Genomics of the Ebola outbreak in Sierra Leone

I am teaching a graduate seminar at SF State on contemporary evolution of human viruses. Colleagues advised me to pick the papers for the entire semester beforehand, to reduce work during the semester. I didn’t do that, however, because I wanted to be flexible and choose (partly) based on what the students liked or what the students had trouble with. The result was that in the second week of class, I could hand out a brand new paper on the 2014 Ebola outbreak. Now that is contemporary!

The only trouble is that from now on, every other paper I choose will seem old; a Dengue outbreak in 2008? How ancient!

Here is some of the homework by the students in my class. I hope you enjoy reading it.

The context and main question of the paper

This paper focused on identifying the transmission route of the Ebola virus disease (EVD) outbreak throughout West Africa, whether the outbreak continues to be supplied by new vectors, and how the virus has changed to infect humans. The scientists used parallel viral sequencing and they ended up generating 99 EBOV genome sequences from 78 confirmed EVD patients. Phylogenetic comparison of all genomes from earlier outbreaks, suggests that the 2014 EBOV likely spread from Middle Africa within 10 years. Patients sharing intrahost variation showed specific transmission patterns in West Africa, and this suggests that transmission of viral genetics may be common.

Something new found in this study was that in contrast to previous EVD outbreaks, human-reservoir exposure is unlikely to have contributed to the growth of this epidemic. In addition, the EBOV catalog of mutations will aid in future studies. One main question that this paper addresses is whether or not future studies can monitor viral changes and adaptation, and understand how to contain this expanding epidemic.

Ryan Marder

The main conclusion of the paper

As this paper was largely descriptive in nature, I am wary to try to define the main scientific conclusion. With regard to concrete discoveries, however, their data suggests quite strongly a single point of origin for the outbreak of Ebola virus disease (EVD) in Sierra Leone, involving two different strains of the virus introduced simultaneously. Additionally, they document with high fidelity possible transmission links between groups of patients.

More important is the demonstration of the utility and information density available through the types of rapid sequencing and analysis employed in this work. Although not a protocol paper, the authors have produced a technical tour de force with a great deal of insight into the disease dynamics involved in the recent Ebola outbreak. I am sure that, as sequencing costs continue their steep decline techniques of this sort will only become more common, and the community will begin to adopt standard practices for these types of studies.

This sort of adoption and standardization will have broad implications for the future of disease mitigation. Tempered by the human genome project’s underwhelming applicability to medical breakthroughs, I remain optimistic that as genetic data is more readily applied to patient treatment, it is likely that information of this kind will contribute to tangible medical interventions which will directly benefit patients around the world.

Graham Larue

The devil’s advocate

The paper mentioned that when the first Sierra Leone case of Ebola virus disease (EVD) was confirmed, the tracing led to 13 more sick females who attended the burial of a traditional healer. It was misleading to seem the females are more prone to contract the disease than the males because the gender ratio of the funeral attendees wasn’t provided.

It was informative but boring to read when a bunch of numbers were given like single nucleotide polymorphisms (SNPs) between the 2014 EBOV genome sequences and the previous EBOV outbreak, and the numbers of intrahost single nucleotide variant (iSNV) in Sierra Leone patients. The wording was a bit confusing sometimes. One ethical issue could be sequencing for other pathogens when the 35 EDV suspected cases turned out negative for EBOV.

Emily Chang

Make a graphical abstract of the paper

Nicolas Cole

Two tweets about the paper

Arturo Altamirano (@articluateartie)