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.
Highlights
Papillomaviruses (PVs) are circular double-stranded DNA viruses containing approximately 8,000 base pairs[1,2]
next generation sequencing (NGS) from rolling circle amplification (RCA) products of one papilloma lesion enabled the amplification of seven full-length PV genomes
In comparison to Human PV (HPV), only 15 Bos taurus papillomavirus (BPV) types have been detected and fully sequenced far (PaVE). This scenario is probably pictured because of the lower efforts in BPV studies when compared to HPV due clinical relevance and funding applied
Summary
Papillomaviruses (PVs) are circular double-stranded DNA viruses containing approximately 8,000 base pairs (bp)[1,2] They belong to the Papillomaviridae family and these complex viruses can infect a wide range of amniotes[1,2,3]. PVs are usually characterized by PCR amplicon sequencing, which is performed using degenerate primer pairs that amplify a relatively conserved L1 gene region from all known PV types and species[4]. This technique has allowed the identification of divers putative new PVs types in humans and other animals, including BPV types in cattle herds from distinct continents worldwide[5,6,7,8]. PVs could be cultivated only in a sophisticated and arduous raft cell culture system, thereby hampering whole genome analysis due to the lack of necessary adequate amount of purified genomic viral DNA24
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