Multi-ethnic Investigation of Risk and Immune Determinants of COVID-19 Outcomes (preprint)

Background: Disparate COVID-19 outcomes have been observed between Hispanic, Non-Hispanic Black, and White patients. The underlying causes for these disparities are not fully understood. Methods: : This was a retrospective study utilizing electronic medical record data from five hospitals within a single academic health system based in New York City. Multivariable logistic regression models were used to identify demographic, clinical, and lab values associated with in-hospital mortality. Results: : 3,086 adult patients with self-reported race/ethnicity information presenting to the emergency department and hospitalized with COVID-19 up to April 13, 2020 were included in this study. While older age (multivariable OR 1.06, 95% CI 1.05-1.07) and baseline hypoxia (multivariable OR 2.71, 95% CI 2.17-3.36) were associated with increased mortality overall and across all races/ethnicities, Non-Hispanic Black (median age 67, IQR 58-76) and Hispanic (median age 63, IQR 50-74) patients were younger and had different comorbidity profiles compared to Non-Hispanic White patients (median age 73, IQR 62-84; p<0.05 for both comparisons). Among inflammatory markers associated with COVID-19 mortality, there was a significant interaction between the Non-Hispanic Black population and interleukin-1-beta (interaction p-value 0.04). Conclusions: : This analysis of a multi-ethnic cohort highlights the need for inclusion and consideration of diverse popualtions in ongoing COVID-19 trials targeting inflammatory cytokines.

Multi-ethnic Investigation of Risk and Immune Determinants of COVID-19 Outcomes (preprint)

Objectives: To compare risk factors for COVID-19 mortality among hospitalized Hispanic, Non-Hispanic Black, and White patients. Design: Retrospecitve cohort study Setting: Five hosptials within a single academic health system Participants: 3,086 adult patients with self-reported race/ethnicity information presenting to the emergency department and hospitalized with COVID-19 up to April 13, 2020. Main outcome measures: In-hospital mortality Results: While older age (multivariable OR 1.06, 95% CI 1.05-1.07) and baseline hypoxia (multivariable OR 2.71, 95% CI 2.17-3.36) were associated with increased mortality overall and across all races/ethnicities, Non-Hispanic Black (median age 67, IQR 58-76) and Hispanic (median age 63, IQR 50-74) patients were younger and had different comorbidity profiles compared to Non-Hispanic White patients (median age 73, IQR 62-84; p<0.05 for both comparisons). Among inflammatory markers associated with COVID-19 mortality, there was a significant interaction between the Non-Hispanic Black population and interleukin-1-beta (interaction p-value 0.04). Conclusions: This analysis of a multi-ethnic cohort highlights the need for inclusion and consideration of diverse popualtions in ongoing COVID-19 trials targeting inflammatory cytokines.

Quantitative chest CT combined with plasma cytokines predict outcomes in COVID-19 patients (preprint)

Despite extraordinary international efforts to dampen the spread and understand the mechanisms behind SARS-CoV-2 infections, accessible predictive biomarkers directly applicable in the clinic are yet to be discovered. Recent studies have revealed that diverse types of assays bear limited predictive power for COVID-19 outcomes. Here, we harness the predictive power of chest CT in combination with plasma cytokines using a machine learning approach for predicting death during hospitalization and maximum severity degree in COVID-19 patients. Patients (n=152) from the Mount Sinai Health System in New York with plasma cytokine assessment and a chest CT within 5 days from admission were included. Demographics, clinical, and laboratory variables, including plasma cytokines (IL-6, IL-8, and TNF-) were collected from the electronic medical record. We found that chest CT combined with plasma cytokines were good predictors of death (AUC 0.78) and maximum severity (AUC 0.82), whereas CT quantitative was better at predicting severity (AUC 0.81 vs 0.70) while cytokine measurements better predicted death (AUC 0.70 vs 0.66). Finally, we provide a simple scoring system using plasma IL-6, IL-8, TNF-, GGO to aerated lung ratio and age as novel metrics that may be used to monitor patients upon hospitalization and help physicians make critical decisions and considerations for patients at high risk of death for COVID-19.

Development of a federated learning approach to predict acute kidney injury in adult hospitalized patients with COVID-19 in New York City (preprint)

Federated learning is a technique for training predictive models without sharing patient-level data, thus maintaining data security while allowing inter-institutional collaboration. We used federated learning to predict acute kidney injury within three and seven days of admission, using demographics, comorbidities, vital signs, and laboratory values, in 4029 adults hospitalized with COVID-19 at five sociodemographically diverse New York City hospitals, between March-October 2020. Prediction performance of federated models was generally higher than single-hospital models and was comparable to pooled-data models. In the first use-case in kidney disease, federated learning improved prediction of a common complication of COVID-19, while preserving data privacy.

Prediction of COVID-19 status using baseline demographics and lab data (preprint)

The global surge in COVID-19 cases underscores the need for fast, scalable, and reliable testing. Current COVID-19 diagnostic tests are limited by turnaround time, limited availability, or occasional false findings. Here, we developed a machine learning-based framework for predicting COVID-19 positive test status relying only on readily-available baseline data, including patient demographics, comorbidities, and common lab values. Leveraging a cohort of 31,739 adults within an academic health system, we trained and tested multiple types of machine learning models, achieving an area under the curve of 0.75. Feature importance analyses highlighted serum calcium levels, aspartate aminotransferase levels, and oxygen saturation as key predictors. Additionally, we developed a single decision tree model that provided an operable method for stratifying sub-populations. Overall, this study provides a proof-of-concept that COVID-19 status prediction models can be developed using only baseline data. The resulting prediction can complement existing tests to enhance screening and pandemic containment workflows.

Prediction of COVID-19 Status Using Baseline Demographics and Lab Data (preprint)

Background: The global surge in COVID-19 cases underscores the need for fast, scalable, and reliable testing. Current COVID-19 diagnostic tests are limited by turnaround time, limited availability, or occasional false findings.Methods: In this study, we developed a machine learning-based framework for predicting COVID-19 positive test status relying only on readily available baseline data, including patient demographics, comorbidities, and common lab values. Leveraging a cohort of 31,739 adults within an academic health system, we divided the patient data into a training set (patient encounters through April 13, 2020) and a test set (patient encounters from April 13, 2020 through June 2, 2020). We trained our machine learning models on the training set and evaluated model performance on the test set.Findings: We trained and tested multiple types of machine learning models, achieving an area under the curve of 0·75 in the test set. Feature importance analyses highlighted serum calcium levels, aspartate aminotransferase levels, and oxygen saturation as key predictors. Additionally, we identified an optimal probability threshold for patient screening and developed a single decision tree model that provided an operable method for stratifying sub-populations.Interpretation: Overall, this study provides a proof-of-concept that COVID-19 status prediction models can be developed using only baseline data. Our machine learning models can be adapted to a variety of global pandemic scenarios, as the resulting prediction could complement existing tests to enhance screening and pandemic containment workflows.Funding: Icahn School of Medicine at Mount Sinai, New York, NY.Declaration of Interests: J.F. is an employ of Outco Inc. All other authors declare no competing financial interests.Ethics Approval Statement: This study utilized de-identified data extracted from the electronic health record and as such was considered nonhuman subject research. Therefore, this study was exempted from the Mount Sinai IRB review and approval process. All analyses were carried out in accordance with relevant guidelines and regulations.

Physiology of cardiomyocyte injury in COVID-19 (preprint)

COVID-19 affects multiple organs. Clinical data from the Mount Sinai Health System shows that substantial numbers of COVID-19 patients without prior heart disease develop cardiac dysfunction. How COVID-19 patients develop cardiac disease is not known. We integrate cell biological and physiological analyses of human cardiomyocytes differentiated from human induced pluripotent stem cells (hiPSCs) infected with SARS-CoV-2 in the presence of interleukins, with clinical findings, to investigate plausible mechanisms of cardiac disease in COVID-19 patients. We infected hiPSC-derived cardiomyocytes, from healthy human subjects, with SARS-CoV-2 in the absence and presence of interleukins. We find that interleukin treatment and infection results in disorganization of myofibrils, extracellular release of troponin-I, and reduced and erratic beating. Although interleukins do not increase the extent, they increase the severity of viral infection of cardiomyocytes resulting in cessation of beating. Clinical data from hospitalized patients from the Mount Sinai Health system show that a significant portion of COVID-19 patients without prior history of heart disease, have elevated troponin and interleukin levels. A substantial subset of these patients showed reduced left ventricular function by echocardiography. Our laboratory observations, combined with the clinical data, indicate that direct effects on cardiomyocytes by interleukins and SARS-CoV-2 infection can underlie the heart disease in COVID-19 patients.

Mortality and risk factors among US Black, Hispanic, and White patients with COVID-19 (preprint)

Background: Little is known about risk factors for COVID-19 outcomes, particularly across diverse racial and ethnic populations in the United States. Methods: In this prospective cohort study, we followed 3,086 COVID-19 patients hospitalized on or before April 13, 2020 within an academic health system in New York (The Mount Sinai Health System) until June 2, 2020. Multivariable logistic regression was used to evaluate demographic, clinical, and laboratory factors as independent predictors of in-hospital mortality. The analysis was stratified by self-reported race and ethnicity. Findings: A total of 3,086 COVID-19 patients were hospitalized, of whom 680 were excluded (78 due to missing race or ethnicity data, 144 were Asian, and 458 were of other unspecified race/ethnicity). Of the 2,406 patients included, 892 (37.1%) were Hispanic, 825 (34.3%) were black, and 689 (28.6%) were white. Black and Hispanic patients were younger than White patients (median age 67 and 63 vs. 73, p<0.001 for both), and they had different comorbidity profiles. Older age and baseline hypoxia were associated with increased mortality across all races. There were suggestive but non-significant interactions between Black race and diabetes (p=0.09), and obesity (p=0.10). Among inflammatory markers associated with COVID-19 mortality, there was a significant interaction between Black race and interleukin-1-beta (p=0.04), and a suggestive interactions between Hispanic ethnicity and procalcitonin (p=0.07) and interleukin-8 (p=0.09). Interpretation: In this large, racially and ethnically diverse cohort of COVID-19 patients in New York City, we identified similarities and important differences across racial and ethnic groups in risk factors for in-hospital mortality.

Sex-specificity of mortality risk factors among hospitalized COVID-19 patients in New York City: prospective cohort study (preprint)

Objective: To identify sex-specific effects of risk factors for in-hospital mortality among COVID-19 patients admitted to a hospital system in New York City. Design: Prospective observational cohort study with in-hospital mortality as the primary outcome. Setting: Five acute care hospitals within a single academic medical system in New York City. Participants: 3,086 hospital inpatients with COVID-19 admitted on or before April 13, 2020 and followed through June 2, 2020. Follow-up till discharge or death was complete for 99.3% of the cohort. Results: The majority of the cohort was male (59.6%). Men were younger (median 64 vs. 70, p<0.001) and less likely to have comorbidities such as hypertension (32.5% vs. 39.9%, p<0.001), diabetes (22.6% vs. 26%, p=0.03), and obesity (6.9% vs. 9.8%, p=0.004) compared to women. Women had lower median values of laboratory markers associated with inflammation compared to men: white blood cells (5.95 vs. 6.8 K/uL, p<0.001), procalcitonin (0.14 vs 0.21 ng/mL, p<0.001), lactate dehydrogenase (375 vs. 428 U/L, p<0.001), C-reactive protein (87.7 vs. 123.2 mg/L, p<0.001). Unadjusted mortality was similar between men and women (28.8% vs. 28.5%, p=0.84), but more men required intensive care than women (25.2% vs. 19%, p<0.001). Male sex was an independent risk factor for mortality (OR 1.26, 95% 1.04-1.51) after adjustment for demographics, comorbidities, and baseline hypoxia. There were significant interactions between sex and coronary artery disease (p=0.038), obesity (p=0.01), baseline hypoxia (p<0.001), ferritin (p=0.002), lactate dehydrogenase (p=0.003), and procalcitonin (p=0.03). Except for procalcitonin, which had the opposite association, each of these factors was associated with disproportionately higher mortality among women. Conclusions: Male sex was an independent predictor of mortality, consistent with prior studies. Notably, there were significant sex-specific interactions which indicated a disproportionate increase in mortality among women with coronary artery disease, obesity, and hypoxia. These new findings highlight patient subgroups for further study and help explain the recognized sex differences in COVID-19 outcomes.

An inflammatory cytokine signature helps predict COVID-19 severity and death (preprint)

The COVID-19 pandemic caused by infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to more than 100,000 deaths in the United States. Several studies have revealed that the hyper-inflammatory response induced by SARS-CoV-2 is a major cause of disease severity and death in infected patients. However, predictive biomarkers of pathogenic inflammation to help guide targetable immune pathways are critically lacking. We implemented a rapid multiplex cytokine assay to measure serum IL-6, IL-8, TNF-, and IL-1{beta} in hospitalized COVID-19 patients upon admission to the Mount Sinai Health System in New York. Patients (n=1484) were followed up to 41 days (median 8 days) and clinical information, laboratory test results and patient outcomes were collected. In 244 patients, cytokine measurements were repeated over time, and effect of drugs could be assessed. Kaplan-Meier methods were used to compare survival by cytokine strata, followed by Cox regression models to evaluate the independent predictive value of baseline cytokines. We found that high serum IL-6, IL-8, and TNF- levels at the time of hospitalization were strong and independent predictors of patient survival. Importantly, when adjusting for disease severity score, common laboratory inflammation markers, hypoxia and other vitals, demographics, and a range of comorbidities, IL-6 and TNF- serum levels remained independent and significant predictors of disease severity and death. We propose that serum IL-6 and TNF- levels should be considered in the management and treatment of COVID-19 patients to stratify prospective clinical trials, guide resource allocation and inform therapeutic options. We also propose that patients with high IL-6 and TNF- levels should be assessed for combinatorial blockade of pathogenic inflammation in this disease.

Analysis of hospitalized COVID-19 patients in the Mount Sinai Health System using electronic medical records (EMR) reveals important prognostic factors for improved clinical outcomes (preprint)

COVID-19 is a novel threat to human health worldwide. There is an urgent need to understand patient characteristics of having COVID-19 disease and evaluate markers of critical illness and mortality. Objective: To assess association of clinical features on patient outcomes. Design, Setting, and Participants: In this observational case series, patient-level data were extracted from electronic medical records for 28,336 patients tested for SARS-CoV-2 at the Mount Sinai Health System from 2/24/ to 4/15/2020, including 6,158 laboratory-confirmed cases. Exposures: Confirmed COVID-19 diagnosis by RT-PCR assay from nasal swabs. Main Outcomes and Measures: Effects of race on positive test rates and mortality were assessed. Among positive cases admitted to the hospital (N = 3,273), effects of patient demographics, hospital site and unit, social behavior, vital signs, lab results, and disease comorbidities on discharge and death were estimated. Results: Hispanics (29%) and African Americans (25%) had disproportionately high positive case rates relative to population base rates (p<2e-16); however, no differences in mortality rates were observed in the hospital. Outcome differed significantly between hospitals (Gray's T=248.9; p<2e-16), reflecting differences in average baseline age and underlying comorbidities. Significant risk factors for mortality included age (HR=1.05 [95% CI, 1.04-1.06]; p=1.15e-32), oxygen saturation (HR=0.985 [95% CI, 0.982-0.988]; p=1.57e-17), care in ICU areas (HR=1.58 [95% CI, 1.29-1.92]; p=7.81e-6), and elevated creatinine (HR=1.75 [95% CI, 1.47-2.10]; p=7.48e-10), alanine aminotransferase (ALT) (HR=1.002, [95% CI 1.001-1.003]; p=8.86e-5) and body-mass index (BMI) (HR=1.02, [95% CI 1.00-1.03]; p=1.09e-2). Asthma (HR=0.78 [95% CI, 0.62-0.98]; p=0.031) was significantly associated with increased length of hospital stay, but not mortality. Deceased patients were more likely to have elevated markers of inflammation. Baseline age, BMI, oxygen saturation, respiratory rate, white blood cell (WBC) count, creatinine, and ALT were significant prognostic indicators of mortality. Conclusions and Relevance: While race was associated with higher risk of infection, we did not find a racial disparity in inpatient mortality suggesting that outcomes in a single tertiary care health system are comparable across races. We identified clinical features associated with reduced mortality and discharge. These findings could help to identify which COVID-19 patients are at greatest risk and evaluate the impact on survival.

Machine Learning to Predict Mortality and Critical Events in COVID-19 Positive New York City Patients (preprint)

Coronavirus 2019 (COVID-19), caused by the SARS-CoV-2 virus, has become the deadliest pandemic in modern history, reaching nearly every country worldwide and overwhelming healthcare institutions. As of April 20, there have been more than 2.4 million confirmed cases with over 160,000 deaths. Extreme case surges coupled with challenges in forecasting the clinical course of affected patients have necessitated thoughtful resource allocation and early identification of high-risk patients. However, effective methods for achieving this are lacking. In this paper, we present a decision tree-based machine learning model trained on electronic health records from patients with confirmed COVID-19 at a single center within the Mount Sinai Health System in New York City. We then externally validate our model by predicting the likelihood of critical event or death within various time intervals for patients after hospitalization at four other hospitals and achieve strong performance, notably predicting mortality at 1 week with an AUC-ROC of 0.84. Finally, we establish model interpretability by calculating SHAP scores to identify decisive features, including age, inflammatory markers (procalcitonin and LDH), and coagulation parameters (PT, PTT, D-Dimer). To our knowledge, this is one of the first models with external validation to both predict outcomes in COVID-19 patients with strong validation performance and identification of key contributors in outcome prediction that may assist clinicians in making effective patient management decisions.

Clinical Characteristics of Hospitalized Covid-19 Patients in New York City (preprint)

ABSTRACT Background: The coronavirus 2019 (Covid-19) pandemic is a global public health crisis, with over 1.6 million cases and 95,000 deaths worldwide. Data are needed regarding the clinical course of hospitalized patients, particularly in the United States. Methods Demographic, clinical, and outcomes data for patients admitted to five Mount Sinai Health System hospitals with confirmed Covid-19 between February 27 and April 2, 2020 were identified through institutional electronic health records. We conducted a descriptive study of patients who had in-hospital mortality or were discharged alive. Results A total of 2,199 patients with Covid-19 were hospitalized during the study period. As of April 2nd, 1,121 (51%) patients remained hospitalized, and 1,078 (49%) completed their hospital course. Of the latter, the overall mortality was 29%, and 36% required intensive care. The median age was 65 years overall and 75 years in those who died. Pre-existing conditions were present in 65% of those who died and 46% of those discharged. In those who died, the admission median lymphocyte percentage was 11.7%, D-dimer was 2.4 ug/ml, C-reactive protein was 162 mg/L, and procalcitonin was 0.44 ng/mL. In those discharged, the admission median lymphocyte percentage was 16.6%, D-dimer was 0.93 ug/ml, C-reactive protein was 79 mg/L, and procalcitonin was 0.09 ng/mL. Conclusions This is the largest and most diverse case series of hospitalized patients with Covid-19 in the United States to date. Requirement of intensive care and mortality were high. Patients who died typically had pre-existing conditions and severe perturbations in inflammatory markers.