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Waxse BJ, Carrillo FAB, Tran TC, Mo H, Ricotta EE, Denny JC. Computable Phenotypes for Respiratory Viral Infections in the All of Us Research Program. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2025:2025.01.17.25320744. [PMID: 39867363 PMCID: PMC11759596 DOI: 10.1101/2025.01.17.25320744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Electronic health records (EHRs) contain rich temporal data about infectious diseases, but an optimal approach to identify infections remains undefined. Using the All of Us Research Program, we developed computable phenotypes for respiratory viruses by integrating billing codes, prescriptions, and laboratory results within 90-day episodes. Phenotypes computed from 265,222 participants yielded cohorts ranging from 238 (adenovirus) to 28,729 (SARS-CoV-2) cases. Virus-specific billing codes showed varied sensitivity (8-67%) and high positive predictive value (90-97%), except for influenza virus and SARS-CoV-2 where lower PPV (69-70%) improved with increasing billing codes. Identified infections exhibited expected seasonal patterns and virus proportions when compared with CDC data. This integrated approach identified episodic disease more effectively than individual components alone and demonstrated utility in identifying severe infections. The method enables large-scale studies of host genetics, health disparities, and clinical outcomes across episodic diseases.
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Affiliation(s)
- Bennett J Waxse
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Tam C Tran
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Huan Mo
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emily E Ricotta
- Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Joshua C Denny
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
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Pott H, LeBlanc JJ, ElSherif M, Hatchette TF, McNeil SA, Andrew MK. Predicting major clinical events among Canadian adults with laboratory-confirmed influenza infection using the influenza severity scale. Sci Rep 2024; 14:18378. [PMID: 39112632 PMCID: PMC11306731 DOI: 10.1038/s41598-024-67931-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 07/17/2024] [Indexed: 08/10/2024] Open
Abstract
We developed and validated the Influenza Severity Scale (ISS), a standardized risk assessment for influenza, to estimate and predict the probability of major clinical events in patients with laboratory-confirmed infection. Data from the Canadian Immunization Research Network's Serious Outcomes Surveillance Network (2011/2012-2018/2019 influenza seasons) enabled the selecting of all laboratory-confirmed influenza patients. A machine learning-based approach then identified variables, generated weighted scores, and evaluated model performance. This study included 12,954 patients with laboratory-confirmed influenza infections. The optimal scale encompassed ten variables: demographic (age and sex), health history (smoking status, chronic pulmonary disease, diabetes mellitus, and influenza vaccination status), clinical presentation (cough, sputum production, and shortness of breath), and function (need for regular support for activities of daily living). As a continuous variable, the scale had an AU-ROC of 0.73 (95% CI, 0.71-0.74). Aggregated scores classified participants into three risk categories: low (ISS < 30; 79.9% sensitivity, 51% specificity), moderate (ISS ≥ 30 but < 50; 54.5% sensitivity, 55.9% specificity), and high (ISS ≥ 50; 51.4% sensitivity, 80.5% specificity). ISS demonstrated a solid ability to identify patients with hospitalized laboratory-confirmed influenza at increased risk for Major Clinical Events, potentially impacting clinical practice and research.
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Affiliation(s)
- Henrique Pott
- Canadian Centre for Vaccinology, Dalhousie University, Halifax, Canada.
- Department of Medicine, Universidade Federal de São Carlos, Rod. Washington Luis, km 235, São Carlos, SP, 13656-905, Brazil.
| | - Jason J LeBlanc
- Canadian Centre for Vaccinology, Dalhousie University, Halifax, Canada
- Department of Pathology, Dalhousie University, Halifax, Canada
| | - May ElSherif
- Canadian Centre for Vaccinology, Dalhousie University, Halifax, Canada
| | - Todd F Hatchette
- Canadian Centre for Vaccinology, Dalhousie University, Halifax, Canada
- Department of Pathology, Dalhousie University, Halifax, Canada
| | - Shelly A McNeil
- Canadian Centre for Vaccinology, Dalhousie University, Halifax, Canada
- Department of Medicine (Infectious Diseases), Dalhousie University, Halifax, Canada
| | - Melissa K Andrew
- Canadian Centre for Vaccinology, Dalhousie University, Halifax, Canada
- Department of Medicine (Geriatrics), Dalhousie University, Halifax, Canada
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Cipelli R, Falato S, Lusito E, Maifredi G, Montedoro M, Valpondi P, Zucchi A, Azzi MV, Zanetta L, Gualano MR, Xoxi E, Marchisio PG, Castaldi S. The Hospital Burden of Flu in Italy: a retrospective study on administrative data from season 2014-2015 to 2018-2019. BMC Infect Dis 2024; 24:572. [PMID: 38851739 PMCID: PMC11162570 DOI: 10.1186/s12879-024-09446-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/29/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Every year in Italy, influenza affects about 4 million people. Almost 5% of them are hospitalised. During peak illness, enormous pressure is placed on healthcare and economic systems. This study aims to quantify the clinical and economic burden of severe influenza during 5 epidemic seasons (2014-2019) from administrative claims data. METHODS Patients hospitalized with a diagnosis of influenza between October 2014, and April 2019, were analyzed. Clinical characteristics and administrative information were retrieved from health-related Administrative Databases (ADs) of 4 Italian Local Health Units (LHUs). The date of first admission was set as the Index Date (ID). A follow-up period of six months after ID was considered to account for complications and re-hospitalizations, while a lookback period (2 years before ID) was set to assess the prevalence of underlying comorbidities. RESULTS Out of 2,333 patients with severe influenza, 44.1% were adults ≥ 65, and 25.6% young individuals aged 0-17. 46.8% had comorbidities (i.e., were at risk), mainly cardiovascular and metabolic diseases (45.3%), and chronic conditions (24.7%). The highest hospitalization rates were among the elderly (≥ 75) and the young individuals (0-17), and were 37.6 and 19.5/100,000 inhabitants/year, respectively. The average hospital stay was 8 days (IQR: 14 - 4). It was higher for older individuals (≥ 65 years, 11 days, [17 - 6]) and for those with comorbidities (9 days, [16 - 6]), p-value < 0.001. Similarly, mortality was higher in elderly and those at risk (p-value < 0.001). Respiratory complications occurred in 12.7% of patients, and cardiovascular disorders in 5.9%. Total influenza-related costs were €9.7 million with hospitalization accounting for 95% of them. 47.3% of hospitalization costs were associated with individuals ≥ 65 and 52.9% with patients at risk. The average hospitalisation cost per patient was € 4,007. CONCLUSIONS This retrospective study showed that during the 2014-2019 influenza seasons in Italy, individuals of extreme ages and those with pre-existing medical conditions, were more likely to be hospitalized with severe influenza. Together with complications and ageing, they worsen patient's outcome and may lead to a prolonged hospitalization, thus increasing healthcare utilization and costs. Our data generate real-world evidence on the burden of influenza, useful to inform public health decision-making.
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Affiliation(s)
- Riccardo Cipelli
- IQVIA Solutions Italy Srl, Via Fabio Filzi 29, Milan, 20124, Italy.
| | - Serena Falato
- IQVIA Solutions Italy Srl, Via Fabio Filzi 29, Milan, 20124, Italy
| | - Eleonora Lusito
- IQVIA Solutions Italy Srl, Via Fabio Filzi 29, Milan, 20124, Italy
| | - Giovanni Maifredi
- SS Epidemiologia, Agenzia di Tutela della Salute di Brescia, Brescia, Italy
| | | | | | - Alberto Zucchi
- UOC Servizio Epidemiologia presso ATS di Bergamo, Bergamo, Italy
| | | | | | | | - Entela Xoxi
- Università Cattolica del Sacro Cuore, Alta Scuola di Economia e Management dei Sistemi Sanitari (ALTEMS), Rome, Italy
| | - Paola Giovanna Marchisio
- Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti, University of Milan, Milan, Italy
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Silvana Castaldi
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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Ramos-Rincón JM, Pinargote-Celorio H, González-de-la-Aleja P, Sánchez-Payá J, Reus S, Rodríguez-Díaz JC, Merino E. Impact of influenza related hospitalization in Spain: characteristics and risk factor of mortality during five influenza seasons (2016 to 2021). Front Public Health 2024; 12:1360372. [PMID: 38628848 PMCID: PMC11018950 DOI: 10.3389/fpubh.2024.1360372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/12/2024] [Indexed: 04/19/2024] Open
Abstract
Background Estimating the global influenza burden in terms of hospitalization and death is important for optimizing prevention policies. Identifying risk factors for mortality allows for the design of strategies tailored to groups at the highest risk. This study aims to (a) describe the clinical characteristics of hospitalizations with a diagnosis of influenza over five flu seasons (2016-2017 to 2020-2021), (b) assess the associated morbidity (hospitalization rates and ICU admissions rate), mortality and cost of influenza hospitalizations in different age groups and (c) analyze the risk factors for mortality. Methods This retrospective study included all hospital admissions with a diagnosis of influenza in Spain for five influenza seasons. Data were extracted from the Spanish National Surveillance System for Hospital Data from 1 July 2016 to 30 June 2021. We identified cases coded as having influenza as a primary or secondary diagnosis (International Classification of Diseases, 10th revision, J09-J11). The hospitalization rate was calculated relative to the general population. Independent predictors of mortality were identified using multivariable logistic regression. Results Over the five seasons, there were 127,160 hospitalizations with a diagnosis of influenza. The mean influenza hospitalization rate varied from 5/100,000 in 2020-2021 (COVID-19 pandemic) to 92.9/100,000 in 2017-2018. The proportion of influenza hospitalizations with ICU admission was 7.4% and was highest in people aged 40-59 years (13.9%). The case fatality rate was 5.8% overall and 9.4% in those aged 80 years or older. Median length of stay was 5 days (and 6 days in the oldest age group). In the multivariable analysis, independent risk factors for mortality were male sex (odds ratio [OR] 1.14, 95% confidence interval [95% CI] 1.08-1.20), age (<5 years: OR 1; 5-19 years: OR 2.02, 95%CI 1.17-3.49; 20-39 years: OR 4.11, 95% CI 2.67-6.32; 40-59 years: OR 8.15, 95% CI 5.60-11.87; 60-79 years: OR 15.10, 95% CI 10.44-21.84; ≥80 years: OR 33.41, 95% CI 23.10-48.34), neurological disorder (OR 1.97, 95% CI 1.83-2.11), heart failure (OR 1.85, 95% CI 1.74-1.96), chronic kidney disease (OR 1.33, 95% CI 1.25-1.41), chronic liver disease (OR 2.95, 95% CI 2.68-3.27), cancer (OR 1.85, 95% CI 1.48-2.24), coinfection with SARS-CoV2 (OR 3.17, 95% CI 2.34-4.28), influenza pneumonia (OR 1.76, 95% CI 1.66-1.86) and admission to intensive care (OR 7.81, 95% CI 7.31-8.36). Conclusion Influenza entails a major public health burden. People aged over 60-and especially those over 80-show the longest hospital stays. Age is also the most significant risk factor for mortality, along with certain associated comorbidities.
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Affiliation(s)
- José-Manuel Ramos-Rincón
- Internal Medicine Department, Dr. Balmis General University Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
| | - Héctor Pinargote-Celorio
- Unit of Infectious Diseases, Dr. Balmis General University Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
| | - Pilar González-de-la-Aleja
- Unit of Infectious Diseases, Dr. Balmis General University Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
| | - José Sánchez-Payá
- Preventive Service, Dr. Balmis General University Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
| | - Sergio Reus
- Unit of Infectious Diseases, Dr. Balmis General University Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
| | - Juan-Carlos Rodríguez-Díaz
- Microbiology Service, Dr. Balmis General University Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
| | - Esperanza Merino
- Unit of Infectious Diseases, Dr. Balmis General University Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
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Miron VD, Drăgănescu AC, Pițigoi D, Aramă V, Streinu-Cercel A, Săndulescu O. The Impact of Obesity on the Host-Pathogen Interaction with Influenza Viruses - Novel Insights: Narrative Review. Diabetes Metab Syndr Obes 2024; 17:769-777. [PMID: 38371386 PMCID: PMC10874191 DOI: 10.2147/dmso.s434115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/10/2024] [Indexed: 02/20/2024] Open
Abstract
After exposure to a viral pathogen, the host-pathogen interaction is essential to determine whether or not infection will ensue, and what the clinical outline of the infection will be. Recent research has shown that the patient with obesity presents a set of particular pathophysiological changes that lead to higher severity of viral infections, and this is particularly true for infection with influenza viruses. Herein, we describe the main metabolic, endocrine, and immune dysregulations that occur in the presence of obesity and their impact on driving intra-host viral diversity, leading to heightened severity and virulence of influenza. We show that obesity is linked to modified responses of both the innate and adaptive immune systems during viral infections, including influenza. Due to chronic inflammation and metabolic, endocrine, and signaling pathway disruptions, individuals with obesity have a suboptimal immune response. This results in longer illness duration, increased virus shedding, higher risk of hospitalization and complications, and greater mortality rates. Additionally, they may have a blunted response to vaccination and a higher likelihood of genetic mutation selection. Understanding the intricate interplay between obesity and viral pathogenesis is crucial for developing efficacious therapeutic approaches and public health policies, particularly in light of the escalating worldwide incidence of obesity.
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Affiliation(s)
- Victor Daniel Miron
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
- National Institute for Infectious Diseases “Prof. Dr. Matei Balș”, Bucharest, Romania
| | - Anca Cristina Drăgănescu
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
- National Institute for Infectious Diseases “Prof. Dr. Matei Balș”, Bucharest, Romania
| | - Daniela Pițigoi
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
- National Institute for Infectious Diseases “Prof. Dr. Matei Balș”, Bucharest, Romania
| | - Victoria Aramă
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
- National Institute for Infectious Diseases “Prof. Dr. Matei Balș”, Bucharest, Romania
| | - Adrian Streinu-Cercel
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
- National Institute for Infectious Diseases “Prof. Dr. Matei Balș”, Bucharest, Romania
| | - Oana Săndulescu
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
- National Institute for Infectious Diseases “Prof. Dr. Matei Balș”, Bucharest, Romania
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