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.

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.

The novel coronavirus, or COVID-19, has rapidly become a global pandemic. A major cause of morbidity and mortality due to COVID-19 has been the worsening hypoxia that, if untreated, can progress to acute respiratory distress syndrome (ARDS) and respiratory failure. Past work has found that intubated patients with ARDS experience physiological benefits to the prone position, because it promotes better matching of pulmonary perfusion to ventilation, improved secretion clearance, and recruitment of dependent areas of the lungs. We created a systemwide multi-institutional (New York-Presbyterian Hospital enterprise) protocol for placing awake, nonintubated, emergency department patients with suspected or confirmed COVID-19 in the prone position. In this piece, we describe the background literature and the approach we have taken at our institution as we care for a high burden of COVID-19 cases with respiratory symptoms.

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.