title: Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification.
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.
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. malboeuf@broadinstitute.org
authors.forename: Christine M
authors.initials: CM
authors.lastname: Malboeuf
authors.forename: Xiao
authors.initials: X
authors.lastname: Yang
authors.forename: Patrick
authors.initials: P
authors.lastname: Charlebois
authors.forename: James
authors.initials: J
authors.lastname: Qu
authors.forename: Aaron M
authors.initials: AM
authors.lastname: Berlin
authors.forename: Monica
authors.initials: M
authors.lastname: Casali
authors.forename: Kendra N
authors.initials: KN
authors.lastname: Pesko
authors.forename: Christian L
authors.initials: CL
authors.lastname: Boutwell
authors.forename: John P
authors.initials: JP
authors.lastname: DeVincenzo
authors.forename: Gregory D
authors.initials: GD
authors.lastname: Ebel
authors.forename: Todd M
authors.initials: TM
authors.lastname: Allen
authors.forename: Michael C
authors.initials: MC
authors.lastname: Zody
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Henn
authors.forename: Joshua Z
authors.initials: JZ
authors.lastname: Levin
mesh_terms: D001483:Base Sequence; D016679:Genome, Viral; D006678:HIV / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D021141:Nucleic Acid Amplification Techniques; D012367:RNA, Viral / Q000737:chemistry*; D012136:Respiratory Syncytial Viruses / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D014902:West Nile virus / Q000235:genetics
chemical_list: D012367:RNA, Viral