Background/Objectives Human papillomavirus type 16 (HPV 16) is the primary aetiology of cervical cancer.

Risk factors associated to develop of malignant lesions include: infection persistence, specific HPV 16 variants and multiple infections presence.

We had characterised the genomic variability of E6, E7 and L1 genes in HPV 16 multiple infection patients samples and analysed the relationship between intratypic variants and lesion grade.

Methods HPV 16 multiple infection samples were amplified with three region type-specific primers and amplicons were sequenced using the “Big Dye Terminator Cycle Sequencing kit”.

Sequences were aligned using Edit Sequence Alignment Editor and ClustalW, and compared with Genbank reported reference sequences: European (E), African (AF1 and AF2) and Asian-American (AA).

Lesions were divided as negative, low-grade (L-SIL) or high-grade (H-SIL).

Results HPV 16 multiple infections were identified in 125 samples and 78 of them were analysed for intratypic variations: 72 E variants (92.3%), 4 AA variants (5.1%), one AF1 (1.3%) and one AF2 variant (1.3%).

In E6 region, missense mutations (A104del and T350G) were defined in 59% and 41% of samples. In E7 region, a mainly synonymous variation (G849A, 41.33%) was detected. In L1 region, non-synonymous replacements were only identified: 6901insCAT (30%), 6902 insATC (65.7%) and GAT6951del (97.1%).

European variants were mainly detected in samples with no lesion while non-european variants were only found in H-SIL or L-SIL.

Conclusions E6, E7 and L1 genes are useful to determinate among E, AA and AF1/AF2 variants. Non-european variants are also present in our population.

Nucleotide variations different to define variants must be studied owing to their potential impact on pathogenesis. T350G nucleotide substitution is associated with elevated risk of cervical carcinomas. These variations should be taken into consideration.

Funding: S-PC11BF002 project (Saiotek, Department of Industry, Basque Government).