Quantitative analysis of different respiratory specimens on two automated test systems for detection of SARS-CoV-2 RNA

•Reliable detection of SARS-CoV-2 RNA with both the cobas®6800 and NeuMoDx™ SARS-CoV-2 assays.•Highest sensitivity of SARS-CoV-2 RNA detection in hospitalized symptomatic patients in nasopharyngeal swabs.•SARS-CoV-2 viral load in anterior nasal swabs comparable to throat swabs.•High false negative rate of SARS-CoV-2 in saliva swabs and gargle lavages in the advanced phase of COVID-19. Molecular testing of SARS-CoV-2 RNA is essential during the pandemic. Here, we compared the results of different respiratory specimens including anterior nasal swabs, pharyngeal swabs, saliva swabs, and gargle lavage samples to nasopharyngeal swabs on two automated SARS-CoV-2 test systems. Samples were collected and tested simultaneously from a total of 36 hospitalized symptomatic COVID-19 patients. Detection and quantification of SARS-CoV-2 was performed on cobas®6800 (Roche) and NeuMoDx™ (Qiagen) systems. Both assays showed reliable detection and quantification of SARS-CoV-2 RNA, with nasopharyngeal swabs showing the highest sensitivity. SARS-CoV-2 RNA concentrations in other respiratory specimens were lower (mean 2.5 log10 copies/ml) or even undetectable in up to 20%. These data clearly indicate that not all respiratory materials are equally suitable for the management of hospitalized patients, especially, in the late phase of COVID-19, when the viral phase subsides and inflammation becomes the predominant factor, making detection of even lower viral loads increasingly important.