RT Journal Article
SR Electronic
T1 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
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.03.03.433753
DO 10.1101/2021.03.03.433753
A1 Xiaofeng Dong
A1 Rebekah Penrice-Randal
A1 Hannah Goldswain
A1 Tessa Prince
A1 Nadine Randle
A1 Javier Salguero
A1 Julia Tree
A1 Ecaterina Vamos
A1 Charlotte Nelson
A1 ISARIC-4C Investigators
A1 COG-UK Consortium
A1 David A. Matthews
A1 Miles W. Carroll
A1 Alistair C. Darby
A1 Julian A. Hiscox
YR 2021
UL http://biorxiv.org/content/early/2021/03/03/2021.03.03.433753.abstract
AB 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.Competing Interest StatementThe authors have declared no competing interest.