RNA-seq can detect Zika with high sensitivity and specificity for ~$2k per sample

Posted on February 17th, 2016 Dan

I’ve been following this sham closely and it seems to be moving forward in spite of the preliminary data

Zika can be detected easily using RiboNucleic Acid SEQuencing on Illumina platform.  RNA, comprising “the transcriptome” is a molecule transcribed from Deoxyribo Nucleic Acid or DNA in cells. When genes are expressed (creating proteins from RNAs), that involves production of RNAs, which are themselves made from special sequences of amino acids. Most viruses contain at least RNA and proteins, which they use to reverse-transcribe or insert themselves into the DNA of cells.  These unique sequences of amino acids in RNA can be positively identified with a high degree of precision- including known viruses such as Zika.

Give me flash frozen tissue, blood and/or fluid samples stored at -80c (RNA degrades rapidly), and I’ll tell you with high accuracy using RNA-seq whether there is any Zika virus in it. I’ve seen hundreds of viruses from HIV to cucumber viruses to rabbit herpes to mouse leukemia viruses to HPV, in every single RNA seq library I’ve ever looked at, across a whole range of tissues, and never once have I seen a single fragment of Zika.

Sometimes you will see one fragment of HIV. That person has HIV.  Will they develop AIDS?  I don’t know.  But the point is, RNA-seq is more sensitive and specific than antibody tests and broader than electron microscopy.  I can confirm presence of the virus from a single virus particle in a large sample. Electron microscopy can only look at a handful of cells. I can examine millions using sequencing.  RNA-seq is by far the most accurate virus test available.

Now I know what you’re thinking- If you’ve never seen Zika before in samples, how do you know you can detect it?  Simple- we’ll order ourselves a Zika sample from ATCC and do a positive control. What I’m describing is well known technology.  Most viruses contain RNA, including Zika. RNA-seq can detect it reliably for ~$2000 per sample.

The bottom line is there really is no need to freak out and get a Zika vaccine, because the virus is most likely not very pathogenic or widespread, but if we want to be sure this is how to proceed.  My contact information is in the sidebar.   Happy mosquito hunting.


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