Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples.

BMC Genomics
Adrian C PaskeyKimberly A Bishop-Lilly

Abstract

Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and contribution of host or environmental nucleic acids. Hybridization-based target enrichment is one potential method for increasing the sensitivity of viral detection via high-throughput sequencing. This study expands upon two previously developed panels of virus enrichment probes (for filoviruses and for respiratory viruses) to include other viruses of biodefense and/or biosurveillance concern to the U.S. Department of Defense and various international public health agencies. The newly expanded and combined panel is tested using carefully constructed synthetic metagenomic samples that contain clinically relevant amounts of viral genetic material. Target enrichment results in a dramatic increase in sensitivity for virus detection as compared to shotgun sequencing, yielding full, deeply covered viral genomes from materials with Ct values suggesting that amplicon sequencing would be likely to fail. Increased pooling to improve cost- and time-effectiveness does not negatively affect the ability to obtain full-length viral genomes...Continue Reading

References

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Citations

Jan 30, 2020·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·Ignacio Postigo-HidalgoJan Felix Drexler
Dec 17, 2020·Viruses·Xavier Fernandez-CassiRosina Girones
Apr 7, 2021·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Paul D HartleySubhash C Verma
May 22, 2021·Schizophrenia Research·Robert H YolkenSarven Sabunciyan
Jan 20, 2020·The Science of the Total Environment·Sandra Martínez-PucholSílvia Bofill-Mas

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Datasets Mentioned

BETA
KJ614529.1

Methods Mentioned

BETA
Polymerase
amplicon sequencing
PCR
amplicon-based sequencing
nucleic acid spiking
Assay

Software Mentioned

CLC Genomics Workbench
ggplot2 R
BLAST
EDGE Bioinformatic

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