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The complete genome of klassevirus – a novel picornavirus in pediatric stool

Alexander L Greninger1, Charles Runckel1, Charles Y Chiu2, Thomas Haggerty3, Julie Parsonnet3, Donald Ganem1 and Joseph L DeRisi1*

Author Affiliations

1 Howard Hughes Medical Institute, Departments of Medicine, Biochemistry, and Microbiology, University of California, San Francisco, California 94143, USA

2 Departments of Laboratory Medicine and Medicine, Division of Infectious Diseases, University of California, San Francisco, California 94143, USA

3 Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, California 94305, USA

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Virology Journal 2009, 6:82  doi:10.1186/1743-422X-6-82

Published: 18 June 2009

Abstract

Background

Diarrhea kills 2 million children worldwide each year, yet an etiological agent is not found in approximately 30–50% of cases. Picornaviral genera such as enterovirus, kobuvirus, cosavirus, parechovirus, hepatovirus, teschovirus, and cardiovirus have all been found in human and animal diarrhea. Modern technologies, especially deep sequencing, allow rapid, high-throughput screening of clinical samples such as stool for new infectious agents associated with human disease.

Results

A pool of 141 pediatric gastroenteritis samples that were previously found to be negative for known diarrheal viruses was subjected to pyrosequencing. From a total of 937,935 sequence reads, a collection of 849 reads distantly related to Aichi virus were assembled and found to comprise 75% of a novel picornavirus genome. The complete genome was subsequently cloned and found to share 52.3% nucleotide pairwise identity and 38.9% amino acid identity to Aichi virus. The low level of sequence identity suggests a novel picornavirus genus which we have designated klassevirus. Blinded screening of 751 stool specimens from both symptomatic and asymptomatic individuals revealed a second positive case of klassevirus infection, which was subsequently found to be from the index case's 11-month old twin.

Conclusion

We report the discovery of human klassevirus 1, a member of a novel picornavirus genus, in stool from two infants from Northern California. Further characterization and epidemiological studies will be required to establish whether klasseviruses are significant causes of human infection.