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      Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

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          Abstract

          The pandemic from the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) led to hundreds of thousands of deaths, including >15,000 in New York City (NYC). This pandemic highlighted a pressing clinical and public health need for rapid, scalable diagnostics that can detect SARS-CoV-2 infection, interrogate strain evolution, and map host response in patients. To address these challenges, we designed a fast (30 minute) colorimetric test to identify SARS-CoV-2 infection and simultaneously developed a large-scale shotgun metatranscriptomic profiling platform for nasopharyngeal swabs. Both technologies were used to profile 338 clinical specimens tested for SARS-CoV-2 and 86 NYC subway samples, creating a broad molecular picture of the COVID-19 epidemic in NYC. Our results nominate a novel, NYC-enriched SARS-CoV-2 subclade, reveal specific host responses in ACE pathways, and find medication risks associated with SARS-CoV-2 infection and ACE inhibitors. Our findings have immediate applications to SARS-CoV-2 diagnostics, public health monitoring, and therapeutic development.

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          Author and article information

          Journal
          bioRxiv
          April 20 2020
          Article
          10.1101/2020.04.20.048066
          8ccbd182-0e3c-46ab-9361-11a6dca17e14
          © 2020
          History

          Molecular biology
          Molecular biology

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