Cross-hybridization between HPV genotypes in the Linear Array Genotyping Test confirmed by Next-Generation Sequencing
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(2019) 14:31
RESEARCH
Open Access
Cross-hybridization between HPV genotypes in the Linear Array Genotyping Test confirmed by Next-Generation Sequencing Cristina Artaza-Irigaray1†, María Guadalupe Flores-Miramontes1†, Dominik Olszewski2, Verónica Vallejo-Ruiz3, Laura Patricia Limón-Toledo4, Cibeles Sánchez-Roque5, Rocío Mayoral-Torres6, Luis Felipe Jave-Suárez1*† and Adriana Aguilar-Lemarroy1*†
Abstract Background: Linear Array Genotyping Test (LA) is one of the gold standards used for Human Papillomavirus (HPV) genotyping, however, since its launching in 2006, new HPV genotypes are still being characterized with the use of high specificity techniques such as Next-Generation Sequencing (NGS). Derived from a previous study of the IMSS Research Network on HPV, which suggested that there might be cross-reaction of some HPV genotypes in the LA test, the aim of this study was to elucidate this point. Methods: Double stranded L1 fragments (gBlocks) from different HPVs were used to perform LA test, additionally, 14 HPV83+ and 26 HPV84+ cervical samples determined with LA, were individually genotyped by NGS. Results: From the LA HPV83+ samples, 64.3% were truly HPV83+, while 42.9% were found to be HPV102+. On the other hand, 69.2% of the LA HPV84+ samples were HPV84+, while 3.8, 11.5 and 30.8% of the samples were indeed HPV 86, 87 and 114 positive, respectively. Additionally, novel nucleotide changes in L1 gene from HPV genotypes 83, 84, 87, 102 and 114 were determined in Mexican cervical samples, some of them lead to changes in the protein sequence. Conclusions: We demonstrated that there is cross-hybridization between alpha3-HPV genotypes 86, 87 and 114 with HPV84 probe in LA strips and between HPV102 with HPV83 probe; this may be causing over or under estimation in the prevalence of these genotypes. In the upcoming years, a switch to more specific and sensitive genotyping methods that detect a broader spectrum of HPV genotypes needs to be implemented. Keywords: Cervical samples, HPV, L1 mutations, Linear Array HPV Genotyping Test, Next-Generation Sequencing, Cross-hybridization
Background Human Papillomaviruses (HPV) belong to a diverse group of small non-encapsulated dsDNA viruses that have evolved over millions of years [1]. HPV classification and nomenclature is defined by the International * Correspondence: [email protected]; [email protected] † Cristina Artaza-Irigaray, María Guadalupe Flores-Miramontes, Luis Felipe JaveSuárez and Adriana Aguilar-Lemarroy contributed equally to this work. 1 División de Inmunología, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social (IMSS), Sierra Mojada No. 800, Col. Independencia, 44340 Guadalajara, Jalisco, Mexico Full list of author information is available at the end of the article
Committee for the Taxonomy of Viruses (ICTV) and the HPVs described to date are classified in different genera and species based on L1 gene sequence percentages of identity [2]. HPVs belong to five different genera called Alpha-, Beta-, Gamma-, Mu-
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