Virus identification in unknown tropical febrile illness cases using deep sequencing.

PLoS Neglected Tropical Diseases
Nathan L YozwiakJoseph L DeRisi

Abstract

Dengue virus is an emerging infectious agent that infects an estimated 50-100 million people annually worldwide, yet current diagnostic practices cannot detect an etiologic pathogen in ∼40% of dengue-like illnesses. Metagenomic approaches to pathogen detection, such as viral microarrays and deep sequencing, are promising tools to address emerging and non-diagnosable disease challenges. In this study, we used the Virochip microarray and deep sequencing to characterize the spectrum of viruses present in human sera from 123 Nicaraguan patients presenting with dengue-like symptoms but testing negative for dengue virus. We utilized a barcoding strategy to simultaneously deep sequence multiple serum specimens, generating on average over 1 million reads per sample. We then implemented a stepwise bioinformatic filtering pipeline to remove the majority of human and low-quality sequences to improve the speed and accuracy of subsequent unbiased database searches. By deep sequencing, we were able to detect virus sequence in 37% (45/123) of previously negative cases. These included 13 cases with Human Herpesvirus 6 sequences. Other samples contained sequences with similarity to sequences from viruses in the Herpesviridae, Flaviviridae, Circ...Continue Reading

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Datasets Mentioned

BETA
GSE28142

Methods Mentioned

BETA
PCR
enzyme-linked immunosorbent assay
electrophoresis

Software Mentioned

Basic Local Alignment Search Tool ( BLAST )
predict
CD
Geneious Tree Builder
HIT
BLASTx
BLAT
Virochip
BLASTn
Geneious

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