Severe acute respiratory infection-preparedness (Sari-Prep): A multicenter prospective study

OBJECTIVES: We designed a prospective cohort study to systematically study patients with severe acute respiratory infection (SARI) and improve hospital preparedness (SARI-PREP). The goal of this project is to evaluate the natural history, prognostic biomarkers, and characteristics, including hospital stress, associated with SARI clinical outcomes and severity. METHODS: In collaboration with the Society of Critical Care Medicine Discovery Research Network and the National Emerging Special Pathogen Training and Education Center (NETEC), SARIPREP is an ongoing, prospective, observational, multi-center cohort study of hospitalized patients with respiratory viral infections. We collected patient demographics, signs, symptoms, and medications;microbiology, imaging, and other diagnostics;mechanical ventilation, hospital procedures, and other interventions;and clinical outcomes. Hospital leadership completed a weekly hospital stress survey. Respiratory, blood, and urine biospecimens were collected from patients on days 0, 3, 7-14 after study enrollment and at hospital discharge. MEASUREMENTS AND MAIN RESULTS: SARI-PREP enrollment began on April 4, 2020 and currently includes 674 patients. Here we report results from the first 400 patients: 216 are from the University of Washington Hospitals, Seattle WA, 142 from New York University, New York NY and 42 from University of Southern California, Los Angeles, CA. Almost all tested positive for SARS-CoV-2 infection (n=397), whereas 3 patients tested positive for an alternative viral pathogen. The mean (±SD) age of the patients was 57±16 years;72% were men, 62% were White, 14% were Asian, 12% were Black, and 31% were Hispanic. Most of the patients were admitted to the intensive care unit (96%). The median (interquartile range) hospital length of stay was 22 (9-46) days. Rates of invasive mechanical ventilation (72%) and renal replacement therapy (19%) were common and the rate of hospital mortality was 35%. CONCLUSIONS: Initial SARI-PREP analysis indicates enrollment of a diverse population of hospitalized patients primarily with SARSCoV-2 infection. The demographics and clinical outcomes of our cohort mirror other large critically ill cohorts of COVID-19 patients. Results of a concomitant, weekly, hospital stress assessment are reported separately.

Evaluation of the airway viral load in acute sars-cov2 infection as a predictor of clinical outcome

Rationale: Throughout recent studies, data suggests high viral load in the plasma and nasopharynx of patients with severe SARS-CoV2 infection is associated with disease severity (mortality, length of hospitalization, and risk of intubation). Here, we evaluated whether viral load in the airway is associated with poor clinical outcomes in patients with SARS-CoV2. Methods: Lower airway samples in 148 patients from an academic center that were admitted to the ICU (dates: March 10th to May 10th, 2020) with severe respiratory failure requiring mechanical ventilation and underwent bronchoscopy for airway clearance and/or tracheostomy. Clinical outcome was defined as ≤ 28 Day mechanical ventilation vs. > 28 Day mechanical ventilation vs. death. Post-admission followup time was 232 [IQR 226-237] days. RNA was isolated in parallel using zymoBIOMICS™ DNA/RNA Miniprep Kit (Cat: R2002) as per manufacturer's instructions. Viral load was measured by quantitative real-time reverse transcription polymerase chain reaction (rRT -PCR) targeting the virus nucleocapsid (N) gene and an additional primer/probe set to detect the human RNase P gene (RP). Results: Among this bronchoscopy cohort, n=58 39% of the subjects were successfully extubated within 28 days of initiation of mechanical ventilation, n=56 38% required prolonged mechanical ventilation and n=34 23% died. We evaluated the viral load by rRT-PCR for SARSCoV2 N gene adjusted by human RP gene throughout the respiratory tract using supraglottic samples and bronchoalveolar lavage (BAL) samples obtained during bronchoscopy. Paired analysis of upper and lower airway samples shows that there is a subset of subjects (n=31, 21%) where there is greater viral load in the BAL than in the supraglottic area supporting topographical differences in viral replication (Fig 1A). BAL samples from subjects that died had higher viral load in their lower airways than patients that survived, even after adjusting for confounders such as age, gender, BMI and timing of sample collection (Fig 1B magenta dots (deceased) vs. yellow/green dots (alive)). Conclusions: Using samples obtained via bronchoscopy we identified that in a subset of subjects with acute SARS-CoV2 infection, the lower airways are the predominant site for viral replication. From our study, it is unclear if the higher viral load reflects host co-morbidies (e.g., diabetes or immunosuppression) or viral factors favoring higher replication. High viral load can be used as a predictor for disease severity upon hospital admission as viral load in the lower airways correlated with poor outcomes.

Evaluation of the lower airway microbiota in patients with severe sars-cov2

RATIONALE:Secondary infections with bacterial pathogens are thought to be responsible for poor outcomes in the 1918 Spanish and H1N1 pandemics. We postulate that poor prognosis in patients with SARS-CoV2 may be associated with uncontrollable viral replication, co-infection with a secondary pathogen, and over exuberant host immune response. We seek to evaluate whether there is an association between distinct features of the lower airway microbiota and poor clinical outcome in patients with SARS-CoV2. METHODS:We collected lower airway samples in 148 patients from NYU admitted between 3/10/2020 and 5/10/2020 with severe respiratory failure requiring mechanical ventilation and that underwent bronchoscopy for airway clearance and/or tracheostomy. Clinical outcome was defined as dead vs alive. DNA was isolated in parallel using zymoBIOMICS™ DNA/RNA Miniprep Kit (Cat: R2002) as per manufacturer's instructions. The V4 region of the 16S rRNA gene marker was sequenced using Illumina MiSeq. Sequences were analyzed using the Quantitative Insights into Microbial Ecology (QIIME version 1.9.1) pipeline. Total bacterial load was evaluated in lower airway samples using digital droplet PCR targeting the 16S rRNA gene. RESULTS:Of the 148 patients included, 114 survived (77%) and 34 (23%) died. Among those with poor clinical outcome, there was a non-statistically significant trend towards higher age and BMI. Patients who died more commonly had chronic kidney disease and prior cerebrovascular accidents, and more often required dialysis. There was no statistically significant difference in the rate of positive bacterial respiratory or blood cultures among those that survived vs. those that died (75 vs. 73% and 43 vs 38%, respectively). Topographical analysis of the 16S RNA microbiome shows compositional differences between the upper and lower airways based on β diversity comparisons. When comparing across clinical outcomes, the α diversity was lower in the dead group but there was no statistically significant difference in overall community composition (β diversity). Taxonomic differential enrichment analysis using DESeq analysis showed that oral commensals were enriched in the group that survived. Patients that died had a higher bacterial load in their lower airways than those who survived. CONCLUSION:Using samples obtained via bronchoscopy we identified lower airway microbiota signatures associated with mortality among critical patients infected with SARS-CoV2. Taxonomic signals identified as associated with poor prognosis did not reveal bacterial taxa commonly classified as respiratory pathogens. This data is not supportive of the hypothesis that secondary untreated bacterial co-infections are responsible for increased mortality in patients with severe SARS-CoV-2.