Abstract
The classification of human papillomavirus (HPV) intratypic lineages by complete genome sequencing is a determinant in understanding biological differences in association with this disease. In this work, we have characterised complete HPV genomes from southern Brazil. Fifteen cervicovaginal Pap smear negative samples previously categorised as HPV-positive were sequenced using ultradeep sequencing, and 18 complete genomes from 13 different HPV types were assembled. Phylogenetic and genetic distance analyses were performed to classify the HPV genomes into lineages and sublineages. This is the first report describing the distribution of HPV intratype lineages of high and low oncogenic risk in asymptomatic women from southern Brazil.
Highlights
Human papillomavirus (HPV) is the most prevalent sexually transmitted infection worldwide and is a major factor in the development of cervical cancer
Libraries were prepared for each sample using a Nextera® XT DNA Sample Preparation kit (Illumina Inc., San Diego, USA) and tagmentation and polymerase chain reaction (PCR) according to the protocol established by the manufacturer
We showed that the use of next-generation sequencing (NGS) enabled the detection of co-infections with multiple human papillomavirus (HPV) genotypes due to its greater sensitivity when compared to Sanger sequencing, as shown previously by our group and others
Summary
Human papillomavirus (HPV) is the most prevalent sexually transmitted infection worldwide and is a major factor in the development of cervical cancer (zur Hausen 1976). Distinct HPV types differ by more than 10% in their L1 sequences, whereas the classification of intratype lineages and sublineages requires complete genome information. Fifteen samples of cervicovaginal smears originated from HPV-positive women previously typed by Oliveira et al (2013) were studied .
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