Abstract
The discovery of novel viruses in animals expands our knowledge of viral diversity and potentially emerging zoonoses. High-throughput sequencing (HTS) technology gives millions or even billions of sequence reads per run, allowing a comprehensive survey of the genetic content within a sample without prior nucleic acid amplification. In this study, we screened 156 rectal swab samples from apparently healthy bats (n = 96), pigs (n = 9), cattles (n = 9), stray dogs (n = 11), stray cats (n = 11) and monkeys (n = 20) using a HTS metagenomics approach. The complete genome of a novel papillomavirus (PV), Miniopterus schreibersii papillomavirus type 1 (MscPV1), with L1 of 60% nucleotide identity to Canine papillomavirus (CPV6), was identified in a specimen from a Common Bent-wing Bat (M. schreibersii). It is about 7.5kb in length, with a G+C content of 45.8% and a genomic organization similar to that of other PVs. Despite the higher nucleotide identity between the genomes of MscPV1 and CPV6, maximum-likelihood phylogenetic analysis of the L1 gene sequence showed that MscPV1 and Erethizon dorsatum papillomavirus (EdPV1) are most closely related. Estimated divergence time of MscPV1 from the EdPV1/MscPV1 common ancestor was approximately 60.2–91.9 millions of years ago, inferred under strict clocks using the L1 and E1 genes. The estimates were limited by the lack of reliable calibration points from co-divergence because of possible host shifts. As the nucleotide sequence of this virus only showed limited similarity with that of related animal PVs, the conventional approach of PCR using consensus primers would be unlikely to have detected the novel virus in the sample. Unlike the first bat papillomavirus RaPV1, MscPV1 was found in an asymptomatic bat with no apparent mucosal or skin lesions whereas RaPV1 was detected in the basosquamous carcinoma of a fruit bat Rousettus aegyptiacus. We propose MscPV1 as the first member of the novel Dyolambda-papillomavirus genus.
Highlights
More than 70% of the emerging infectious disease agents are caused by microbes jumping from animals into human
We report in this paper the discovery and characterization of a novel bat papillomavirus (PV) from rectal swab samples randomly collected from asymptomatic wild, food and pet animals using a metagenomic approach
Virus discovery has traditionally been done by phenotypic techniques such as animal inoculation or chick embryo inoculation which are later replaced by tissue culture
Summary
More than 70% of the emerging infectious disease agents are caused by microbes jumping from animals into human. This has been well exemplified by the highly fatal human infection due to avian influenza A H5N1 in 1997 [1]. Bats are ideal incubators for new emerging infectious agents as they are mammals which roosted together and can fly over vast geographical distance [5]. This has reignited the interest in seeking for new bat viruses including many bat coronaviruses and the recent discovery of bat influenza virus [6]. We report in this paper the discovery and characterization of a novel bat papillomavirus (PV) from rectal swab samples randomly collected from asymptomatic wild, food and pet animals using a metagenomic approach
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