Tracking ebolavirus genomic drift with a resequencing microarray

PLoS One. 2022 Feb 10;17(2):e0263732. doi: 10.1371/journal.pone.0263732. eCollection 2022.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antibodies, Neutralizing / pharmacology*
  • Ebolavirus / classification*
  • Ebolavirus / drug effects
  • Ebolavirus / genetics
  • Genetic Drift
  • Genome, Viral
  • Glycoproteins / genetics*
  • High-Throughput Nucleotide Sequencing
  • Oligonucleotide Array Sequence Analysis
  • Phylogeny
  • Sequence Analysis, RNA / methods*
  • Viral Proteins / genetics

Substances

  • Antibodies, Neutralizing
  • Glycoproteins
  • Viral Proteins

Grants and funding

Irina Tiper, Moussa Kourout and Bryan Lanning were supported in part by an appointment to the Oak Ridge Institute for Science and Education (ORISE) Research Fellowship Program at the Center for Biologics Evaluation and Research administered by the ORISE through an interagency agreement between the U.S. Department of Energy and the U.S. Food and Drug Administration. Funding for this research was partially provided by the FDA Medical Countermeasures Initiative (MCMi). Received by RD There is no grant number. https://www.fda.gov/emergency-preparedness-and-response/counterterrorism-and-emerging-threats/medical-countermeasures-initiative-mcmi. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.