Metagenomic virus detection in clinical specimens : a new era

As seen in this Chinese doll picture, the organisms in our nature is not only they look like, they live in an intermingling fashion, which calls for the whole study of them , or the Metagenomics. With the advancement of newer sequencing methods, the area of metagenomics has largely expanded, or on the other way, the broad-range studies of microorganisms in genetic level has geared up the newer and newer inventions of high-throughput sequencing systems. Okay, what it is, Metagenomics is a beautiful study, nothings less important here.

But when we come to the world of viruses, they are not the main ones in the environmental pool. Sure they are present there, but the main sphere of viruses are living cells as they only live well in intracellular condition. In many cases, viruses enter in a body, replicate here, fight with each other or live in peace, spread infections, and when they are shed, from the host body, they are not the same, they have mutated and changed by this time. This made the theory of Quasispecies. So, the environmental study of metagenomics can not be applied here.

Another matter is the studies of Zoonosis. Everyday, there is a new evidence coming out, about, this or that newly emerged disease has come from this or that animals. When a case is found, with no former case, its very difficult to find out the causative agent. So, the specific and effective study of Metagenomics from clinical sample is very important.

This study comes forward with a very new method, tissue-based unbiased virus detection for viral metagenomics (TUViD-VM). Formerly there were many methods available for viral metagenomic study as Hybridization, Sequence independent single primer amplification( SISPA), Arbitrary primed PCR (AP-PCR), Rolling circle amplification etc. This study group from Robert Koch Institute, Germany, not only established a new protocol, but also have shown the efficacy very well.

Schematic description of tissue-based universal virus detection for viral metagenomics protocol. Estimated durations of each step are shown in parentheses. The protocol takes 12 h to complete

This study compared the protocol in different virus groups, different hosts, different extraction, PCR and sequencing methods. The only limitation of this study might be the higher cost for sample processing. It also need high capacity computational analyses as both the viral and host genomes are mixed in a clinical sample gene pool. The researchers nullified the constrain, as sequence data for mammalian hosts are very limited.

This study opened a new era of viral study. Where a newly emerged disease call for an outbreak, and we find nothing in our hands to search the causative agent, as we saw for Ebola just a few days earlier, an established protocol of tissue based viral metagenomics can  help a lot!

Links : http://wwwnc.cdc.gov/eid/article/21/1/14-0766_article

            http://onlinelibrary.wiley.com/doi/10.1002/rmv.532/abstract

also posted at : http://www.sciencenutshell.com/metagenomic-virus-detection-clinical-specimens-new-era/

Advertisements

5 thoughts on “Metagenomic virus detection in clinical specimens : a new era

  1. thanks for putting this on your blog Sadia. you have managed to write something very complex in such a readable way that even non-scientists like me can understand and find interesting!
    Debbie

    Like

  2. really?? I thought I made it complicated! actually these all are quite new to me as well! I told my little brother about you “mao-bi” blog, and prawn-crab soldiers.. we enjoyed it! you write things more nice way than me

    Like

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s