COVID-19 study with RNA-Seq data on dbGaP (729 participants)

phs002258 — Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection    Reveals Unique Host Responses, Viral Diversification, and Drug    Interactions

<p>In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has killed hundreds of thousands of people, including >23,000 in New York City (NYC) alone. The pandemic's sudden emergence highlights the clinical need to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we provide large-scale shotgun metatranscriptomics (total-RNA-seq) for host, viral, and microbial profiling. In version 1, we sequenced a total of 732 clinical specimens (nasopharyngeal (NP) swabs) gathered from 669 unique patients in New York City during the first two months of the outbreak. In version 2, we sequenced an additional 168 clinical specimens from autopsy tissues (lung, heart, kidney, liver, and lymph node) from 60 patients, yielding a broad molecular portrait of the emerging COVID-19 disease across 900 clinical specimens and 729 patients. </p>

Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection    Reveals Unique Host Responses, Viral Diversification, and Drug    Interactions