Phylogeography of 2014-2015 Ebola virus epidemic


Being even more serious - the big problem with pathogen discovery studies in the past have just been the lack of sensible negative controls! But PCR studies are potentially even worse than sequencing because of false positives from mispriming and contamination from stuff being handled in the lab. Sequencing data at least lets you know you are on-target, and the sequence information helps you clue into whether you are looking at a natural population.

What would be nice about the field sequencing is that over time you’d build a nice picture of what is intrinsic to host, what is environment and what is reagent contamination. But yes, in the wrong hands I dread to think what you’d find :slight_smile:


What you’d find? Even more platypus I suspect - or maybe opossum…

Since we’re being all serious, I totally agree on all these points. At the Broad we sequenced 48 healthy individuals 2 months after having completed our Ebola sequencing. What turned up in all samples? You guessed it - Ebola.

It’s amazing what a simple water control can tell you though and is definitely something that needs to be done every single time. Low input seems to be the main issue with contaminants cropping up - used to be Pseudomonas, the it was E. coli, then Bradyrhizobium (the ones causing colitis…), but now it seems to be some weird viruses. Changes all the time.

Being able to do in-field sequencing using disposable reagents and equipment would be a big leap forward. @ig299 has a Sequencing Tent, I want a Sequencing Truck!