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Open AccessArticle

Evaluation of Signature Erosion in Ebola Virus Due to Genomic Drift and Its Impact on the Performance of Diagnostic Assays

1
Critical Reagents Program, Medical Countermeasure Systems Annex, 110 Thomas Johnson Drive, Frederick, MD 21702, USA
2
The Tauri Group, LLC, Alexandria, VA 22310, USA
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Noblis, Inc., 3150 Fairview Park Drive South, Falls Church, VA 22042, USA
4
Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
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DCE consulting, Vienna, VA 22181, USA
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Medical Countermeasure Systems, Ft. Belvoir, VI 22060, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Jens H. Kuhn
Viruses 2015, 7(6), 3130-3154; https://doi.org/10.3390/v7062763
Received: 25 March 2015 / Revised: 11 May 2015 / Accepted: 11 June 2015 / Published: 17 June 2015
(This article belongs to the Collection Advances in Ebolavirus, Marburgvirus, and Cuevavirus Research)
Genome sequence analyses of the 2014 Ebola Virus (EBOV) isolates revealed a potential problem with the diagnostic assays currently in use; i.e., drifting genomic profiles of the virus may affect the sensitivity or even produce false-negative results. We evaluated signature erosion in ebolavirus molecular assays using an in silico approach and found frequent potential false-negative and false-positive results. We further empirically evaluated many EBOV assays, under real time PCR conditions using EBOV Kikwit (1995) and Makona (2014) RNA templates. These results revealed differences in performance between assays but were comparable between the old and new EBOV templates. Using a whole genome approach and a novel algorithm, termed BioVelocity, we identified new signatures that are unique to each of EBOV, Sudan virus (SUDV), and Reston virus (RESTV). Interestingly, many of the current assay signatures do not fall within these regions, indicating a potential drawback in the past assay design strategies. The new signatures identified in this study may be evaluated with real-time reverse transcription PCR (rRT-PCR) assay development and validation. In addition, we discuss regulatory implications and timely availability to impact a rapidly evolving outbreak using existing but perhaps less than optimal assays versus redesign these assays for addressing genomic changes. View Full-Text
Keywords: EBOV; Western African outbreak; WGS; qRT-PCR; signature erosion; PSET; BioVelocity EBOV; Western African outbreak; WGS; qRT-PCR; signature erosion; PSET; BioVelocity
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Sozhamannan, S.; Holland, M.Y.; Hall, A.T.; Negrón, D.A.; Ivancich, M.; Koehler, J.W.; Minogue, T.D.; Campbell, C.E.; Berger, W.J.; Christopher, G.W.; Goodwin, B.G.; Smith, M.A. Evaluation of Signature Erosion in Ebola Virus Due to Genomic Drift and Its Impact on the Performance of Diagnostic Assays. Viruses 2015, 7, 3130-3154.

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