How many papillomavirus species can go undetected in papilloma lesions?

Abstract

A co-infection comprising to at least seven papillomavirus (PV) types was detected by next generation sequencing (NGS) of randomly primed rolling circle amplification (RCA) products of a bovine (Bos taurus) papilloma lesion from the Brazilian Amazon region. Six putative new PV types that could not be detected by commonly used PCR protocols were identified. Their overall L1 nucleotide identities were less than 90% compared to described PV species and types. L1 nucleotide BLAST sequence hits showed that each new type was related to Beta, Gamma, Dyokappa, Dyoeta, and Xipapillomavirus, as well as two likely new unclassified genera. Our results show that the employment of NGS is relevant to the detection and characterization of distantly related PV and is of major importance in co-infection studies. This knowledge will help us understand the biology and pathogenesis of PV, as well as contribute to disease control. Moreover, we can also conclude that there are many unknown circulating PVs.

Papillomaviruses in ruminants: An update

“…The majority of BPV type‐specific prevalence data are from Japan and Brazil. Brazil is one of the largest beef and milk producer in the world, and 21 of 23 BPV types were detected and described here, as well as a great number of putative new types (Batista et al., ; Carvalho, Batista, Silva, Balbino, & Freitas, ; Da Silva et al., , ; Daudt, da Silva, Cibulski, et al., ; Daudt, da Silva, Streck, et al., ; Lunardi, Alfieri, et al., ; Lunardi et al., ). The BPV type‐specific distribution and their association with specific lesions in cattle are summarized in Table .…”

“…The genetic characterization by PCR using the degenerated primer pairs originally designed for HPV detection (FAP59/FAP64 or MY09/MY11), which amplifies a highly conserved region of PV L1 gene (Forslund, Antonsson, Nordin, Stenquist, & Hansson, ; Snijders et al., ), has enabled the identification and characterization of several PV types in almost all affected PV species (Antonsson & Hansson, ; Gottschling, Wibbelt, Wittstatt, Stockfleth, & Nindl, ; Munday, Dunowska, Hills, & Laurie, ; Rector et al., ), as well as in new BPV types in both dairy and beef cattle from distinct geographical regions worldwide (Lunardi, De Alcântara, et al., ; Ogawa et al., ). Also, putative and new BPV types, partially or totally sequenced by Sanger or NGS, have been published recently (Da Silva et al., ; Daudt, da Silva, Streck, et al., ; Lunardi et al., ). However, the development of NGS has enabled the discovery of new BPV types that were not amplified using FAP or MY primer pairs (Da Silva et al., ; Daudt, da Silva, Streck, et al., ).…”

“…Also, putative and new BPV types, partially or totally sequenced by Sanger or NGS, have been published recently (Da Silva et al., ; Daudt, da Silva, Streck, et al., ; Lunardi et al., ). However, the development of NGS has enabled the discovery of new BPV types that were not amplified using FAP or MY primer pairs (Da Silva et al., ; Daudt, da Silva, Streck, et al., ).…”

“…In contrast, only 39 ruminant PV types are recognized up to now (https://pave.niaid.nih.gov/), which leads us to support the importance of improving the efforts to characterize animal PVs. Recent studies, some using high‐throughput sequencing platforms have shown that animal PVs were underestimated and new types have been characterized (Bauermann et al., ; Da Silva et al., ; Daudt, da Silva, Streck, et al., ; López‐Bueno et al., ; Tore et al., ).…”

“…Due to the complex and the difficulty of tissue culture systems for the in vitro propagation of the PV (Bienkowska‐haba et al., ), detailed genetic and molecular information has been accumulated, especially in human and bovine papillomavirus, using cloning and Sanger sequencing. Lately, the new technology of high efficiency sequencing has enabled the characterization of new and putative new BPVs (Da Silva et al., ; Daudt, da Silva, Streck, et al., ; Munday et al., ). As PVs are cosmopolitan viruses, they have been detected in many regions of almost all continents infecting a large range of amniote species (Rector & Van Ranst, ).…”