title: Evaluation of Signature Erosion in Ebola Virus Due to Genomic Drift and Its Impact on the Performance of Diagnostic Assays.
abstract: 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.
authors.affiliation: Critical Reagents Program, Medical Countermeasure Systems Annex, 110 Thomas Johnson Drive, Frederick, MD 21702, USA. shanmuga.sozhamannan.ctr@mail.mil.|The Tauri Group, LLC, Alexandria, VA 22310, USA. shanmuga.sozhamannan.ctr@mail.mil.
authors.forename: Shanmuga
authors.initials: S
authors.lastname: Sozhamannan
authors.affiliation: Noblis, Inc., 3150 Fairview Park Drive South, Falls Church, VA 22042, USA. mitchell.holland@noblis.org.
authors.forename: Mitchell Y
authors.initials: MY
authors.lastname: Holland
authors.affiliation: Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA. adrienne.t.hall2.civ@mail.mil.
authors.forename: Adrienne T
authors.initials: AT
authors.lastname: Hall
authors.affiliation: Noblis, Inc., 3150 Fairview Park Drive South, Falls Church, VA 22042, USA. daniel.negron@noblis.org.
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Negrón
authors.affiliation: Noblis, Inc., 3150 Fairview Park Drive South, Falls Church, VA 22042, USA. mychal.ivancich@noblis.org.
authors.forename: Mychal
authors.initials: M
authors.lastname: Ivancich
authors.affiliation: Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA. jeff.w.koehler.ctr@mail.mil.
authors.forename: Jeffrey W
authors.initials: JW
authors.lastname: Koehler
authors.affiliation: Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA. timothy.d.minogue.civ@mail.mil.
authors.forename: Timothy D
authors.initials: TD
authors.lastname: Minogue
authors.affiliation: DCE consulting, Vienna, VA 22181, USA. dceconsulting@verizon.net.
authors.forename: Catherine E
authors.initials: CE
authors.lastname: Campbell
authors.affiliation: Noblis, Inc., 3150 Fairview Park Drive South, Falls Church, VA 22042, USA. walter.berger@noblis.org.
authors.forename: Walter J
authors.initials: WJ
authors.lastname: Berger
authors.affiliation: Medical Countermeasure Systems, Ft. Belvoir, VI 22060, USA. george.w.christopher.civ@mail.mil.
authors.forename: George W
authors.initials: GW
authors.lastname: Christopher
authors.affiliation: Critical Reagents Program, Medical Countermeasure Systems Annex, 110 Thomas Johnson Drive, Frederick, MD 21702, USA. bruce.g.goodwin4.civ@mail.mil.
authors.forename: Bruce G
authors.initials: BG
authors.lastname: Goodwin
authors.affiliation: Critical Reagents Program, Medical Countermeasure Systems Annex, 110 Thomas Johnson Drive, Frederick, MD 21702, USA. michael.a.smith215.civ@mail.mil.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Smith
mesh_terms: D003951:Diagnostic Errors; D029043:Ebolavirus / Q000235:genetics*; D040961:Genetic Drift; D016679:Genome, Viral; D019142:Hemorrhagic Fever, Ebola / Q000175:diagnosis* / Q000821:virology*; D006801:Humans; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D012680:Sensitivity and Specificity
keywords: BioVelocity; EBOV; PSET; WGS; Western African outbreak; qRT-PCR; signature erosion