One common problem in public health
is the detection of pathogenic organisms, so it could be considered as a
critical component in public health diagnosis. Thus, viruses detection and
identification in clinical samples is always complicated. Traditionally, culture
isolations and electron microscopy methods were used in order to find virus
identity, but these common techniques have been replaced with PCR and other
molecular tools. However, the problem with our attempts of identifying viruses is that these don't present ubiquitous characteristics,
similar to ribosomal DNA in organisms; consequently, there isn't an universal protocol to diagnose and track
viruses, and with the usage of different methods different viruses are
described.
Svaraka and its team tried, in 2010,
to propose a tool to diagnose viruses in clinical samples. They used
metagenomic analysis in samples collected by EVS program in Netherlands, which
goal was the detection of poliovirus circulation among Netherlands' hospitals.
About the method suggested, metagenomics was amply used in the detection of
different environmental samples , principally in the searching of Bacteria as
pollution indicators or its ecological roles. The scientific team suggested
this method due to its powerful detection of complete sequences from genomes of
a sample, then it overcomes some limitations from other methods like too
specificity in PCR (specific and global sequences that viruses don't present)
and difficulties on isolation certain viruses.
Investigators found some interesting
results. Firstly, it was suggested to use an method to separate viral fraction
from all the sample because virus represents only a fraction from the microbial
community and this analysis must be focused only in virus sequences. Secondly, sequences
from different types of viruses were detected, from Enterovirus, detected with
traditional methods, to new and scarce viruses at that moment like Saffold
Viruses (SAFV). Third, complete sequences of all viruses, especially those
which are new non-identified, were able to be related toward phylogeny to known
viruses and make predictions such as if they are pathogenic or possibly
pathogenic for humans. Finally, metagenomics provides large amounts of data
which could be used on the study of proteins involved in the pathogenicity of
certain viruses.
In conclusion, metagenomic is a
powerful tool for virus detection in clinical samples. This method, could deal
with the limitations in other molecular and traditional diagnosis techniques.
Furthermore, the most notable implications is that sequencing technology is
becoming more and more cheaper everyday, and it could be applied to distinct
samples like feces, blood, cell cultures and more.
References
Svraka, S., Rosario, K., Duizer, E.,
van der Avoort, H., Breitbart, M., & Koopmans, M. (2010). Metagenomic
sequencing for virus identification in a public-health setting. Journal
of General Virology, 91(11), 2846-2856.
