Identification of a Novel Bat Papillomavirus by Metagenomics

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...

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Main Authors:	Tse, Herman, Tsang, Alan K. L., Tsoi, Hoi-Wah, Leung, Andy S. P., Ho, Chi-Chun, Lau, Susanna K. P., Woo, Patrick C. Y., Yuen, Kwok-Yung
Format:	Online
Language:	English
Published:	Public Library of Science 2012
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427170/

id	pubmed-3427170
recordtype	oai_dc
spelling	pubmed-34271702012-08-30 Identification of a Novel Bat Papillomavirus by Metagenomics Tse, Herman Tsang, Alan K. L. Tsoi, Hoi-Wah Leung, Andy S. P. Ho, Chi-Chun Lau, Susanna K. P. Woo, Patrick C. Y. Yuen, Kwok-Yung Research Article 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. Public Library of Science 2012-08-24 /pmc/articles/PMC3427170/ /pubmed/22937142 http://dx.doi.org/10.1371/journal.pone.0043986 Text en © 2012 Tse et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Tse, Herman Tsang, Alan K. L. Tsoi, Hoi-Wah Leung, Andy S. P. Ho, Chi-Chun Lau, Susanna K. P. Woo, Patrick C. Y. Yuen, Kwok-Yung
spellingShingle	Tse, Herman Tsang, Alan K. L. Tsoi, Hoi-Wah Leung, Andy S. P. Ho, Chi-Chun Lau, Susanna K. P. Woo, Patrick C. Y. Yuen, Kwok-Yung Identification of a Novel Bat Papillomavirus by Metagenomics
author_facet	Tse, Herman Tsang, Alan K. L. Tsoi, Hoi-Wah Leung, Andy S. P. Ho, Chi-Chun Lau, Susanna K. P. Woo, Patrick C. Y. Yuen, Kwok-Yung
author_sort	Tse, Herman
title	Identification of a Novel Bat Papillomavirus by Metagenomics
title_short	Identification of a Novel Bat Papillomavirus by Metagenomics
title_full	Identification of a Novel Bat Papillomavirus by Metagenomics
title_fullStr	Identification of a Novel Bat Papillomavirus by Metagenomics
title_full_unstemmed	Identification of a Novel Bat Papillomavirus by Metagenomics
title_sort	identification of a novel bat papillomavirus by metagenomics
description	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.
publisher	Public Library of Science
publishDate	2012
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427170/
_version_	1611552084956545024

Identification of a Novel Bat Papillomavirus by Metagenomics

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