TY - JOUR
T1 - Enhanced virome sequencing using targeted sequence capture
AU - Wylie, Todd N.
AU - Wylie, Kristine M.
AU - Herter, Brandi N.
AU - Storch, Gregory A.
N1 - Funding Information:
We thank Richard Hotchkiss and Andrew Walton for providing samples for the anellovirus work, Maria Cannella and Richard Buller for carrying out the virus-specific PCR assays on the samples from the research study, Stephanie Bledsoe and the staff of the Virology Laboratory at St. Louis Children’s Hospitals for supplying remnant specimen material, Elena Deych and William Shannon for assisting with statistical analysis, and The McDonnell Genome Institute for generating sequence data. We thank Efrem Lim and David Wang for performing the PCR validation test on the HPyV10 virus. This study was supported by grant number R01AI097213 from the National Institute of Allergy and Infectious Diseases, awarded to G.A.S.
Publisher Copyright:
© 2015 Robin et al.
PY - 2015/12
Y1 - 2015/12
N2 - Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ~1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications.
AB - Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ~1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications.
UR - http://www.scopus.com/inward/record.url?scp=84956624157&partnerID=8YFLogxK
U2 - 10.1101/gr.191049.115
DO - 10.1101/gr.191049.115
M3 - Article
C2 - 26395152
AN - SCOPUS:84956624157
SN - 1088-9051
VL - 25
SP - 1910
EP - 1920
JO - Genome research
JF - Genome research
IS - 12
ER -