Multiplex viral genome detection

We used commercial kits to detect viral genomes. For pooled collections, we used Allplex Seegene (Eurobio, https://www.eurobio-scientific.com) on the sample of collected liquid, according to the manufacturer’s recommendations. The kit detects influenza A virus; influenza A(H1) virus; influenza A(H1N1)pdm09 virus; influenza A(H3) virus; influenza B virus; respiratory syncytial viruses A and B; adenovirus; enterovirus; human metapneumovirus (hMPV); parainfluenza viruses 1–4; bocaviruses 1–4; coronaviruses 229E, NL63, and OC43; and human rhinovirus. For individual testing, and particularly to detect SARS-CoV-2 RNA, we used TaqPath (ThermoFisher Scientific, https://www.thermofisher.com), Alinity (Abbott, https://www.corelaboratory.abbott), GeneXpert (Cepheid, https://info.cepheid.com), and FilmArray (bioMérieux, https://www.biomerieux.com). To detect cytomegalovirus (CMV), Epstein-Barr virus, and human parvovirus B19 genome, as part of our routine daily workflow we used RealStar assays (Altona, https://www.altona-diagnostics.com). All products were used as recommended by the manufacturers. For the kinetic study on SARS-CoV-2–positive samples and the comparison of signals between nasopharyngeal swab samples and tissues, we obtained all Ct values from a SARS-CoV-2 AMP Kit automatized on Alinity. This test amplifies 2 genome target genes (RNA polymerase and nucleocapsid), and the obtained signal is provided as a single Ct. Concordance between the signals obtained by the different commercial techniques routinely used in our laboratory is excellent. Our laboratory is certified according to COFRAC NF EN ISO 15189.

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Lagathu G., Grolhier C., Besombes J., Maillard A., Comacle P., Pronier C, & Thibault V. (2023). Using Discarded Facial Tissues to Monitor and Diagnose Viral Respiratory Infections. Emerging Infectious Diseases, 29(3), 511-518.

Publication 2023

Adenovirus Assays Bocaviruses Coronaviruses 229e Cytomegalovirus Diagnostics Enterovirus Epstein barr virus Genes Genome Human Human metapneumovirus Human parvovirus b19 Influenza Influenza a h1n1 virus Influenza a virus Influenza b virus Kinetic Nasopharyngeal Nucleocapsid Parainfluenza viruses 1 Parainfluenza viruses 4 Respiratory syncytial viruses Rhinovirus Rna polymerase Sars cov 2 Tissues Viral genomes Virus

Corresponding Organization :

Other organizations : Centre Hospitalier Universitaire de Rennes, Institut de Recherche en Santé, Environnement et Travail

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Variable analysis

independent variables

Not explicitly mentioned

dependent variables

Viral genomes detected by the commercial kits (influenza A virus, influenza A(H1) virus, influenza A(H1N1)pdm09 virus, influenza A(H3) virus, influenza B virus, respiratory syncytial viruses A and B, adenovirus, enterovirus, human metapneumovirus (hMPV), parainfluenza viruses 1–4, bocaviruses 1–4, coronaviruses 229E, NL63, and OC43, and human rhinovirus)
SARS-CoV-2 RNA
Cytomegalovirus (CMV), Epstein-Barr virus, and human parvovirus B19 genome

control variables

Not explicitly mentioned

positive controls

Not explicitly mentioned

negative controls

Not explicitly mentioned

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