1793 viruses!
In case you missed it, I spent ten days in hospital this past May (2013).
When they took the skin biopsy from my arm, I got them to take 2 samples. One of them, along with a throat and skin swab was later sent to the virologists I do some work with in the Viroscience Lab at the Erasmus Medical Center (EMC).
I got the sequence data back about a week ago and have been looking at them, firstly via BLAST and then using a bunch of code I’ve been writing lately. There are 115K reads from 6 preparations (RNA and DNA protocols for each of the 3 samples). These come from a “next generation” sequencer, a Roche 454. The next generation sequencing involves using random primers to indiscriminately match genetic material. My BLAST output files are about 82Mb in total (this is relatively small, some of my other data sets are about 30Gb). I BLASTed against a viral subset alias nucleotide database that I made from the full NCBI Nucleotide Database, excluding all bacteriophage viruses. There are about 1.3M viral sequences in the subset db.
I wont go into details, but wanted to dump a bit of data that’s pretty amusing / interesting. Just to give the EMC folks an idea of the scale of diversity I am seeing, I grepped out all “complete genome” hits from all the BLAST output. I chucked out suffixes in the sequence titles that matched the regex (nearly )?complete genome|isolate|strain|subtype).* and then stripped the titles of any text beyond the string “virus” in the title (this step collapses a lot of virus strain information that should really be kept). Then, do a unique sort and…. it turns out I have reads matching at least 1793 viruses.
I feel like the subject of a metagenomics study. At the hospital, once the chickenpox tests had come back negative, they threw a ton of tests at my samples and everything was negative. Otherwise, I’d really be worried :-)
Given the list of sequence matches, it feels like the only plausible explanation is that I’m actually dead and that this is all just a simulation.
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July 30th, 2013 at 9:48 pm
Glad to know you are still alive or at least being simulated on the same model into which I am projected.
It’s not unlikely that you matched all that large list, because of a highly conserved sequence stretches.
If I’d look up matches to my mitochondrial genome, I’d probably come to the conclusion that there is a blue whale inside my epidermis. XD
July 30th, 2013 at 9:54 pm
Hey Axel! :-)
Yes, you’re right. I just found it amusing to hit so many things. I haven’t had time to write more code to look everything up, but in previous data sets (and in the pieces of mine I’ve looked at) there are indeed many instances of hits against things like ribosomal RNA and polymerases and nothing else at all in the matched sequence. I do still find it interesting and don’t really understand it all, but it’s clear that a huge number of the cases (possibly all) can be ignored. I just have to figure out which ones…
Are you in Barcelona at all before Sept? I’ll be there Aug 8-19.
July 30th, 2013 at 10:18 pm
I just read about your rash in May and, wow!
Lucy had mentioned it briefly, but I didn’t realize it had been so serious and such a scary nightmare!
I’ll be in BCN from 9th to 23rd.
August 9th, 2013 at 4:59 am
Hey, this looks like you have ROCKY MOUNTAIN SPOTTED FEVER. I find it surprising that they tested you for everything under the sun.. and most of which is very unlikely for you to have, such as plant virus’s and such. I got a kick out of them testing you for Rabies because it can’t be tested unless they take a sample of your brain tissue.. THIS IS KNOW FOR FACT… So obviously they didn’t do that to you if your still breathing right now… LOL… So either your list here is bogus or your doctor is a quack and I suggest you run now. I find it strange that they didn’t test you for tick borne illnesses such as Lyme and RMSF. Lyme testing is tricky.. many tests aren’t accurate for Lyme’s unless you have a western blot. I’d put money that you have RMSF… but.. hey… I’m not a doctor.. what do I know???