Characterization and Whole Genome Analysis of Human Papillomavirus Type 16 E1-1374∧63nt Variants

Background: The variation of the most common Human papillomavirus (HPV) type found in cervical cancer, the HPV16, has been extensively investigated in almost all viral genes. The E1 gene variation, however, has been rarely studied. The main objective of the present investigation was to analyze the variability of the E6 and E1 genes, focusing on the recently identified E1-1374(boolean AND)63nt variant. Methodology/Principal Findings: Variation within the E6 of 786 HPV16 positive cervical samples was analyzed using high-resolution melting, while the E1-1374(boolean AND)63nt duplication was assayed by PCR. Both techniques were supplemented with sequencing. The E1-1374(boolean AND)63nt duplication was linked with the E-G350 and the E-C109/G350 variants. In comparison to the referent HPV16, the E1-1374(boolean AND)63nt E-G350 variant was significantly associated with lower grade cervical lesions (p = 0.029), while the E1-1374(boolean AND)63nt E-C109/G350 variant was equally distributed between high and low grade lesions. The E1-1374(boolean AND)63nt variants were phylogenetically closest to E-G350 variant lineage (A2 sub-lineage based on full genome classification). The major differences between E1-1374(boolean AND)63nt variants were within the LCR and the E6 region. On the other hand, changes within the E1 region were the major differences from the A2 sub-lineage, which has been historically but inconclusively associated with high grade cervical disease. Thus, the shared variations cannot explain the particular association of the E1-1374(boolean AND)63nt variant with lower grade cervical lesions. Conclusions/Significance: The E1 region has been thus far considered to be well conserved among all HPVs and therefore uninteresting for variability studies. However, this study shows that the variations within the E1 region could possibly affect cervical disease, since the E1-1374(boolean AND)63nt E-G350 variant is significantly associated with lower grade cervical lesions, in comparison to the A1 and A2 sub-lineage variants. Furthermore, it appears that the silent variation 109T>C of the E-C109/G350 variant might have a significant role in the viral life cycle and warrants further study.