Real-time RT-PCR assay to differentiate clades of H5N1 avian influenza viruses circulating in Vietnam

  • Kis Z
  • Jones J
  • Creanga A
 et al. 
  • 23


    Mendeley users who have this article in their library.
  • 9


    Citations of this article.


Continued circulation and geographical expansion of highly pathogenic avian influenza H5N1 virus have led to the emergence of numerous clades in Vietnam. Although viral RNA sequencing and phylogenetic analysis are the gold standard for H5N1 HA clade designation, limited sequencing capacity in many laboratories precludes rapid H5N1 clade identification and detection of novel viruses. Therefore, a Taqman real-time RT-PCR assay for rapid differentiation of the four major H5N1 clades detected in Vietnam was developed. Using HA sequence alignments of clades 1.1,, 2.3.4, and 7 viruses, primers and FAM-labeled probes were designed to target conserved regions characteristic of each clade. The assay was optimized and evaluated using circulating clades of H5N1 collected in Vietnam from 2007 to 2012 and shown to be both sensitive and specific for the differentiation of the four H5N1 clades. The assay provides a useful tool for screening of large specimen collections for HA gene sequencing and phylogenetic analysis and for the rapid identification of molecular clade signatures to support outbreak investigations and surveillance activities. Finally, this assay may be useful to monitor for the emergence of novel or variant clades of H5N1 in Vietnam in the future or in other countries where these particular clades may circulate. © 2013 Elsevier B.V.

Author-supplied keywords

  • Clade-differentiation
  • H5N1
  • Highly pathogenic avian influenza
  • Real-time RT-PCR
  • Vietnam

Get free article suggestions today

Mendeley saves you time finding and organizing research

Sign up here
Already have an account ?Sign in

Find this document


  • Z. Kis

  • J. Jones

  • A. Creanga

  • K. Ferdinand

  • K. Inui

  • N. Gerloff

Cite this document

Choose a citation style from the tabs below

Save time finding and organizing research with Mendeley

Sign up for free