Monitoring of Ebola Virus Makona Evolution through Establishment of Advanced Genomic Capability in Liberia

Abstract

To support Liberia's response to the ongoing Ebola virus (EBOV) disease epidemic in Western Africa, we established in-country advanced genomic capabilities to monitor EBOV evolution. Twenty-five EBOV genomes were sequenced at the Liberian Institute for Biomedical Research, which provided an in-depth view of EBOV diversity in Liberia during September 2014-February 2015. These sequences were consistent with a single virus introduction to Liberia; however, shared ancestry with isolates from Mali indicated at least 1 additional instance of movement into or out of Liberia. The pace of change is generally consistent with previous estimates of mutation rate. We observed 23 nonsynonymous mutations and 1 nonsense mutation. Six of these changes are within known binding sites for sequence-based EBOV medical countermeasures; however, the diagnostic and therapeutic impact of EBOV evolution within Liberia appears to be low.

Keywords: Ebola virus; Liberia; filovirus; genomics; negative-strand RNA virus; viral countermeasures; viral hemorrhagic fever; viruses.

Figure 1

A) Median-joining haplotype network constructed from a full-genome alignment of 122 clinical Ebola virus Makona (EBOV/Mak) isolates (list of isolates in Technical Appendix 3). Each colored vertex represents a sampled viral haplotype, with the numbered vertices representing the centers of the 3 clusters described in (12). All sampled isolates from Liberia originated from cluster 2. The size of each vertex is relative to the number of sampled isolates, and the colors indicate country of origin. Hatch marks indicate the number of mutations along each edge. Because of missing data, 2,764 sites (14.6% of total genome) were excluded from the analysis, including 26 sites with variability among isolates (16.7% of all variable sites). B) Root-to-tip distance correlates well with test date and estimates a rate of evolution equal to 9.17 × 10⁻⁴ substitutions/site/year. This analysis comprises 110 clinical EBOV/Mak isolates collected during March 17, 2014–January 20, 2015 (Technical Appendix 3, isolates with dates).

Figure 2

Mutation analysis of candidate therapeutic drug and diagnostic binding sites used in outbreak of Ebola virus (EBOV) disease, Western Africa. A single-nucleotide polymorphism (SNP) table is combined with a heat map based on 2 categories: 1) mutations tolerated by the therapeutic drug or diagnostic target (highlighted in green); 2) mutations within the binding region of a therapeutic drug or diagnostic assay that have not yet been tested (highlighted in yellow/orange) (–24,27,30,31). Changes previously described are highlighted in yellow; changes that appeared during circulation in Liberia are highlighted in orange. The reference nucleotide positions reported here are in relation to EBOV/Kik-9510621 (GenBank accession no. AY354458), which is one of the primary isolates used as reference for developing these therapeutic drugs and diagnostic assays. A summary of the changes to the probes is available in Technical Appendix 1 Table. PMO, phosphorodiaminate morpholino oligomer, mAB, monoclonal antibody; siRNA, small interfering RNA; Ref pos, reference positive; VP, viral protein.