Virology. Mutation rate and genotype variation of Ebola virus from Mali case sequences

Abstract

The occurrence of Ebola virus (EBOV) in West Africa during 2013-2015 is unprecedented. Early reports suggested that in this outbreak EBOV is mutating twice as fast as previously observed, which indicates the potential for changes in transmissibility and virulence and could render current molecular diagnostics and countermeasures ineffective. We have determined additional full-length sequences from two clusters of imported EBOV infections into Mali, and we show that the nucleotide substitution rate (9.6 × 10(-4) substitutions per site per year) is consistent with rates observed in Central African outbreaks. In addition, overall variation among all genotypes observed remains low. Thus, our data indicate that EBOV is not undergoing rapid evolution in humans during the current outbreak. This finding has important implications for outbreak response and public health decisions and should alleviate several previously raised concerns.

Fig. 1.. Phylogenetic relationship among viruses from the ongoing outbreak.

A Bayesian tree of all currently published sequences from the ongoing outbreak is shown. Branch colors indicate posterior probability, with terminal branches shown in black. The x axis indicates time in years before acquisition of the last sample (21 November 2014). Although clade structure in the analysis is ambivalent for some of the Sierra Leone viruses, there is strong support for the placement of the Malian viruses as a distinct lineage originating from the main group of Sierra Leone sequences and distinct from both the Guinean viruses, as well as another well-supported clade of Sierra Leone viruses.

Fig. 2.. Nucleotide substitution rate in the current outbreak.

The probability distribution of substitution rates in the current EBOV outbreak in West Africa based on all currently published sequences from this outbreak, including those from Mali, is shown as a gray shaded area. Previously reported substitution rates for EBOVs from four different publications (, –9) are indicated by dotted lines (further qualifying information is provided in brackets if several rates were reported in those publications).