Limited Cross-Species Virus Transmission in a Spatially Restricted Coral Reef Fish Community

Costa, Vincenzo A; Bellwood, David R.; Mifsud, Jonathon C O; Geoghegan, Jemma L.; Holmes, Edward C.; Harvey, Erin

doi:10.1101/2022.05.17.492384

Cited by 6 publications

(6 citation statements)

References 77 publications

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“…2022 ), hepaci- and pesti-like viruses in cartilaginous fish (Chondrichthyes) ( Shi et al 2018 ), and hepaciviruses in reptiles and bony fish (Osteichthyes) ( Shi et al 2018 ; Porter et al. 2020 ; Costa et al. 2022 ; Harding et al.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians

et al. 2022

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The flavivirids (family Flaviviridae) are a group of positive-sense RNA viruses that include well-documented agents of human disease. Despite their importance and ubiquity, the time-scale of flavivirid evolution is uncertain. An ancient origin, spanning millions of years, is supported by their presence in both vertebrates and invertebrates and by the identification of a flavivirus-derived endogenous viral element in the peach blossom jellyfish genome (Craspedacusta Sowerby, phylum Cnidaria), implying that the flaviviruses arose early in the evolution of the Metazoa. To date, however, no exogenous flavivirid sequences have been identified in these hosts. To help resolve the antiquity of the Flaviviridae, we mined publicly available transcriptome data across the Metazoa. From this, we expanded the diversity within the family through the identification of 32 novel viral sequences and extended the host range of the pestiviruses to include amphibians, reptiles, and ray-finned fish. Through cophylogenetic analysis we found cross-species transmission to be the predominate macroevolutionary event across the non-vectored flavivirid genera (median, 68%), including a cross-species transmission event between bats and rodents, although long-term virus-host co-divergence was still a regular occurrence (median, 23%). Notably, we discovered flavivirus-like sequences in basal metazoan species, including the first associated with Cnidaria. This sequence formed a basal lineage to the genus Flavivirus and was closer to arthropod and crustacean flaviviruses than those in the tamanavirus group that include a variety of invertebrate and vertebrate viruses. Combined, these data attest an ancient origin of the flaviviruses, likely close to the emergence of the metazoans 750–800 million years ago.

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Section: Introductionmentioning

confidence: 99%

Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians

et al. 2022

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“…The Great Barrier Reef in Australia, for example, boasts almost four times the number of fish species compared to the Southern Ocean (De'ath et al, 2012). Contrary to their limited host diversity, however, the observed viral family richness and number and types of viral families infecting Ross Sea fishes were comparable to those of this coral reef system (Costa, Bellwood, et al, 2023;Costa et al, 2024). In fact, similar questions have also been asked of penguins and their ticks from the Antarctic Peninsula, revealing RNA virome diversity akin to that in Australian waterbirds .…”

Section: Discussionmentioning

confidence: 90%

Viromes of Antarctic fish resembles the diversity found at lower latitudes

Grimwood,

Waller,

Wierenga

et al. 2024

Preprint

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Antarctica harbours some of the most isolated and extreme environments on Earth, concealing a largely unexplored and unique component of the global animal virosphere. To understand the diversity and evolutionary histories of viruses in these polar species we determined the viromes of 11 Antarctic fish species with 248 samples collected from the Ross Sea region spanning the Perciformes, Gadiformes, and Scorpaeniformes orders. The continent's shift southward and cooling temperatures over 20 million years ago led to a reduction in biodiversity and subsequent radiation of some marine fauna, such as the notothenioid fishes. Despite decreased host species richness in polar regions, we revealed a surprisingly complex virome diversity in Ross Sea fish, with the types and numbers of viruses per host species and individuals sampled comparable to that of fish in warmer marine environments with higher host community diversity. We also observed a higher number of closely related viruses likely representing instances of recent and historic host-switching events among Perciformes (all notothenioids) than in the Gadiformes, suggesting that rapid speciation events within this order generated closely related host species with few genetic barriers to cross-species transmission. Additionally, we identified novel genomic variation in an arenavirus with a split nucleoprotein sequence containing a stable helical structure, indicating potential adaptation of viral proteins to extreme temperatures. These findings enhance our understanding of virus evolution and virus-host interactions in response to environmental shifts, especially in less diverse ecosystems more vulnerable to the impacts of anthropogenic and climate changes.

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“…While we detected MrNV in combined liver and gill samples of the common carp ( C. carpio ), it is likely that these viruses were derived from environmental contamination of gill tissue, which often leads to the identification of a large diversity of viruses associated with aquatic invertebrates [ 32 , 33 ]. This is supported by the identification of M. australiense in two of the five MrNV-positive libraries ( Figure 1 ).…”

Section: Discussionmentioning

confidence: 99%

Genetic Reassortment between Endemic and Introduced Macrobrachium rosenbergii Nodaviruses in the Murray-Darling Basin, Australia

Costa

Geoghegan

Holmes

et al. 2022

Viruses

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Macrobrachium rosenbergii nodavirus (MrNV)—the aetiological agent of white tail disease—is a major limiting factor of crustacean aquaculture as it causes up to 100% mortality in M. rosenbergii larvae and juveniles. Despite the importance of MrNV, there have been few studies on the phylogenetic diversity and geographic range of this virus in Australian waterways. Here, we detected MrNV genomes in common carp (Cyprinus carpio) metatranscriptomes sampled at five freshwater sites across the Murray-Darling Basin (MDB), Australia. We identified genetic divergence of the RNA-dependent RNA polymerase gene between MrNV sequences identified in the northern and southern rivers of the MDB. Northern viruses exhibited strong phylogenetic clustering with MrNV from China, whereas the southern viruses were more closely related to MrNV from Australia. However, all five viruses were closely related in the capsid protein, indicative of genetic reassortment of the RNA1 and RNA2 segments between Australian and introduced MrNV. In addition, we identified Macrobrachium australiense in two of the five MrNV-positive libraries, suggesting that these species may be important reservoir hosts in the MDB. Overall, this study reports the first occurrence of MrNV outside of the Queensland region in Australia and provides evidence for genetic reassortment between endemic and introduced MrNV.

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Limited Cross-Species Virus Transmission in a Spatially Restricted Coral Reef Fish Community

Cited by 6 publications

References 77 publications

Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians

Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians

Viromes of Antarctic fish resembles the diversity found at lower latitudes

Genetic Reassortment between Endemic and Introduced Macrobrachium rosenbergii Nodaviruses in the Murray-Darling Basin, Australia

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