Rapid investigation of hepatitis A virus outbreak by single strand conformation polymorphism analysis

J Med Virol. 2005 Jun;76(2):271-8. doi: 10.1002/jmv.20355.


Investigation of hepatitis A virus (HAV) outbreaks often implies nucleotide sequence analysis. As an alternative method for the identification of related strains, single strand conformation polymorphism method (SSCP) was compared to sequence analysis. Twenty-three strains from sporadic and outbreak cases were studied retrospectively. SSCP, sequence identity and phylogenetic analyses were conducted on a 267 bp fragment of the VP1-2A variable region. The results of SSCP pattern comparison and sequence identity were highly correlated (r = 0.92, P < 0.001). If SSCP showed similar patterns, the VP1-2A fragments had a high and significant probability to have a sequence identity over 99.6%. Results were concordant for outbreak strains. The only discordant result concerned a cluster of three sporadic cases evidenced by phylogenetic analysis while SSCP showed similar patterns for only two of these three cases. A prospective SSCP analysis of a recent HAV outbreak confirmed the reliability of this technique. SSCP may thus provide a rapid and cost-effective tool for preliminary investigation of HAV outbreaks, before undertaking exhaustive nucleotide sequence analysis.

Publication types

  • Comparative Study

MeSH terms

  • Adolescent
  • Adult
  • Child
  • Child, Preschool
  • Cysteine Endopeptidases / genetics
  • Disease Outbreaks*
  • Female
  • Hepatitis A / epidemiology*
  • Hepatitis A / virology*
  • Hepatitis A virus / classification*
  • Hepatitis A virus / genetics*
  • Hepatitis A virus / isolation & purification
  • Humans
  • Male
  • Middle Aged
  • Molecular Epidemiology
  • Phylogeny
  • Polymorphism, Single-Stranded Conformational*
  • Retrospective Studies
  • Sequence Analysis, DNA
  • Viral Proteins / genetics
  • Viral Structural Proteins / genetics


  • VP1 protein, hepatitis A virus
  • Viral Proteins
  • Viral Structural Proteins
  • Cysteine Endopeptidases
  • picornain 2A, Picornavirus