Quantitative SARS-CoV-2 subgenomic RNA as a surrogate marker for viral infectivity: Comparison between culture isolation and direct sgRNA quantification
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 nasoph...
| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2023-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10473502/?tool=EBI |
| _version_ | 1797690819289808896 |
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| author | Rossana Scutari Silvia Renica Valeria Cento Alice Nava Josè Camilla Sammartino Alessandro Ferrari Arianna Pani Marco Merli Diana Fanti Chiara Vismara Francesco Scaglione Massimo Puoti Alessandra Bandera Andrea Gori Antonio Piralla Fausto Baldanti Carlo Federico Perno Claudia Alteri |
| author_facet | Rossana Scutari Silvia Renica Valeria Cento Alice Nava Josè Camilla Sammartino Alessandro Ferrari Arianna Pani Marco Merli Diana Fanti Chiara Vismara Francesco Scaglione Massimo Puoti Alessandra Bandera Andrea Gori Antonio Piralla Fausto Baldanti Carlo Federico Perno Claudia Alteri |
| author_sort | Rossana Scutari |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-12T02:05:37Z |
| format | Article |
| id | doaj.art-d648066fbd4547f78644b9dae588e65b |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-03-12T02:05:37Z |
| publishDate | 2023-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-d648066fbd4547f78644b9dae588e65b2023-09-07T05:31:44ZengPublic Library of Science (PLoS)PLoS ONE1932-62032023-01-01189Quantitative SARS-CoV-2 subgenomic RNA as a surrogate marker for viral infectivity: Comparison between culture isolation and direct sgRNA quantificationRossana ScutariSilvia RenicaValeria CentoAlice NavaJosè Camilla SammartinoAlessandro FerrariArianna PaniMarco MerliDiana FantiChiara VismaraFrancesco ScaglioneMassimo PuotiAlessandra BanderaAndrea GoriAntonio PirallaFausto BaldantiCarlo Federico PernoClaudia AlteriDetection 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.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10473502/?tool=EBI |
| spellingShingle | Rossana Scutari Silvia Renica Valeria Cento Alice Nava Josè Camilla Sammartino Alessandro Ferrari Arianna Pani Marco Merli Diana Fanti Chiara Vismara Francesco Scaglione Massimo Puoti Alessandra Bandera Andrea Gori Antonio Piralla Fausto Baldanti Carlo Federico Perno Claudia Alteri Quantitative SARS-CoV-2 subgenomic RNA as a surrogate marker for viral infectivity: Comparison between culture isolation and direct sgRNA quantification PLoS ONE |
| title | Quantitative SARS-CoV-2 subgenomic RNA as a surrogate marker for viral infectivity: Comparison between culture isolation and direct sgRNA quantification |
| title_full | Quantitative SARS-CoV-2 subgenomic RNA as a surrogate marker for viral infectivity: Comparison between culture isolation and direct sgRNA quantification |
| title_fullStr | Quantitative SARS-CoV-2 subgenomic RNA as a surrogate marker for viral infectivity: Comparison between culture isolation and direct sgRNA quantification |
| title_full_unstemmed | Quantitative SARS-CoV-2 subgenomic RNA as a surrogate marker for viral infectivity: Comparison between culture isolation and direct sgRNA quantification |
| title_short | Quantitative SARS-CoV-2 subgenomic RNA as a surrogate marker for viral infectivity: Comparison between culture isolation and direct sgRNA quantification |
| title_sort | quantitative sars cov 2 subgenomic rna as a surrogate marker for viral infectivity comparison between culture isolation and direct sgrna quantification |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10473502/?tool=EBI |
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