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), 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.

Rainfall and sentinel chicken seroconversions predict human cases of Murray Valley encephalitis in the north of Western Australia.

BACKGROUND: Murray Valley encephalitis virus (MVEV) is a flavivirus that occurs in Australia and New Guinea. While clinical cases are uncommon, MVEV can cause severe encephalitis with high mortality. Sentinel chicken surveillance is used at many sites around Australia to provide an early warning system for risk of human infection in areas that have low population density and geographical remoteness. MVEV in Western Australia occurs in areas of low population density and geographical remoteness, resulting in logistical challenges with surveillance systems and few human cases. While epidemiological data has suggested an association between rainfall and MVEV activity in outbreak years, it has not been quantified, and the association between rainfall and sporadic cases is less clear. In this study we analysed 22 years of sentinel chicken and human case data from Western Australia in order to evaluate the effectiveness of sentinel chicken surveillance for MVEV and assess the association between rainfall and MVEV activity. METHODS: Sentinel chicken seroconversion, human case and rainfall data from the Kimberley and Pilbara regions of Western Australia from 1990 to 2011 were analysed using negative binomial regression. Sentinel chicken seroconversion and human cases were used as dependent variables in the model. The model was then tested against sentinel chicken and rainfall data from 2012 and 2013. RESULTS: Sentinel chicken seroconversion preceded all human cases except two in March 1993. Rainfall in the prior three months was significantly associated with both sentinel chicken seroconversion and human cases across the regions of interest. Sentinel chicken seroconversion was also predictive of human cases in the models. The model predicted sentinel chicken seroconversion in the Kimberley but not in the Pilbara, where seroconversions early in 2012 were not predicted. The latter may be due to localised MVEV activity in isolated foci at dams, which do not reflect broader virus activity in the region. CONCLUSIONS: We showed that rainfall and sentinel chickens provide a useful early warning of MVEV risk to humans across endemic and epidemic areas, and that a combination of the two indicators improves the ability to assess MVEV risk and inform risk management measures.

Ross River virus infection surveillance in the Greater Perth Metropolitan area--has there been an increase in cases in the winter months?

An increase in off-season (June to September) Ross River virus (RRV) notifications from the greater Perth metropolitan area was observed from 2006 to 2009. We investigated the increase to determine whether it is likely to have reflected a true increase in off-season cases. A single positive RRV IgM test result is sufficient for RRV notification but where follow-up testing was performed, the positive predictive value of an IgM test where IgG was negative was very low in the off-season and also in the season when using the only commercially available test kit. The increase in off-season notifications was not associated with an increase in off-season testing. Some Perth laboratories use more stringent notification criteria than the nationally agreed RRV case definition, and the geographical distribution of samples tested varies between laboratories. Our findings make a strong case to change the nationally agreed case definition for RRV to not accept a single IgM positive test result as laboratory definitive evidence where the IgG is negative. Our study also identified a range of challenges in interpreting changes in seasonal patterns and geographical distribution of RRV. Any such observed changes should be investigated through further data analysis and/or mosquito trapping and testing in order to assess validity.

Discovery of Jogalong virus, a novel hepacivirus identified in a Culex annulirostris (Skuse) mosquito from the Kimberley region of Western Australia.

The discovery of hepaciviruses in non-human hosts has accelerated following the advancement of high-throughput sequencing technology. Hepaciviruses have now been described in reptiles, fish, birds, and an extensive array of mammals. Using metagenomic sequencing on pooled samples of field-collected Culex annulirostris mosquitoes, we discovered a divergent hepacivirus-like sequence, named Jogalong virus, from the Kimberley region in northern Western Australia. Using PCR, we screened the same 300 individual mosquitoes and found just a single positive sample (1/300, 0.33%). Phylogenetic analysis of the hepacivirus NS5B protein places Jogalong virus within the genus Hepacivirus but on a distinct and deeply rooted monophyletic branch shared with duck hepacivirus, suggesting a notably different evolutionary history. Vertebrate barcoding PCR targeting two mitochondrial genes, cytochrome c oxidase subunit I and cytochrome b, indicated that the Jogalong virus-positive mosquito had recently fed on the tawny frogmouth (Podargus strigoides), although it is currently unknown whether this bird species contributes to the natural ecology of this virus.

The Diversity and Distribution of Viruses Associated with Culex annulirostris Mosquitoes from the Kimberley Region of Western Australia.

Metagenomics revealed an impressive breadth of previously unrecognized viruses. Here, we report the virome of the Culex annulirostris Skuse mosquito, an important vector of pathogenic arboviruses in Australia. Mosquitoes were collected from three sites in the Kimberley region of Western Australia. Unbiased high-throughput sequencing (HTS) revealed the presence of 16 novel viral sequences that share less than 90% identity with known viruses. None were closely related to pathogenic arboviruses. Viruses were distributed unevenly across sites, indicating a heterogeneous Cx. annulirostris virome. Polymerase chain reaction assays confirmed HTS data and identified marked variation between the virus prevalence identified at each site.

Phylogenetic and Timescale Analysis of Barmah Forest Virus as Inferred from Genome Sequence Analysis.

Barmah Forest virus (BFV) is a medically important mosquito-borne alphavirus endemic to Australia. Symptomatic disease can be a major cause of morbidity, associated with fever, rash, and debilitating arthralgia. BFV disease is similar to that caused by Ross River virus (RRV), the other major Australian alphavirus. Currently, just four BFV whole-genome sequences are available with no genome-scale phylogeny in existence to robustly characterise genetic diversity. Thirty novel genome sequences were derived for this study, for a final 34-taxon dataset sampled over a 44 year period. Three distinct BFV genotypes were characterised (G1-3) that have circulated in Australia and Papua New Guinea (PNG). Evidence of spatio-temporal co-circulation of G2 and G3 within regions of Australia was noted, including in the South West region of Western Australia (WA) during the first reported disease outbreaks in the state's history. Compared with RRV, the BFV population appeared more stable with less frequent emergence of novel lineages. Preliminary in vitro assessment of RRV and BFV replication kinetics found that RRV replicates at a significantly faster rate and to a higher, more persistent titre compared with BFV, perhaps indicating mosquitoes may be infectious with RRV for longer than with BFV. This investigation resolved a greater diversity of BFV, and a greater understanding of the evolutionary dynamics and history was attained.

Evaluation of a Health Communication Campaign to Improve Mosquito Awareness and Prevention Practices in Western Australia.

Fight the Bite represents the Department of Health's first attempt to actively raise awareness and improve prevention practices related to mosquitoes in Western Australia (WA). The multi-faceted campaign model involved a range of stakeholders and delivery methods over a 2 year period, achieving a recall rate of 8.2% among 2,500 survey participants. Significant regional differences were noted in campaign exposure, reflecting the variation in mosquito management issues throughout the State, and subsequent engagement by local government. Of those individuals with campaign recall, 43.8% reported an increase in awareness and 27.4% reported a change in behavior, which equated to a 1.7 and 1.2% change across the total survey population, respectively. The results of this study demonstrate that Fight the Bite has significantly improved awareness and prevention practices among those individuals who were exposed to the campaign. This was particularly promising, given the modest budget, resources, and time period over which the campaign was run prior to evaluation. This outcome means that Fight the Bite can be confidently adopted as a proven and standardized but regionally adaptable campaign approach to raising awareness about mosquito avoidance and mosquito-borne diseases by the Department of Health and its stakeholders. Future campaign aims include increasing reach through heightened and sustained promotion of Fight the Bite by both the Department and local government, as well as expanded collaboration with a range of stakeholders within the community.

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.

The ecology and epidemiology of Ross River and Murray Valley encephalitis viruses in Western Australia: examples of One Health in Action.

Arboviruses are maintained and transmitted through an alternating biological cycle in arthropods and vertebrates, with largely incidental disease in humans and animals. As such, they provide excellent examples of One Health, as their health impact is inextricably linked to their vertebrate hosts, their arthropod vectors and the environment. Prevention and control requires a comprehensive understanding of these interactions, and how they may be effectively and safely modified. This review concentrates on human disease due to Ross River and Murray Valley encephalitis viruses, the two major arboviral pathogens in Australia. It describes how their pattern of infection and disease is influenced by natural climatic and weather patterns, and by anthropogenic activities. The latter includes human-mediated environmental manipulations, such as water impoundment infrastructures, human movements and migration, and community and social changes, such as urban spread into mosquito larval habitats. Effective interventions need to be directed at the environmental precursors of risk. This can best be achieved using One Health approaches to improve collaboration and coordination between different disciplines and cross-sectoral jurisdictions in order to develop more holistic mitigation and control procedures, and to address poorly understood ecological issues through multidisciplinary research.

Discovery of a widespread infestation of Aedes albopictus in the Torres Strait, Australia.

Aedes albopictus is a container-breeding Stegomyia mosquito that has dispersed widely from its origins in Southeast Asia. Because Ae. albopictus is a known dengue vector and a potential vector of a variety of arboviruses and it can tolerate cooler climates than Aedes aegypti, Australian quarantine and health authorities have strategies to detect and eliminate it from international ports. Following the detection of 42 adult Ae. albopictus in BG-Sentinel traps set on Yorke island in the Torres Strait of Australia in April 2005, extensive surveys were conducted to determine the distribution of Ae. albopictus in the Torres Strait and adjoining Cape York Peninsula. A total of 17 islands and the northern peninsula area of Cape York Peninsula were surveyed by collection of larvae and pupae from flooded containers and human bait collections of adult mosquitoes with aspirators and sweep nets. Aedes albopictus was detected on 10 islands and comprised 100% of the day-biting container-breeding mosquitoes on Yorke and Stephens Islands. No Ae. albopictus were detected in the mainland sites on Cape York. Retrospective genetic analysis of larvae collected in April 2004 and April 2005 on Yorke Island indicated that Ae. albopictus was present in low densities in 2004 and that there were 3 genetically distinct mitochondrial haplotypes on Yorke Island in April 2005. Additionally, on Yorke Island there is evidence that Ae. albopictus is displacing Aedes scutellaris.

First record of Aedes (Aedimorphus) vexans vexans (Meigen) in Australia.

Aedes (Aedimorphus) vexans vexans has become widely distributed in the Australasian and Oceanic Islands zoogeographic regions, and in this paper, we describe the 1st confirmed report of Ae. vexans vexans in Australia. A total of 45 adult individuals were collected around the town of Kununurra in the northeast Kimberley region of Western Australia during the late wet seasons between 1996 and 2003. The majority (84%) was collected at trap sites in or near the Ord Stage I Irrigation Area. Aedes vexans vexans was a minor component of the mosquito population, comprising <0.1% of the total number of adults collected during the study period. The absence of Ae. vexans vexans in earlier collections suggests that it has been recently introduced into northeast Kimberley, most likely by wind currents from the Indonesian archipelago or on occasional light aircraft arriving in Kununurra from nearby islands. The collection of adult Ae. vexans vexans every year since 2001 could indicate that this mosquito has become established in the Kununurra environs, possibly facilitated by the presence of year-round breeding sites created by the irrigation area. Encephalitogenic flaviviruses have been isolated from this species in North America, Europe, and Taiwan, and the vector competence of Ae. vexans vexans for arboviruses prevalent in northern Western Australia, particularly the flaviviruses Murray Valley encephalitis and Kunjin, should be investigated.

Proximity to mosquito breeding habitat and Ross River virus risk in the Peel region of Western Australia.

It is intuitive that vector-borne disease exposure risk is related to proximity to sources of vector breeding, but this aspect rarely receives empirical testing. The population of Western Australia (WA) is increasing rapidly, with many new residential developments proposed in close proximity to mosquito breeding habitat. However, potential mosquito-borne disease risks for future residents are given little consideration by planning authorities. The Peel region is one of the fastest growing regions in WA and regularly experiences a large number of cases of the mosquito-borne Ross River virus (RRV) disease with epidemics occuring in the region every few years. A spatial analysis of RRV disease data in the Peel region was undertaken to determine the risk associated with proximity to a mosquito breeding habitat. Geographic Information Systems (GIS) software was used to create buffers between 1 and 6 km from the breeding habitat. The number of cases per 1000 dwellings in each buffer was calculated between 2002/03 to 2011/12 for years with >100 cases across all buffers (n=5) in addition to the cumulative rate over the entire period in each buffer. Residents living within 1 km of a mosquito breeding habitat had a significantly higher rate of RRV disease compared to the background rate across the Peel region in all individual years investigated. The cumulative data over the 10-year study period showed that residents in the 1- and 2-km buffers had a significantly higher rate, whereas those living between 3 and 6 km away did not. This study demonstrates an increased mosquito-borne disease risk associated with living in close proximity to a mosquito breeding habitat in a rapidly expanding region of WA and highlights the importance of considering mosquito-borne disease risks when planning authorities assess new residential development applications. Known mosquito breeding wetlands should be incorporated into land use planning scheme maps to ensure that they are accurately delineated and the implications are considered when planning decisions are made.

Investigation of the First Case of Dengue Virus Infection Acquired in Western Australia in Seven Decades: Evidence of Importation of Infected Mosquitoes?

In October 2013, a locally-acquired case of dengue virus (DENV) infection was reported in Western Australia (WA) where local dengue transmission has not occurred for over 70 years. Laboratory testing confirmed recent DENV infection and the case demonstrated a clinically compatible illness. The infection was most likely acquired in the Pilbara region in the northwest of WA. Follow up investigations did not detect any other locally-acquired dengue cases or any known dengue vector species in the local region, despite intensive adult and larval mosquito surveillance, both immediately after the case was notified in October 2013 and after the start of the wet season in January 2014. The mechanism of infection with DENV in this case cannot be confirmed. However, it most likely followed a bite from a single infected mosquito vector that was transiently introduced into the Pilbara region but failed to establish a local breeding population. This case highlights the public health importance of maintaining surveillance efforts to ensure that any incursions of dengue vectors into WA are promptly identified and do not become established, particularly given the large numbers of viraemic dengue fever cases imported into WA by travellers returning from dengue-endemic regions.

Epizootic activity of Murray Valley encephalitis and Kunjin viruses in an aboriginal community in the southeast Kimberley region of Western Australia: results of mosquito fauna and virus isolation studies.

We undertook annual surveys of flavivirus activity in the community of Billiluna in the southeast Kimberley region of Western Australia between 1989 and 2001 [corrected]. Culex annulirostris was the dominant mosquito species, particularly in years of above average rains and flooding. Murray Valley encephalitis (MVE) virus was isolated in 8 of the 13 years of the study from seven mosquito species, but more than 90% of the isolates were from Cx. annulirostris. The results suggest that MVE virus is epizootic in the region, w ith activity only apparent in years with average or above average rainfall and increased numbers of Cx. annulirostris. High levels of MVE virus activity and associated human cases were detected only once (in 1993) during the survey period. Activity of MVE virus could only be partially correlated with wet season rainfall and flooding, suggesting that a number of other factors must also be considered to accurately predict MVE virus activity at such communities.

Epizootic activity of Murray Valley encephalitis virus in an aboriginal community in the southeast Kimberley region of Western Australia: results of cross-sectional and longitudinal serologic studies.

Murray Valley encephalitis (MVE) virus is a mosquito-borne flavivirus causing severe encephalitis with a resultant high morbidity and mortality. In the period 1989-1993, we undertook a cross-sectional and longitudinal study by annually screening members of a small remote Aboriginal community in northwestern Australia for MVE virus antibodies. Of the estimated 250-300 people in the community, 249 were tested, and 52.6% had positive serology to MVE. The proportion testing positive increased with increasing age group, and males were slightly more likely to be positive than females. During the study period, a high proportion of the population seroconverted to MVE; the clinical/subclinical ratio seems to be lower than previously reported. Although MVE is mostly asymptomatic, the devastating consequences of clinical illness indicate that advice should be provided regarding the avoidance of mosquito bites. Our longitudinal study showed that the risk of seroconversion was similar for each age group, not just the young.

Antigenic and genetic typing of Whataroa viruses in Australia.

We recently characterized three novel alphaviruses isolated from mosquitoes captured in New South Wales, Australia. Initial cross-neutralization studies revealed antigenic similarity to the Sindbis virus (SINV)-like Whataroa virus (WHAV), heretofore found only in New Zealand. Nucleotide sequence analysis showed that the WHAV-like viruses shared >99% nucleotide sequence similarity with each other, and 96-97% similarity with prototype WHAV. Enzyme-linked immunosorbent assay reactions of a panel of monoclonal antibodies to SINV showed that the novel WHAV-like viruses displayed identical binding patterns and were antigenically distinct from all SINV isolates examined. Although these viruses displayed a similar binding pattern to prototype WHAV, three monoclonal antibodies discriminated them from the New Zealand virus. Our results suggest that these novel alphaviruses are antigenic variants of WHAV and represent the first reported isolations of this virus from outside New Zealand. The monoclonal antibodies used in this study will be useful for typing new SINV and SINV-like isolates.

Investigation of the southern limits of Murray Valley encephalitis activity in Western Australia during the 2000 wet season.

Western Australia experienced its worst-ever outbreak of the mosquito-borne Murray Valley encephalitis (MVE) virus during the 2000 wet season. Highest-on-record rainfall throughout much of the state during the 2000 wet season gave rise to extensive mosquito breeding and increased MVE virus transmission, resulting in nine cases of encephalitis. Activity of MVE virus in Western Australia is monitored by detecting MVE virus-specific antibodies in serum from sentinel chickens, located at towns and communities throughout the north of the state. However, during 2000, all 28 flocks of chickens seroconverted to MVE virus, including a flock located >600 km further south than MVE virus activity had ever previously been recorded. Furthermore, the majority of the nine cases of encephalitis occurred outside the enzootic Kimberley region. We therefore undertook a major serosurvey of domestic chicken flocks both south and east of the previously defined regions of virus activity. The results suggest that MVE virus activity extended as far south as the Midwest and northern Goldfields during 2000. A new southern limit of activity of MVE virus is therefore proposed. The results have implications for managing outbreaks of MVE virus in Western Australia and have enabled us to locate additional sentinel flocks as part of the MVE surveillance program for future years.

The seroprevalence and factors associated with Ross river virus infection in western grey kangaroos (Macropus fuliginosus) in Western Australia.

A serosurvey was undertaken in 15 locations in the midwest to southwest of Western Australia (WA) to investigate the seroprevalence of Ross River virus (RRV) neutralizing antibodies and factors associated with infection in western grey kangaroos (Macropus fuliginosus). The estimated seroprevalence in 2632 kangaroo samples, using a serum neutralization test, was 43.9% (95% CI 42.0, 45.8). Location was significantly associated with seroprevalence (p<0.001). There was a strong positive correlation between seroprevalence and the average log-transformed neutralizing antibody titer (r=0.98, p<0.001). The seroprevalence among adult kangaroos was significantly higher than in subadult kangaroos (p<0.05). No significant association was observed between seroprevalence and the sex of kangaroos (p>0.05). The results of this study indicate that kangaroos in WA are regularly infected with RRV and may be involved in the maintenance and transmission of RRV.

Ross River virus risk associated with dispersal of Aedes (Ochlerotatus) camptorhynchus (Thomson) from breeding habitat into surrounding residential areas: muddy lakes, Western Australia.

Rapid population growth in Western Australia has resulted in increased development of land for residential housing, and new developments are often proposed close to water because of intrinsic aesthetic values. However, this placement may place future residents at risk of mosquito-borne disease, of which Ross River virus (RRV) disease is the most common in Australia. Mosquito dispersal data were combined with a spatial analysis of human RRV cases to show that mosquitoes dispersed readily from larval habitat into surrounding low- and high-density residential areas and that residents living within 2 km of mosquito breeding habitat had a significantly higher rate of RRV disease. This finding highlights the importance of planning authorities in state and local governments to consider the implications of mosquito-borne disease risks when assessing residential development applications.