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. 2019 Apr 22;14(1):31.
doi: 10.1186/s13000-019-0808-2.

Cross-hybridization between HPV genotypes in the Linear Array Genotyping Test confirmed by Next-Generation Sequencing

Cristina Artaza-Irigaray  1 , María Guadalupe Flores-Miramontes  1 , Dominik Olszewski  2 , Verónica Vallejo-Ruiz  3 , Laura Patricia Limón-Toledo  4 , Cibeles Sánchez-Roque  5 , Rocío Mayoral-Torres  6 , Luis Felipe Jave-Suárez  7 , Adriana Aguilar-Lemarroy  8
Affiliations

Cross-hybridization between HPV genotypes in the Linear Array Genotyping Test confirmed by Next-Generation Sequencing

Cristina Artaza-Irigaray et al. Diagn Pathol. .

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; Cross-hybridization; HPV; L1 mutations; Linear Array HPV Genotyping Test; Next-Generation Sequencing.

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Conflict of interest statement

Ethics approval and consent to participate

All subjects gave their informed consent for inclusion before they participated in the study. The study was conducted in accordance with the Declaration of Helsinki, and the protocols were approved by the National Committee on Health Research and Ethics of the IMSS (with the registration numbers R-2012-785-090 and R-2014-785-036).

Consent for publication

Not applicable

Competing interests

The Authors declare that they have no competing interests

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Linear array Genotyping test performed individually with different L1 gBlocks (double stranded genomic blocks). The gBlocks were designed from HPV genotypes 102 (a), 114 (b), 86 (c) and 87 (d) and taken as template for the LA test
Fig. 2
Fig. 2
Phylogenetic tree based on alpha-3 HPVs L1 sequences. The analysis involved the 11 reference HPVs from alpha-3 species (REF) and 39 L1 sequences from HPVs 83, 84, 86, 87, 102 and 114 that infect Mexican woman. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site
See this image and copyright information in PMC

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