Recent advances in the inference of deep viral evolutionary history.

The rapid rate of virus evolution, while useful for outbreak investigations, poses a challenge for accurately estimating long-term viral evolutionary divergence and leaves us with little genomic traces at deep evolutionary timescales, complicating the reconstruction of deep virus evolutionary history. Recent advancements in protein structure prediction and computational biology have opened up new avenues and enabled us to peer back further in time and with greater clarity than ever before. Here, we review recent approaches to reconstructing the deep evolutionary history of viruses.

Diverse viral pathogens in Australian canines: limited geographic structure and the first detection of an RNA virus in dingoes.

Viruses impose a substantial disease burden on dogs, and the close relationship between dogs and humans may facilitate zoonotic disease emergence. Australia's geographic isolation, strict biosecurity measures, and native dingo populations present a unique model for understanding the spread and evolution of canine viruses. However, aside from a few well-characterized pathogens, genomic data are scarce for many common dog viruses, limiting our understanding of their evolution and disease ecology.

Tunicate metatranscriptomes reveal evidence of ancient co-divergence between viruses and their hosts.

Tunicates are a key transitional taxon in animal evolution as the closest extant invertebrate relatives of the vertebrates. Their RNA viruses may also reflect this transitional state, but this has not been tested. In particular, it is not known whether tunicate RNA viruses form a sister group to those found in vertebrates, indicative of virus-host co-divergence throughout the entire evolutionary history of the chordates.

Limited similarity in microbial composition among coral reef fishes from the Great Barrier Reef, Australia.

Reef fishes exhibit enormous biodiversity within a highly interactive ecosystem. Relatively little is known about the diversity and evolution of microbial species associated with reef fish, even though this may provide valuable insights into the factors that shape microbial communities. Through metatranscriptomic sequencing, we characterized the viruses, bacteria, and single-celled eukaryotes from 126 reef fish species inhabiting Lizard Island and Orpheus Island on the Great Barrier Reef, Australia.

Integrated analysis of protein sequence and structure redefines viral diversity and the taxonomy of the .

The are a family of non-segmented positive-sense enveloped RNA viruses containing significant pathogens including hepatitis C virus and yellow fever virus. Recent large-scale metagenomic surveys have identified many diverse RNA viruses related to classical orthoflaviviruses and pestiviruses but quite different genome lengths and configurations, and with a hugely expanded host range that spans multiple animal phyla, including molluscs, cnidarians and stramenopiles,, and plants. Grouping of RNA-directed RNA polymerase (RdRP) hallmark gene sequences of flavivirus and 'flavi-like' viruses into four divergent clades and multiple lineages within them was congruent with helicase gene phylogeny, PPHMM profile comparisons, and comparison of RdRP protein structure predicted by AlphFold2.

A ~40-kb flavi-like virus does not encode a known error-correcting mechanism.

It is commonly held that there is a fundamental relationship between genome size and error rate, manifest as a notional "error threshold" that sets an upper limit on genome sizes. The genome sizes of RNA viruses, which have intrinsically high mutation rates due to a lack of mechanisms for error correction, must therefore be small to avoid accumulating an excessive number of deleterious mutations that will ultimately lead to population extinction. The proposed exceptions to this evolutionary rule are RNA viruses from the order (such as coronaviruses) that encode error-correcting exonucleases, enabling them to reach genome lengths greater than 40 kb.

A novel papillomavirus in a New Zealand fur seal (Arctocephalus forsteri) with oral lesions.

Despite being the predominant seal species in the Australian-New Zealand region and serving as a key indicator of marine environmental health, little is known about infectious diseases in New Zealand fur seals (Long-nosed fur seal; Arctocephalus forsteri). Several papillomaviruses have been identified in earless seals and sea lions, with the latter linked to cutaneous plaques and invasive squamous cell carcinoma. To date, no papillomaviruses have been reported in fur seals.

Host adaptive radiation is associated with rapid virus diversification and cross-species transmission in African cichlid fishes.

Adaptive radiations are generated through a complex interplay of biotic and abiotic factors. Although adaptive radiations have been widely studied in the context of animal and plant evolution, little is known about how they impact the evolution of the viruses that infect these hosts, which in turn may provide insights into the drivers of cross-species transmission and hence disease emergence. We examined how the rapid adaptive radiation of the cichlid fishes of African Lake Tanganyika over the last 10 million years has shaped the diversity and evolution of the viruses they carry.

Australian terrestrial environments harbour extensive RNA virus diversity.

Australia is home to a diverse range of unique native fauna and flora. To address whether Australian ecosystems also harbour unique viruses, we performed meta-transcriptomic sequencing of 16 farmland and sediment samples taken from the east and west coasts of Australia. We identified 2460 putatively novel RNA viruses across 18 orders, the vast majority of which belonged to the microbe-associated phylum Lenarviricota.

Divergent hepaciviruses, delta-like viruses, and a chu-like virus in Australian marsupial carnivores (dasyurids).

Although Australian marsupials are characterised by unique biology and geographic isolation, little is known about the viruses present in these iconic wildlife species. The Dasyuromorphia are an order of marsupial carnivores found only in Australia that include both the extinct Tasmanian tiger (thylacine) and the highly threatened Tasmanian devil. Several other members of the order are similarly under threat of extinction due to habitat loss, hunting, disease, and competition and predation by introduced species such as feral cats.

Evidence for an ancient aquatic origin of the RNA viral order .

The emergence of previously unknown disease-causing viruses in mammals is in part the result of a long-term evolutionary process. Reconstructing the deep phylogenetic histories of viruses helps identify major evolutionary transitions and contextualizes the emergence of viruses in new hosts. We used a combination of total RNA sequencing and transcriptome data mining to extend the diversity and evolutionary history of the RNA virus order , which includes the influenza viruses.

Limited cross-species virus transmission in a spatially restricted coral reef fish community.

The Great Barrier Reef (GBR)-the largest coral reef ecosystem in the world-supports over 1,200 fish species with some of the highest population densities and diversities observed in vertebrates, offering a high potential for virus transmission among species. As such, the GBR represents an exceptional natural ecosystem to determine the impact of host community diversity on virus evolution and emergence. In recent decades, the GBR has also experienced significant threats of extinction, making it one of the most vulnerable ecosystems on the planet.

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

The flavivirids (family ) are a group of positive-sense RNA viruses that include well-documented agents of human disease. Despite their importance and ubiquity, the timescale 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 (, phylum ), implying that the flaviviruses arose early in the evolution of the Metazoa.

Transcriptome Mining Expands Knowledge of RNA Viruses across the Plant Kingdom.

Our current understanding of plant viruses stems largely from those affecting economically important plants. Yet plant species in cultivation represent a small and biased subset of the plant kingdom. Here, we describe virus diversity and abundance in 1,079 transcriptomes from species across the breadth of the plant kingdom (Archaeplastida) by analyzing open-source data from the 1000 Plant Transcriptomes Initiative (1KP).

Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the .

The comprise a genetically diverse group of positive-sense single-stranded RNA virus families that infect a range of invertebrate and vertebrate hosts. Recent metagenomic studies have identified nido-like virus sequences, particularly those related to the , in a range of aquatic hosts including fish, amphibians, and reptiles. We sought to identify additional members of the in both bony and jawless fish through a combination of total RNA sequencing (meta-transcriptomics) and data mining of published RNA sequencing data and from this reveal more of the long-term patterns and processes of coronavirus evolution.

Erratum: Virome composition in marine fish revealed by meta-transcriptomics.

[This corrects the article DOI: 10.1093/ve/veab005.].

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

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 (). This invasive species now occupies up to ninety per cent of fish biomass, with hugely detrimental impacts on native fauna and flora.

Virome composition in marine fish revealed by meta-transcriptomics.

Revealing the determinants of virome composition is central to placing disease emergence in a broader evolutionary context. Fish are the most species-rich group of vertebrates and so provide an ideal model system to study the factors that shape virome compositions and their evolution. We characterized the viromes of nineteen wild-caught species of marine fish using total RNA sequencing (meta-transcriptomics) combined with analyses of sequence and protein structural homology to identify divergent viruses that often evade characterization.