Rapid and Ultra-Sensitive SARS-CoV-2 Subgenomic RNA Detection Using Single-Molecule With a Large Transistor-SiMoT Bioelectronic Platform

Eleonora Macchia; Anna Maria D'Erchia; Mariapia Caputo; Angelica Bianco; Claudia Leoni; Francesca Intranuovo; Cecilia Scandurra; Lucia Sarcina; Cinzia Di Franco; Paolo Bollella; Gaetano Scamarcio; Luisa Torsi; Graziano Pesole

doi:10.1002/aelm.202400908

Rapid and Ultra-Sensitive SARS-CoV-2 Subgenomic RNA Detection Using Single-Molecule With a Large Transistor-SiMoT Bioelectronic Platform

Eleonora Macchia
, Anna Maria D'Erchia^*
, Mariapia Caputo
, Angelica Bianco
, Claudia Leoni
, Francesca Intranuovo
, Cecilia Scandurra
, Lucia Sarcina
, Cinzia Di Franco
, Paolo Bollella
, Gaetano Scamarcio
, Luisa Torsi^*
, Graziano Pesole

^*Corresponding author for this work

Physics

Research output: Contribution to journal › Article › Scientific › peer-review

1 Citation (Scopus)

1 Downloads (Pure)

Abstract

The replication of Coronaviridae viruses depends on the synthesis of structural proteins expressed through the discontinuous transcription of subgenomic RNAs (sgRNAs). Thus, detecting sgRNAs, which reflect active viral replication, provides valuable insights into infection status. Current diagnostic methods, such as PCR-based assays, often involve high costs, complex equipment, and reliance on highly trained personnel. Additionally, their specificity can be compromised by technical limitations in kit design. While viral culture remains highly accurate, it is impractical for routine diagnostics. In this study, the single-molecule-with-a-large-transistor (SiMoT) technology is presented for detecting sgRNA encoding the nucleocapsid (N) protein in clinical samples. SiMoT incorporates a stable layer of complementary DNA strands on the sensing gate electrode, facilitating rapid, sensitive, and specific sgRNA detection. Among 90 tested samples, SiMoT achieved a diagnostic sensitivity of 98.0% and a specificity of 87.8%, delivering results within 30 min. This user-friendly platform requires minimal sample preparation and offers a cost-effective point-of-care (POC) diagnostic solution. With its demonstrated diagnostic accuracy and scalability, SiMoT represents a promising tool for detecting active viral replication in SARS-CoV-2 and other coronaviruses. It addresses the limitations of existing molecular and culture-based methods while enhancing accessibility to reliable diagnostics.

Original language	English
Article number	2400908
Journal	Advanced Electronic Materials
Volume	11
Issue number	17
DOIs	https://doi.org/10.1002/aelm.202400908
Publication status	Published - 20 Oct 2025
MoE publication type	A1 Journal article-refereed

Funding

The authors thank Dr. Annunziata De Luisi and Dr. Petronilla Frugis for their laboratory support. The Centro di Innovazione Regionale Digital Assay, Regione PUGLIA Delibera Regionale n 702 del 08/11/2022 CUP B93C22000840001; NoOne-A binary sensor with single-molecule digit to discriminate biofluids enclosing zero or at least one biomarker, ERC Stg2021, GA:101040383; PRIN project prot.2017RHX2E4 “At the forefront of Analytical ChemisTry: disrUptive detection technoLogies to improve; Italian network of excellence for advanced diagnosis (INNOVA), Ministero della Salute-code PNC-E3-2022-23683266 PNC-HLS-DA, CUP: C43C22001630001; Complementary National Plan PNC-I.1 ″Research initiatives for innovative technologies and pathways in the health and welfare sector” D.D. 931 of 06/06/2022, DARE—DigitAl lifelong pRevEntion initiative, code PNC0000002, CUP: B53C22006420001; Tecnologie portatili e protocolli innovativi per la diagnosi ultrasensibile di Xylella fastidiosa direttamente in piante e vettori (1LIVEXYLELLA) Ministero dell'agricoltura, della sovranità alimentare e delle foreste—MIPAAF D.M. n.419161 del 13/09/2022; Research actions for reducing the impact on agricultural and natural ecosystems of the harmful plant pathogen Xylella fastidiosa (REACH-XY)—CUP B93C22001920001; the National Center for Gene Therapy and Drugs Based on RNA Technology (Project no. CN_00000041) and ELIXIR-IT through the empowering project ELIXIRNextGenIT (Grant Code IR0000010) are acknowledged for partial financial support. The authors thank Dr. Annunziata De Luisi and Dr. Petronilla Frugis for their laboratory support. The Centro di Innovazione Regionale Digital Assay, Regione PUGLIA Delibera Regionale n 702 del 08/11/2022 CUP B93C22000840001; NoOne‐A binary sensor with single‐molecule digit to discriminate biofluids enclosing zero or at least one biomarker, ERC Stg2021, GA:101040383; PRIN project prot.2017RHX2E4 “At the forefront of Analytical ChemisTry: disrUptive detection technoLogies to improve; Italian network of excellence for advanced diagnosis (INNOVA), Ministero della Salute‐code PNC‐E3‐2022‐23683266 PNC‐HLS‐DA, CUP: C43C22001630001; Complementary National Plan PNC‐I.1 ″Research initiatives for innovative technologies and pathways in the health and welfare sector” D.D. 931 of 06/06/2022, DARE—DigitAl lifelong pRevEntion initiative, code PNC0000002, CUP: B53C22006420001; Tecnologie portatili e protocolli innovativi per la diagnosi ultrasensibile di Xylella fastidiosa direttamente in piante e vettori (1LIVEXYLELLA) Ministero dell'agricoltura, della sovranità alimentare e delle foreste—MIPAAF D.M. n.419161 del 13/09/2022; Research actions for reducing the impact on agricultural and natural ecosystems of the harmful plant pathogen Xylella fastidiosa (REACH‐XY)—CUP B93C22001920001; the National Center for Gene Therapy and Drugs Based on RNA Technology (Project no. CN_00000041) and ELIXIR‐IT through the empowering project ELIXIRNextGenIT (Grant Code IR0000010) are acknowledged for partial financial support.

Keywords

bioelectronics
biomarkers
early-detections
SiMoT
subgenomic RNA

Access to Document

10.1002/aelm.202400908Licence: CC BY

Adv Elect Materials - 2025 - Macchia - Rapid and Ultra‐Sensitive SARS‐CoV‐2 Subgenomic RNA Detection Using Single‐MoleculeFinal published version, 1.64 MBLicence: CC BY

https://urn.fi/URN:NBN:fi-fe2026021814044

Cite this

Macchia, E., D'Erchia, A. M., Caputo, M., Bianco, A., Leoni, C., Intranuovo, F., Scandurra, C., Sarcina, L., Di Franco, C., Bollella, P., Scamarcio, G., Torsi, L., & Pesole, G. (2025). Rapid and Ultra-Sensitive SARS-CoV-2 Subgenomic RNA Detection Using Single-Molecule With a Large Transistor-SiMoT Bioelectronic Platform. Advanced Electronic Materials, 11(17), Article 2400908. https://doi.org/10.1002/aelm.202400908

@article{c58b86e9861a423397d44f5ee94b0400,

title = "Rapid and Ultra-Sensitive SARS-CoV-2 Subgenomic RNA Detection Using Single-Molecule With a Large Transistor-SiMoT Bioelectronic Platform",

abstract = "The replication of Coronaviridae viruses depends on the synthesis of structural proteins expressed through the discontinuous transcription of subgenomic RNAs (sgRNAs). Thus, detecting sgRNAs, which reflect active viral replication, provides valuable insights into infection status. Current diagnostic methods, such as PCR-based assays, often involve high costs, complex equipment, and reliance on highly trained personnel. Additionally, their specificity can be compromised by technical limitations in kit design. While viral culture remains highly accurate, it is impractical for routine diagnostics. In this study, the single-molecule-with-a-large-transistor (SiMoT) technology is presented for detecting sgRNA encoding the nucleocapsid (N) protein in clinical samples. SiMoT incorporates a stable layer of complementary DNA strands on the sensing gate electrode, facilitating rapid, sensitive, and specific sgRNA detection. Among 90 tested samples, SiMoT achieved a diagnostic sensitivity of 98.0\% and a specificity of 87.8\%, delivering results within 30 min. This user-friendly platform requires minimal sample preparation and offers a cost-effective point-of-care (POC) diagnostic solution. With its demonstrated diagnostic accuracy and scalability, SiMoT represents a promising tool for detecting active viral replication in SARS-CoV-2 and other coronaviruses. It addresses the limitations of existing molecular and culture-based methods while enhancing accessibility to reliable diagnostics.",

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author = "Eleonora Macchia and D'Erchia, \{Anna Maria\} and Mariapia Caputo and Angelica Bianco and Claudia Leoni and Francesca Intranuovo and Cecilia Scandurra and Lucia Sarcina and \{Di Franco\}, Cinzia and Paolo Bollella and Gaetano Scamarcio and Luisa Torsi and Graziano Pesole",

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Macchia, E, D'Erchia, AM, Caputo, M, Bianco, A, Leoni, C, Intranuovo, F, Scandurra, C, Sarcina, L, Di Franco, C, Bollella, P, Scamarcio, G, Torsi, L & Pesole, G 2025, 'Rapid and Ultra-Sensitive SARS-CoV-2 Subgenomic RNA Detection Using Single-Molecule With a Large Transistor-SiMoT Bioelectronic Platform', Advanced Electronic Materials, vol. 11, no. 17, 2400908. https://doi.org/10.1002/aelm.202400908

TY - JOUR

T1 - Rapid and Ultra-Sensitive SARS-CoV-2 Subgenomic RNA Detection Using Single-Molecule With a Large Transistor-SiMoT Bioelectronic Platform

AU - Macchia, Eleonora

AU - D'Erchia, Anna Maria

AU - Caputo, Mariapia

AU - Bianco, Angelica

AU - Leoni, Claudia

AU - Intranuovo, Francesca

AU - Scandurra, Cecilia

AU - Sarcina, Lucia

AU - Di Franco, Cinzia

AU - Bollella, Paolo

AU - Scamarcio, Gaetano

AU - Torsi, Luisa

AU - Pesole, Graziano

PY - 2025/10/20

Y1 - 2025/10/20

N2 - The replication of Coronaviridae viruses depends on the synthesis of structural proteins expressed through the discontinuous transcription of subgenomic RNAs (sgRNAs). Thus, detecting sgRNAs, which reflect active viral replication, provides valuable insights into infection status. Current diagnostic methods, such as PCR-based assays, often involve high costs, complex equipment, and reliance on highly trained personnel. Additionally, their specificity can be compromised by technical limitations in kit design. While viral culture remains highly accurate, it is impractical for routine diagnostics. In this study, the single-molecule-with-a-large-transistor (SiMoT) technology is presented for detecting sgRNA encoding the nucleocapsid (N) protein in clinical samples. SiMoT incorporates a stable layer of complementary DNA strands on the sensing gate electrode, facilitating rapid, sensitive, and specific sgRNA detection. Among 90 tested samples, SiMoT achieved a diagnostic sensitivity of 98.0% and a specificity of 87.8%, delivering results within 30 min. This user-friendly platform requires minimal sample preparation and offers a cost-effective point-of-care (POC) diagnostic solution. With its demonstrated diagnostic accuracy and scalability, SiMoT represents a promising tool for detecting active viral replication in SARS-CoV-2 and other coronaviruses. It addresses the limitations of existing molecular and culture-based methods while enhancing accessibility to reliable diagnostics.

AB - The replication of Coronaviridae viruses depends on the synthesis of structural proteins expressed through the discontinuous transcription of subgenomic RNAs (sgRNAs). Thus, detecting sgRNAs, which reflect active viral replication, provides valuable insights into infection status. Current diagnostic methods, such as PCR-based assays, often involve high costs, complex equipment, and reliance on highly trained personnel. Additionally, their specificity can be compromised by technical limitations in kit design. While viral culture remains highly accurate, it is impractical for routine diagnostics. In this study, the single-molecule-with-a-large-transistor (SiMoT) technology is presented for detecting sgRNA encoding the nucleocapsid (N) protein in clinical samples. SiMoT incorporates a stable layer of complementary DNA strands on the sensing gate electrode, facilitating rapid, sensitive, and specific sgRNA detection. Among 90 tested samples, SiMoT achieved a diagnostic sensitivity of 98.0% and a specificity of 87.8%, delivering results within 30 min. This user-friendly platform requires minimal sample preparation and offers a cost-effective point-of-care (POC) diagnostic solution. With its demonstrated diagnostic accuracy and scalability, SiMoT represents a promising tool for detecting active viral replication in SARS-CoV-2 and other coronaviruses. It addresses the limitations of existing molecular and culture-based methods while enhancing accessibility to reliable diagnostics.

KW - bioelectronics

KW - biomarkers

KW - early-detections

KW - SiMoT

KW - subgenomic RNA

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DO - 10.1002/aelm.202400908

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AN - SCOPUS:85216534056

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VL - 11

JO - Advanced Electronic Materials

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IS - 17

M1 - 2400908

ER -

Rapid and Ultra-Sensitive SARS-CoV-2 Subgenomic RNA Detection Using Single-Molecule With a Large Transistor-SiMoT Bioelectronic Platform

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