Cadhla Firth

Water buffaloes in northern Australia occupy tropical wetlands where conditions favour the proliferation of arthropod vectors and the transmission of vector-borne livestock diseases. However, their role in maintaining economically important arboviruses such as Akabane virus (AKAV), bluetongue virus (BTV), and bovine ephemeral fever virus (BEFV) remains poorly understood. These three viruses cause significant production losses in cattle and pose ongoing surveillance challenges in remote areas. To assess exposure to these viruses, a convenience sample of feral water buffaloes from the Northern Territory, Australia, was collected. Commercial enzyme-linked immunosorbent assays (ELISAs) were used to detect antibodies against AKAV, BTV, and BEFV in 119 samples stored as dried blood on filter paper. Seroprevalence was 18.5% for AKAV, 66.4% for BTV, and 15.1% for BEFV. These results are consistent with previous serological studies in northern Australian cattle, confirming the circulation of these pathogens in the region. Our findings demonstrate that water buffaloes are exposed to these economically important arboviruses and may contribute to their maintenance, highlighting the need to consider feral buffalo populations in regional arbovirus surveillance strategies and livestock disease management.

Environmental surveillance has emerged as a pivotal strategy for early detection of pathogens that pose a threat to humans. In Asia, live-bird markets (LBMs) are key human-animal interfaces for zoonotic virus transmission. Traditional sampling strategies are time-consuming, expensive and carry significant biosafety risks. Here, we assess the performance of metagenomics on environmental samples (ES) versus traditional poultry swabs for detecting viral pathogens in two Cambodian LBMs between January 2022 and April 2023. ES, including air (n = 35), cage swabs (n = 17), carcass wash water (n = 17) and drinking water (n = 9) are collected alongside oropharyngeal and cloacal swabs from chickens (n = 30) and ducks (n = 29). ES is sensitive in detecting 40 viruses from pathogen families including Orthomyxoviridae and Coronaviridae . Air samples capture the greatest diversity of poultry viruses. Viral contigs from ES show high sequence identity to poultry swab contigs when aligned to the same gene. We show ES outperforms poultry samples in detecting the highly pathogenic influenza A/H5N1, including clades 2.3.4.4b and 2.3.2.1c, which are found in the environment but are missed by poultry swabs. Our findings show metagenomics on ES replicates traditional surveillance, offering broader coverage and improved pathogen detection. This approach could be pivotal for mitigating zoonotic spillover and enhancing pandemic preparedness.

Several animal species, including horses and pigs, can be infected with Japanese encephalitis virus (JEV). Feral pigs ( Sus scrofa ) are considered an effective amplifying host for JEV in natural habitats. In this study, 265 dried blood spots were collected from feral pigs in four selected North Queensland local government areas, and antibodies against JEV were detected using a competitive enzyme‐linked immunosorbent assay (cELISA). The results showed that 26.4% (70/265) of the feral pigs had antibodies specific to JEV. We found a significant difference in the seroprevalence of JEV in the Wet Tropics ( p < 0.05), compared to the Dry Tropics region of North Queensland. The results indicate that feral pigs in North Queensland have been exposed to JEV, suggesting that they may play an important role as an amplifying host. These findings may inform the planning of mitigation measures through a multisectoral One Health approach.

Bats are the reservoir hosts of emerging coronaviruses (CoVs) affecting human and livestock health. We assessed the diversity, evolution, and geographic distribution of two alphacoronaviruses (subgenus Rhinacovirus ) with considerable potential for emergence: swine acute diarrhea syndrome coronavirus (SADS-CoV), which has caused large outbreaks in pigs in China and can infect primary human airway epithelial cells in vitro ; and the related Rhinolophus bat coronavirus HKU2 (HKU2-CoV). Phylogenetic analyses of 523 rhinacovirus sequences from bats in China and Southeast Asia suggest these viruses should be reclassified into at least two distinct CoV species representing two well-supported monophyletic clades. Stronger phylogenetic clustering by sampling location than by host species suggests infrequent long-distance transmission of rhinacoviruses in southern China. Ancestral state reconstruction analysis indicates that R. sinicus/thomasi and R. affinis have played an important role in rhinacovirus evolution in southern China and that R. affinis is the likely reservoir host of SADS-CoV that spilled over into pigs. We used species distribution modeling of Rhinolophus spp. bat hosts of rhinacoviruses, combined with pig and human density data, to identify potential geographic rhinacovirus spillover risk in Southeast Asia. Areas of high pig density within suitable bat habitat exist primarily in southern China and northern Vietnam, and hotspots of the highest human density within suitable bat habitat are primarily along the southern coast of China, Java, and central Thailand. Targeted surveillance of pigs and people in these regions may facilitate the timely detection of bat CoV spillover events and mitigate the risk of future outbreaks. IMPORTANCE: Bats are the reservoir or ancestral hosts of important emerging coronaviruses affecting people (e.g., SARS-CoV and SARS-CoV-2) and livestock (e.g., PEDV, SADS-CoV). Here, we analyzed 523 genetic sequences of SADS-CoV that caused large-scale die-offs of pigs in China, which is known to be able to infect human cells and related HKU2-CoVs. We used this information to identify the horseshoe bat Rhinolophus affinis as the likely spillover host for the outbreak in pigs, and identified the bat species within which these viruses evolved. We then modeled the distribution of these host species and their overlap with dense human and pig populations to identify the regions where surveillance programs can help identify spillover events and prevent future outbreaks.

Traditional food markets (TFMs) are dynamic and complex systems that play a vital role in societies across the globe. They provide fresh, affordable food, help preserve cultural traditions, and support the livelihoods of millions. However, these markets also present inherent risks associated with the trade of live animals and animal-derived products, including the emergence and spread of zoonotic diseases, which are underreported in these settings. This review explores the dual role of TFMs as essential societal hubs and hotspots for zoonotic diseases, emphasizing the need for surveillance and targeted One Health research on pathogens in these environments. By assessing the health risks associated with the presence of specific animals and their pathogens in TFMs, this review lays the foundation for developing the evidence-based risk assessments and mitigation strategies needed to reduce zoonotic disease risk. Enhancing the safety and sustainability of TFMs through integrated One Health approaches will be crucial for balancing the cultural and economic importance of TFMs with the need for increased global health security.

The Lacey Act of 1900, in its contemporary form, authorizes the US Fish and Wildlife Service (USFWS) to regulate wildlife species as “injurious,” thereby prohibiting their importation into the United States without a USFWS import permit. To date, most injurious species have been listed because of their potential ecological impacts. In response to the COVID-19 pandemic, the American Rescue Plan Act of 2021 directed the USFWS to assess the zoonotic disease risk associated with wildlife imported into the United States for potential injurious listing. In this Forum, we explore the Lacey Act's role in preventing zoonotic pathogens from entering the United States via the international wildlife trade. We give particular attention to the act's capacity to unify human, animal, and environmental regulatory goals, including by identifying ways in which the novel use of historic regulations may assist other governments with promulgating One Health legal or policy frameworks.

Over the last decade metagenomic sequencing has facilitated an increasing number of virome-scale studies, leading to an exponential expansion in understanding of virus diversity. This is partially driven by the decreasing costs of metagenomic sequencing, improvements in computational tools for revealing novel viruses, and an increased understanding of the key role that viruses play in human and animal health. A central concern associated with this remarkable increase in the number of virome-scale studies is the lack of broadly accepted “gold standards” for reporting the data and results generated. This is of particular importance for animal virome studies as there are a multitude of nuanced approaches for both data presentation and analysis, all of which impact the resulting outcomes. As such, the results of published studies can be difficult to contextualise and may be of reduced utility due to reporting deficiencies. Herein, we aim to address these reporting issues by outlining recommendations for the presentation of virome data, encouraging a transparent communication of findings that can be interpreted in evolutionary and ecological contexts.

Urbanization is rapidly transforming much of Southeast Asia, altering the structure and function of the landscape, as well as the frequency and intensity of the interactions between people, animals, and the environment. In this study, we explored the impact of urbanization on zoonotic disease risk by simultaneously characterizing changes in the ecology of animal reservoirs (rodents), ectoparasite vectors (ticks), and pathogens across a gradient of urbanization in Kuching, a city in Malaysian Borneo. We sampled 863 rodents across rural, developing, and urban locations and found that rodent species diversity decreased with increasing urbanization—from 10 species in the rural location to 4 in the rural location. Notably, two species appeared to thrive in urban areas, as follows: the invasive urban exploiter Rattus rattus ( n = 375) and the native urban adapter Sundamys muelleri ( n = 331). R. rattus was strongly associated with built infrastructure across the gradient and carried a high diversity of pathogens, including multihost zoonoses capable of environmental transmission (e.g., Leptospira spp.). In contrast, S. muelleri was restricted to green patches where it was found at high densities and was strongly associated with the presence of ticks, including the medically important genera Amblyomma , Haemaphysalis , and Ixodes . Our analyses reveal that zoonotic disease risk is elevated and heterogeneously distributed in urban environments and highlight the potential for targeted risk reduction through pest management and public health messaging.

Nanopore sequencing and phylodynamic modeling have been used to reconstruct the transmission dynamics of viral epidemics, but their application to bacterial pathogens has remained challenging. Cost-effective bacterial genome sequencing and variant calling on nanopore platforms would greatly enhance surveillance and outbreak response in communities without access to sequencing infrastructure. Here, we adapt random forest models for single nucleotide polymorphism (SNP) polishing developed by Sanderson and colleagues (2020. High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic nanopore sequencing. Genome Res. 30(9):1354–1363) to estimate divergence and effective reproduction numbers (R_e) of two methicillin-resistant Staphylococcus aureus (MRSA) outbreaks from remote communities in Far North Queensland and Papua New Guinea (PNG; n = 159). Successive barcoded panels of S. aureus isolates (2 × 12 per MinION) sequenced at low coverage (>5× to 10×) provided sufficient data to accurately infer genotypes with high recall when compared with Illumina references. Random forest models achieved high resolution on ST93 outbreak sequence types (>90% accuracy and precision) and enabled phylodynamic inference of epidemiological parameters using birth–death skyline models. Our method reproduced phylogenetic topology, origin of the outbreaks, and indications of epidemic growth (R_e > 1). Nextflow pipelines implement SNP polisher training, evaluation, and outbreak alignments, enabling reconstruction of within-lineage transmission dynamics for infection control of bacterial disease outbreaks on portable nanopore platforms. Our study shows that nanopore technology can be used for bacterial outbreak reconstruction at competitive costs, providing opportunities for infection control in hospitals and communities without access to sequencing infrastructure, such as in remote northern Australia and PNG.