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Intrahepatic cholestasis of pregnancy (ICP) is the most common liver-specific disorder affecting pregnant women, with an Australian incidence of 0.6% pa and recurring in 70% of those affected. ICP causes mild to severe pruritus, often resulting in considerable skin excoriations, profound sleep disturbances, and severe anxiety, and yet the aetiology and optimal treatment or management of this condition remains unknown. In this review, we consider the role of viruses in causing or exacerbating ICP and discuss viruses that have been most closely implicated in the disease, including the role of Hepatitis B and Hepatitis C viruses in ICP. [ABSTRACT FROM AUTHOR]

Simple Summary: In this review, we present the differences between viral diagnostic studies in psittacines and their progress. The aim of this study was to analyze the evolution of published studies on viruses in psittacines up to 2022. We found that: (i) on average, 2.5 articles per year on viral diagnosis in psittacines have been published since 1975; (ii) the most productive research groups are concentrated in Australia, the United States, and Germany; (iii) the most important virus for psittacines is Circovirus; (iv) the diagnostic method of choice is polymerase chain reaction (PCR); and (v) the most studied psittacines belong to the Psittacidae family kept in captivity. This study provides information to guide future work on viruses in psittacines and encourages broad viral research in wild and domestic animals to prevent future outbreaks and the emergence of new viral diseases. The first reports of viruses in psittacine birds date back to the early 1970s. Here, we elucidate the differences among these previous studies and the advances achieved. The objective of this study was to carry out a comprehensive review using both scientometric and systematic methods to analyze the evolution of published studies on viruses in psittacine birds up to 2022. The search descriptors "virus", "diagnosis", and "Psittaciformes" were used to find the articles of interest for this study. A total of 118 articles were manually selected, and the scientometric data were organized using the software VOSviewer® version 1.6.18. The present review revealed that: (i) on average, 2.5 articles/year on the diagnosis of viral infection in psittacine birds were published since 1975; (ii) the most productive research groups are concentrated in three countries: Australia, the United States, and Germany; (iii) the most important virus in psittacine birds is the Circovirus, which causes psittacine beak and feather disease; (iv) the diagnostic method of choice is polymerase chain reaction (PCR); and (v) the most studied psittacine birds were those in the Psittacidae family that were kept in captivity. [ABSTRACT FROM AUTHOR]

Objectives: To identify factors which influence the intraoral prevalence of human herpes viruses (HHVs) using mucosal swabs, saliva samples and qPCR analysis. Methodology: In this cross‐sectional observational study, matched saliva and oral swabs were collected from a total of 115 subjects: 70 immunocompetent subjects with no mucosal abnormalities, 22 with mucosal abnormalities and 23 therapeutically immunocompromised individuals. Extracted DNA was analysed by multiplex qPCR for detection and quantification of HHVs 1–6. Results: At least one human herpes virus was detected in 77.1% of immunocompetent individuals with no mucosal abnormalities, with EBV the most commonly detected at 61.4%. HHV‐6 was detected in 17.1%, HSV‐1 in 4.3% and CMV in 1.1%. Detection was higher in saliva than in oral swabs. There was no detection of HSV‐2 or VZV. Neither presence of oral mucosal abnormality nor therapeutic immunocompromise was related to increased detection of human herpes virus. Conclusion: Commensal detection rates of EBV are high, and caution in clinical correlation of positive detection is warranted. Commensal CMV rates are low, and detection is likely to be clinically relevant. This study presents a comprehensive commensal detection rate of HHVs 1–6 by qPCR in saliva and swabs. [ABSTRACT FROM AUTHOR]

Philosopher and anthropologist Elizabeth Povinelli is the author of several books criticising multicultural late liberalism in Australia and the United States. Over the past few years she has created the Karrabing Film Collective with Indigenous people from Northern Australia to produce short experimental narrations filmed using smart phones, partly improvised and inspired by what she calls the animist strategy. This article discusses how, in Geontologies: A Requiem to Late Liberalism, Povinelli articulates her figure of Animism, with two others, the Desert and the Virus, so as to portray the projections of the life and death of humanity within our current geological era that some call or denounce as the Anthropocene. [ABSTRACT FROM AUTHOR]

Ectoparasites play an important role in virus transmission among vertebrates. Little, however, is known about the nature of those viruses that pass between invertebrates and vertebrates. In Australia, flies and fleas support the mechanical transmission of two viral biological controls against wild rabbits--rabbit hemorrhagic disease virus (RHDV) and myxoma virus. We compared virome compositions in rabbits and these ectoparasites, sequencing total RNA from multiple tissues and gut contents of wild rabbits, fleas collected from these rabbits, and flies trapped sympatrically. Metatranscriptomic analyses identified 50 novel viruses from multiple RNA virus families. Rabbits and their ectoparasites were characterized by markedly different viromes, with virus abundance greatest in flies. Although viral contigs from six virus families/groups were found in both rabbits and ectoparasites, they clustered in distinct hostdependent lineages. A novel calicivirus and a picornavirus detected in rabbit cecal content were vertebrate specific; the newly detected calicivirus was distinct from known rabbit caliciviruses, while the picornavirus clustered with sapeloviruses. Several picobirnaviruses were also identified that fell in diverse phylogenetic positions, compatible with the idea that they are associated with bacteria. Further comparative analysis revealed that the remaining viruses found in rabbits, and all those from ectoparasites, were likely associated with invertebrates, plants, and coinfecting endosymbionts. While no full genomes of vertebrate-associated viruses were detected in ectoparasites, small numbers of reads from rabbit astrovirus, RHDV, and other lagoviruses were present in flies. This supports a role for flies in the mechanical transmission of RHDV, while their involvement in astrovirus transmission merits additional exploration. [ABSTRACT FROM AUTHOR]

Infectious diseases are significant demographic and evolutionary drivers of populations, but studies about the genetic basis of disease resistance and susceptibility are scarce in wildlife populations. Cetacean morbillivirus (CeMV) is a highly contagious disease that is increasing in both geographic distribution and incidence, causing unusual mortality events (UME) and killing tens of thousands of individuals across multiple cetacean species worldwide since the late 1980s. The largest CeMV outbreak in the Southern Hemisphere reported to date occurred in Australia in 2013, where it was a major factor in a UME, killing mainly young Indo‐Pacific bottlenose dolphins (Tursiops aduncus). Using cases (nonsurvivors) and controls (putative survivors) from the most affected population, we carried out a genome‐wide association study to identify candidate genes for resistance and susceptibility to CeMV. The genomic data set consisted of 278,147,988 sequence reads and 35,493 high‐quality SNPs genotyped across 38 individuals. Association analyses found highly significant differences in allele and genotype frequencies among cases and controls at 65 SNPs, and Random Forests conservatively identified eight as candidates. Annotation of these SNPs identified five candidate genes (MAPK8, FBXW11, INADL, ANK3 and ACOX3) with functions associated with stress, pain and immune responses. Our findings provide the first insights into the genetic basis of host defence to this highly contagious disease, enabling the development of an applied evolutionary framework to monitor CeMV resistance across cetacean species. Biomarkers could now be established to assess potential risk factors associated with these genes in other CeMV‐affected cetacean populations and species. These results could also possibly aid in the advancement of vaccines against morbilliviruses. [ABSTRACT FROM AUTHOR]

This is a personal account of one man's experience of the months during which COVID-19 spread in Australia. Though personal, it aims to also be representative, so that readers will find in it reflections of their own experiences. Various social incidents are described, some in which social distancing is involved. The altering states of the author's mind as time passes are carefully described in sequence, and the impact of continued anxiety and isolation on his mental well-being is presented as a form of madness, in one dramatic incident. [ABSTRACT FROM AUTHOR]

Abstract The Great Australian Bight (GAB) is a region of great economic and ecological importance to southern Australia, supporting fisheries of national and international importance, and large populations of small pelagic fish and iconic apex predators. There is, however, limited information on the plankton forming the base of the food web and their links to higher trophic levels in the GAB. Bacteria [inclusive of Archaea ], picophytoplankton (Prochlorococcus , Synechococcus and picoeukaryotes) and viruses were investigated in the central through to the eastern GAB for the first time, across five shelf edge to offshore transects in the austral Autumn of 2013. Downwelling conditions were evident over the region prior to and during the study period. Prochlorococcus numerically dominated picophytoplankton, exceeding Synechococcus and picoeukaryotes on average, by 5-fold and 30-fold respectively. Synechococcus and picoeukaryotes showed a clear shelf edge to offshore trend with highest abundances occurring at the shelf edge. Bacterial abundances showed low variation over the region, but with highest percent of high DNA bacteria (%HDNA) occurring at the shelf edge. Viral abundances closely followed bacteria, however individual viral groups were positively correlated with picophytoplankton groups, suggesting all picoplankton groups were subject to viral infection in GAB waters. Highest total picoplankton biomass occurred in surface waters at the shelf edge (26.5 ± 1.49 µg C L−1), with picophytoplankton carbon biomass (PB) and bacterial carbon biomass (BB) each accounting for ~50% of the total picoplankton biomass in the upper 60 m of the water column. Total picoplankton biomass was ~2-fold lower offshore waters, with BB comprising the bulk of the biomass (~72%). For the upper 60 m of the water column, picoeukaryotes accounted for ~51% of PB at the shelf edge, compared to ~24% in offshore waters. Based on our estimated C:Chl a ratios, picoeukaryotes accounted for 32.7 ± 3.0% of Chl a at the shelf edge, compared to 9.1 ± 0.6% in offshore waters. Prochlorococcus dominated PB in offshore waters (~67%), accounting for ~28% of Chl a. Multivariate analyses showed that the best predictors of the picoplankton community were a combination of nitrate and salinity (ρ = 0.704), indicating strong environmental forcing of the picophytoplankton community across the GAB. The elevated PB at the shelf edge, due to the dominance of picoeukaryotes, was a regional feature of the central and eastern GAB during the time of this study. We hypothesize that picoeukaryotes play a critical role in supporting higher trophic levels in GAB shelf edge waters. This study highlights the importance of small plankton in food web dynamics in GAB waters. [ABSTRACT FROM AUTHOR]

Hendra virus (HeV) and Nipah virus (NiV) are highly pathogenic paramyxoviruses, which have emerged in recent decades and cause sporadic outbreaks of respiratory and encephalitic disease in Australia and Southeast Asia, respectively. Over two billion people currently live in regions potentially at risk due to the wide range of the Pteropus fruit bat reservoir, yet there are no approved vaccines or therapeutics to protect against or treat henipavirus disease. In recent years, significant progress has been made toward developing various experimental vaccine platforms and therapeutics. Here, we describe these advances for both human and livestock vaccine candidates and discuss the numerous preclinical studies and the few that have progressed to human phase 1 clinical trial and the one approved veterinary vaccine., (© 2023. Springer Science+Business Media, LLC, part of Springer Nature.)

The international trade in ornamental fish is considered a major factor for the transboundary spread of aquatic pathogens that can affect both wild and farmed fish populations. Nearly 18 million ornamental fish were imported into Australia in 2007, including approximately 3.9 million goldfish. Despite quarantine regulations during importation, there have been several incidents in Australia where exotic pathogens from ornamental fish have become established in farmed or free-living fish species. The exotic virus Cyprinid herpesvirus 2 (CyHV2) was first found in Australia in 2003 in goldfish, suggesting that sub-clinically infected goldfish were passing through quarantine regardless of health certification and three weeks of quarantine. Repeated cross sectional surveys were conducted to determine whether CyHV2 has already established in farmed or wild ornamental fish in Australia. Goldfish populations were tested to OIE standard to detect 2% prevalence with 95% confidence assuming a test of 100% sensitivity and specificity. CyHV2 was found at retail outlets, farms and in several populations of wild goldfish in the ACT and Victoria. The prevalence and moderate to high viral loads in sub-clinically infected goldfish from different domestic populations suggested the introduction was not a recent event. This study demonstrated that CyHV2 has established in Australia and informed quarantine policy to revoke the requirement for goldfish exported to Australia to be certified free of CyHV2. The results provided clear evidence that an aquatic pathogen from imported ornamental fish can become established in farmed and wild populations. This is of particular significance to Australia as there are many endemic and ecologically sensitive populations of fish that may be severely affected by exotic pathogens. The incursion of CyHV2 in Australia should be considered a case study to inform pathway analysis for pathogen establishment. [ABSTRACT FROM AUTHOR]

Abstract: Globally, cyanobacterial blooms are increasing along with observations of the controlling influence of viruses. Our aim here was to test whether viruses from an Australian freshwater lake could lyse the cyanobacterium Cylindrospermopsis raciborskii (Woloszynska) Seenaya and Subba Raju. C. raciborskii was selectively isolated from Lake Samsonvale southeast Queensland Australia using a Modified Jaworski Medium (without any form of inorganic nitrogen). Microscopy confirmed the resulting culture of a single cyanobacterial species. Natural viral-like particles (VLPs) were incubated with C. raciborskii cells, the host abundance decreased by 86% in 5 days, while the number of VLPs increased stepwise. As a cell lysed, the filaments of cells split into smaller, but viable, fragments. This process may help disperse the cyanobacterium in the wild. Hence the use of this virus to control blooms may inadvertently encourage the dispersal of toxic filamentous cyanobacteria. The cyanophage (virus infecting cyanobacteria) replication time was 21 h, with an average burst size of 64 viruses cell−1. Transmission Electron Microscopy showed this cyanophage for C. raciborskii, with its long, non-contractile tail and a capsid diameter of 70 nm, belongs to the Siphoviridae family of viruses. This cyanophage can affect the abundance and distribution of the cyanobacterium C. raciborskii in this Australian freshwater lake. [Copyright &y& Elsevier]

Transmission electron microscopy (TEM) was used to determine whether Acropora muricata coral colonies from the Great Barrier Reef (GBR), Australia, harboured virus-like particles (VLPs). VLPs were present in all coral colonies sampled at Heron Island (southern GBR) and in tagged coral colonies sampled in at least two of the three sampling periods at Lizard Island (northern GBR). VLPs were observed within gastrodermal and epidermal tissues, and on rarer occasions, within the mesoglea. These VLPs had similar morphologies to known prokaryotic and eukaryotic viruses in other systems. Icosahedral VLPs were observed most frequently, however, filamentous VLPs (FVLPs) and phage were also noted. There were no clear differences in VLP size, morphology or location within the tissues with respect to sample date, coral health status or site. The most common VLP morphotype exhibited icosahedral symmetry, 120-150 nm in diameter, with an electron-dense core and an electronlucent membrane. Larger VLPs of similar morphology were also common. VLPs occurred as single entities, in groups, or in dense clusters, either as free particles within coral tissues, or within membrane-bound vacuoles. VLPs were commonly observed within the perinuclear region, with mitochondria, golgi apparatus and crescent-shaped particles frequently observed within close proximity. The host(s) of these observed VLPs was not clear; however, the different sizes and morphologies of VLPs observed within A. muricata tissues suggest that viruses are infecting either the coral animal, zooxanthellae, intracellular bacteria and/or other coral-associated microbiota, or that the one host is susceptible to infection from more than one type of virus. These results add to the limited but emerging body of evidence that viruses represent another potentially important component of the coral holobiont. [ABSTRACT FROM AUTHOR]

Encephalitis is most often caused by a variety of infectious agents identified through diagnostic tests utilizing cerebrospinal fluid. We investigated the clinical characteristics and potential aetiological agents of unexplained encephalitis through metagenomic sequencing of residual clinical samples from multiple tissue types and independent clinical review. Forty-three specimens were collected from 18 encephalitis cases with no cause identified by the Australian Childhood Encephalitis study. Samples were subjected to total RNA sequencing ('metatranscriptomics') to determine the presence and abundance of potential pathogens, and to describe the possible aetiologies of unexplained encephalitis. Using this protocol, we identified five RNA and two DNA viruses associated with human infection from both non-sterile and sterile sites, which were confirmed by PCR. These comprised two human rhinoviruses, two human seasonal coronaviruses, two polyomaviruses and one picobirnavirus. Human rhinovirus and seasonal coronaviruses may be responsible for five of the encephalitis cases. Immune-mediated encephalitis was considered likely in six cases and metatranscriptomics did not identify a possible pathogen in these cases. The aetiology remained unknown in nine cases. Our study emphasizes the importance of respiratory viruses in the aetiology of unexplained child encephalitis and suggests that non-central-nervous-system sampling in encephalitis clinical guidelines and protocols could improve the diagnostic yield.

Currently, due to the global pandemic caused by severe acute respiratory syndrome coronavirus SARS-CoV-2, new procedures and devices for effective disinfection of indoor air are of obvious interest. Various studies demonstrated quite broad ranges of the efficiency of essential oils in the control of biological aerosols. This project reports the results of investigation of the antimicrobial activity of essential oils natural for Australia (tea tree oil, eucalyptus oil and lemon myrtle) distributed by newly developed VaxiPod device for various scenarios, including bacterial, viral and fungal inactivation on various surfaces and in aerosol form. It was found that the device was capable of operating continuously over 24-h periods, providing sufficient aerosol concentration to efficiently inactivate microorganisms both on the surface and in airborne form. Twenty-four to forty-eight hours were required to achieve inactivation above 90% of most of the tested microbes on solid surfaces (stainless steel discs and agar plates), whilst similar efficiency of inactivation on fibrous filter surface as well as in aerosol form was achieved over 30–60 min of the process run. The results look very promising for further development of bioaerosol inactivating procedures and technologies for air quality control applications. [ABSTRACT FROM AUTHOR]

The Northern Australia Quarantine Strategy (NAQS) is a biosecurity initiative operated by the Australian federal government's Department of Agriculture, Water and the Environment (DAWE). It is unique worldwide because it deals specifically with the potential arrival via unregulated pathways of exotic threats from overseas in a vast and sparsely populated region. It aims to protect the nation's animal- and plant-based production industries, as well as the environment, from incursions of organisms from countries that lie immediately to the north. These are diseases, pests, and weeds present in these countries that are currently either absent from, or under active containment in, Australia and may arrive by natural or human-assisted means. This review article focuses on the plant viruses and virus-like diseases that are most highly targeted by the NAQS program. It presents eight pathogen species/group entries in the NAQS A list of target pathogens, providing an overview of the historical and current situation, and collates some new data obtained from surveillance activities conducted in northern Australia and collaborative work overseas. [ABSTRACT FROM AUTHOR]

Molluscs are major contributors to the international and Australian aquaculture industries, however, their immune systems remain poorly understood due to limited access to draft genomes and evidence of divergences from model organisms. As invertebrates, molluscs lack adaptive immune systems or 'memory', and rely solely on innate immunity for antimicrobial defence. Hemolymph, the circulatory fluid of invertebrates, contains hemocytes which secrete effector molecules with immune regulatory functions. Interactions between mollusc effector molecules and bacterial and fungal pathogens have been well documented, however, there is limited knowledge of their roles against viruses, which cause high mortality and significant production losses in these species. Of the major effector molecules, only the direct acting protein dicer-2 and the antimicrobial peptides (AMPs) hemocyanin and myticin-C have shown antiviral activity. A better understanding of these effector molecules may allow for the manipulation of mollusc proteomes to enhance antiviral and overall antimicrobial defence to prevent future outbreaks and minimize economic outbreaks. Moreover, effector molecule research may yield the description and production of novel antimicrobial treatments for a broad host range of animal species.

• BQCV and SBV were prevalent in apparently healthy adult worker bees (Apis mellifera). • These were also the most commonly detected pathogens in co-foraging native species. • Similar variants were detected across species suggesting interspecies transmission. Australia remains the last significant land mass free of Varroa , a parasitic mite which has caused dramatic honey bee (Apis mellifera) colony losses across the globe, due to its association with the pathogenic deformed wing virus (DWV). As such, Australia continues to maintain relatively healthy honey bee populations, despite recent work showing apiaries harbor a surprisingly high prevalence of microbial pathogens. We sought to determine the prevalence of these microbial pathogens in honey bees and native pollinators actively co-foraging on mass flowering crops and to understand the extent to which they may be shared between taxa. We found high prevalences of black queen cell virus (BQCV) and sacbrood virus (SBV) in the honey bees (88% and 41% respectively), and correspondingly, these were the most common honey bee pathogens detected in native pollinator taxa, albeit at much lower prevalence; the maximum prevalence for any pathogen in a native pollinator group was 24% (BQCV in Halictidae spp.). The viral pathogens Israeli acute paralysis virus and Lake Sinai viruses 1 and 2, and the fungal parasites Nosema apis and Nosema ceranae , were only rarely detected. Phylogenetic analyses of the most common pathogens revealed similar genotypes circulating between species. Our data suggest that, in Australian orchards, pathogen prevalence in honey bees is a good predictor of pathogen prevalence in native pollinators, which raises concerns about how the viral landscape may change in native taxa if, or when, Varroa arrives. [ABSTRACT FROM AUTHOR]

This article provides an up-to-date review of disease-causing viruses and phytoplasmas of currants including symptoms, transmission, detection, economic impact, and control measures. Currants are widely cultivated in more than 30 countries in the temperate zones of Europe, Asia, South America, Australia, and New Zealand. Ribes spp. can be infected by more than 20 virus species and four Candidatus Phytoplasma species, with more to be described in the future. High-throughput sequencing opened a new era of deciphering virus variants and mixed infections, leading to the characterization of several new species. The use of clean propagation material is the basis for control of Ribes graft-transmissible diseases, but this has become a challenging task given the ever-growing number of newly discovered pathogens.

As of 1 May 2020, there had been 6808 confirmed cases of COVID-19 in Australia. Of these, 98 had died from the disease. The epidemic had been in decline since mid-March, with 308 cases confirmed nationally since 14 April. This suggests that the collective actions of the Australian public and government authorities in response to COVID-19 were sufficiently early and assiduous to avert a public health crisis - for now. Analysing factors that contribute to individual country experiences of COVID-19, such as the intensity and timing of public health interventions, will assist in the next stage of response planning globally. We describe how the epidemic and public health response unfolded in Australia up to 13 April. We estimate that the effective reproduction number was likely below one in each Australian state since mid-March and forecast that clinical demand would remain below capacity thresholds over the forecast period (from mid-to-late April)., Competing Interests: DP, FS, MM, EM, RM, NG, EC, PD, DC, JW, SA, JM, JM This work was undertaken with direct funding support from the Australian Government Department of Health, Office of Health Protection and has assisted the Australian Government in its epidemic response activities., (© 2020, Price et al.)

The Tasmanian devil is an endangered carnivorous marsupial threatened by devil facial tumor disease (DFTD). While research on DFTD has been extensive, little is known about viruses in devils and whether any are of potential conservation relevance for this endangered species. Using both metagenomics based on virion enrichment and sequence-independent amplification (virion-enriched metagenomics) and metatranscriptomics based on bulk RNA sequencing, we characterized and compared the fecal viromes of captive and wild devils. A total of 54 fecal samples collected from two captive and four wild populations were processed for virome characterization using both approaches. In total, 24 novel marsupial-related viruses, comprising a sapelovirus, astroviruses, rotaviruses, picobirnaviruses, parvoviruses, papillomaviruses, polyomaviruses, and a gammaherpesvirus, were identified, as well as known mammalian pathogens such as rabbit hemorrhagic disease virus 2. Captive devils showed significantly lower viral diversity than wild devils. Comparison of the two virus discovery approaches revealed substantial differences in the number and types of viruses detected, with metatranscriptomics better suited for RNA viruses and virion-enriched metagenomics largely identifying more DNA viruses. Thus, the viral communities revealed by virion-enriched metagenomics and metatranscriptomics were not interchangeable and neither approach was able to detect all viruses present. An integrated approach using both virion-enriched metagenomics and metatranscriptomics constitutes a powerful tool for obtaining a complete overview of both the taxonomic and functional profiles of viral communities within a sample. IMPORTANCE The Tasmanian devil is an iconic Australian marsupial that has suffered an 80% population decline due to a contagious cancer, devil facial tumor disease, along with other threats. Until now, viral discovery in this species has been confined to one gammaherpesvirus (dasyurid herpesvirus 2 [DaHV-2]), for which captivity was identified as a significant risk factor. Our discovery of 24 novel marsupial-associated RNA and DNA viruses, and that viral diversity is lower in captive than in wild devils, has greatly expanded our knowledge of gut-associated viruses in devils and provides important baseline information that will contribute to the conservation and captive management of this endangered species. Our results also revealed that a combination of virion-enriched metagenomics and metatranscriptomics may be a more comprehensive approach for virome characterization than either method alone. Our results thus provide a springboard for continuous improvements in the way we study complex viral communities., (Copyright © 2019 Chong et al.)

Background: Differentiating bacterial from viral pneumonia is important for guiding targeted management and judicious use of antibiotics. We assessed if clinical characteristics and blood inflammatory biomarkers could be used to distinguish bacterial from viral pneumonia., Methods: Western Australian children (≤17 years) hospitalized with radiologically-confirmed community-acquired pneumonia were recruited and clinical symptoms and management data were collected. C-reactive protein (CRP), white cell counts (WCC) and absolute neutrophil counts (ANC) were measured as part of routine care. Clinical characteristics and biomarker levels were compared between cases with definite bacterial pneumonia (clinical empyema and/or bacteria detected in blood or pleural fluid), presumed viral pneumonia (presence of ≥1 virus in nasopharyngeal swab without criteria for definite bacterial pneumonia), and other pneumonia cases (pneumonia in the absence of criteria for either definite bacterial or presumed viral pneumonia). The area-under-curve (AUC) of the receiver operating characteristic (ROC) curve for varying biomarker levels were used to characterise their utility for discriminating definite bacterial from presumed viral pneumonia. For biomarkers with AUC > 0.8 (fair discriminator), Youden index was measured to determine the optimal cut-off threshold, and sensitivity, specificity, predictive values (positive and negative) were calculated. We investigated whether better discrimination could be achieved by combining biomarker values with the presence/absence of symptoms., Results: From May 2015 to October 2017, 230 pneumonia cases were enrolled: 30 with definite bacterial pneumonia, 118 with presumed viral pneumonia and 82 other pneumonia cases. Differences in clinical signs and symptoms across the groups were noted; more definite bacterial pneumonia cases required intravenous fluid and oxygen supplementation than presumed viral or other pneumonia cases. CRP, WCC and ANC were substantially higher in definite bacterial cases. For a CRP threshold of 72 mg/L, the AUC of ROC was 0.82 for discriminating definite bacterial pneumonia from presumed viral pneumonia. Combining the CRP with either the presence of fever (≥38 ο C) or the absence of rhinorrhea improved the discrimination., Conclusions: Combining elevated CRP with the presence or absence of clinical signs/ symptoms differentiates definite bacterial from presumed viral pneumonia better than CRP alone. Further studies are required to explore combination of biomarkers and symptoms for use as definitive diagnostic tool.

High-throughput transcriptome sequencing allows for the unbiased detection of viruses in host tissues. The application of this technique to immunosuppressed animals facilitates the detection of viruses that might otherwise be excluded or contained in immunocompetent individuals. To identify potential viral pathogens infecting domestic cats we performed high-throughput transcriptome sequencing of tissues from cats infected with feline immunodeficiency virus (FIV). A novel member of the Hepadnaviridae, tentatively named domestic cat hepadnavirus, was discovered in a lymphoma sample and its complete 3187 bp genome characterized. Phylogenetic analysis placed the domestic cat hepadnavirus as a divergent member of mammalian orthohepadnaviruses that exhibits no close relationship to any other virus. DNA extracted from whole blood from pet cats was positive for the novel hepadnavirus by PCR in 6 of 60 (10%) FIV-infected cats and 2 of 63 (3.2%) FIV-uninfected cats. The higher prevalence of hepadnavirus viraemia detected in FIV-infected cats mirrors that seen in human immunodeficiency virus-infected humans coinfected with hepatitis B virus. In summary, we report the first hepadnavirus infection in a carnivore and the first in a companion animal. The natural history, epidemiology and pathogenic potential of domestic cat hepadnavirus merits additional investigation. [ABSTRACT FROM AUTHOR]

Acute lower respiratory infection (ALRI) is a major cause of hospitalization for Indigenous children in remote regions of Australia. The associated microbiology remains unclear. Our aim was to determine whether the microbes present in the nasopharynx before an ALRI were associated with its onset. A retrospective case-control/crossover study among Indigenous children aged up to 2 years. ALRI cases identified by medical note review were eligible where nasopharyngeal swabs were available: (1) 0-21 days before ALRI onset (case); (2) 90-180 days before ALRI onset (same child controls); and (3) from time and age-matched children without ALRI (different child controls). PCR assays determined the presence and/or load of selected respiratory pathogens. Among 104 children (182 recorded ALRI episodes), 120 case-same child control and 170 case-different child control swab pairs were identified. Human adenoviruses (HAdV) were more prevalent in cases compared to same child controls (18 vs 7%; OR = 3.08, 95% CI 1.22-7.76, p = 0.017), but this association was not significant in cases versus different child controls (15 vs 10%; OR = 1.93, 95% CI 0.97-3.87 (p = 0.063). No other microbes were more prevalent in cases compared to controls. Streptococcus pneumoniae (74%), Haemophilus influenzae (75%) and Moraxella catarrhalis (88%) were commonly identified across all swabs. In a pediatric population with a high detection rate of nasopharyngeal microbes, HAdV was the only pathogen detected in the period before illness presentation that was significantly associated with ALRI onset. Detection of other potential ALRI pathogens was similar between cases and controls.

Thermal biology predicts that vector-borne disease transmission peaks at intermediate temperatures and declines at high and low temperatures. However, thermal optima and limits remain unknown for most vector-borne pathogens. We built a mechanistic model for the thermal response of Ross River virus, an important mosquito-borne pathogen in Australia, Pacific Islands, and potentially at risk of emerging worldwide. Transmission peaks at moderate temperatures (26.4°C) and declines to zero at thermal limits (17.0 and 31.5°C). The model accurately predicts that transmission is year-round endemic in the tropics but seasonal in temperate areas, resulting in the nationwide seasonal peak in human cases. Climate warming will likely increase transmission in temperate areas (where most Australians live) but decrease transmission in tropical areas where mean temperatures are already near the thermal optimum. These results illustrate the importance of nonlinear models for inferring the role of temperature in disease dynamics and predicting responses to climate change., Competing Interests: MS, SR, EM No competing interests declared, (© 2018, Shocket et al.)

Sir Mac Farlane Burnet was the most honored of all Australian scientists. In 1960, Burnet shared the Nobel Prize for Medicine with Peter Medawar of Britain for the discovery of acquired immunological tolerance. He developed techniques for growing influenza viruses in the chorioallantoic membrane of the chick embryo. This became a standard laboratory practice. He continued to work with chick embryos long after the use of cell cultures had become general. His virology research resulted in significant discoveries concerning the nature and replication of viruses and their interaction with the immune system., (Copyright © 2018 European Federation of Immunological Societies. Published by Elsevier B.V. All rights reserved.)

Wolbachia is an endosymbiotic bacterium that can block viral infections in arthropods, generating interest in its potential to control the spread of mosquito-borne disease. Drosophila melanogaster is model organism for Wolbachia infection, and the w Mel strain of Wolbachia can improve host survival following viral infection. However, it is unclear whether w Mel induces anti-viral blocking against the broader native virome of D. melanogaster , or whether the major effect of Wolbachia is a reduction in viral abundance rather than viral clearance. We examined the effect of Wolbachia on viral abundance by comparing the total transcriptome of w Mel-positive and w Mel-negative D. melanogaster populations sampled from six locations in Australia. In addition, we examined the impact of w Mel on individual flies by obtaining transcriptome data from 20 w Mel-positive and 20 w Mel-negative D. melanogaster from the location (Melbourne) with highest density of w Mel. These data revealed high viral abundance in both Wolbachia -positive and -negative populations and individuals. Notably, none of the viral species identified, representing RNA viruses from at least nine families/floating genera, showed evidence of protection by w Mel. Although the viral loads of picorna-like viruses are reduced by w Mel under experimental conditions, we observed no such effect here. These data show that D. melanogaster can harbour abundant RNA viruses regardless of its Wolbachia status and imply that the interaction between Wolbachia and viruses in nature is more complex than simple blocking., (© 2018 The Author(s).)

Although viral emergence is commonly associated with cross-species transmission, the processes and determinants of viral evolution in a novel host environment are poorly understood. We address key questions in virus emergence and evolution using data generated from two unique natural experiments: the deliberate release of myxoma virus (MYXV) and rabbit hemorrhagic disease virus (RHDV) as biological control (biocontrol) agents against the European rabbit in Australia, and which have been of enormous benefit to Australia's ecosystem and agricultural industries. Notably, although virulence evolution in MYXV and RHDV followed different trajectories, a strongly parallel evolutionary process was observed in Australia and Europe. These biocontrol agents were also characterized by a lack of transmission to nontarget host species, suggesting that there are major barriers to successful emergence., (Copyright © 2014 Elsevier Ltd. All rights reserved.)