Application of Causal Discovery Algorithms in Studying the Nephrotoxicity of Remdesivir Using Longitudinal Data from the EHR

Remdesivir has been widely used for the treatment of Coronavirus (COVID) in hospitalized patients, but its nephrotoxicity is still under investigation1. Given the paucity of knowledge regarding the mechanism and optimal treatment of the development of acute kidney injury (AKI) in the setting of COVID, we analyzed the role of remdesivir and built multifactorial causal models of COVID-AKI by applying causal discovery machine learning techniques. Risk factors of COVID-AKI and renal function measures were represented in a temporal sequence using longitudinal data from EHR. Our models successfully recreated known causal pathways to changes in renal function and interactions with each other and examined the consistency of high-level causal relationships over a 4-day course of remdesivir. Results indicated a need for assessment of renal function on day 2 and 3 use of remdesivir, while uncovering that remdesivir may pose less risk to AKI than existing conditions of chronic kidney disease.

Protection From COVID-19 mRNA Vaccination and Prior SARS-CoV-2 Infection Against COVID-19-Associated Encounters in Adults During Delta and Omicron Predominance.

BACKGROUND: Data assessing protection conferred from COVID-19 mRNA vaccination and/or prior SARS-CoV-2 infection during Delta and Omicron predominance periods in the United States are limited. METHODS: This cohort study included persons ≥18 years who had ≥1 health care encounter across 4 health systems and had been tested for SARS-CoV-2 before 26 August 2021. COVID-19 mRNA vaccination and prior SARS-CoV-2 infection defined the exposure. Cox regression estimated hazard ratios (HRs) for the Delta and Omicron periods; protection was calculated as (1-HR)×100%. RESULTS: Compared to unvaccinated and previously uninfected persons, during Delta predominance, protection against COVID-19-associated hospitalizations was high for those 2- or 3-dose vaccinated and previously infected, 3-dose vaccinated alone, and prior infection alone (range, 91%-97%, with overlapping 95% confidence intervals [CIs]); during Omicron predominance, estimates were lower (range, 77%-90%). Protection against COVID-19-associated emergency department/urgent care (ED/UC) encounters during Delta predominance was high for those exposure groups (range, 86%-93%); during Omicron predominance, protection remained high for those 3-dose vaccinated with or without a prior infection (76%; 95% CI = 67%-83% and 71%; 95% CI = 67%-73%, respectively). CONCLUSIONS: COVID-19 mRNA vaccination and/or prior SARS-CoV-2 infection provided protection against COVID-19-associated hospitalizations and ED/UC encounters regardless of variant. Staying up-to-date with COVID-19 vaccination still provides protection against severe COVID-19 disease, regardless of prior infection.

COVID-19 Vaccination Of People Experiencing Homelessness And Incarceration In Minnesota.

We used data from a statewide public health-health system collaboration to describe trends in COVID-19 vaccination rates by racial and ethnic groups among people experiencing homelessness or incarceration in Minnesota. Vaccination completion rates among the general population and people incarcerated in state prisons were substantially higher than those among people experiencing homelessness or jail incarceration.

Effectiveness of BNT162b2 and mRNA-1273 Second Doses and Boosters for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection and SARS-CoV-2-Related Hospitalizations: A Statewide Report From the Minnesota Electronic Health Record Consortium.

Using vaccine data combined with electronic health records, we report that mRNA boosters provide greater protection than a 2-dose regimen against SARS-CoV-2 infection and related hospitalizations. The benefit of a booster was more evident in the elderly and those with comorbidities.

Trends in COVID-19 Vaccine Administration and Effectiveness Through October 2021.

Importance: COVID-19 vaccines are effective, but inequities in vaccine administration and waning immunity may limit vaccine effectiveness. Objectives: To report statewide trends in vaccine administration and vaccine effectiveness in Minnesota. Design, Setting, and Participants: This cohort study used COVID-19 vaccine data from the Minnesota Immunization Information Connection from October 25, 2020, through October 30, 2021 that were linked with electronic health record (EHR) data from health systems collaborating as part of the Minnesota EHR Consortium (MNEHRC). Participants included individuals who were seen at a participating health system in Minnesota. Exposures: Individuals were considered fully vaccinated in the second week after receipt of a second dose of a BNT162b2 or mRNA-1273 vaccine or a single dose of an Ad26.COV.2.S vaccine. Main Outcomes and Measures: A completed vaccination series and vaccine breakthrough, defined as either a positive SARS-CoV-2 polymerase chain reaction (PCR) test or a hospital admission the same week or within the 3 weeks following a positive SARS-CoV-2 PCR test. A test-negative design and incident rate ratio were used to evaluate COVID-19 vaccine effectiveness separately for the BNT162b2, mRNA-1273, and Ad26.COV.2.S vaccines. Rurality and social vulnerability index were assessed at the area level. Results: This study included 4 431 190 unique individuals at participating health systems, and 3 013 704 (68%) of the individuals were fully vaccinated. Vaccination rates were lowest among Minnesotans who identified as Hispanic (116 422 of 217 019 [54%]), multiracial (30 066 of 57 412 [52%]), American Indian or Alaska Native (22 190 of 41 437 [54%]), and Black or African American (158 860 of 326 595 [49%]) compared with Minnesotans who identified as Asian or Pacific Islander (159 999 of 210 994 [76%]) or White (2 402 928 of 3 391 747 [71%]). Among individuals aged 19 to 64 years, vaccination rates were lower in rural areas (196 479 of 308 047 [64%]) compared with urban areas (151 541 of 1 951 265 [77%]) and areas with high social vulnerability (544 433 of 774 952 [70%]) compared with areas with low social vulnerability (571 613 of 724 369 [79%]). In the 9 weeks ending October 30, 2021, vaccine effectiveness as assessed by a test-negative design was 33% (95% CI, 30%-37%) for Ad26.COV.2.S; 53% (95% CI, 52%-54%) for BNT162b2; and 66% (95% CI, 65%-67%) for mRNA-1273. For SARS-CoV-2-related hospitalizations, vaccine effectiveness in the 9 weeks ending October 30, 2021, was 78% (95% CI, 75%-81%) for Ad26.COV.2.S; 81% (95% CI, 79%-82%) for BNT162b2; and 81% (95% CI, 79%-82%) for mRNA-1273. Conclusions and Relevance: This cohort study of data from a Minnesota statewide consortium suggests disparities in vaccine administration and effectiveness. Vaccine effectiveness against infection was lower for Ad26.COV.2.S and BNT162b2 but was associated with protection against SARS-CoV-2-related hospitalizations despite the increased prevalence of the Delta variant in Minnesota.

Minnesota Electronic Health Record Consortium COVID-19 Project: Informing Pandemic Response Through Statewide Collaboration Using Observational Data.

OBJECTIVE: Robust disease and syndromic surveillance tools are underdeveloped in the United States, as evidenced by limitations and heterogeneity in sociodemographic data collection throughout the COVID-19 pandemic. To monitor the COVID-19 pandemic in Minnesota, we developed a federated data network in March 2020 using electronic health record (EHR) data from 8 multispecialty health systems. MATERIALS AND METHODS: In this serial cross-sectional study, we examined patients of all ages who received a COVID-19 polymerase chain reaction test, had symptoms of a viral illness, or received an influenza test from January 3, 2016, through November 7, 2020. We evaluated COVID-19 testing rates among patients with symptoms of viral illness and percentage positivity among all patients tested, in aggregate and by zip code. We stratified results by patient and area-level characteristics. RESULTS: Cumulative COVID-19 positivity rates were similar for people aged 12-64 years (range, 15.1%-17.6%) but lower for adults aged ≥65 years (range, 9.3%-10.7%). We found notable racial and ethnic disparities in positivity rates early in the pandemic, whereas COVID-19 positivity was similarly elevated across most racial and ethnic groups by the end of 2020. Positivity rates remained substantially higher among Hispanic patients compared with other racial and ethnic groups throughout the study period. We found similar trends across area-level income and rurality, with disparities early in the pandemic converging over time. PRACTICE IMPLICATIONS: We rapidly developed a distributed data network across Minnesota to monitor the COVID-19 pandemic. Our findings highlight the utility of using EHR data to monitor the current pandemic as well as future public health priorities. Building partnerships with public health agencies can help ensure data streams are flexible and tailored to meet the changing needs of decision makers.