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

Viruses

Shanmuga Sozhamannan¹  Michael A. Smith¹  Bruce G. Goodwin¹  Catherine E. Campbell²  Adrienne T. Hall³  Timothy D. Minogue³  Jeffrey W. Koehler³  George W. Christopher⁴  Walter J. Berger⁵  Mychal Ivancich⁵  Daniel A. Negrón⁵  Mitchell Y. Holland⁵ 

[1] Critical Reagents Program, Medical Countermeasure Systems Annex, 110 Thomas Johnson Drive, Frederick, MD 21702, USA;DCE consulting, Vienna, VA 22181, USA;Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA;Medical Countermeasure Systems, Ft. Belvoir, VI 22060, USA;Noblis, Inc., 3150 Fairview Park Drive South, Falls Church, VA 22042, USA;

关键词: EBOV;    Western African outbreak;    WGS;    qRT-PCR;    signature erosion;    PSET;    BioVelocity;   

DOI  :  10.3390/v7062763

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown