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Phenotyping coronavirus disease 2019 during a global health pandemic: Lessons learned from the characterization of an early cohort.

ABSTRACT: From the start of the coronavirus disease 2019 (COVID-19) pandemic, researchers have looked to electronic health record (EHR) data as a way to study possible risk factors and outcomes. To ensure the validity and accuracy of research using these data, investigators need to be confident that the phenotypes they construct are reliable and accurate, reflecting the healthcare settings from which they are ascertained. We developed a COVID-19 registry at a single academic medical center and used data from March 1 to June 5, 2020 to assess differences in population-level characteristics in pandemic and non-pandemic years respectively. Median EHR length, previously shown to impact phenotype performance in type 2 diabetes, was significantly shorter in the SARS-CoV-2 positive group relative to a 2019 influenza tested group (median 3.1 years vs 8.7; Wilcoxon rank sum P = 1.3e-52). Using three phenotyping methods of increasing complexity (billing codes alone and domain-specific algorithms provided by an EHR vendor and clinical experts), common medical comorbidities were abstracted from COVID-19 EHRs, defined by the presence of a positive laboratory test (positive predictive value 100%, recall 93%). After combining performance data across phenotyping methods, we observed significantly lower false negative rates for those records billed for a comprehensive care visit (p = 4e-11) and those with complete demographics data recorded (p = 7e-5). In an early COVID-19 cohort, we found that phenotyping performance of nine common comorbidities was influenced by median EHR length, consistent with previous studies, as well as by data density, which can be measured using portable metrics including CPT codes. Here we present those challenges and potential solutions to creating deeply phenotyped, acute COVID-19 cohorts.

SUBMITTER: DeLozier S

PROVIDER: S-EPMC8026248 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:ObjectivesTo describe the impact of coronavirus disease 2019 on family engagement among ICUs participating in a multicenter collaborative promoting implementation of family-centered care projects and to report sites' experiences with the collaborative itself prior to its cancelation due to the pandemic in March 2020.DesignCross-sectional survey.SettingTwenty-seven academic and community ICUs in the United States and South Korea.SubjectsSite leaders.InterventionsPrior to March 2020, all sites had participated in 6 months of webinars, monthly calls, and listserv communication to facilitate projects and to collect preimplementation family satisfaction and clinician perception data.Measurements and main resultsPlanned projects included ICU orientation initiatives (12, 44.4%), structured family care conferences (6, 22.2%), and ICU diaries (5, 18.5%). After cancelation of the collaborative, 22 site leaders (81.5%) were surveyed by phone from June 2020 to July 2020. Twenty (90.1%) reported having stopped their site project; projects that continued were 1) a standardized palliative extubation protocol and 2) daily written clinical summaries for families. Sites described significant variability in visitor restriction policies and uncertainty regarding future policy changes. Four sites (18.2%) reported that their hospital did not provide personal protective equipment to visitors. Regarding video conferencing with families, 11 sites (52.4%) reported clinicians' using their own personal devices. Two-hundred twelve family surveys and 346 clinician surveys collected prior to cancelation highlighted a broad need for family support. When leaders were asked on a scale from 0 to 10 how helpful collaborative activities had been prior to cancelation, mean response was 8.0 (sd 2.5).ConclusionsWhile the collaborative model can help promote ICU family engagement initiatives, coronavirus disease 2019 has impeded implementation of these initiatives even among motivated units. ICUs need adequate personal protective equipment for visitors and video conferencing capabilities on hospital devices while strict visitor restrictions continue to evolve.

Project description:The occurrence of coronavirus disease 2019 (COVID-19) was followed by a small burst of cases around the world; afterward, due to a series of emergency non-pharmaceutical interventions (NPIs), the increasing number of confirmed cases slowed down in many countries. However, the lifting of control measures by the government and the public's loosening of precautionary behaviors led to a sudden increase in cases, arousing deep concern across the globe. arousing deep concern across the globe. This study evaluates the situation of the COVID-19 pandemic in countries and territories worldwide from January 2020 to February 2021. According to the time-varying reproduction number (R(t)) of each country or territory, the results show that almost half of the countries and territories in the world have never controlled the epidemic. Among the countries and territories that had once contained the occurrence, nearly half failed to maintain their prevention and control, causing the COVID-19 pandemic to rebound across the world-resulting in even higher waves in half of the rebounding countries or territories. This work also proposes and uses a time-varying country-level transmission risk score (CTRS), which takes into account both R(t) and daily new cases, to demonstrate country-level or territory-level transmission potential and trends. Time-varying hierarchical clustering of time-varying CTRS values was used to successfully reveal the countries and territories that contributed to the recent aggravation of the global pandemic in the last quarter of 2020 and the beginning of 2021, and to identify countries and territories with an increasing risk of COVID-19 transmission in the near future. Furthermore, a regression analysis indicated that the introduction and relaxation of NPIs, including workplace closure policies and stay-at-home requirements, appear to be associated with recent global transmission changes. In conclusion, a systematic evaluation of the global COVID-19 pandemic over the past year indicates that the world is now in an unexpected situation, with limited lessons learned. Summarizing the lessons learned could help in designing effective public responses for constraining future waves of COVID-19 worldwide.

Project description:Background: Industrialised countries had varied responses to the COVID-19 pandemic, which may lead to different death tolls from COVID-19 and other diseases. Methods: We applied an ensemble of 16 Bayesian probabilistic models to vital statistics data to estimate the number of weekly deaths if the pandemic had not occurred for 40 industrialised countries and US states from mid-February 2020 through mid-February 2021. We subtracted these estimates from the actual number of deaths to calculate the impacts of the pandemic on all-cause mortality. Results: Over this year, there were 1,410,300 (95% credible interval 1,267,600-1,579,200) excess deaths in these countries, equivalent to a 15% (14-17) increase, and 141 (127-158) additional deaths per 100,000 people. In Iceland, Australia and New Zealand, mortality was lower than would be expected in the absence of the pandemic, while South Korea and Norway experienced no detectable change. The USA, Czechia, Slovakia and Poland experienced >20% higher mortality. Within the USA, Hawaii experienced no detectable change in mortality and Maine a 5% increase, contrasting with New Jersey, Arizona, Mississippi, Texas, California, Louisiana and New York which experienced >25% higher mortality. Mid-February to the end of May 2020 accounted for over half of excess deaths in Scotland, Spain, England and Wales, Canada, Sweden, Belgium, the Netherlands and Cyprus, whereas mid-September 2020 to mid-February 2021 accounted for >90% of excess deaths in Bulgaria, Croatia, Czechia, Hungary, Latvia, Montenegro, Poland, Slovakia and Slovenia. In USA, excess deaths in the northeast were driven mainly by the first wave, in southern and southwestern states by the summer wave, and in the northern plains by the post-September period. Conclusions: Prior to widespread vaccine-acquired immunity, minimising the overall death toll of the pandemic requires policies and non-pharmaceutical interventions that delay and reduce infections, effective treatments for infected patients, and mechanisms to continue routine health care.

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Phenotyping coronavirus disease 2019 during a global health pandemic: Lessons learned from the characterization of an early cohort.

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