Edward Charles Holmes

This study identifies 86 viruses in Australian dogs and dingoes, revealing limited geographic structure and the first detection of rotavirus A in dingoes, suggesting cross-species transmission.

The paper identifies 162 viral species in small mammals from Yunnan, China, including 102 novel species and 24 with potential human health risks.

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

VirID improves RNA virus discovery and characterization from metagenomic data by reducing false positives, accurately estimating diversity, and identifying virus-host associations.

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

Reanalysis of public environmental metatranscriptomes from the Huanan market links SARS-CoV-2 positivity to one wildlife stall containing raccoon dog, civet and bamboo rat genetic material.

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.

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

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.

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.

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.

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.

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

The paper compares two avian influenza virus incursions in Australia, showing contrasting evolutionary dynamics between H4 and H10 viruses.

The paper identifies a novel RNA virus in zoonotic Plasmodium knowlesi isolates, showing it belongs to an unclassified viral taxon called ormycoviruses.

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.

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 paper analyzes viromes of Antarctic fish to compare viral diversity with lower latitude fish, finding comparable complexity and evidence of host-switching and viral adaptation.

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

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

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.

The paper uses genomic data to analyze how national and international restrictions affected SARS-CoV-2 transmission in Brazil and Paraguay, showing the spread of variants and the role of importation.

The paper identifies novel viruses in introduced passerine birds in New Zealand and highlights potential risks to endemic species.

The paper identifies viral sequences in laboratory reagents using metagenomic sequencing and reports their presence in negative control libraries.

The paper identifies and characterizes genetic diversity and host range of rodent-borne coronaviruses in China, revealing new subtypes and genomic complexity.

CCMetagen improves metagenomic classification by using weighted read mappings, outperforming existing tools in precision and F1 scores for species-level identification.

This study evaluates metatranscriptomics for identifying fungal species and subspecies in mixed communities using a mock community of 17 fungal isolates, showing high accuracy at species and strain levels when low-abundance taxa are excluded.

The paper identifies a novel RNA virus, MaRNAV-1, associated with Plasmodium vivax in humans and mosquitoes, and a related virus in birds infected with Leucocytozoon parasites.

The paper identifies a novel HDV-like agent in ducks, showing genetic divergence but structural and functional similarities to HDV, challenging current understanding of HDV origins.

This study characterizes the faecal virome of captive and wild Tasmanian devils using VLP metagenomics and meta-transcriptomics, revealing novel viruses and highlighting differences in viral diversity between populations.