Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak

Abstract

Members of the genus Ebolavirus have caused outbreaks of haemorrhagic fever in humans in Africa. The most recent outbreak in Guinea, which began in February of 2014, is still ongoing. Recently published analyses of sequences from this outbreak suggest that the outbreak in Guinea is caused by a divergent lineage of Zaire ebolavirus. We report evidence that points to the same Zaire ebolavirus lineage that has previously caused outbreaks in the Democratic Republic of Congo, the Republic of Congo and Gabon as the culprit behind the outbreak in Guinea.

Keywords: Guinea; disease outbreak; ebolavirus; zoonoses.

ML tree of complete genomes.

ML tree of complete genomes without accommodating for rate heterogeneity shows the Guinea outbreak sequences (highlighted) as belonging to a divergent EBOV lineage. Tips belonging to the EBOV lineage are not collapsed. Numbers above key nodes in the EBOV clade are bootstrap values (100 replicates).

MrBayes tree of concatenated coding sequences.

When only the coding sequences are used, the Guinea outbreak sequences appear to be derived from within the diversity of Gabon/DRC EBOV lineages.

Expanded view of a MrBayes tree of concatenated coding sequences.

Expanding the EBOV region of the tree (same tree as Figure 2, but with the divergent ebolavirus species cropped out) we see that the Guinea outbreak sequences are nested within the EBOV clade.

MrBayes tree of intergenic sequences.

Intergenic regions show a similar picture with the Guinea sequences nested within EBOV.

Root-to-tip regression of a MrBayes tree of concatenated coding regions.

Sequences from the 1976 Zaire outbreak are very close to the root.

MrBayes tree of concatenated coding sequences rooted by least squares regression.

The Bayesian posterior support for all the groupings between the outbreaks are 1.0 including for the grouping of Guinea 2014 with DRC 2007 and Gabon 2002. This demonstrates that the uncertainty about the position of the Guinea 2014 lineage in the complete ebolavirus trees was down to the rooting of the EBOV clade (i.e., where the divergent outgroups connect to the EBOV tree). The relationships of the EBOV outbreaks is completely consistent for the simple whole genome alignment, the coding regions only and the intergenic regions only but the position of the root changes. In the figure A) denotes the position of the root for the full genome maximum likelihood tree, B) for the Bayesian coding-sequence only tree, C) the Bayesian intergenic regions only tree and D) the combined coding-sequence and intergenic region accommodating different rates of evolution.

Maximum clade credibility tree of GP sequences.

Although the closest relatives of the Guinea lineage are not entirely certain (posterior probability 0.92), its relationship with Central African EBOV lineages is well-supported (posterior probability 1.0).