E. C. Holmes

Meta-transcriptomic analysis of companion animal infectomes reveals their diversity and potential roles in animal and human disease

The paper analyzes meta-transcriptomic data from companion animals to identify microbial communities and assess zoonotic risks.

Limited transmission of microbial species among coral reef fishes from the Great Barrier Reef, Australia

The paper investigates microbial transmission among reef fishes in the Great Barrier Reef, finding limited cross-species transmission despite ecological interactions.

Mapping glycoprotein structure reveals defining events in the evolution of the Flaviviridae

The paper maps glycoprotein structures across Flaviviridae to identify evolutionary events shaping their virology and ecology.

Genomic and phylogenetic features of the Picobirnaviridae suggest microbial rather than animal hosts

This study analyzes genomic and phylogenetic data of picobirnaviruses to suggest they are bacterial rather than animal pathogens, identifying seven potential genera and showing frequent cross-species transmission.

The diverse viromes of Australian lizards are shaped by host taxonomy and habitat

This study identifies novel viruses in Australian lizards, showing that virome diversity is shaped by host taxonomy, habitat, and range size.

A 39.8kb flavi-like virus uses a novel strategy for overcoming the RNA virus error threshold

This paper identifies a 39.8kb flavi-like virus without an exonuclease that overcomes the RNA virus error threshold by using bacterial nucleic acid metabolism domains.

Identification of a novel papillomavirus from a New Zealand fur seal (Arctocephalus forsteri) with oral papilloma-like lesions

The paper identifies a novel papillomavirus, AfPV1, in New Zealand fur seals with oral papilloma-like lesions and detects a novel gammaherpesvirus, AfGHV1, in another individual.

Australian terrestrial environments harbour extensive RNA virus diversity

The paper identifies extensive RNA virus diversity in Australian soils and sediments, revealing novel viral clades and highlighting environmental factors influencing viral abundance and diversity.

Metagenomic analysis of individual mosquitos reveals the ecology of insect viruses

The paper analyzes the virome of 2,438 individual mosquitoes across China to reveal viral diversity, geographic hotspots, and the impact of host phylogeny on viral composition.

Total infectome investigation of diphtheritic stomatitis in yellow-eyed penguins (Megadyptes antipodes) reveals a novel and abundant megrivirus

The paper investigates the infectome of diphtheritic stomatitis in yellow-eyed penguins, identifying a novel megrivirus associated with the disease.

Host specificity shapes fish viromes across lakes on an isolated remote island

The paper investigates fish viromes on Chatham Island, identifying 19 viruses including 16 novel species and finding that virome composition is not influenced by ecological factors.

Viral capsid, antibody, and receptor interactions: experimental analysis of the antibody escape evolution of canine parvovirus

This study uses in vitro selection and deep sequencing to identify escape mutations in canine parvovirus selected by two antibodies, revealing mechanisms of antibody and receptor binding interactions.

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

The paper examines how the adaptive radiation of African cichlid fishes influenced viral diversity and evolution, finding accelerated hepacivirus diversification during periods of rapid cichlid diversification.

Divergent hepaciviruses, chuvirus and deltaviruses in Australian marsupial carnivores (Dasyurids) identified through transcriptome mining

The paper identifies novel viruses in Australian marsupial carnivores using transcriptome data, revealing divergent hepaciviruses, chuviruses, and deltaviruses.

Virome analysis of New Zealand's bats reveals cross-species viral transmission among the Coronaviridae

This study analyzes the viromes of New Zealand's bats to investigate cross-species viral transmission, finding evidence of alphacoronavirus jumps between species and a novel short-genome coronavirus.

Using artificial intelligence to document the hidden RNA virosphere

This study uses a deep learning algorithm to discover highly divergent RNA viruses in metatranscriptomes, identifying 161,979 potential species and 180 supergroups.

Understanding the Divergent Evolution and Epidemiology of H3N8 Influenza Viruses in Dogs and Horses

This paper compares the evolution and epidemiology of H3N8 influenza viruses in dogs and horses to understand their distinct evolutionary fates and potential zoonotic risks.

Evidence for an aquatic origin of influenza virus and the order Articulavirales

The paper traces the evolutionary history of the Articulavirales order, identifying aquatic origins and host jumps, including a sturgeon-associated influenza virus and a new family in Cnidaria.

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

The paper identifies 32 novel flavivirus sequences in non-bilaterian hosts, extending the host range and supporting an ancient origin of flaviviruses near the emergence of metazoans.

Individual bat viromes reveal the co-infection, spillover and emergence risk of potential zoonotic viruses

The study analyzes viral diversity in individual bats to assess co-infection, spillover, and zoonotic risk of potential viruses.

Gammaretroviruses, novel viruses and pathogenic bacteria in Australian bats with neurological signs, pneumonia and skin lesions

This study identifies pathogens in Australian bats with neurological signs, pneumonia, and skin lesions using metatranscriptomic sequencing and traditional diagnostics.

Host Phylogeny Shapes Viral Transmission Networks in an Island Ecosystem

The paper analyzes the virome of an island ecosystem to show that host phylogenetic relatedness shapes viral transmission networks, increasing disease emergence risk among closely related species.

A novel gyrovirus associated with a fatal respiratory disease in yellow-eyed penguin (Megadyptes antipodes) chicks

The paper identifies a novel gyrovirus associated with respiratory distress syndrome in yellow-eyed penguin chicks through metatranscriptomic analysis of tissue samples.

Novel Viral and Microbial Species in a Translocated Toutouwai (Petroica longipes) Population from Aotearoa/New Zealand

The paper characterizes the infectome of translocated toutouwai, identifying novel viruses and microbes, and suggests translocations may help restore native infectious communities.

Re-emergence of Severe Acute Diarrhea Syndrome Coronavirus (SADS-CoV) in Guangxi, China, 2021

The paper identifies the re-emergence of SADS-CoV in pigs in Guangxi, China, through qPCR and metagenomic analysis, suggesting undetected circulation since 2019.

Faecal virome of the Australian grey-headed flying fox from urban/suburban environments contains novel coronaviruses, retroviruses and sapoviruses

The paper characterizes the faecal virome of Australian grey-headed flying foxes, identifying novel coronaviruses, retroviruses, and sapoviruses.

Cloacal virome of an ancient host lineage - the tuatara (Sphenodon punctatus) - reveals abundant and diverse diet-related viruses

The paper identifies 49 novel viral species in tuatara cloacal samples, most likely dietary related, and discovers a novel Picornaviridae virus potentially infecting tuatara.

Divergent Evolutionary Pathways of Myxoma Virus in Australia: Virulence Phenotypes in Susceptible and Partially Resistant Rabbits Indicate Possible Selection for Transmissibility

This study examines the evolution of myxoma virus in Australian rabbits through experimental infections, revealing diverse virulence phenotypes and suggesting selection for transmissibility over inflammation.

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

The study analyzes viromes of 61 reef fish species in the Great Barrier Reef, finding limited cross-species virus transmission despite high biodiversity.

Diverse RNA viruses associated with diatom, eustigmatophyte, dinoflagellate and rhodophyte microalgae cultures

This study identifies ten new RNA virus species in microalgal cultures, expanding the known diversity of viruses infecting unicellular eukaryotes.