Edward Charles Holmes

Quantitative host-response mapping enables phenotypic profiling of viruses detected by virome sequencing

ViroChart maps host responses from virome RNA-seq data to identify phenotypic profiles of viruses, revealing host response patterns in animal infections.

Metatranscriptomic Identification of Co- and Incidental Infections in Marine Turtles Reveals Complex Disease Aetiologies

The paper uses metatranscriptomic sequencing to identify co- and incidental infections in marine turtles, revealing complex disease aetiologies involving multiple pathogens.

Metagenomic identification of novel Hepaciviridae in Australian birds reveals pegivirus recombination

The paper identifies two novel pegiviruses and two orthohepaciviruses in Australian birds, revealing recombination events and co-infections among avian hepaciviruses.

A divergent betacoronavirus with a functional furin cleavage site in South American bats

The paper reports a new bat betacoronavirus from Brazil with a functional furin cleavage site in its spike protein, highlighting its phylogenetic distinctiveness and potential zoonotic risk.

Multi-kingdom microbial diversity and interaction landscapes in mosquitoes revealed by 5,163 individual meta-transcriptomes

The paper analyzes 5,163 mosquito meta-transcriptomes to characterize microbial diversity and interactions, identifying pathogens and cross-kingdom associations.

The RNA virome of early metazoans sheds light on long-term virus-host relationships

The paper analyzes RNA viromes of ctenophores and placozoans to explore virus-host relationships, identifying novel viruses and their evolutionary patterns.

Cryo-EM structure of piscine orthoreovirus reveals structural conservation across 450 million years of viral evolution

The paper reports the cryo-EM structure of piscine orthoreovirus, showing structural conservation with mammalian orthoreoviruses despite low sequence identity.

RVPSD: A comprehensive and user-friendly web database for RNA viral protein structures

RVPSD provides a web database of 154,716 AlphaFold2-predicted RNA viral protein structures from 5,263 species, enabling structural and functional analysis of RNA viral proteomes.

Hidden diversity and expanded host range of sarthroviruses, including terrestrial vertebrates

The paper identifies ten new sarthrovirus species from diverse hosts in Australia, expanding the family to 11 species and seven genera, and suggests alternative replication strategies and helper virus associations.

Co-Circulation of Multiple Kolmiovirus Lineages Through Vertebrate Evolution

This paper identifies novel kolmioviruses in vertebrates, showing multiple lineages co-circulated through vertebrate evolution, with HDV-HBV association emerging recently.

Predicting the Evolutionary and Functional Landscapes of Viruses with a Unified Nucleotide-Protein Language Model: LucaVirus

LucaVirus predicts viral evolution and function using a unified nucleotide-protein language model, achieving state-of-the-art results in key virology tasks.

Detection and genomic characterisation of a novel hantavirus in Australian dolphins

The paper detects a novel hantavirus in Australian dolphins and places it within the Mobatvirus genus, indicating hantaviruses can infect non-terrestrial mammals.

Alignment-free phylogenetic inference via hyperbolic protein language models

LucaPhylo infers phylogenetic trees from unaligned protein sequences using hyperbolic geometry and protein language models, achieving accuracy comparable to alignment-based methods for divergent RNA viruses.

Host innate immune response profiling reveals hidden viral infections across diverse animal species

The paper develops a host-response-based framework to detect viral infections by analyzing ISG expression in RNA-seq data from diverse species, revealing hidden infections missed by conventional methods.

RNA virus discovery in Australian camelids reveals divergent picornaviruses and the convergent evolution of upstream ORFs

This study identifies new RNA viruses in invasive camelids in Australia, revealing convergent evolution of upstream ORFs across divergent picornaviruses.

Limited effect of short- to mid-term storage conditions on an Australian farmland soil RNA virome

This study identifies 1,475 novel RNA viruses in Australian soils and demonstrates that snap-freezing is a viable storage method for at least three months.

Viral diversity, ecological interconnectedness, and the identification of mammalian chuviruses in Australian microbats

The paper identifies a new lineage of chuviruses in Australian microbats and reveals high viral diversity and connectivity among microbat species.

Mapping the global distribution and spread of the Plasmodium vivax-associated virus MaRNAV-1

The paper maps the geographic distribution and host associations of MaRNAV-1, a virus linked to Plasmodium vivax, using metatranscriptomic data.

SegFinder: an automated tool for identifying RNA virus genome segments through co-occurrence in multiple sequenced samples

SegFinder identifies RNA virus genome segments by analyzing co-occurrence across samples, discovering novel segments and expanding known segmented virus families.

Isolation of an infectious mammalian chu-like virus from tumor cells of the endangered Tasmanian devil (Sarcophilus harrisii)

The paper isolates a new jingchuvirus, TDCV, from Tasmanian devil tumor cells, showing it infects these cells but not mosquito cells, and suggests it belongs to a novel virus family.

Generalized Biological Foundation Model with Unified Nucleic Acid and Protein Language

This paper introduces LucaOne, a foundation model trained on nucleic acid and protein sequences, demonstrating understanding of biological principles and performing well on related tasks.

Tunicate metatranscriptomes reveal ancient virus-host co-divergence and inter-order recombination in the evolutionary history of disease-causing viruses

The paper analyzes tunicate metatranscriptomes to show that some disease-causing RNA viruses evolved before vertebrates and that recombination between viral orders shaped their evolution.

Limited diversity of bat-associated RNA viruses in endangered and geographically isolated Christmas Island flying foxes

This study characterizes the RNA virome of endangered Christmas Island flying foxes, finding limited diversity dominated by dietary viruses and identifying novel viruses related to mainland Australia and invertebrates.

Infectome Analysis of Small Mammals in Southern China Reveals Ecological Associations and Emerging Threats from Diverse Pathogens

The paper analyzes the pathogen infectome of small mammals in southern China, identifying new pathogens and factors influencing their distribution and diversity.

Insect-specific Alphamesonivirus-1 (Mesoniviridae) in lymph node and lung tissues from two horses with acute respiratory syndrome

This paper reports the first detection of Alphamesonivirus-1 in mammals, specifically horses with acute respiratory syndrome, challenging the belief that mesoniviruses are insect-specific.

Infectome analysis of bat kidneys from Yunnan province, China, reveals close relatives of Hendra-Nipah viruses and prevalent bacterial and eukaryotic pathogens

The paper analyzes the infectome of bat kidneys from Yunnan, China, identifying novel viruses, a protozoan parasite, and bacterial species, including henipaviruses related to Hendra and Nipah viruses.

Comprehensive Infectome Analysis Reveals Diverse Infectious Agents with Zoonotic Potential in Wildlife

The paper analyzes wildlife infectomes to identify zoonotic pathogens, finding 62 novel pathogens including a new coronavirus genus and highlighting high pathogen diversity in Carnivora and Rodentia.

Detection of exotic biosecurity threat ribgrass mosaic virus and novel tobamoviruses through metatranscriptomic sequencing of animal gut content

This paper detects RMV and novel tobamoviruses in Australia using metatranscriptomic sequencing of animal gut content, revealing new viral threats to horticultural systems.

Genome sizes of animal RNA viruses reflect phylogenetic constraints

This study examines genome size variation in animal RNA viruses and finds that phylogenetic constraints, not host type or genome segmentation, primarily influence genome size across viral orders.

Diverse Viral Pathogens in Australian Canines: Limited Geographic Structure and the First Detection of an RNA Virus in Dingoes

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.