Molecular evolution of viruses of the family Filoviridae based on 97 whole-genome sequences

Outbreaks of Ebola virus disease in Africa: the beginnings of a tragic saga

The tremendous outbreak of Ebola virus disease occurring in West Africa since the end of 2013 surprises by its remoteness from previous epidemics and dramatic extent. This review aims to describe the 27 manifestations of Ebola virus that arose after its discovery in 1976. It provides an update on research on the ecology of Ebola viruses, modes of contamination and human transmission of the disease that are mainly linked to close contact with an infected animal or a patient suffering from the disease. The recommendations to contain the epidemic and challenges to achieve it are reminded.

Clinical features and pathobiology of Ebolavirus infection

There has clearly been a deluge of international press coverage of the recent outbreak of Ebolavirus in Africa and is partly related to the "fear factor" that comes across when one is confronted with the fact that once infected, not only is the speed of death in a majority of cases rapid but also the images of the cause of death such as bleeding from various orifices gruesome and frightening. The fact that it leads to infection and death of health care providers (10% during the current epidemic) and the visualization of protective gear worn by these individuals to contain such infection adds to this "fear factor". Finally, there is a clear perceived notion that such an agent can be utilized as a bioterrorism agent that adds to the apprehension. Thus, in efforts to gain an objective view of the growing threat Ebolavirus poses to the general public, it is important to provide some basic understanding for the lethality of Ebolavirus infection that is highlighted in Fig. 1. This virus infection first appears to disable the immune system (the very system needed to fight the infection) and subsequently disables the vascular system that leads to blood leakage (hemorrhage), hypotension, drop in blood pressure, followed by shock and death. The virus appears to sequentially infect dendritic cells disabling the interferon system (one of the major host anti-viral immune systems) then macrophages (that trigger the formation of blood clots, release of inflammatory proteins and nitric oxide damaging the lining of blood vessels leading to blood leakage) and finally endothelial cells that contribute to blood leakage. The virus also affects organs such as the liver (that dysregulates the formation of coagulation proteins), the adrenal gland (that destroys the ability of the patient to synthesize steroids and leads to circulation failure and disabling of regulators of blood pressure) and the gastro-intestinal tract (leading to diarrhea). The ability of the virus to disable such major mechanisms in the body facilitates the ability of the virus to replicate in an uncontrolled fashion leading to the rapidity by which the virus can cause lethality. Various laboratories have been working on defining such mechanisms utilizing in vitro culture systems, a variety of animal models including inbred strains of normal and select gene knock out mice, guinea pigs and nonhuman primates that have led to a better understanding of the potential mechanisms involved. There have also been some major advances made in the identification of therapies from the very simple (major supportive type of therapy), to the identification of a number of highly effective chemotherapeutic agents, a variety of highly effective preventive (demonstrating 100% effectiveness in nonhuman primate models) recombinant formulations (adenovirus based, VSV-based, rabies virus based), therapeutic candidate vaccines (cocktail of monoclonal antibodies such as ZMAPP) and alternate approaches (RNAi-based such as TKM-Ebola and antisense based such as AVI-7537) that show great promise and at an unprecedented rate of discovery that speaks well for the scientific research community at large.

Evidence that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the Miocene

An understanding of the timescale of evolution is critical for comparative virology but remains elusive for many RNA viruses. Age estimates based on mutation rates can severely underestimate divergences for ancient viral genes that are evolving under strong purifying selection. Paleoviral dating, however, can provide minimum age estimates for ancient divergence, but few orthologous paleoviruses are known within clades of extant viruses. For example, ebolaviruses and marburgviruses are well-studied mammalian pathogens, but their comparative biology is difficult to interpret because the existing estimates of divergence are controversial. Here we provide evidence that paleoviral elements of two genes (ebolavirus-like VP35 and NP) in cricetid rodent genomes originated after the divergence of ebolaviruses and cuevaviruses from marburgviruses. We provide evidence of orthology by identifying common paleoviral insertion sites among the rodent genomes. Our findings indicate that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the early Miocene.

Challenges, progress, and opportunities: proceedings of the filovirus medical countermeasures workshop

On August 22–23, 2013, agencies within the United States Department of Defense (DoD) and the Department of Health and Human Services (HHS) sponsored the Filovirus Medical Countermeasures (MCMs) Workshop as an extension of the activities of the Filovirus Animal Non-clinical Group (FANG). The FANG is a federally-recognized multi-Agency group established in 2011 to coordinate and facilitate U.S. government (USG) efforts to develop filovirus MCMs. The workshop brought together government, academic and industry experts to consider the needs for filovirus MCMs and evaluate the status of the product development pipeline. This report summarizes speaker presentations and highlights progress and challenges remaining in the field.

Clock Rooting Further Demonstrates that Guinea 2014 EBOV is a Member of the Zaïre Lineage

While initial phylogenetic analyses concluded to Guinea 2014 EBOV falling outside the Zaïre lineage (ZEBOV), a recent re-analysis of the same dataset by Dudas and Rambaut (2014) suggested that Guinea 2014 EBOV actually is ZEBOV. Under the same hypothesis as used by these authors (the molecular clock hypothesis), we reinforce their conclusion by providing a statistical assessment of the location of the root of the Zaïre lineage. Our analysis unambiguously supports Guinea 2014 EBOV as a member of the Zaïre lineage. In addition, we also show that some uncertainty exists so as to the location of the root of the genus Ebolavirus. We release the software we used for these re-analyses. RootAnnotator allows for the easy determination of branch root posterior probability from any posterior sample of clocked trees and is freely available at http://sourceforge.net/projects/rootannotator/.

Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak

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.

Filoviruses in bats: current knowledge and future directions

Filoviruses, including Ebolavirus and Marburgvirus, pose significant threats to public health and species conservation by causing hemorrhagic fever outbreaks with high mortality rates. Since the first outbreak in 1967, their origins, natural history, and ecology remained elusive until recent studies linked them through molecular, serological, and virological studies to bats. We review the ecology, epidemiology, and natural history of these systems, drawing on examples from other bat-borne zoonoses, and highlight key areas for future research. We compare and contrast results from ecological and virological studies of bats and filoviruses with those of other systems. We also highlight how advanced methods, such as more recent serological assays, can be interlinked with flexible statistical methods and experimental studies to inform the field studies necessary to understand filovirus persistence in wildlife populations and cross-species transmission leading to outbreaks. We highlight the need for a more unified, global surveillance strategy for filoviruses in wildlife, and advocate for more integrated, multi-disciplinary approaches to understand dynamics in bat populations to ultimately mitigate or prevent potentially devastating disease outbreaks.

Emerging targets and novel approaches to Ebola virus prophylaxis and treatment

Ebola is a highly virulent pathogen causing severe hemorrhagic fever with a high case fatality rate in humans and non-human primates (NHPs). Although safe and effective vaccines or other medicinal agents to block Ebola infection are currently unavailable, a significant effort has been put forth to identify several promising candidates for the treatment and prevention of Ebola hemorrhagic fever. Among these, recombinant adenovirus-based vectors have been identified as potent vaccine candidates, with some affording both pre- and post-exposure protection from the virus. Recently, Investigational New Drug (IND) applications have been approved by the US Food and Drug Administration (FDA) and phase I clinical trials have been initiated for two small-molecule therapeutics: anti-sense phosphorodiamidate morpholino oligomers (PMOs: AVI-6002, AVI-6003) and lipid nanoparticle/small interfering RNA (LNP/siRNA: TKM-Ebola). These potential alternatives to vector-based vaccines require multiple doses to achieve therapeutic efficacy, which is not ideal with regard to patient compliance and outbreak scenarios. These concerns have fueled a quest for even better vaccination and treatment strategies. Here, we summarize recent advances in vaccines or post-exposure therapeutics for prevention of Ebola hemorrhagic fever. The utility of novel pharmaceutical approaches to refine and overcome barriers associated with the most promising therapeutic platforms are also discussed.