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Journal of Virology, May 2009, p. 4642-4651, Vol. 83, No. 9
0022-538X/09/$08.00+0     doi:10.1128/JVI.02301-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis{triangledown}

Joseph G. Victoria,1,2 Amit Kapoor,1,2 Linlin Li,1,2 Olga Blinkova,1,2 Beth Slikas,1,2 Chunlin Wang,3 Asif Naeem,4 Sohail Zaidi,4 and Eric Delwart1,2*

Blood Systems Research Institute, San Francisco, California 94118,1 Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94118,2 Stanford Genome Technology Center, Stanford, California,3 National Institute of Health, Department of Virology, Islamabad, Pakistan4

Received 3 November 2008/ Accepted 2 February 2009

We analyzed viral nucleic acids in stool samples collected from 35 South Asian children with nonpolio acute flaccid paralysis (AFP). Sequence-independent reverse transcription and PCR amplification of capsid-protected, nuclease-resistant viral nucleic acids were followed by DNA sequencing and sequence similarity searches. Limited Sanger sequencing (35 to 240 subclones per sample) identified an average of 1.4 distinct eukaryotic viruses per sample, while pyrosequencing yielded 2.6 viruses per sample. In addition to bacteriophage and plant viruses, we detected known enteric viruses, including rotavirus, adenovirus, picobirnavirus, and human enterovirus species A (HEV-A) to HEV-C, as well as numerous other members of the Picornaviridae family, including parechovirus, Aichi virus, rhinovirus, and human cardiovirus. The viruses with the most divergent sequences relative to those of previously reported viruses included members of a novel Picornaviridae genus and four new viral species (members of the Dicistroviridae, Nodaviridae, and Circoviridae families and the Bocavirus genus). Samples from six healthy contacts of AFP patients were similarly analyzed and also contained numerous viruses, particularly HEV-C, including a potentially novel Enterovirus genotype. Determining the prevalences and pathogenicities of the novel genotypes, species, genera, and potential new viral families identified in this study in different demographic groups will require further studies with different demographic and patient groups, now facilitated by knowledge of these viral genomes.

* Corresponding author. Mailing address: BSRI, 270 Masonic Ave., San Francisco, CA 94118. Phone: (415) 923-5763. Fax: (415) 567-5899. E-mail: delwarte{at}medicine.ucsf.edu

{triangledown} Published ahead of print on 11 February 2009.

Journal of Virology, May 2009, p. 4642-4651, Vol. 83, No. 9
0022-538X/09/$08.00+0     doi:10.1128/JVI.02301-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.



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