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1.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-318395

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 a 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 RNAs from anonymized COVID-19 positive subjects and we found a recurrent and characteristic pattern of sgmRNAs expression in relation to the total viral RNA content. Further, we observed that expression profiles of sgmRNAs analyzed in a subset of 110 samples subjected to meta-transcriptomics sequencing were highly correlated with those obtained by ddPCR. Our results, providing a comprehensive and dynamic snapshot of SARS-CoV-2 sgmRNAs expression and replication, may contribute to provide a better understanding of SARS-CoV-2 transcription and expression mechanisms, and support the development of more accurate molecular diagnostic tools and for the stratification of COVID-19 patients.

2.
Commun Biol ; 4(1): 1215, 2021 10 22.
Article in English | MEDLINE | ID: covidwho-1479821

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.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/genetics , COVID-19/metabolism , Coronavirus Nucleocapsid Proteins , Polymerase Chain Reaction/methods , RNA, Viral/metabolism , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Transcriptome , Computational Biology , Humans , Limit of Detection , Open Reading Frames , Phosphoproteins , RNA, Messenger/metabolism , Real-Time Polymerase Chain Reaction , Reproducibility of Results
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