Journal: Nature Communications

Article Title: Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions

doi: 10.1038/s41467-021-21361-7

Figure Lengend Snippet: a Reads mapping to SARS-CoV-2 (red), other viruses (pink), human (blue), bacteria (light blue), archaea (black), fungi (dark gray), across samples with high/medium/low viral load according to qRT-PCR (“High”, “Medium”, and “Low”, respectively), qRT-PCR negative samples with no detection of other respiratory viruses (“None”), and qRT-PCR negative samples in which other respiratory viruses were detected by RNA sequencing and/or by a BioFire panel (“Other viral infection”). b Heatmap of abundance of a selection of viral pathogens across samples. c BioFire viral validation of the detection of viral pathogens using RNA sequencing across 669 samples. Box plots to compare relative abundance of viral pathogens in RNA sequencing between samples that were found as positive or negative for each virus in a BioFire PCR panel. Box plots show the median as center, first and third quartiles as the box hinges, and whiskers extend to the smallest and largest value no further than the 1.5× interquartile range (IQR) away from the hinges.

Article Snippet: Overall, we found close concordance between these results and the findings of a transcriptomics based viral detection to the results of a standard (BioFire) respiratory pathogen PCR panel performed within 7 days of the NP swab used for RNA sequencing ( N = 356 patients across 404 tests) (Fig. ).

Techniques: Bacteria, Quantitative RT-PCR, RNA Sequencing, Infection, Selection, Biomarker Discovery, Virus