There are only a few places in the world where polio is still endemic. Polio normally infects the gut and is usually asymptomatic, but sometimes spreads to the nervous system and causes acute flaccid paralysis (AFP).  In South Asia, AFP keeps cropping up, but it turns out many of these cases are not being caused by poliovirus.  So what is causing these cases of AFP?  A recent study did a metagenomic analysis of the virus population from stool samples from AFP cases in Pakistan.  Metagenomics is an approach where you can sequence all the nucleic acid from a particular sample to see whats there.  In this case they filtered samples to remove cells, digested the filtrate with nucleases to destroy free nucleic acids, leaving them with the genetic material of viruses in their protective capsids.

They found lots of bacteriophages (presumably infecting gut bacteria), lots of plant viruses (probably from eating veggies), and lots of animal viruses.  They identified a new genus of picornaviruses, closely related to poliovirus.  This new genus, which they called Cosavirus, appears to be highly prevalent in samples from Pakistan but not in samples from the UK.  But is it the cause of AFP?  Its found in 49% of AFP cases and in 44% of healthy controls.  So are healthy controls asymptomatic infections, like we see in polio?  Are there other causes for the other 51% of AFP cases? Lots of questions obviously remain in understanding the epidemiology of AFP here, but this study is a good start and a very practical application of metagenomics for virus discovery.