Rapid investigation of hepatitis A virus outbreak by single strand conformation polymorphism analysis.
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.
Mackiewicz
Vincent
V
Centre National de Référence du Virus de l'Hépatite A, Laboratoire de Virologie, Hôpital Paul Brousse, Assistance Publique-Hôpitaux de Paris, Villejuif, France. vincent.mackiew@pbr.ap-hop-paris.fr
Roque-Afonso
Anne-Marie
AM
Marchadier
Eric
E
Nicand
Elisabeth
E
Fki-Berrajah
Lamia
L
Dussaix
Elisabeth
E
D000293:Adolescent; D000328:Adult; D002648:Child; D002675:Child, Preschool; D003546:Cysteine Endopeptidases / Q000235:genetics; D004196:Disease Outbreaks; D005260:Female; D006506:Hepatitis A / Q000453:epidemiology* / Q000821:virology*; D030041:Hepatitis A virus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D010802:Phylogeny; D018807:Polymorphism, Single-Stranded Conformational; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA; D014764:Viral Proteins / Q000235:genetics; D015678:Viral Structural Proteins / Q000235:genetics
C096539:VP1 protein, hepatitis A virus; D014764:Viral Proteins; D015678:Viral Structural Proteins; D003546:Cysteine Endopeptidases; C057400:picornain 2A, Picornavirus