Journal articles on the topic 'Viral carcinogenesis – New South Wales'

Australia’s response to the human immunodeficiency virus type 1 (HIV-1) pandemic led to effective control of HIV transmission and one of the world’s lowest HIV incidence rates—0.14%. Although there has been a recent decline in new HIV diagnoses in New South Wales (NSW), the most populous state in Australia, there has been a concomitant increase with non-B subtype infections, particularly for the HIV-1 circulating recombinant form CRF01_AE. This aforementioned CRF01_AE sampled in NSW, were combined with those sampled globally to identify NSW-specific viral clades. The population growth of these clades was assessed in two-year period intervals from 2009 to 2017. Overall, 109 NSW-specific clades were identified, most comprising pairs of sequences; however, five large clades comprising ≥10 sequences were also found. Forty-four clades grew over time with one or two sequences added to each in different two-year periods. Importantly, while 10 of these clades have seemingly discontinued, the remaining 34 were still active in 2016/2017. Seven such clades each comprised ≥10 sequences, and are representative of individual sub-epidemics in NSW. Thus, although the majority of new CRF01_AE infections were associated with small clades that rarely establish ongoing chains of local transmission, individual sub-epidemics are present and should be closely monitored.

The objective of the present study was to describe use of health services for sexually transmitted infections (STI), blood borne viral infections (BBV) and drug and alcohol issues by young Aboriginal people in New South Wales (NSW). A cross-sectional survey was conducted at two Aboriginal sports and cultural events in NSW, in 2007 and 2008, among Aboriginal people aged 16–30 years to ascertain their knowledge of STI, BBV, associated risk behaviours and health service access in NSW. A total of 293 young Aboriginal people completed the survey; 58% were female, the mean age was 20 years, and almost 70% were single. Just over one-third (34%) of participants had been tested for an STI in the past 12 months, and over half (58%) reported that they had ever had an STI test (including HIV). Of respondents who had had an STI test in the past 12 months, 54.0% had done so at an Aboriginal Community Controlled Health Service (ACCHS) and 29% by a GP. Just over one-third (36%) of participants had ever had a test for hepatitis C, 45% of whom had received their test at an ACCHS. Participants were also asked about the types of services they had used for advice about STI and BBV. Of the 69% who had sought STI advice, ACCHS was the most common clinical location for doing so (36% for STI and 26% for hepatitis C). This study highlights the important role that ACCHS play in the provision of STI and BBV testing care and management for a cohort of young Aboriginal people in NSW.

Aedes vigilax mosquitoes, collected from the south coast of New South Wales, were fed on a blood-meal containing the T48 strain of Ross River virus. Viral infection and multiplication in this major vector were studied, together with dissemination of the virus in organs and tissues as determined by immunofluorescence. Individuals of this field mosquito population were highly susceptible to infection (ID50 = 10(3.4) BHK-21 TCID50 per mosquito) and virus replicated rapidly, reaching a maximum level 5-6 days after feeding. Specific viral antigens were detected in sections of abdominal midgut, abdominal fat bodies, thoracic fat bodies, cerebral ganglia and head fat bodies 2-4 days after ingestion of the virus-containing bloodmeal. Antigens were also detected 5-7 days after feeding in abdominal ganglia, thoracic ganglia, salivary glands and foregut. Antigens were demonstrated in sections of eggs from the ovary of one mosquito, which provided further evidence of transovarial transmission of Ross River virus in Ae. vigilax.

Multiple viruses with zoonotic potential have been isolated from bats globally. Here we describe the isolation and characterization of a novel paramyxovirus, Alston virus (AlsPV), isolated from urine collected from an Australian pteropid bat colony in Alstonville, New South Wales. Characterization of AlsPV by whole-genome sequencing and analyzing antigenic relatedness revealed it is a rubulavirus that is closely related to parainfluenza virus 5 (PIV5). Intranasal exposure of mice to AlsPV resulted in no clinical signs of disease, although viral RNA was detected in the olfactory bulbs of two mice at 21 days post exposure. Oronasal challenge of ferrets resulted in subclinical upper respiratory tract infection, viral shedding in respiratory secretions, and detection of viral antigen in the olfactory bulb of the brain. These results imply that AlsPV may be similar to PIV5 in its ability to infect multiple mammalian host species. This isolation of a novel paramyxovirus with the potential to transmit from bats to other mammalian species reinforces the importance of continued surveillance of bats as a source of emerging viruses.

Bovine ephemeral fever is an important viral disease of cattle in Australia. The disease occurred each year, principally in summer and autumn, between 1981 and 1985. Queensland and the northern half of New South Wales were areas of greatest activity with only sporadic cases being reported from the Northern Territory and the northern third of Western Australia. Since 1981, the disease has been endemic in an extensive area of eastern Australia and has tended to occur in widely scattered outbreaks rather than the north-south advancing wave form of the epidemics of 1936-37, 1967-68, 1970-71 and 1972-74. The southernmost outbreaks between 1981 and 1985 were well within the limits of these earlier epidemics. The pattern of disease appears to have become seasonally endemic rather than periodically endemic in the northern two-thirds of eastern Australia. Ephemeral fever was not recorded in Victoria, Tasmania, South Australia or the southern part of Western Australia between 1981 and 1985

Norovirus is an important human pathogen that is now recognized as the leading cause of acute gastroenteritis globally. Six viral genogroups have been described, although only genogroups GI, GII, and GIV are known to infect humans, with the GII viruses most commonly identified in both outbreak and sporadic settings. In contrast, infections by GIV viruses are rarely reported, and their overall prevalence in the community is unknown. Here, we report the complete genome sequence of the human GIV.1 strain Lake Macquarie virus, which caused two linked outbreaks of acute gastroenteritis in aged-care facilities in the Hunter region of New South Wales, Australia. The Lake Macquarie virus genome was 7,527 nucleotides (nt) in length and shared highest identity (70%) with the recently completed feline GIV.2 virus genome.

SUMMARYMeasles mortality fell prior to the introduction of vaccines or antibiotics. By examining historical mortality reports we sought to determine how much measles mortality was due to epidemiological factors such as isolation from major population centres or increased age at time of infection. Age-specific records were available from Aberdeen; Scotland; New Zealand and the states of Australia at the end of the 19th and beginning of the 20th centuries. Despite the relative isolation of Australia, measles mortality was concentrated in very young children similar to Aberdeen. In the more isolated states of Tasmania, Western Australia and Queensland adults made up 14–15% of measles deaths as opposed to 8–9% in Victoria, South Australia and New South Wales. Mortality in Iceland and Faroe Islands during the 1846 measles epidemic was used as an example of islands isolated from respiratory pathogens. The transition from crisis mortality across all ages to deaths concentrated in young children occurred prior to the earliest age-specific mortality data collected. Factors in addition to adult age of infection and epidemiological isolation such as nutritional status and viral virulence may have contributed to measles mortality outcomes a century ago.

This study is the first report of experimental infection and transmission of Menangle virus (MenPV) in pigs. Isolated in 1997 from piglets that were stillborn at a large commercial piggery in New South Wales, Australia, MenPV is a recently identified paramyxovirus of bat origin that causes severe reproductive disease in pigs and an influenza-like illness, with a rash, in humans. Although successfully eradicated from the infected piggery, the virus was only isolated from affected fetuses and stillborn piglets during the period of reproductive disease, and thus the mode of transmission between pigs was not established. To investigate the pathogenesis of MenPV, we undertook time-course studies in 6-week-old pigs following intranasal administration of a low-passage, non-plaque-purified isolate from the lung of an infected stillborn piglet. Viraemia was of short duration and low titre, as determined by real-time RT-PCR and virus isolation. Following an incubation period of 2–3 days, virus was shed in nasal and oral secretions, faeces and urine, typically for less than 1 week. Cessation of shedding correlated with the development of neutralizing antibodies in sera. Secondary lymphoid organs and intestine were identified, using quantitative real-time RT-PCR, as major sites of viral replication and dissemination, and this was confirmed by positive immunolabelling of viral antigen within various lymphoid tissues and intestinal epithelium. These data provide new insights into the pathogenesis of MenPV in weaned pigs, and will facilitate future control and eradication programmes should it ever re-emerge in the pig population.

Human enteroviruses evolve quickly. The 5′ untranslated region (UTR) is fundamentally important for efficient viral replication and for virulence; the VP1 region correlates well with antigenic typing by neutralization, and can be used for virus identification and evolutionary studies. In order to investigate the molecular diversity in EV-B species, the 5′ UTR and VP1 regions were analysed for 208 clinical isolates from a single public-health laboratory (serving New South Wales, Australia), representing 28 EV-B types. Sequences were compared with the 5′ UTR and VP1 regions of 98 strains available in GenBank, representing the same 28 types. The genetic relationships were analysed using two types of software (mega and BioNumerics). The sequence analyses of the 5′ UTR and VP1 regions of 306 EV-B strains demonstrated that: (i) comparing the two regions gives strong evidence of epidemiological linkage of strains in some serotypes; (ii) the intraserotypic genetic variation within each gene reveals that they evolve distinctly largely due to their different functions; and (iii) mutation and possible recombination in the two regions play significant roles in the molecular diversity of EV-B. Understanding the tempo and pattern of molecular diversity and evolution is of great importance in the pathogenesis of EV-B enteroviruses, information which will assist in disease prevention and control.

Background.Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized.Results.To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized.Conclusions.Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small.

ObjectiveTo determine the contribution of respiratory syncytial virus (RSV) to the subsequent development of severe asthma in different subgroups of children at risk of severe RSV disease.SettingsThe study was conducted in New South Wales (NSW), Australia.ParticipantsThe study comprised all children born in NSW between 2000 and 2010 with complete follow-up till 31 December 2011. The cohort was divided into three subgroups: (1) non-Indigenous high-risk children: non-Indigenous children born preterm or born with a low birth weight; (2) Indigenous children: children of mothers whose Indigenous status was recorded as Aboriginal and/or Torres Strait Islander and (3) non-Indigenous standard risk children: all other non-Indigenous term children.Primary outcome measureRisk of development of severe asthma in different subgroups of children who had RSV hospitalisation in the first 2 years of life compared with those who did not.DesignWe performed a retrospective cohort analysis using population-based linked administrative data. Extended Cox model was used to determine HR and 95% CI around the HR for first asthma hospitalisation in different subgroups of children.ResultsThe cohort comprised 847 516 children born between 2000 and 2010. In the adjusted Cox model, the HR of first asthma hospitalisation was higher and comparable across all subgroups of children who had RSV hospitalisation compared with those who did not. The HR (95% CI) was highest in children aged 2–3 years; 4.3 (95% CI 3.8 to 4.9) for high-risk, 4.0 (95% CI 3.3 to 4.8) for Indigenous and 3.9 (95% CI 3.7 to 4.1) for non-Indigenous standard risk children. This risk persisted beyond 7 years of age.ConclusionThis large study confirms a comparable increased risk of first asthma hospitalisation following RSV disease in the first 2 years of life across different subgroups children at risk.

Over 2 growing seasons, the incidences of infection with beet western yellows (BWYV), cauliflower mosaic (CaMV), and turnip mosaic (TuMV) viruses were determined in canola (Brassica napus) crops growing in the agricultural area of south-west Australia. Tissue blot immunoassay was used to detect BWYV and enzyme-linked immunosorbent assay to detect CaMV and TuMV. In 1998, BWYV was detected in 59% of 159 crops surveyed, whereas in 1999 it was found in 66% of 56 crops. Incidences within individual infected crops were 1–65% (1998) and 1–61% (1999). Infection occurred widely in high and medium rainfall zones, but was also readily detected in the low rainfall zone. In addition, BWYV was found in canola samples from 5 sites in New South Wales. Most cultivars tested (9 of 10) in the canola crop survey were infected with BWYV. No clear relationship was found between BWYV infection and any particular type of disease symptom. Overall, the incidence of BWYV at the crop edge was marginally greater than that inside the crop. CaMV was detected in 27% of 143 crops in 1998 but in only 2 of 47 in 1999. Incidences within individual infected crops were 1–17% in 1998 but only 1% in 1999. CaMV infected 6 of 10 cultivars and was present in high, medium, and low rainfall zones. Obvious chlorotic ringspot symptoms were associated with CaMV infection. TuMV was detected in 5% of 139 crops in 1998 but in only 1 of 47 from 1999. Incidences within the individual infected crops were 1–5% in 1998 and 1% in 1999; 3 of 10 cultivars were infected and it was found in high and medium rainfall zones. BWYV, CaMV, and TuMV were all found infecting wild radish (Raphanus raphinistrum). In general, incidences of BWYV were greater in wild radish than in canola. In 1998, BWYV was detected in wild radish at 9 of 12 sites sampled in 5 of 6 districts, with infection incidences up to 48%. In 1999, it was detected at all 10 sites sampled in 7 districts, with incidences up to 96%. Infected samples came from all rainfall zones, and from several different types of sites, some of which were distant from canola crops. Despite the presence of possible viral symptoms in wild radish, none was clearly associated with BWYV infection. In contrast, TuMV caused obvious mottle and ‘oak leaf’ patterns in wild radish plants. The finding of widespread virus infection in canola crops and a substantial virus reservoir in wild radish weeds is cause for concern to the canola industry.

Objectives: To determine if there were any differences in antiretroviral treatment (ART) use across the three eastern states of Australia, New South Wales (NSW), Victoria and Queensland, during the period 1997 to 2006. Methods: We used data from a clinic-based cohort, the Australian HIV Observational Database (AHOD), to determine the proportion of HIV-infected patients on ART in selected clinics in each state and the proportion of treated patients with an undetectable viral load. Data from the national Highly Specialised Drugs program and AHOD were used to estimate total numbers of individuals on ART and the proportion of individuals living with HIV on ART nationally and by state. Data from the HIV Futures Survey and the Gay Community Periodic Survey were used to determine the proportion of community-based men who have sex with men on ART. The proportion of patients with primary HIV infection (PHI) who commenced ART within 1 year of diagnosis was obtained from the Acute Infection and Early Disease Research Program (AIEDRP) CORE01 protocol and Primary HIV and Early Disease Research: Australian Cohort (PHAEDRA) cohorts. Results: We estimated that the numbers of individuals on ART increased from 3181 to 4553 in NSW, 1309 to 1926 in Victoria and 809 to 1615 in Queensland between 2000 and 2006. However, these numbers may reflect a lower proportion of individuals living with HIV on ART in NSW compared with the other states (37% compared with 49 and 55% in 2000). We found similar proportions of HIV-positive men who have sex with men participants were on ART in all three states over the study period in the clinic-based AHOD cohort (81–92%) and two large, community-based surveys in Australia (69–85% and 49–83%). Similar proportions of treated patients had an undetectable viral load across the three states, with a consistently increasing trend over time observed in all states. We found that more PHI patients commenced treatment in the first year following HIV diagnosis in NSW compared with Victoria; however, the sample size was very small. Conclusions: For the most part, patterns of ART use were similar across NSW, Victoria and Queensland using a range of available data from cohort studies, community surveys and national prescription databases in Australia. However, there may be a lower proportion of individuals living with HIV on ART in NSW compared with the other states, and there is some indication of a more aggressive treatment approach with PHI patients in NSW compared with Victoria.

Background The proportion of births via cesarean section (CS) varies worldwide and in many countries exceeds WHO-recommended rates. Long-term health outcomes for children born by CS are poorly understood, but limited data suggest that CS is associated with increased infection-related hospitalisation. We investigated the relationship between mode of birth and childhood infection-related hospitalisation in high-income countries with varying CS rates. Methods and findings We conducted a multicountry population-based cohort study of all recorded singleton live births from January 1, 1996 to December 31, 2015 using record-linked birth and hospitalisation data from Denmark, Scotland, England, and Australia (New South Wales and Western Australia). Birth years within the date range varied by site, but data were available from at least 2001 to 2010 for each site. Mode of birth was categorised as vaginal or CS (emergency/elective). Infection-related hospitalisations (overall and by clinical type) occurring after the birth-related discharge date were identified in children until 5 years of age by primary/secondary International Classification of Diseases, 10th Revision (ICD-10) diagnosis codes. Analysis used Cox regression models, adjusting for maternal factors, birth parameters, and socioeconomic status, with results pooled using meta-analysis. In total, 7,174,787 live recorded births were included. Of these, 1,681,966 (23%, range by jurisdiction 17%–29%) were by CS, of which 727,755 (43%, range 38%–57%) were elective. A total of 1,502,537 offspring (21%) had at least 1 infection-related hospitalisation. Compared to vaginally born children, risk of infection was greater among CS-born children (hazard ratio (HR) from random effects model, HR 1.10, 95% confidence interval (CI) 1.09–1.12, p < 0.001). The risk was higher following both elective (HR 1.13, 95% CI 1.12–1.13, p < 0.001) and emergency CS (HR 1.09, 95% CI 1.06–1.12, p < 0.001). Increased risks persisted to 5 years and were highest for respiratory, gastrointestinal, and viral infections. Findings were comparable in prespecified subanalyses of children born to mothers at low obstetric risk and unchanged in sensitivity analyses. Limitations include site-specific and longitudinal variations in clinical practice and in the definition and availability of some data. Data on postnatal factors were not available. Conclusions In this study, we observed a consistent association between birth by CS and infection-related hospitalisation in early childhood. Notwithstanding the limitations of observational data, the associations may reflect differences in early microbial exposure by mode of birth, which should be investigated by mechanistic studies. If our findings are confirmed, they could inform efforts to reduce elective CS rates that are not clinically indicated.

AbstractGiardiasis is one of the most important non-viral causes of human diarrhoea. Yet, little is known about the epidemiology of giardiasis in the context of developed countries such as Australia and there is a limited information about local sources of exposure to inform prevention strategies in New South Wales. This study aimed to (1) describe the epidemiology of giardiasis and (2) identify potential modifiable risk factors associated with giardiasis that are unique to south-western Sydney, Australia. A 1:2 matched case-control study of 190 confirmed giardiasis cases notified to the South-Western Local Health District Public Health Unit from January to December 2016 was employed to investigate the risk factors for giardiasis. Two groups of controls were selected to increase response rate; Pertussis cases and neighbourhood (NBH) controls. A matched analysis was carried out for both control groups separately. Variables with a significant odds ratio (OR) in the univariate analysis were placed into a multivariable regression for each matched group, respectively. In the regression model with the NBH controls, age and sex were controlled as potential confounders. Identified risk factors included being under 5 years of age (aOR = 7.08; 95% confidence intervals (CI) 1.02–49.36), having a household member diagnosed with a gastrointestinal illness (aOR = 15.89; 95% CI 1.53–164.60) and having contact with farm animals, domestic animals or wildlife (aOR = 3.03; 95% CI 1.08–8.54). Cases that travelled overseas were at increased risk of infection (aOR = 19.89; 95% CI 2.00–197.37) when compared with Pertussis cases. This study provides an update on the epidemiology and associated risk factors of a neglected tropical disease, which can inform enhanced surveillance and prevention strategies in the developed metropolitan areas.

Abstract A new distribution map is provided for Polymyxa graminis Ledingham. Cercozoa: Plasmodiophorida. Hosts: groundnut (Arachis hypogaea), oats (Avena sativa), barley (Hordeum vulgare), rice (Oryza sativa), rye (Secale cereale), wheat (Triticum aestivum), millet (Panicum miliaceum) and sorghum (Sorghum bicolor). Information is given on the geographical distribution in Europe (Belgium, France, Mainland France, Germany, Greece, Mainland Greece, Italy, Mainland Italy, Netherlands, Spain, Mainland Spain, UK, England and Wales), Asia (China, Anhui, Gansu, Henan, Hubei, Hunan, Jiangsu, Jiangxi, Shaanxi, Shandong, Shanxi, Sichuan, Zhejiang, India, Andhra Pradesh, Gujarat, Punjab, Rajasthan, Iran, Japan, Honshu, Lebanon, Pakistan, Syria, Turkey), Africa (Burkina Faso, Cote d'Ivoire, Mali, Niger, Senegal), North America (Canada, Manitoba, Ontario, Prince Edward Island, USA, Arkansas, Florida, Georgia, Illinois, Iowa, Kansas, Kentucky, Maryland, Missouri, Nebraska, New Mexico, New York, Oklahoma, Pennsylvania, South Carolina, Virginia, Washington), South America (Bolivia, Brazil, Rio Grande do Sul, Colombia), Oceania (New Zealand). Vector of numerous plant viruses, including Soil-borne wheat mosaic virus, Wheat yellow mosaic virus, Wheat spindle streak mosaic virus, Barley yellow mosaic virus, Oat mosaic virus, Rice stripe necrosis virus and Peanut clump virus. Several viruses transmitted by P. graminis cause major widespread diseases on barley, wheat and groundnut. P. graminis is presumed to be present in all fields infested with the viral diseases it transmits, but is also present in virus-free soils. The distribution of the viruses transmitted by P. graminis is greater than the confirmed distribution of P. graminis shown on the map.

Abstract Respiratory syncytial virus (RSV) is an important human respiratory pathogen. In temperate regions, a distinct seasonality is observed, where peaks of infections typically occur in early winter, often preceding the annual influenza season. Infections are associated with high rates of morbidity and mortality and in some populations exceed that of influenza. Two subtypes, RSV-A and RSV-B, have been described, and molecular epidemiological studies have shown that both viruses mostly co-circulate. This trend also appears to be the case for Australia; however, previous genomic studies have been limited to cases from one Eastern state—New South Wales. As such, the broader spatial patterns and viral traffic networks across the continent are not known. Here, we conducted a whole-genome study of RSV comparing strains across eastern and Western Australia during the period January 2016 to June 2017. In total, 96 new RSV genomes were sequenced, compiled with previously generated data, and examined using a phylodynamic approach. This analysis revealed that both RSV-A and RSV-B strains were circulating, and each subtype was dominated by a single genotype, RSV-A ON1-like and RSV-B BA10-like viruses. Some geographical clustering was evident in strains from both states with multiple distinct sub-lineages observed and relatively low mixing across jurisdictions, suggesting that endemic transmission was likely seeded from imported, unsampled locations. Overall, the RSV phylogenies reflected a complex pattern of interactions across multiple epidemiological scales from fluid virus traffic across global and regional networks to fine-scale local transmission events.

Abstract The diversity of lagoviruses (Caliciviridae) in Australia has increased considerably in recent years. By the end of 2017, five variants from three viral genotypes were present in populations of Australian rabbits, while prior to 2014 only two variants were known. To understand the evolutionary interactions among these lagovirus variants we monitored their geographical distribution and relative incidence over time in a continental-scale competition study. Within three years of the incursion of rabbit haemorrhagic disease virus 2 (RHDV2, denoted genotype GI.1bP-GI.2 [polymerase genotype]P-[capsid genotype]) into Australia, two novel recombinant lagovirus variants emerged: RHDV2-4e (genotype GI.4eP-GI.2) in New South Wales and RHDV2-4c (genotype GI.4cP-GI.2) in Victoria. Although both novel recombinants contain non-structural genes related to those from benign, rabbit-specific, enterotropic viruses, these variants were recovered from the livers of both rabbits and hares that had died acutely. This suggests that the determinants of host and tissue tropism for lagoviruses are associated with the structural genes, and that tropism is intricately connected with pathogenicity. Phylogenetic analyses demonstrated that the RHDV2-4c recombinant emerged independently on multiple occasions, with five distinct lineages observed. Both the new RHDV2-4e and 4c recombinant variants replaced the previous dominant parental RHDV2 (genotype GI.1bP-GI.2) in their respective geographical areas, despite sharing an identical or near-identical (i.e. single amino acid change) VP60 major capsid protein with the parental virus. This suggests that the observed replacement by these recombinants was not driven by antigenic variation in VP60, implicating the non-structural genes as key drivers of epidemiological fitness. Molecular clock estimates place the RHDV2-4e recombination event in early to mid-2015, while the five RHDV2-4c recombination events occurred from late 2015 through to early 2017. The emergence of at least six viable recombinant variants within a two-year period highlights the high frequency of these events, detectable only through intensive surveillance, and demonstrates the importance of recombination in lagovirus evolution.

ABSTRACT A standard multiplex PCR offers comprehensive testing for respiratory viruses. However, it has traditionally been performed in a referral laboratory with a lengthy turnaround time, which can reduce patient flow through the hospital. We aimed to determine whether the introduction of a rapid PCR, but with limited targets (Cepheid Xpert Flu/RSV XC), was associated with improved outcomes for adults hospitalized with respiratory illness. A controlled quasi-experimental study was conducted across three hospitals in New South Wales, Australia. Intervention groups received standard multiplex PCR during the preimplementation, July to December 2016 (n = 953), and rapid PCR during the postimplementation, July to December 2017 (n = 1,209). Control groups (preimplementation, n = 937, and postimplementation, n = 1,102) were randomly selected from adults hospitalized with respiratory illness during the same periods. The outcomes were hospital length of stay (LOS) and microbiology test utilization (blood culture, urine culture, sputum culture, and respiratory bacterial and virus serologies). The introduction of rapid PCR was associated with a nonsignificant 8.9-h reduction in median LOS (95% confidence interval [CI], −21.5 h to 3.7 h; P = 0.17) for all patients and a significant 21.5-h reduction in median LOS (95% CI, −36.8 h to −6.2 h; P < 0.01) among patients with positive test results in an adjusted difference-in-differences analysis. For patients receiving test results before disposition, rapid PCR use was associated with a significant reduction in LOS, irrespective of test results. Compared with standard PCR testing, rapid PCR use was significantly associated with fewer blood culture (adjusted odds ratio [aOR], 0.67; 95% CI, 0.5 to 0.82; P < 0.001), sputum culture (aOR, 0.56; 95% CI, 0.47 to 0.68, P < 0.001), bacterial serology (aOR, 0.44; 95% CI, 0.35 to 0.55, P < 0.001) and viral serology (aOR, 0.42; 95% CI, 0.33 to 0.53, P < 0.001) tests, but not with fewer urine culture tests (aOR, 0.94; 95% CI, 0.78 to 1.12, P = 0.48). Rapid PCR testing of adults hospitalized with respiratory illnesses can deliver benefits to patients and reduce resource utilization. Future research should consider a formal economic analysis and assess its potential impacts on clinical decision making.

BackgroundHepatitis E virus (HEV) is a common cause of acute viral hepatitis with significant morbidity and mortality, particularly in pregnant women. There are four major genotypes which can cause disease in humans. Genotypes 1 and 2 are usually associated with outbreaks and spread via facal/oral route or contaminated water. Genotypes 3 and 4 are zoonotic and usually associated with handling of pigs or consumption of contaminated pork. The strains circulating in Australia have never been characterized.Rationale/AimsThe aims for this project are to identify the HEV genotypes found in Australia and link them to possible sources of transmission by phylogenetic analysis.Materials and MethodsBetween 2015 and 2020, 91 HEV isolates were sequenced and genotyped using an in-house PCR. Sixty-six of these were also sequenced by using the international HEVnet primers. Genotypes were determined using the BLASTn program. Relatedness to other strains in Australia was determined by phylogenetic analyses of the HEVnet sequences. Isolates were also stratified by state of origin, gender, age, predisposing factors and travel history (if known).ResultsOf the 91 HEV isolates sequenced, 55 (60.4%) were genotype 1. There were 34 (37.4%) genotype 3 strains and two genotype 4 (2.2%). At least 20 of the genotype 1 strains have been linked to travel in India, and another three with Pakistan. Five of the “Indian” strains were closely related and are suspected to have originated in Gujarat. Phylogenetic analysis also showed that 12 genotype 3 strains were genetically related and potentially acquired in/from New South Wales, Australia. The two genotype 4 strains may have originated in China.DiscussionThis is the first study to describe the HEV isolates identified in Australia. The results infer that HEV may be acquired during overseas travel as well as locally, presumably from consumption of pork or pork-related products. The phylogenetic analyses also reveal clusters of infection originating from India and Pakistan. This study provides some insight into the source and epidemiology of HEV infection in Australia which may be used to guide public health procedure and enable the implementation of measures to deal with potential outbreaks of infection.

Wandering the aisles of my local Woolworths in April this year, I noticed a large number of chocolate bilbies replacing chocolate rabbits. In these harsh economic times it seems that even the Easter bunny is in danger of losing his Easter job. While the changing shape of Easter chocolate may seem to be a harmless affair, the expulsion of the rabbit from Easter celebrations has a darker side. In this paper I look at the campaign to replace the Easter bunny with the Easter bilby, and the implications this mediated conservation move has for living rabbits in the Australian ecosystem. Essential to this discussion is the premise that studies of ecology must take into account the impact of media and culture on environmental issues. Of particular interest is the role of narrative, and the way the stories we tell about rabbits determine how they are treated in real life. While I recognise that the Australian bilby’s struggle for survival is a tale which should be told, I also argue that the vilification of the European-Australian rabbit is part of the native/invasive dualism which has ceased to be helpful, and has instead become a motivator of unproductive violence. In place of this simplified dichotomous narrative, I propose an ethic of "ecological remembrance" to combat the totalising eradication of the European rabbit from the Australian environment and culture. The Bilby vs the Bunny: A Case Study in "Media Selection" Easter Bunny says, ‘Bilby, I want you to have my job.You know about sharing and taking care.I think Australia should have an Easter Bilby.We rabbits have become too greedy and careless.Rabbits must learn from bilbies and other bush creatures’. The lines above are taken from Ali Garnett and Kaye Kessing’s children’s story, Easter Bilby, co-published by the Australian Anti-Rabbit Research Foundation as part of the campaign to replace the Easter bunny with the eco-politically correct Easter bilby. The first chocolate bilbies were made in 1982, but the concept really took off when major chocolate retailer Darrell Lea became involved in 2002. Since this time Haigh’s chocolate, Cadbury, and Pink Lady have also released delicious cocoa natives for consumption, and both Darrell Lea and Haigh’s use their profits to support bilby assistance programs, creating the “pleasant Easter sensation” that “eating a chocolate bilby is helping save the real thing” (Phillips). The Easter bilby campaign is a highly mediated approach to conservation which demonstrates the new biological principle Phil Bagust has recognised as “media selection.” Bagust observes that in our “hybridised global society” it is impossible to separate “the world of genetic selection from the world of human symbolic and material diversity as if they exist in different universes” (8). The Australian rabbit thrives in “natural selection,” having adapted to the Australian environment so successfully it threatens native species and the economic productivity of farmers. But the rabbit loses out in “cultural selection” where it is vilified in the media for its role in environmental degradation. The campaign to conserve the bilby depends, in a large part, on the rabbit’s failures in “media selection”. On Good Friday 2012 Sky News Australia quoted Mike Drinkwater of Wild Life Sydney’s support of the Easter bilby campaign: Look, the reason that we want to highlight the bilby as an iconic Easter animal is, number one, rabbits are a pest in Australia. Secondly, the bilby has these lovely endearing rabbit-like qualities. And thirdly, the bilby is a beautiful, iconic, native animal that is struggling. It is endangered so it’s important that we do all we can to support that. Drinkwater’s appeal to the bilby’s “endearing rabbit-like qualities” demonstrates that it is not the Australian rabbit’s individual embodiment which detracts from its charisma in Australian society. In this paper I will argue that the stories we tell about the European-Australian rabbit’s alienation from Indigenous country diminish the species cultural appeal. These stories are told with passionate conviction to save and protect native flora and fauna, but, too often, this promotion of the native relies on the devaluation of non-native life, to the point where individual rabbits are no longer morally considerable. Such a hierarchical approach to conservation is not only ethically problematic, but can also be ineffective because the native/invasive approach to ecology is overly simplistic. A History of Rabbit Stories In the Easter Bilby children’s book the illustrated rabbit offers to make itself disappear from the “Easter job.” The reason for this act of self-destruction is a despairing recognition of its “greedy and careless” nature, and at the same time, its selfless offer to be replaced by the ecologically conscious Bilby. In this sacrificial gesture is the implicit offering of all rabbit life for the salvation of native ecosystems and animal life. This plot line slots into a much larger series of stories we have been telling about the Australian environment. Libby Robin has observed that settler Australians have always had a love-hate relationship with the native flora and fauna of the continent (6), either devaluing native plants, animals, and ecosystems, or launching into an “overcompensating patriotic strut about the Australian biota” (Robin 9). The colonising dynamic of early Australian society was built on the devaluation of animals such as the bilby. This was reflected in the introduction of feral animals by “acclimatisation societies” and the privileging of “pets” such as cats and dogs over native animals (Plumwood). Alfred Crosby has made the persuasive argument that the invasion of Australia, and other “neo-European” countries, was, necessarily, more-than-human. In his work, Ecological Imperialism, Crosby charts the historical partnership between human European colonisers in Indigenous lands and the “grunting, lowing, neighing, crowing, chirping, snarling, buzzing, self-replicating and world-altering avalanche” (194) of introduced life that they brought with them. In response to this “guilt by association” Australians have reversed the values in the dichotomous colonial dynamic to devalue the introduced and so “empower” the colonised native. In this new “anti-colonial” story, rabbits signify a wound of colonisation which has spread across and infected indigenous country. J. M. Arthur’s (130) analysis of language in relation to colonisation highlights some of the important lexical characteristics in the rabbit stories we now tell. He observes that the rabbits’ impact on the county is described using a vocabulary of contamination: “It is a ‘menace’, a ‘problem’, an ‘infestation’, a ‘nuisance’, a ‘plague’” (170). This narrative of disease encourages a redemptive violence against living rabbits to “cure” the rabbit problem in order to atone for human mistakes in a colonial past. Redemptive Violence in Action Rabbits in Australia have been subject to a wide range of eradication measures over the past century including shooting, the destruction of burrows, poisoning, ferreting, trapping, and the well-known rabbit proof fence in Western Australia. Particularly noteworthy in this slaughter has been the introduction of biological control measures with the release of the savage and painful disease Myxomatosis in late December 1950, followed by the release of the Calicivirus (Rabbit Haemorrhage Disease, or RHD) in 1996. As recently as March 2012 the New South Wales Department of Primary Industries announced a 1.5 million dollar program called “RHD Boost” which is attempting to develop a more effective biological control agent for rabbits who have become immune to the Calicivirus. In this perverse narrative, disease becomes a cure for the rabbit’s contamination of Australian environments. Calicivirus is highly infectious, spreads rapidly, and kills rabbits en masse. Following the release of Calicivirus in 1995 it killed 10 million rabbits in eight weeks (Ponsonby Veterinary Centre). While Calicivirus appears to be more humane than the earlier biological control, Myxomatosis, there are indications that it causes rabbits pain and stress. Victims are described as becoming very quiet, refusing to eat, straining for breath, losing coordination, becoming feverish, and excreting bloody nasal discharge (Heishman, 2011). Post-mortem dissection generally reveals a “pale and mottled liver, many small streaks or blotches on the lungs and an enlarged spleen... small thrombi or blood clots” (Coman 173). Public criticism of the cruel methods involved in killing rabbits is often assuaged with appeals to the greater good of the ecosystem. The Anti-Rabbit research foundation state on their Website, Rabbit-Free Australia, that: though killing rabbits may sound inhumane, wild rabbits are affecting the survival of native Australian plants and animals. It is our responsibility to control them. We brought the European rabbit here in the first place — they are an invasive pest. This assumption of personal and communal responsibility for the rabbit “problem” has a fundamental blind-spot. Arthur (130) observes that the progress of rabbits across the continent is often described as though they form a coordinated army: The rabbit extends its ‘dominion’, ‘dispossesses’ the indigenous bilby, causes sheep runs to be ‘abandoned’ and country ‘forfeited’, leaving the land in ‘ecological tatters’. While this language of battle pervades rabbit stories, humans rarely refer to themselves as invaders into Aboriginal lands. Arthur notes that, by taking responsibility for the rabbit’s introduction and eradication, the coloniser assumes an indigenous status as they defend the country against the exotic invader (134). The apprehension of moral responsibility can, in this sense, be understood as the assumption of settler indigeneity. This does not negate the fact that assuming human responsibility for the native environment can be an act of genuine care. In a country scarred by a history of ecocide, movements like the Easter Bilby campaign seek to rectify the negligent mistakes of the past. The problem is that reactive responses to the colonial devaluation of native life can be unproductive because they preserve the basic structure of the native/invasive dichotomy by simplistically reversing its values, and fail to respond to more complex ecological contexts and requirements (Plumwood). This is also socially problematic because the native/invasive divide of nonhuman life overlays more complex human politics of colonisation in Australia. The Native/Invasive Dualism The bilby is currently listed as an “endangered” species in Queensland and as “vulnerable” nationally. Bilbies once inhabited 70% of the Australian landscape, but now inhabit less than 15% of the country (Save the Bilby Fund). This dramatic reduction in bilby numbers has multiple causes, but the European rabbit has played a significant role in threatening the bilby species by competing for burrows and food. Other threats come from the predation of introduced species, such as feral cats and foxes, and the impact of farmed introduced species, such as sheep and cattle, which also destroy bilby habitats. Because the rabbit directly competes with the bilby for food and shelter in the Australian environment, the bilby can be classed as the underdog native, appealing to that larger Australian story about “the fair go”. It seems that the Easter bilby campaign is intended to level out the threat posed by the highly successful and adaptive rabbit through promoting the bilby in the “cultural selection” stakes. This involves encouraging bilby-love, while actively discouraging love and care for the introduced rabbits which threaten the bilby’s survival. On the Rabbit Free Australia Website, the campaign rationale to replace the Easter bunny with the Easter bilby claims that: Very young children are indoctrinated with the concept that bunnies are nice soft fluffy creatures whereas in reality they are Australia’s greatest environmental feral pest and cause enormous damage to the arid zone. In this statement the lived corporeal presence of individual rabbits is denied as the “soft, fluffy” body disappears behind the environmentally problematic species’ behaviour. The assertion that children are “indoctrinated” to find rabbits love-able, and that this conflicts with the “reality” of the rabbit as environmentally destructive, denies the complexity of the living animal and the multiple possible responses to it. That children find rabbits “fluffy” is not the result of pro-rabbit propaganda, but because rabbits are fluffy! That Rabbit Free Australia could construe this to be some kind of elaborate falsehood demonstrates the disappearance of the individual rabbit in the native/invasive tale of colonisation. Rabbit-Free Australia seeks to eradicate the animal not only from Australian ecosystems, but from the hearts and minds of children who are told to replace the rabbit with the more fitting native bilby. There is no acceptance here of the rabbit as a complex animal that evokes ambivalent responses, being both worthy of moral consideration, care and love, and also an introduced and environmentally destructive species. The native/invasive dualism is a subject of sustained critique in environmental philosophy because it depends on a disjunctive temporal division drawn at the point of European settlement—1788. Environmental philosopher Thom van Dooren points out that the divide between animals who belong and animals who should be eradicated is “fundamentally premised on the reification of a specific historical moment that ignores the changing and dynamic nature of ecologies” (11). Mark Davis et al. explain that the practical value of the native/invasive dichotomy in conservation programs is seriously diminished and in some cases is becoming counterproductive (153). They note that “classifying biota according to their adherence to cultural standards of belonging, citizenship, fair play and morality does not advance our understanding of ecology” (153). Instead, they promote a more inclusive approach to conservation which accepts non-native species as part of Australia’s “new nature” (Low). Recent research into wildlife conservation indicates a striking lack of evidence for the case that pest control protects native diversity (see Bergstromn et al., Davis et al., Ewel & Putz, Reddiex & Forsyth). The problematic justification of “killing for conservation” becomes untenable when conservation outcomes are fundamentally uncertain. The mass slaughter which rabbits have been subjected to in Australia has been enacted with the goal of fostering life. This pursuit of creation through destruction, of re-birth through violent death, enacts a disturbing twist where death comes to signal the presence of life. This means, perversely, that a rabbit’s dead body becomes a valuable sign of environmental health. Conservation researchers Ben Reddiex and David M. Forsyth observe that this leads to a situation where environmental managers are “more interested in estimating how many pests they killed rather than the status of biodiversity they claimed to be able to protect” (715). What Other Stories Can We Tell about the Rabbit? With an ecological narrative that is failing, producing damage and death instead of fostering love and life, we are left with the question—what other stories can we tell about the place of the European rabbit in the Australian environment? How can the meaning ecologies of media and culture work in harmony with an ecological consciousness that promotes compassion for nonhuman life? Ignoring the native/invasive distinction entirely is deeply problematic because it registers the ecological history of Australia as continuity, and fails to acknowledge the colonising impact of European settlement on the environment. At the same time, continually reinforcing that divide through pro-invasive or pro-native stories drastically simplifies complex and interconnected ecological systems. Instead of the unproductive native/invasive dualism, ecologists and philosophers alike are suggesting “reconciliatory” approaches to the inhabitants of our shared environments which emphasise ecology as relational rather than classificatory. Evolutionary ecologist Scott P. Carroll uses the term “conciliation biology” as an alternative to invasion biology which focuses on the eradication of invasive species. “Conciliation biology recognises that many non-native species are permanent, that outcomes of native-nonnative interactions will vary depending on the scale of assessment and the values assigned to the biotic system, and that many non-native species will perform positive functions in one or more contexts” (186). This hospitable approach aligns with what Michael Rosensweig has termed “reconciliation ecology”—the modification and diversification of anthropogenic habitats to harbour a wider variety of species (201). Professor of Ecology and Evolutionary Biology Mark Bekoff encourages a “compassionate conservation” which avoids the “numbers game” of species thinking where certain taxonomies are valued above others and promotes approaches which “respect all life; treat individuals with respect and dignity; and tread lightly when stepping into the lives of animals”(24). In a similar vein environmental philosopher Deborah Bird Rose offers the term “Eco-reconciliation”, to describe a mode of “living generously with others, singing up relationships so that we all flourish” (Wild Dog 59). It may be that the rabbit cannot live in harmony with the bilby, and in this situation I am unsure of what a conciliation approach to ecology might look like in terms of managing both of these competing species. But I am sure what it should not look like if we are to promote approaches to ecology and conservation which avoid the simplistic dualism of native/invasive. The devaluation of rabbit life to the point of moral inconsiderability is fundamentally unethical. By classifying certain lives as “inappropriate,” and therefore expendable, the process of rabbit slaughter is simply too easy. The idea that the rabbit should disappear is disturbing in its abstract approach to these living, sentient creatures who share with us both place and history. A dynamic understanding of ecology dissipates the notion of a whole or static “nature.” This means that there can be no simple or comprehensive directives for how humans should interact with their environments. One of the most insidious aspects of the native/invasive divide is the way it makes violent death appear inevitable, as though rabbits must be culled. This obscures the many complex and contingent choices which determine the fate of nonhuman life. Understanding the dynamism of ecology requires an acceptance that nature does not provide simple prescriptive responses to problems, and instead “people are forced to choose the kind of environment they want” (189) and then take actions to engender it. This involves difficult decisions, one of which is culling to maintain rabbit numbers and facilitate environmental resilience. Living within a world of “discordant harmonies”, as Daniel Botkin evocatively describes it, environmental decisions are necessarily complex. The entanglement of ecological systems demands that we reject simplistic dualisms which offer illusory absolution from the consequences of the difficult choices humans make about life, ecologies, and how to manage them. Ecological Remembrance The vision of a rabbit-free Australia is unrealistic. As organisation like the Anti-Rabbit Research Foundation pursue this future ideal, they eradicate rabbits from the present, and seek to remove them from the past by replacing them culturally with the more suitable bilby. Culled rabbits lie rotting en masse in fields, food for no one, and even their cultural impact in human society is sought to be annihilated and replaced with more appropriate native creatures. The rabbits’ deaths do not turn back to life in transformative and regenerative processes that are ecological and cultural, but rather that death becomes “an event with no future” (Rose, Wild Dog 25). This is true oblivion, as the rabbit is entirely removed from the world. In this paper I have made a case for the importance of stories in ecology. I have argued that the kinds of stories we tell about rabbits determines how we treat them, and so have positioned stories as an essential part of an ecological system which takes “cultural selection” seriously. In keeping with this emphasis on story I offer to the conciliation push in ecological thinking the term “ecological remembrance” to capture an ethic of sharing time while sharing space. This spatio-temporal hospitality is focused on maintaining heterogeneous memories and histories of all beings who have impacted on the environment. In Deborah Bird Rose’s terms this is a “recuperative work” which commits to direct dialogical engagement with the past that is embedded in the present (Wild Country 23). In this sense it is a form of recuperation that promotes temporal and ecological continuity. Eco-remembrance aligns with dynamic understandings of ecology because it is counter-linear. Instead of approaching the past as a static idyll, preserved and archived, ecological remembrance celebrates the past as an ongoing, affective presence which is lived and performed. Ecological remembrance, applied to the European rabbit in Australia, would involve rejecting attempts to extricate the rabbit from Australian environments and cultures. It would seek acceptance of the rabbit as part of Australia’s “new nature” (Low), and aim for recognition of the rabbit’s impact on human society as part of dynamic multi-species ecologies. In this sense ecological remembrance of the rabbit directly opposes the goal of the Foundation for Rabbit Free Australia to eradicate the European rabbit from Australian environment and culture. On the Rabbit Free Australia website, the section on biological controls states that “the point is not how many rabbits are killed, but how many are left behind”. The implication is that the millions upon millions of rabbit lives extinguished have vanished from the earth, and need not be remembered or considered. However, as Deborah Rose argues, “all deaths matter” (Wild Dog 21) and “no death is a mere death” (Wild Dog 22). Every single rabbit is an individual being with its own unique life. To deny this is tantamount to claiming that each rabbit that dies from shooting or poisoning is the same rabbit dying again and again. Rose has written that “death makes claims upon all of us” (Wild Dog 19). These are claims of ethics and compassion, a claim that “we look into the eyes of the dying and not flinch, that we reach out to hold and to help” (Wild Dog 20). This claim is a duty of remembrance, a duty to “bear witness” (Wiesel 160) to life and death. The Nobel Peace Prize winning author, Elie Wiesel, argued that memory is a reconciliatory force that creates bonds as mass annihilation seeks to destroy them. Memory ensures that no life becomes truly life-less as it wrests the victims of mass slaughter from “oblivion” and allows the dead to “vanquish death” (21). 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