Sunday, 20 April 2014

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