Isolates of Zaire ebolavirus from wild apes reveal genetic lineage and recombinants

Abstract

Over the last 30 years, Zaire ebolavirus (ZEBOV), a virus highly pathogenic for humans and wild apes, has emerged repeatedly in Central Africa. Thus far, only a few virus isolates have been characterized genetically, all belonging to a single genetic lineage and originating exclusively from infected human patients. Here, we describe the first ZEBOV sequences isolated from great ape carcasses in the Gabon/Congo region that belong to a previously unrecognized genetic lineage. According to our estimates, this lineage, which we also encountered in the two most recent human outbreaks in the Republic of the Congo in 2003 and 2005, diverged from the previously known viruses around the time of the first documented human outbreak in 1976. These results suggest that virus spillover from the reservoir has occurred more than once, as predicted by the multiple emergence hypothesis. However, the young age of both ZEBOV lineages and the spatial and temporal sequence of outbreaks remain at odds with the idea that the virus simply emerged from a long-established and widespread reservoir population. Based on data from two ZEBOV genes, we also demonstrate, within the family Filoviridae , recombination between the two lineages. According to our estimates, this event took place between 1996 and 2001 and gave rise to a group of recombinant viruses that were responsible for a series of outbreaks in 2001–2003. The potential for recombination adds an additional level of complexity to unraveling and potentially controlling the emergence of ZEBOV in humans and wildlife species.

Molecular Evolution of Viruses of the Family Filoviridae Based on 97 Whole-Genome Sequences

“…An independent root-to-tip regression analysis using the Path-O-Gen program resulted in an estimate contained within the 95% highest posterior density (HPD) interval from the Bayesian coalescent analysis (2.2 ϫ 10 Ϫ4 nucleotide substitutions/site/year; correlation coefficient ϭ 0.89). While it is possible that Ebola virus emerged only recently, the low level of genetic diversity despite a moderately fast molecular evolutionary rate, coupled with the previously hypothesized ancestral age of the filoviruses overall, suggests that Ebola virus has more likely undergone a recent genetic bottleneck, a hypothesis that others have proposed as well (29,30,32). Given the dependence of a zoonotic virus on its host population, it is easy to envision a scenario in which the number of susceptible hosts declines, for a variety of possible reasons, and results in a small effective viral population size and a subsequent loss of genetic diversity that would limit our ability to trace the virus back through time.…”

“…Further confusing the issue, some authors have presented data indicating that viruses of at least one filovirus species (Zaire ebolavirus) share a most recent common ancestor (MRCA) in the very recent past (29)(30)(31)(32). Previous studies have attempted to estimate rates of nonsynonymous substitutions and divergence times among viruses within the Filoviridae; however, most have been limited in terms of sample size (25) or have examined only a single species, in particular, Zaire ebolavirus (29,31,32). Here, we perform detailed Bayesian coalescent phylogenetic analyses on 97 virus whole-genome sequences (55 of which are newly reported here) to comprehensively examine the evolutionary rates of the filoviruses and estimate dates of common ancestry within this family.…”

Ebolavirus Classification Based on Natural Vectors

“…The switched positions of the species in the two trees indicate that there is a recombination of GP and NP between species Zaire ebolavirus and Bundibugyo ebolavirus. The recombination between GP and NP was also studied previously (Wittmann et al, 2007;Domazet-Lošo and Haubold, 2011).…”

Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses?

“…The Ebola virus shows three 'groups' A, B and R (near-clades), with some indices of recombination (Wittmann et al, 2007).…”