A highly prevalent and genetically diversified Picornaviridae genus in South Asian children

Abstract

Viral metagenomics focused on particle-protected nucleic acids was used on the stools of South Asian children with nonpolio acute flaccid paralysis (AFP). We identified sequences distantly related to Seneca Valley virus and cardioviruses that were then used as genetic footholds to characterize multiple viral species within a previously unreported genus of the Picornaviridae family. The picornaviruses were detected in the stools of >40% of AFP and healthy Pakistani children. A genetically diverse and highly prevalent enteric viral infection, characteristics similar to the Enterovirus genus, was therefore identified substantially expanding the genetic diversity of the RNA viral flora commonly found in children.Cardiovirus ͉ Cosavirus ͉ metagenomics ͉ Picornavirus ͉ polio M etagenomics analyses have revealed a high degree of microbial genetic diversity in environmental and human samples. Human stool, containing numerous bacteriophages and plant viruses (1, 2), also appears to be a readily accessible source of novel eukaryotic viruses (3). Stools from children with acute flaccid paralysis (AFP) are being systematically analyzed by using cell cultures to identify and control remaining foci of poliovirus in 4 endemic countries (www.who.int/ immunizationmonitoring/laboratorypolio/en/index.html and www.polioeradication.org/content/general/infectedistricts.pdf). Inoculated cell cultures from nonpolio AFP cases show the presence of other, nonpoliovirus, human enteroviruses (HEVs) (4, 5), some serotypes of which have been associated with neurological symptoms. Because HEVs are detected in less than half of the nonpolio AFP cases a majority of these cases remain without a potential etiological agent. To characterize the viruses circulating in this population we used viral particle nucleic acid purification and limited shotgun sequencing, a method initially reported for animal viruses by Allander et al. (6) and extensively used for environmental viral metagenomics (7-9). We genetically characterized multiple picornavirus species (themselves diversified into serotypes) belonging to a previously unreported genus of the Picornaviridae family. Members of this genus were detected in the stools of nearly half of the AFP and healthy children. This high level of viral genetic diversity and prevalence, reminiscent of that observed for HEV infections, indicate that this genus of picornaviruses has the potential to be involved in a variety of diseases. Results Metagenomic Identification and Sequencing of a Highly DivergentPicornavirus. Stool samples from cases of nonpolio AFP were analyzed by using a simple viral particle nucleic acid purification method involving filtration at 450 nm and DNA and RNA nuclease treatment to reduce contamination from bacteria, eukaryotic cells, and nonviral capsid protected nucleic acids. Extracted viral nucleic acids where then amplified in a sequenceindependent manner by using 3Ј randomized oligonucleotides for reverse transcription, Klenow fragment DNA polymerase extension, and PCR. Amplified DNA libr...

Characterization of a canine homolog of hepatitis C virus

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Two Closely Related Novel Picornaviruses in Cattle and Sheep in Hungary from 2008 to 2009, Proposed as Members of a New Genus in the Family Picornaviridae

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Non-Polio Enteroviruses, the Neglected and Emerging Human Pathogens:Are we Waiting for the Sizzling Enterovirus Volcano to Erupt?

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