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.

Benchmarking TriadAb using targets from the second antibody modeling assessment.

Computational modeling and design of antibodies has become an integral part of today's research and development in antibody therapeutics. Here we describe the Triad Antibody Homology Modeling (TriadAb) package, a functionality of the Triad protein design platform that predicts the structure of any heavy and light chain sequences of an antibody Fv domain using template-based modeling. To gauge the performance of TriadAb, we benchmarked against the results of the Second Antibody Modeling Assessment (AMA-II). On average, TriadAb produced main-chain carbonyl root-mean-square deviations between models and experimentally determined structures at 1.10 Å, 1.45 Å, 1.41 Å, 3.04 Å, 1.47 Å, 1.27 Å, 1.63 Å in the framework and the six complementarity-determining regions (H1, H2, H3, L1, L2, L3), respectively. The inaugural results are comparable to those reported in AMA-II, corroborating with our internal bench-based experiences that models generated using TriadAb are sufficiently accurate and useful for antibody engineering using the sequence design capabilities provided by Triad.

Use of adrenaline to manage suspected anaphylaxis following COVID-19 vaccination: An Australian retrospective cohort study.

BACKGROUND: The rate of anaphylaxis following COVID-19 vaccinations is estimated to be 2-11 cases per million doses administered. However, adrenaline is occasionally used in individuals who are later diagnosed with immunisation stress-related responses, as their initial presenting signs and symptoms can appear similar to that of anaphylaxis. This study aims to describe the clinical profile of individuals who had received adrenaline following a COVID-19 vaccine and their subsequent revaccination outcomes. METHODS: We examined notifications of cases who had received adrenaline following a COVID-19 vaccine in New South Wales, Australia. The cases were classified into Brighton Collaboration Case Definition (BCCD) for anaphylaxis, their clinical presentation, management and subsequent revaccination outcomes were compared. RESULTS: From 22 February 2021 to 30 September 2021, there were 222 cases where adrenaline was administered. Of these, 32 (14 %) fulfilled Level 1 BCCD, 59 (27%) Level 2, 2 (1%) Level 3, 97 (44%) Level 4 and 32 (14 %) Level 5. The most commonly reported symptoms were sensation of throat closure (n = 116, 52%), difficulty breathing (n = 82, 37%) and nausea (n = 55, 25 %). Of the 176 (79%) individuals who proceeded to further vaccination, 89 (51%) received the same vaccine formulation and only 14 (8%) experienced another allergic adverse event with 9 (5%) receiving adrenaline. CONCLUSION: Less than one in five individuals who received adrenaline met Level 1 BCCD criteria for anaphylaxis. Many reactions that were treated with adrenaline had little to no diagnostic certainty of anaphylaxis and in such cases repeat vaccination had a high likelihood of being tolerated. Increased awareness and education on objective signs and symptoms of anaphylaxis is required to ensure appropriate use of adrenaline.

Spatiotemporal variations of river water turbidity in responding to rainstorm-streamflow processes and farming activities in a mountainous catchment, Lai Chi Wo, Hong Kong, China.

River turbidity is an important factor in evaluating environmental water quality, and turbidity dynamics can reflect water sediment changes. During rainfall periods, specifically in mountainous areas, river turbidity varies dramatically, and knowledge of spatiotemporal turbidity variations in association with rainfall features and farming activities is valuable for soil erosion prevention and catchment management. However, due to the difficulties in collecting reliable field turbidity data during rainstorms at a fine temporal scale, our understanding of the features of turbidity variations in mountainous rivers is still vague. This study conducted field measurements of hydrological and environmental variables in a mountainous river, the Lai Chi Wo river, in Hong Kong, China. The study results revealed that variations of turbidity graphs during rainstorms closely match variations of streamflow hydrographs, and the occurrence of the turbidity peaks and water level peaks are almost at the same time. Moreover, the study disclosed that the increasing rates of the turbidity values are closely related to the rainfall intensity at temporal scales of 15 and 20 min, and the impact of farming activities on river turbidity changes is largely dependent on rainfall intensity. In the study area, when the rainfall intensity is larger than 35 mm/hr at a time interval of 15 min, the surface runoff over the farmland would result in higher river water turbidity downstream than that upstream. The study results would enrich our understanding of river water turbidity dynamics at minute scales and be valuable for further exploration of the river water environment in association with turbidity.

HIV: the changing paradigm.

The past four decades have seen enormous progress in the diagnosis and management of human immunodeficiency virus (HIV) infection. There have been significant advances spanning the approval of the first antiretroviral agents, the advent of combination antiretroviral therapy to single tablet regimens with minimal toxicity. Although these remarkable developments have on the surface led to the 'end of AIDS', there are still key populations being left behind. This clinical update will describe the diagnosis and management of HIV, and the changing paradigms that have seen HIV transform from a life-limiting condition to a manageable chronic disease over a few decades.

Lack of standardisation in interpretation and reporting of autoantibody assays: a survey analysis of Australasian laboratories with focus on line immunoassays.

Autoantibody assays are reported in a variety of formats. Results only slightly above established cut-offs provide lower likelihood ratios; therefore, their clinical significance may be more uncertain, which is not readily communicated with dichotomous qualitative reporting. Line immunoassays (LIA) are a common method for detecting antibodies to extractable nuclear antigens (ENA) and myositis-associated antibodies. However, recommended positive cut-offs are contentious. We distributed a survey via e-mail to participants in the Royal College of Pathologists of Australasia Quality Assurance Program (RCPAQAP) Immunology modules and to a dedicated immunology mailing list in Australasia. Questions explored general viewpoints surrounding autoantibody reporting, as well as current laboratory practices, with particular focus on interpretation and reporting of the most commonly used ENA LIA manufactured by Euroimmun. There were 31 responders, representative of at least 17 unique laboratories across Australia (8 public, 5 private) and New Zealand (4 laboratories). Responses suggest that autoantibody reporting is not standardised; there was variation in general viewpoints and reporting practices, particularly regarding the interpretation of and positive cut-offs used for the Euroimmun ENA LIA, which were contrary to the manufacturer's guidelines in a majority of the responses. Interpretative qualitative reporting based on results from other investigations and the clinical history was a common theme. There is large variation in the reporting of autoantibody assays within Australasia, especially by LIA. A majority of respondents report the most commonly used ENA LIA contrary to manufacturer's guidelines; alternative positive cut-offs are commonly utilised. LIA reports should indicate the level of positivity to enhance their relevance in the clinical decision-making process.

Subtype-specific differences in transmission cluster dynamics of HIV-1 B and CRF01_AE in New South Wales, Australia.

INTRODUCTION: The human immunodeficiency virus 1 (HIV-1) pandemic is characterized by numerous distinct sub-epidemics (clusters) that continually fuel local transmission. The aims of this study were to identify active growing clusters, to understand which factors most influence the transmission dynamics, how these vary between different subtypes and how this information might contribute to effective public health responses. METHODS: We used HIV-1 genomic sequence data linked to demographic factors that accounted for approximately 70% of all new HIV-1 notifications in New South Wales (NSW). We assessed differences in transmission cluster dynamics between subtype B and circulating recombinant form 01_AE (CRF01_AE). Separate phylogenetic trees were estimated using 2919 subtype B and 473 CRF01_AE sequences sampled between 2004 and 2018 in combination with global sequence data and NSW-specific clades were classified as clusters, pairs or singletons. Significant differences in demographics between subtypes were assessed with Chi-Square statistics. RESULTS: We identified 104 subtype B and 11 CRF01_AE growing clusters containing a maximum of 29 and 11 sequences for subtype B and CRF01_AE respectively. We observed a > 2-fold increase in the number of NSW-specific CRF01_AE clades over time. Subtype B clusters were associated with individuals reporting men who have sex with men (MSM) as their transmission risk factor, being born in Australia, and being diagnosed during the early stage of infection (p < 0.01). CRF01_AE infections clusters were associated with infections among individuals diagnosed during the early stage of infection (p < 0.05) and CRF01_AE singletons were more likely to be from infections among individuals reporting heterosexual transmission (p < 0.05). We found six subtype B clusters with an above-average growth rate (>1.5 sequences / 6-months) and which consisted of a majority of infections among MSM. We also found four active growing CRF01_AE clusters containing only infections among MSM. Finally, we found 47 subtype B and seven CRF01_AE clusters that contained a large gap in time (>1 year) between infections and may be indicative of intermediate transmissions via undiagnosed individuals. CONCLUSIONS: The large number of active and growing clusters among MSM are the driving force of the ongoing epidemic in NSW for subtype B and CRF01_AE.

Increased HIV Subtype Diversity Reflecting Demographic Changes in the HIV Epidemic in New South Wales, Australia.

Changes over time in HIV-1 subtype diversity within a population reflect changes in factors influencing the development of local epidemics. Here we report on the genetic diversity of 2364 reverse transcriptase sequences from people living with HIV-1 in New South Wales (NSW) notified between 2004 and 2018. These data represent >70% of all new HIV-1 notifications in the state over this period. Phylogenetic analysis was performed to identify subtype-specific transmission clusters. Subtype B and non-B infections differed across all demographics analysed (p < 0.001). We found a strong positive association for infections among females, individuals not born in Australia or reporting heterosexual transmission being of non-B origin. Further, we found an overall increase in non-B infections among men who have sex with men from 50 to 79% in the last 10 years. However, we also found differences between non-B subtypes; heterosexual transmission was positively associated with subtype C only. In addition, the majority of subtype B infections were associated with clusters, while the majority of non-B infections were singletons. However, we found seven non-B clusters (≥5 sequences) indicative of local ongoing transmission. In conclusion, we present how the HIV-1 epidemic has changed over time in NSW, becoming more heterogeneous with distinct subtype-specific demographic associations.

Geospatial evaluation of trade-offs between equity in physical access to healthcare and health systems efficiency.

INTRODUCTION: Decisions regarding the geographical placement of healthcare services require consideration of trade-offs between equity and efficiency, but few empirical assessments are available. We applied a novel geospatial framework to study these trade-offs in four African countries. METHODS: Geolocation data on population density (a surrogate for efficiency), health centres and cancer referral centres in Kenya, Malawi, Tanzania and Rwanda were obtained from online databases. Travel time to the closest facility (a surrogate for equity) was estimated with 1 km resolution using the Access Mod 5 least cost distance algorithm. We studied associations between district-level average population density and travel time to closest facility for each country using Pearson's correlation, and spatial autocorrelation using the Global Moran's I statistic. Geographical clusters of districts with inefficient resource allocation were identified using the bivariate local indicator of spatial autocorrelation. RESULTS: Population density was inversely associated with travel time for all countries and levels of the health system (Pearson's correlation range, health centres: -0.89 to -0.71; cancer referral centres: -0.92 to -0.43), favouring efficiency. For health centres, negative spatial autocorrelation (geographical clustering of dissimilar values of population density and travel time) was weaker in Rwanda (-0.310) and Tanzania (-0.292), countries with explicit policies supporting equitable access to rural healthcare, relative to Kenya (-0.579) and Malawi (-0.543). Stronger spatial autocorrelation was observed for cancer referral centres (Rwanda: -0.341; Tanzania: -0.259; Kenya: -0.595; Malawi: -0.666). Significant geographical clusters of sparsely populated districts with long travel times to care were identified across countries. CONCLUSION: Negative spatial correlations suggested that the geographical distribution of health services favoured efficiency over equity, but spatial autocorrelation measures revealed more equitable geographical distribution of facilities in certain countries. These findings suggest that even when prioritising efficiency, thoughtful decisions regarding geographical allocation could increase equitable physical access to services.

Regulation of axial and head patterning during planarian regeneration by a commensal bacterium.

Some animals, such as planaria, can regenerate complex anatomical structures in a process regulated by genetic and biophysical factors, but additional external inputs into regeneration remain to be uncovered. Microbial communities inhabiting metazoan organisms are important for metabolic, immune, and disease processes, but their instructive influence over host structures remains largely unexplored. Here, we show that Aquitalea sp. FJL05, an endogenous commensal bacterium of Dugesia japonica planarians, and one of the small molecules it produces, indole, can influence axial and head patterning during regeneration, leading to regeneration of permanently two-headed animals. Testing the impact of indole on planaria tissues via RNA sequencing, we find that indole alters the regenerative outcomes in planarians through changes in expression to patterning genes, including a downregulation of Wnt pathway genes. These data provide a unique example of the product of a commensal bacterium modulating transcription of patterning genes to affect the host's anatomical structure during regeneration.

Attempts to develop an enzyme converting DHIV to KIV.

Dihydroxy-acid dehydratase (DHAD) catalyzes the dehydration of R-2,3-dihydroxyisovalerate (DHIV) to 2-ketoisovalerate (KIV) using an Fe-S cluster as a cofactor, which is sensitive to oxidation and expensive to synthesize. In contrast, sugar acid dehydratases catalyze the same chemical reactions using a magnesium ion. Here, we attempted to substitute the high-cost DHAD with a cost-efficient engineered sugar acid dehydratase using computational protein design (CPD). First, we tried without success to modify the binding pocket of a sugar acid dehydratase to accommodate the smaller, more hydrophobic DHIV. Then, we used a chemically activated substrate analog to react with sugar acid dehydratases or other enolase superfamily enzymes. Mandelate racemase from Pseudomonas putida (PpManR) and the putative sugar acid dehydratase from Salmonella typhimurium (StPutD) showed beta-elimination activity towards chlorolactate (CLD). CPD combined with medium-throughput selection improved the PpManR kcat/KM for CLD by four-fold. However, these enzyme variants did not show dehydration activity towards DHIV. Lastly, assuming phosphorylation could also be a good activation mechanism, we found that mevalonate-3-kinase (M3K) from Picrophilus torridus (PtM3K) exhibited adenosine triphosphate (ATP) hydrolysis activity when mixed with DHIV, indicating phosphorylation activity towards DHIV. Engineering PpManR or StPutD to accept 3-phospho-DHIV as a substrate was performed, but no variants with the desired activity were obtained.

Limited Sustained Local Transmission of HIV-1 CRF01_AE in New South Wales, Australia.

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.

NMDA receptor antibody in teratoma-related opsoclonus-myoclonus syndrome.

Opsoclonus-myoclonus syndrome (OMS) is a brainstem/cerebellar syndrome producing disabling multi-directional saccadic oscillations with oscillopsia, with or without somatic myoclonus and cerebellar ataxia (Wong et al., 2001; Armangué et al., 2016). OMS is presumed to have an autoimmune basis and patients with it are tested for antineuronal antibodies and have imaging to locate any tumors. Here we report a unusual case of a young woman who had NMDAR antibody (NMDAR-ab) positive, teratoma-related, isolated OMS without encephalopathy. Removal of her ovarian teratoma, and immunotherapy with steroids, intravenous immunoglobulin (IVIg), plasma exchange (PLEX), and ultimately with B-cell depletion with rituximab resulted in total recovery after 3 months. Patients with teratoma-related OMS very rarely have NMDAR-ab which suggests that it is not the NMDAR-ab per se that causes the OMS.

T-cell-mediated drug hypersensitivity: immune mechanisms and their clinical relevance.

T-cell-mediated drug hypersensitivity represents a significant proportion of immune mediated drug hypersensitivity reactions. In the recent years, there has been an increase in understanding the immune mechanisms behind T-cell-mediated drug hypersensitivity. According to hapten mechanism, drug specific T-cell response is stimulated by drug-protein conjugate presented on major histocompatibility complex (MHC) as it is presented as a new antigenic determinant. On the other hand, p-i concept suggests that a drug can stimulate T cells via noncovalent direct interaction with T-cell receptor and/or peptide-MHC. The drug binding site is quite variable and this leads to several different mechanisms within p-i concept. Altered peptide repertoire can be regarded as an 'atypical' subset of p-i concept since the mode of the drug binding and the binding site are essentially identical to p-i concept. However, the intracellular binding of abacavir to HLA-B(*)57:01 additionally results in alteration in peptide repertoire. Furthermore the T-cell response to altered peptide repertoire model is only shown for abacavir and HLA-B(*)57:01 and therefore it may not be generalised to other drug hypersensitivity. Danger hypothesis has been postulated to play an important role in drug hypersensitivity by providing signal 2 but its experimental data is lacking at this point in time. Furthermore, the recently described allo-immune response suggests that danger signal may be unnecessary. Finally, in view of these new understanding, the classification and the definition of type B adverse drug reaction should be revised.