 (FilmArray method) in this sequence for emergency examinations from April 2020. The detection rates of these test methods for 163 samples measured by the GeneXpert method and 493 samples measured by the FilmArray method from their introduction to December 2020 were compared with those measured by the Ampdirect method. The detection rate within 10 days from onset was 90% and above. By focusing on the COVID-19-specialized clinical department and the general clinical department, the tests of 8,416 samples measured from July to December 2020 at our hospital were evaluated. The positivity rates (regular examinations/emergency examinations) were 11.6%/29.9% in the COVID-19-specialized clinical department and 0.13%/3.50% in the general clinical department. The positivity rate of the emergency examinations was higher than that of the regular examinations, and it was considered that the rapid result indicating positivity helped in deciding whether a patient requires admission in a general hospital or transfer to a COVID-19-specialized clinical department, thereby preventing the spread of infection. By using different test methods, we were able to quickly obtain the results and respond to the rapid increase in the number of cases to be tested. Regarding the testing system during the COVID-19 epidemic, it was considered very useful to apply multiple SARS-CoV-2 nucleic acid kits to make the best use of their respective characteristics.