Quantitative SARS-CoV-2 subgenomic RNA as a surrogate marker for viral infectivity: Comparison between culture isolation and direct sgRNA quantification.

Publication date: Sep 01, 2023

Detection of subgenomic (sg) SARS-CoV-2 RNAs are frequently used as a correlate of viral infectiousness, but few data about correlation between sg load and viable virus are available. Here, we defined concordance between culture isolation and E and N sgRNA quantification by ddPCR assays in 51 nasopharyngeal swabs collected from SARS-CoV-2 positive hospitalized patients. Among the 51 samples, 14 were SARS-CoV-2 culture-positive and 37 were negative. According to culture results, the sensitivity and specificity of E and N sgRNA assays were 100% and 100%, and 84% and 86%, respectively. ROC analysis showed that the best E and N cut-offs to predict positive culture isolation were 32 and 161 copies/mL respectively, with an AUC (95% CI) of 0. 96 (0. 91-1. 00) and 0. 96 (0. 92-1. 00), and a diagnostic accuracy of 88% and 92%, respectively. Even if no significant correlations were observed between sgRNA amount and clinical presentation, a higher number of moderate/severe cases and lower number of days from symptoms onset characterized patients with sgRNA equal to or higher than sgRNA cut-offs. Overall, this study suggests that SARS-CoV-2 sgRNA quantification could be helpful to estimate the replicative activity of SARS-CoV-2 and can represent a valid surrogate marker to efficiently recognize patients with active infection. The inclusion of this assay in available SARS-CoV-2 diagnostics procedure might help in optimizing fragile patients monitoring and management.

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Concepts Keywords
Clinical Assays
Rnas Cov
Virus Culture


Type Source Name
disease IDO infectivity
disease VO viable
drug DRUGBANK Saquinavir
drug DRUGBANK Aspartame
disease MESH infection
disease IDO assay
disease MESH Infectious Diseases
disease IDO history
disease IDO process
pathway REACTOME Reproduction
disease VO time
drug DRUGBANK Nonoxynol-9
drug DRUGBANK Gold
pathway KEGG Viral replication
disease IDO replication
disease IDO production
disease VO population
disease MESH viral shedding
disease MESH COVID 19
disease VO protocol
pathway KEGG RNA polymerase
drug DRUGBANK Creatinolfosfate
drug DRUGBANK Indoleacetic acid
drug DRUGBANK Medical air
drug DRUGBANK Streptomycin
drug DRUGBANK L-Glutamine
drug DRUGBANK Trypsin
disease VO gene

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