Australian Laboratory Research Articles

Novel HLA-DQB1, DQA1, DPA1 and DPB1 alleles identified in the Australian New South Wales tissue typing laboratory

Introduction of NGS into clinical histocompatibility laboratories has greatly increased the frequency of novel HLA allele discovery. We identified 9 DQA1, 7 DQB1, 8 DPA1 and 2 DPB1 novel alleles over the last 2 years. 92% (24 of 26) differed from their closest allele by single nucleotide substitutions detected in coding regions and 84% (22 of 26) contained polymorphism outside of exon 2. Identification of novel alleles in non-coding intronic regions were restricted to splice sites. Two novel alleles arising from nucleotide substitution affecting splicing were identified and named with questionable expression status. Novel alleles with polymorphism detected only in non-coding regions (introns and UTRs) were not reported. 21 additional DQA1, DQB1 and DPA1 alleles detected in multiple individuals as novel at the time of testing, were also detected in other laboratories. The number of novel alleles detected further emphasises the role of NGS in novel allele discovery.

Assessing the carbon footprint of the agriculture, forestry, and fishing industry of Australia

Purpose This study examines the carbon emissions of Australia’s agriculture, forestry and fishing sectors from a consumption perspective to develop effective policy frameworks. The objective is to identify key supply chains, industries and products contributing to these emissions and provide recommendations for sustainable development. Design/methodology/approach A multiregional input-output lifecycle assessment was conducted using the Australian Industrial Ecology Virtual Laboratory (IELab) platform to disaggregate sectors and enable benchmarking against other economic sectors. Findings In 2018, the “agriculture, forestry, and fishing” sector was responsible for 12.15% of Australia’s carbon footprint. Major contributors included the “electricity, gas, water, and waste” category (26.1%) and the sector’s activities (24.3%). The “transport, postal, and warehousing” sector also contributed 18.4%. Within the industry, the agriculture subsector had the highest impact (71.3%), followed by forestry and logging (15%) and fishing, hunting and trapping (7.6%). Aquaculture and supporting services contributed 6.1%. Research limitations/implications The principal constraint encountered by the present study pertained to the availability of up-to-date data. The latest accessible data for quantifying the carbon footprint within Australia’s agriculture, forestry and fishing sector, utilizing the Input-Output analysis methodology through the Australian Industrial Ecology Virtual Laboratory (IELab) platform, about 2018. Practical implications The findings of this study provide policymakers with detailed insights into the carbon footprints of key sectors, highlighting the contributions from each subsector. This information can be directly used to develop effective emission-reduction policies, with a focus on reducing emissions in utility services, transport and warehousing. Social implications The study, by raising public awareness of the significant role of industrial agricultural methods in Australia’s carbon footprint and emphasizing the importance of renewable energy and sustainable fuels for electricity generation and road transport, underscores the urgent need for action to mitigate climate change. Originality/value This study stands out by not only identifying the most impactful industries but also by providing specific strategies to reduce their emissions. It offers a comprehensive breakdown of specific agricultural activities and outlines mitigation strategies for utility services, agricultural operations and transport, thereby adding a unique perspective to the existing knowledge.

KV reference dosimetry in Australia and New Zealand: Survey results and trends.

To assess the number of radiotherapy kilovoltage (kV) units in service, their clinical utilization, and methodology and equipment used for absorbed dose determination across Australia and New Zealand. A survey was sent to 61 Australian and New Zealand radiotherapy providers in the second half of 2023. Fifty-seven responses were received, with 43 departments having kV units and providing beam quality data for 185 therapeutic kV beams 20-300kVp. Percentage depth dose curves were compared between five clinical beams with 100 kVp and 2.13-6.28mm Aluminum half value layers (HVLs), demonstrating large differences that can occur between beams with the same kVp. Eighteen departments provided clinical utilization data for their kV units, with a total of 4458 treatment courses and their corresponding kVp reported. All departments complied with national and international recommendations with respect to the equipment used for reference dosimetry of kV beams; 77% of ionization chambers used for absorbed dose determination were of Farmer-type, with the remaining 23% being plane parallel soft x-ray chambers. Methods of derivation of air-kerma calibration factors varied, with 73% of respondents using a draft document disseminated by the Australian Primary Standards laboratory, 23% using HVL alone, and 6% using other methods. The results of this survey provide a snapshot of kilovoltage radiation therapy use and the number of kV units across Australia and New Zealand. This data can be used as a point of reference for future investigations into clinical utilization and reference dosimetry methods across Australia and New Zealand or for comparisons with other countries, facilitating standardization of reference dosimetry practice for kilovoltage units.

Development and preliminary validation of a MERS-CoV ELISA for serological testing of camels and alpacas

This study describes the development and preliminary validation of a new serological assay using MERS-CoV S1 protein in an indirect enzyme-linked immunosorbent assay (ELISA) format. This assay has the advantage of being able to test MERS-CoV serum samples in a PC2 laboratory without the need for a high-level biocontainment laboratory (PC3 or PC4), which requires highly trained and skilled staff and a high level of resources and equipment. Furthermore, this MERS-CoV S1 ELISA enables a larger number of samples to be tested quickly, with results obtained in approximately five hours. The MERS-CoV S1 ELISA demonstrated high analytical specificity, with no cross-reactivity observed in serum of animals infected with other viruses, including different coronaviruses. We tested 166 positive and 40 negative camel serum samples and have estimated the diagnostic sensitivity (DSe) to be 99.4% (95% CI: 96.7 – 100.0%) and diagnostic specificity (DSp) to be 100% (95% CI: 97.2%-100.0%) relative to the assigned serology results (ppNT and VNT) using a S/P ratio cut-off value of >0.58. The findings of this study showed that our MERS-CoV S1 ELISA was more sensitive than the commercial EUROIMMUN ELISA (Se 99.4% vs 84.9%) and comparable to the ppNT assay, and therefore could be used as a diagnostic aid in countries in the Middle East where MERS-CoV is endemic in dromedary camels. The assay reagents and protocol were easily adapted and transferred from an Australian laboratory to a laboratory in the University of Hong Kong. Thus, the results described here show that the MERS-CoV S1 ELISA represents a cheap, rapid, robust, and reliable assay to support surveillance of MERS-CoV in camels in endemic regions.

Epidemiological and Clinical Features of Rickettsial Infection Among Australian Individuals from 2015 to 2018

Objective: In this study, the clinical, laboratory and epidemiological features of rickettsial infection in Australian patients were examined. Methods: Patients with Rickettsia spp. seropositivity were selected from the database of the Australian Rickettsial Reference Laboratory. Questionnaires were sent to each referring physician with a request for information regarding the patient’s illness. Results: A retrospective analysis of 178 patients revealed the following common features in Australian rickettsial infection: fever, headache, myalgia, rash and a history of recent exposure to the Australian bush. The history included tick bites, eschar presence, respiratory abnormalities and acute fatigue, accompanied by abnormal haematology and liver function tests. Conclusions: A differential diagnosis including rickettsial infection should be confirmed (or refuted) by rickettsial serology.

Validation of an HIV whole genome sequencing method for HIV drug resistance testing in an Australian clinical microbiology laboratory.

Detection of HIV drug resistance (HIVDR) is vital to successful anti-retroviral therapy (ART). HIVDR testing to determine drug-resistance mutations is routinely performed in Australia to guide ART choice in newly diagnosed people living with HIV or in cases of treatment failure. In 2022, our clinical microbiology laboratory sought to validate a next-generation sequencing (NGS)-based HIVDR assay to replace the previous Sanger-sequencing (SS)-based ViroSeq. NGS solutions for HIVDR offer higher throughput, lower costs and higher sensitivity for variant detection. We sought to validate the previously described low-cost probe-based NGS method (veSEQ-HIV) for whole-genome recovery and HIVDR-testing in a diagnostic setting. veSEQ-HIV displayed 100% and 98% accuracy in major and minor mutation detection, respectively, and 100% accuracy of subtyping (provided > 1000 mapped reads were obtained). Pairwise comparison exhibited low inter-and intrarun variability across the whole-genome (Jaccard index [J] = 0.993; J = 0.972) and the Pol gene (J = 0.999; J = 0.999), respectively. veSEQ-HIV met all our pre-set criteria based on WHO recommendations and successfully replaced ViroSeq in our laboratory. Scaling-down veSEQ-HIV to a limited batch size and sequencing on Illumina iSeq. 100, allowed easy implementation of the assay into the workflow of a small sequencing laboratory with minimal staff and equipment and the ability to meet clinically relevant test turn-around times. As HIVDR-testing moves from SS- to NGS-based methods and new ART drugs come to market (particularly those with targets outside the Pol region), whole-genome recovery using veSEQ-HIV provides a robust, cost-effective and "future-proof" NGS method for HIVDR-testing.

P084 Characteristics of sleep hypoventilation during polysomnography in a large Australian clinical sleep laboratory cohort.

Abstract BACKGROUND Sleep hypoventilation complicates a range of neurological and respiratory conditions. However, robust definitions are based mainly on expert consensus, and clinically significant thresholds remain unclear. This study thus aims to provide a descriptive analysis of capnography results in a large clinical cohort of patients referred for overnight polysomnography (PSG). METHODS Retrospective clinical audit of overnight in-lab PSGs, between Jan 2015 and June 2023, at a tertiary hospital housing the State-wide referral centre for chronic domiciliary ventilation. Diagnostic PSGs with transcutaneous CO2 (PTcCO2) monitoring and without supplemental oxygen were included. The following data will be extracted from each PSG: Patient demographics: -Primary and secondary clinical diagnoses -PTcCO2 values (e.g. Mean, Minimum and Maximum PTcCO2 in Wake, Sleep, NREM and REM) -Sleep fragmentation measures -Sleep macro-architecture measures -AHI -SpO2 values Data analysis will be performed with IBM SPSS Statistics software, version 26 (Armonk, NY: IBM Corp) PROGRESS TO DATE 525 PSGs meeting initial criteria have been identified. Currently processing PSG data files to extract parameters and complete exploratory data cleaning and analysis. INTENDED OUTCOME AND IMPACT We aim to explore and clarify: -Differences in patterns of hypoventilation between different diagnostic groups. -Relationships between awake hypoventilation, sleep hypoventilation and REM-isolated hypoventilation. -Effects of applying differing criteria for hypoventilation available in the literature. -Relationships between measures of sleep fragmentation, AHI, SpO2 and hypoventilation parameters. The results of this study will also support and inform future research into associations between severity, duration and patterns of hypoventilation and clinically significant outcomes including morbidity and mortality.

Evaluation of commercially available methamphetamine presumptive tests for site contamination

Presumptive tests or lateral flow immunoassay testing kits are increasingly being utilised as a fast, portable, cost-effective method to detect an array of analytes, particularly illicit drugs. In Australia, the methamphetamine and decontamination industry regularly use presumptive testing kits to determine whether a property is contaminated. These presumptive test kits advertise a detection limit of 0.5 µg/100 cm2 and above for methamphetamine. The performance of seven methamphetamine presumptive test brands and their kit components were analysed in this study. Following the kit instructions, each kit was analysed using a ceramic tile that was spiked with a known concentration of methamphetamine. These presumptive test kits were highly sensitive, with positive results also found below the limit of detection. Therefore, if there is a negative result it is likely that there is no methamphetamine present. Those that return a positive result require further quantitative assessment. Thus, the presumptive test kits may detect the presence of methamphetamine that is below the Australian Clandestine Drug Laboratory Remediation Guideline of 0.5 µg/100 cm2. This indicates these tests might be useful as a screening assessment but should not be relied upon to develop a remediation action plan.

Enteric Aeromonas Infection: a Common Enteric Bacterial Infection with a Novel Infection Pattern Detected in an Australian Population with Gastroenteritis.

Aeromonas species are emerging human enteric pathogens. However, they are currently not routinely detected in many diagnostic laboratories, and information regarding Aeromonas enteric infections detected using molecular methods is lacking. Here, we investigated the detection of Aeromonas species and four other enteric bacterial pathogens in 341,330 fecal samples from patients with gastroenteritis processed in a large Australian diagnostic laboratory between 2015 and 2019. These enteric pathogens were detected using quantitative real-time PCR (qPCR) methods. Furthermore, we compared the qPCR cycle threshold (CT) values obtained from fecal samples that tested positive for Aeromonas only by molecular detection with those of samples that tested positive by both molecular detection and bacterial isolation methods. Aeromonas species were found to be the second most common bacterial enteric pathogens among patients with gastroenteritis. We observed a unique pattern of three infection peaks for Aeromonas, which correlated with the age of the patients. Aeromonas species were the most common enteric bacterial pathogens in children younger than 18 months. Fecal samples that tested positive for Aeromonas only by molecular detection had significantly higher CT values than fecal samples that tested positive by both molecular detection and bacterial culture. In conclusion, our findings reveal that Aeromonas enteric pathogens exhibit an age-related three-peak infection pattern, distinguishing them from other enteric bacterial pathogens. Moreover, the high rate of Aeromonas enteric infection discovered in this study suggests that Aeromonas species should be routinely tested in diagnostic laboratories. Our data also show that combining qPCR with bacterial culture can enhance the detection of enteric pathogens. IMPORTANCE Aeromonas species are emerging human enteric pathogens. However, these species are currently not routinely detected in many diagnostic laboratories, and no studies have reported the detection of Aeromonas enteric infection using molecular methods. We investigated the presence of Aeromonas species and four other enteric bacterial pathogens in 341,330 fecal samples from patients with gastroenteritis using quantitative real-time PCR (qPCR) methods. Interestingly, we discovered that Aeromonas species were the second most common bacterial enteric pathogens in patients with gastroenteritis, exhibiting a novel infection pattern compared to those of other enteric pathogens. Furthermore, we found that Aeromonas species were the most prevalent enteric bacterial pathogens in children aged 6 to 18 months. Our data also revealed that qPCR methods exhibit higher sensitivity in detecting enteric pathogens compared to that of bacterial culture alone. Moreover, combining qPCR with bacterial culture enhances the detection of enteric pathogens. These findings emphasize the importance of Aeromonas species in public health.

A surge in human metapneumovirus paediatric respiratory admissions in Western Australia following the reduction of SARS-CoV-2 non-pharmaceutical interventions.

Western Australian laboratory data demonstrated a decrease in human metapneumovirus (hMPV) detections through 2020 associated with SARS-CoV-2-related non-pharmaceutical interventions (NPIs), followed by a subsequent surge in metropolitan region in mid-2021. We aimed to assess the impact of the surge in hMPV on paediatric hospital admissions and the contribution of changes in testing. All respiratory-coded admissions of children aged <16 years at a tertiary paediatric centre between 2017 and 2021 were matched with respiratory virus testing data. Patients were grouped by age at presentation and by ICD-10 AM codes into bronchiolitis, other acute lower respiratory infection (OALRI), wheeze and upper respiratory tract infection (URTI). For analysis, 2017-2019 was utilised as a baseline period. hMPV-positive admissions in 2021 were more than 2.8 times baseline. The largest increase in incidence was observed in the 1-4 years group (incidence rate ratio (IRR) 3.8; 95% confidence interval (CI): 2.5-5.9) and in OALRI clinical phenotype (IRR 2.8; 95% CI: 1.8-4.2). The proportion of respiratory-coded admissions tested for hMPV in 2021 doubled (32-66.2%, P < 0.001), with the greatest increase in wheeze (12-75% in 2021, P < 0.001). hMPV test percentage positivity in 2021 was higher than in the baseline period (7.6% vs. 10.1% in 2021, P = 0.004). The absence and subsequent surge underline the susceptibility of hMPV to NPIs. Increased hMPV-positive admissions in 2021 can be partially attributable to testing, but test-positivity remained high, consistent with a genuine increase. Continued comprehensive testing will help ascertain true burden of hMPV respiratory diseases.

Evaluation of glutamic acid decarboxylase (GAD) 65 antibody detection methods for neurological and diabetic investigation in an Australian diagnostic laboratory

The role of anti-glutamic acid decarboxylase (GAD) 65 autoantibodies in autoimmune neurological conditions is evolving, but testing recommendations remain unchanged in Australia with GAD enzyme-linked immunosorbent assay (ELISA) and immunoblot as the only two Therapeutic Goods Administration approved testing methods available in Australia. Common practice is for use of ELISA in diagnosis of type 1 diabetes mellitus (T1DM) and use of immunoblot for diagnosis of GAD65-associated neurological disease. We observed a cohort of patients with negative immunoblot results and positive ELISA in the context of GAD-associated neurological disease without T1DM. In the absence of robust consensus guidelines on preferred testing modalities, we sought to determine if ELISA could have a superior role in the diagnosis of GAD-associated neurological disease when compared to immunoblot in this paper. We tested for anti-GAD65 autoantibodies on 55 patient samples, 40 samples requested for neurological disease and 15 type 1 diabetes samples with detectable anti-GAD65, using two testing platforms: Euroimmun anti-GAD enzyme-linked immunosorbent assay (ELISA) and. Euroimmun EuroLine immunoblot for paraneoplastic neurologic syndromes. These results were correlated against the clinical scenario. Positive ELISA results had a sensitivity of 100% and specificity of 91% for GAD65-related neurological disease. Immunoblot showed sensitivity of 43% and specificity of 76% for GAD65-related neurological disease. ELISA proved more sensitive and specific for GAD65-related neurological disease compared to immunoblot, raising questions about the role of this testing modality in neurological disease. We propose that ELISA should be used as a sole diagnostic method for all GAD65 antibody-related neurological disease over immunoblot. The presence of anti-GAD65 antibody on immunoblot is of doubtful clinical significance.

Australian National Enterovirus Reference Laboratory annual report, 2022.

Australia monitors its polio-free status by conducting surveillance for cases of acute flaccid paralysis (AFP) in children less than 15 years of age, as recommended by the World Health Organization (WHO). Cases of AFP in children are notified to the Australian Paediatric Surveillance Unit or the Paediatric Active Enhanced Disease Surveillance System, and faecal specimens are referred for virological investigation to the National Enterovirus Reference Laboratory. In 2022, no cases of poliomyelitis were reported from clinical surveillance and Australia reported 1.69 non-polio AFP cases per 100,000 children, thereby meeting the WHO's performance criterion for a sensitive surveillance system. The non-polio enteroviruses coxsackievirus A2, coxsackievirus A6, coxsackievirus A10, echovirus 18, enterovirus A71 and enterovirus C96 were identified from clinical specimens collected from AFP cases. Australia also performs enterovirus and environmental surveillance to complement the clinical system focussed on children. In 2022, thirty cases of wild poliovirus were reported from three countries (Afghanistan, Mozambique and Pakistan); 24 countries also reported cases of poliomyelitis due to circulating vaccine-derived poliovirus.

Australian National Enterovirus Reference Laboratory annual report, 2021.

Australia monitors its polio-free status by conducting surveillance for cases of acute flaccid paralysis (AFP) in children less than 15 years of age, as recommended by the World Health Organization (WHO). Cases of AFP in children are notified to the Australian Paediatric Surveillance Unit or the Paediatric Active Enhanced Disease Surveillance System, and faecal specimens are referred for virological investigation to the National Enterovirus Reference Laboratory. In 2021, no cases of poliomyelitis were reported from clinical surveillance and Australia reported 1.31 non-polio AFP cases per 100,000 children, thereby meeting the WHO's performance criterion for a sensitive surveillance system. The non-polio enteroviruses coxsackievirus A4, coxsackievirus A10, coxsackievirus A13 and enterovirus A71 were identified from clinical specimens collected from AFP cases. Australia also performs enterovirus and environmental surveillance to complement the clinical system focussed on children. In 2021, there were five cases of wild poliovirus reported from the two remaining endemic countries: Afghanistan and Pakistan. Including Afghanistan and Pakistan, 22 countries also reported cases of AFP due to circulating vaccine-derived poliovirus.

Nutrient-sensitive approach for sustainability assessment of different dietary patterns in Australia

Understanding the relation between sustainability and nutrients is important in devising healthy and sustainable diets. However, there are no prevailing methodologies to assess sustainability at the nutrient level. The aim was to examine and demonstrate the potential of integrating input-output analysis with nutritional geometry to link environmental, economic, and health associations of dietary scenarios in Australia with macronutrients. One-day dietary recalls of 9341 adult respondents (age ≥18 y) of the latest available cross-sectional National Nutrition and Physical Activity Survey-2011/12 of Australia were integrated with the input-output data obtained from the Australian Industrial Ecology Virtual Laboratory to calculate the environmental and economic impacts of dietary intakes in Australia. Australian adults' dietary intakes were classified into 3 dietary scenarios: "vegan," "pescatarian," and "omnivorous." Then, the relations between nutritional, economic, and environmental characteristics of the 3 dietary scenarios were demonstrated with the diets' macronutrient composition in a multidimensional nutritional geometry representation to link the sustainability indicators with macronutrients. Nutrient density and economic and environmental indicators increased as the percentage of energy from proteins increased and decreased as the percentage of energy from fats increased for the 3 dietary scenarios, except for the nutrient density and water use of the "vegan" dietary scenario. Energy density increased as the percentage of energy from fats increased and decreased as the percentage of energy from proteins increased for "pescatarian" and "omnivorous" dietary scenarios. In the "vegan" dietary scenario, nutrient density and water use increased as the percentage of energy from proteins increased; however, these decreased as the percentage of energy from carbohydrates increased, instead of fats. The study presents a new approach to analyzing the relations between sustainability indicators, foods, and macronutrients and establishes that proteins, irrespective of the source of protein, are driving dietary environmental and economic impacts.

Gluten-free diet adherence and implications for the diagnosis of coeliac disease

Coeliac disease (CD) is an autoimmune disorder caused by the ingestion of gluten containing foods in genetically susceptible individuals, with a worldwide prevalence of up to 1%. Currently, the only available treatment is a gluten-free diet (GFD). Screening for CD is primarily performed using serum based testing for anti-tissue transglutaminase (tTG) antibodies. Patients must be on a gluten containing diet at the time of testing to ensure an accurate serological result. We investigated the prevalence of a GFD in hospital clinic settings and the general population using survey data to estimate the proportion of CD patients that may be misdiagnosed for CD based on serological tests. Data were collected at clinics of a metropolitan hospital in Sydney, Australia, and the general population. Data from Medicare Benefits Scheme and tTG results from a large Australian private laboratory were reviewed for comparison. Of 778 participants who responded to the survey, 58 (7.5%) were on a GFD. More patients attending the immunology (15.9%) and gastroenterology (12.1%) clinics adopted a GFD than those attending the diabetes (2.6%) or endocrinology (6.1%) clinics, or in the general population (4.3%). More females than males excluded gluten from their diet (p<0.0001). Medicare statistics between 2013 and 2019 demonstrated an increase in CD serological testing; however, tTG data from a private pathology highlighted a stable level of elevated tTG antibodies of 3% of total tests performed. The high number of individuals on a GFD is likely impacting the ability to accurately diagnose CD using serum-based testing.

A history of CSIRO’S Central Australian Laboratory, 1: 1953–80: pastoral land research

CSIRO’s research in the arid zone was initiated after World War 2 when a strong push to develop the sparsely populated and isolated region of northern Australia was promoted as being in the national interest. This impetus had social and political origins but implementation depended on scientific insights into regional ‘potential’, which was couched at the time in terms of agronomic and pastoral use. Ray Perry was a key figure in early land resource surveys of the region and later a key motivator for, and supporter of, research in the arid and semi-arid rangelands of Australia. His commitment was fundamental to the establishment of CSIRO’s Central Australian Laboratory. Pastoral land use and improving the land for that purpose were the primary concerns when CSIRO’s presence in Alice Springs was established in 1953. From an initial focus on ‘making the desert bloom’, in particular making the vast spinifex grasslands more ‘useful’, the focus of research shifted to maintaining the productivity of country preferred by cattle and establishing methods for monitoring its health. It was not until the 1970s that Aboriginal and conservation land management appeared in the laboratory’s research agenda, somewhat intermittently, in response to important social and political changes in the wider Australian community.

Performance characteristics of two real-time TaqMan polymerase chain reaction assays for the detection of WSSV in clinically diseased and apparently healthy prawns.

This study aimed to generate data on performance characteristics for 2 real-time TaqMan PCR assays (CSIRO and WOAH WSSV qPCRs) for the purposes of (1) detection of white spot syndrome virus (WSSV) in clinically diseased prawns and (2) detection of WSSV in apparently healthy prawns. Analytical sensitivity of both assays was 2 to 20 genome copies per reaction, and analytical specificity was 100% after testing nucleic acid from 9 heterologous prawn pathogens and 4 prawn species. Results obtained after testing more than 20 000 samples in up to 559 runs with the CSIRO WSSV qPCR and up to 293 runs with the WOAH WSSV qPCR demonstrated satisfactory repeatability for both assays. Both assays demonstrated median diagnostic sensitivity (DSe) 100% (95% CI: 94.9-100%) when testing clinically diseased prawns. When 1591 test results from apparently healthy prawns were analysed by Bayesian latent class analysis, median DSe and diagnostic specificity (DSp) were 82.9% (95% probability interval [PI]: 75.0-90.2%) and 99.7% (95% PI: 98.6-99.99%) for the CSIRO WSSV qPCR and 76.8% (95% PI: 68.9-84.9%) and 99.7% (95% PI: 98.7-99.99%) for the WOAH WSSV qPCR. When both assays were interpreted in parallel, median DSe increased to 98.3 (95% PI: 91.6-99.99%), and median DSp decreased slightly to 99.4% (95% PI: 97.9-99.99%). Routine testing of quantified positive controls by laboratories in the Australian laboratory network demonstrated satisfactory reproducibility of the CSIRO WSSV qPCR assay. Both assays demonstrated comparable performance characteristics, and the results contribute to the validation data required in the WOAH validation pathway for the purposes of detection of WSSV in clinically diseased and apparently healthy prawns.

PETROGRAPHIC AND GEOCHEMICAL CONSTRAINTS ON TECTONIC SETTINGS OF THE BIRIMIAN SUPERGROUP VOLCANIC ROCKS, EVIDENCE FROM NEW DROBO ENVIRONS SOUTH OF JAMAN DISTRICT IN THE BONO REGION OF GHANA

The petrographic and geochemical studies of Birimian Supergroup meta-volcanic rocks in the New Drobo environs in Ghana help to decipher the tectonic settings at the study area. Twenty thin sections were prepared with rock samples from the field at the KNUST Geological Engineering Laboratory and petrographic microscope used to determine the different types of minerals in the samples and also the rock type. Whole rock geochemical analysis was done, using both X-Ray Fluorescence and Inductively Coupled Plasma Mass Spectrometer methods at Australian Laboratory Services in Canada. The main volcanic rock types at the study area comprise of basalt, andesite, dacite and rhyo-dacite with porphyritic mineralogical composition such as plagioclase feldspar, augite, olivine, hornblende, biotite, quartz, rutile, chlorite. The average concentrations of Zr &lt; 150 ppm, TiO2 &lt; 1.5 % and P2O5 &lt; 0.25 % and the ratios of Nb/Y &lt; 1.2 and Y/Nb &gt; 1 reveal the magma type in the study area to be continental tholeiitic basalt in nature. The mafic volcanic basalt is from a plate margin tectonic setting and thus of normal MORB and volcanic arc basalts. Also, the low basaltic values of the ratios of Ti/Y and Nb/Y confirm the tectonic setting of the area to be of plate margin. Zr is highly incompatible with respect to Ti and renders the ratio of Zr/TiO2 to be influenced by partial melting and causes heterogeneity in the mantle. The heterogeneity in the source of the mantle can be confirmed with the high value of the ratio of Zr/Y.

A history of CSIRO’s Central Australian Laboratory 2, 1980–2018: interdisciplinary land research

In the first 27 years of the Central Australian Laboratory (CAL), to 1980, research focussed almost entirely on the needs of the pastoral industry. By the 1980s, ongoing campaigns for Aboriginal land rights and demands to conserve biodiversity plainly showed that there were other land uses deserving research attention. Initially CAL’s research agenda expanded to include conservation in spinifex grasslands and grazing lands but remained biophysical in nature. It subsequently became clear that people’s roles in decision-making about land use and management should be part of research. By the 2000s, scientists were able to build trusting relationships with Aboriginal people and organisations and undertake collaborative studies to improve livelihoods and wellbeing on country. Over the 38 years from 1980 to 2018, CAL’s research activities responded to diverse societal expectations but it was not enough to prevent the laboratory’s eventual closure as public investment in rangelands dwindled.

Australian National Enterovirus Reference Laboratory annual report, 2020.

Australia monitors its polio-free status by conducting surveillance for cases of acute flaccid paralysis (AFP) in children less than 15 years of age, as recommended by the World Health Organization (WHO). Cases of AFP in children are notified to the Australian Paediatric Surveillance Unit or the Paediatric Active Enhanced Disease Surveillance System and faecal specimens are referred for virological investigation to the National Enterovirus Reference Laboratory. In 2020, no cases of poliomyelitis were reported from clinical surveillance; Australia reported 1.09 non-polio AFP cases per 100,000 children, thereby meeting the WHO's performance criterion for a sensitive surveillance system. The non-polio enteroviruses coxsackievirus A10 and coxsackievirus A16 were identified from clinical specimens collected from AFP cases. Australia also performs enterovirus surveillance and environmental surveillance to complement the clinical system focussed on children. In 2020, there were 140 cases of wild poliovirus reported from the two remaining endemic countries: Afghanistan and Pakistan. Another 28 countries reported cases of circulating vaccine-derived poliovirus.