Resequencing microarray technology for genotyping human papillomavirus in cervical smears.
There are more than 40 human papillomaviruses (HPVs) belonging to the alpha genus that cause sexually transmitted infections; these infections are among the most frequent and can lead to condylomas and anogenital intra-epithelial neoplasia. At least 18 of these viruses are causative agents of anogenital carcinomas. We evaluated the performance of a resequencing microarray for the detection and genotyping of alpha HPV of clinical significance using cloned HPV DNA. To reduce the number of HPV genotypes tiled on microarray, we used reconstructed ancestral sequences (RASs) as they are more closely related to the various genotypes than the current genotypes are among themselves. The performance of this approach was tested by genotyping with a set of 40 cervical smears already genotyped using the commercial PapilloCheck kit. The results of the two tests were concordant for 70% (28/40) of the samples and compatible for 30% (12/40). Our findings indicate that RASs were able to detect and identify one or several HPV in clinical samples. Associating RASs with homonym sequences improved the genotyping of HPV present in cases of multiple infection. In conclusion, we demonstrate the diagnostic potential of resequencing technology for genotyping of HPV, and illustrate its value both for epidemiological studies and for monitoring the distribution of HPV in the post-vaccination era.
Institut Pasteur, Epidémiologie et Physiopathologie des Virus Oncogènes, 75724 Paris Cedex 15, France; Centre National de la Recherche Scientifique, UMR 3569, 75724 Paris Cedex 15, France.
Nicolas
N
Berthet
Institut Pasteur, Centre National de Référence des Papillomavirus, 75724 Paris Cedex 15, France.
Michael
M
Falguières
Institut Pasteur, Epidémiologie et Physiopathologie des Virus Oncogènes, 75724 Paris Cedex 15, France; Centre National de la Recherche Scientifique, UMR 3569, 75724 Paris Cedex 15, France.
Claudia
C
Filippone
AP-HP, Hôpital Pitié-Salpêtrière, Service de Chirurgie Maxillo-Faciale et Stomatologie, 75013 Paris, France; UPMC, Université Paris 06, CIMI-Paris, UMRS CR7, INSERM U1135, 75005, Paris, France.
Chloé
C
Bertolus
Imagine, Institut des maladies génétiques - Plateforme Génomique, Hôpital Necker - Enfants Malades, 75743 Paris cedex 15, France.
Christine
C
Bole-Feysot
Institut Pasteur, Plate-forme Génotypage des Pathogènes et Santé Publique, 75724 Paris Cedex 15, France.
Sylvain
S
Brisse
Institut Pasteur, Epidémiologie et Physiopathologie des Virus Oncogènes, 75724 Paris Cedex 15, France; Centre National de la Recherche Scientifique, UMR 3569, 75724 Paris Cedex 15, France.
Antoine
A
Gessain
Institut Pasteur, Centre National de Référence des Papillomavirus, 75724 Paris Cedex 15, France; UPMC Université Paris 06, Groupe hospitalier Pitié-Salpêtrière, Paris Cedex 13, France.
Isabelle
I
Heard
Institut Pasteur, Centre National de Référence des Papillomavirus, 75724 Paris Cedex 15, France; Institut Pasteur, Unité de Génétique, Papillomavirus et Cancer humain, 75724 Paris Cedex 15, France.
Michel
M
Favre
D052685:Alphapapillomavirus / Q000235:genetics*; D001483:Base Sequence; D016000:Cluster Analysis; D017931:DNA Primers / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics*; D005260:Female; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010802:Phylogeny; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D014626:Vaginal Smears / Q000379:methods*
D017931:DNA Primers; D004279:DNA, Viral