Viral genome sequencing by random priming methods

Appolinaire Djikeng*, Rebecca Halpin, Ryan Kuzmickas, Jay DePasse, Jeremy Feldblyum, Naomi Sengamalay, Claudio Afonso, Xinsheng Zhang, Norman G. Anderson, Elodie Ghedin, David J. Spiro

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Background: Most emerging health threats are of zoonotic origin. For the overwhelming majority, their causative agents are RNA viruses which include but are not limited to HIV, Influenza, SARS, Ebola, Dengue, and Hantavirus. Of increasing importance therefore is a better understanding of global viral diversity to enable better surveillance and prediction of pandemic threats; this will require rapid and flexible methods for complete viral genome sequencing.

Results: We have adapted the SISPA methodology [1-3] to genome sequencing of RNA and DNA viruses. We have demonstrated the utility of the method on various types and sources of viruses, obtaining near complete genome sequence of viruses ranging in size from 3,000-15,000 kb with a median depth of coverage of 14.33. We used this technique to generate full viral genome sequence in the presence of host contaminants, using viral preparations from cell culture supernatant, allantoic fluid and fecal matter.

Conclusion: The method described is of great utility in generating whole genome assemblies for viruses with little or no available sequence information, viruses from greatly divergent families, previously uncharacterized viruses, or to more fully describe mixed viral infections.

Original languageEnglish
Article number5
Number of pages9
JournalBMC Genomics
Volume9
DOIs
Publication statusPublished - 7 Jan 2008

Keywords

  • VIRUS DISCOVERY
  • DNA VIRUSES
  • IDENTIFICATION
  • RNA
  • AMPLIFICATION
  • PARVOVIRUS
  • REVEALS

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