The Ebola outbreak of 2014 (Contd.)

Following up on the previous post here are some more detail on the recent Science paper along with a round-up of “what do we know, what have we learned” thus far.

The Gire et al paper in Science was huge amount of work and a giant collaborative research effort. Being a computational biology researcher, I appreciate their in-depth and detailed evaluation utilizing numerous bioinformatics software tools. Gleaning through the supplemental text, I created the flowchart below as a summary of all the analysis that went into the eventual results and interpretations. This was created using the wonderful Gliffy tool.

ebolaFlowchart of the impressive work accomplished by the Gire et al Science paper (I made this using notes from their Supplemental Data)

A slew of articles summarizing the recent Science paper came out as the hype surrounding WHO warning of this current outbreak hitting 20,000 people caught on. This is huge!! Peter Piot, who co-discovered the Ebola virus during the 1976 outbreak never imagined an outbreak like this, but is confident of ‘high-income countries’ doing just fine.

The Broad Institute and Harvard University worked with Sierra Leone Ministry of Health and Sanitation along with other researchers to provide the comprehensive paper in Science describing the sequencing of current Ebola genomes. Simultaneously, the human trial on NIH and GSK’s investigational Ebola vaccine is to begin this week, as it performed well on primate studies. Hopefully this one will be faster than the usual 10-year turn-around observed for a vaccine trial. Although the experimental drug ZMapp is being used on the cases, it is with mixed results and much and more still needs to be done. Interestingly the drug is a three-mouse monoclonal antibody and the primate research itself was published in Nature last week. Details of how it seemed to have worked on the 2 US health care workers in the midst of this outbreak is a pretty ‘miraculous’ story!

The major points to note thus far:

  • First Ebola Virus Disease of 2014 confirmed in Sierra Leone on May 25
  • It seems like there was one instance of the EBOV transmitting from the ‘natural reservoir’ to humans and has since been transmitted from human to human (implying there is rare, though present, chance of non-human transmission)
  • Substitution rate is twice as high implying that continued progression of this epidemic could allow a viral adaptation, thus the need for rapid containment
  • The 2014 outbreak has a doubling period of about 35 days!!
  • Complicating matters, positive diagnosis for malaria does not necessarily rule out Ebola Virus Disease
  • Senegal just became the 5th West African country with a confirmed case of Ebola
  • Breaking News: samples from Ebola outbreak in Congo (DRC) were evaluated to have a distinct and independent transmission event, likely via a bushmeat consumption!

Hopefully this is contained sooner rather than later…

Solving the Ebola Virus Genome and Identifying Possible Diagnosis

If you have ever played the card game Killer Bunnies and your Bunnies in the Bunny circle have died because of the Level 11 Weapon of Ebola Virus you want to read this.

047_The_Ebola_Virus-thumbnail

Research community is making strides to understand whether the virus is adapting to its host or changing as it spreads through the different populations as more countries get in its warp, in West Africa.

5 of the 50 co-authors on this Science article were infected with the deadly Zaire Ebola Virus (EBOV) themselves. Nothing short of a thriller, the events trace back to the funeral of a healer which kick-started the spread of Ebola in the region. Also reviewed here is a paper from 2008 in which the authors have pointed the VP35 protein, which during their experiments was identified as a critical component of this hemorrhagic fever.

Ebola’s genomic sequence:

  • Linear, single-stranded genome
  • Inverse-complementary 3′ and 5′ termini
  • ~19 kb (19 thousand nucleotides long compared to 3 billion human genome)
  • Seven genes (compared to ~20k in humans)

The current outbreak is due to the EBOV virus, one of the five Ebola virus known to infect humans. Research groups are trying to identify whether the genetic sequence of this virus is changing fast enough in regions that are key for the accuracy of the PCR based diagnostic tests.

This EBOV virus in the 2014 epidemic has been reported to be 97% similar to the virus that first emerged in 1976. Articles across the web estimate that EBOV is set to evolve at about 7×10-4 substitutions per site per year suggesting that the current strain of EBOV would have accumulated many substitutions over the 40 year time period since 1976.

In this article Gire et al use genomic data and inferences by using next generation sequencing technologies to explain whether the virus is accumulating significant mutations as it changes hosts.

  • Methods compared to ascertain choice for sequencing:
    • Library preparation: Nugen and Nextera
    • Sequencing instruments: PacBio and Illumina
  • Nextera and Illumina provided most complete genome assembly and intrahost SNV identification
  • 99 virus genomes, 78 patients in Sierra Leone sequenced at a median coverage >2,000x across 99.9% of EBOV coding regions
  • Intra and Interhost genetic variations to characterize transmission patterns
  • 341 fixed substitutions identified between previous and 2014 EBOV
    • 35 nonsynonymous, 173 synonymous, 133 noncoding
  • 55 single nucleotide polymorphisms (SNPs) among this West African outbreak
    • 15 nonsynonymous, 25 synonymous, 15 noncoding
  • Genetic similarity across sequenced 2014 samples suggests single transmission

 

Josh Herr of Michigan State University and Daniel Park of Broad Institute aim to maintain an analysis wiki for solving the underlying genomic riddle, by studying the different strains of the virus and are encouraging contributors (ebola-crowdsource).

Screen shot 2014-08-30 at 8.01.22 PM

In an earlier paper published in Journal of Virology in 2008, Hartman et al discuss how whole genome expression profiling reveals that the innate immune response of the host can be inhibited and reversed by single amino acid change in VP35 Protein.

  • Two reverse genetic-generated Ebola virus strains
    • Encode wild-type VP35 protein or VP35 with an arginine (R)-to-alanine (A) amino acid substitution at position 312
  • Whole-genome expression profiling of the host cells in human liver
  • Host cells reveal differences in response to introduction of these viruses differing by a single amino acid
  • VP35 protein plays a vital role in inhibiting immune responses of the host
  • Single amino acid change exhibits the ability to eliminate this inhibitory effect
  • VP35 Protein demonstrates a critical role in the severity of the disease

 

Dr. Lipkin professor of epidemiology at the Columbia University discusses a pertinent question of whether ‘Ebola can travel to the United States’ . He explains in a matter-of-fact way that although there is a possibility of the virus traveling to US like anywhere else, there’s also a high likelihood of it being monitored and isolated by health authorities at the earliest possible.

Lets get to a round of that card game now, shall we.