Characterisation of complete high- and low-risk human papillomavirus genomes isolated from cervical specimens in southern Brazil

Oliveira, Gisele R de; Siqueira, Juliana D; Finger-Jardim, Fabiana; Vieira, Valdimara C; Silva, Ronald L; Gonçalves, Carla V; Soares, Esmeralda A; Martinez, Ana Maria Barral de; Soares, Marcelo A

doi:10.1590/0074-02760170121

GENOME ANNOUNCEMENTS AND HIGHLIGHTS • Mem. Inst. Oswaldo Cruz 112 (10) • Oct 2017 • https://doi.org/10.1590/0074-02760170121 linkcopy

Characterisation of complete high- and low-risk human papillomavirus genomes isolated from cervical specimens in southern Brazil

Authorship SCIMAGO INSTITUTIONS RANKINGS

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.

human papillomavirus; lineage; complete genome; southern Brazil

Sample	HPV type by Sanger sequencing*	HPV type(s) by NGS	Complete genomes assembled	Distance (%)	Lineage(s)/ sublineage(s) assigned
01	6	6	6	0.1	B3
02	6	6	6	0.1	B1
03	6	6	6	0.2	A
04	16	16, 31	---	---	---
05	18	18	18	0.1	A3
06	31	31, 68	31 68	0.3 0.3	C2 C1
07	33	68	68	0.2	C1
08	35	35, 39	35 39	0.3 0.1	A1 A1
09	58	51, 58	51	0.2	A1
10	58	58	58	0.1	A2
11	67	31, 67, 85	67 85 31	0.1 0.1 0.3	A2 A B2
12	82	56, 61, 82	56 61 82	0.2 0.1 0.1	A2 A1 A2
13	82	82	82	0.1	A2
14	83	31, 82, 83,	---	---	---
15	83	6, 74, 82, 83	---	---	---

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[TFN1] *: HPV previously typed by Oliveira et al. (2013); NGS: next-generation sequencing.