Biology subjects

Williams, D. T.

Publications and source records attributed to Williams, D. T..

6 recordsLinked to original sources

bioRxiv2026

First detected incursions of avian influenza H5N1 clade 2.3.4.4b into mainland Australia from the Southern Ocean

High pathogenicity avian influenza H5N1 clade 2.3.4.4b has caused a panzootic of devastating impact to poultry and wildlife globally. The Australian continent and broader Oceania until recently remained the last major region without confirmed detections. Here we report the first H5N1 clade 2.3.4.4b detections from two live seabirds - a brown skua and a southern giant petrel - found on the south coast of Western Australia in June 2026. Virus genome sequencing showed that both viruses were most closely related to H5N1 viruses detected recently on sub-Antarctic islands in the Southern Indian Ocean. In time-calibrated phylogeographic analyses, both viruses sampled in Western Australia clustered with viruses from Heard Island, a sub-Antarctic external territory of Australia. Ancestral location reconstruction also identified Heard Island as the most probable source location, although unsampled intermediate locations cannot be excluded. The two Western Australian detections were estimated to be independent incursions from Heard Island, rather than local transmission on mainland Australia. There was no evidence of reassortment with endemic avian influenza viruses in Australia, and both virus sequences retained key avian-like genetic markers and lacked known substitutions for reduced antiviral susceptibility. These detections revealed a Southern Ocean pathway of recurrent H5N1 incursions into Australia, highlighting the risk of potential establishment on the mainland and the need for heightened surveillance and rapid, nationally-coordinated, virus genomic characterisation.

microbiology↗

bioRxiv2025

Detection of Japanese Encephalitis (JE) Virus in Piggery effluent from an Australian Farm Prior to Outbreaks of JE

Japanese encephalitis virus (JEV), a mosquito-borne orthoflavivirus, raises concerns about its seasonal re-emergence. Pigs are a major amplifying host and JEV infection can manifest as significant reproductive disease and losses, necessitating robust surveillance. This study evaluated effluent surveillance for early JEV detection in piggery effluent from a Victorian farm between December 2024 and March 2025. Effluent samples were tested using JEV-specific real-time reverse transcription (RT)-PCR, with positive detections found on four separate sampling days, despite an absence of clinical signs in livestock through the testing period. Subsequent veterinary investigations for JEV in litters born on 17/05/2025 (suspect cases only) aligned with a positive effluent sample collected during the estimated JEV infection exposure periods of the sows. With the single clinically confirmed JEV case (which farrowed on 1/06/2025) collection of the same positive effluent sample fell just outside, but near, the estimated exposure period for the affected sow. These findings highlight ability of effluent monitoring to detect JEV infection 2 to 4 months before clinical manifestations present, offering potential for a non-invasive, herd-level early warning system. Intermittent detections may suggest limitations in grab sampling and low viral loads in effluent samples. Integrating effluent surveillance with veterinary clinical testing of litters suspected of being exposed to JEV or during high-risk periods could enhance JEV management in Australias enzootic regions, supporting One Health strategies.

molecular biology↗

bioRxiv2025

Surveillance of Japanese Encephalitis Virus in Piggery Effluent and Environmental Samples: A Complementary Tool for Outbreak Detection

Japanese encephalitis virus (JEV) is an emerging public health and biosecurity concern in Australia, with recent human cases and detections in mosquitoes and pigs across multiple states highlight the risk to susceptible human and animal populations. While traditional surveillance methods such as mosquito trapping, sentinel chicken programs and direct testing of pig specimens remain essential, monitoring effluent offers a valuable complementary approach for detecting infections within animal populations. This study presents the first evidence of JEV in Australian piggery effluents/environmental waters, demonstrating the feasibility of effluent and environmental water surveillance for JEV monitoring. Effluent/environmental samples from multiple piggery sites were analyzed using real-time reverse transcription polymerase chain reaction (RT-PCR), revealing the presence of JEV genetic fragments in solid and liquid fractions of effluents at three farms, with corresponding veterinary cases in some herds. Viral RNA was detected more frequently in solid fraction of effluent samples, aligning with previous findings on the partitioning behaviour of mosquito-borne viruses. The detection of JEV in the borrow pit (i.e., a man-made excavation that holds water) water sample highlights potential transmission pathways via mosquito vectors. These findings demonstrate the value of effluent monitoring as an additional tool for JEV surveillance in piggery settings, supporting potential early warning systems and mitigation strategies. Integrating effluent-based monitoring with traditional surveillance approaches could improve livestock industry related disease detection, risk assessments, and response efforts for human and animal health in endemic and emerging regions. Wastewater/effluent surveillance may have important applications for the management of a wide range of emerging animal diseases. IMPORTANCEThis study presents the first evidence of Japanese encephalitis virus (JEV) detection in Australian piggery effluents, establishing effluent surveillance as a valuable complementary tool for monitoring viral pathogens in animal populations. Our findings support the integration of effluent monitoring with traditional surveillance systems to improve early warning capabilities, enhance biosecurity, and mitigate risks to both animal and human health.

molecular biology↗

bioRxiv2024

Australian Culex annulirostris mosquitoes are competent vectors for Japanese encephalitis virus genotype IV

Japanese encephalitis virus (JEV) is transmitted by Culex species of mosquitoes. In 2022, JEV belonging to a previously unrecognised lineage of genotype IV (GIV) caused a major outbreak of JE in South-eastern Australia, resulting in human cases and affecting piggeries. Cx. annulirostris has previously been implicated as the major vector of JEV in northern Australia where the virus has circulated since its first detection in 1995. Here, we showed that experimental infection of a laboratory colony of Australian Cx. annulirostris with the isolate JEV NSW/22 resulted in a 100% mosquito infection rate, with 87% of mosquito saliva samples testing positive by RT-qPCR at 14 days post-infection. Immunohistochemistry confirmed the presence of a replicating virus in the mosquito midgut and dissemination throughout the body, including the salivary glands. Our results also showed evidence of transovarial transmission of this virus; however, transstadial transmission from the eggs to the adult stage was not found. Comparison with an Indonesian isolate of GIV JEV and previous Australian isolates belonging to genotypes I and II showed that infection with JEV NSW/22 resulted in higher viral titres in the early stage of infection and higher proportions of mosquitoes with JEV-positive saliva, indicating a greater transmission potential compared to other isolates. This study provides compelling experimental evidence that Australian Cx. annulirostris is a highly efficient vector for the 2022 Australian JEV GIV outbreak strain.

microbiology↗

bioRxiv2021

A novel and highly divergent Canine Distemper Virus lineage causing distemper in ferrets in Australia

Canine distemper virus (CDV) is a highly contagious systemic viral disease of dogs, that regularly spills-over into other animal species. Despite widespread vaccination, CDV remains endemic in many parts of the world. In this study we report an outbreak of distemper in ferrets in two independent research facilities in Australia. We found that disease severity varied, although most animals had mild to moderate disease signs. Histopathology results of animals with severe disease presented the typical profile of distemper pathology with multi-system virus replication. Through the development of a discriminatory PCR paired with full genome sequencing we revealed that the outbreak at both facilities was caused by a single, novel lineage of CDV. This lineage was highly divergent across the H gene, F signal peptide and full genome and had less than 93% similarity across the H gene to other described lineages, including the vaccine strain. Molecular analysis indicates that this strain belongs to a distinct lineage that diverged from other clades approximately 140 to 400 years ago, and appears to be unique to Australia. Given the differences in key viral proteins of this novel CDV strain, a review of the efficacy of the CDV vaccines currently in use in Australia is warranted to ensure maximum protection of dogs and other vulnerable species. In addition, enhanced surveillance to determine the prevalence of CDV in ferrets, dogs and other at-risk species in Australia would be useful to better understand the diversity of CDV in Australia. ImportanceCanine distemper virus (CDV) is highly contagious and while dogs are the main reservoir, it may spill over into a number of other animal species. In this study we report an outbreak of distemper in ferrets in two research facilities in Australia. Outcomes of pathology and histopathology suggest ferrets have widespread multi-systemic infection, consistent with previously reported distemper infections in ferrets and dogs. Critically, through sequencing and phylogenetic analysis, we revealed that the outbreak at both facilities was caused by a single, novel and highly divergent lineage of CDV. This virus had less than 93% nucleotide similarity to other described lineages and the vaccine strain. This manuscript adds considerably to the epidemiology, ecology and evolution of this virus, and is one of few reports of distemper in Australia in the literature.

microbiology↗

bioRxiv2021

Novel Hendra virus variant detected by sentinel surveillance of Australian horses.

A novel Hendra virus (HeV) variant, not detected by routine testing, was identified and isolated from a Queensland horse that suffered acute, fatal disease consistent with HeV infection. Whole genome sequencing and phylogenetic analysis demonstrated the variant to have ~83% nucleotide identity to the prototype HeV strain. An updated RT-qPCR assay was designed for routine HeV surveillance. In silico and in vitro comparison of the receptor-binding protein with prototypic HeV showed that the human monoclonal antibody m102.4 used for post-exposure prophylaxis, as well as the current equine vaccine, should be effective against this variant. Genetic similarity of this virus to sequences detected from grey-headed flying-foxes suggests the variant circulates at-least in this species. Studies determining infection kinetics, pathogenicity, reservoir-species associations, viral-host co-evolution and spillover dynamics for this virus are urgently needed. Surveillance and biosecurity practices should be updated to appreciate HeV spillover risk across all regions frequented by flying foxes.

molecular biology↗