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Metagenomic identification of diverse animal hepaciviruses and pegiviruses

Ashleigh F. Porter, John H.-O. Pettersson, Wei-Shan Chang, Erin Harvey, Karrie Rose, Mang Shi, John-Sebastian Eden, Jan Buchmann, Craig Moritz, View ORCID ProfileEdward C. Holmes
doi: https://doi.org/10.1101/2020.05.16.100149
Ashleigh F. Porter
1Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
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John H.-O. Pettersson
1Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
2Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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Wei-Shan Chang
1Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
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Erin Harvey
1Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
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Karrie Rose
3Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman, Australia
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Mang Shi
5School of Medicine, Sun Yat-sen University, Guangzhou, China
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John-Sebastian Eden
1Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
4Centre for Virus Research, Westmead Institute for Medical Research, Westmead, Australia
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Jan Buchmann
1Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
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Craig Moritz
6Research School of Biology, and Centre for Biodiversity Analysis, Australian National University, Acton, ACT, Australia
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Edward C. Holmes
1Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
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  • ORCID record for Edward C. Holmes
  • For correspondence: edward.holmes@sydney.edu.au
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Abstract

The RNA virus family Flaviviridae harbours several important pathogens of humans and other animals, including Zika virus, dengue virus and hepatitis C virus. The Flaviviridae are currently divided into four genera - Hepacivirus, Pegivirus, Pestivirus and Flavivirus – each of which have a diverse host range. Members of the genus Hepacivirus are associated with a diverse array of animal species, including humans and non-human primates, other mammalian species, as well as birds and fish, while the closely related pegiviruses have been identified in a variety of mammalian taxa including humans. Using a combination of meta-transcriptomic and whole genome sequencing we identified four novel hepaciviruses and one novel variant of a known virus, in five species of native Australian wildlife, expanding our knowledge of the diversity in this important group of RNA viruses. The infected hosts comprised native Australian marsupials and birds, as well as a native gecko (Gehyra lauta). The addition of these novel viruses led to the identification of a distinct marsupial clade within the hepacivirus phylogeny that also included an engorged Ixodes holocyclus tick collected while feeding on Australian long-nosed bandicoots (Perameles nasuta). Gecko and avian associated hepacivirus lineages were also identified. In addition, by mining the short-read archive (SRA) database we identified another five novel members of Flaviviridae, comprising three new hepaciviruses from avian and primate hosts, as well as two primate-associated pegiviruses. The large-scale phylogenetic analysis of these novel hepacivirus and pegivirus genomes provides additional support for virus-host co-divergence over evolutionary time-scales.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 17, 2020.
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Metagenomic identification of diverse animal hepaciviruses and pegiviruses
Ashleigh F. Porter, John H.-O. Pettersson, Wei-Shan Chang, Erin Harvey, Karrie Rose, Mang Shi, John-Sebastian Eden, Jan Buchmann, Craig Moritz, Edward C. Holmes
bioRxiv 2020.05.16.100149; doi: https://doi.org/10.1101/2020.05.16.100149
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Metagenomic identification of diverse animal hepaciviruses and pegiviruses
Ashleigh F. Porter, John H.-O. Pettersson, Wei-Shan Chang, Erin Harvey, Karrie Rose, Mang Shi, John-Sebastian Eden, Jan Buchmann, Craig Moritz, Edward C. Holmes
bioRxiv 2020.05.16.100149; doi: https://doi.org/10.1101/2020.05.16.100149

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