Project description:To elucidate key pathways in the host transcriptome of patients infected with SARS-CoV-2, we used RNA sequencing (RNA Seq) to analyze nasopharyngeal (NP) swab and whole blood (WB) samples from 333 COVID-19 patients and controls, including patients with other viral and bacterial infections. Analyses of differentially expressed genes (DEGs) and pathways was performed relative to other infections (e.g. influenza, other seasonal coronaviruses, bacterial sepsis) in both NP swabs and WB. Comparative COVID-19 host responses between NP swabs and WB were examined. Both hospitalized patients and outpatients exhibited upregulation of interferon-associated pathways, although heightened and more robust inflammatory and immune responses were observed in hospitalized patients with more clinically severe disease. A two-layer machine learning-based classifier, run on an independent test set of NP swab samples, was able to discriminate between COVID-19 and non-COVID-19 infectious or non-infectious acute respiratory illness using complete (>1,000 genes), medium (<100) and small (<20) gene biomarker panels with 85.1%-86.5% accuracy, respectively. These findings demonstrate that SARS-CoV-2 infection has a distinct biosignature that differs between NP swabs and WB and can be leveraged for differential diagnosis of COVID-19 disease.

2020-12-15 | GSE163151 | GEO

uncultured 16S rRNA gene sequences from bird cloacal swabs

Project description:Rufous collared sparrow cloacal bacterial community raw sequence reads

| PRJNA478210 | ENA

Vaginal Swabs

Project description:Vaginal Swabs Raw sequence reads

| PRJNA814210 | ENA

Metatranscriptomes of human oral peri-implant biofilms

Project description:Metatranscriptomes of human oral peri-implant biofilms

| PRJEB43417 | ENA

Cloacal microbiota of barn swallow

Project description:Cloacal microbiota of barn swallow