Abstract

SARS-CoV-2 replication requires the synthesis of a set of structural proteins expressed through discontinuous transcription of ten subgenomic mRNAs (sgmRNAs). Here, we have fine-tuned droplet digital PCR (ddPCR) assays to accurately detect and quantify SARS-CoV-2 genomic ORF1ab and sgmRNAs for the nucleocapsid (N) and spike (S) proteins. We analyzed 166 RNA samples from anonymized SARS-CoV-2 positive subjects and we observed a recurrent and characteristic pattern of sgmRNAs expression in relation to the total viral RNA content. Additionally, expression profiles of sgmRNAs, as determined by meta-transcriptomics sequencing of a subset of 110 RNA samples, were highly correlated with those obtained by ddPCR. By providing a comprehensive and dynamic snapshot of the levels of SARS-CoV-2 sgmRNAs in infected individuals, our results may contribute a better understanding of the dynamics of transcription and expression of the genome of SARS-CoV-2 and facilitate the development of more accurate molecular diagnostic tools for the stratification of COVID-19 patients.

Oranger et al use digital droplet PCR to develop an assay that provides a dynamic snapshot of the levels of SARS-CoV-2 sub-genomic messanger RNA in infected individuals. This has the potential to improve diagnostic accuracy for COVID-19

Details

Title
Accurate detection and quantification of SARS-CoV-2 genomic and subgenomic mRNAs by ddPCR and meta-transcriptomics analysis
Author
Oranger Annarita 1   VIAFID ORCID Logo  ; Manzari Caterina 1 ; Chiara Matteo 2 ; Notario Elisabetta 1 ; Fosso Bruno 3   VIAFID ORCID Logo  ; Parisi, Antonio 4 ; Bianco, Angelica 4 ; Iacobellis Michela 5 ; d’Avenia Morena 5 ; D’Erchia Anna Maria 6   VIAFID ORCID Logo  ; Pesole Graziano 6   VIAFID ORCID Logo 

1  University of Bari Aldo Moro, Department of Biosciences, Biotechnology and Biopharmaceutics, Bari, Italy (GRID:grid.7644.1) (ISNI:0000 0001 0120 3326) 
2  National Research Council, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy (GRID:grid.5326.2) (ISNI:0000 0001 1940 4177); University of Milan, Department of Biosciences, Milan, Italy (GRID:grid.4708.b) (ISNI:0000 0004 1757 2822) 
3  National Research Council, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy (GRID:grid.5326.2) (ISNI:0000 0001 1940 4177) 
4  Istituto Zooprofilattico Sperimentale della Puglia e Basilicata, Putignano (Bari), Italy (GRID:grid.508082.7) (ISNI:0000 0004 1755 4106) 
5  Servizio Centralizzato Aziendale di Citopatologia e Screening- PO “Di Venere” - ASL, Bari, Italy (GRID:grid.508082.7) 
6  University of Bari Aldo Moro, Department of Biosciences, Biotechnology and Biopharmaceutics, Bari, Italy (GRID:grid.7644.1) (ISNI:0000 0001 0120 3326); National Research Council, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy (GRID:grid.5326.2) (ISNI:0000 0001 1940 4177); Consorzio Interuniversitario Biotecnologie, Trieste, Italy (GRID:grid.441025.6) (ISNI:0000 0004 1759 487X) 
Publication year
2021
Publication date
2021
Publisher
Nature Publishing Group
e-ISSN
23993642
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s42003-021-02748-0
ProQuest document ID
2584639285
Copyright
© The Author(s) 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.