Research Publications and Outputs

Soil Moisture Data 4/16/2025 from Narrabri NSW LLara2 Farm

2026-04-23T01:18:25Z

Soil Moisture Data 4/16/2025 from Narrabri NSW LLara2 Farm Harwood, Richard 6 CSVS and 1 .kml file which contains lat/lon positions for each 6 sensors (1 CSV for a sensor). Raw time series data of soil moisture at 30 minute intervals.

Beyond 2025: Navigating Challenges and Opportunities in Global Nutrition

2026-04-28T02:04:48Z

Beyond 2025: Navigating Challenges and Opportunities in Global Nutrition Branca, Francesco With ultra-processed foods increasingly at the heart of global nutrition debates, Professor Branca highlights emerging evidence and anticipates strengthened international guidance and policy measures. He will further address the complex challenge of managing powerful corporate influences within food systems, advocating for greater accountability and robust frameworks to tackle conflicts of interest in nutrition governance. Join us for a thought-provoking discussion on shaping a resilient and equitable global nutrition future.

Review: "The future of unions and worker representation: The digital picket line" by Anthony Forsyth, Hart Publishing, Oxford, 2022.

2026-04-28T02:06:59Z

Review: "The future of unions and worker representation: The digital picket line" by Anthony Forsyth, Hart Publishing, Oxford, 2022. McCrystal, Shae The 'digital picket line', the subtitle of this significant new monograph by Professor Anthony Forsyth, nicely evokes the themes that permeate this study of the future of trade unions and worker representation. As Forsyth observes, the term is 'emblematic of the transformation in union forms and tactics ... needed to ensure that unions continue to play an effective role as the representative of workers into the future'. Forsyth sets out the challenge for the trade union movement to identify 'how the revitalisation of unions can be achieved and what collectivism must look like to ensure the effective representation of workers' interests into the future'. Adopting Visser’s categorisation of four possible futures for the union movement (marginalisation, dualisation, replacement, revitalisation), Forsyth contends that revitalisation for unions is viable provided the union movement commits to the underlying preconditions to enable revitalisation to occur.

Plasma Activation of Microplates Optimized for One-Step Reagent-Free Immobilization of DNA and Protein

2024-03-15T05:40:03Z

Plasma Activation of Microplates Optimized for One-Step Reagent-Free Immobilization of DNA and Protein Coffi Dit Gleize, Kanako; Tran, Clara T. H.; Waterhouse, Anna; Bilek, Marcela M. M.; Wickham, Shelley F. J. Activated microplates are widely used in biological assays and cell culture to immobilize biomolecules, either through passive physical adsorption or covalent cross-linking. Covalent attachment gives greater stability in complex biological mixtures. However, current multistep chemical activation methods add complexity and cost, require specific functional groups, and can introduce cytotoxic chemicals that affect downstream cellular applications. Here, we show a method for one-step linker-free activation of microplates by energetic ions from plasma for covalent immobilization of DNA and protein. Two types of energetic ion plasma treatment were shown to be effective: plasma immersion ion implantation (PIII) and plasma-activated coating (PAC). This is the first time that PIII and PAC have been reported in microwell plates with nonflat geometry. We confirm that the plasma treatment generates radical-activated surfaces at the bottom of wells despite potential shadowing from the walls. Comprehensive surface characterization studies were used to compare the PIII and PAC microplate surface composition, wettability, radical density, optical properties, stability, and biomolecule immobilization density. PAC plates were found to have more nitrogen and lower radical density and were more hydrophobic and more stable over 3 months than PIII plates. Optimal conditions were obtained for high-density DNA (PAC, 0 or 21% nitrogen, pH 3–4) and streptavidin (PAC, 21% nitrogen, pH 5–7) binding while retaining optical properties required for typical high-throughput biochemical microplate assays, such as low autofluorescence and high transparency. DNA hybridization and protein activity of immobilized molecules were confirmed. We show that PAC activation allows for high-density covalent immobilization of functional DNA and protein in a single step on both 96- and 384-well plates without specific linker chemistry. These microplates could be used in the future to bind other user-selected ligands in a wide range of applications, for example, for solid phase polymerase chain reaction and stem cell culture and differentiation.

Design Optimization of Perfluorinated Liquid-Infused Surfaces for Blood-Contacting Applications

2026-04-22T01:50:35Z

Design Optimization of Perfluorinated Liquid-Infused Surfaces for Blood-Contacting Applications Hong, Jun Ki; Mathur, Kavya; Ruhoff, Alexander; Akhavan, B.; Waterhouse, Anna; Neto, Chiara Tethered-liquid perfluorocarbon (TLP) coatings show promise for bloodcontacting medical device applications to reduce blood adhesion and delay thrombosis. However, their fabrication and longevity under external fluid flow is not well characterized. A vapor phase silanization reaction leading to the formation of tethered-perfluorocarbon (TP) layers containing large bumpy aggregates, 300 ± 200 nm thick, on top of an underlying 35 ± 15 nm thick uniform coating is reported. The vapor phase method compares favorably to the well-established liquid phase deposition to reproducibly create slippery coatings on silicon and polystyrene with very low water sliding angles (2° ± 1°), without the need to control humidity conditions. The TP layer retains perfluorinated lubricants up to 20 000 s–1, using a cone-and-plate rheometer, with the higher viscosity lubricant perfluoroperhydrophenanthrene being more resistant to depletion than perfluorodecalin. TLP infused with either of the lubricants effectively reduces adhesion of fibrin from human whole blood relative to TP and control hydrophilic and hydrophobic surfaces. The combination of highly fluorinated TP coatings grafted from the vapor phase to create nanoscale structured surfaces infused with higher viscosity lubricant may be the most suitable combination for clinical applications of liquid-infused surfaces to reduce thrombosis in blood-contacting medical devices under flow.

An interlaboratory collection of datasets and test cases

2026-05-27T02:26:04Z

An interlaboratory collection of datasets and test cases Ceguerra, Anna Gives the ability for new atom probe users to get training on specific computational programs using the test case document and the sample datasets. The test cases also give sample outputs for the researcher to verify their own running of the test case.

Low-angle boundary in Zircon DN5 dataset for Deformation-induced trace element redistribution in zircon revealed using atom probe tomography

2026-04-23T01:18:25Z

Low-angle boundary in Zircon DN5 dataset for Deformation-induced trace element redistribution in zircon revealed using atom probe tomography Cairney, Julie; La Fontaine, Alex; Piazolo, Sandra; Trimby, Patrick; Yang, Limei Direct contact alex.lafontaine@sydney.edu.au Source of data (who collected it, at what organisation, etc.) The University of Sydney - Julie Cairney, Alex La Fontaine, Sandra Piazolo, Patrick Trimby, Limei Yang Significance (Why is this data significant?) Showing deformation-induced trace element segregation in Zircons Citation details (Has this data been used for a publication prior to sharing?) Nature communication - doi:10.1038/ncomms10490

Human tooth enamel dataset for Atomic-scale compositional mapping reveals Mg-rich amorphous calcium phosphate in human dental enamel

2026-05-06T03:24:24Z

Human tooth enamel dataset for Atomic-scale compositional mapping reveals Mg-rich amorphous calcium phosphate in human dental enamel La Fontaine, Alex; Cairney, Julie Direct contact alex.lafontaine@sydney.edu.au Source of data (who collected it, at what organisation, etc.) The University of Sydney - Julie Cairney - Alex La Fontaine Significance (Why is this data significant?) First APT data from human tooth enamel - Showing amorphous calcium phosphate intergranular phase Citation details (Has this data been used for a publication prior to sharing?) Published in Science Advances: DOI: 10.1126/sciadv.1601145

Cu plates and Sn precipitates in Al-1.7%Cu-0.05%Sn alloy

2026-04-23T01:18:25Z

Cu plates and Sn precipitates in Al-1.7%Cu-0.05%Sn alloy La Fontaine, Alex; Marceau, Ross Direct contact alex.lafontaine@sydney.edu.au Source of data (who collected it, at what organisation, etc.) The University of Sydney - Alex La Fontaine and Ross Marceau Significance (Why is this data significant?) First time APT was used to reveal Cu-plates and Sn nanoprecipitates in Al-1.7%Cu-0.05%Sn alloy

Pure aluminium datasets

2026-04-23T01:18:25Z

Pure aluminium datasets Ceguerra, Anna R4_02574 ("Roger"), 05601 ("Geoff"), and other pure Al datasets Used for testing reconstruction calibration and reconstruction protocols

Reference Zircon Round Robin

2026-04-23T01:18:25Z

Reference Zircon Round Robin La Fontaine, Alex Direct contact: alex.lafontaine@sydney.edu.au. Source of data: Australian Centre for Microscopy & Microanalysis (ACMM), University of Sydney lead the round robin experiment with 9 international institutes. Significance: Round robin data on reference zircon.

IFI27 transcription is an early predictor for COVID-19 outcomes; a multi-cohort observational study

2026-04-23T01:18:25Z

IFI27 transcription is an early predictor for COVID-19 outcomes; a multi-cohort observational study Shojaei, Maryam; Shamshirian, Amir; Monkman, James; Grice, Laura; Tran, Minh; Tan, Chin Wee; Rossi, Gustavo Rodrigues; McCulloch, Timothy R.; Nalos, Marek; Chew, Keng Yih; Zhu, Yanshan; Xia, Yao; Wells, Timothy J.; Senegaglia, Alexandra Cristina; Rebelatto, Carmen Lúcia Kuniyoshi; Franck, Claudio Luciano; dos Santos, Anna Flavia Ribeiro; de Noronha, Lucia; Motamen, Sepideh; Valadan, Reza; Amjadi, Omolbanin; Gogna, Rajan; Madan, Esha; Alizadeh-Navaei, Reza; Lamperti, Liliana; Zuñiga, Felipe; Nova-Lamperti, Estefania; Labarca, Gonzalo; Knippenberg, Ben; Herwanto, Velma; Wang, Ya; Phu, Amy; Chew, Tracy; Kwan, Timothy; Kim, Karan; Teoh, Sally; Pelaia, Tiana M; Kuan, Win Sen; Jee, Yvette; Iredell, Jon; O’Byrne, Ken; Fraser, John F.; Davis, Melissa J.; Belz, Gabrielle; Warkiani, Majid; Gallo, Carlos Salomon; Souza-Fonseca-Guimaraes, Fernando; Nguyen, Quan; Mclean, Anthony; Kulasinghe, Arutha; Short, Kirsty R.; Tang, Benjamin Robust biomarkers that predict disease outcomes amongst COVID-19 patients are necessary for both patient triage and resource prioritisation. Numerous candidate biomarkers have been proposed for COVID-19. However, at present, there is no consensus on the best diagnostic approach to predict outcomes in infected patients. Moreover, it is not clear whether such tools would apply to other potentially pandemic pathogens and therefore of use as stockpile for future pandemic preparedness. We conducted a multi-cohort observational study to investigate the biology and the prognostic role of interferon alpha-inducible protein 27 (IFI27) in COVID-19 patients. We show that IFI27 is expressed in the respiratory tract of COVID-19 patients and elevated IFI27 expression is associated with the presence of a high viral load. We further demonstrate that systemic host response, as measured by blood IFI27 expression, is associated with COVID-19 severity. For clinical outcome prediction (e.g. respiratory failure), IFI27 expression displays a high positive (0.83) and negative (0.95) predictive value, outperforming all other known predictors of COVID-19 severity. Furthermore, IFI27 is upregulated in the blood of infected patients in response to other respiratory viruses. For example, in the pandemic H1N1/09 swine influenza virus infection, IFI27-like genes were highly upregulated in the blood samples of severely infected patients. These data suggest that prognostic biomarkers targeting the family of IFI27 genes could potentially supplement conventional diagnostic tools in future virus pandemics, independent of whether such pandemics are caused by a coronavirus, an influenza virus or another as yet-to-be discovered respiratory virus. We searched the scientific literature using PubMed to identify studies that used the IFI27 biomarker to predict outcomes in COVID-19 patients. We used the search terms “IFI27”, “COVID-19, “gene expression” and “outcome prediction”. We did not identify any study that investigated the role of IFI27 biomarker in outcome prediction. Although ten studies were identified using the general terms of “gene expression” and “COVID-19”, IFI27 was only mentioned in passing as one of the identified genes. All these studies addressed the broader question of the host response to COVID-19; none focused solely on using IFI27 to improve the risk stratification of infected patients in a pandemic. Here, we present the findings of a multi-cohort study of the IFI27 biomarker in COVID-19 patients. Our findings show that the host response, as reflected by blood IFI27 gene expression, accurately predicts COVID-19 disease progression (positive and negative predictive values; 0.83 and 0.95, respectively), outperforming age, comorbidity, C-reactive protein and all other known risk factors. The strong association of IFI27 with disease severity occurs not only in SARS-CoV-2 infection, but also in other respiratory viruses with pandemic potential, such as the influenza virus. These findings suggest that host response biomarkers, such as IFI27, could help identify high-risk COVID-19 patients - those who are more likely to develop infection complications - and therefore may help improve patient triage in a pandemic. This is the first systemic study of the clinical role of IFI27 in the current COVID-19 pandemic and its possible future application in other respiratory virus pandemics. The findings not only could help improve the current management of COVID-19 patients but may also improve future pandemic preparedness.

Tuning Ta coating properties through chemical and plasma etching pre-treatment of NiTi wire substrates

2026-04-28T02:05:17Z

Tuning Ta coating properties through chemical and plasma etching pre-treatment of NiTi wire substrates Pace, Ben; Bendavid, Avi; Ahsan, Mohammed; Dargusch, Matthew; Bhatia, Vijay; Byrnes, Jacob; Cairney, Julie Tantalum coatings have wide applications including as corrosion resistant coatings and radiopaque films for biomedical implants. However, producing coatings of sufficient thickness with the desired mechanical properties remains a substantial challenge. In this study, we show that the microstructure and properties of thick Ta films deposited on NiTi wires can be controlled significantly by pre-treating the substrate surface via ultrasonication followed by Aqua Regia etchant, or by plasma-based etching alone, while maintaining overall adhesive strength. Films from plasma and chemically etched samples exhibited substantially greater bulk texturing in the <111> direction than the control film, also yielding more elongated and columnar grains. The extent of <111> texturing in each sample was reflected in differences in Σ3 CSL boundary density. Additionally, only plasma etching yielded a β-Ta secondary phase. These microstructural observations demonstrate that film phase composition, texturing, grain shape distribution and grain boundary characteristics can be optimised for particular applications, simply by applying different NiTi substrate pretreatment regimes. It is suggested that this bears significant implications for influencing bulk properties such as cohesive and shear strength, as well as ductility, conductivity and cohesion in thick tantalum coatings.

Immune responses in COVID-19 respiratory tract and blood reveal mechanisms of disease severity

2026-04-28T02:01:06Z

Immune responses in COVID-19 respiratory tract and blood reveal mechanisms of disease severity Zhang, Wuji; Chua, Brendon Y.; Selva, Kevin J.; Kedzierski, Lukasz; Ashhurst, Thomas M.; Haycroft, Ebene R.; Shoffner, Suzanne K.; Hensen, Luca; Boyd, David F.; James, Fiona; Mouhtouris, Effie; Kwong, Jason C.; Chua, Kyra Y. L.; Drewett, George; Copaescu, Ana; Dobson, Julie E.; Rowntree, Louise C.; Habel, Jennifer R.; Allen, Lilith F.; Koay, Hui-Fern; Neil, Jessica A.; Gartner, Matthew; Lee, Christina Y.; Andersson, Patiyan; Seemann, Torsten; Sherry, Norelle L.; Amanat, Fatima; Krammer, Florian; Londrigan, Sarah L.; Wakim, Linda M.; King, Nicholas J.C.; Godfrey, Dale I.; Mackay, Laura K.; Thomas, Paul G.; Nicholson, Suellen; Arnold, Kelly B.; Chung, Amy W.; Holmes, Natasha E.; Smibert, Olivia C.; Trubiano, Jason A.; Gordon, Claire L.; Nguyen, Thi H.O.; Kedzierska, Katherine ABSTRACT Although the respiratory tract is the primary site of SARS-CoV-2 infection and the ensuing immunopathology, respiratory immune responses are understudied and urgently needed to understand mechanisms underlying COVID-19 disease pathogenesis. We collected paired longitudinal blood and respiratory tract samples (endotracheal aspirate, sputum or pleural fluid) from hospitalized COVID-19 patients and non-COVID-19 controls. Cellular, humoral and cytokine responses were analysed and correlated with clinical data. SARS-CoV-2-specific IgM, IgG and IgA antibodies were detected using ELISA and multiplex assay in both the respiratory tract and blood of COVID-19 patients, although a higher receptor binding domain (RBD)-specific IgM and IgG seroconversion level was found in respiratory specimens. SARS-CoV-2 neutralization activity in respiratory samples was detected only when high levels of RBD-specific antibodies were present. Strikingly, cytokine/chemokine levels and profiles greatly differed between respiratory samples and plasma, indicating that inflammation needs to be assessed in respiratory specimens for the accurate assessment of SARS-CoV-2 immunopathology. Diverse immune cell subsets were detected in respiratory samples, albeit dominated by neutrophils. Importantly, we also showed that dexamethasone and/or remdesivir treatment did not affect humoral responses in blood of COVID-19 patients. Overall, our study unveils stark differences in innate and adaptive immune responses between respiratory samples and blood and provides important insights into effect of drug therapy on immune responses in COVID-19 patients.

Assessment of COVID-19 intervention strategies in the Nordic countries using genomic epidemiology

2026-04-28T02:03:10Z

Assessment of COVID-19 intervention strategies in the Nordic countries using genomic epidemiology Duchene, Sebastian; Featherstone, Leo; de Blasio, Birgitte Freiesleben; Holmes, Edward C.; Bohlin, Jon; Pettersson, John H.-O. Abstract The Nordic countries, defined here as Norway, Sweden, Denmark, Finland and Iceland, are known for their comparable demographics and political systems. Since these countries implemented different COVID-19 intervention strategies, they provide a natural laboratory for examining how COVID-19 policies and mitigation strategies affected the propagation, evolution and spread of the SARS-CoV-2 virus. We explored how the duration, the size and number of transmission clusters, defined as country-specific monophyletic groups in a SARS-CoV-2 phylogenetic tree, differed between the Nordic countries. We found that Sweden had the largest number of COVID-19 transmission clusters followed by Denmark, Norway, Finland and Iceland. Moreover, Sweden and Denmark had the largest, and most enduring, transmission clusters followed by Norway, Finland and Iceland. In addition, there was a significant positive association between transmission cluster size and duration, suggesting that the size of transmission clusters could be reduced by rapid and effective contact tracing. Thus, these data indicate that to reduce the general burden of COVID-19 there should be a focus on limiting dense gatherings and their subsequent contacts to keep the number, size and duration of transmission clusters to a minimum. Our results further suggest that although geographical connectivity, population density and openness influence the spread and the size of SARS-CoV-2 transmission clusters, country-specific intervention strategies had the largest single impact.

Binding of a pyrimidine RNA base-mimic to SARS-CoV-2 nonstructural protein 9.

2026-04-23T01:18:25Z

Binding of a pyrimidine RNA base-mimic to SARS-CoV-2 nonstructural protein 9. Littler, Dene R; Mohanty, Biswaranjan; Lowery, Shea A; Colson, Rhys N; Gully, Benjamin S; Perlman, Stanley; Scanlon, Martin J; Rossjohn, Jamie The coronaviral nonstructural protein 9 (Nsp9) is essential for viral replication; it is the primary substrate of Nsp12's pseudokinase domain within the viral replication transcription complex, an association that also recruits other components during different stages of RNA reproduction. In the unmodified state, Nsp9 forms an obligate homodimer via an essential GxxxG protein-interaction motif, but its ssRNA-binding mechanism remains unknown. Using structural biological techniques, here we show that a base-mimicking compound identified from a small molecule fragment screen engages Nsp9 via a tetrameric Pi-Pi stacking interaction that induces the formation of a parallel trimer-of-dimers. This oligomerization mechanism allows an interchange of "latching" N-termini, the charges of which contribute to a series of electropositive channels that suggests a potential interface for viral RNA. The identified pyrrolo-pyrimidine compound may also serve as a potential starting point for the development of compounds seeking to probe Nsp9's role within SARS-CoV-2 replication.

Sars-CoV-2 Genome Sequencing Methods Differ In Their Ability To Detect Variants From Low Viral Load Samples.

2026-04-28T02:07:33Z

Sars-CoV-2 Genome Sequencing Methods Differ In Their Ability To Detect Variants From Low Viral Load Samples. Lam, C.; Gray, K.; Gall, M.; Sadsad, R.; Arnott, A.; Johnson-Mackinnon, J.; Fong, W.; Basile, K.; Kok, J.; Dwyer, D. E.; Sintchenko, V.; Rockett, R.J. SARS-CoV-2 genomic surveillance has been vital in understanding the spread of COVID-19, the emergence of viral escape mutants and variants of concern. However, low viral loads in clinical specimens affect variant calling for phylogenetic analyses and detection of low frequency variants, important in uncovering infection transmission chains. We systematically evaluated three widely adopted SARS-CoV-2 whole genome sequencing methods for their sensitivity, specificity, and ability to reliably detect low frequency variants. Our analyses highlight that the ARTIC v3 protocol consistently displays high sensitivity for generating complete genomes at low viral loads compared with the probe-based Illumina respiratory viral oligo panel, and a pooled long-amplicon method. We show substantial variability in the number and location of low-frequency variants detected using the three methods, highlighting the importance of selecting appropriate methods to obtain high quality sequence data from low viral load samples for public health and genomic surveillance purposes.

Intracardiac Echocardiography for Point-of-Care Guided Left Ventricular Assist Device Implantation: Surgical Implications for COVID-19.

2026-03-16T05:46:13Z

Intracardiac Echocardiography for Point-of-Care Guided Left Ventricular Assist Device Implantation: Surgical Implications for COVID-19. Yastrebov, Konstantin; Brunel, Laurencie; Paterson, Hugh S; Williams, Zoe A; Wise, Innes K; Burrows, Christopher S; Bannon, Paul G Data from animal models is now available to initiate assessment of human safety and feasibility of wide-angle three-dimensional intracardiac echocardiography (3D ICE) to guide point-of-care implantation of percutaneous left ventricular assist devices in critical care settings. Assessment of these combined new technologies could be best achieved within a surgical institution with pre-existing expertise in separate utilization of ICE and Impella.

Risk awareness during operation of analytical flow cytometers and implications throughout the COVID-19 pandemic

2026-04-28T02:04:18Z

Risk awareness during operation of analytical flow cytometers and implications throughout the COVID-19 pandemic Aspland, A.; Chew, C.; Douagi, I.; Galland, T.; Marvin, J.; Monts, J.; Nance, D.; Smith, A.L.; Solga, M. The COVID-19 pandemic has brought biosafety to the forefront of many life sciences. The outbreak has compelled research institutions to re-evaluate biosafety practices and potential at-risk areas within research laboratories and more specifically within Shared Resource Laboratories (SRLs). In flow cytometry facilities, biological safety assessment encompasses known hazards based on the biological sample and associated risk group, as well as potential or unknown hazards, such as aerosol generation and instrument “failure modes.” Cell sorting procedures undergo clearly defined biological safety assessments and adhere to well-established biosafety guidelines that help to protect SRL staff and users against aerosol exposure. Conversely, benchtop analyzers are considered low risk due to their low sample pressure and enclosed fluidic systems, although there is little empirical evidence to support this assumption of low risk. To investigate this, we evaluated several regions on analyzers using the Cyclex-d microsphere assay, a recently established method for cell sorter aerosol containment testing. We found that aerosol and/or droplet hazards were detected on all benchtop analyzers predominantly during operation in “failure modes.” These results indicate that benchtop analytical cytometers present a more complicated set of risks than are commonly appreciated.

Integrated immune dynamics define correlates of COVID-19 severity and antibody responses

2026-04-23T01:18:25Z

Integrated immune dynamics define correlates of COVID-19 severity and antibody responses Koutsakos, Marios; Rowntree, Louise C; Hensen, Luca; Chua, Brendon Y; van de Sandt, Carolien E; Habel, Jennifer R; Zhang, Wuji; Jia, Xiaoxiao; Kedzierski, Lukasz; Ashhurst, Thomas M; Putri, Givanna H; Marsh-Wakefield, Felix; Read, Mark N; Edwards, Davis N; Clemens, E Bridie; Wong, Chinn Yi; Mordant, Francesca L; Juno, Jennifer A; Amanat, Fatima; Audsley, Jennifer; Holmes, Natasha E; Gordon, Claire L; Smibert, Olivia C; Trubiano, Jason A; Hughes, Carly M; Catton, Mike; Denholm, Justin T; Tong, Steven Y C; Doolan, Denise L; Kotsimbos, Tom C; Jackson, David C; Krammer, Florian; Godfrey, Dale I; Chung, Amy W; King, Nicholas J C; Lewin, Sharon R; Wheatley, Adam K; Kent, Stephen J; Subbarao, Kanta; McMahon, James; Thevarajan, Irani; Nguyen, Thi H O; Cheng, Allen C; Kedzierska, Katherine SARS-CoV-2 causes a spectrum of COVID-19 disease, the immunological basis of which remains ill defined. We analyzed 85 SARS-CoV-2-infected individuals at acute and/or convalescent time points, up to 102 days after symptom onset, quantifying 184 immunological parameters. Acute COVID-19 presented with high levels of IL-6, IL-18, and IL-10 and broad activation marked by the upregulation of CD38 on innate and adaptive lymphocytes and myeloid cells. Importantly, activated CXCR3+cTFH1 cells in acute COVID-19 significantly correlate with and predict antibody levels and their avidity at convalescence as well as acute neutralization activity. Strikingly, intensive care unit (ICU) patients with severe COVID-19 display higher levels of soluble IL-6, IL-6R, and IL-18, and hyperactivation of innate, adaptive, and myeloid compartments than patients with moderate disease. Our analyses provide a comprehensive map of longitudinal immunological responses in COVID-19 patients and integrate key cellular pathways of complex immune networks underpinning severe COVID-19, providing important insights into potential biomarkers and immunotherapies.