The Institute of Environmental Science and Research (ESR) has changed its name to the New Zealand Institute for Public Health and Forensic Science (PHF Science) as of 1 July 2025. The website address is now www.phfscience.nz. Visitors are automatically redirected to the new address. Please check and update any links and bookmarks.
Use our research, insights & resources
Our intelligence hub hosts all our information, from disease surveillance dashboards to environmental risk assessments. Explore and use PHF Science’s research, insights, tools and resources to make a difference for Aotearoa New Zealand.
PHF Science is working to actively co-design with Māori in research, science and innovation to improve Māori economic, social and wellbeing outcomes and impacts.
PHF Science is a New Zealand Government owned research organisation that plays a critical national role in public health and forensics, and is a key contributor to environment and biosecurity outcomes.
Metagenomic sequencing reveals a lack of virus exchange between native and invasive freshwater fish across the Murray-Darling Basin, Australia
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.
