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

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-Ian

Where the Guinea ebolaviruses hang in the jungle of the genus Ebolavirus

The 3 complete genomes from the NEJM article are boxed in pink.
Viruses that belong to the species Zaire ebolavirus, are boxed in blue
(including the Gueckedou and Kissidougou isolates).
With my thanks to Dr Stephan Gunther for providing these 3
genome sequences for this tree. Alignments were made using Geneious v6.1.6.
Neighbor-joining tree with 500 bootstraps made using Mega 6.06.
GenBank accession numbers are shown for each entry. Two representatives of the genus Marburgvirus are also included at the bottom of the tree.
Click on image to enlarge.

References...

1. Emergence of Zaire Ebola Virus Disease in Guinea — Preliminary Report
   http://www.nejm.org/doi/pdf/10.1056/NEJMoa1404505

Naming the new Zaire ebolavirus variants

The recent NEJM paper [1,2] on the Guinea Ebola outbreak listed 3 full genome sequences (detected from infected people using standard "Filioviridae-specific RT-PCR assays" and published "real-time RT-PCR assays targeting the glycoprotein (GP) or nucleoprotein (NP) gene".

My thanks to Dr Stephen Gunther for answering my email and giving permission to list these names. They should be on Genbank now he tells me (I have not found them as yet). We now know that these virus variants of the species Zaire ebolavirus are called:

• Ebola virus H.sapiens-wt/GIN/2014/Gueckedou-C05
  GenBank accession number: KJ660346, KJ660347 or KJ660348
• Ebola virus H.sapiens-wt/GIN/2014/Gueckedou-C07
  GenBank accession number: KJ660346, KJ660347 or KJ660348
• Ebola virus H.sapiens-wt/GIN/2014/Kissidougou-C15
  GenBank accession number: KJ660346, KJ660347 or KJ660348

See more one the way the Filioviridae Study Group prefers to name ebolaviruses in a recent post here.[2]

On the issue of whether these variants can still be detected using published diagnostic PCRs, the answer is yes they can (they were detected using them after all!). To look more closely at that, I aligned the 3 new full genomes and also the primer sequences for 2 diagnostic reverse-transcription real-time polymerase chain reaction (RT-rtPCR) assays mentioned in the NEJM article by Baize and colleagues [3,4]. They target the nucleoprotein (NP; [4]) region of the genome and the glycoprotein (GP; [3])

The two PCR assay regions targeting GP and NP PCR oligonucleotides
(primers and fluorogenic probes) primers. The yellow stars in the NP assay
highlight a 2 nucleotide mismatches between the forward primer or probe
(T in oligo, A in genome) and the 3 genomes. These shouldn't decrease
assay sensitivity too much at all.
Click on image to enlarge.

References...

1. Emergence of Zaire Ebola Virus Disease in Guinea — Preliminary Report
   http://www.nejm.org/doi/pdf/10.1056/NEJMoa1404505
2. http://virologydownunder.blogspot.com.au/2014/04/update-on-ebola-virus-disease-evd-case_17.html
3. Development and Evaluation of a Fluorogenic 5 ' Nuclease Assay To Detect and Differentiate between Ebola Virus Subtypes Zaire and Sudan | Gibb and colleagues | J Clin Microbiol. 2001 p4125-30
   http://jcm.asm.org/content/39/11/4125.full.pdf+html
4. Rapid detection of filoviruses by real-time TaqMan polymerase chain reaction assays.| Huang and colleagues | Virologica sinica 2012 p273-7
   http://www.ncbi.nlm.nih.gov/pubmed/23001480

Media MER muttering more than murmurs.

Ouch. Anyway, before you finish typing or reading that coronavirus outbreak story make sure it doesn't use the names human betacoronavirus 2c EMC, human betacoronavirus 2c England-Qatar, human betacoronavirus 2C Jordan-N3, betacoronavirus England 1 or (especially the short-sighted) novel coronavirus (NCoV)-they are so, like, yesterday's name. 

Prof Raoul J. de Groot and a host of coronavirus (CoV) experts, comprising the CoV Study Group, have penned a scientific article that has just been accepted into the Journal of Virology. The name of the newest spiky little killer is officially Middle East respiratory syndrome coronavirus or MERS-CoV for short. New variants (the same virus detected in other people/animals) will be given a name using the influenza virus naming system:

Virus name host/country of virus detection/variant identifier/year detected e.g. MERS-CoV Hu/Jordan-N3/2012).

That's as official as it gets anyway so this is how we should label it from here on in.

We're also avoiding calling it a human CoV until we know how humans get the infections. Since the virus is similar to a bat version one of many question is whether the cases all got it directly from bats (unlikely) or from human contact with another, intermediate, host. This builds on the media reports noted on 07.05.13.

It's an nHCoV, its an EMC...no...its MERS?

It was an unusual move that apparently required "a great deal of effort to find a name that all parties involved could agree on". Avian Flu Diary reports on a ScienceInsider article noting that the Coronavirus Study Group will propose an entirely new name for the latest human coronavirus type that seems to cause respiratory disease in humans and belongs to a new coronavirus species. 

Usually the International Committee on Taxonomy of Viruses (ICTV) doesn't fiddle around with naming below the level of species and the new human coronavirus type seems to be part of a group of viruses (including bat coronaviruses) that together will likely form a novel species. Do the bat viruses also cause respiratory syndrome in humans...or other animals? There is likely to be some (more) confusion caused by this name change, and it is very possible that the press will not strictly adhere to the new name any more than the old one (an argument that supports either side of the debate).

So far the virus has been called novel coronavirus (NCOV-a name that never should have stuck-what do we call the next one....more novel CoV?) and in the scientific, peer-reviewed literature, HCoV-EMC after the laboratory that characterized the virus (Erasmus Medical Center). Still, its only about 8 months since we learned of the first case subsequently attributed to this virus in Sept 2012 (the patient presented in June 2012). How big could the body of literature be on EMC at this point? Apparently its 23 papers strong according to PubMED.

The new name for the disease and the virus group will change to MERS-CoV (Middle East respiratory syndrome). It will next go before the ICTV for ratification.