Analysis of the genetic diversity and phylogenetic relationships of putative human papillomavirus types

Abstract

More than 170 human papillomavirus (HPV) types have been completely sequenced, curated and divided into five genera: Alphapapillomavirus, Betapapillomavirus, Gammapapillomavirus, Mupapillomavirus and Nupapillomavirus. With the application of PCR methods, hundreds of putative novel HPV types have been identified as PCR amplicons in mucosa and skin. However, at present there are no studies reporting a systematic search of the currently known L1 amplicons and their phylogenetic relationships. This survey revealed the existence of at least 202 different putative HPV types that are pending for full-genome characterization: five alphapapillomaviruses, 37 betapapillomaviruses, 159 gammapapillomaviruses and one mupapillomavirus. All potential viruses of the genera Alphapapillomavirus and Betapapillomavirus were grouped in the defined species, while 59 putative gammapapillomaviruses types were segregated in 21 unidentified putative species. These data highlight the need for progress in the identification of additional taxa of the family Papillomaviridae in order to elucidate the diversity, evolution and medical implications of these viruses.Papillomaviruses (PVs) are small non-enveloped DNA tumour viruses with a circular genome of nearly 8 kb. PVs infect the epithelia of vertebrates and are host specific (Bernard et al., 2010). By convention, designation of a novel PV type requires the genome to be cloned and curated by the Papillomavirus Reference Center and show less than 90 % identity in the L1 ORF with respect to any known PV type, while PV types belonging to new species within a genus share 60-70 % nucleotide identity with PV types within this genus (de Villiers et al., 2004).Presently, 170 human PV (HPV) types have been officially designated and completely sequenced (de Villiers, 2013; http://www.hpvcenter.se/html/refclones.html), and divided into five genera according to their L1 ORF phylogenetic relationships: Alphapapillomavirus, Betapapillomavirus, Gammapapillomavirus, Mupapillomavirus and Nupapillomavirus. There is diversity in the pathology of the HPV types across the genera and species, in particular in relation to the epithelium infected and the oncogenic potential of the viral type. The genus Alphapapillomavirus is heterogeneous, containing: (i) the high-risk mucosal HPV types in species a-7 and a-9; (ii) low-risk mucocutaneous genital types in species a-10; and (iii) viruses grouped in the species a-4, which are most frequently associated with common skin warts (Bernard et al., 2010;de Villiers et al., 2004).Other HPV-containing genera are less heterogeneous. The betapapillomavirus (b-PV) types cause flat lesions in epidermodysplasia verruciformis patients, but evident HPV lesions are rare in immune-competent individuals (Pfister et al., 2003). The mupapillomavirus (m-PV) and some gammapapillomavirus (c-PV) types cause proliferative cutaneous lesions in humans, although the recently identified c-PV types are not associated with known lesions. In addition, c-PV and m-PV types differ from each other in that...

Diversity of human papillomavirus in the anal canal of men: the HIM Study

“…In fact, more than 200 different presumed new HPV types are waiting for full genome characterization of which the majority clusters within the γ-HPV genus [4-6]. Some differences were observed regarding the prevalence of individual types among the three geographical locations.…”

“…Whereas α-HPV types have been mainly isolated from mucosal and genital lesions and thus categorized as mucosal types, β- and γ-HPV types were mostly isolated from the skin and have been grouped together as cutaneous HPV [4]. β- and γ-HPV genera have more genotypes than the α-HPV genus, and partial DNA sequence information points to the existence of hundreds of putative novel HPV types of both viral genera [5-6]. Recent data describe high prevalence of cutaneous HPV at diverse anatomic sites that are different from those in which they were isolated [7-11].…”

A large spectrum of alpha and beta papillomaviruses are detected in human stool samples

“…These are divided into five genera according to the phylogenetic relationship of their L1 ORF: alpha (a), beta (b), gamma (c), mu (m) and nu (n) (de Villiers, 2013). Hundreds of putative novel HPVs have recently been identified in mucosa and skin by innovative and advanced technologies in DNA sequencing and bioinformatics (Chouhy et al, 2013a).…”

Evaluation of Human Papillomavirus Genotyping from Formalin-fixed Paraffin-embedded Specimens in Cervical Cancers

“…외피가 없는 55 nm의 정이십면체 바이러스이고, 사람 외에도 여러 동물에 게 유두종을 일으킨다 [19]. HPV는 약 200여종의 유전형이 있 고 지금까지 170여종에 달하는 유전형의 염기서열이 완전히 밝혀졌다 [5]. …”