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Identification and quantification of SARS-CoV-2 leader subgenomic mRNA gene junctions in nasopharyngeal samples shows phasic transcription in animal models of COVID-19 and aberrant pattens in humans (preprint)
biorxiv; 2021.
Preprint in English | bioRxiv | ID: ppzbmed-10.1101.2021.03.03.433753
ABSTRACT

Introduction:

SARS-CoV-2 has a complex strategy for the transcription of viral subgenomic mRNAs (sgmRNAs), which are targets for nucleic acid diagnostics. Each of these sgRNAs has a unique 5 sequence, the leader-transcriptional regulatory sequence gene junction (leader-TRS-junction), that can be identified using sequencing.

Results:

High resolution sequencing has been used to investigate the biology of SARS-CoV-2 and the host response in cell culture models and from clinical samples. LeTRS, a bioinformatics tool, was developed to identify leader-TRS-junctions and be used as a proxy to quantify sgmRNAs for understanding virus biology. This was tested on published datasets and clinical samples from patients and longitudinal samples from animal models with COVID-19.

Discussion:

LeTRS identified known leader-TRS-junctions and identified novel species that were common across different species. The data indicated multi-phasic abundance of sgmRNAs in two different animal models, with spikes in sgmRNA abundance reflected in human samples, and therefore has implications for transmission models and nucleic acid-based diagnostics.
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Full text: Available Collection: Preprints Database: bioRxiv Main subject: COVID-19 Language: English Year: 2021 Document Type: Preprint

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Full text: Available Collection: Preprints Database: bioRxiv Main subject: COVID-19 Language: English Year: 2021 Document Type: Preprint