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Unbiased Deep Sequencing of RNA Viruses from Clinical Samples
Published on: July 2, 2016
Virus identification in unknown tropical febrile illness cases using deep sequencing.
Nathan L Yozwiak1, Peter Skewes-Cox, Mark D Stenglein
1Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, United States of America.
Plos Neglected Tropical Diseases
|February 21, 2012
Summary
Metagenomic deep sequencing identified viruses in 37% of patients with dengue-like illness who tested negative for dengue virus. This approach reveals diverse viral infections, including Human Herpesvirus 6, aiding tropical febrile illness diagnosis.
Area of Science:
- Virology
- Genomics
- Infectious Diseases
Background:
- Dengue virus causes millions of infections globally, but current diagnostics miss the cause in about 40% of dengue-like illnesses.
- Metagenomic methods like viral microarrays and deep sequencing offer powerful tools for identifying unknown or emerging pathogens.
- Unidentified viral agents contribute to the burden of tropical febrile illnesses, highlighting the need for advanced diagnostic capabilities.
Purpose of the Study:
- To characterize the viral spectrum in Nicaraguan patients with dengue-like symptoms but negative dengue virus tests.
- To evaluate the efficacy of deep sequencing and microarray techniques for detecting diverse viral infections in human serum.
- To identify known and potentially novel viruses contributing to undiagnosed febrile illnesses.
Main Methods:
- Utilized the Virochip microarray and deep sequencing on serum from 123 patients with dengue-like symptoms.
- Employed a barcoding strategy for simultaneous deep sequencing of multiple samples, generating over 1 million reads per sample.
- Implemented a bioinformatic filtering pipeline to remove human and low-quality sequences, enabling efficient, unbiased database searches.
Main Results:
- Deep sequencing detected viral sequences in 37% (45/123) of patients previously negative for dengue virus.
- Identified Human Herpesvirus 6 sequences in 13 cases.
- Detected viral sequences related to Herpesviridae, Flaviviridae, Circoviridae, Anelloviridae, Asfarviridae, and Parvoviridae families, including some potentially novel viruses.
Conclusions:
- Unbiased metagenomic approaches are highly effective for detecting a wide range of known and divergent viruses in tropical febrile illnesses.
- Deep sequencing significantly improves the diagnostic yield for patients presenting with dengue-like symptoms but testing negative for dengue virus.
- This methodology holds promise for uncovering the etiology of undiagnosed infectious diseases and understanding viral diversity.
