Anchored Pan Dengue RT-PCR and fast sanger sequencing for detection of dengue RNA in human serum

Zhe Hu, Henrik Nordström, Norbert Nowotny, Kerstin I. Falk, Gunnar Sandström

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

A large number of human infections are caused by different dengue virus strains, mainly in the tropical and subtropical parts of the world, but also outside the endemic regions. RT-PCR methods are used widely for detection of dengue virus RNA in acute-phase serum samples; however, new sequence variation can inhibit these methods. An assay was developed integrating an anchored Pan Dengue RT-PCR with a new Fast Sanger sequencing protocol. For broad detection and identification of dengue virus RNA, including new strains of all serotypes, the conserved 30 genome end was targeted for highly specific cDNA synthesis. A combination of degenerated primers was used for second strand synthesis, followed by tag primed amplification. The mixture of generated amplicons was identified directly by the Fast Sanger sequencing from the anchored 30 genome end. Evaluating the assay on human serum RNA spiked with viral RNA representing the four dengue serotypes demonstrated a detection limit of 44-124 copies viral RNA per reaction for a two-step format of the anchored Pan Dengue RT-PCR and 100-500 copies for a one-step protocol, respectively. The different serotypes were clearly identified from the generated sequences. Further, the 5-hr procedure was evaluated and compared to standard real-time RT-PCR protocols on acute-phase serum samples from patients with confirmed dengue infections. This assay demonstrates a strategy for virus detection, which combines nucleic acid amplification adapted for dengue virus RNA with direct and rapid sequencing. It provides a tolerance for new sequence variation and the strategy should be applicable for other RNA viruses.

Original languageEnglish
Pages (from-to)1701-1710
Number of pages10
JournalJournal of Medical Virology
Volume82
Issue number10
DOIs
Publication statusPublished - Oct 2010

Fingerprint

Dengue Virus
Dengue
RNA
Polymerase Chain Reaction
Viral RNA
Serum
Genome
RNA Viruses
Infection
Nucleic Acids
Limit of Detection
Real-Time Polymerase Chain Reaction
Complementary DNA
Viruses
Serogroup

Keywords

  • 3′ genome end
  • Dengue virus
  • Fast sanger sequencing
  • Human serum
  • Pan Dengue RT-PCR
  • Viral RNA

ASJC Scopus subject areas

  • Virology
  • Infectious Diseases

Cite this

Anchored Pan Dengue RT-PCR and fast sanger sequencing for detection of dengue RNA in human serum. / Hu, Zhe; Nordström, Henrik; Nowotny, Norbert; Falk, Kerstin I.; Sandström, Gunnar.

In: Journal of Medical Virology, Vol. 82, No. 10, 10.2010, p. 1701-1710.

Research output: Contribution to journalArticle

Hu, Zhe ; Nordström, Henrik ; Nowotny, Norbert ; Falk, Kerstin I. ; Sandström, Gunnar. / Anchored Pan Dengue RT-PCR and fast sanger sequencing for detection of dengue RNA in human serum. In: Journal of Medical Virology. 2010 ; Vol. 82, No. 10. pp. 1701-1710.
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