scholarly journals Automated Real-Time Collection of Pathogen-Specific Diagnostic Data: Syndromic Infectious Disease Epidemiology (Preprint)

2018 ◽  
Author(s):  
Lindsay Meyers ◽  
Christine C Ginocchio ◽  
Aimie N Faucett ◽  
Frederick S Nolte ◽  
Per H Gesteland ◽  
...  
Keyword(s):  
Infectious Disease ◽  
United States ◽  
Real Time ◽  
Large Scale ◽  
The United States ◽  
Molecular Diagnostic ◽  
Respiratory Pathogens ◽  
Test Results ◽  
Patient Privacy ◽  
Clinical Laboratories

BACKGROUND Health care and public health professionals rely on accurate, real-time monitoring of infectious diseases for outbreak preparedness and response. Early detection of outbreaks is improved by systems that are comprehensive and specific with respect to the pathogen but are rapid in reporting the data. It has proven difficult to implement these requirements on a large scale while maintaining patient privacy. OBJECTIVE The aim of this study was to demonstrate the automated export, aggregation, and analysis of infectious disease diagnostic test results from clinical laboratories across the United States in a manner that protects patient confidentiality. We hypothesized that such a system could aid in monitoring the seasonal occurrence of respiratory pathogens and may have advantages with regard to scope and ease of reporting compared with existing surveillance systems. METHODS We describe a system, BioFire Syndromic Trends, for rapid disease reporting that is syndrome-based but pathogen-specific. Deidentified patient test results from the BioFire FilmArray multiplex molecular diagnostic system are sent directly to a cloud database. Summaries of these data are displayed in near real time on the Syndromic Trends public website. We studied this dataset for the prevalence, seasonality, and coinfections of the 20 respiratory pathogens detected in over 362,000 patient samples acquired as a standard-of-care testing over the last 4 years from 20 clinical laboratories in the United States. RESULTS The majority of pathogens show influenza-like seasonality, rhinovirus has fall and spring peaks, and adenovirus and the bacterial pathogens show constant detection over the year. The dataset can also be considered in an ecological framework; the viruses and bacteria detected by this test are parasites of a host (the human patient). Interestingly, the rate of pathogen codetections, on average 7.94% (28,741/362,101), matches predictions based on the relative abundance of organisms present. CONCLUSIONS Syndromic Trends preserves patient privacy by removing or obfuscating patient identifiers while still collecting much useful information about the bacterial and viral pathogens that they harbor. Test results are uploaded to the database within a few hours of completion compared with delays of up to 10 days for other diagnostic-based reporting systems. This work shows that the barriers to establishing epidemiology systems are no longer scientific and technical but rather administrative, involving questions of patient privacy and data ownership. We have demonstrated here that these barriers can be overcome. This first look at the resulting data stream suggests that Syndromic Trends will be able to provide high-resolution analysis of circulating respiratory pathogens and may aid in the detection of new outbreaks.

scholarly journals Automated collection of pathogen-specific diagnostic data for real-time syndromic epidemiological studies

2017 ◽  
Author(s):  
Lindsay Meyers ◽  
Christine C. Ginocchio ◽  
Aimie N. Faucett ◽  
Frederick S. Nolte ◽  
Per H. Gesteland ◽  
...  
Keyword(s):  
Real Time ◽  
Standard Of Care ◽  
The United States ◽  
Epidemiological Studies ◽  
Respiratory Pathogen ◽  
Molecular Diagnostic ◽  
Patient Privacy ◽  
Public Health Professionals ◽  
Clinical Laboratories ◽  
Molecular Diagnostic Test

AbstractHealth-care and public health professionals rely on accurate, real-time monitoring of infectious diseases for outbreak preparedness and response. Early detection of outbreaks is improved by systems that are pathogen-specific. We describe a system, FilmArray® Trend, for rapid disease reporting that is syndrome-based but pathogen-specific. Results from a multiplex molecular diagnostic test are sent directly to a cloud database. www.syndromictrends.com presents these data in near real-time. Trend preserves patient privacy by removing or obfuscating patient identifiers. We summarize the respiratory pathogen results, for 20 organisms from 344,000 patient samples acquired as standard of care testing over the last four years from 20 clinical laboratories in the United States. The majority of pathogens show influenza-like seasonality, rhinovirus has fall and spring peaks and adenovirus and bacterial pathogens show constant detection over the year. Interestingly, the rate of pathogen co-detections, on average 7.7%, matches predictions based on the relative abundance of organisms present.

scholarly journals Tracking and predicting U.S. influenza activity with a real-time surveillance network

2020 ◽  
Vol 16 (11) ◽  
pp. e1008180
Author(s):  
Sequoia I. Leuba ◽  
Reza Yaesoubi ◽  
Marina Antillon ◽  
Ted Cohen ◽  
Christoph Zimmer
Keyword(s):  
United States ◽  
Real Time ◽  
Logistic Models ◽  
The United States ◽  
Test System ◽  
Test Results ◽  
Surveillance Network ◽  
Physician Visits ◽  
National Network ◽  
Influenza Activity

Each year in the United States, influenza causes illness in 9.2 to 35.6 million individuals and is responsible for 12,000 to 56,000 deaths. The U.S. Centers for Disease Control and Prevention (CDC) tracks influenza activity through a national surveillance network. These data are only available after a delay of 1 to 2 weeks, and thus influenza epidemiologists and transmission modelers have explored the use of other data sources to produce more timely estimates and predictions of influenza activity. We evaluated whether data collected from a national commercial network of influenza diagnostic machines could produce valid estimates of the current burden and help to predict influenza trends in the United States. Quidel Corporation provided us with de-identified influenza test results transmitted in real-time from a national network of influenza test machines called the Influenza Test System (ITS). We used this ITS dataset to estimate and predict influenza-like illness (ILI) activity in the United States over the 2015-2016 and 2016-2017 influenza seasons. First, we developed linear logistic models on national and regional geographic scales that accurately estimated two CDC influenza metrics: the proportion of influenza test results that are positive and the proportion of physician visits that are ILI-related. We then used our estimated ILI-related proportion of physician visits in transmission models to produce improved predictions of influenza trends in the United States at both the regional and national scale. These findings suggest that ITS can be leveraged to improve “nowcasts” and short-term forecasts of U.S. influenza activity.

scholarly journals Near Real-time Surveillance of Disease during 2016-17 Influenza Season in the U.S.

2018 ◽  
Vol 10 (1) ◽  
Author(s):  
Sushruth K. Reddy ◽  
Jhobe Steadman ◽  
John Tamerius
Keyword(s):  
Public Health ◽  
Infectious Disease ◽  
Real Time ◽  
Influenza A ◽  
Influenza Season ◽  
The United States ◽  
Influenza B ◽  
Test Results ◽  
Influenza Activity ◽  
The U.S

ObjectiveDemonstrate performance of the Virena Global Wireless Surveillance System, an automated platform utilized in conjunction with the Sofia FIA Analyzer, for near real-time transmission of infectious disease test results to public health and other healthcare organizations.IntroductionPublic health agencies worldwide all enjoy the same mission—providing healthcare warnings, guidance, and support to the public and healthcare professionals they represent. A critical element in achieving this mission is accessing timely and comprehensive surveillance information about disease in their regions of responsibility. Advances in diagnostic technologies for infectious disease and in the wireless conveyance of information hold great promise for advancing the quality of surveillance information and in facilitating the delivery of timely, accurate, and impactful public health information. Quidel Corporation has developed a cloud–based, wireless communications system that is fully integrated with its Sofia fluorescence immunoassay (FIA) platform for rapid, point-of-care diagnosis of infectious disease. The system, called the Virena Global Wireless Surveillance System (hereinafter, Virena) provides test results to public health organizations and other appropriate entities in near-real time. Currently, more than 4,000 Sofia instruments are transmitting results automatically by Virena. This presentation describes the use of Virena in surveilling influenza in the U.S. in the 2016-2017 influenza season, when over 700,000 influenza-like-illness (ILI) patient results were transmitted. The methods employed, results, and the promise of this innovative system will be discussed.MethodsThe Sofia Fluorescent Immunoassay Analyzer (FIA) is a small FDA-cleared, CLIA-waived bench top device that uses immunofluorescence-based, lateral-flow technology for rapid analyte detection within 15 minutes for influenza. With Sofia2, a recent upgrade, positive influenza test results can be obtained in as few as 3 minutes, depending on virus levels. The results are encrypted, and automatically transmitted by Virena--often within 5 seconds--to a dual cloud system for further encryption and formatting. The test results (also including location, date, and patient age) are subsequently pushed to participating public health and healthcare organizations for daily collection and analysis. Healthcare providers utilizing the Virena system may also access their own data and facility-de-identified regional and national data, using a password-enabled internet application called MyVirena.com.ResultsBetween August 1, 2016 and October 6, 2017, 706,654 ILI patient results were transmitted by Virena from over 3,000 clinical sites in the United States. The influenza positivity rate (influenza A and B combined) peaked on February 9th at 33% and maintained this level for two weeks (Figure 1). During this period, as many as 7,048 results were transmitted by Virena per day. Influenza A activity peaked on the same day at 26%, and influenza B peaked at 18% nearly 6.5 weeks later. In the six months from December 15th to June 15th, the influenza positivity rate for patients with ILI was 10% or greater in the United States. Data analysis for individual states revealed significant differences in time of onset of influenza and in the peak positivity rates. For example, the state of Arizona experienced peak positivity rates for influenza activity (42%) as late as mid-May, driven largely by influenza B. In California, influenza A peaked at 43% on January 16th and maintained a positivity rate greater than 15% for nearly three months, while influenza B averaged below 4% for the entire period. Age-specific analysis showed that children in the 2 to 18 year old group had the highest positivity rate (44%, n=251,756) and the longest incidence period. Virena data demonstrated similar influenza activity trends on national and regional levels as that depicted by the clinical laboratory and NREVSS data collected by the CDC; however, the Virena data were collected and reported sooner (Figure 2).ConclusionsThe Virena system represents a major stride for disease surveillance, providing clinical testing data in near real-time time, with local, national, and global scope. This first substantial evaluation of the Virena system, with over 4,000 transmitting Sofia Analyzers, demonstrates capabilities for near real-time assessment of disease onset, regionally varying positivity rates, durations of outbreaks, differential assessment of influenza A and B prevalence, and dynamic mapping throughout the year. With expanding regional and metropolitan coverage, the Virena system holds promise as both a powerful surveillance tool, and as a valuable resource for healthcare quality initiatives, epidemiological research, and the development of new mathematical models for influenza forecasting .

Quality Control of Data in a Large-Scale Cancer Register Program

1966 ◽  
Vol 05 (02) ◽  
pp. 67-74 ◽  
Author(s):  
W. I. Lourie ◽  
W. Haenszeland
Keyword(s):  
United States ◽  
Quality Control ◽  
Cancer Patients ◽  
Large Scale ◽  
The United States ◽  
Newly Diagnosed ◽  
Related Data ◽  
Cancer Register ◽  
Independent Review ◽  
End Results

Quality control of data collected in the United States by the Cancer End Results Program utilizing punchcards prepared by participating registries in accordance with a Uniform Punchcard Code is discussed. Existing arrangements decentralize responsibility for editing and related data processing to the local registries with centralization of tabulating and statistical services in the End Results Section, National Cancer Institute. The most recent deck of punchcards represented over 600,000 cancer patients; approximately 50,000 newly diagnosed cases are added annually.Mechanical editing and inspection of punchcards and field audits are the principal tools for quality control. Mechanical editing of the punchcards includes testing for blank entries and detection of in-admissable or inconsistent codes. Highly improbable codes are subjected to special scrutiny. Field audits include the drawing of a 1-10 percent random sample of punchcards submitted by a registry; the charts are .then reabstracted and recoded by a NCI staff member and differences between the punchcard and the results of independent review are noted.

Utopias of One

2019 ◽  
Author(s):  
Joshua Kotin
Keyword(s):  
United States ◽  
Soviet Union ◽  
World War I ◽  
Large Scale ◽  
Jim Crow ◽  
Personal Autonomy ◽  
The United States ◽  
Soviet Period ◽  
Original Research ◽  
The Soviet Union

This book is a new account of utopian writing. It examines how eight writers—Henry David Thoreau, W. E. B. Du Bois, Osip and Nadezhda Mandel'shtam, Anna Akhmatova, Wallace Stevens, Ezra Pound, and J. H. Prynne—construct utopias of one within and against modernity's two large-scale attempts to harmonize individual and collective interests: liberalism and communism. The book begins in the United States between the buildup to the Civil War and the end of Jim Crow; continues in the Soviet Union between Stalinism and the late Soviet period; and concludes in England and the United States between World War I and the end of the Cold War. In this way it captures how writers from disparate geopolitical contexts resist state and normative power to construct perfect worlds—for themselves alone. The book contributes to debates about literature and politics, presenting innovative arguments about aesthetic difficulty, personal autonomy, and complicity and dissent. It models a new approach to transnational and comparative scholarship, combining original research in English and Russian to illuminate more than a century and a half of literary and political history.

Situational Breakdowns

2019 ◽  
Author(s):  
Anne Nassauer
Keyword(s):  
United States ◽  
Large Scale ◽  
Contextual Factors ◽  
The United States ◽  
Social Outcomes ◽  
Dynamic Processes ◽  
Collective Decisions ◽  
Different Types ◽  
The Impact

This book provides an account of how and why routine interactions break down and how such situational breakdowns lead to protest violence and other types of surprising social outcomes. It takes a close-up look at the dynamic processes of how situations unfold and compares their role to that of motivations, strategies, and other contextual factors. The book discusses factors that can draw us into violent situations and describes how and why we make uncommon individual and collective decisions. Covering different types of surprise outcomes from protest marches and uprisings turning violent to robbers failing to rob a store at gunpoint, it shows how unfolding situations can override our motivations and strategies and how emotions and culture, as well as rational thinking, still play a part in these events. The first chapters study protest violence in Germany and the United States from 1960 until 2010, taking a detailed look at what happens between the start of a protest and the eruption of violence or its peaceful conclusion. They compare the impact of such dynamics to the role of police strategies and culture, protesters’ claims and violent motivations, the black bloc and agents provocateurs. The analysis shows how violence is triggered, what determines its intensity, and which measures can avoid its outbreak. The book explores whether we find similar situational patterns leading to surprising outcomes in other types of small- and large-scale events: uprisings turning violent, such as Ferguson in 2014 and Baltimore in 2015, and failed armed store robberies.

Ban Ki-moon, 2007–2016

2018 ◽  
Author(s):  
Richard Gowan
Keyword(s):  
United States ◽  
Decision Making ◽  
Security Council ◽  
Large Scale ◽  
Central African Republic ◽  
The United States ◽  
Cautious Approach ◽  
Peacekeeping Operations ◽  
Council Decision ◽  
The Face

During Ban Ki-moon’s tenure, the Security Council was shaken by P5 divisions over Kosovo, Georgia, Libya, Syria, and Ukraine. Yet it also continued to mandate and sustain large-scale peacekeeping operations in Africa, placing major burdens on the UN Secretariat. The chapter will argue that Ban initially took a cautious approach to controversies with the Council, and earned a reputation for excessive passivity in the face of crisis and deference to the United States. The second half of the chapter suggests that Ban shifted to a more activist pressure as his tenure went on, pressing the Council to act in cases including Côte d’Ivoire, Libya, and Syria. The chapter will argue that Ban had only a marginal impact on Council decision-making, even though he made a creditable effort to speak truth to power over cases such as the Central African Republic (CAR), challenging Council members to live up to their responsibilities.

A Nationwide Survey of COVID-19 Testing in LGBTQ+ Populations in the United States

2021 ◽  
pp. 003335492110181
Author(s):  
Richard J. Martino ◽  
Kristen D. Krause ◽  
Marybec Griffin ◽  
Caleb LoSchiavo ◽  
Camilla Comer-Carruthers ◽  
...  
Keyword(s):  
United States ◽  
Gay Men ◽  
Antibody Test ◽  
Nationwide Survey ◽  
The United States ◽  
Sociodemographic Characteristics ◽  
Full Time ◽  
Test Results ◽  
Antibody Testing ◽  
And Gender

Objectives Lesbian, gay, bisexual, transgender, or queer and questioning (LGBTQ+) people and populations face myriad health disparities that are likely to be evident during the COVID-19 pandemic. The objectives of our study were to describe patterns of COVID-19 testing among LGBTQ+ people and to differentiate rates of COVID-19 testing and test results by sociodemographic characteristics. Methods Participants residing in the United States and US territories (N = 1090) aged ≥18 completed an internet-based survey from May through July 2020 that assessed COVID-19 testing and test results and sociodemographic characteristics, including sexual orientation and gender identity (SOGI). We analyzed data on receipt and results of polymerase chain reaction (PCR) and antibody testing for SARS-CoV-2 and symptoms of COVID-19 in relation to sociodemographic characteristics. Results Of the 1090 participants, 182 (16.7%) received a PCR test; of these, 16 (8.8%) had a positive test result. Of the 124 (11.4%) who received an antibody test, 45 (36.3%) had antibodies. Rates of PCR testing were higher among participants who were non–US-born (25.4%) versus US-born (16.3%) and employed full-time or part-time (18.5%) versus unemployed (10.8%). Antibody testing rates were higher among gay cisgender men (17.2%) versus other SOGI groups, non–US-born (25.4%) versus US-born participants, employed (12.6%) versus unemployed participants, and participants residing in the Northeast (20.0%) versus other regions. Among SOGI groups with sufficient cell sizes (n > 10), positive PCR results were highest among cisgender gay men (16.1%). Conclusions The differential patterns of testing and positivity, particularly among gay men in our sample, confirm the need to create COVID-19 public health messaging and programming that attend to the LGBTQ+ population.

scholarly journals 1068. Large-Scale Migration and the Changing Viral Hepatitis Prevalences in North America: A modeling approach

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S563-S563
Author(s):  
Kenneth A Valles ◽  
Lewis R Roberts
Keyword(s):  
United States ◽  
Viral Hepatitis ◽  
Large Scale ◽  
Country Of Origin ◽  
Human Movement ◽  
High Volume ◽  
The United States ◽  
The Philippines ◽  
Outcome Data ◽  
Treatment Programs

Abstract Background Infection by hepatitis B and C viruses causes inflammation of the liver and can lead to cirrhosis, liver failure, and hepatocellular carcinoma. The WHO’s ambition to eliminate viral hepatitis by 2030 requires strategies specific to the dynamic disease profiles each nation faces. Large-scale human movement from high-prevalence nations to the United States and Canada have altered the disease landscape, likely warranting adjustments to present elimination approaches. However, the nature and magnitude of the new disease burden remains unknown. This study aims to generate a modeled estimate of recent HBV and HCV prevalence changes to the United States and Canada due to migration. Methods Total migrant populations from 2010-2019 were obtained from United Nations Migrant Stock database. Country-of-origin HBV and HCV prevalences were obtained for the select 40 country-of-origin nations from the Polaris Observatory and systematic reviews. A standard pivot table was used to evaluate the disease contribution from and to each nation. Disease progression estimates were generated using the American Association for the Study of the Liver guidelines and outcome data. Results Between 2010 and 2019, 7,676,937 documented migrants arrived in US and Canada from the selected high-volume nations. Primary migrant source regions were East Asia and Latin America. Combined, an estimated 878,995 migrants were HBV positive, and 226,428 HCV positive. The majority of both migrants (6,477,506) and new viral hepatitis cases (HBV=840,315 and HCV=215,359) were found in the United States. The largest source of HBV cases stemmed from the Philippines, and HCV cases from El Salvador. Conclusion Massive human movement has significantly changed HBV and HCV disease burdens in both the US and Canada over the past decade and the long-term outcomes of cirrhosis and HCC are also expected to increase. These increases are likely to disproportionally impact individuals of the migrant and refugee communities and screening and treatment programs must be strategically adjusted in order to reduce morbidity, mortality, and healthcare expenses. Disclosures All Authors: No reported disclosures

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