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Virome heterogeneity and connectivity in waterfowl and shorebird communities

View ORCID ProfileMichelle Wille, View ORCID ProfileMang Shi, View ORCID ProfileMarcel Klaassen, View ORCID ProfileAeron C. Hurt, View ORCID ProfileEdward C. Holmes
doi: https://doi.org/10.1101/528174
Michelle Wille
1WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
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  • For correspondence: michelle.wille@influenzacentre.org edward.holmes@sydney.edu.au
Mang Shi
2Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.
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Marcel Klaassen
3Centre for Integrative Ecology, Deakin University, Geelong, Australia.
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Aeron C. Hurt
1WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
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Edward C. Holmes
2Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.
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  • For correspondence: michelle.wille@influenzacentre.org edward.holmes@sydney.edu.au
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Abstract

Models of host-microbe dynamics typically assume a single-host population infected by a single pathogen. In reality, many hosts form multi-species aggregations and may be infected with an assemblage of pathogens. We used a meta-transcriptomic approach to characterize the viromes of nine avian species in the Anseriformes (ducks) and Charadriiformes (shorebirds). This revealed the presence of 27 viral species, of which 24 were novel, including double-stranded RNA viruses (Picobirnaviridae and Reoviridae), single-stranded RNA viruses (Astroviridae, Caliciviridae, Picornaviridae), a retro-transcribing DNA virus (Hepadnaviridae), and a single-stranded DNA virus (Parvoviridae). These viruses comprise multi-host generalist viruses and those that are host-specific, indicative of both virome connectivity and heterogeneity. Virome connectivity was apparent in two well described multi-host virus species (avian coronavirus and influenza A virus) and a novel Rotavirus species that were shared among some Anseriform species, while heterogeneity was reflected in the absence of viruses shared between Anseriformes and Charadriiformes. Notably, within avian host families there was no significant relationship between either host taxonomy or foraging ecology and virome composition, although Anseriform species positive for influenza A virus harboured more additional viruses than those negative for influenza virus. Overall, we demonstrate complex virome structures across host species that co-exist in multi-species aggregations.

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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 January 29, 2019.
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Virome heterogeneity and connectivity in waterfowl and shorebird communities
Michelle Wille, Mang Shi, Marcel Klaassen, Aeron C. Hurt, Edward C. Holmes
bioRxiv 528174; doi: https://doi.org/10.1101/528174
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Virome heterogeneity and connectivity in waterfowl and shorebird communities
Michelle Wille, Mang Shi, Marcel Klaassen, Aeron C. Hurt, Edward C. Holmes
bioRxiv 528174; doi: https://doi.org/10.1101/528174

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