Last data update: Sep 23, 2024. (Total: 47723 publications since 2009)
Records 1-8 (of 8 Records) |
Query Trace: Soroka S [original query] |
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Tracking COVID-19 in the United States with surveillance of aggregate cases and deaths
Khan D , Park M , Burkholder J , Dumbuya S , Ritchey MD , Yoon P , Galante A , Duva JL , Freeman J , Duck W , Soroka S , Bottichio L , Wellman M , Lerma S , Lyons BC , Dee D , Haile S , Gaughan DM , Langer A , Gundlapalli AV , Suthar AB . Public Health Rep 2023 333549231163531 Early during the COVID-19 pandemic, the Centers for Disease Control and Prevention (CDC) leveraged an existing surveillance system infrastructure to monitor COVID-19 cases and deaths in the United States. Given the time needed to report individual-level (also called line-level) COVID-19 case and death data containing detailed information from individual case reports, CDC designed and implemented a new aggregate case surveillance system to inform emergency response decisions more efficiently, with timelier indicators of emerging areas of concern. We describe the processes implemented by CDC to operationalize this novel, multifaceted aggregate surveillance system for collecting COVID-19 case and death data to track the spread and impact of the SARS-CoV-2 virus at national, state, and county levels. We also review the processes established to acquire, process, and validate the aggregate number of cases and deaths due to COVID-19 in the United States at the county and jurisdiction levels during the pandemic. These processes include time-saving tools and strategies implemented to collect and validate authoritative COVID-19 case and death data from jurisdictions, such as web scraping to automate data collection and algorithms to identify and correct data anomalies. This topical review highlights the need to prepare for future emergencies, such as novel disease outbreaks, by having an event-agnostic aggregate surveillance system infrastructure in place to supplement line-level case reporting for near-real-time situational awareness and timely data. |
Improving efficiency of COVID-19 aggregate case and death surveillance data transmission for jurisdictions: current and future role of application programming interfaces (APIs).
Khan D , Park M , Lerma S , Soroka S , Gaughan D , Bottichio L , Bray M , Fukushima M , Bregman B , Wiedeman C , Duck W , Dee D , Gundlapalli A , Suthar AB . J Am Med Inform Assoc 2022 29 (10) 1807-1809 During the coronavirus disease-2019 (COVID-19) pandemic, the Centers for Disease Control and Prevention (CDC) supplemented traditional COVID-19 case and death reporting with COVID-19 aggregate case and death surveillance (ACS) to track daily cumulative numbers. Later, as public health jurisdictions (PHJs) revised the historical COVID-19 case and death data due to data reconciliation and updates, CDC devised a manual process to update these records in the ACS dataset for improving the accuracy of COVID-19 case and death data. Automatic data transfer via an application programming interface (API), an intermediary that enables software applications to communicate, reduces the time and effort in transferring data from PHJs to CDC. However, APIs must meet specific content requirements for use by CDC. As of March 2022, CDC has integrated APIs from 3 jurisdictions for COVID-19 ACS. Expanded use of APIs may provide efficiencies for COVID-19 and other emergency response planning efforts as evidenced by this proof-of-concept. In this article, we share the utility of APIs in COVID-19 ACS. |
Protecting Privacy and Transforming COVID-19 Case Surveillance Datasets for Public Use.
Lee B , Dupervil B , Deputy NP , Duck W , Soroka S , Bottichio L , Silk B , Price J , Sweeney P , Fuld J , Weber JT , Pollock D . Public Health Rep 2021 136 (5) 333549211026817 OBJECTIVES: Federal open-data initiatives that promote increased sharing of federally collected data are important for transparency, data quality, trust, and relationships with the public and state, tribal, local, and territorial partners. These initiatives advance understanding of health conditions and diseases by providing data to researchers, scientists, and policymakers for analysis, collaboration, and use outside the Centers for Disease Control and Prevention (CDC), particularly for emerging conditions such as COVID-19, for which data needs are constantly evolving. Since the beginning of the pandemic, CDC has collected person-level, de-identified data from jurisdictions and currently has more than 8 million records. We describe how CDC designed and produces 2 de-identified public datasets from these collected data. METHODS: We included data elements based on usefulness, public request, and privacy implications; we suppressed some field values to reduce the risk of re-identification and exposure of confidential information. We created datasets and verified them for privacy and confidentiality by using data management platform analytic tools and R scripts. RESULTS: Unrestricted data are available to the public through Data.CDC.gov, and restricted data, with additional fields, are available with a data-use agreement through a private repository on GitHub.com. PRACTICE IMPLICATIONS: Enriched understanding of the available public data, the methods used to create these data, and the algorithms used to protect the privacy of de-identified people allow for improved data use. Automating data-generation procedures improves the volume and timeliness of sharing data. |
Initial public health laboratory response after Hurricane Maria - Puerto Rico, 2017
Concepcion-Acevedo J , Patel A , Luna-Pinto C , Pena RG , Cuevas Ruiz RI , Arbolay HR , Toro M , Deseda C , De Jesus VR , Ribot E , Gonzalez JQ , Rao G , De Leon Salazar A , Ansbro M , White BB , Hardy MC , Georgi JC , Stinnett R , Mercante AM , Lowe D , Martin H , Starks A , Metchock B , Johnston S , Dalton T , Joglar O , Stafford C , Youngblood M , Klein K , Lindstrom S , Berman L , Galloway R , Schafer IJ , Walke H , Stoddard R , Connelly R , McCaffery E , Rowlinson MC , Soroka S , Tranquillo DT , Gaynor A , Mangal C , Wroblewski K , Muehlenbachs A , Salerno RM , Lozier M , Sunshine B , Shapiro C , Rose D , Funk R , Pillai SK , O'Neill E . MMWR Morb Mortal Wkly Rep 2018 67 (11) 333-336 Hurricane Maria made landfall in Puerto Rico on September 20, 2017, causing major damage to infrastructure and severely limiting access to potable water, electric power, transportation, and communications. Public services that were affected included operations of the Puerto Rico Department of Health (PRDOH), which provides critical laboratory testing and surveillance for diseases and other health hazards. PRDOH requested assistance from CDC for the restoration of laboratory infrastructure, surveillance capacity, and diagnostic testing for selected priority diseases, including influenza, rabies, leptospirosis, salmonellosis, and tuberculosis. PRDOH, CDC, and the Association of Public Health Laboratories (APHL) collaborated to conduct rapid needs assessments and, with assistance from the CDC Foundation, implement a temporary transport system for shipping samples from Puerto Rico to the continental United States for surveillance and diagnostic and confirmatory testing. This report describes the initial laboratory emergency response and engagement efforts among federal, state, and nongovernmental partners to reestablish public health laboratory services severely affected by Hurricane Maria. The implementation of a sample transport system allowed Puerto Rico to reinitiate priority infectious disease surveillance and laboratory testing for patient and public health interventions, while awaiting the rebuilding and reinstatement of PRDOH laboratory services. |
Detection of anthrax protective antigen (PA) using europium labeled anti-PA monoclonal antibody and time-resolved fluorescence
Stoddard RA , Quinn CP , Schiffer JM , Boyer AE , Goldstein J , Bagarozzi DA , Soroka SD , Dauphin LA , Hoffmaster AR . J Immunol Methods 2014 408 78-88 Inhalation anthrax is a rare but acute infectious disease following adsorption of Bacillus anthracis spores through the lungs. The disease has a high fatality rate if untreated, but early and correct diagnosis has a significant impact on case patient recovery. The early symptoms of inhalation anthrax are, however, non-specific and current anthrax diagnostics are primarily dependent upon culture and confirmatory real-time PCR. Consequently, there may be a significant delay in diagnosis and targeted treatment. Rapid, culture-independent diagnostic tests are therefore needed, particularly in the context of a large scale emergency response. The aim of this study was to evaluate the ability of monoclonal antibodies to detect anthrax toxin proteins that are secreted early in the course of B. anthracis infection using a time-resolved fluorescence (TRF) immunoassay. We selected monoclonal antibodies that could detect protective antigen (PA), as PA83 and also PA63 and LF in the lethal toxin complex. The assay reliable detection limit (RDL) was 6.63 x 10-6muM (0.551ng/ml) for PA83 and 2.51 x 10-5muM (1.58ng/ml) for PA63. Despite variable precision and accuracy of the assay, PA was detected in 9 out of 10 sera samples from anthrax confirmed case patients with cutaneous (n=7), inhalation (n=2), and gastrointestinal (n=1) disease. Anthrax Immune Globulin (AIG), which has been used in treatment of clinical anthrax, interfered with detection of PA. This study demonstrates a culture-independent method of diagnosing anthrax through use of monoclonal antibodies to detect PA and LF in the lethal toxin complex. |
Validation and long term performance characteristics of a quantitative enzyme linked immunosorbent assay (ELISA) for human anti-PA IgG
Semenova VA , Schiffer J , Steward-Clark E , Soroka S , Schmidt DS , Brawner MM , Lyde F , Thompson R , Brown N , Foster L , Fox S , Patel N , Freeman AE , Quinn CP . J Immunol Methods 2012 376 97-107 Accurate, reliable and standardized quantification of anti-protective antigen (PA) IgG antibody levels is essential for comparative analyses of anti-toxin immune responses in anthrax cases, recipients of PA-based anthrax vaccines and for evaluation of anti-PA based immunotherapies. We have previously reported the early performance characteristics and application of a quantitative anti-PA IgG enzyme linked immunosorbent assay. The principal application of this assay was in a Phase 4 human clinical trial of anthrax vaccine adsorbed (AVA, BioThrax), the central component of the CDC Anthrax Vaccine Research Program (AVRP) and in humans following bioterrorism associated Bacillus anthracis infection (Quinn et al., 2002; Quinn et al., 2004; Marano et al., 2008). The objective of the AVRP was to determine the feasibility of reducing the number of priming series and booster doses of the licensed Anthrax Vaccine Adsorbed (AVA) (BioThrax(R); Emergent BioSolutions, Lansing, MI) and changing the route of administration from subcutaneous (SC) to intramuscular (IM) (Marano et al., 2008). In this paper we report the validation and long term performance characteristics of the assay during its six year application in the AVRP (2002-2008). The critical features are 1) extensive validation of the assay using two standard reference sera; 2) long term stability and 3) consistency of the data for quantitative analysis of human long term anti-PA IgG responses. The reportable value (RV) of the assay was expressed as anti-PA IgG concentration (mcg/ml). Accuracy of the assay was high with a percent error (%ER) range of 1.6-11.4%. Overall intra-operator and intermediate precision were high with Coefficients of Variation (%CVs) of 2.5-15.4% and 6.3-13.2%, respectively. The assay demonstrated excellent dilutional linearity for human sera using log(10) transformed data with the slope=0.95 to 0.99, intercept=0.02 to 0.06 and r(2)=0.980-0.987. The assay was robust, tolerating changes in serum incubation temperatures from 35 to 39 degrees C, serum incubation times from 55 to 65min and changes in key reagents. The long-term assay stability over 6years using consecutive reference sera AVR414 and AVR801 demonstrated sustained high accuracy and precision for the assay, confirming its suitability for long term studies of PA protein-based anthrax vaccines. |
Sensitivity and specificity of serologic assays for the detection of human infection with 2009 pandemic H1N1 virus in U.S. populations
Veguilla V , Hancock K , Schiffer J , Gargiullo P , Lu X , Aranio D , Branch A , Dong L , Holiday C , Liu F , Steward-Clark E , Sun H , Tsang B , Wang D , Whaley M , Bai Y , Cronin L , Browning P , Dababneh H , Noland H , Thomas L , Foster L , Quinn CP , Soroka SD , Katz JM . J Clin Microbiol 2011 49 (6) 2210-5 Swine origin 2009 H1N1 influenza virus has spread globally to cause the first influenza pandemic of the 21(st) century. Serological studies can improve our understanding of the extent of human infection and risk factors associated with transmission of this pandemic virus. The "gold standard" for serodiagnosis of human influenza infection is the detection of seroconversion between acute and convalescent stage samples. However, timing of seroepidemiologic investigations often precludes collection of truly acute phase sera, requiring development of serologic criteria for evaluating convalescent phase sera that optimize detection of true positives and true negatives. To guide seroepidemiologic investigations into the spread of the novel 2009 pandemic H1N1 virus, we characterized serum antibody responses to 2009 H1N1 virus in 87 individuals with confirmed viral infection and 227 non-exposed U.S. individuals using microneutralization (MN) and hemagglutination-inhibition (HI) assays. Sensitivity and specificity were determined for each assay alone, and in combination, for detection of 2009 H1N1-specific antibodies in convalescent sera. Although the HI assay was more specific for detecting antibody to 2009 H1N1, the MN was more sensitive, particularly for detecting low titer seroconversions. A combination of titers (MN ≥40 and HI ≥20) provided highest sensitivity (90%) and specificity (96%) for individuals aged < 60 years and 92% specificity for adults aged ≥60 years for detection of serologically confirmed 2009 H1N1 infections in U.S. populations during the first pandemic waves. These studies provide an approach to optimize timely serologic investigations for future pandemics or outbreaks of novel influenza viruses among humans. |
A two-stage, multilevel quality control system for serological assays in anthrax vaccine clinical trials
Soroka SD , Schiffer JM , Semenova VA , Li H , Foster L , Quinn CP . Biologicals 2010 38 (6) 675-83 A two-stage, multilevel assay quality control (QC) system was designed and implemented for two high stringency QC anthrax serological assays; a quantitative anti-PA IgG enzyme-linked immunosorbent assay (ELISA) and an anthrax lethal toxin neutralization activity (TNA) assay. The QC system and the assays were applied for the congressionally mandated Centers for Disease Control and Prevention (CDC) Phase 4 human clinical trial of anthrax vaccine adsorbed (AVA, BioThrax). A total of 57,284 human serum samples were evaluated by anti-PA enzyme-linked immunosorbent assay (ELISA) and 11,685 samples by anthrax lethal toxin neutralization activity (TNA) assay. The QC system demonstrated overall sample acceptance rates of 86% for ELISA and 90% for the TNA assays respectively. Monitoring of multiple assay and test sample variables showed no significant long term trends or degradation in any of the critical assay reagents or reportable values for both assays. Assay quality control data establish the functionality of the quality control system and demonstrates the reliability of the serological data generated using these assays. |
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- Page last updated:Sep 23, 2024
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