Metagenomic sequencing reveals a lack of virus exchange between native and invasive freshwater fish across the Murray-Darling Basin, Australia

Vincenzo A Costa; Jonathon C O Mifsud; Dean Gilligan; Jane E Williamson; Edward C Holmes; Jemma L Geoghegan

doi:10.1093/ve/veab034

Metagenomic sequencing reveals a lack of virus exchange between native and invasive freshwater fish across the Murray-Darling Basin, Australia

Virus Evol. 2021 Apr 13;7(1):veab034. doi: 10.1093/ve/veab034. eCollection 2021 Jan.

Authors

Vincenzo A Costa¹, Jonathon C O Mifsud¹, Dean Gilligan², Jane E Williamson¹, Edward C Holmes³, Jemma L Geoghegan^{1

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Affiliations

¹ Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.
² NSW Department of Primary Industries, Batemans Bay Fisheries Office, Batemans Bay 2536, Australia.
³ Marie 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, NSW 2006, Australia.
⁴ Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand.
⁵ Institute of Environmental Science and Research, Wellington, Porirua 5022, New Zealand.

Abstract

Biological invasions are among the biggest threats to freshwater biodiversity. This is increasingly relevant in the Murray-Darling Basin, Australia, particularly since the introduction of the common carp (Cyprinus carpio). This invasive species now occupies up to ninety per cent of fish biomass, with hugely detrimental impacts on native fauna and flora. To address the ongoing impacts of carp, cyprinid herpesvirus 3 (CyHV-3) has been proposed as a potentially effective biological control agent. Crucially, however, it is unknown whether CyHV-3 and other cyprinid herpesviruses already exist in the Murray-Darling. Further, little is known about those viruses that naturally occur in wild freshwater fauna, and the frequency with which these viruses jump species boundaries. To document the evolution and diversity of freshwater fish viromes and better understand the ecological context to the proposed introduction of CyHV-3, we performed a meta-transcriptomic viral survey of invasive and native fish across the Murray-Darling Basin, covering over 2,200 km of the river system. Across a total of thirty-six RNA libraries representing ten species, we failed to detect CyHV-3 nor any closely related viruses. Rather, meta-transcriptomic analysis identified eighteen vertebrate-associated viruses that could be assigned to the Arenaviridae, Astroviridae, Bornaviridae, Caliciviridae, Coronaviridae, Chuviridae, Flaviviridae, Hantaviridae, Hepeviridae, Paramyxoviridae, Picornaviridae, Poxviridae, Reoviridae and Rhabdoviridae families, and a further twenty-seven that were deemed to be associated with non-vertebrate hosts. Notably, we revealed a marked lack of viruses that are shared among invasive and native fish sampled here, suggesting that there is little virus transmission from common carp to native fish species, despite co-existing for over fifty years. Overall, this study provides the first data on the viruses naturally circulating in a major river system and supports the notion that fish harbour a large diversity of viruses with often deep evolutionary histories.

Keywords: RNA sequencing; fish virus; freshwater fish; meta-transcriptomics; virome; virus evolution.