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Hotel quarantine for international travelers has been used to prevent coronavirus disease spread into Australia. A quarantine hotel–associated community outbreak was detected in South Australia. Real-time genomic sequencing enabled rapid confirmation tracking the outbreak to a recently returned traveler and linked 2 cases of infection in travelers at the same facility.

The gold standard for diagnostics of SARS-CoV-2 (COVID-19) virus is based on real-time polymerase chain reaction (RT-PCR) using centralized PCR facilities and commercial viral RNA extraction kits. One of the key components of these kits are magnetic beads composed of silica coated magnetic iron oxide (Fe2O3 or Fe3O4) nanoparticles, needed for the selective extraction of RNA. At the beginning of the pandemic in 2019, due to a high demand across the world there were severe shortages of many reagents and consumables, including these magnetic beads required for testing for SARS-CoV-2. Laboratories needed to source these products elsewhere, preferably at a comparable or lower cost. Here, we describe the development of a simple, low-cost and scalable preparation of magnetic nanoparticles (MNPs) from biowaste and demonstrate their successful application in viral RNA extraction and the detection of COVID-19. These MNPs have a unique nanoplatelet shape with a high surface area, which are beneficial features, expected to provide improved RNA adsorption, better dispersion and processing ability compared with commercial spherical magnetic beads. Their performance in COVID-19 RNA extraction was evaluated in comparison with commercial magnetic beads and the results presented here showed comparable results for high throughput PCR analysis. The presented magnetic nanoplatelets generated from biomass waste are safe, low-cost, simple to produce in large scale and could provide a significantly reduced cost of nucleic acid extraction for SARS-CoV-2 and other DNA and RNA viruses.

This study evaluated the feasibility of utilising general practitioner (GP)-initiated, laboratory-confirmed self-collected home swab data (iSwab) for estimating influenza vaccine effectiveness (VE), compared to traditional health practitioner-collected swabs for surveillance. Demographic, clinical, and vaccination profiles of iSwab patients were compared to patients whose swabs were collected by a practitioner in an established GP surveillance network (Australian Sentinel Practices REsearch Network, ASPREN). VE estimates for both groups were calculated using a test-negative design and logistic regression. ASPREN patients had a lower median age (37 years) compared to iSwab (42 years) and a lower vaccination rate (37 % vs. 47 %). iSwab patients were more likely to have missing data than the ASPREN cohort. Pathogen detection rates varied between the two sampling methods. ASPREN had higher influenza positivity compared to iSwab, especially in 2022. VE estimates varied between the two methods, with ASPREN demonstrating moderate effectiveness in both years. iSwab VE was unable to be calculated in 2022 due to small sample size, while in 2023 it was higher than the ASPREN estimates. Combining data from both methods provided more precise VE estimates. However, population differences in the iSwab cohort question the validity of the combined estimates. Self-collected home swabs, initiated by GPs, have the potential to complement traditional systems for VE estimation. Differences in demographics, vaccination rates, and data completeness between the two methods highlight the need for systematic sampling to prevent selection bias in the self-swabbing cohort to ensure accuracy of VE estimates before combining data from these two methods.

New HIV-1 infections are genotyped as part of standard of care testing to ensure that antiretroviral treatment will be efficacious against the virus. Historically this has been performed by sequencing the pol region of the HIV-1 genome only. The popularity of next-generation sequencing (NGS) methods during the SARS-CoV-2 pandemic has resulted in a shift towards using NGS in diagnostic sequencing, but there remain limited methodologies utilising the strengths of NGS for robust diagnostic sequencing of longer regions of the HIV-1 genome. Given the acceptance and success of tiling PCR methodologies during the SARS-CoV-2 pandemic, we aimed to design and verify a novel tiling PCR method for routine HIV-1 sequencing. A set of tiling PCR primers was designed to amplify the 5’ half of HIV-1 in six overlapping segments of 1,000 bp in only two PCR reactions. The assay can move from sample to sequencer in under a day. The tiling PCR was able to generate HIV-1 sequences from 90 (100%) samples in a comparison panel, and complete protease-reverse transcriptase and integrase regions were amplified in > 90% of samples with a viral load > 5000 copies/mL. Seven additional drug resistance mutations were identified when using this novel method. As such, this novel designer tiling PCR is a promising method for the routine NGS-based diagnostic sequencing of HIV-1.

Background Vaccine effectiveness (VE) estimates provide important post‐marketing assessment of how well seasonal influenza vaccines prevent medically attended influenza disease. We present VE estimates for primary care in Australia for the 2017–2019 seasons. Methods The study used a test‐negative design. Influenza VE was estimated from adjusted logistic regression models comparing the odds of vaccination among influenza‐test‐positive cases and test‐negative non‐cases. Estimates were made overall and separately by influenza type, subtype, lineage and clade and stratified by age group. Antigenic similarity of influenza viruses to vaccine strains was assessed using the haemagglutination inhibition assay, and phylogenetic analysis was performed on sequenced viruses. Results The study included 2879, 1973 and 3371 general practice patients with swabs collected during 2017, 2018 and 2019 respectively. Influenza A(H3N2) was predominant in 2017 and 2019, while influenza A(H1N1)pdm09 predominated in 2018. VE was estimated at 37% (95% CI 22, 48) for the 2017 season, 53% (95% CI 33, 67) for 2018 and 50% (95% CI 40, 58) for 2019. In general, estimates were higher against A(H1N1)pdm09 and influenza B viruses and lower against A(H3N2) viruses. Across the three seasons, antigenic data identified a greater proportion of A(H1N1)pdm09 and influenza B viruses than A(H3N2) viruses as antigenically similar to the cell‐propagated reference viruses. VE estimates by clade generally indicated higher VE among viruses in the same clade as the vaccine viruses. Conclusions Influenza VE varied across influenza seasons and by influenza type/subtype. Given the ongoing evolution of circulating influenza viruses, vaccine improvements are needed, especially for influenza A(H3N2).

Background In a previous study of a Q fever outbreak in Birmingham, our group identified a non-infective complex of Coxiella burnetii ( C.b. ) antigens able to survive in the host and provoked aberrant humoral and cell-mediated immunity responses. The study led to recognition of a possible pathogenic link between C.b. infection and subsequent long-term post Q fever fatigue syndrome (QFS). This report presents an unusually severe case of C.b. antigen and DNA detection in post-mortem specimens from a patient with QFS. Case presentation We report a 19-year old female patient who became ill with an acute unexplained febrile encephalitis-like illness, followed by increasingly severe multisystem dysfunction and death 10 years later. During life, extensive clinical and laboratory investigations from different disciplinary stand points failed to deliver a definitive identification of a cause. Given the history of susceptibility to infection from birth, acute fever and the diagnosis of “post viral syndrome”, tests for infective agents were done starting with C.b. and Legionella pneumophila . The patient had previously visited farms a number of times. Comprehensive neuropathological assessment at the time of autopsy had not revealed gross or microscopic abnormalities. The aim was to extend detailed studies with the post-mortem samples and identify possible factors driving severe disturbance of homeostasis and organ dysfunction exhibited by the course of the patient’s ten-year illness. Immunohistochemistry for C.b. antigen and PCR for DNA were tested on paraffin embedded blocks of autopsy tissues from brain, spleen, liver, lymph nodes (LN), bone marrow (BM), heart and lung. Standard H&E staining of brain sections was unrevealing. Immuno-staining analysis for astrocyte cytoskeleton proteins using glial fibrillary acidic protein (GFAP) antibodies showed a reactive morphology. C oxiella antigens were demonstrated in GFAP immuno-positive grey and white matter astrocytes, spleen, liver, heart, BM and LN. PCR analysis (COM1/IS1111 genes) confirmed the presence of C.b. DNA in heart, lung, spleen, liver & LN, but not in brain or BM. Conclusion The study revealed the persistence of C. b. cell components in various organs, including astrocytes of the brain, in a post-infection QFS. The possible mechanisms and molecular adaptations for this alternative C.b. life style are discussed.

ObjectivesTo investigate the performance of the fully automated cobas 4800 CT/NG test for detection of Chlamydia trachomatis and Neisseria gonorrhoeae.MethodsThe study was conducted using 900 clinical specimens (496 urine and 404 swab specimens) for C trachomatis testing, of which 498 specimens (318 urine and 180 swab specimens) were also tested for N gonorrhoeae. The results of the cobas 4800 CT/NG test were compared with those obtained from the Roche COBAS AMPLICOR CT/NG and COBAS TaqMan CT assays. N gonorrhoeae-positive specimens were further tested using in-house, real-time PCR assays. A panel of 223 Neisseria isolates was used to further investigate the performance of the cobas 4800 N gonorrhoeae assay.ResultsFor urine specimens, the sensitivity, specificity and negative and positive predictive values of the cobas 4800 CT/NG test were 94.5%, 99.5%, 98.8% and 97.7%, respectively, for C trachomatis, and 92.9%, 100%, 99.7% and 100%, respectively, for N gonorrhoeae. For swab specimens, the sensitivity, specificity and negative and positive predictive values were 92.0%, 100%, 99.5% and 100%, respectively, for C trachomatis, and 100%, 99.4%, 100% and 90.0%, respectively, for N gonorrhoeae. All N gonorrhoeae isolates were positive and all non-gonococcal Neisseria strains were negative by the cobas 4800 N gonorrhoeae assay.ConclusionsThe cobas 4800 CT/NG test is suitable for high through-put identification of C trachomatis and N gonorrhoeae infections.

Background: Hepatic chemosaturation for inoperable liver tumors is a palliative treatment option with a beneficial effect on survival. However, the procedure regularly leads to circulatory failure during the filtration phase, and hemodynamic management is challenging. Our study aimed to compare two different strategies for hemodynamic management during chemosaturation to develop hypotheses for improving patient care and reducing peri-interventional morbidity. Methods: We conducted a single-center retrospective cohort study including 66 procedures of chemosaturation between May 2016 and March 2024. Procedures were divided into two groups: group 1 was managed with norepinephrine as the only vasopressor and liberal use of hydroxyethyl starch (HES). Group 2 was managed with norepinephrine and vasopressin and the preferred use of balanced crystalloids. We compared these two groups with respect to hemodynamic parameters, laboratory values, and post-interventional complications. Results: The heart rate was highest and the mean arterial pressure (MAP) was lowest during the filtration phase in both groups (p = 0.868, p = 0.270). The vasoactive inotropic score (VIS) was significantly higher in group 2 during the filtration phase (31.5 vs. 89, p < 0.001). Group 1 received significantly more HES overall (1000 mL vs. 0 mL, p < 0.001). Lactate levels at admission to the ICU were higher in group 1 (22.9 vs. 14.45 mg/dL, p = 0.041). Platelet counts were lower in group 2 from directly after chemosaturation through day 2 (p = 0.022, p = 0.001, p = 0.032). The INR differed significantly directly after chemosaturation (1.13 vs. 1.26, p = 0.015). Overall, group 1 received significantly more blood products peri-interventionally. There were two bleedings and one ischemic stroke in the overall cohort. There was no peri-interventional mortality. Conclusions: Advanced hemodynamic management ensures low peri-interventional mortality and morbidity. High-dose vasopressors, including vasopressin and the preferred use of balanced crystalloids, are sufficient to stabilize circulatory function during chemosaturation.