Ross River Virus: Many Vectors and Unusual Hosts Make for an Unpredictable Pathogen

Long-term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring and viral whole-genome sequencing

Arbovirus surveillance of wild-caught mosquitoes is an affordable and sensitive means of monitoring virus transmission dynamics at various spatial-temporal scales, and emergence and re-emergence during epidemic and interepidemic periods. A variety of molecular diagnostics for arbovirus screening of mosquitoes (known as xeno-monitoring) are available, but most provide limited information about virus diversity. Polymerase chain reaction (PCR)-based screening coupled with RNA sequencing is an increasingly affordable and sensitive pipeline for integrating complete viral genome sequencing into surveillance programs. This enables large-scale, high-throughput arbovirus screening from diverse samples. We collected mosquitoes in CO2-baited light traps from five urban parks in Brisbane from March 2021 to May 2022. Mosquito pools of ≤200 specimens were screened for alphaviruses and flaviviruses using virus genus-specific primers and reverse transcription quantitative PCR (qRT-PCR). A subset of virus-positive samples was then processed using a mosquito-specific ribosomal RNA depletion method and then sequenced on the Illumina NextSeq. Overall, 54,670 mosquitoes representing 26 species were screened in 382 pools. Thirty detections of arboviruses were made in 28 pools. Twenty of these positive pools were further characterized using RNA sequencing generating 18 full-length genomes. These full-length sequences belonged to four medically relevant arboviruses: Barmah Forest, Ross River, Sindbis-like, and Stratford viruses. Phylogenetic and evolutionary analyses revealed the evolutionary progression of arbovirus lineages over the last 100 years, demonstrating that different epidemiological, immunological, and evolutionary processes may actively shape the evolution of Australian arboviruses. These results underscore the need for more genomic surveillance data to explore the complex evolutionary pressures acting on arboviruses. Overall, our findings highlight the effectiveness of our methodology, which can be applied broadly to enhance arbovirus surveillance in various ecological contexts and improve understanding of transmission dynamics.

Independent repeated mutations within the alphaviruses Ross River virus and Barmah Forest virus indicates convergent evolution and past positive selection in ancestral populations despite ongoing purifying selection

Ross River virus (RRV) and Barmah Forest virus (BFV) are arthritogenic arthropod-borne viruses (arboviruses) that exhibit generalist host associations and share distributions in Australia and Papua New Guinea (PNG). Using stochastic mapping and discrete-trait phylogenetic analyses, we profiled the independent evolution of RRV and BFV signature mutations. Analysis of 186 RRV and 88 BFV genomes demonstrated their viral evolution trajectories have involved repeated selection of mutations, particularly in the nonstructural protein 1 (nsP1) and envelope 3 (E3) genes suggesting convergent evolution. Convergent mutations in the nsP1 genes of RRV (residues 248 and 441) and BFV (residues 297 and 447) may be involved with catalytic enzyme mechanisms and host membrane interactions during viral RNA replication and capping. Convergent E3 mutations (RRV site 59 and BFV site 57) may be associated with enzymatic furin activity and cleavage of E3 from protein precursors assisting viral maturation and infectivity. Given their requirement to replicate in disparate insect and vertebrate hosts, convergent evolution in RRV and BFV may represent a dynamic link between their requirement to selectively 'fine-tune' intracellular host interactions and viral replicative enzymatic processes. Despite evidence of evolutionary convergence, selection pressure analyses did not reveal any RRV or BFV amino acid sites under strong positive selection and only weak positive selection for nonstructural protein sites. These findings may indicate that their alphavirus ancestors were subject to positive selection events which predisposed ongoing pervasive convergent evolution, and this largely supports continued purifying selection in RRV and BFV populations during their replication in mosquito and vertebrate hosts.

The Stop Codon after the nsp3 Gene of Ross River Virus (RRV) Is Not Essential for Virus Replication in Three Cell Lines Tested, but RRV Replication Is Attenuated in HEK 293T Cells

A recombinant Ross River virus (RRV) that contains the fluorescent protein mCherry fused to the non-structural protein 3 (nsP3) was constructed, which allowed real-time imaging of viral replication. RRV-mCherry contained either the natural opal stop codon after the nsP3 gene or was constructed without a stop codon. The mCherry fusion protein did not interfere with the viral life cycle and deletion of the stop codon did not change the replication capacity of RRV-mCherry. Comparison of RRV-mCherry and chikungunya virus-mCherry infections, however, showed a cell type-dependent delay in RRV-mCherry replication in HEK 293T cells. This delay was not caused by differences in cell entry, but rather by an impeded nsP expression caused by the RRV inhibitor ZAP (zinc finger CCCH-Type, antiviral 1). The data indicate that viral replication of alphaviruses is cell-type dependent, and might be unique for each alphavirus.

Testing the intrinsic mechanisms driving the dynamics of Ross River Virus across Australia

The mechanisms driving dynamics of many epidemiologically important mosquito-borne pathogens are complex, involving combinations of vector and host factors (e.g., species composition and life-history traits), and factors associated with transmission and reporting. Understanding which intrinsic mechanisms contribute most to observed disease dynamics is important, yet often poorly understood. Ross River virus (RRV) is Australia's most important mosquito-borne disease, with variable transmission dynamics across geographic regions. We used deterministic ordinary differential equation models to test mechanisms driving RRV dynamics across major epidemic centers in Brisbane, Darwin, Mandurah, Mildura, Gippsland, Renmark, Murray Bridge, and Coorong. We considered models with up to two vector species (Aedes vigilax, Culex annulirostris, Aedes camptorhynchus, Culex globocoxitus), two reservoir hosts (macropods, possums), seasonal transmission effects, and transmission parameters. We fit models against long-term RRV surveillance data (1991-2017) and used Akaike Information Criterion to select important mechanisms. The combination of two vector species, two reservoir hosts, and seasonal transmission effects explained RRV dynamics best across sites. Estimated vector-human transmission rate (average β = 8.04x10-4per vector per day) was similar despite different dynamics. Models estimate 43% underreporting of RRV infections. Findings enhance understanding of RRV transmission mechanisms, provide disease parameter estimates which can be used to guide future research into public health improvements and offer a basis to evaluate mitigation practices.

Prediction of Ross River Virus Incidence Using Mosquito Data in Three Cities of Queensland, Australia

Ross River virus (RRV) is the most common mosquito-borne disease in Australia, with Queensland recording high incidence rates (with an annual average incidence rate of 0.05% over the last 20 years). Accurate prediction of RRV incidence is critical for disease management and control. Many factors, including mosquito abundance, climate, weather, geographical factors, and socio-economic indices, can influence the RRV transmission cycle and thus have potential utility as predictors of RRV incidence. We collected mosquito data from the city councils of Brisbane, Redlands, and Mackay in Queensland, together with other meteorological and geographical data. Predictors were selected to build negative binomial generalised linear models for prediction. The models demonstrated excellent performance in Brisbane and Redlands but were less satisfactory in Mackay. Mosquito abundance was selected in the Brisbane model and can improve the predictive performance. Sufficient sample sizes of continuous mosquito data and RRV cases were essential for accurate and effective prediction, highlighting the importance of routine vector surveillance for disease management and control. Our results are consistent with variation in transmission cycles across different cities, and our study demonstrates the usefulness of mosquito surveillance data for predicting RRV incidence within small geographical areas.

Susceptibility of Aedes albopictus, Ae. aegypti and human populations to Ross River virus in Kuala Lumpur, Malaysia

BACKGROUND

Emerging arboviruses such as chikungunya and Zika viruses have unexpectedly caused widespread outbreaks in tropical and subtropical regions recently. Ross River virus (RRV) is endemic in Australia and has epidemic potential. In Malaysia, Aedes mosquitoes are abundant and drive dengue and chikungunya outbreaks. We assessed risk of an RRV outbreak in Kuala Lumpur, Malaysia by determining vector competence of local Aedes mosquitoes and local seroprevalence as a proxy of human population susceptibility.

METHODOLOGY/PRINCIPAL FINDINGS

We assessed oral susceptibility of Malaysian Ae. aegypti and Ae. albopictus by real-time PCR to an Australian RRV strain SW2089. Replication kinetics in midgut, head and saliva were determined at 3 and 10 days post-infection (dpi). With a 3 log10 PFU/ml blood meal, infection rate was higher in Ae. albopictus (60%) than Ae. aegypti (15%; p<0.05). Despite similar infection rates at 5 and 7 log10 PFU/ml blood meals, Ae. albopictus had significantly higher viral loads and required a significantly lower median oral infectious dose (2.7 log10 PFU/ml) than Ae. aegypti (4.2 log10 PFU/ml). Ae. albopictus showed higher vector competence, with higher viral loads in heads and saliva, and higher transmission rate (RRV present in saliva) of 100% at 10 dpi, than Ae. aegypti (41%). Ae. aegypti demonstrated greater barriers at either midgut escape or salivary gland infection, and salivary gland escape. We then assessed seropositivity against RRV among 240 Kuala Lumpur inpatients using plaque reduction neutralization, and found a low rate of 0.8%.

CONCLUSIONS/SIGNIFICANCE

Both Ae. aegypti and Ae. albopictus are susceptible to RRV, but Ae. albopictus displays greater vector competence. Extensive travel links with Australia, abundant Aedes vectors, and low population immunity places Kuala Lumpur, Malaysia at risk of an imported RRV outbreak. Surveillance and increased diagnostic awareness and capacity are imperative to prevent establishment of new arboviruses in Malaysia.

Fine-scale genomic tracking of Ross River virus using nanopore sequencing

BACKGROUND

Ross River virus (RRV) is Australia's most common and widespread mosquito-transmitted arbovirus and is of significant public health concern. With increasing anthropogenic impacts on wildlife and mosquito populations, it is important that we understand how RRV circulates in its endemic hotspots to determine where public health efforts should be directed. Current surveillance methods are effective in locating the virus but do not provide data on the circulation of the virus and its strains within the environment. This study examined the ability to identify single nucleotide polymorphisms (SNPs) within the variable E2/E3 region by generating full-length haplotypes from a range of mosquito trap-derived samples.

METHODS

A novel tiled primer amplification workflow for amplifying RRV was developed with analysis using Oxford Nanopore Technology's MinION and a custom ARTIC/InterARTIC bioinformatic protocol. By creating a range of amplicons across the whole genome, fine-scale SNP analysis was enabled by specifically targeting the variable region that was amplified as a single fragment and established haplotypes that informed spatial-temporal variation of RRV in the study site in Victoria.

RESULTS

A bioinformatic and laboratory pipeline was successfully designed and implemented on mosquito whole trap homogenates. Resulting data showed that genotyping could be conducted in real time and that whole trap consensus of the viruses (with major SNPs) could be determined in a timely manner. Minor variants were successfully detected from the variable E2/E3 region of RRV, which allowed haplotype determination within complex mosquito homogenate samples.

CONCLUSIONS

The novel bioinformatic and wet laboratory methods developed here will enable fast detection and characterisation of RRV isolates. The concepts presented in this body of work are transferable to other viruses that exist as quasispecies in samples. The ability to detect minor SNPs, and thus haplotype strains, is critically important for understanding the epidemiology of viruses their natural environment.

Vaccine development for zoonotic viral diseases caused by positive‑sense single‑stranded RNA viruses belonging to the Coronaviridae and Togaviridae families (Review)

Outbreaks of zoonotic viral diseases pose a severe threat to public health and economies worldwide, with this currently being more prominent than it previously was human history. These emergency zoonotic diseases that originated and transmitted from vertebrates to humans have been estimated to account for approximately one billion cases of illness and have caused millions of deaths worldwide annually. The recent emergence of severe acute respiratory syndrome coronavirus-2 (coronavirus disease 2019) is an excellent example of the unpredictable public health threat causing a pandemic. The present review summarizes the literature data regarding the main vaccine developments in human clinical phase I, II and III trials against the zoonotic positive-sense single-stranded RNA viruses belonging to the Coronavirus and Alphavirus genera, including severe acute respiratory syndrome, Middle east respiratory syndrome, Venezuelan equine encephalitis virus, Semliki Forest virus, Ross River virus, Chikungunya virus and O'nyong-nyong virus. That there are neither vaccines nor effective antiviral drugs available against most of these viruses is undeniable. Therefore, new explosive outbreaks of these zoonotic viruses may surely be expected. The present comprehensive review provides an update on the status of vaccine development in different clinical trials against these viruses, as well as an overview of the present results of these trials.

Pathogens and disease vectors/hosts monitoring in aquatic environments: Potential of using eDNA/eRNA based approach

Infectious diseases are spreading in to previously unreported geographical regions, and are reappeared in regions 75 or 100 years after their last reported case, as a result of environmental changes caused by anthropogenic activities. A pathogen, vector/host monitoring methodology is therefore indispensable in identifying potential transmission sites, providing early warnings and evaluating the human health risks of these infectious diseases in a given area. Recently, environmental DNA (eDNA) and environmental RNA approach (eRNA) have become widespread in monitoring organisms in the environment due to advantages like lower cost, time, and labour requirements. However, eDNA/eRNA based monitoring of pathogens and vectors/hosts using aquatic samples is limited to very few studies. In this review, we summarized the currently available eDNA/eRNA based human and non-human pathogens and vectors/hosts detection studies in aquatic samples. Species-specific shedding, transport, and decay of eDNA/eRNA in aquatic environments which is essential in estimating the abundance of pathogen, vectors/host in focus is also summarized. We also suggest the usage of eDNA/eRNA approach in urban aquatic samples like runoff in identifying the disease vectors/hosts inhabiting in locations which are not accessible easily.

Zoonotic and reverse zoonotic transmission of viruses between humans and pigs

Humans and pigs share a close contact relationship, similar biological traits, and one of the highest estimated number of viruses compared to other mammalian species. The contribution and directionality of viral exchange between humans and pigs remain unclear for some of these viruses, but their transmission routes are important to characterize in order to prevent outbreaks of disease in both host species. This review collects and assesses the evidence to determine the likely transmission route of 27 viruses between humans and pigs.

Physiology and ecology combine to determine host and vector importance for Ross River virus

Identifying the key vector and host species that drive the transmission of zoonotic pathogens is notoriously difficult but critical for disease control. We present a nested approach for quantifying the importance of host and vectors that integrates species' physiological competence with their ecological traits. We apply this framework to a medically important arbovirus, Ross River virus (RRV), in Brisbane, Australia. We find that vertebrate hosts with high physiological competence are not the most important for community transmission; interactions between hosts and vectors largely underpin the importance of host species. For vectors, physiological competence is highly important. Our results identify primary and secondary vectors of RRV and suggest two potential transmission cycles in Brisbane: an enzootic cycle involving birds and an urban cycle involving humans. The framework accounts for uncertainty from each fitted statistical model in estimates of species' contributions to transmission and has has direct application to other zoonotic pathogens.

Impact of COVID-19 Mitigation Measures on Mosquito-Borne Diseases in 2020 in Queensland, Australia

We describe the impact of COVID-19 mitigation measures on mosquito-borne diseases in Queensland, Australia, during the first half of 2020. Implementation of restrictions coincided with an atypical late season outbreak of Ross River virus (RRV) characterized by a peak in notifications in April (1173) and May (955) which were greater than 3-fold the mean observed for the previous four years. We propose that limitations on human movement likely resulted in the majority of RRV infections being acquired at or near the place of residence, and that an increase in outdoor activities, such as gardening and bushwalking in the local household vicinity, increased risk of exposure to RRV-infected mosquitoes. In contrast, the precipitous decline in international passenger flights led to a reduction in the number of imported dengue and malaria cases of over 70% and 60%, respectively, compared with the previous five years. This substantial reduction in flights also reduced a risk pathway for importation of exotic mosquitoes, but the risk posed by importation via sea cargo was not affected. Overall, the emergence of COVID-19 has had a varied impact on mosquito-borne disease epidemiology in Queensland, but the need for mosquito surveillance and control, together with encouragement of personal protective measures, remains unchanged.

Response of Mosquitoes Associated with Estuarine Wetlands to Bushfire in Australia

The response of mosquitoes to bushfire is poorly understood. During the 2019-20 summer, many regions of Australia were impacted by devastating bushfires. An area of estuarine and brackish-water wetlands alongside the Georges River, Sydney, New South Wales, was burned in January 2020. Mosquito populations within the area were monitored as part of the local authority's mosquito management program, providing a unique opportunity to record the response of key mosquitoes of pest and public health concern to bushfire. Ground pools within a tidally influenced swamp oak forest dominated by Casuarina glauca and associated wetlands dominated by Phragmites australis and Bolboschoenus spp. had been identified as suitable habitat for a range of mosquitoes, including Aedes alternans, Ae. vigilax, and Verrallina funerea. Surveys of immature stages of mosquitoes within recently burned habitats inundated by tides demonstrated that mosquito eggs survived the direct and indirect impacts of fire and immature stages successfully completed development as reflected in concomitant changes in adult mosquito populations following the bushfire. This unique observation has implications for mosquito management following bushfire in Australia and internationally.

The Putative Roles and Functions of Indel, Repetition and Duplication Events in Alphavirus Non-Structural Protein 3 Hypervariable Domain (nsP3 HVD) in Evolution, Viability and Re-Emergence

Alphavirus non-structural proteins 1–4 (nsP1, nsP2, nsP3, and nsP4) are known to be crucial for alphavirus RNA replication and translation. To date, nsP3 has been demonstrated to mediate many virus–host protein–protein interactions in several fundamental alphavirus mechanisms, particularly during the early stages of replication. However, the molecular pathways and proteins networks underlying these mechanisms remain poorly described. This is due to the low genetic sequence homology of the nsP3 protein among the alphavirus species, especially at its 3′ C-terminal domain, the hypervariable domain (HVD). Moreover, the nsP3 HVD is almost or completely intrinsically disordered and has a poor ability to form secondary structures. Evolution in the nsP3 HVD region allows the alphavirus to adapt to vertebrate and insect hosts. This review focuses on the putative roles and functions of indel, repetition, and duplication events that have occurred in the alphavirus nsP3 HVD, including characterization of the differences and their implications for specificity in the context of virus–host interactions in fundamental alphavirus mechanisms, which have thus directly facilitated the evolution, adaptation, viability, and re-emergence of these viruses.

Ross River Virus Infection: A Cross-Disciplinary Review with a Veterinary Perspective

Ross River virus (RRV) has recently been suggested to be a potential emerging infectious disease worldwide. RRV infection remains the most common human arboviral disease in Australia, with a yearly estimated economic cost of $4.3 billion. Infection in humans and horses can cause chronic, long-term debilitating arthritogenic illnesses. However, current knowledge of immunopathogenesis remains to be elucidated and is mainly inferred from a murine model that only partially resembles clinical signs and pathology in human and horses. The epidemiology of RRV transmission is complex and multifactorial and is further complicated by climate change, making predictive models difficult to design. Establishing an equine model for RRV may allow better characterization of RRV disease pathogenesis and immunology in humans and horses, and could potentially be used for other infectious diseases. While there are no approved therapeutics or registered vaccines to treat or prevent RRV infection, clinical trials of various potential drugs and vaccines are currently underway. In the future, the RRV disease dynamic is likely to shift into temperate areas of Australia with longer active months of infection. Here, we (1) review the current knowledge of RRV infection, epidemiology, diagnostics, and therapeutics in both humans and horses; (2) identify and discuss major research gaps that warrant further research.

Genome Sequence Analysis of First Ross River Virus Isolate from Papua New Guinea Indicates Long-Term, Local Evolution

Ross River virus (RRV) is the most medically significant mosquito-borne virus of Australia, in terms of human morbidity. RRV cases, characterised by febrile illness and potentially persistent arthralgia, have been reported from all Australian states and territories. RRV was the cause of a large-scale epidemic of multiple Pacific Island countries and territories (PICTs) from 1979 to 1980, involving at least 50,000 cases. Historical evidence of RRV seropositivity beyond Australia, in populations of Papua New Guinea (PNG), Indonesia and the Solomon Islands, has been documented. We describe the genomic characterisation and timescale analysis of the first isolate of RRV to be sampled from PNG to date. Our analysis indicates that RRV has evolved locally within PNG, independent of Australian lineages, over an approximate 40 year period. The mean time to most recent common ancestor (tMRCA) of the unique PNG clade coincides with the initiation of the PICTs epidemic in mid-1979. This may indicate that an ancestral variant of the PNG clade was seeded into the region during the epidemic, a period of high RRV transmission. Further epidemiological and molecular-based surveillance is required in PNG to better understand the molecular epidemiology of RRV in the general Australasian region.

Assessing the Risk of Exotic Mosquito Incursion through an International Seaport, Newcastle, NSW, Australia

Exotic mosquitoes, especially container-inhabiting species such as Aedes aegypti and Aedes albopictus, pose a risk to Australia as they bring with them potentially significant pest and public health concerns. Notwithstanding the threat to public health and wellbeing, significant economic costs associated with the burden of mosquito control would fall to local authorities. Detection of these mosquitoes at airports and seaports has highlighted pathways of introduction but surveillance programs outside these first ports of entry are not routinely conducted in the majority of Australian cities. To assist local authorities to better prepare response plans for exotic mosquito incursions, an investigation was undertaken to determine the extent of habitats suitable for container-inhabiting mosquitoes in over 300 residential properties adjacent to the Port of Newcastle, Newcastle, NSW. More than 1500 water-holding containers were recorded, most commonly pot plant saucers, roof gutters, and water-holding plants (e.g., bromeliads). There were significantly more containers identified for properties classified as untidy but there was no evidence visible that property characteristics could be used to prioritise property surveys in a strategic eradication response. The results demonstrate that there is potential for local establishment of exotic mosquitoes and that considerable effort would be required to adequately survey these environments for the purpose of surveillance and eradication programs.

Mosquito-Borne Viruses and Non-Human Vertebrates in Australia: A Review

Mosquito-borne viruses are well recognized as a global public health burden amongst humans, but the effects on non-human vertebrates is rarely reported. Australia, houses a number of endemic mosquito-borne viruses, such as Ross River virus, Barmah Forest virus, and Murray Valley encephalitis virus. In this review, we synthesize the current state of mosquito-borne viruses impacting non-human vertebrates in Australia, including diseases that could be introduced due to local mosquito distribution. Given the unique island biogeography of Australia and the endemism of vertebrate species (including macropods and monotremes), Australia is highly susceptible to foreign mosquito species becoming established, and mosquito-borne viruses becoming endemic alongside novel reservoirs. For each virus, we summarize the known geographic distribution, mosquito vectors, vertebrate hosts, clinical signs and treatments, and highlight the importance of including non-human vertebrates in the assessment of future disease outbreaks. The mosquito-borne viruses discussed can impact wildlife, livestock, and companion animals, causing significant changes to Australian ecology and economy. The complex nature of mosquito-borne disease, and challenges in assessing the impacts to non-human vertebrate species, makes this an important topic to periodically review.

The Insect-Specific Parramatta River Virus Is Vertically Transmitted by Aedes vigilax Mosquitoes and Suppresses Replication of Pathogenic Flaviviruses In Vitro

Insect-specific flaviviruses (ISFs) have been isolated from a range of mosquito species from different parts of the world. These viruses replicate efficiently in mosquitoes but do not appear to replicate in vertebrates. There is increasing evidence that ISFs persist in nature through vertical transmission, and that they interfere with the replication and transmission of pathogenic flaviviruses in the mosquito host. A novel ISF species, Parramatta River virus (PaRV), was previously shown to occur at high rates in Aedes (Ae.) vigilax mosquitoes collected from Sydney, Australia. We investigated whether vertical transmission was the mechanism of viral persistence in Ae. vigilax populations and whether PaRV affected replication of the pathogenic flaviviruses, West Nile virus (WNV), and dengue virus type 3 (DENV-3) in cultured mosquito cells. Progeny reared from eggs obtained from field-collected infected females had infection rates as high as 142 and 85 per 1000 for females and males, respectively. In vitro experiments showed that replication of both WNV and DENV-3 was significantly suppressed in Aedes albopictus (C6/36) cells persistently infected with PaRV. Our studies with PaRV support the findings of previous investigations that ISFs persist in nature through vertical transmission and that ISFs can suppress the replication of pathogenic flaviviruses in coinfected mosquito cells.

Infectious disease and sickness behaviour: tumour progression affects interaction patterns and social network structure in wild Tasmanian devils

Infectious diseases, including transmissible cancers, can have a broad range of impacts on host behaviour, particularly in the latter stages of disease progression. However, the difficulty of early diagnoses makes the study of behavioural influences of disease in wild animals a challenging task. Tasmanian devils (Sarcophilus harrisii) are affected by a transmissible cancer, devil facial tumour disease (DFTD), in which tumours are externally visible as they progress. Using telemetry and mark-recapture datasets, we quantify the impacts of cancer progression on the behaviour of wild devils by assessing how interaction patterns within the social network of a population change with increasing tumour load. The progression of DFTD negatively influences devils' likelihood of interaction within their network. Infected devils were more active within their network late in the mating season, a pattern with repercussions for DFTD transmission. Our study provides a rare opportunity to quantify and understand the behavioural feedbacks of disease in wildlife and how they may affect transmission and population dynamics in general.

Arthritogenic alphaviruses: epidemiological and clinical perspective on emerging arboviruses

Mosquito-borne viruses, or arboviruses, have been part of the infectious disease landscape for centuries, and are often, but not exclusively, endemic to equatorial and subtropical regions of the world. The past two decades saw the re-emergence of arthritogenic alphaviruses, a genus of arboviruses that includes several members that cause severe arthritic disease. Recent outbreaks further highlight the substantial public health burden caused by these viruses. Arthritogenic alphaviruses are often reported in the context of focused outbreaks in specific regions (eg, Caribbean, southeast Asia, and Indian Ocean) and cause debilitating acute disease that can extend to chronic manifestations for years after infection. These viruses are classified among several antigenic complexes, span a range of hosts and mosquito vectors, and can be distributed along specific geographical locations. In this Review, we highlight key features of alphaviruses that are known to cause arthritic disease in humans and outline the present findings pertaining to classification, immunogenicity, pathogenesis, and experimental approaches aimed at limiting disease manifestations. Although the most prominent alphavirus outbreaks in the past 15 years featured chikungunya virus, and a large body of work has been dedicated to understanding chikungunya disease mechanisms, this Review will instead focus on other arthritogenic alphaviruses that have been identified globally and provide a comprehensive appraisal of present and future research directions.

Sequencing of Historical Isolates, K-mer Mining and High Serological Cross-Reactivity with Ross River Virus Argue against the Presence of Getah Virus in Australia

Getah virus (GETV) is a mosquito-transmitted alphavirus primarily associated with disease in horses and pigs in Asia. GETV was also reported to have been isolated from mosquitoes in Australia in 1961; however, retrieval and sequencing of the original isolates (N544 and N554), illustrated that these viruses were virtually identical to the 1955 GETV_MM2021 isolate from Malaysia. K-mer mining of the >40,000 terabases of sequence data in the Sequence Read Archive followed by BLASTn confirmation identified multiple GETV sequences in biosamples from Asia (often as contaminants), but not in biosamples from Australia. In contrast, sequence reads aligning to the Australian Ross River virus (RRV) were readily identified in Australian biosamples. To explore the serological relationship between GETV and other alphaviruses, an adult wild-type mouse model of GETV was established. High levels of cross-reactivity and cross-protection were evident for convalescent sera from mice infected with GETV or RRV, highlighting the difficulties associated with the interpretation of early serosurveys reporting GETV antibodies in Australian cattle and pigs. The evidence that GETV circulates in Australia is thus not compelling.

Spatial and temporal patterns of Ross River virus in south east Queensland, Australia: identification of hot spots at the rural-urban interface

Background

Ross River virus (RRV) is responsible for the most common vector-borne disease of humans reported in Australia. The virus circulates in enzootic cycles between multiple species of mosquitoes, wildlife reservoir hosts and humans. Public health concern about RRV is increasing due to rising incidence rates in Australian urban centres, along with increased circulation in Pacific Island countries. Australia experienced its largest recorded outbreak of 9544 cases in 2015, with the majority reported from south east Queensland (SEQ). This study examined potential links between disease patterns and transmission pathways of RRV.

Methods

The spatial and temporal distribution of notified RRV cases, and associated epidemiological features in SEQ, were analysed for the period 2001–2016. This included fine-scale analysis of disease patterns across the suburbs of the capital city of Brisbane, and those of 8 adjacent Local Government Areas, and host spot analyses to identify locations with significantly high incidence.

Results

The mean annual incidence rate for the region was 41/100,000 with a consistent seasonal peak in cases between February and May. The highest RRV incidence was in adults aged from 30 to 64 years (mean incidence rate: 59/100,000), and females had higher incidence rates than males (mean incidence rates: 44/100,000 and 34/100,000, respectively). Spatial patterns of disease were heterogeneous between years, and there was a wide distribution of disease across both urban and rural areas of SEQ. Overall, the highest incidence rates were reported from predominantly rural suburbs to the north of Brisbane City, with significant hot spots located in peri-urban suburbs where residential, agricultural and conserved natural land use types intersect.

Conclusions

Although RRV is endemic across all of SEQ, transmission is most concentrated in areas where urban and peri-urban environments intersect. The drivers of RRV transmission across rural-urban landscapes should be prioritised for further investigation, including identification of specific vectors and hosts that mediate human spillover.

Species Traits and Hotspots Associated with Ross River Virus Infection in Nonhuman Vertebrates in South East Queensland

Ross River virus (RRV) is a mosquito-borne zoonotic arbovirus associated with high public health and economic burdens across Australia, but particularly in South East Queensland (SEQ). Despite this high burden, humans are considered incidental hosts. Transmission of RRV is maintained among mosquitoes and many nonhuman vertebrate reservoir hosts, although the relative contributions of each of these hosts are unclear. To clarify the importance of a range of vertebrates in RRV transmission in SEQ, a total of 595 serum samples from 31 species were examined for RRV exposure using a gold-standard plaque reduction neutralization test. Data were analyzed statistically using generalized linear models and a coefficient inference tree, and spatially. RRV exposure was highly variable between and within species groups. Critically, species group ("placental mammal," "marsupial," and "bird"), which has previously been used as a proxy for reservoir hosts, was a poor correlate for exposure. Instead, we found that generalized "diet" and greater "body mass" were most strongly correlated with seropositivity. We also identified significant differences in seropositivity between the two major possum species (ringtail possums and brushtail possums), which are ecologically and taxonomically different. Finally, we identified distinct hotspots and coldspots of seropositivity in nonhuman vertebrates, which correlated with human notification data. This is the largest diversity of species tested for RRV in a single study to date. The analysis methods within this study provide a framework for analyzing serological data in combination with species traits for other zoonotic disease, but more specifically for RRV highlight areas to target further public health research and surveillance effort.

Multiple capsid protein binding sites mediate selective packaging of the alphavirus genomic RNA

The alphavirus capsid protein (Cp) selectively packages genomic RNA (gRNA) into the viral nucleocapsid to produce infectious virus. Using photoactivatable ribonucleoside crosslinking and an innovative biotinylated Cp retrieval method, here we comprehensively define binding sites for Semliki Forest virus (SFV) Cp on the gRNA. While data in infected cells demonstrate Cp binding to the proposed genome packaging signal (PS), mutagenesis experiments show that PS is not required for production of infectious SFV or Chikungunya virus. Instead, we identify multiple Cp binding sites that are enriched on gRNA-specific regions and promote infectious SFV production and gRNA packaging. Comparisons of binding sites in cytoplasmic vs. viral nucleocapsids demonstrate that budding causes discrete changes in Cp-gRNA interactions. Notably, Cp’s top binding site is maintained throughout virus assembly, and specifically binds and assembles with Cp into core-like particles in vitro. Together our data suggest a model for selective alphavirus genome recognition and assembly.

Alphaviruses need to selectively package genomic viral RNA for transmission, but the packaging mechanism remains unclear. Here, Brown et al. combine PAR-CLIP with biotinylated capsid protein (Cp) retrieval and identify multiple Cp binding sites on genomic viral RNA that promote virion formation.

Antiviral Strategies against Arthritogenic Alphaviruses

Alphaviruses are members of the Togaviridae family that are mainly transmitted by arthropods such as mosquitoes. In the last decades, several alphaviruses have re-emerged, causing outbreaks worldwide. One example is the re-emergence of chikungunya virus (CHIKV) in 2004, which caused massive epidemics in the Indian Ocean region after which the virus dramatically spread to the Americas in late 2013. Besides CHIKV, other alphaviruses, such as the Ross River virus (RRV), Mayaro virus (MAYV), and Venezuelan equine encephalitis virus (VEEV), have emerged and have become a serious public health concern in recent years. Infections with the Old World alphaviruses (e.g., CHIKV, RRV) are primarily associated with polyarthritis and myalgia that can persist for months to years. On the other hand, New World alphaviruses such as VEEV cause mainly neurological disease. Despite the worldwide (re-)emergence of these viruses, there are no antivirals or vaccines available for the treatment or prevention of infections with alphaviruses. It is therefore of utmost importance to develop antiviral strategies against these viruses. We here provided an overview of the reported antiviral strategies against arthritogenic alphaviruses. In addition, we highlighted the future perspectives for the development and the proper use of such antivirals.

How do local differences in saltmarsh ecology influence disease vector mosquito populations?

Saltmarsh breeding mosquitoes are an important source of vectors for arboviral transmission. In southern Australia, the most prominent vector borne disease, Ross River virus (Togaviridae: Alphavirus) (RRV), is transmitted by the saltmarsh mosquito (Diptera: Culicidae) Aedes camptorhynchus (Thomson). However, the factors driving the abundance of this mosquito within and among saltmarshes are poorly understood. To predict the abundance of this mosquito within saltmarshes, the environmental conditions and aquatic invertebrate ecology of three temperate saltmarshes habitats were monitored over two seasons. Up to 44% of first-instar mosquito numbers and 21% of pupal numbers were accounted for by environmental variables. Samphire vegetation cover was a common predictor of first-instar numbers across sites although, between saltmarshes, aquatic factors such as high salinity, temperatures less than 22 °C and water body volume were important predictors. The identified predictors of pupal numbers were more variable and included high tides, waterbody volume and alkalinity. The composition of invertebrate functional feeding groups differed between saltmarshes and showed that an increased diversity led to fewer mosquitoes. It was evident that apparently similar saltmarshes can vary markedly in invertebrate assemblages, water availability and conditions through tidal inundations, rainfall or waterbody permanency. The present study advances insight into predictors of vector mosquito numbers that drive the risk of RRV outbreaks.

Epidemiological models for predicting Ross River virus in Australia: A systematic review

Ross River virus (RRV) is the most common and widespread arbovirus in Australia. Epidemiological models of RRV increase understanding of RRV transmission and help provide early warning of outbreaks to reduce incidence. However, RRV predictive models have not been systematically reviewed, analysed, and compared. The hypothesis of this systematic review was that summarising the epidemiological models applied to predict RRV disease and analysing model performance could elucidate drivers of RRV incidence and transmission patterns. We performed a systematic literature search in PubMed, EMBASE, Web of Science, Cochrane Library, and Scopus for studies of RRV using population-based data, incorporating at least one epidemiological model and analysing the association between exposures and RRV disease. Forty-three articles, all of high or medium quality, were included. Twenty-two (51.2%) used generalised linear models and 11 (25.6%) used time-series models. Climate and weather data were used in 27 (62.8%) and mosquito abundance or related data were used in 14 (32.6%) articles as model covariates. A total of 140 models were included across the articles. Rainfall (69 models, 49.3%), temperature (66, 47.1%) and tide height (45, 32.1%) were the three most commonly used exposures. Ten (23.3%) studies published data related to model performance. This review summarises current knowledge of RRV modelling and reveals a research gap in comparing predictive methods. To improve predictive accuracy, new methods for forecasting, such as non-linear mixed models and machine learning approaches, warrant investigation.

A cross-reactive antibody protects against Ross River virus musculoskeletal disease despite rapid neutralization escape in mice

Arthritogenic alphaviruses cause debilitating musculoskeletal disease and historically have circulated in distinct regions. With the global spread of chikungunya virus (CHIKV), there now is more geographic overlap, which could result in heterologous immunity affecting natural infection or vaccination. Here, we evaluated the capacity of a cross-reactive anti-CHIKV monoclonal antibody (CHK-265) to protect against disease caused by the distantly related alphavirus, Ross River virus (RRV). Although CHK-265 only moderately neutralizes RRV infection in cell culture, it limited clinical disease in mice independently of Fc effector function activity. Despite this protective phenotype, RRV escaped from CHK-265 neutralization in vivo, with resistant variants retaining pathogenic potential. Near the inoculation site, CHK-265 reduced viral burden in a type I interferon signaling-dependent manner and limited immune cell infiltration into musculoskeletal tissue. In a parallel set of experiments, purified human CHIKV immune IgG also weakly neutralized RRV, yet when transferred to mice, resulted in improved clinical outcome during RRV infection despite the emergence of resistant viruses. Overall, this study suggests that weakly cross-neutralizing antibodies can protect against heterologous alphavirus disease, even if neutralization escape occurs, through an early viral control program that tempers inflammation.

The induction of broadly neutralizing antibodies is a goal of many antiviral vaccine programs. In this study, we show that cross-reactive monoclonal and polyclonal antibodies developed after CHIKV infection or immunization with relatively weak cross-neutralizing activity can protect against RRV-induced musculoskeletal disease in mice. Even though RRV rapidly escaped from neutralization, antibody therapy reduced inflammation in musculoskeletal tissues and decreased viral burden near the site of infection in a manner that required type I interferon signaling. These studies in mice show that broadly reactive antibodies with limited neutralizing activity still can confer protection against heterologous alphaviruses.

Epidemic Alphaviruses: Ecology, Emergence and Outbreaks

Over the past century, the emergence/reemergence of arthropod-borne zoonotic agents has been a growing public health concern. In particular, agents from the genus Alphavirus pose a significant risk to both animal and human health. Human alphaviral disease presents with either arthritogenic or encephalitic manifestations and is associated with significant morbidity and/or mortality. Unfortunately, there are presently no vaccines or antiviral measures approved for human use. The present review examines the ecology, epidemiology, disease, past outbreaks, and potential to cause contemporary outbreaks for several alphavirus pathogens.

A micro-PRNT for the detection of Ross River virus antibodies in mosquito blood meals: A useful tool for inferring transmission pathways

Introduction

Many arboviruses of public health significance are maintained in zoonotic cycles with complex transmission pathways. The presence of serum antibody against arboviruses in vertebrates provides evidence of their historical exposure but reveals nothing about the vector-reservoir relationship. Moreover, collecting blood or tissue samples from vertebrate hosts is ethically and logistically challenging. We developed a novel approach for screening the immune status of vertebrates against Ross River virus that allows us to implicate the vectors that form the transmission pathways for this commonly notified Australian arboviral disease.

Methods

A micro-plaque reduction neutralisation test (micro-PRNT) was developed and validated on koala (Phascolarctos cinereus) sera against a standard PRNT. The ability of the micro-PRNT to detect RRV antibodies in mosquito blood meals was then tested using two mosquito models. Laboratory-reared Aedes aegypti were fed, via a membrane, on sheep blood supplemented with RRV seropositive and seronegative human sera. Aedes notoscriptus were fed on RRV seropositive and seronegative human volunteers. Blood-fed mosquitoes were harvested at various time points after feeding and their blood meals analysed for the presence of RRV neutralising antibodies using the micro-PRNT.

Results

There was significant agreement of the plaque neutralisation resulting from the micro-PRNT and standard PRNT techniques (R² = 0.65; P<0.0001) when applied to RRV antibody detection in koala sera. Sensitivity and specificity of the micro-PRNT assay were 88.2% and 96%, respectively, in comparison with the standard PRNT. Blood meals from mosquitoes fed on sheep blood supplemented with RRV antibodies, and on blood from RRV seropositive humans neutralised the virus by ≥50% until 48 hr post feeding. The vertebrate origin of the blood meal was also ascertained for the same samples, in parallel, using established molecular techniques.

Conclusions

The small volumes of blood present in mosquito abdomens can be used to identify RRV antibodies and therefore host exposure to arbovirus infection. In tandem with the accurate identification of the mosquito, and diagnostics for the host origin of the blood meal, this technique has tremendous potential for exploring RRV transmission pathways. It can be adapted for similar studies on other mosquito borne zoonoses.

Localized Outbreaks of Epidemic Polyarthritis among Military Personnel Caused by Different Sublineages of Ross River Virus, Northeastern Australia, 2016-2017

Two outbreaks of epidemic polyarthritis occurred among Australian Defence Force personnel during and following short military exercises in the Shoalwater Bay Training Area, northeastern Australia, in 2016 and 2017. Ross River virus (RRV) IgM was detected in acute-phase serum samples from most patients (28/28 in 2016 and 25/31 in 2017), and RRV was recovered from 4/38 serum samples assayed (1/21 in 2016 and 3/17 in 2017). Phylogenetic analyses of RRV envelope glycoprotein E2 and nonstructural protein nsP3 nucleotide sequences segregated the RRV isolates obtained in 2016 and 2017 outbreaks into 2 distinct sublineages, suggesting that each outbreak was caused by a different strain of RRV. The spatiotemporal characteristics of the 2016 outbreak suggested that some of the infections involved human-mosquito-human transmission without any intermediate host. These outbreaks highlight the importance of personal protective measures in preventing vectorborne diseases for which no vaccine or specific prophylaxis exists.

Ross River Virus Infection of Horses: Appraisal of Ecological and Clinical Consequences

Ross River virus (RRV) is a mosquito-borne arbovirus of the genus Alphavirus that causes disease in humans and horses in Australia. A temporal association of RRV infection in horses with clinical signs including pyrexia, malaise, and polyarthralgia has been reported, along with reduced athletic performance, often for extended periods. Despite these reports, disease due to RRV remains somewhat controversial as experimental infection of horses has resulted in obvious viraemia yet minimal signs of clinical disease. The relatively high viraemia demonstrated by horses infected with RRV has led to speculation that they could act as an important reservoir host of the virus, although this remains unclear. This review sought to appraise the existing literature relating to RRV infection of horses and to summarize the ecological and clinical consequences of RRV of relevance to the equine industry and to public health more broadly.

Associations Between Ross River Virus Infection in Humans and Vector-Vertebrate Community Ecology in Brisbane, Australia

Transmission of vector-borne pathogens can vary in complexity from single-vector, single-host systems through to multivector, multihost vertebrate systems. Understanding the dynamics of transmission is important for disease prevention efforts, but is dependent on disentangling complex interactions within coupled natural systems. Ross River virus (RRV) is a multivector multihost pathogen responsible for the greatest number of notified vector-borne pathogen infections in humans in Australia. Current evidence suggests that nonhuman vertebrates are critical for the maintenance and spillover of RRV into mosquito populations. Yet, there is a limited knowledge of which mosquito vector species and amplifying vertebrate host species are most important for transmission of RRV to humans. We conducted field surveys of nonhuman vertebrates and mosquitoes in the RRV endemic city of Brisbane, Australia, to assess the effect of vector and host community structure on human RRV notifications. Six suburbs were selected across a gradient of human disease notification rates. Differences in vertebrate and mosquito compositions were observed across all suburbs. Suburbs with higher RRV notification rates contained greater vertebrate biomass (dominated by the presence of horses) and higher mosquito abundances. This study suggests that horse-mosquito interactions should be considered in more detail and that vertebrate biomass and mosquito abundance be incorporated into future RRV modeling studies and considered in public health strategies for RRV management.

Human monoclonal antibodies against Ross River virus target epitopes within the E2 protein and protect against disease

Ross River fever is a mosquito-transmitted viral disease that is endemic to Australia and the surrounding Pacific Islands. Ross River virus (RRV) belongs to the arthritogenic group of alphaviruses, which largely cause disease characterized by debilitating polyarthritis, rash, and fever. There is no specific treatment or licensed vaccine available, and the mechanisms of protective humoral immunity in humans are poorly understood. Here, we describe naturally occurring human mAbs specific to RRV, isolated from subjects with a prior natural infection. These mAbs potently neutralize RRV infectivity in cell culture and block infection through multiple mechanisms, including prevention of viral attachment, entry, and fusion. Some of the most potently neutralizing mAbs inhibited binding of RRV to Mxra8, a recently discovered alpahvirus receptor. Epitope mapping studies identified the A and B domains of the RRV E2 protein as the major antigenic sites for the human neutralizing antibody response. In experiments in mice, these mAbs were protective against cinical disease and reduced viral burden in multiple tissues, suggesting a potential therapeutic use for humans.

Epidemiologic, Entomologic, and Virologic Factors of the 2014-15 Ross River Virus Outbreak, Queensland, Australia

Australia experienced its largest recorded outbreak of Ross River virus (RRV) during the 2014-15 reporting year, comprising >10,000 reported cases. We investigated epidemiologic, entomologic, and virologic factors that potentially contributed to the scale of the outbreak in Queensland, the state with the highest number of notifications (6,371). Spatial analysis of human cases showed that notifications were geographically widespread. In Brisbane, human case notifications and virus detections in mosquitoes occurred across inland and coastal locations. Viral sequence data demonstrated 2 RRV lineages (northeastern genotypes I and II) were circulating, and a new strain containing 3 unique amino acid changes in the envelope 2 protein was identified. Longitudinal mosquito collections demonstrated unusually high relative abundance of Culex annulirostris and Aedes procax mosquitoes, attributable to extensive freshwater larval habitats caused by early and persistent rainfall during the reporting year. Increased prevalence of these mosquitoes probably contributed to the scale of this outbreak.

Modulation of Monocyte-Driven Myositis in Alphavirus Infection Reveals a Role for CX3CR1+ Macrophages in Tissue Repair

Arthritogenic alphaviruses cause debilitating inflammatory disease, and current therapies are restricted to palliative approaches. Here, we show that following monocyte-driven muscle inflammation, tissue recovery is associated with the accumulation of CX₃CR1⁺ macrophages in the muscle. Modulating inflammatory monocyte infiltration using immune-modifying microparticles (IMP) reduced tissue damage and inflammation and enhanced the formation of tissue repair-associated CX₃CR1⁺ macrophages in the muscle. This shows that modulating key effectors of viral inflammation using microparticles can alter the outcome of disease by facilitating the accumulation of macrophage subsets associated with tissue repair.

Arthritogenic alphaviruses such as Ross River and Chikungunya viruses cause debilitating muscle and joint pain and pose significant challenges in the light of recent outbreaks. How host immune responses are orchestrated after alphaviral infections and lead to musculoskeletal inflammation remains poorly understood. Here, we show that myositis induced by Ross River virus (RRV) infection is driven by CD11b^hi Ly6C^hi inflammatory monocytes and followed by the establishment of a CD11b^hi Ly6C^lo CX₃CR1⁺ macrophage population in the muscle upon recovery. Selective modulation of CD11b^hi Ly6C^hi monocyte migration to infected muscle using immune-modifying microparticles (IMP) reduced disease score, tissue damage, and inflammation and promoted the accumulation of CX₃CR1⁺ macrophages, enhancing recovery and resolution. Here, we detail the role of immune pathology, describing a poorly characterized muscle macrophage subset as part of the dynamics of alphavirus-induced myositis and tissue recovery and identify IMP as an effective immunomodulatory approach. Given the lack of specific treatments available for alphavirus-induced pathologies, this study highlights a therapeutic potential for simple immune modulation by IMP in infected individuals in the event of large alphavirus outbreaks.

Novel monoclonal antibodies against Australian strains of negeviruses and insights into virus structure, replication and host -restriction

We report the isolation of Australian strains of Bustos virus and Ngewotan virus, two insect-specific viruses in the newly identified taxon Negevirus, originally isolated from Southeast Asian mosquitoes. Consistent with the expected insect-specific tropism of negeviruses, these isolates of Ngewotan and Bustos viruses, alongside the Australian negevirus Castlerea virus, replicated exclusively in mosquito cells but not in vertebrate cells, even when their temperature was reduced to 34 °C. Our data confirmed the existence of two structural proteins, putatively one membrane protein forming the majority of the virus particle, and one glycoprotein forming a projection on the apex of the virions. We generated and characterized 71 monoclonal antibodies to both structural proteins of the two viruses, most of which were neutralizing. Overall, these data increase our knowledge of negevirus mechanisms of infection and replication in vitro.

Genome-Scale Phylogeny and Evolutionary Analysis of Ross River Virus Reveals Periodic Sweeps of Lineage Dominance in Western Australia, 1977-2014

Ross River virus (RRV) causes the most common mosquito-borne infection in Australia and causes a significant burden of suffering to infected individuals as well as being a large burden to the Australian economy. The genetic diversity of RRV and its evolutionary history have so far only been studied using partial E2 gene analysis with a limited number of isolates. Robust whole-genome analysis has not yet been conducted. This study generated 94 novel near-whole-genome sequences to investigate the evolutionary history of RRV to better understand its genetic diversity through comprehensive whole-genome phylogeny. A better understanding of RRV genetic diversity will enable better diagnostics, surveillance, and potential future vaccine design.

Ross River virus (RRV), an alphavirus of the Togaviridae family, is the most medically significant mosquito-borne virus of Australia. Past RRV phylogenetic and evolutionary analyses have been based on partial genome analyses only. Three geographically distinct RRV lineages, the Eastern, the Western, and the supposedly extinct North-Eastern lineage, were classified previously. We sought to expand on past phylogenies through robust genome-scale phylogeny to better understand RRV genetic diversity and evolutionary dynamics. We analyzed 106 RRV complete coding sequences, which included 13 genomes available on NCBI and 94 novel sequences derived for this study, sampled throughout Western Australia (1977–2014) and during the substantial Pacific Islands RRV epidemic (1979–1980). Our final data set comprised isolates sampled over 59 years (1959–2018) from a range of locations. Four distinct genotypes were defined, with the newly described genotype 4 (G4) found to be the contemporary lineage circulating in Western Australia. The prior geographical classification of RRV lineages was not supported by our findings, with evidence of geographical and temporal cocirculation of distinct genetic groups. Bayesian Markov chain Monte Carlo (MCMC) analysis revealed that RRV lineages diverged from a common ancestor approximately 94 years ago, with distinct lineages emerging roughly every 10 years over the past 50 years in periodic bursts of genetic diversity. Our study has enabled a more robust analysis of RRV evolutionary history and resolved greater genetic diversity that had been previously defined by partial E2 gene analysis.

IMPORTANCE Ross River virus (RRV) causes the most common mosquito-borne infection in Australia and causes a significant burden of suffering to infected individuals as well as being a large burden to the Australian economy. The genetic diversity of RRV and its evolutionary history have so far only been studied using partial E2 gene analysis with a limited number of isolates. Robust whole-genome analysis has not yet been conducted. This study generated 94 novel near-whole-genome sequences to investigate the evolutionary history of RRV to better understand its genetic diversity through comprehensive whole-genome phylogeny. A better understanding of RRV genetic diversity will enable better diagnostics, surveillance, and potential future vaccine design.

Viral Febrile Illnesses and Emerging Pathogens

Emerging or emerged diseases and viral pathogens are responsible historically and currently for large epidemics, global pandemics, and significant morbidity and mortality. Our civilization will continue to face the emergence of new pathogens and viruses: viruses will continue to evolve and adapt to new environments at a high rate; our population continues to grow through birth rate, land development, and migration; climate change will continue to increase the vector burden and spread and change the migratory pattern of animals; and our societal mobility will continue to increase through rapid transportation. The clinical evaluation of the febrile patient with a potential emerging viral pathogen involves documenting the likelihood for an infection by a detailed travel history, calculation of an incubation time by exposure, and an understanding of the disease progression though the clinical illness, which drives the differential diagnosis and the type of diagnostics ordered. Ultimately, the proper identification and diagnosis of a patient with a viral febrile illness due to an emerging pathogen will elicit the appropriate precautions to protect health care providers and communities, deliver appropriate therapeutic interventions, and initiate a targeted public health response.

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The majority of emerging diseases are caused by viruses, with many that are transmitted by insect vectors or are zoonotic.

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RNA viruses in particular have high mutation rates and can evolve rapidly in new and changing environments. This, in combination with societal factors, climate change, and rapid travel, has increased the number of epidemics from emerging pathogens in the last several decades.

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Understanding the travel history, incubation time of potential viruses, and the clinical presentation by illness day is essential in making the right diagnosis and identifying the infecting virus.

Antiviral drug discovery against arthritogenic alphaviruses: Tools and molecular targets

Alphaviruses are (mainly) arthropod-borne viruses that belong to the family of the Togaviridae. Based on the disease they cause, alphaviruses are divided into an arthritogenic and an encephalitic group. Arthritogenic alphaviruses such as the chikungunya virus (CHIKV), the Ross River virus (RRV) and the Mayaro virus (MAYV) have become a serious public health concern in recent years. Epidemics are associated with high morbidity and the infections cause in many patients debilitating joint pain that can persist for months to years. The recent (2013-2014) introduction of CHIKV in the Americas resulted in millions of infected persons. Massive outbreaks of CHIKV and other arthritogenic alphaviruses are likely to occur in the future. Despite the worldwide (re-)emergence of these viruses, there are no antivirals or vaccines available for the treatment or prevention of infections with alphaviruses. It is therefore of utmost importance to develop antiviral strategies against these viruses. We here review the possible molecular targets in the replication cycle of these viruses for the development of antivirals. In addition, we provide an overview of the currently available in vitro systems and mouse infection models that can be used to assess the potential antiviral effect against these viruses.

Mosquito and Virus Surveillance as a Predictor of Human Ross River Virus Infection in South-West Western Australia: How Useful Is It?

Mosquito and virus surveillance systems are widely used in Western Australia (WA) to support public health efforts to reduce mosquito-borne disease. However, these programs are costly to maintain on a long-term basis. Therefore, we aimed to assess the validity of mosquito numbers and Ross River virus (RRV) isolates from surveillance trap sites as predictors of human RRV cases in south-west WA between 2003 and 2014. Using negative binomial regression modeling, mosquito surveillance was found to be a useful tool for predicting human RRV cases. In eight of the nine traps, when adjusted for season, there was an increased risk of RRV cases associated with elevated mosquito numbers detected 1 month before the onset of human cases for at least one quartile compared with the reference group. The most predictive urban trap sites were located near saltmarsh mosquito habitat, bushland that could sustain macropods and densely populated residential suburbs. This convergence of environments could allow enzootic transmission of RRV to spillover and infect the human population. Close proximity of urban trap sites to each other suggested these sites could be reduced. Ross River virus isolates were infrequent at some trap sites, so ceasing RRV isolation from mosquitoes at these sites or where isolates were not predictive of human cases could be considered. In future, trap sites could be reduced for routine surveillance, allowing other environments to be monitored to broaden the understanding of RRV ecology in the region. A more cost-effective and efficient surveillance program may result from these modifications.

Dispersal of the Mosquito Aedes vigilax (Diptera: Culicidae) From Urban Estuarine Wetlands in Sydney, Australia

Aedes vigilax (Skuse) is a pest and vector species associated with coastal wetlands and the abundance of this mosquito has been identified as contributing to increased risk of mosquito-borne disease outbreaks. As urban development continues to encroach on these coastal wetlands, pest and public health impacts are becoming of increasing concern and in the absence of broadscale mosquito control. Urban planners are looking to buffer zones and other land use planning options to minimize contact between mosquitoes and humans but gaps in the understanding of dispersal ranges of mosquitoes hamper the adoption of these strategies. A mark-release-recapture experiment was conducted to measure the dispersal of this mosquito from an urban estuarine wetland in Sydney, Australia. An estimated total of over 150,000 wild caught female mosquitoes were marked with fluorescent dust and then released. A network of 38 traps was then operated for 5 d within an area of 28 km2. A total of 280 marked mosquitoes was recaptured, representing less than 1% of the estimate 250,000 marked mosquitoes released. Marked mosquitoes were recaptured up to 3 km from the release point, providing an insight into the dispersal range of these mosquitoes. The mean distance traveled by marked mosquitoes was 0.83 km, a result reflecting the greater proportion of marked mosquitoes recaptured near release point. The findings of this study indicate that effective buffer zones between estuarine wetlands and high-density urban developments would be an impractical approach to minimizing pest and public health impacts associated with this mosquito.

Establishment of an Alphavirus-Specific Neutralization Assay to Distinguish Infections with Different Members of the Semliki Forest complex

Background: Alphaviruses are transmitted by arthropod vectors and can be found worldwide. Alphaviruses of the Semliki Forest complex such as chikungunya virus (CHIKV), Mayaro virus (MAYV) or Ross River virus (RRV) cause acute febrile illness and long-lasting arthralgia in humans, which cannot be clinically discriminated from a dengue virus or Zika virus infection. Alphaviruses utilize a diverse array of mosquito vectors for transmission and spread. For instance, adaptation of CHIKV to transmission by Aedes albopictus has increased its spread and resulted in large outbreaks in the Indian Ocean islands. For many alphaviruses commercial diagnostic tests are not available or show cross-reactivity among alphaviruses. Climate change and globalization will increase the spread of alphaviruses and monitoring of infections is necessary and requires virus-specific methods. Method: We established an alphavirus neutralization assay in a 384-well format by using pseudotyped lentiviral vectors. Results: MAYV-specific reactivity could be discriminated from CHIKV reactivity. Human plasma from blood donors infected with RRV could be clearly identified and did not cross-react with other alphaviruses. Conclusion: This safe and easy to use multiplex assay allows the discrimination of alphavirus-specific reactivity within a single assay and has potential for epidemiological surveillance. It might also be useful for the development of a pan-alphavirus vaccine.

Ecological and life history traits are associated with Ross River virus infection among sylvatic mammals in Australia

Background

Ross River virus (RRV) is Australia’s most important arbovirus given its annual burden of disease and the relatively large number of Australians at risk for infection. This mosquito-borne arbovirus is also a zoonosis, making its epidemiology and infection ecology complex and cryptic. Our grasp of enzootic, epizootic, and zoonotic RRV transmission dynamics is imprecise largely due to a poor understanding of the role of wild mammalian hosts in the RRV system.

Methods

The current study applied a piecewise structural equation model (PSEM) toward an interspecific comparison of sylvatic Australian mammals to characterize the ecological and life history profile of species with a history of RRV infection relative to those species with no such history among all wild mammalian species surveyed for RRV infection. The effects of species traits were assessed through multiple causal pathways within the PSEM framework.

Results

Sylvatic mammalian species with a history of RRV infection tended to express dietary specialization and smaller population density. These species were also characterized by a longer gestation length.

Conclusions

This study provides the first interspecific comparison of wild mammals for RRV infection and identifies some potential targets for future wildlife surveys into the infection ecology of this important arbovirus. An applied RRV macroecology may prove invaluable to the epidemiological modeling of RRV epidemics across diverse sylvatic landscapes, as well as to the development of human and animal health surveillance systems.

Electronic supplementary material

The online version of this article (10.1186/s12898-019-0220-5) contains supplementary material, which is available to authorized users.

Accurate identification of Australian mosquitoes using protein profiling

Australian mosquito species significantly impact human health through nuisance biting and the transmission of endemic and exotic pathogens. Surveillance programmes designed to provide an early warning of mosquito-borne disease risk require reliable identification of mosquitoes. This study aimed to investigate the viability of Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) as a rapid and inexpensive approach to the identification of Australian mosquitoes and was validated using a three-step taxonomic approach. A total of 300 mosquitoes representing 21 species were collected from south-eastern New South Wales and morphologically identified. The legs from the mosquitoes were removed and subjected to MALDI-TOF MS analysis. Fifty-eight mosquitoes were sequenced at the cytochrome c oxidase subunit I (cox1) gene region and genetic relationships were analysed. We create the first MALDI-TOF MS spectra database of Australian mosquito species including 19 species. We clearly demonstrate the accuracy of MALDI-TOF MS for identification of Australian mosquitoes. It is especially useful for assessing gaps in the effectiveness of DNA barcoding by differentiating closely related taxa. Indeed, cox1 DNA barcoding was not able to differentiate members of the Culex pipiens group, Cx. quinquefasciatus and Cx. pipiens molestus, but these specimens were correctly identified using MALDI-TOF MS.

Temperature explains broad patterns of Ross River virus transmission

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.

Mosquitoes cannot control their body temperature, so their survival and performance depend on the temperature where they live. As a result, outside temperatures can also affect the spread of diseases transmitted by mosquitoes. This has left scientists wondering how climate change may affect the spread of mosquito-borne diseases. Predicting the effects of climate change on such diseases is tricky, because many interacting factors, including temperatures and rainfall, affect mosquito populations. Also, rising temperatures do not always have a positive effect on mosquitoes – they may help mosquitoes initially, but it can get too warm even for these animals.

Climate change could affect the Ross River virus, the most common mosquito-borne disease in Australia. The virus infects 2,000 to 9,000 people each year and can cause long-term joint pain and disability. Currently, the virus spreads year-round in tropical, northern Australia and seasonally in temperate, southern Australia. Large outbreaks have occurred outside of Australia, and scientists are worried it could spread worldwide.

Now, Shocket et al. have built a model that predicts how the spread of Ross River virus changes with temperature. Shocket et al. used data from laboratory experiments that measured mosquito and virus performance across a broad range of temperatures. The experiments showed that ~26°C (80°F) is the optimal temperature for mosquitoes to spread the Ross River virus. Temperatures below 17°C (63°F) and above 32°C (89°F) hamper the spread of the virus. These temperature ranges match the current disease patterns in Australia where human cases peak in March. This is two months after the country’s average temperature reaches the optimal level and about how long it takes mosquito populations to grow, infect people, and for symptoms to develop.

Because northern Australia is already near the optimal temperature for mosquitos to spread the Ross River virus, any climate warming should decrease transmission there. But warming temperatures could increase the disease’s transmission in the southern part of the country, where most people live. The model Shocket et al. created may help the Australian government and mosquito control agencies better plan for the future.