HPV Direct Flow CHIP: A new human papillomavirus genotyping method based on direct PCR from crude-cell extracts

• Published in: Journal of virological methods 2013-10, Vol.193 (1), p.9-17
• Main Authors: Herraez-Hernandez, Elsa, Alvarez-Perez, Martina, Navarro-Bustos, Gloria, Esquivias, Javier, Alonso, Sonia, Aneiros-Fernandez, Jose, Lacruz-Pelea, Cesar, Sanchez-Aguera, Magdalena, Santamaria, Javier Saenz, de Antonio, Jesus Chacon, Rodriguez-Peralto, Jose Luis
• Format: Article
• Language: English
• Subjects: Adolescent; Adult; Aged; Aged, 80 and over; cell biology; CLART HPV2; colorimetry; Colorimetry - methods; DNA; DNA, Viral - genetics; epidemiology; Female; Genotype; genotyping; HPV Direct Flow CHIP; HPV Genotyping; Human papillomavirus; Humans; Hybrid Capture 2; hybrid capture methods; Linear Array; Middle Aged; Nucleic Acid Hybridization - methods; Papillomaviridae; Papillomaviridae - classification; Papillomaviridae - genetics; Papillomaviridae - isolation & purification; Papillomavirus Infections - virology; polymerase chain reaction; Polymerase Chain Reaction - methods; screening; Spain; tissues; Virology - methods; Young Adult
• ISSN: 0166-0934; 1879-0984
• DOI: 10.1016/j.jviromet.2013.04.018

•The analytical performance of HPV Direct Flow CHIP was studied.•The new HPV Direct Flow CHIP uses crude-cell extracts as PCR template.•Comparison with other commercial systems showed a high agreement between methods.•HPV Direct Flow CHIP could be used for sensitive HPV detection. HPV Direct Flow CHIP is a newly developed test for identifying 18 high-risk and 18 low-risk human papillomavirus (HPV) genotypes. It is based on direct PCR from crude-cell extracts, automatic flow-through hybridization, and colorimetric detection. The aim of this study was to evaluate the performance of HPV Direct Flow CHIP in the analysis of 947 samples from routine cervical screening or the follow-up of abnormal Pap smears. The specimens were dry swab samples, liquid-based cytology samples, or formalin-fixed paraffin-embedded tissues. The genotype distribution was in agreement with known epidemiological data for the Spanish population. Three different subgroups of the samples were also tested by Linear Array (LA) HPV Genotyping Test (n=108), CLART HPV2 (n=82), or Digene Hybrid Capture 2 (HC2) HPV DNA Test (n=101). HPV positivity was 73.6% by HPV Direct Flow CHIP versus 67% by LA, 65.9% by HPV Direct Flow CHIP versus 59.8% by CLART, and 62.4% by HPV Direct Flow CHIP versus 42.6% by HC2. HPV Direct Flow CHIP showed a positive agreement of 88.6% with LA (k=0.798), 87.3% with CLART (k=0.818), and 68.2% with HC2 (k=0.618). In conclusion, HPV Direct Flow CHIP results were comparable with those of the other methods tested. Although further investigation is needed to compare the performance of this new test with a gold-standard reference method, these preliminary findings evidence the potential value of HPV Direct Flow CHIP in HPV vaccinology and epidemiology studies.