Wednesday, 13 August 2014

Behind the naming of ebolaviruses... [UPDATE 2]

Just don't call me a taxi
Virus taxonomy is the classification of viruses into groups based on similarities. 

Today classification is supported by viral gene and genome sequence information.

The International Committee on Taxonomy of Viruses (ICTV) takes care of the official virus taxonomy. It has a pretty friendly website with a good search engine and the latest (2013 at writing) virus taxonomy can be found here. [1]

So what does it, and its tome, Virus Taxonomy, Ninth Report of the International Committee on Taxonomy of Viruses [2], have to say about ebolaviruses? Well, not as much as you might like, if you want to be able to name them, talk conversationally about them and discuss the issues around the disease resulting from infection by most of them. Sure, you can just call it all "Ebola" (which is a river in Africa by the way) and be done with it, but you'd be wrong. And some smart alec will correct you for sure. Here is where the ICTV Filoviridae Study Group fills in a lot of blanks.

One thing to get on top of first up. When talking or writing about these    looking little pathogens, we can just call lump them together under the conversational term "ebolaviruses" thus..."Hey Jeanette, did you hear about the latest ebolavirus infection numbers over the weekend?" is a question that could refer to any of the 5 very different viruses.

So, let's try and make that tearoom conversation a little more accurate.

The very dry detailed stuff down to the level of a species.

The italicization and the capitalization below are really important to taxonomy guys - so, ya know, care

Also, the ICTV reminds us that the name of the species is not the name of a virus - they are 2 different things. The species is a broad term for all the measurably different viruses out in the wild, that it contains. Here, species is to viruses what Mitsubishi Sigma is to identifying my old car. A virus name,

e.g. Ebola virus (see below), is like identifying my car as "a silver 1988 Mitsubishi Sigma". 

What if we used taxonomy on cars? A different way to explain how to name ebolaviruses.
Click to enlarge


The viruses we are talking about here belong to the order Mononegavirales, family Filoviridae, genus Ebolavirus. 

There are 5 species within the genus. The species names are in italics below. Underneath is the name of the virus (the virus belongs to the species container) and its abbreviation. The viruses in bold have caused outbreaks of human disease.
  • Taï Forest ebolavirus
    • Taï Forest virus (TAFV)
  • Reston ebolavirus
    • Reston virus (RESTV)
  • Sudan ebolavirus
    • Sudan virus (SUDV)
  • Zaire ebolavirus
    • Ebola virus (EBOV)
  • Bundibugyo ebolavirus
    • Bundibugyo virus (BDBV)

But what should I call the latest ebolavirus strain, variant, genotype, subtype, serotype, isolate thingy?


In the case of the current outbreak, that latest virus is an Ebola virus (EBOV), which we can now say belongs to the species Zaire ebolavirus (a Mitsubishi Sigma). 


But back to the car analogy. The silver 1989 Mitsubishi Sigma name is still not enough to tell it apart from any other silver Mitsubishi Sigma parked at the same shopping centre. How do you choose yours in a way that won't get you arrested for breaking into someone else's car? They both look like silver Mitsubishi Sigmas. But the silver Mitsubishi Sigma with license plate ABC 321 is yours and your alone, and that code differentiates your car from any other anywhere in the world.


We know from genome sequencing studies that the virus circulating in Guinea is an EBOV (a silver Mitsubishi Sigma) and is not identical to the one in (what was called) Zaire in 1976 (this silver Mitsubishi Sigma car has a different license plate). They couldn't be the same physical virus anyway, because each person hosts millions and millions of virions, each cell has a varied population of viruses in it, and each virion has a relatively short life. 

There is no universal definition for classification of viruses below the level of a species. But there are lots of terms that are used - most are listed in the heading to this section. In filovirus-land, the Study Group has sought to impart some order upon the chaos [3]. 


A virus strain needs to have 1 or more observable, genetically stable and unique differences compared to other viruses in the same species. For instance, one might cause a disease that is different from the one we know. So apart from a different license plate, it might also have an Awesome Mix #1 CD in the tray. 


From Kuhn et al.[5]
Viruses  2014, 6(11), 4760-4799
Click on image to enlarge.
variant has some genetic sequence or other differences that may result in a slightly different observable change. The West African EBOV is a variant and not a strain of Zaire ebolavirus and was named after the Makona river (see figure) which makes contact with all three countries that have had widespread and intense transmission.[5] For example, these from Guinea and Sierra Leone:

A virus isolate is a virus sample resulting from growing or culturing it in cells or tissues. Variants can therefore be represented by isolates. These isolates can be identical or slightly different (your neighbour could order the exact same car as you did-but he would still have a different license plate and no bobble-heads and fluffy dice).

The naming schemes do go into further detail, but you can read that in [3].

The disease.

The disease caused by EBOV, SUDV, TAFV and BDBV is called Ebola virus disease (EVD). Frankly, that is a tough one to explain after all of the above. It reads as though we are talking about just 1 virus causing disease (EBOV). But not so. Viruses from 4 species cause EVD - EBOV, SUDV, TAFV and BDBV. Diseases are named by World Health Organization's International Classification of Diseases (ICD) site, (4) and the name of this disease goes back many years and has not been updated yet. The disease has been called Ebola haemorrhagic fever, but is not now. Ebola virus disease is, by itself, a proper noun - that is its name - so it always gets the capital 'E'. And to continue from the taxonomy above, EVD is caused by a virus that can be ascribed to a species. In West Africa right now, EVD is due to infection by an Ebola virus variant classified in the species  Zaire ebolavirus.

Navigating a tree in the ebolavirus jungle.

Lastly, I've cobbled together a tree of genomes from each of the 5 ebolavirus species. It may help. Or not.


A phylogenetic tree of some genome sequences of the 5 species of ebolavirus, each indicated with a specific coloured dot.

References...
  1. ICTV Virus Taxonomy: 2013 Release
    http://www.ictvonline.org/virusTaxonomy.asp
  2. Ebola virus disease World Helath Organization fact sheet
    http://www.who.int/mediacentre/factsheets/fs103/en/
  3. Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae.Arch Virol (2013) 158:301–311.
    http://download.springer.com/static/pdf/619/art%253A10.1007%252Fs00705-012-1454-0.pdf?auth66=1408093824_af9d701ab93574066469a6f6745c11d7&ext=.pdf
  4. International Classification of Diseases (ICD)
    http://www.who.int/classifications/icd/en/
  5. Nomenclature- and Database-Compatible Names for the Two Ebola Virus Variants that Emerged in Guinea and the Democratic Republic of the Congo in 2014
    http://www.mdpi.com/1999-4915/6/11/4760
Updates...
  1. 05AUG2015: Added comment about Ebola virus disease being a proper noun

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