Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification

Christine M. Malboeuf, Xiao Yang, Patrick Charlebois, James Qu, Aaron M. Berlin, Monica Casali, Kendra N. Pesko, Christian L. Boutwell, John Devincenzo, Gregory D. Ebel, Todd M. Allen, Michael C. Zody, Matthew R. Henn, Joshua Z. Levin

Research output: Contribution to journalArticle

52 Citations (Scopus)

Abstract

RNA viruses are the causative agents for AIDS, influenza, SARS, and other serious health threats. Development of rapid and broadly applicable methods for complete viral genome sequencing is highly desirable to fully understand all aspects of these infectious agents as well as for surveillance of viral pandemic threats and emerging pathogens. However, traditional viral detection methods rely on prior sequence or antigen knowledge. In this study, we describe sequence-independent amplification for samples containing ultra-low amounts of viral RNA coupled with Illumina sequencing and de novo assembly optimized for viral genomes. With 5 million reads, we capture 96 to 100% of the viral protein coding region of HIV, respiratory syncytial and West Nile viral samples from as little as 100 copies of viral RNA. The methods presented here are scalable to large numbers of samples and capable of generating full or near full length viral genomes from clone and clinical samples with low amounts of viral RNA, without prior sequence information and in the presence of substantial host contamination.

Original languageEnglish (US)
JournalNucleic acids research
Volume41
Issue number1
DOIs
StatePublished - Jan 1 2013

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RNA Sequence Analysis
Viral Genome
Viral RNA
RNA Viruses
Viral Proteins
Pandemics
Human Influenza
Open Reading Frames
Acquired Immunodeficiency Syndrome
Clone Cells
HIV
Antigens
Health

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Malboeuf, C. M., Yang, X., Charlebois, P., Qu, J., Berlin, A. M., Casali, M., ... Levin, J. Z. (2013). Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification. Nucleic acids research, 41(1). https://doi.org/10.1093/nar/gks794

Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification. / Malboeuf, Christine M.; Yang, Xiao; Charlebois, Patrick; Qu, James; Berlin, Aaron M.; Casali, Monica; Pesko, Kendra N.; Boutwell, Christian L.; Devincenzo, John; Ebel, Gregory D.; Allen, Todd M.; Zody, Michael C.; Henn, Matthew R.; Levin, Joshua Z.

In: Nucleic acids research, Vol. 41, No. 1, 01.01.2013.

Research output: Contribution to journalArticle

Malboeuf, CM, Yang, X, Charlebois, P, Qu, J, Berlin, AM, Casali, M, Pesko, KN, Boutwell, CL, Devincenzo, J, Ebel, GD, Allen, TM, Zody, MC, Henn, MR & Levin, JZ 2013, 'Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification', Nucleic acids research, vol. 41, no. 1. https://doi.org/10.1093/nar/gks794
Malboeuf, Christine M. ; Yang, Xiao ; Charlebois, Patrick ; Qu, James ; Berlin, Aaron M. ; Casali, Monica ; Pesko, Kendra N. ; Boutwell, Christian L. ; Devincenzo, John ; Ebel, Gregory D. ; Allen, Todd M. ; Zody, Michael C. ; Henn, Matthew R. ; Levin, Joshua Z. / Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification. In: Nucleic acids research. 2013 ; Vol. 41, No. 1.
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