Target-dependent enrichment of virions determines the reduction of high-throughput sequencing in virus discovery

• Published in: PloS one Vol. 10; no. 4; p. e0122636
• Main Authors: Jensen, Randi Holm, Mollerup, Sarah, Mourier, Tobias, Hansen, Thomas Arn, Fridholm, Helena, Nielsen, Lars Peter, Willerslev, Eske, Hansen, Anders Johannes, Vinner, Lasse
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 08.04.2015; Public Library of Science (PLoS)
• Subjects: Analysis; Base Sequence; Care and treatment; Cell culture; Complications and side effects; Deoxyribonucleic acid; DNA; DNA sequencing; Enrichment; Epidemics; Gene Library; Gene sequencing; Genomes; Health aspects; Hepatitis; High-Throughput Nucleotide Sequencing; High-throughput screening (Biochemical assaying); Human papillomavirus 18 - genetics; Human papillomavirus 18 - isolation & purification; Human papillomavirus 18 - pathogenicity; Humans; Infections; Museums; Nucleic acids; Nucleotide sequence; Respiratory diseases; Ribonucleic acid; Ribosomal DNA; RNA; RNA viruses; RNA, Viral - genetics; RNA, Viral - isolation & purification; Sentinel surveillance; Target detection; Target recognition; Viral infections; Virion - genetics; Virion - isolation & purification; Virions; Virology; Virus diseases; Virus Diseases - genetics; Virus Diseases - virology; Viruses
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0122636

Viral infections cause many different diseases stemming both from well-characterized viral pathogens but also from emerging viruses, and the search for novel viruses continues to be of great importance. High-throughput sequencing is an important technology for this purpose. However, viral nucleic acids often constitute a minute proportion of the total genetic material in a sample from infected tissue. Techniques to enrich viral targets in high-throughput sequencing have been reported, but the sensitivity of such methods is not well established. This study compares different library preparation techniques targeting both DNA and RNA with and without virion enrichment. By optimizing the selection of intact virus particles, both by physical and enzymatic approaches, we assessed the effectiveness of the specific enrichment of viral sequences as compared to non-enriched sample preparations by selectively looking for and counting read sequences obtained from shotgun sequencing. Using shotgun sequencing of total DNA or RNA, viral targets were detected at concentrations corresponding to the predicted level, providing a foundation for estimating the effectiveness of virion enrichment. Virion enrichment typically produced a 1000-fold increase in the proportion of DNA virus sequences. For RNA virions the gain was less pronounced with a maximum 13-fold increase. This enrichment varied between the different sample concentrations, with no clear trend. Despite that less sequencing was required to identify target sequences, it was not evident from our data that a lower detection level was achieved by virion enrichment compared to shotgun sequencing.