New Ebola case in Sierra Leone - additional information and sequencing?

By now you have probably all heard about the new Ebola case in Sierra Leone:

This is devastating news since Sierra Leone has been Ebola-free for quite some time (last case Sep. 13, Bombali; last case in Kambia Sep. 9). Given that this appears to be a male case that came from the border region with Guinea (Kambia - although he died in Tonkolili) the question is whether this is a lingering transmission chain from Sierra Leone/Guinea or resurgence from a survivor (as has been observed in Liberia). I am leaning towards lingering transmission, since the last reported case was Oct. 29 in Forecariah, Guinea, which is <50 miles from Kambia and on the same main road. For sexual transmission the case would also likely have to be female.

It will be important to distinguish between the two scenarios since a lingering transmission chain would likely have several more cases, whereas survivor transmission could be limited to this single case. Does anybody have any additional information on this case? Sequencing information would also be critical as that should allow us to distinguish between the two scenarios.

@arambaut just pointed out to me that the case is likely a female student (BBC got it wrong):

This changes the balance towards sexual transmission similar to what has been observed previously in Liberia. Sequencing should give a definitive answer.

Totally agree with your assessments! Yes a woman makes the sexual transmission scenario a bit more likely.

Sequencing will tell the tale.

Turns out that all the little “nuances” of virus evolution, adaption etc that the good old boys in the field can’t seem to grasp are important.

This is a real downer. But I’m glad IG’s team is fast on it.

Here are some possible scenarios that the sequence result can distinguish between:

  1. Lingering/hidden transmission chain within Sierra Leone. It should be pretty clear phylogenetically in that it wouldn’t look like any of the below scenarios.
  2. Lingering/hidden transmission chain within Guinea, popping over to Sierra Leone. The most recent Guinean sequences (including Oct 24, 2015 from Forecariah via Nick Loman) fall in a distinct clade, so this should stick out pretty clearly.
  3. Really lingering/hidden transmission chain within Guinea. If this thing ends up being “Lineage A”, I’d be pretty upset: that would underscore how underreported and undersampled Guinea is as a whole.
  4. Sexual transmission. This would look like a strangely low substitution rate as we’ve seen in Liberia before.
  5. New zoonosis (genome doesn’t fall under the original Baize et al sequences). While I would’ve said this was less likely in the past, at some point, as the epidemic truly dies off, it’s inevitable that we’ll encounter this one day.

My guess is #2 or #4.

How long does an Ion Torrent run take?


More thoughts on why this matters in terms of informing response. The implications of the sequencing result would be:

  1. Would necessitate a strong epidemiological investigation by SL MOHS.
  2. Would necessitate a strong epidemiological investigation by Guinean MOH.
  3. Would require a serious and fundamentally different approach in Guinea and point to some big deficiencies in what’s happening there.
  4. Would imply a general lesson of continued vigilance in all countries with survivors, especially male ones (incl US/UK).
  5. Would mean we need to dump resources into ecological studies sooner than later.

Nice summary - FWIW I would think #4 is the most likely. At the start of doing the real-time surveillance we detected a few cases which looked linked from Kambia in SL and Forecariah in Guinea. We haven’t seen this since March-April 2015. Of course that doesn’t mean it couldn’t have happened this time.

As you say, sequencing should reveal the answer!

Ion Torrent only takes a few hours. Apparently sequencing is done and worked well. Critical issue now is uploading the data to Sanger for assembly - the internet connection is being extremely problematic.

Do they have a Mac/Linux box available? A reference-based mapping approach would give them a high quality consensus and should be easy to do locally - wouldn’t take long with Novoalign.

That’s right - do it old school, call the SNPs by eye and shout them down the phone!

Any update on the sequencing from this important case?