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Title: Surveillance for Emerging Diseases with Multiplexed Point-of-Care Diagnostics

Abstract

Here, we present an analysis of the diagnostic technologies that were used to identify historical outbreaks of ebola virus disease and consider systematic surveillance strategies that may greatly reduce the peak size of future epidemics. We observe that clinical signs and symptoms alone are often insufficient to recognize index cases of diseases of global concern against the considerable background infectious disease burden that is present throughout the developing world. We propose a simple sampling strategy to enrich in especially dangerous pathogens with a low background for molecular diagnostics by targeting blood borne pathogens in the healthiest age groups. With existing multiplexed diagnostic technologies, such a system could be combined with existing public health screening and reference laboratory systems for malaria, dengue, and common bacteremia or be used to develop such an infrastructure in less-developed locations. Because the needs for valid samples and accurate recording of patient attributes are aligned with needs for global biosurveillance, local public health needs, and improving patient care, co-development of these capabilities appears to be quite natural, flexible, and extensible as capabilities, technologies, and needs evolve over time. Furthermore, implementation of multiplexed diagnostic technologies to enhance fundamental clinical lab capacity will increase public health monitoring andmore » biosurveillance as a natural extension.« less

Authors:
 [1];  [2];  [1];  [1];  [3];  [3];  [4]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Analytics, Intelligence and Technology Division
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division
  3. Dept. of Homeland Security, Washington, DC (United States). Homeland Security Advanced Research Projects Agency (HSARPA)
  4. US Food and Drug Administration, Washington, DC (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE; US Department of Homeland Security (DHS)
OSTI Identifier:
1340961
Report Number(s):
LA-UR-16-20747
Journal ID: ISSN 2326-5094
Grant/Contract Number:
AC52-06NA25396; HSHQPM- 14-X-00069
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Health Security
Additional Journal Information:
Journal Volume: 14; Journal Issue: 3; Journal ID: ISSN 2326-5094
Publisher:
Mary Ann Liebert, Inc.
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Biological Science; disease surveillance; multiplex diagnostics

Citation Formats

Deshpande, Alina, McMahon, Benjamin, Daughton, Ashlynn Rae, Abeyta, Esteban Luis, Anderson, Kevin, Hodge, David, and Pillai, Segaran. Surveillance for Emerging Diseases with Multiplexed Point-of-Care Diagnostics. United States: N. p., 2016. Web. doi:10.1089/hs.2016.0005.
Deshpande, Alina, McMahon, Benjamin, Daughton, Ashlynn Rae, Abeyta, Esteban Luis, Anderson, Kevin, Hodge, David, & Pillai, Segaran. Surveillance for Emerging Diseases with Multiplexed Point-of-Care Diagnostics. United States. doi:10.1089/hs.2016.0005.
Deshpande, Alina, McMahon, Benjamin, Daughton, Ashlynn Rae, Abeyta, Esteban Luis, Anderson, Kevin, Hodge, David, and Pillai, Segaran. 2016. "Surveillance for Emerging Diseases with Multiplexed Point-of-Care Diagnostics". United States. doi:10.1089/hs.2016.0005. https://www.osti.gov/servlets/purl/1340961.
@article{osti_1340961,
title = {Surveillance for Emerging Diseases with Multiplexed Point-of-Care Diagnostics},
author = {Deshpande, Alina and McMahon, Benjamin and Daughton, Ashlynn Rae and Abeyta, Esteban Luis and Anderson, Kevin and Hodge, David and Pillai, Segaran},
abstractNote = {Here, we present an analysis of the diagnostic technologies that were used to identify historical outbreaks of ebola virus disease and consider systematic surveillance strategies that may greatly reduce the peak size of future epidemics. We observe that clinical signs and symptoms alone are often insufficient to recognize index cases of diseases of global concern against the considerable background infectious disease burden that is present throughout the developing world. We propose a simple sampling strategy to enrich in especially dangerous pathogens with a low background for molecular diagnostics by targeting blood borne pathogens in the healthiest age groups. With existing multiplexed diagnostic technologies, such a system could be combined with existing public health screening and reference laboratory systems for malaria, dengue, and common bacteremia or be used to develop such an infrastructure in less-developed locations. Because the needs for valid samples and accurate recording of patient attributes are aligned with needs for global biosurveillance, local public health needs, and improving patient care, co-development of these capabilities appears to be quite natural, flexible, and extensible as capabilities, technologies, and needs evolve over time. Furthermore, implementation of multiplexed diagnostic technologies to enhance fundamental clinical lab capacity will increase public health monitoring and biosurveillance as a natural extension.},
doi = {10.1089/hs.2016.0005},
journal = {Health Security},
number = 3,
volume = 14,
place = {United States},
year = 2016,
month = 6
}

Journal Article:
Free Publicly Available Full Text
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  • We have developed a nucleic acid-based assay that is rapid, sensitive, specific, and can be used for the simultaneous detection of 5 common human respiratory pathogens including influenza A, influenza B, parainfluenza type 1 and 3, respiratory syncytial virus, and adenovirus group B, C, and E. Typically, diagnosis on an un-extracted clinical sample can be provided in less than 3 hours, including sample collection, preparation, and processing, as well as data analysis. Such a multiplexed panel would enable rapid broad-spectrum pathogen testing on nasal swabs, and therefore allow implementation of infection control measures, and timely administration of antiviral therapies. Thismore » article presents a summary of the assay performance in terms of sensitivity and specificity. Limits of detection are provided for each targeted respiratory pathogen, and result comparisons are performed on clinical samples, our goal being to compare the sensitivity and specificity of the multiplexed assay to the combination of immunofluorescence and shell vial culture currently implemented at the UCDMC hospital. Overall, the use of the multiplexed RT-PCR assay reduced the rate of false negatives by 4% and reduced the rate of false positives by up to 10%. The assay correctly identified 99.3% of the clinical negatives, 97% of adenovirus, 95% of RSV, 92% of influenza B, and 77% of influenza A without any extraction performed on the clinical samples. The data also showed that extraction will be needed for parainfluenza virus, which was only identified correctly 24% of the time on un-extracted samples.« less
  • Although adoption of newer Point-of-Care (POC) diagnostics is increasing, there is a significant challenge using POC diagnostics data to improve epidemiological models. In this work, we propose a method to process zip-code level POC datasets and apply these processed data to calibrate an epidemiological model. We specifically develop a calibration algorithm using simulated annealing and calibrate a parsimonious equation-based model of modified Susceptible-Infected-Recovered (SIR) dynamics. The results show that parsimonious models are remarkably effective in predicting the dynamics observed in the number of infected patients and our calibration algorithm is sufficiently capable of predicting peak loads observed in POC diagnosticsmore » data while staying within reasonable and empirical parameter ranges reported in the literature. Additionally, we explore the future use of the calibrated values by testing the correlation between peak load and population density from Census data. Our results show that linearity assumptions for the relationships among various factors can be misleading, therefore further data sources and analysis are needed to identify relationships between additional parameters and existing calibrated ones. As a result, calibration approaches such as ours can determine the values of newly added parameters along with existing ones and enable policy-makers to make better multi-scale decisions.« less
  • Inorganic persistent luminescent phosphors are an excellent class of optical reporters for enabling sensitive point-of-care diagnostics, particularly with smartphone-based biosensing devices in testing formats such as the lateral flow assay (LFA). Here, the development of persistent phosphors for this application is focused on the solid solution (Sr 1-δBa δ) 2MgSi 2O 7:Eu 2+,Dy 3+ (δ = 0, 0.125, 0.25, 0.375), which is prepared using a high-temperature solid-state reaction as confirmed by synchrotron X-ray powder diffraction. The substitution of barium for strontium enables control over the Eu 2+ 5d-orbital crystal field splitting (CFS) as a tool for tuning the emission wavelengthmore » while maintaining luminescence lifetimes >9 min across the composition range. Thermoluminescence measurements of the solid solution provide evidence that trap states contribute to the persistent lifetimes with the trap depths also remaining constant as a function of composition. Time-gated luminescence images of these compounds are captured on a smartphone arranged in a layout to mimic a point-of-care test and demonstrate the viability of using these materials as optical reporters. Moreover, comparing the blue-emitting (Sr 0.625Ba 0.375) 2MgSi 2O 7:Eu 2+,Dy 3+ and the green-emitting SrAl 2O 4:Eu 2+,Dy 3+ in a single LFA-type format shows these two compounds can be detected and resolved simultaneously, thereby permitting the development of a multiplexed LFA.« less
  • Although adoption of newer Point-of-Care (POC) diagnostics is increasing, there is a significant challenge using POC diagnostics data to improve epidemiological models. In this work, we propose a method to process zip-code level POC datasets and apply these processed data to calibrate an epidemiological model. We specifically develop a calibration algorithm using simulated annealing and calibrate a parsimonious equation-based model of modified Susceptible-Infected-Recovered (SIR) dynamics. The results show that parsimonious models are remarkably effective in predicting the dynamics observed in the number of infected patients and our calibration algorithm is sufficiently capable of predicting peak loads observed in POC diagnosticsmore » data while staying within reasonable and empirical parameter ranges reported in the literature. Additionally, we explore the future use of the calibrated values by testing the correlation between peak load and population density from Census data. Our results show that linearity assumptions for the relationships among various factors can be misleading, therefore further data sources and analysis are needed to identify relationships between additional parameters and existing calibrated ones. As a result, calibration approaches such as ours can determine the values of newly added parameters along with existing ones and enable policy-makers to make better multi-scale decisions.« less
  • A new DNA diagnostic and sequencing system has been developed that uses time-of-flight resonance ionization mass spectrometry (TOF-RIMS) to provide a rapid method of analyzing stable isotope-labeled oligonucleotides in form 1 sequencing by hybridization (SBH). With form 1, the DNA is immobilized on a nylon membrane and enriched isotope-labeled individual oligonucleotide probes are free to seek out complementary DNAs during hybridization. The major advantage of this new approach is that multiple oligonucleotides can be labeled with different enriched isotopes and can all be simultaneously hybridized to the genosensor matrix. The probes can then be simultaneously detected with TOF-RIMS with highmore » selectivity, sensitivity, and efficiency. By using isotopically enriched tin labels, up to 10 labeled oligonucleotides could be examined in a single hybridization to the DNA matrix. Greater numbers of labels are available if rare earth isotopes are employed. In the present study, matrices containing three different DNAs were prepared and simultaneously hybridized with two different probes under a variety of conditions. The results show that DNAs, immobilized on nylon surfaces, can be specifically hybridized to probes labeled with different enriched tin isotopes. Discrimination between complementary and noncomplementary sites of better than 100 was obtained in multiplexed samples. 34 refs., 5 figs.« less