Ebola could mutate as rapidly as the flu

© Science Magazine

The largest genomic data collected on the Ebola virus to date has been recently published in Science [1], giving unique insights on the origin and spread of the greatest Ebola outbreak so far.

The Ebola virus was first discovered in 1976, when it caused 318 cases: until now, it was the largest outbreak.

"The current outbreak started in February 2014 in Guinea, West Africa, and spread into Liberia in March, Sierra Leone in May, and Nigeria in late July. It is the largest known EVD outbreak and is expanding exponentially [1]."

In a recent Science paper [1], researchers sequenced 99 Ebola genomes from 78 patients from Sierra Leone. By analyzing the genetic make-up of the viral population, scientists can retrace the spread of the outbreak. It's a bit like looking at the DNA of a large group of people to find out who's related to whom. In the case of Ebola, we want to know if there was only one "parent", so to speak, or if there were several animal-to-human reinsertions.

According to the paper, the event that brought the virus to Sierra Leone at the end of May was the burial of a healer from Guinea who had treated Ebola patients. Local practices at funerals include touching and kissing the corpse, and given that Ebola can survive in a dead host for up to three days, you can see how a single funeral can infect dozens of people, especially when the dead is a popular healer as in this particular case. Thirteen cases were traced back to this funeral, two of which stemmed the outbreak in Sierra Leone.

The researchers analyzed the viral genomes using phylogenetic trees, a technique that enabled them to retrace the history of the virus.

"Phylogenetic comparison to all 20 genomes from earlier outbreaks suggests that the 2014 West African virus likely spread from central Africa within the past decade [1]."

They were able to see that the "ancestor" originated from a single transmission event back in February. This finding contradicts previous hypothesis that the unprecedented spread of the outbreak was due to multiple transmission events from animal to humans. Contrary to this hypothesis, after that first transmission, in which the virus jumped from animals to human back in February, Ebola has been spreading among people alone.

"Genetic similarity across the sequenced 2014 samples suggests a single transmission from the natural reservoir, followed by human-to-human transmission during the outbreak. Molecular dating places the common ancestor of all sequenced Guinea and Sierra Leone lineages around late February 2014, 3 months after the earliest suspected cases in Guinea; this coalescence would be unlikely had there been multiple transmissions from the natural reservoir [1]."

But the most interesting point (to me at least) that the paper addresses is the virus's mutation rate. Since viruses replicate quite rapidly, it's important to know how high is the chance that at every replication cycle, errors (i.e. mutations) are introduced. Rapidly mutating viruses have a greater chance to escape the immune system (see HIV, for example) and are also much harder to target with a vaccine. The Science paper claims that

"The observed substitution rate is roughly twice as high within the 2014 outbreak as between outbreaks [1]."

In fact, they estimate the mutation rate to be roughly the same as that of the seasonal flu, which, if confirmed, would greatly hamper the creation of a vaccine.

Unfortunately the odds are still against poor countries. I attended a talk this week where the speaker reported that while the mortality rate in the affected African countries is at 95%, in the Western world it drops down to 75-80%. This is due to prompt intervention, the use of serum from people who survived the infection (and hence developed good antibodies against the virus), and the use of IVs. Unfortunately, people living in the affected countries tend to be skeptical of westerners and, just like it happened with HIV, beliefs that Ebola is yet another virus introduced by Westerners to hurt the locals are rampant.

When I finished reading the Science paper, I was saddened to find this final paragraph:

"In memoriam: Tragically, five co-authors, who contributed greatly to public health and re- search efforts in Sierra Leone, contracted EVD and lost their battle with the disease before this manuscript could be published: Mohamed Fullah, Mbalu Fonnie, Alex Moigboi, Alice Kovoma, and S. Humarr Khan. We wish to honor their memory."

[1] Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang PP, Nekoui M, Colubri A, Coomber MR, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, Saffa S, Sellu J, Jalloh AA, Kovoma A, Koninga J, Mustapha I, Kargbo K, Foday M, Yillah M, Kanneh F, Robert W, Massally JL, Chapman SB, Bochicchio J, Murphy C, Nusbaum C, Young S, Birren BW, Grant DS, Scheiffelin JS, Lander ES, Happi C, Gevao SM, Gnirke A, Rambaut A, Garry RF, Khan SH, & Sabeti PC (2014). Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science (New York, N.Y.), 345 (6202), 1369-72 PMID: 25214632

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A mosaic vaccine that could potentially protect from different ebola strains

Disclaimer: The mosaic vaccine paper discussed in this article is from my own group and overlaps with some of the research I do. 

I'm sure you've been following the latest news about the Ebola virus outbreak in Africa.

"The Ebola outbreak in West Africa is the world's deadliest to date and the World Health Organization has declared an international health emergency as more than 1,000 people have died of the virus in Guinea, Liberia, Sierra Leone and Nigeria this year." [Source: BBC News]

The ebola virus was first described in 1976, with outbreaks reported starting from 1967 [3]. It's part of the Filovirus family and its natural reservoir is believed to be fruit bats, though there is evidence that it could be wider than we think. In fact, ebola can infect other animals like monkeys and pigs. Because the virus is transmitted through bodily fluids and it can survive for a few days after the host's death, it can be easily spread through the butchering and consumption of bushmeat.

You've probably heard from the news that two infected Americans were treated with "serum". Some headlines even dubbed it a "secret serum." The serum is actually no secret and has been used not just for ebola but also for other viruses like RSV [1]. The treatment, called passive transfer of antibodies (or antibody serum), is based on the transfer of antibody serum from one organism to another. The idea behind it is that the immune system of a person previously exposed to the virus has developed antibodies that can help other immunologically naive patients fight the infection. For the ebola virus, the therapy is still in the experimental phase and, up to these two patients, had only been tested in animals.

There are several vaccines currently being tested, each one at various experimental phases. Friedrich et al. [1] list a nice summary of all the current testing in their review. The one they do not mention in their review is a mosaic vaccine being developed by my group, which is based on ideas originally designed for an HIV vaccine.

What is a mosaic vaccine?

A vaccine is an attenuated form of a virus. Even though unable to start a full infection, when injected into the body, the attenuated virus is detected by the immune system, which can then mount the appropriate response and "create" neutralizing antibodies. Typically, the attenuated virus is created from the natural virus found in organisms.

And then came HIV and baffled everyone.

The problem with HIV is that every single HIV-infected person has a different virus. In order to protect from every possible infection, one would need to put into a vaccine the over half a million genetically distinct circulating strains. Clearly, that's not possible. How do you protect people from a viral population that's so diverse? Natural strains are no longer sufficient. You have to come up with clever ways to 'summarize' the whole population of viruses with just 2-3 viral strains.

That's when computers come in handy: the mosaic vaccine is a vaccine created in silico. Suppose you want to create one genetic sequence that "summarizes" all the genetic variants found in a population of 100 strains. The algorithm that creates the mosaic starts from the 100 strains and it literally reshuffles them bit by bit. The "bits" are not cut out randomly but in a way that, when reassembled in a full genome, the proteins are still functional and working. In other words, you want to make sure that after the reshuffling you still have functioning viruses. You repeat the reshuffling for a few times and at the end of the iterations you pick the one strain that best represents the original pool of 100 genomes.

HIV-1 mosaic vaccines have given great results in guinea pigs and monkeys. But what would be the advantage of using them for ebola?

If you are familiar with phylogenetics, you will certainly object that the two viruses (HIV and ebola) are quite different: while HIV spreads out in a star-like fashion (which translates into the fact that no two individuals have the same virus), ebola evolves more like the flu, with new emerging viruses causing new outbreaks. So, why would the mosaic vaccine help with ebola?

"While the techniques used here are very similar to those used for HIV-1 mosaic vaccine design, a pattern of repeated introductions of the filoviruses into humans (and primates generally) gives a crucial difference from HIV-1. HIV-1 shows great diversity within the pandemic, but that diversity has developed continuously, leaving intermediate isolates in its wake. In contrast, known filovirus diversity has episodically increased as new outbreaks are found to result from novel viruses, lacking intermediates." [3]

The fact that the ebola virus "lacks intermediates" seems to indicate that there are reservoirs that we don't know of where the virus accumulates diversity. This is worrisome: we not only need to protect from the current outbreaks, but also be prepared for new viruses that might emerge in the future. In [3], Fenimore et al show how the mosaic algorithm can be readapted from HIV to ebola, accounting for the evolutionary differences between the two viruses.

A mosaic vaccine would protect from all ebola subspecies and also against new strains that could potentially develop from the current outbreaks. The problem with ebola is that its reservoir could be wider than we think. The viral diversity found in bats has not matched the diversity of the ebola strains found in humans. So, where are the new viruses coming from? There are likely pockets of diversity that come from reservoirs we don't know of.

"The implication is that a vaccine against the filoviruses should strive for good coverage of common epitopes from the maximum number of types and strains currently available, in the hope that future outbreaks will retain these elements, so the vaccine will still be effective when challenged by a novel strain in a new outbreak." [3]

The authors tested the ebola mosaic vaccine on a mouse model and compared it with a vaccine created with a single natural strain from Zaire. All vaccinated mice in either group (mosaic or natural) survived the challenge. The natural strain vaccine provided 82.8% coverage of other Zaire strains, but only 14.0% coverage of non-Zaire strains. On the other hand, the single mosaic vaccine provided 54.7% coverage of other Zaire strains (still sufficient to protect the mice from infection) and 23.2% coverage of non-Zaire ebola virus strains, proving that a mosaic can indeed improve protection against different subtypes. Furthermore, comparing a cocktail of a two-mosaic vaccine with a two-protein natural cocktail and a vaccine that was previously tested in macaques (Hensley et al., 2010), the mosaic cocktail achieved the highest coverage.


[1] Friedrich BM, Trefry JC, Biggins JE, Hensley LE, Honko AN, Smith DR, & Olinger GG (2012). Potential vaccines and post-exposure treatments for filovirus infections. Viruses, 4 (9), 1619-50 PMID: 23170176

[2] Fischer W, Perkins S, Theiler J, Bhattacharya T, Yusim K, Funkhouser R, Kuiken C, Haynes B, Letvin NL, Walker BD, Hahn BH, & Korber BT (2007). Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants. Nature medicine, 13 (1), 100-6 PMID: 17187074

[3] Fenimore PW, Muhammad MA, Fischer WM, Foley BT, Bakken RR, Thurmond JR, Yusim K, Yoon H, Parker M, Hart MK, Dye JM, Korber B, & Kuiken C (2012). Designing and testing broadly-protective filoviral vaccines optimized for cytotoxic T-lymphocyte epitope coverage. PloS one, 7 (10) PMID: 23056184