Rapid differential diagnosis of SARS-CoV-2, influenza A/B and respiratory syncytial viruses: Validation of a novel RT-PCR assay

Alexander Domnich; Bianca Bruzzone; Carlo-Simone Trombetta; Vanessa De Pace; Valentina Ricucci; Serena Varesano; Giada Garzillo; Matilde Ogliastro; Andrea Orsi; Giancarlo Icardi

doi:10.1016/j.jcv.2023.105402

Rapid differential diagnosis of SARS-CoV-2, influenza A/B and respiratory syncytial viruses: Validation of a novel RT-PCR assay

J Clin Virol. 2023 Apr:161:105402. doi: 10.1016/j.jcv.2023.105402. Epub 2023 Feb 14.

Affiliations

¹ Hygiene Unit, San Martino Policlinico Hospital - IRCCS for Oncology and Neurosciences, Genoa, Italy. Electronic address: alexander.domnich@hsanmartino.it.
² Hygiene Unit, San Martino Policlinico Hospital - IRCCS for Oncology and Neurosciences, Genoa, Italy.
³ Department of Health Sciences, University of Genoa, Genoa, Italy.
⁴ Hygiene Unit, San Martino Policlinico Hospital - IRCCS for Oncology and Neurosciences, Genoa, Italy; Department of Health Sciences, University of Genoa, Genoa, Italy; Interuniversity Research Center on Influenza and Other Transmissible Infections (CIRI-IT), Genoa, Italy.

PMID: 36805601
DOI: 10.1016/j.jcv.2023.105402

Abstract

Background: Influenza and respiratory syncytial (RSV) viruses are expected to co-circulate with SARS-CoV-2 in the upcoming seasons and clinical differential diagnosis between them is difficult. Laboratory-based RT-PCR is a gold standard diagnostic method for influenza, RSV and SARS-CoV-2. The objective of this study was to estimate the diagnostic performance of a novel point-of-care RT-PCR assay STANDARD M10 Flu/RSV/SARS-CoV-2 (SD Biosensor) in a large number of clinical specimens with diversified (co)-infection patterns and viral loads.

Methods: This was a retrospective study, in which all samples were tested in both STANDARD M10 Flu/RSV/SARS-CoV-2 index and Allplex SARS-CoV-2/Respiratory Panel 1 (Seegene) reference kits. Samples with discordant results were further processed in a third resolver test (Resp-4-Plex, Abbott).

Results: A total of 1,019 naso-/oropharyngeal samples (50.3% positive for at least one virus) were processed in both STANDARD M10 Flu/RSV/SARS-CoV-2 and Allplex assays and the overall between-assay agreement was as high as 94.6%. Positive percent agreement of the STANDARD M10 Flu/RSV/SARS-CoV-2 was 100%, 96.6%, 97.3% and 99.4% for influenza A, B, RSV and SARS-CoV-2, respectively. The corresponding negative percent agreement was 99.7%. 100%, 100% and 98.4%, respectively. The expected positive and negative predictive values for all viruses were constantly above 96% in a reasonable range of disease prevalence.

Conclusions: STANDARD M10 Flu/RSV/SARS-CoV-2 is a reliable RT-PCR assay able to detect influenza A, influenza B, RSV and SARS-CoV-2 in one hour or less, fostering a rapid differential diagnosis of common respiratory viruses.

Keywords: Diagnostic accuracy; Influenza; RSV; SARS-CoV-2; point-of-care testing; rapid RT-PCR.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19* / diagnosis
Coinfection* / diagnosis
Diagnosis, Differential
Humans
Influenza A virus* / genetics
Influenza B virus / genetics
Influenza, Human* / diagnosis
Molecular Diagnostic Techniques / methods
Real-Time Polymerase Chain Reaction / methods
Respiratory Syncytial Virus Infections* / diagnosis
Respiratory Syncytial Virus, Human* / genetics
Respiratory Syncytial Viruses
Retrospective Studies
Reverse Transcriptase Polymerase Chain Reaction
SARS-CoV-2 / genetics
Sensitivity and Specificity