title: Identification of novel human papillomavirus lineages and sublineages in HIV/HPV-coinfected pregnant women by next-generation sequencing.
abstract: Infection by human papillomavirus (HPV) is a necessary condition for development of cervical cancer, and has also been associated with malignancies of other body anatomical sites. Specific HPV types have been associated with premalignant lesions and invasive carcinoma, but mounting evidence suggests that within-type lineages and sublineages also display distinct biological characteristics associated with persistent infections and evolution to cervical cancer. In the present study, we have assessed HPV multiple infection and variation from a cohort of highly susceptible, HIV(+) pregnant women using next-generation sequencing and an in-house pipeline for HPV full-length genome assembly. Seventy-two consensus sequences representing complete or near-complete (>97%) HPV genomes were assembled, spanning 28 different types. Genetic distance and phylogenetic analyses allowed us to propose the classification of novel HPV lineages and sublineages across nine HPV types, including two high-risk types. HPV diversity may be a hallmark of immunosuppressed patients upon HIV infection and AIDS progression.
authors.affiliation: Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.
authors.forename: Juliana D
authors.initials: JD
authors.lastname: Siqueira
authors.affiliation: Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.
authors.forename: Brunna M
authors.initials: BM
authors.lastname: Alves
authors.affiliation: Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.
authors.forename: Isabel M
authors.initials: IM
authors.lastname: Prellwitz
authors.affiliation: Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.
authors.forename: Carolina
authors.initials: C
authors.lastname: Furtado
authors.affiliation: Instituto de Ginecologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Ângela R
authors.initials: ÂR
authors.lastname: Meyrelles
authors.affiliation: Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Elizabeth S
authors.initials: ES
authors.lastname: Machado
authors.affiliation: Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil; Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Héctor N
authors.initials: HN
authors.lastname: Seuánez
authors.affiliation: Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil; Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Marcelo A
authors.initials: MA
authors.lastname: Soares
authors.affiliation: Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil. Electronic address: esoares@inca.gov.br.
authors.forename: Esmeralda A
authors.initials: EA
authors.lastname: Soares
mesh_terms: D000328:Adult; D015331:Cohort Studies; D060085:Coinfection; D005260:Female; D016679:Genome, Viral; D015658:HIV Infections / Q000150:complications / Q000821:virology*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D027383:Papillomaviridae / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D030361:Papillomavirus Infections / Q000150:complications / Q000821:virology*; D011247:Pregnancy; D011251:Pregnancy Complications, Infectious / Q000821:virology*
keywords: Coinfection; Full-length sequence; HPV; High-risk types; Immunosuppression; Pregnancy