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Brown JF, Dye JM, Tozay S, Jeh-Mulbah G, Wohl DA, Fischer WA, Cunningham CK, Rowe K, Zacharias P, van Hasselt J, Norwood DA, Thielman NM, Zak SE, Hoover DL. Anti-Ebola Virus Antibody Levels in Convalescent Plasma and Viral Load After Plasma Infusion in Patients With Ebola Virus Disease. J Infect Dis 2019; 218:555-562. [PMID: 29659889 DOI: 10.1093/infdis/jiy199] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/03/2018] [Indexed: 11/14/2022] Open
Abstract
Background Ebola virus (EBOV) neutralizing antibody in plasma may reduce viral load following administration of plasma to patients with Ebola virus disease (EVD), but measurement of these antibodies is complex. Methods Anti-EBOV antibody was measured by 2 neutralization and 2 enzyme-linked immunosorbent assays (ELISAs) in convalescent plasma (ECP) from 100 EVD survivor donors in Liberia. Viral load was assessed repetitively in patients with EVD participating in a clinical trial of enhanced standard of care plus ECP. Results All 4 anti-EBOV assays were highly concordant for detection of EBOV antibody. Antibodies were not detected in plasma specimens obtained from 15 of 100 donors, including 7 with documented EBOV-positive reverse-transcription polymerase chain reaction during EVD. Viral load was reduced following each dose in the 2 clinical trial participants who received ECP with higher antibody levels but not in the 2 who received ECP with lower antibody levels. Conclusions Recovery from EVD can occur with absence of detectable anti-EBOV antibody several months after disease onset. ELISAs may be useful to select ECP donors or identify ECP units that contain neutralizing antibody. ECP with higher anti-EBOV antibody levels may have greater effect on EBOV load-an observation that requires further investigation. Clinical Trials Registration NCT02333578.
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Affiliation(s)
- Jerry F Brown
- Eternal Love Winning Africa Hospital, Paynesville, Liberia
| | - John M Dye
- US Army Medical Research Institute of Infectious Disease, Frederick, Maryland
| | - Sam Tozay
- Eternal Love Winning Africa Hospital, Paynesville, Liberia
| | | | - David A Wohl
- University of North Carolina School of Medicine, Chapel Hill
| | | | | | - Kathleen Rowe
- Blood Centers of America, West Warwick, Rhode Island
| | - Peter Zacharias
- Safe Blood for Africa Foundation, Washington, District of Columbia, Hinckley, Ohio
| | - James van Hasselt
- Safe Blood for Africa Foundation, Washington, District of Columbia, Hinckley, Ohio
| | - David A Norwood
- US Army Medical Research Institute of Infectious Disease, Frederick, Maryland
| | | | - Samantha E Zak
- US Army Medical Research Institute of Infectious Disease, Frederick, Maryland
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2
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Shah K, Bentley E, Tyler A, Richards KSR, Wright E, Easterbrook L, Lee D, Cleaver C, Usher L, Burton JE, Pitman JK, Bruce CB, Edge D, Lee M, Nazareth N, Norwood DA, Moschos SA. Field-deployable, quantitative, rapid identification of active Ebola virus infection in unprocessed blood. Chem Sci 2017; 8:7780-7797. [PMID: 29163915 PMCID: PMC5694917 DOI: 10.1039/c7sc03281a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/20/2017] [Indexed: 01/01/2023] Open
Abstract
The West African Ebola virus outbreak underlined the importance of delivering mass diagnostic capability outside the clinical or primary care setting in effectively containing public health emergencies caused by infectious disease. Yet, to date, there is no solution for reliably deploying at the point of need the gold standard diagnostic method, real time quantitative reverse transcription polymerase chain reaction (RT-qPCR), in a laboratory infrastructure-free manner. In this proof of principle work, we demonstrate direct performance of RT-qPCR on fresh blood using far-red fluorophores to resolve fluorogenic signal inhibition and controlled, rapid freeze/thawing to achieve viral genome extraction in a single reaction chamber assay. The resulting process is entirely free of manual or automated sample pre-processing, requires no microfluidics or magnetic/mechanical sample handling and thus utilizes low cost consumables. This enables a fast, laboratory infrastructure-free, minimal risk and simple standard operating procedure suited to frontline, field use. Developing this novel approach on recombinant bacteriophage and recombinant human immunodeficiency virus (HIV; Lentivirus), we demonstrate clinical utility in symptomatic EBOV patient screening using live, infectious Filoviruses and surrogate patient samples. Moreover, we evidence assay co-linearity independent of viral particle structure that may enable viral load quantification through pre-calibration, with no loss of specificity across an 8 log-linear maximum dynamic range. The resulting quantitative rapid identification (QuRapID) molecular diagnostic platform, openly accessible for assay development, meets the requirements of resource-limited countries and provides a fast response solution for mass public health screening against emerging biosecurity threats.
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Affiliation(s)
- Kavit Shah
- Westminster Genomic Services , Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
- BGResearch Ltd. , 6 The Business Centre, Harvard Way, Harvard Industrial Estate , Kimbolton , Huntingdon PE28 0NJ , UK
| | - Emma Bentley
- Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
| | - Adam Tyler
- BioGene Ltd. , 8 The Business Centre, Harvard Way, Harvard Industrial Estate , Kimbolton , Huntingdon PE28 0NJ , UK
| | - Kevin S R Richards
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - Edward Wright
- Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
| | - Linda Easterbrook
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - Diane Lee
- Fluorogenics LIMITED , Building 227, Tetricus Science Park, Dstl Porton Down , Salisbury , Wiltshire SP4 0JQ , UK
| | - Claire Cleaver
- Fluorogenics LIMITED , Building 227, Tetricus Science Park, Dstl Porton Down , Salisbury , Wiltshire SP4 0JQ , UK
| | - Louise Usher
- Westminster Genomic Services , Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
| | - Jane E Burton
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - James K Pitman
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - Christine B Bruce
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - David Edge
- BioGene Ltd. , 8 The Business Centre, Harvard Way, Harvard Industrial Estate , Kimbolton , Huntingdon PE28 0NJ , UK
| | - Martin Lee
- Fluorogenics LIMITED , Building 227, Tetricus Science Park, Dstl Porton Down , Salisbury , Wiltshire SP4 0JQ , UK
| | - Nelson Nazareth
- BioGene Ltd. , 8 The Business Centre, Harvard Way, Harvard Industrial Estate , Kimbolton , Huntingdon PE28 0NJ , UK
| | - David A Norwood
- Diagnostic Systems Division and Virology Division , United States Army Medical Research Institute of Infectious Diseases , Fort Detrick , MD 21701-5011 , USA
| | - Sterghios A Moschos
- Westminster Genomic Services , Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
- Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
- Department of Applied Sciences , Faculty of Health and Life Sciences , Northumbria University , C4.03 Ellison Building, Ellison Place , Newcastle Upon Tyne , Tyne and Wear NE1 8ST , UK . ; Tel: +44(0) 191 215 6623
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3
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Minogue TD, Koehler JW, Norwood DA. Targeted Next-Generation Sequencing for Diagnostics and Forensics. Clin Chem 2016; 63:450-452. [PMID: 27932415 DOI: 10.1373/clinchem.2016.256065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/29/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Timothy D Minogue
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, MD.
| | - Jeffrey W Koehler
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, MD
| | - David A Norwood
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, MD
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4
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Cnops L, van Griensven J, Honko AN, Bausch DG, Sprecher A, Hill CE, Colebunders R, Johnson JC, Griffiths A, Palacios GF, Kraft CS, Kobinger G, Hewlett A, Norwood DA, Sabeti P, Jahrling PB, Formenty P, Kuhn JH, Ariën KK. Essentials of filoviral load quantification. Lancet Infect Dis 2016; 16:e134-e138. [PMID: 27296694 DOI: 10.1016/s1473-3099(16)30063-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/07/2016] [Accepted: 04/20/2016] [Indexed: 11/29/2022]
Abstract
Quantitative measurement of viral load is an important parameter in the management of filovirus disease outbreaks because viral load correlates with severity of disease, survival, and infectivity. During the ongoing Ebola virus disease outbreak in parts of Western Africa, most assays used in the detection of Ebola virus disease by more than 44 diagnostic laboratories yielded qualitative results. Regulatory hurdles involved in validating quantitative assays and the urgent need for a rapid Ebola virus disease diagnosis precluded development of validated quantitative assays during the outbreak. Because of sparse quantitative data obtained from these outbreaks, opportunities for study of correlations between patient outcome, changes in viral load during the course of an outbreak, disease course in asymptomatic individuals, and the potential for virus transmission between infected patients and contacts have been limited. We strongly urge the continued development of quantitative viral load assays to carefully evaluate these parameters in future outbreaks of filovirus disease.
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Affiliation(s)
- Lieselotte Cnops
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Johan van Griensven
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Anna N Honko
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | | | - Armand Sprecher
- Médecins Sans Frontières-Operational Center of Brussels, Brussels, Belgium
| | - Charles E Hill
- Molecular Diagnostics Laboratory, Emory University Hospital, Atlanta, GA, USA
| | - Robert Colebunders
- International Health Unit, Global Health Institute, Faculty of Medicine and Health Sciences, Antwerp University, Antwerp, Belgium
| | - Joshua C Johnson
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Anthony Griffiths
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Gustavo F Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Colleen S Kraft
- Pathology and Laboratory Medicine, Emory University Medical School, Atlanta, GA, USA
| | - Gary Kobinger
- National Microbiology Laboratory, Public Health Agency of Canada, University of Manitoba, Winnipeg, MB, Canada
| | | | - David A Norwood
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Pardis Sabeti
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Peter B Jahrling
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | | | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Kevin K Ariën
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
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5
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Hartman LJ, Heinrich ML, Zovanyi AM, Ingram MF, Hobson JP, Kulesh DA, Craw PD, Jaissle JG, Norwood DA, Minogue TD. Demonstration of the Pre-Emergency Use Authorization Path Using 3 Minor Groove Binder-Hydrolysis Probe Assays to Detect Escherichia coli O104:H4. Clin Chem 2015; 61:1391-8. [PMID: 26384353 DOI: 10.1373/clinchem.2015.242750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 08/27/2015] [Indexed: 11/06/2022]
Abstract
BACKGROUND The Department of Defense (DoD) and the Food and Drug Administration (FDA) have collaboratively worked on a pre-Emergency Use Authorization (pre-EUA) process for in vitro diagnostic (IVD) devices, using FDA's regulatory flexibilities under the EUA authorities. The pre-EUA process enables FDA review of data in anticipation of a request for an EUA, advancing US government public health emergency preparedness efforts. METHODS The IVD device developed to detect Escherichia coli O104:H4, for which an EUA has not been issued, serves as an example to illustrate that process. Specifically, DoD designed real-time PCR assays to target the virulent E. coli strain O104:H4 (etiological agent of the 2011 German outbreak) including: fliC (flagellin), Agg3C (AAF), and rfb (wbwC) on the basis of the published sequences. RESULTS After development and optimization of these 3 specific assays, a defined protocol was followed to determine and document the sensitivity and specificity of each assay analytically. CONCLUSIONS FDA reviewed these data and returned commentary on additional required experiments to complete the pre-EUA process and expedite the use of the device should there be an emergency need for an IVD device to detect this virulent E. coli strain before such a test is cleared by FDA.
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Affiliation(s)
- Laurie J Hartman
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD; Clinical RM, Hinckley, OH
| | - Megan L Heinrich
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD
| | - Ashley M Zovanyi
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD
| | - Michael F Ingram
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD
| | | | - David A Kulesh
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD
| | - Philip D Craw
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD
| | - James G Jaissle
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD
| | - David A Norwood
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD
| | - Timothy D Minogue
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD;
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6
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Rossi CA, Kearney BJ, Olschner SP, Williams PL, Robinson CG, Heinrich ML, Zovanyi AM, Ingram MF, Norwood DA, Schoepp RJ. Evaluation of ViroCyt® Virus Counter for rapid filovirus quantitation. Viruses 2015; 7:857-72. [PMID: 25710889 PMCID: PMC4379551 DOI: 10.3390/v7030857] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/06/2015] [Accepted: 02/16/2015] [Indexed: 11/16/2022] Open
Abstract
Development and evaluation of medical countermeasures for diagnostics, vaccines, and therapeutics requires production of standardized, reproducible, and well characterized virus preparations. For filoviruses this includes plaque assay for quantitation of infectious virus, transmission electron microscopy (TEM) for morphology and quantitation of virus particles, and real-time reverse transcription PCR for quantitation of viral RNA (qRT-PCR). The ViroCyt® Virus Counter (VC) 2100 (ViroCyt, Boulder, CO, USA) is a flow-based instrument capable of quantifying virus particles in solution. Using a proprietary combination of fluorescent dyes that stain both nucleic acid and protein in a single 30 min step, rapid, reproducible, and cost-effective quantification of filovirus particles was demonstrated. Using a seed stock of Ebola virus variant Kikwit, the linear range of the instrument was determined to be 2.8E+06 to 1.0E+09 virus particles per mL with coefficient of variation ranging from 9.4% to 31.5% for samples tested in triplicate. VC particle counts for various filovirus stocks were within one log of TEM particle counts. A linear relationship was established between the plaque assay, qRT-PCR, and the VC. VC results significantly correlated with both plaque assay and qRT-PCR. These results demonstrated that the VC is an easy, fast, and consistent method to quantify filoviruses in stock preparations.
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Affiliation(s)
- Cynthia A Rossi
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Brian J Kearney
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Scott P Olschner
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Priscilla L Williams
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Camenzind G Robinson
- Pathology Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Megan L Heinrich
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Ashley M Zovanyi
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Michael F Ingram
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - David A Norwood
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Randal J Schoepp
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
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7
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Buzard GS, Baker D, Wolcott MJ, Norwood DA, Dauphin LA. Multi-platform comparison of ten commercial master mixes for probe-based real-time polymerase chain reaction detection of bioterrorism threat agents for surge preparedness. Forensic Sci Int 2012; 223:292-7. [PMID: 23107058 DOI: 10.1016/j.forsciint.2012.10.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 08/14/2012] [Accepted: 10/03/2012] [Indexed: 01/18/2023]
Abstract
The Centers for Disease Control and Prevention and United States Army Research Institute for Infectious Diseases have developed real-time PCR assays for the detection of bioterrorism threat agents. These assays all rely on a limited number of approved real-time PCR master mixes. Because the availability of these reagents is a critical element of bioterrorism preparedness, we undertook a joint national preparedness exercise to address the potential surge needs resulting from a large-scale bio-emergency. We identified 9 commercially-available potential alternatives to an existing approved master mix (LightCycler FastStart DNA Master HybProbes): the TaqMan Fast Universal PCR master mix, OmniMix HS, FAST qPCR master mix, EXPRESS qPCR SuperMix kit, QuantiFast Probe PCR kit, LightCycler FastStart DNA Master(PLUS) HybProbe, Brilliant II FAST qPCR master mix, ABsolute Fast QPCR Mix and the HotStart IT Taq master mix. The performances of these kits were evaluated by the use of real-time PCR assays for four bioterrorism threat agents: Bacillus anthracis, Brucella melitensis, Burkholderia mallei and Francisella tularensis. The master mixes were compared for target-specific detection levels, as well as consistency of results among three different real-time PCR platforms (LightCycler, SmartCycler and 7500 Fast Dx). Real-time PCR analysis revealed that all ten kits performed well for agent detection on the 7500 Fast Dx instrument; however, the QuantiFast Probe PCR kit yielded the most consistently positive results across multiple real-time PCR platforms. We report that certain combinations of commonly used master mixes and instruments are not as reliable as others at detecting low concentrations of target DNA. Furthermore, our study provides laboratories the option to select from the commercial kits we evaluated to suit their preparedness needs.
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Affiliation(s)
- Gregory S Buzard
- Bioterrorism Rapid Response and Advanced Technology (BRRAT) Laboratory, Division of Preparedness and Emerging Infections (DPEI), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA 30333, United States
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8
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Burke RL, Vest KG, Eick AA, Sanchez JL, Johns MC, Pavlin JA, Jarman RG, Mothershead JL, Quintana M, Palys T, Cooper MJ, Guan J, Schnabel D, Waitumbi J, Wilma A, Daniels C, Brown ML, Tobias S, Kasper MR, Williams M, Tjaden JA, Oyofo B, Styles T, Blair PJ, Hawksworth A, Montgomery JM, Razuri H, Laguna-Torres A, Schoepp RJ, Norwood DA, MacIntosh VH, Gibbons T, Gray GC, Blazes DL, Russell KL. Department of Defense influenza and other respiratory disease surveillance during the 2009 pandemic. BMC Public Health 2011; 11 Suppl 2:S6. [PMID: 21388566 PMCID: PMC3092416 DOI: 10.1186/1471-2458-11-s2-s6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The Armed Forces Health Surveillance Center's Division of Global Emerging Infections Surveillance and Response System (AFHSC-GEIS) supports and oversees surveillance for emerging infectious diseases, including respiratory diseases, of importance to the U.S. Department of Defense (DoD). AFHSC-GEIS accomplishes this mission by providing funding and oversight to a global network of partners for respiratory disease surveillance. This report details the system's surveillance activities during 2009, with a focus on efforts in responding to the novel H1N1 Influenza A (A/H1N1) pandemic and contributions to global public health. Active surveillance networks established by AFHSC-GEIS partners resulted in the initial detection of novel A/H1N1 influenza in the U.S. and several other countries, and viruses isolated from these activities were used as seed strains for the 2009 pandemic influenza vaccine. Partners also provided diagnostic laboratory training and capacity building to host nations to assist with the novel A/H1N1 pandemic global response, adapted a Food and Drug Administration-approved assay for use on a ruggedized polymerase chain reaction platform for diagnosing novel A/H1N1 in remote settings, and provided estimates of seasonal vaccine effectiveness against novel A/H1N1 illness. Regular reporting of the system's worldwide surveillance findings to the global public health community enabled leaders to make informed decisions on disease mitigation measures and controls for the 2009 A/H1N1 influenza pandemic. AFHSC-GEIS's support of a global network contributes to DoD's force health protection, while supporting global public health.
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Affiliation(s)
- Ronald L Burke
- Armed Forces Health Surveillance Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Kelly G Vest
- Armed Forces Health Surveillance Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Angelia A Eick
- Armed Forces Health Surveillance Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Jose L Sanchez
- Armed Forces Health Surveillance Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Matthew C Johns
- Armed Forces Health Surveillance Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Julie A Pavlin
- Armed Forces Research Institute of Medical Sciences, 315/6 Rajavithi Road, Bangkok, Thailand 10400
| | - Richard G Jarman
- Armed Forces Research Institute of Medical Sciences, 315/6 Rajavithi Road, Bangkok, Thailand 10400
| | - Jerry L Mothershead
- Center for Disaster and Humanitarian Assistance Medicine, Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Miguel Quintana
- Public Health Region-South, Building 2472, Schofield Road, Fort Sam Houston, TX 78234, USA
| | - Thomas Palys
- Landstuhl Regional Medical Center, Department of Pathology and Area Laboratory Services, CMR 402, APO AE 09180, USA
| | | | - Jian Guan
- Public Health Region-Pacific, Unit 45006, APO AE 96343, USA
| | - David Schnabel
- U.S. Embassy, Attention: MRU, United Nations Avenue, Post Office Box 606, Village Market 00621 Nairobi, Kenya
| | - John Waitumbi
- U.S. Embassy, Attention: MRU, United Nations Avenue, Post Office Box 606, Village Market 00621 Nairobi, Kenya
| | - Alisa Wilma
- Department of Defense Veterinary Food Analysis & Diagnostic Laboratory, 2472 Schofield Road, Suite 2630, Fort Sam Houston, TX 78234, USA
| | - Candelaria Daniels
- Department of Defense Veterinary Food Analysis & Diagnostic Laboratory, 2472 Schofield Road, Suite 2630, Fort Sam Houston, TX 78234, USA
| | - Matthew L Brown
- USAMEDDAC-Korea, Microbiology Section, Unit 15244, Box 459, APO AP 96205, USA
| | - Steven Tobias
- Naval Medical Research Unit Number 2, Kompleks Pergudangan DEPKES R.I., JI. Percetakan Negara II No. 23, Jakarta 10560, Indonesia
| | - Matthew R Kasper
- Naval Medical Research Unit Number 2, Kompleks Pergudangan DEPKES R.I., JI. Percetakan Negara II No. 23, Jakarta 10560, Indonesia
| | - Maya Williams
- Naval Medical Research Unit Number 2, Kompleks Pergudangan DEPKES R.I., JI. Percetakan Negara II No. 23, Jakarta 10560, Indonesia
| | - Jeffrey A Tjaden
- Naval Medical Research Unit No. 3, Extension of Ramses Street, Adjacent to Abbassia Fever Hospital, Postal Code 11517, Cairo, Egypt
| | - Buhari Oyofo
- Naval Medical Research Unit No. 3, Extension of Ramses Street, Adjacent to Abbassia Fever Hospital, Postal Code 11517, Cairo, Egypt
| | - Timothy Styles
- U.S. Navy Environmental Preventive Medicine Unit No. 2, 1887 Powhatan Street, Norfolk, VA 23511, USA
| | - Patrick J Blair
- Naval Health Research Center, 140 Sylvester Road, San Diego, CA 92106, USA
| | - Anthony Hawksworth
- Naval Health Research Center, 140 Sylvester Road, San Diego, CA 92106, USA
| | - Joel M Montgomery
- Naval Medical Research Center Detachment, Centro Medico Naval “CMST,” Av. Venezuela CDRA 36, Callao 2, Lima, Peru
| | - Hugo Razuri
- Naval Medical Research Center Detachment, Centro Medico Naval “CMST,” Av. Venezuela CDRA 36, Callao 2, Lima, Peru
| | - Alberto Laguna-Torres
- Naval Medical Research Center Detachment, Centro Medico Naval “CMST,” Av. Venezuela CDRA 36, Callao 2, Lima, Peru
| | - Randal J Schoepp
- U.S. Army Medical Research Institute of Infectious Diseases, Diagnostic Systems Division, 1425 Porter Street, Fort Detrick, MD 21702, USA
| | - David A Norwood
- U.S. Army Medical Research Institute of Infectious Diseases, Diagnostic Systems Division, 1425 Porter Street, Fort Detrick, MD 21702, USA
| | - Victor H MacIntosh
- U.S. Air Force School of Aerospace Medicine, 2513 Kennedy Circle, Building 180, Brooks City Base, TX 78235, USA
| | - Thomas Gibbons
- U.S. Air Force School of Aerospace Medicine, 2513 Kennedy Circle, Building 180, Brooks City Base, TX 78235, USA
| | - Gregory C Gray
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Post Office Box 100188, Gainesville, FL 32610, USA
| | - David L Blazes
- Armed Forces Health Surveillance Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Kevin L Russell
- Armed Forces Health Surveillance Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - AFHSC-GEIS Influenza Surveillance Writing Group
- Armed Forces Health Surveillance Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
- Armed Forces Research Institute of Medical Sciences, 315/6 Rajavithi Road, Bangkok, Thailand 10400
- Center for Disaster and Humanitarian Assistance Medicine, Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
- Landstuhl Regional Medical Center, Department of Pathology and Area Laboratory Services, CMR 402, APO AE 09180, USA
- U.S. Embassy, Attention: MRU, United Nations Avenue, Post Office Box 606, Village Market 00621 Nairobi, Kenya
- Naval Medical Research Unit Number 2, Kompleks Pergudangan DEPKES R.I., JI. Percetakan Negara II No. 23, Jakarta 10560, Indonesia
- Naval Medical Research Unit No. 3, Extension of Ramses Street, Adjacent to Abbassia Fever Hospital, Postal Code 11517, Cairo, Egypt
- U.S. Navy Environmental Preventive Medicine Unit No. 2, 1887 Powhatan Street, Norfolk, VA 23511, USA
- Naval Health Research Center, 140 Sylvester Road, San Diego, CA 92106, USA
- Naval Medical Research Center Detachment, Centro Medico Naval “CMST,” Av. Venezuela CDRA 36, Callao 2, Lima, Peru
- U.S. Air Force School of Aerospace Medicine, 2513 Kennedy Circle, Building 180, Brooks City Base, TX 78235, USA
- Walter Reed Army Institute of Research, Emerging Infectious Diseases Research Unit, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
- Australian Army Malaria Institute, Gallipoli Barracks, Enoggera, QLD 4051, Australia
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723, USA
- U.S. Navy and Marine Corps Public Health Center, 620 John Paul Jones Circle, Suite 1100, Portsmouth, VA 23708, USA
- Laboratory for Emerging Infectious Diseases, University of Buea, Post Office Box 63, Buea, Cameroon
- Global Viral Forecasting Initiative, 1 Sutter, Suite 600, San Francisco, CA 94104, USA
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9
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Trombley AR, Wachter L, Garrison J, Buckley-Beason VA, Jahrling J, Hensley LE, Schoepp RJ, Norwood DA, Goba A, Fair JN, Kulesh DA. Comprehensive panel of real-time TaqMan polymerase chain reaction assays for detection and absolute quantification of filoviruses, arenaviruses, and New World hantaviruses. Am J Trop Med Hyg 2010; 82:954-60. [PMID: 20439981 DOI: 10.4269/ajtmh.2010.09-0636] [Citation(s) in RCA: 170] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Viral hemorrhagic fever is caused by a diverse group of single-stranded, negative-sense or positive-sense RNA viruses belonging to the families Filoviridae (Ebola and Marburg), Arenaviridae (Lassa, Junin, Machupo, Sabia, and Guanarito), and Bunyaviridae (hantavirus). Disease characteristics in these families mark each with the potential to be used as a biological threat agent. Because other diseases have similar clinical symptoms, specific laboratory diagnostic tests are necessary to provide the differential diagnosis during outbreaks and for instituting acceptable quarantine procedures. We designed 48 TaqMan-based polymerase chain reaction (PCR) assays for specific and absolute quantitative detection of multiple hemorrhagic fever viruses. Forty-six assays were determined to be virus-specific, and two were designated as pan assays for Marburg virus. The limit of detection for the assays ranged from 10 to 0.001 plaque-forming units (PFU)/PCR. Although these real-time hemorrhagic fever virus assays are qualitative (presence of target), they are also quantitative (measure a single DNA/RNA target sequence in an unknown sample and express the final results as an absolute value (e.g., viral load, PFUs, or copies/mL) on the basis of concentration of standard samples and can be used in viral load, vaccine, and antiviral drug studies.
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Affiliation(s)
- Adrienne R Trombley
- Diagnostic Systems Division, and Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21701-5011, USA
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10
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Satterfield BC, Kulesh DA, Norwood DA, Wasieloski LP, Caplan MR, West JAA. Tentacle Probes: differentiation of difficult single-nucleotide polymorphisms and deletions by presence or absence of a signal in real-time PCR. Clin Chem 2007; 53:2042-50. [PMID: 17932130 DOI: 10.1373/clinchem.2007.091488] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND False-positive results are a common problem in real-time PCR identification of DNA sequences that differ from near neighbors by a single-nucleotide polymorphism (SNP) or deletion. Because of a lack of sufficient probe specificity, post-PCR analysis, such as a melting curve, is often required for mutation differentiation. METHODS Tentacle Probes, cooperative reagents with both a capture and a detection probe based on specific cell-targeting principles, were developed as a replacement for 2 chromosomal TaqMan-minor groove binder (MGB) assays previously developed for Yersinia pestis and Bacillus anthracis detection. We compared TaqMan-MGB probes to Tentacle Probes for SNP and deletion detection based on the presence or absence of a growth curve. RESULTS With the TaqMan-MGB Y. pestis yp48 assays, false-positive results for Yersinia pseudotuberculosis occurred at every concentration tested, and with the TaqMan-MGB B. anthracis gyrA assays, false-positive results occurred in 21 of 29 boil preps of environmental samples of near neighbors. With Tentacle Probes no false-positive results occurred. CONCLUSIONS The high specificity exhibited by Tentacle Probes may eliminate melting curve analysis for SNP and deletion mutation detection, allowing the diagnostic use of previously difficult targets.
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Affiliation(s)
- Brent C Satterfield
- Harrington Department of Bioengineering, Arizona State University, Tempe, AZ 85287-9709, USA
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11
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Ulrich MP, Christensen DR, Coyne SR, Craw PD, Henchal EA, Sakai SH, Swenson D, Tholath J, Tsai J, Weir AF, Norwood DA. Evaluation of the Cepheid GeneXpert system for detecting Bacillus anthracis. J Appl Microbiol 2006; 100:1011-6. [PMID: 16630001 DOI: 10.1111/j.1365-2672.2006.02810.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS The Cepheid GeneXpert is a four-site, automated sample preparation and real-time PCR detection system. In this study, the capability of the GeneXpert to isolate and detect nucleic acid from Bacillus anthracis Ames spores was assessed. METHODS AND RESULTS A four-plex, dried-down bead cartridge containing PCR reagents specific for the pXO1 and pXO2 plasmids as well as sample processing and inhibition controls was evaluated. For B. anthracis Ames spores harbouring pXO1 and pXO2, samples containing 68 CFU per ml (148 spores per ml) were positive in all four replicates. A limited cross-reactivity panel, which included closely related Bacillus species, was also tested to determine the specificity of the pXO1 and pXO2 assays. No cross-reactivity occurred. Further, B. anthracis Sterne spore samples were analysed to compare results when processed using the GeneXpert to those run directly on the Cepheid SmartCycler without sample processing. The GeneXpert detection capability was three logs lower than the SmartCycler indicating the benefit of incorporating a nucleic acid extraction procedure. CONCLUSIONS This study demonstrates that the GeneXpert is a rapid and reliable system for simultaneously detecting the B. anthracis virulence plasmids pXO1 and pXO2. SIGNIFICANCE AND IMPACT OF THE STUDY The GeneXpert is the only platform currently available that is capable of both nucleic acid purification and real-time PCR detection enclosed within a single system. Further, all sample manipulations are automated, thus reducing errors associated with manual processing.
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Affiliation(s)
- M P Ulrich
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702-5011, USA
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12
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Hepburn MJ, Purcell BK, Lawler JV, Coyne SR, Petitt PL, Sellers KD, Norwood DA, Ulrich MP. Live vaccine strain Francisella tularensis is detectable at the inoculation site but not in blood after vaccination against tularemia. Clin Infect Dis 2006; 43:711-6. [PMID: 16912944 DOI: 10.1086/506348] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Accepted: 05/16/2006] [Indexed: 11/03/2022] Open
Abstract
INTRODUCTION Live vaccine strain (LVS) Francisella tularensis is a live, attenuated investigational tularemia vaccine that has been used by the US Army for decades to protect laboratory workers. Postvaccination bacterial kinetic characteristics of LVS at the inoculation site and in the blood are unknown and, therefore, were assessed in a prospective study. LVS vaccination of laboratory workers provided the opportunity to compare culture with polymerase chain reaction (PCR) for the detection of F. tularensis in human clinical samples. METHODS Blood and skin swab samples were prospectively collected from volunteers who received the LVS tularemia vaccine at baseline (negative controls) and at 5 specified time points (days 1, 2, 7 or 8, 14 or 15, and 35 after vaccination). Bacterial culture and PCR of whole blood samples (17 volunteers) and inoculation site swabs (41 volunteers) were performed. RESULTS The culture and PCR results of all blood samples were negative. Results of real-time PCR from the inoculation site samples were positive for 41 (100%) of 41 volunteers on day 1, for 40 (97.6%) of 41 volunteers on day 2, for 24 (58.5%) of 41 on day 7 or 8, for 6 (16.7%) of 36 on day 14 or 15, and for 0 (0%) of 9 on day 35. Positive results of bacterial cultures of the inoculation site samples occurred significantly less frequently, compared with PCR testing, with 4 (9.8%) of 41 volunteers having positive results on day 1 (P<.001) and 4 (9.8%) of 41 on day 2 (P<.001); all results from subsequent days were negative. CONCLUSIONS F. tularensis LVS genomic DNA was detected in the majority of samples from the inoculation site up to 1 week after LVS vaccination, with real-time PCR being more sensitive than culture. Our data suggest that bacteremia does not occur after LVS vaccination in normal, healthy human volunteers.
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Affiliation(s)
- Matthew J Hepburn
- Division of Medicine, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA.
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13
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Abstract
Burkholderia mallei is the causative agent of human and animal glanders and is a category B biothreat agent. Rapid diagnosis of B. mallei and immediate prophylactic treatment are essential for patient survival. The majority of current bacteriological and immunological techniques for identifying B. mallei from clinical samples are time-consuming, and cross-reactivity with closely related organisms (i.e. Burkholderia pseudomallei) is a problem. In this investigation, two B. mallei-specific real-time PCR assays targeting the B. mallei bimA(ma) gene (Burkholderia intracellular motility A; BMAA0749), which encodes a protein involved in actin polymerization, were developed. The PCR primer and probe sets were tested for specificity against a collection of B. mallei and B. pseudomallei isolates obtained from numerous clinical and environmental (B. pseudomallei only) sources. The assays were also tested for cross-reactivity using template DNA from 14 closely related Burkholderia species. The relative limit of detection for the assays was found to be 1 pg or 424 genome equivalents. The authors also analysed the applicability of assays to detect B. mallei within infected BALB/c mouse tissues. Beginning 1 h post aerosol exposure, B. mallei was successfully identified within the lungs, and starting at 24 h post exposure, in the spleen and liver. Surprisingly, B. mallei was not detected in the blood of acutely infected animals. This investigation provides two real-time PCR assays for the rapid and specific identification of B. mallei.
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14
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Lawler JV, Endy TP, Hensley LE, Garrison A, Fritz EA, Lesar M, Baric RS, Kulesh DA, Norwood DA, Wasieloski LP, Ulrich MP, Slezak TR, Vitalis E, Huggins JW, Jahrling PB, Paragas J. Cynomolgus macaque as an animal model for severe acute respiratory syndrome. PLoS Med 2006; 3:e149. [PMID: 16605302 PMCID: PMC1435788 DOI: 10.1371/journal.pmed.0030149] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Accepted: 01/10/2006] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The emergence of severe acute respiratory syndrome (SARS) in 2002 and 2003 affected global health and caused major economic disruption. Adequate animal models are required to study the underlying pathogenesis of SARS-associated coronavirus (SARS-CoV) infection and to develop effective vaccines and therapeutics. We report the first findings of measurable clinical disease in nonhuman primates (NHPs) infected with SARS-CoV. METHODS AND FINDINGS In order to characterize clinically relevant parameters of SARS-CoV infection in NHPs, we infected cynomolgus macaques with SARS-CoV in three groups: Group I was infected in the nares and bronchus, group II in the nares and conjunctiva, and group III intravenously. Nonhuman primates in groups I and II developed mild to moderate symptomatic illness. All NHPs demonstrated evidence of viral replication and developed neutralizing antibodies. Chest radiographs from several animals in groups I and II revealed unifocal or multifocal pneumonia that peaked between days 8 and 10 postinfection. Clinical laboratory tests were not significantly changed. Overall, inoculation by a mucosal route produced more prominent disease than did intravenous inoculation. Half of the group I animals were infected with a recombinant infectious clone SARS-CoV derived from the SARS-CoV Urbani strain. This infectious clone produced disease indistinguishable from wild-type Urbani strain. CONCLUSIONS SARS-CoV infection of cynomolgus macaques did not reproduce the severe illness seen in the majority of adult human cases of SARS; however, our results suggest similarities to the milder syndrome of SARS-CoV infection characteristically seen in young children.
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Affiliation(s)
- James V Lawler
- 1Infectious Diseases Department, National Naval Medical Center (NNMC), Bethesda, Maryland, United States of America
| | - Timothy P Endy
- 2Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - Lisa E Hensley
- 2Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - Aura Garrison
- 2Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - Elizabeth A Fritz
- 2Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - May Lesar
- 3Radiology Division, National Naval Medical Center (NNMC); Bethesda, Maryland, United States of America
| | - Ralph S Baric
- 4Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - David A Kulesh
- 5Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - David A Norwood
- 5Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - Leonard P Wasieloski
- 5Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - Melanie P Ulrich
- 5Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - Tom R Slezak
- 6Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Elizabeth Vitalis
- 6Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - John W Huggins
- 2Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - Peter B Jahrling
- 7Headquarters Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - Jason Paragas
- 2Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail:
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15
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Christensen DR, Hartman LJ, Loveless BM, Frye MS, Shipley MA, Bridge DL, Richards MJ, Kaplan RS, Garrison J, Baldwin CD, Kulesh DA, Norwood DA. Detection of biological threat agents by real-time PCR: comparison of assay performance on the R.A.P.I.D., the LightCycler, and the Smart Cycler platforms. Clin Chem 2006; 52:141-5. [PMID: 16391330 DOI: 10.1373/clinchem.2005.052522] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Rapid detection of biological threat agents is critical for timely therapeutic administration. Fluorogenic PCR provides a rapid, sensitive, and specific tool for molecular identification of these agents. We compared the performance of assays for 7 biological threat agents on the Idaho Technology, Inc. R.A.P.I.D., the Roche LightCycler, and the Cepheid Smart Cycler. METHODS Real-time PCR primers and dual-labeled fluorogenic probes were designed to detect Bacillus anthracis, Brucella species, Clostridium botulinum, Coxiella burnetii, Francisella tularensis, Staphylococcus aureus, and Yersinia pestis. DNA amplification assays were optimized by use of Idaho Technology buffers and deoxynucleotide triphosphates supplemented with Invitrogen Platinum Taq DNA polymerase, and were subsequently tested for sensitivity and specificity on the R.A.P.I.D., the LightCycler, and the Smart Cycler. RESULTS Limit of detection experiments indicated that assay performance was comparable among the platforms tested. Exclusivity and inclusivity testing with a general bacterial nucleic acid cross-reactivity panel containing 60 DNAs and agent-specific panels containing nearest neighbors for the organisms of interest indicated that all assays were specific for their intended targets. CONCLUSION With minor supplementation, such as the addition of Smart Cycler Additive Reagent to the Idaho Technology buffers, assays for DNA templates from biological threat agents demonstrated similar performance, sensitivity, and specificity on all 3 platforms.
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Affiliation(s)
- Deanna R Christensen
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
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16
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Hartman LJ, Coyne SR, Norwood DA. “Development of a novel internal positive control for TaqmanR based assays” [YMCPR 19(1):51–9]. Mol Cell Probes 2005. [DOI: 10.1016/j.mcp.2005.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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Hartman LJ, Coyne SR, Norwood DA. Development of a novel internal positive control for Taqman® based assays. Mol Cell Probes 2005; 19:51-9. [PMID: 15652220 DOI: 10.1016/j.mcp.2004.07.006] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2004] [Revised: 07/30/2004] [Accepted: 07/30/2004] [Indexed: 10/26/2022]
Abstract
Development of rapid amplification assays for the detection and identification of biological threat agents has become a focus of diagnostic efforts in recent years. The use of real-time PCR assays as diagnostic tools depends upon two critical processes. First, nucleic acid purification must provide template that is both amplifiable and free of PCR inhibitors. Second, the assays themselves must be sensitive and specific for their nucleic acid targets. A differentiation must be made between results achieved due to the lack of target nucleic acid (true negatives) and those produced due to the inability to amplify target DNA (false negatives) so confidence in negative reactions is possible. False negatives can occur when inhibitors are present in the sample being tested, especially if clinical samples such as blood are analyzed. To address the problem of detecting inhibition in purified nucleic acids, an exogenous internal positive control (IPC) based on Taqman chemistry was developed. A previously optimized assay was cloned and the primer and probe sites were mutated to produce novel sequences with no known homology to published sequence data. The IPC was sensitive to a variety of inhibitors, including hemoglobin, heparin, EDTA, humic acids, and fulvic acid. It was also equally sensitive to inhibition when labeled with either 6FAM or ROX dyes. In addition, the IPC was successfully multiplexed with agent specific assays without any loss in their sensitivity. The designed IPC assay has proven to be an effective tool for monitoring inhibitors of PCR and builds confidence in negative results obtained with agent specific assays.
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Affiliation(s)
- Laurie J Hartman
- US Army Medical Research Institute of Infectious Diseases, Diagnostic Systems Division, 1425 Porter Street, Fort Detrick, MD 21702, USA
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18
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Draghici S, Khatri P, Liu Y, Chase KJ, Bode EA, Kulesh DA, Wasieloski LP, Norwood DA, Reifman J. Identification of genomic signatures for the design of assays for the detection and monitoring of anthrax threats. Pac Symp Biocomput 2005:248-59. [PMID: 15759631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Sequences that are present in a given species or strain while absent from or different in any other organisms can be used to distinguish the target organism from other related or un-related species. Such DNA signatures are particularly important for the identification of genetic source of drug resistance of a strain or for the detection of organisms that can be used as biological agents in warfare or terrorism. Most approaches used to find DNA signatures are laboratory based, require a great deal of effort and can only distinguish between two organisms at a time. We propose a more efficient and cost-effective bioinformatics approach that allows identification of genomic fingerprints for a target organism. We validated our approach using a custom microarray, using sequences identified as DNA fingerprints of Bacillus anthracis. Hybridization results showed that the sequences found using our algorithm were truly unique to B. anthracis and were able to distinguish B. anthracis from its close relatives B. cereus and B. thuringiensis.
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Affiliation(s)
- Sorin Draghici
- Dept of Computer Science, Wayne State University, Detroit, MI 48202, USA
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19
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Coyne SR, Craw PD, Norwood DA, Ulrich MP. Comparative analysis of the Schleicher and Schuell IsoCode Stix DNA isolation device and the Qiagen QIAamp DNA Mini Kit. J Clin Microbiol 2004; 42:4859-62. [PMID: 15472363 PMCID: PMC522347 DOI: 10.1128/jcm.42.10.4859-4862.2004] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Efficient, rapid, and reproducible procedures for isolating high-quality DNA before PCR gene amplification are essential for the diagnostic and molecular identification of pathogenic bacteria. This study evaluated the Qiagen QIAamp DNA Mini Kit and the Schleicher and Schuell IsoCode Stix DNA isolation device for isolating nucleic acid. Buffer, serum, and whole-blood samples were spiked with Bacillus anthracis Sterne vegetative cells and Yersinia pestis, while water was spiked with B. anthracis Sterne spores. Although minimal variations in limit of detection occurred among matrices, both the IsoCode Stix extraction method and the Qiagen procedure have comparable detection limits.
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Affiliation(s)
- Susan R Coyne
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702-5011, USA
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20
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Gibb TR, Norwood DA, Woollen N, Henchal EA. Viral replication and host gene expression in alveolar macrophages infected with Ebola virus (Zaire strain). Clin Diagn Lab Immunol 2002; 9:19-27. [PMID: 11777824 PMCID: PMC119875 DOI: 10.1128/cdli.9.1.19-27.2002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In order to characterize the cellular response to and identify potential diagnostic markers for the early detection of Ebola virus, an in vitro culture system involving nonhuman primate alveolar macrophages was developed. Ebola virus replication in the alveolar macrophages was characterized by plaque assay, immunohistochemical analysis, and in situ hybridization. Fluorogenic 5'-nuclease assays specific for nonhuman primate proinflammatory cytokines and chemokines were designed and used to evaluate mRNA transcription in macrophages infected with Ebola virus. Transient increases in cytokine and chemokine mRNA levels were observed immediately following exposure to Ebola virus. At 2 h postexposure, levels of cytokine and chemokine mRNAs were markedly reduced. Although Ebola virus infection of alveolar macrophages failed to induce a sustained increase in proinflammatory cytokine and chemokine mRNA transcription (potentially reducing the use of these markers as diagnostic tools), the fluorogenic 5'-nuclease assays developed may have prognostic value for individuals infected with Ebola virus. Recently published data have indicated that persons who remain asymptomatic after exposure to Ebola virus are capable of mounting an early proinflammatory cytokine response and that those who become clinically ill are not. If implemented immediately after exposure, these assays could be used to predict which individuals will be more likely to remain asymptomatic as opposed to those who will be more likely to develop clinical signs and eventually succumb to the virus.
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Affiliation(s)
- Tammy R Gibb
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702-5011, USA.
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21
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Gibb TR, Norwood DA, Woollen N, Henchal EA. Development and evaluation of a fluorogenic 5' nuclease assay to detect and differentiate between Ebola virus subtypes Zaire and Sudan. J Clin Microbiol 2001; 39:4125-30. [PMID: 11682540 PMCID: PMC88497 DOI: 10.1128/jcm.39.11.4125-4130.2001] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2001] [Accepted: 08/19/2001] [Indexed: 11/20/2022] Open
Abstract
The ability to rapidly recognize Ebola virus infections is critical to quickly limit further spread of the disease. A rapid, sensitive, and specific laboratory diagnostic test is needed to confirm outbreaks of Ebola virus infection and to distinguish it from other diseases that can cause similar clinical symptoms. A one-tube reverse transcription-PCR assay for the identification of Ebola virus subtype Zaire (Ebola Zaire) and Ebola virus subtype Sudan (Ebola Sudan) was developed and evaluated by using the ABI PRISM 7700 sequence detection system. This assay uses one common primer set and two differentially labeled fluorescent probes to simultaneously detect and differentiate these two subtypes of Ebola virus. The sensitivity of the primer set was comparable to that of previously designed primer sets, as determined by limit-of-detection experiments. This assay is unique in its ability to simultaneously detect and differentiate Ebola Zaire and Ebola Sudan. In addition, this assay is compatible with emerging rapid nucleic acid analysis platforms and therefore may prove to be a very useful diagnostic tool for the control and management of future outbreaks.
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Affiliation(s)
- T R Gibb
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702-5011, USA.
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22
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Abstract
The ability to rapidly recognize Marburg virus infections is critical to quickly institute proper barrier nursing precautions and limit further spread of the disease. A rapid, sensitive, and specific laboratory diagnostic test is necessary to confirm outbreaks of Marburg virus and to distinguish it from other diseases that can present with similar clinical symptoms. A one-tube reverse transcriptase-polymerase chain reaction (RT-PCR) assay for the identification of Marburg virus was developed and evaluated using the ABI PRISM 7700 Sequence Detection System and TaqMan chemistry. The sensitivity and specificity of the newly designed primer/probe set (MBGGP3) was evaluated. MBGGP3 was equivalent to or 10-100-fold more sensitive than previously designed primer sets as determined by limit of detection experiments. In addition, the MBGGP3 assay was able to detect all strains of Marburg virus tested, but gave negative results with other haemorrhagic fever and genetically related viruses. The results of this study indicate that the MBGGP3 primer/probe set is both sensitive and specific. In addition, this assay is compatible with emerging rapid nucleic acid analysis platforms and therefore may prove to be a useful diagnostic tool for the control and management of future outbreaks.
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Affiliation(s)
- T R Gibb
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, MD 21702-5011, USA
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23
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Abstract
Clostridium difficile is a causative agent in antibiotically induced diarrhea and pseudomembraneous colitis. The ability of strains of C. difficile to cause disease depends upon the presence of two toxin genes and their corresponding proteins, designated toxin A and toxin B. Previous studies conducted in this laboratory indicated that toxigenic strains of C. difficile possess both toxin genes, whereas non-toxigenic strains do not. Likewise, the studies showed that toxigenic and non-toxigenic strains of C. difficile differ significantly in chromosomal organization by ribotype analysis. Therefore, the chromosomal organization of a reference strain was investigated. Pulsed field gel electrophoresis was utilized to generate a physical map of the chromosome of the toxigenic Clostridium difficile strain ATCC 43594. Restriction digestions of whole chromosomes with the enzymes NruI and SacII generated consistent macrofragment profiles. NruI digestion resulted in 14 discernible bands containing 16 fragments of DNA. SacII digestions resulted in 14 discernible bands containing 15 fragments of DNA. Restriction digestions with both SacII and NruI resulted in 21 discernible bands containing 31 fragments of DNA. Probing of single and double digests with an extensive set of NruI and SacII single- and double-digest bands clarified the location of individual fragments in relation to one another, resulting in a restriction map of the chromosome. PCR-generated probes of five loci of C. difficile were used to map the location of seven genes on the chromosome. Finally, the addition of all fragments from NruI, SacII and NruI/SacII digestions resulted in an approximate chromosome size of 4.4 Mb.
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Affiliation(s)
- D A Norwood
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
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24
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Abstract
We report the physical mapping of the toxin A and B genes to the bacterial chromosome of Clostridium difficile ATCC 43594 by pulsed-field gel electrophoresis. Single and double digestions with restriction endonucleases NruI and SacII allowed localization of the toxin genes to a specific 577-kb fragment and estimation of genome size to be approximately 3.8 megabases. This effort represents the initial step in the construction of a physical map of the whole genome.
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Affiliation(s)
- D A Norwood
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, USA.
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