Just yesterday I was reading about how metagenomics is proving to be a better choice for many questions than many traditional DNA amplification centric molecular techniques like many microarray and other PCR based approaches.
Metagenomics , which is a fancy way of saying ” sequence everything ” directly from the sample and then figure out what that everything is , now has another feather in its cap , the identification of the possible causative agent for the honeybee colony collapse disorder.
CCD is a scary disease which has been affecting bee populations across the US . CCD is the name given to the end result , a colony of bees collapses because almost its entire adult bee population essentially disappears. The collapsed hives have the queen bee and a few newly emerged adult bees and considering the social structure of bees the colony withers away.
Without bees there is no pollination and without pollination agriculture will suffer..and without agriculture ..well there will be no food. Scientists have therefore been struggling to find out why these colonies were collapsing and the bees disappearing ever since the first signs of CCD appeared in 2004.
In the paper by Cox-Foster et al in Science Magazine ( Science Express) scientists obtained by pyrosequencing DNA sequence data from CCD and non-CCD bees from the US and Australia as well as DNA from royal jelly from china . The strategy they followed was to first get all the sequence data from CCD and non-CCD bee pools and then look for unusual sequences for bacteria and viruses and other pathogens which may signal an infection. Once the sequence data was obtained they got some initial clues as to the component foreign sequences in these pools. The final pathogen quantitation was obtained by directing PCR primers designed using the asembled metagneomics derived sequence against RNA pools from both samples.
Of all candiate pathogens an as yet unclasified virus from the dicistroviridae family called the Israeli Acute Paralysis virus ( IAPV) was the only one found predomiantly in the CCD samples. The IAPV is a relative of the KBV ( Kashmir Bee virus) and ABPV ( Acute Bee Paralysis virus) and possibly represents an emergent virus that is causative agent of the colony collapse disorder.
This combination approach – i.e metagnomics to get at raw sequence data followed by precise diagnostic primers and QPCR is a powerful approach which I am sure will significantly cut down the time to identify the causative agents behind future emerging infections in all organisms including humans. The rate limiting step would be the time it takes to get the metageomic sequence data which promises to get shorter and shorter.
The paper in Science by Cox-Foster DL et. al.
Other feathers in the metagenomics cap in the sequencing of large segments of the Neanderthal genome