Human Papillomavirus (HPV) genotype 18 variants in patients with clinical manifestations of HPV related infections in Bilbao, Spain

Abstract

BackgroundHuman papillomavirus (HPV) variants differ in their biological and chemical properties, and therefore, may present differences in pathogenicity. Most authors classified variants based on the phylogenetic analysis of L1 region. Nevertheless, recombination in HPV samples is becoming a usual finding and thus, characterizing genetic variability in other regions should be essential.ObjectivesWe aimed to characterize the genetic variability of HPV 18 in 5 genomic regions: E6, E7, E4, L1 and the Upstream Regulatory Region (URR), working with both single infection and multiple HPV infection samples. Furthermore, we aimed to assess the prevalence of HPV 18 variants in our region and look for possible existence of recombination as well as analyze the relationship between these variants and the type of lesion.MethodsFrom 2007 to 2010, Clinical Microbiology and Infection Control Department analyzed 44 samples which were positive for HPV 18. Genetic variability was determined in PCR products and variants were assigned to European, Asian-amerindian or African lineage. Recombination and association of variants with different types of lesion was studied.ResultsGenetic analysis of the regions revealed a total of 56 nucleotide variations. European, African and Asian-amerindian variants were found in 25/44 (56.8%), 10/44 (22.7%) and 5/44 (11.4%) samples, respectively. We detected the presence of recombinant variants in 2/44 (4.5%) cases. Samples taken from high-grade squamous intraepithelial lesions (H-SIL) only presented variants with specific-african substitutions.ConclusionsMultiple HPV infection, non-european HPV variants prevalence and existence of recombination are considered risk factors for HPV persistence and progression of intraepithelial abnormalities, and therefore, should be taken into consideration in order to help to design and optimize diagnostics protocols as well as improve epidemiologic studies.Our study is one of the few studies in Spain which analyses the genetic variability of HPV18 and we showed the importance of characterizing more than one genomic region in order to detect recombination and classify HPV variants properly.

Human Papillomavirus 18 Genetic Variation and Cervical Cancer Risk Worldwide

“…Our LCR/E6 classification fits with other HPV18 sequences reported in the literature (10,12,(40)(41)(42)(43)(44)(45)(46)(47)(48)(49)(50) and is consistent with lineage definitions based on the gold standard approach of HPV18 whole-genome sequencing (13). Although based on LCR and E6 only, our analysis included many novel variants, particularly among previously underrepresented A5 and B (sub)lineages, which would warrant sequencing the whole genomes in order to strengthen the full picture of HPV18 genetic evolution.…”

Genetic diversity of HPV16 and HPV18 in Brazilian patients with invasive cervical cancer

“…Of the 80 HPV18 samples, nine were excluded from the analyses due to the unsuccessful PCR amplification of LCR and/or E6 . For the remaining 71 samples, lineage identification was based on an approach similar to that used for HPV16; that is, based on sequencing a region encompassing LCR and E6 and identifying nucleotide signatures based on the SNVs described by Arias‐Pulido et al [] and Arroyo et al []. Fifty‐five samples (∼70 % of the HPV18 samples) were identified as belonging to lineage A and 16 samples (∼19 % of the HPV18 samples) were identified as belonging to lineage B (Table ).…”

“…Two strategies were employed. First, HPV16 lineages were identified based on single nucleotide variants (SNVs) at specific LCR and E6 sites according to the method of Cornet et al [], and HPV18 lineages were characterized by identifying lineage‐distinctive SNVs [Arias‐Pulido et al, ; Arroyo et al, ]. Second, a phylogenetic reconstruction was performed using a dataset of 1,300 bp LCR + E6 sequences, including the reference sequences proposed by Burk et al [].…”

“…A small proportion of oncogenic infections are persistent and progress to invasive cancer; however, the factors associated with progression are poorly understood. One important hypothesis suggested by several studies relates to intra‐type diversity [Sichero et al, ; Gheit et al, ; Smith et al, ; Arroyo et al, ; Cornet et al, ; Chen et al, ]. These studies suggested that intra‐type lineages differ in their biological characteristics and pathogenicity.…”

Human Papillomavirus 16 Variants May Be Identified by <b><i>E6 </i></b>Gene Analysis

“…In this study all samples had multiple HPV-16 infections, and this could affect the appearance of nucleotide substitutions. Moreover, although most authors have analyzed only one genomic region to identify HPV-16 variants, it would probably not be enough for an appropriate variant identification since it may be impossible to detect recombination [24,25]. Furthermore, Angulo et al [26 ]have proved that E6 is one of the genes with the highest recombination value in the HPV genome and, as recombination, is a great evolutionary mechanism that could have an effect on pharmacogenomics and vaccine strategies.…”