Tracking ebolavirus genomic drift with a resequencing microarray

Journal Article · 09 February 2022 · PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0263732 · OSTI ID:1904900

Tiper, Irina ^[1]; Kourout, Moussa ^[2]; Fisher, Carolyn ^[2]; Konduru, Krishnamurthy ^[2]; Purkayastha, Anjan ^[3]; Kaplan, Gerardo ^[2]; Duncan, Robert  ^[2]

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1. U.S. Food and Drug Administration (FDA), Silver Spring, MD (United States); OSTI
2. U.S. Food and Drug Administration (FDA), Silver Spring, MD (United States)
3. OpenBox Bio, Vienna, VA (United States)

Filoviruses are emerging pathogens that cause acute fever with high fatality rate and present a global public health threat. During the 2013–2016 Ebola virus outbreak, genome sequencing allowed the study of virus evolution, mutations affecting pathogenicity and infectivity, and tracing the viral spread. In 2018, early sequence identification of the Ebolavirus as EBOV in the Democratic Republic of the Congo supported the use of an Ebola virus vaccine. However, field-deployable sequencing methods are needed to enable a rapid public health response. Resequencing microarrays (RMA) are a targeted method to obtain genomic sequence on clinical specimens rapidly, and sensitively, overcoming the need for extensive bioinformatic analysis. This study presents the design and initial evaluation of an ebolavirus resequencing microarray (Ebolavirus-RMA) system for sequencing the major genomic regions of four Ebolaviruses that cause disease in humans. The design of the Ebolavirus-RMA system is described and evaluated by sequencing repository samples of three Ebolaviruses and two EBOV variants. The ability of the system to identify genetic drift in a replicating virus was achieved by sequencing the ebolavirus glycoprotein gene in a recombinant virus cultured under pressure from a neutralizing antibody. Comparison of the Ebolavirus-RMA results to the Genbank database sequence file with the accession number given for the source RNA and Ebolavirus-RMA results compared to Next Generation Sequence results of the same RNA samples showed up to 99% agreement.

• Research Organization: Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States)
• Sponsoring Organization: USDOE Office of Science (SC); US Food and Drug Administration; FDA Medical Countermeasures Initiative (MCMi)
• Grant/Contract Number: SC0014664
• OSTI ID: 1904900
• Journal Information: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 2 Vol. 17; ISSN 1932-6203
• Publisher: Public Library of ScienceCopyright Statement
• Country of Publication: United States
• Language: English