ABSTRACT
Real-time PCR plays a key role in the diagnosis of viral infections. Multiple kits can detect or quantify genomes of various viruses with the same thermocycling program. Detection of RNA viruses includes an additional step of reverse transcription and challenge their detection in a single run with DNA viruses. We investigated the analytical performance of HSV-1, HSV-2 and VZV DNA quantification with Altona RealStar® PCR kits using the RT-PCR program for RNA viruses instead of the PCR program for DNA viruses. For each three viruses, Bland-Altman distribution did not show differences between both programs, and quantification curves generated with both thermocycling programs confirmed high correlation (R2 ≥ 0.9983). Detection of low viral load samples was evaluated, on 10-times repeat-test. All replicate samples were detected with both thermocycling programs and were quantified at similar viral loads (bias in log10 copies/mL: +0.05 (HSV-1), -0.01 (HSV-2) and +0.25 (VZV)). This confirms the feasibility of using the RT-PCR thermocycling program to detect and quantify the genome of RNA and DNA viruses in a single run.
Subject(s)
RNA Viruses , Humans , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity , Real-Time Polymerase Chain Reaction , DNA VirusesABSTRACT
PREDIMED, Clinical Data Warehouse of Grenoble Alps University Hospital, is currently participating in daily COVID-19 epidemic follow-up via spatial and chronological analysis of geographical maps. This monitoring is aimed for cluster detection and vulnerable population discovery. Our real-time geographical representations allow us to track the epidemic both inside and outside the hospital.
Subject(s)
COVID-19 , COVID-19/epidemiology , Data Warehousing , Geography , Hospitals, University , HumansSubject(s)
Coronavirus Infections/physiopathology , Guillain-Barre Syndrome/physiopathology , Pneumonia, Viral/physiopathology , Adult , Aged , Ageusia/etiology , Asthenia/etiology , Ataxia/etiology , COVID-19 , Coronavirus Infections/complications , Diarrhea/etiology , Facial Paralysis/etiology , Female , Guillain-Barre Syndrome/cerebrospinal fluid , Guillain-Barre Syndrome/complications , Guillain-Barre Syndrome/therapy , Humans , Immunoglobulins, Intravenous/therapeutic use , Immunologic Factors/therapeutic use , Male , Middle Aged , Myalgia/etiology , Neural Conduction , Olfaction Disorders/etiology , Pandemics , Paraparesis/etiology , Paresthesia/etiology , Pneumonia, Viral/complications , Quadriplegia/etiology , Reflex, Abnormal , Respiratory Insufficiency/etiologyABSTRACT
Robust antigen point-of-care SARS-CoV-2 tests have been proposed as an efficient tool to address the COVID-19 pandemic. This requirement was raised after acknowledging the constraints that are brought by molecular biology. However, worldwide markets have been flooded with cheap and potentially underperforming lateral flow assays. Herein we retrospectively compared the overall performance of five qualitative rapid antigen SARS-CoV-2 assays and one quantitative automated test on 239 clinical swabs. While the overall sensitivity and specificity are relatively similar for all tests, concordance with molecular based methods varies, ranging from 75,7% to 83,3% among evaluated tests. Sensitivity is greatly improved when considering patients with higher viral excretion (Ct≤33), proving that antigen tests accurately distinguish infectious patients from viral shedding. These results should be taken into consideration by clinicians involved in patient triage and management, as well as by national authorities in public health strategies and for mass campaign approaches.