Peter Doherty Institute

Older people mount poorer adaptive immune responses to mRNA vaccines, leaving them more vulnerable to infection with SARS-CoV-2. To design better mRNA vaccines for older people, we need to understand how aging alters mechanisms of adjuvancy that shape immunogenicity. To first define age-related changes in immunogenicity, we vaccinated young (< 5 months old) and aged (> 18 months old) C57BL/6 mice with an mRNA vaccine encoding the SARS-CoV-2 spike protein. Tcell responses were markedly reduced in aged mice at peak and memory timepoints, using intracellular cytokine staining or activation-induced marker assays. Spike and receptor-binding domain binding and neutralizing antibody titers were also markedly reduced in aged mice, consistent with deficits seen in older humans. To define age-related changes in adjuvancy mechanisms, we vaccinated young and aged mice with mRNA vaccines loaded with DiD lipid dye or mScarlet mRNA, then tracked dendritic cell (DC) numbers, phenotype, vaccine uptake, antigen expression, and activation, as well as local and systemic cytokine production. DC numbers in the draining lymph nodes (dLN) were dramatically reduced before and early after vaccination in aged compared to young mice, with delayed recruitment of DCs to the dLN. Vaccine uptake was not impacted by age, but the frequency of DCs expressing antigen increased with age and DC activation decreased with age. Aging accelerated the expression of some cytokines (IL-1α, IL-6), while delaying others (IFNγ, MCP-1) in dLNs and sera. This illustrates that aging impairs multiple adjuvancy mechanisms but mRNA vaccine strategies that address these age-related deficits could improve responses in older people.

Excessive cell death in the epithelium due to prolonged immune activation is associated with intestinal diseases such as Crohn’s disease. Mice with mutations in the Crohn’s disease susceptibility gene Atg16l1 are susceptible to inflammation associated with intestinal epithelial cell (IEC) death, including loss of antimicrobial Paneth cells triggered by infection with murine norovirus (MNV). Here, we show that intestinal disease downstream of MNV depends on IFN-α/β and IFN-λ signaling in IECs. In mouse organoids, IFNs synergize with TNF to induce RIPK1-dependent cell death, amplified by ATG16L1 deficiency. We further show that human intestinal organoids harboring the ATG16L1 risk allele exhibit heightened sensitivity to TNF and IFN co-stimulation and to serum from severe COVID-19 patients. Our findings reveal that virally triggered cytokines including IFNs exacerbate epithelial vulnerability in genetically predisposed hosts.

While organellar genomes are typically a single circular molecule, some have undergone extreme evolutionary changes, such as fragmentation. Among plastid genomes, extensive fragmentation is rare but has been observed in the green alga Boodlea composita (Cladophorales), wherein single-stranded chromosomes adopt an unusual hairpin structure, stabilized by inverted repeats. This plastome is also highly reduced in coding content, containing only 21 protein-coding genes that are highly divergent in sequence, yet the plastome comprises a numerous and heterogeneous chromosome population. The lack of plastomes among close relatives has stymied our understanding of the evolutionary origins of Boodlea's unique plastome characteristics. Here, we report plastomes from three additional Cladophorales families. We show that elevated mutation rates and a massive reduction in coding content preceded fragmentation and that fragmentation resulted in a highly heterogeneous population with hundreds of minicircular chromosomes and a concomitant increase in GC content. Long inverted repeats are absent in minicircular chromosomes, suggesting the repetitive sequences that facilitate the formation of hairpin structures are unique to the Boodlea clade. Codon reassignments also occurred concurrently among fragmented and non-fragmented Cladophorales plastomes. Our findings document a clear stepwise progression of plastid topologies and sequence characteristics in Cladophorales. This assists in our understanding of the evolution of fragmented organellar genomes in general, as well as the limits to coding capacity reduction and sequence divergence able to be withstood by a functioning plastid.

The global spread of viruses highlights the need for timely and effective genomic surveillance to detect new variants and inform rapid public health responses. However, high costs and uneven sequencing capacity hinder equitable global implementation. Surveillance focused on international travelers at major travel hubs has been proposed as a way to complement robust local surveillance, but its potential benefits have not been fully quantified. Here, we develop and calibrate a multiple-strain metapopulation model of global SARS-CoV-2 transmission using extensive epidemiological, phylogenetic, and high-resolution air travel data. Retrospective analyses of the Omicron BA.1/BA.2 emergence and forward simulations for hypothetical novel variants show that targeted enhancement of traveler surveillance at key hubs can shorten variant detection delays, with reduced total surveillance efforts. Practical "non-disruptive" strategies, such as prioritizing a small number of highly connected hubs, consistently outperformed baseline approaches and remained effective across a range of variant transmissibility and vaccine effectiveness scenarios. These results provide a quantitative framework for strengthening global genomic surveillance through targeted, complementary strategies that preserve local capacity while improving preparedness for future pandemics.

Summary The role of the peripheral immune system in Alzheimer’s Disease (AD) remains insufficiently resolved, limiting the understanding of systemic disease effects and mechanisms. Here, we employed three high-resolution single-cell techniques, including flow cytometry, single-cell RNA- and ATAC-sequencing, to investigate peripheral immunity in AD dementia and earlier stages of the AD trajectory in over 100 patients. We identified reduced humoral immune responses in AD, characterized by a diminished B cell compartment displaying an impaired activation phenotype. Classical monocytes expanded in mild cognitive impairment and early AD dementia, acquiring a NF- k B/AP-1-mediated low-grade inflammation phenotype. Our findings link peripheral dysregulation in innate and adaptive immunity at cell frequency, transcriptional and epigenetic levels to the AD trajectory and provide insights into distinct phenotypes that define AD progression in contrast to healthy aging across cohorts.

ObjectivesOur previous study in hospitalised patients infected with avian A(H7N9) influenza virus identified CD84 amongst several genes associated with recovery. Yet, the correlation between CD84 and respiratory viral infection outcomes is far from established. We aimed to define CD84 dynamics in patient cohorts of respiratory disease and immune cell populations in influenza virus‐infected mice.MethodsExpression dynamics of CD84 and association with previously identified correlates of severe and fatal respiratory disease outcomes, OLAH and IL18R1, were analysed in A(H7N9) and COVID‐19 patient cohorts across disease severities. Using mouse models of influenza virus infection, CD84 expression on immune cell subsets was analysed over the course of infection.ResultsElevated CD84 levels in recovered A(H7N9) patients were accompanied by increased expression of genes for CD84‐associated adaptor proteins and other SLAM receptor family members. In these patients, high CD84 expression persisted until discharge, while remaining low throughout the disease in patients that succumbed. We found inverse correlations between CD84 with OLAH and IL18R1 levels in our A(H7N9) cohort, and in hospitalised COVID‐19 patients across respiratory disease severities. In influenza virus‐infected mice, CD84 was upregulated on a broad range of immune cell populations, particularly on activated and influenza virus‐specific T‐cell populations and correlated with less disease severity.ConclusionOur findings revealed the link between high CD84 expression in humans and recovery from respiratory viral infections. In mice, CD84 expression increased across a broad range of immune cell populations, with CD84 expression on activated T‐cell populations correlating with less severe disease.

The Australian Commission on Safety and Quality in Healthcare developed a list of sixteen potentially preventable Hospital-Acquired Complications (HACs) and an algorithm using International Classification of Disease (ICD) codes to detect them. We evaluated this algorithm's performance for diagnosing hospital-onset bloodstream infections (HO-BSI). Administrative records were extracted for episodes of admitted patient care from July 2016 to June 2017 at five Australian principal referral hospitals. We applied the BSI HAC algorithm to each episode, then randomly selected 50 patients deemed positive and negative for HO-BSI at each site. Reviewers blinded to HAC status applied the reference surveillance definition for HO-BSI. The positive predictive value (PPV) and negative predictive value (NPV) for the BSI HAC were calculated. We explored changes to the HAC algorithm to improve these metrics. Overall, 352 917 episodes were included; median (IQR) age was 54 (33-71) years, 49.6 % were female, and 43.8 % were elective admissions. Of these, 2229 (0.6 %) had a HO-BSI according to the HAC algorithm. Among manually reviewed episodes, the PPV for the HAC algorithm was 0.28 (95 % CI, 0.23-0.34) and the NPV was 1.00 (95 % CI, 0.98-1.00). The codes 'Sepsis, unspecified' and 'bacterial sepsis of newborn, unspecified' were both common triggers for HO-BSI HACs (accounting for 35.8 % and 18.4 % of HO-BSIs, respectively) and had poor PPV (0.06 and 0.03, respectively). Removal of these codes from the algorithm increased PPV to 0.53 (0.45-0.62). The HAC algorithm had sub-optimal PPV for HO-BSI. This performance was improved by removing the 'unspecified sepsis' ICD codes.

Human influenza viruses rapidly acquire mutations in their hemagglutinin (HA) protein that erode neutralization by antibodies from prior exposures. Here, we use a sequencing-based assay to measure neutralization titers for 78 recent H3N2 HA strains against a large set of children and adult sera, measuring ~10,000 total titers. There is substantial person-to-person heterogeneity in the titers against different viral strains, both within and across age cohorts. The growth rates of H3N2 strains in the human population in 2023 are highly correlated with the fraction of sera with low titers against each strain. Notably, strain growth rates are less correlated with neutralization titers against pools of human sera, demonstrating the importance of population heterogeneity in shaping viral evolution. Overall, these results suggest that high-throughput neutralization measurements of human sera against many different viral strains can help explain the evolution of human influenza.

The data that supports the findings of this study are available in the supplementary material of this article. Supplementary Table S1. High vs Standard/Other Dosing of Janus kinase Inhibitors. Derived from the “Monthly Index of Medical Specialties”, accessed November 2024. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

The emergence and spread of antimicrobial-resistant organisms is a major global health challenge. We report on the approach and outcomes of a programme which aimed to take a One Health approach, incorporating an understanding that the health of humans, animals and the environment are linked. Combating the Threat of Antimicrobial Resistance in Pacific Island Countries (COMBAT-AMR) was funded by the Australian Department of Foreign Trade and designed to build capacity across human and animal health to address the threat of antimicrobial resistance (AMR) in Fiji, Samoa, Papua New Guinea and the Solomon Islands between 2020 and 2023.Semi-structured interviews were undertaken with implementers, key stakeholders and participants across the programme themes (n=53). Evaluation of specific activities included participant surveys, competency assessments and document reviews.Both the human health and animal health sectors made significant progress in capacity-building and mentoring of local staff and collection and analysis of surveillance data. However, the sectors largely operated in parallel, with limited planning or resources allocated for explicit intersectoral activities. Resources allocated to animal health were also insufficient to compensate for under-resourced animal health sectors in comparison to human health sectors in the target countries.The increasing use of One Health approaches to address AMR necessitates careful consideration of strategies to support intersectoral collaboration at the design and implementation stages. The comprehensive evaluation of the COMBAT-AMR programme contributes to the current evidence base regarding operationalising One Health principles in building capacity in AMR in low- and middle-income countries.