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

In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin-angiotensin-aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinct ACE2 expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies.

Utilizing Telemedicine in a Novel Approach to COVID-19 Management and Patient Experience in the Emergency Department

Background: The COVID-19 crisis has highlighted telemedicine as a care delivery tool uniquely suited for a disaster pandemic. Introduction: With support from emergency department (ED) leadership, our institution rapidly deployed telemedicine in a novel approach to large-scale ED infectious disease management at NewYork-Presbyterian/Weill Cornell Medical Center (NYP/WCMC) and NewYork-Presbyterian/Lower Manhattan Hospital (NYP/LMH). Materials and Methods: Nineteen telemedicine carts were placed in COVID-19 isolation rooms to conserve personal protective equipment (PPE) and mitigate infectious risk for patients and providers by decreasing in-person exposures. Results: The teleisolation carts were used for 261 COVID-19 patient interactions from March to May 2020, with 79% of overall use in March. Our urban academic site (NYP/WCMC) had 173 of these cases, and the urban community hospital (NYP/LMH) had 88. This initiative increased provider/patient communication and attention to staff safety, improved palliative care and patient support services, lowered PPE consumption, and streamlined clinical workflows. The carts also increased patient comfort and reduced the psychological toll of isolation. Discussion: Deploying customized placement strategies in these two EDs maximized cart availability for isolation patients and demonstrates the utility of telemedicine in various ED settings. Conclusions: The successful introduction of this program in both academic and urban community hospitals suggests that widespread adoption of similar initiatives could improve safe ED evaluation of potentially infectious patients. In the longer term, our experience underscores the critical role of telemedicine in disaster preparedness planning, as building these capabilities in advance allows for the agile scaling needed to manage unforeseen catastrophic scenarios.

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

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused thousands of deaths worldwide, including >18,000 in New York City (NYC) alone. The sudden emergence of this pandemic has highlighted a pressing clinical need for rapid, scalable diagnostics that can detect infection, interrogate strain evolution, and identify novel patient biomarkers. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs, plus a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, bacterial, and viral profiling. We applied both technologies across 857 SARS-CoV-2 clinical specimens and 86 NYC subway samples, providing a broad molecular portrait of the COVID-19 NYC outbreak. Our results define new features of SARS-CoV-2 evolution, nominate a novel, NYC-enriched viral subclade, reveal specific host responses in interferon, ACE, hematological, and olfaction pathways, and examine risks associated with use of ACE inhibitors and angiotensin receptor blockers. Together, these findings have immediate applications to SARS-CoV-2 diagnostics, public health, and new therapeutic targets.