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Open AccessArticle

SARS-CoV-2 Subgenomic N (sgN) Transcripts in Oro-Nasopharyngeal Swabs Correlate with the Highest Viral Load, as Evaluated by Five Different Molecular Methods

1
CEINGE, Biotecnologie Avanzate, 80131 Naples, Italy
2
Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, 80138 Naples, Italy
3
Department of Medicina di Laboratorio e Trasfusionale, AOU Federico II, 80138 Naples, Italy
4
Dipartimento di Clinica e Medicina Sperimentale, Università degli Studi di Foggia “Emanuele Altomare” Via Napoli, 121, 71122 Foggia FG, Italy
*
Author to whom correspondence should be addressed.
Academic Editor: Chao-Min Cheng
Diagnostics 2021, 11(2), 288; https://doi.org/10.3390/diagnostics11020288
Received: 12 January 2021 / Revised: 5 February 2021 / Accepted: 5 February 2021 / Published: 12 February 2021
The COVID-19 pandemic has forced diagnostic laboratories to focus on the early diagnostics of SARS-CoV-2. The positivity of a molecular test cannot respond to the question regarding the viral capability to replicate, spread, and give different clinical effects. Despite the fact that some targets are covered by commercially-available assays, the identification of new biomarkers is desired in order to improve the quality of the information given by these assays. Therefore, since the subgenomic transcripts (sgN and sgE) are considered markers of viral activity, we evaluated these subgenomic transcripts in relation to the genomic amplification obtained using five different commercial CE-IVD tools. Methods: Five CE-IVD kits were compared in terms of their capability to detect both synthetic SARS-CoV-2 viral constructs (spiked in TMB or PBS medium) and targets (N, E, RdRp and Orf1ab genes) in twenty COVID-19–positive patients’ swabs. The sgN and sgE were assayed by real-time RT-qPCR and digital PCR. Results: None of the diagnostic kits missed the viral target genes when they were applied to targets spiked in TMB or PBS (at dilutions ranging from 100 pg to 0.1 pg). Nevertheless, once they were applied to RNA extracted from the patients’ swabs, the superimposability ranged from 50% to 100%, regardless of the extraction procedure. The sgN RNA transcript was detected only in samples with a higher viral load (Ct ≤ 22.5), while sgE was within all of the Ct ranges. Conclusions: The five kits show variable performances depending on the assay layout. It is worthy of note that the detection of the sgN transcript is associated with a higher viral load, thus representing a new marker of early and more severe infection. View Full-Text
Keywords: SARS-CoV-2 subgenomic regions; viral load; CE-IVD SARS-CoV-2 subgenomic regions; viral load; CE-IVD
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MDPI and ACS Style

Zollo, M.; Ferrucci, V.; Izzo, B.; Quarantelli, F.; Domenico, C.D.; Comegna, M.; Paolillo, C.; Amato, F.; Siciliano, R.; Castaldo, G.; Capoluongo, E. SARS-CoV-2 Subgenomic N (sgN) Transcripts in Oro-Nasopharyngeal Swabs Correlate with the Highest Viral Load, as Evaluated by Five Different Molecular Methods. Diagnostics 2021, 11, 288. https://doi.org/10.3390/diagnostics11020288

AMA Style

Zollo M, Ferrucci V, Izzo B, Quarantelli F, Domenico CD, Comegna M, Paolillo C, Amato F, Siciliano R, Castaldo G, Capoluongo E. SARS-CoV-2 Subgenomic N (sgN) Transcripts in Oro-Nasopharyngeal Swabs Correlate with the Highest Viral Load, as Evaluated by Five Different Molecular Methods. Diagnostics. 2021; 11(2):288. https://doi.org/10.3390/diagnostics11020288

Chicago/Turabian Style

Zollo, Massimo; Ferrucci, Veronica; Izzo, Barbara; Quarantelli, Fabrizio; Domenico, Carmela D.; Comegna, Marika; Paolillo, Carmela; Amato, Felice; Siciliano, Roberto; Castaldo, Giuseppe; Capoluongo, Ettore. 2021. "SARS-CoV-2 Subgenomic N (sgN) Transcripts in Oro-Nasopharyngeal Swabs Correlate with the Highest Viral Load, as Evaluated by Five Different Molecular Methods" Diagnostics 11, no. 2: 288. https://doi.org/10.3390/diagnostics11020288

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