E. C. Holmes

This study uses metagenomic sequencing to identify viral and immune-mediated causes of unexplained childhood encephalitis in Australia, finding respiratory viruses in five cases and immune-mediated causes in six.

This study investigates the impact of Wolbachia wAu strain on RNA virome composition in Drosophila simulans and identifies novel viruses in the species.

This study identifies 30 new RNA virus species from microalgal transcriptomes, revealing their phylogenetic diversity and highlighting the need for improved detection methods.

The paper identifies divergent coronaviruses in bony and jawless fish, revealing cross-species transmission and distinct evolutionary patterns within the Coronaviridae family.

The paper identifies novel bat coronaviruses, including relatives of SARS-CoV-2, from a region in China, providing insights into their evolutionary origins and geographic distribution.

The paper uses metagenomic sequencing to analyze viruses in native and invasive fish in the Murray-Darling Basin, finding no evidence of CyHV-3 or shared viruses between species.

This study identifies frequent recombination between non-structural and structural genes in lagoviruses as a key driver of epidemiological fitness, leading to the emergence of multiple recombinant variants that outcompete parental strains.

The paper identifies a novel rubella-like virus in Pacific electric rays, revealing a complex evolutionary history of the Matonaviridae family.

The paper identifies two new Amnoonviridae viruses in fish and finds additional TiLV transcripts, suggesting a broad host range for the family.

The paper shows that incorporating occurrence data with birth-death models improves estimates of the basic reproductive number in phylodynamic analyses, while coalescent models are less affected by sampling biases but cannot use occurrence data.

The paper identifies novel viruses in urban wild birds with paresis using meta-transcriptomic analysis and finds potential viral causes of neurological and muscular diseases.

The paper identifies five divergent influenza-like viruses in amphibians and fish, suggesting an ancient evolutionary association between influenza viruses and vertebrates.

The paper identifies two novel viruses in captive bearded dragons with respiratory disease using meta-transcriptomic sequencing.

The paper was withdrawn due to the non-publication of a zoonotic risk prediction tool mentioned in the manuscript.

This study examines SARSr-CoV-2 in Malayan pangolins, showing lung infection, vertical transmission, and immune response similarities to COVID-19 in humans.

This study compares viromes of urban and rural red foxes, finding differences in viral abundance and diversity, and identifies novel viruses with potential zoonotic relevance.

This study identifies 18 novel RNA viruses in green and chlorarachniophyte algae using meta-transcriptomic and structural homology methods, suggesting horizontal transfer and evolutionary links to plant and fungal viruses.

The paper identifies a divergent Articulavirus in an Australian gecko using meta-transcriptomics and protein structure comparisons, revealing a new genus in the Amnoonviridae family.

The paper identifies novel hepaciviruses and pegiviruses in Australian wildlife and supports virus-host co-divergence through phylogenetic analysis.

The paper uses meta-transcriptomics to analyze virome composition in marine fish, identifying new viruses and factors shaping virome diversity.

This study identifies RNA viruses in Ixodes uriae ticks from both hemispheres, finding shared viruses suggesting cross-circumpolar dispersal via migratory birds, while host populations remain geographically distinct.

The paper uses SARS-CoV-2 genome sequencing and agent-based modeling to estimate local transmission rates during the early stages of the COVID-19 outbreak in New South Wales.

This paper proposes a dynamic nomenclature system for SARS-CoV-2 to improve genomic epidemiology by tracking active lineages and their spread.

The paper identifies a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand through whole genome sequencing and phylogenetic analysis.

This study examines how residential energy retrofits affect indoor air quality and microbial exposure by comparing weatherized and non-weatherized homes.

This paper identifies a novel bat coronavirus, RmYN02, with sequence similarities to HCoV-19 and natural insertions at the S1/S2 cleavage site, suggesting a possible recombinant origin for HCoV-19.

This study passaged influenza A viruses in different MDCK cell lines and found limited genome-wide sequence variation, with most mutations occurring in the hemagglutinin gene.

The paper identifies 2019-nCoV related coronaviruses in Malayan pangolins, suggesting they may be intermediate hosts for the virus.

The paper characterizes the complete genome of a novel coronavirus, WHCV, linked to a respiratory outbreak in Wuhan, finding it closely related to SARS-like bat coronaviruses.

The paper analyzes virome diversity in Antarctic penguins and their ticks, finding comparable diversity to Australian waterbirds and rejecting the idea of low pathogen pressure in penguins.