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1.
Sci Rep ; 11(1): 20987, 2021 10 25.
Article in English | MEDLINE | ID: covidwho-1483149

ABSTRACT

Acid suppressants are widely-used classes of medications linked to increased risks of aerodigestive infections. Prior studies of these medications as potentially reversible risk factors for COVID-19 have been conflicting. We aimed to determine the impact of chronic acid suppression use on COVID-19 infection risk while simultaneously evaluating the influence of social determinants of health to validate known and discover novel risk factors. We assessed the association of chronic acid suppression with incident COVID-19 in a 1:1 case-control study of 900 patients tested across three academic medical centers in California, USA. Medical comorbidities and history of chronic acid suppression use were manually extracted from health records by physicians following a pre-specified protocol. Socio-behavioral factors by geomapping publicly-available data to patient zip codes were incorporated. We identified no evidence to support an association between chronic acid suppression and COVID-19 (adjusted odds ratio 1.04, 95% CI 0.92-1.17, P = 0.515). However, several medical and social features were positive (Latinx ethnicity, BMI ≥ 30, dementia, public transportation use, month of the pandemic) and negative (female sex, concurrent solid tumor, alcohol use disorder) predictors of new infection. These findings demonstrate the value of integrating publicly-available databases with medical data to identify critical features of communicable diseases.


Subject(s)
COVID-19/epidemiology , COVID-19/therapy , Gastroesophageal Reflux/complications , Social Determinants of Health , Aged , Behavior , COVID-19/psychology , California , Case-Control Studies , Computational Biology/methods , Databases, Factual , Female , Gastroenterology , Gastroesophageal Reflux/drug therapy , Geography , Histamine H2 Antagonists/pharmacology , Humans , Incidence , Male , Middle Aged , Odds Ratio , Proton Pump Inhibitors/pharmacology , Risk Factors , Social Class
2.
Front Immunol ; 12: 647536, 2021.
Article in English | MEDLINE | ID: covidwho-1264331

ABSTRACT

The field of immunology is rapidly progressing toward a systems-level understanding of immunity to tackle complex infectious diseases, autoimmune conditions, cancer, and beyond. In the last couple of decades, advancements in data acquisition techniques have presented opportunities to explore untapped areas of immunological research. Broad initiatives are launched to disseminate the datasets siloed in the global, federated, or private repositories, facilitating interoperability across various research domains. Concurrently, the application of computational methods, such as network analysis, meta-analysis, and machine learning have propelled the field forward by providing insight into salient features that influence the immunological response, which was otherwise left unexplored. Here, we review the opportunities and challenges in democratizing datasets, repositories, and community-wide knowledge sharing tools. We present use cases for repurposing open-access immunology datasets with advanced machine learning applications and more.


Subject(s)
Allergy and Immunology , Computational Biology/methods , Datasets as Topic , Immune System , Machine Learning , Humans , Meta-Analysis as Topic
3.
Biochem Biophys Res Commun ; 538: 173-179, 2021 01 29.
Article in English | MEDLINE | ID: covidwho-1125837

ABSTRACT

There is an urgent need to identify therapies that prevent SARS-CoV-2 infection and improve the outcome of COVID-19 patients. Although repurposed drugs with favorable safety profiles could have significant benefit, widely available prevention or treatment options for COVID-19 have yet to be identified. Efforts to identify approved drugs with in vitro activity against SARS-CoV-2 resulted in identification of antiviral sigma-1 receptor ligands, including antihistamines in the histamine-1 receptor binding class. We identified antihistamine candidates for repurposing by mining electronic health records of usage in population of more than 219,000 subjects tested for SARS-CoV-2. Usage of diphenhydramine, hydroxyzine and azelastine was associated with reduced incidence of SARS-CoV-2 positivity in subjects greater than age 61. We found diphenhydramine, hydroxyzine and azelastine to exhibit direct antiviral activity against SARS-CoV-2 in vitro. Although mechanisms by which specific antihistamines exert antiviral effects is not clear, hydroxyzine, and possibly azelastine, bind Angiotensin Converting Enzyme-2 (ACE2) and the sigma-1 receptor as off-targets. Clinical studies are needed to measure the effectiveness of diphenhydramine, hydroxyzine and azelastine for disease prevention, for early intervention, or as adjuvant therapy for severe COVID-19.


Subject(s)
Angiotensin-Converting Enzyme 2/chemistry , Antiviral Agents/chemistry , COVID-19/drug therapy , Drug Repositioning , Histamine Antagonists/chemistry , SARS-CoV-2/drug effects , Angiotensin-Converting Enzyme 2/genetics , Angiotensin-Converting Enzyme 2/metabolism , Animals , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , Catalytic Domain , Chlorocebus aethiops , HEK293 Cells , Histamine Antagonists/pharmacology , Histamine Antagonists/therapeutic use , Humans , Ligands , Protein Binding , Receptors, Histamine/chemistry , Receptors, sigma/chemistry , Vero Cells
5.
J Am Med Inform Assoc ; 28(2): 393-401, 2021 02 15.
Article in English | MEDLINE | ID: covidwho-1054313

ABSTRACT

Our goal is to summarize the collective experience of 15 organizations in dealing with uncoordinated efforts that result in unnecessary delays in understanding, predicting, preparing for, containing, and mitigating the COVID-19 pandemic in the US. Response efforts involve the collection and analysis of data corresponding to healthcare organizations, public health departments, socioeconomic indicators, as well as additional signals collected directly from individuals and communities. We focused on electronic health record (EHR) data, since EHRs can be leveraged and scaled to improve clinical care, research, and to inform public health decision-making. We outline the current challenges in the data ecosystem and the technology infrastructure that are relevant to COVID-19, as witnessed in our 15 institutions. The infrastructure includes registries and clinical data networks to support population-level analyses. We propose a specific set of strategic next steps to increase interoperability, overall organization, and efficiencies.


Subject(s)
COVID-19 , Electronic Health Records , Information Dissemination , Information Systems/organization & administration , Public Health Practice , Academic Medical Centers , Humans , Registries , United States
6.
Sci Data ; 7(1): 405, 2020 11 16.
Article in English | MEDLINE | ID: covidwho-926927

ABSTRACT

Management of the COVID-19 pandemic has proven to be a significant challenge to policy makers. This is in large part due to uneven reporting and the absence of open-access visualization tools to present local trends and infer healthcare needs. Here we report the development of CovidCounties.org, an interactive web application that depicts daily disease trends at the level of US counties using time series plots and maps. This application is accompanied by a manually curated dataset that catalogs all major public policy actions made at the state-level, as well as technical validation of the primary data. Finally, the underlying code for the site is also provided as open source, enabling others to validate and learn from this work.


Subject(s)
Coronavirus Infections/epidemiology , Pneumonia, Viral/epidemiology , Software , Betacoronavirus , COVID-19 , Data Curation/methods , Datasets as Topic , Humans , Internet , Pandemics , SARS-CoV-2 , United States/epidemiology
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