Simon Mallal

Mutations in human immunodeficiency virus type 1 (HIV-1) enable the virus to evade recognition and killing by human leucocyte antigen (HLA)-restricted T cells. These viral adaptations are specific to the HLA type of individuals and are therefore evident as HLA allele-HIV sequence associations at the population level. Most studies of HLA associations have been cross-sectional and may not capture selective changes that have accumulated to reach fixation at the population level, with potential impacts on viral replication and clinical outcomes. In this study, we examined the population from Western Australia, where HLA-HIV-1 associations were first demonstrated, to determine if ongoing evolution has occurred over more than 30 years of observation.
Cross-sectional HIV-1 subtype B sequences sampled at two time points, early in the epidemic (1992 - 2002, n = 182) and recently (2017 - 2022, n = 119) was utilised to examine HIV-1 evolutionary dynamics overtime. In addition, HIV-1 subtype B viral load records (one measurement per individual) from a five-year period early in the epidemic (1997 - 2002, n = 673) were compared with recent data (2017 - 2022, n = 363) to determine whether any population level HIV-1 adaptation has functional impact.
The analysis identified 120 amino acid positions across the Gag, Pol and Nef genes that showed significant change in proportion over time, with most (100/120; 83.3%) showing an increase in the proportion of one or more of the non-consensus amino acids. Of these positions, 35% (42/120) included one or more amino acids (48; 34 in Pol, 9 in Gag and 5 in Nef) reported as HLA-associated viral adaptations (35/48; 72.9%) or putative compensatory adaptations (11/48, 22.9%). Over two thirds of these adaptations (68.8%; 33/48) increased in proportion over time (range 5.8% to 46%), with eight becoming the consensus sequence. We also observed the accumulation of specific compensatory mutations within epitopes presented by protective HLA alleles. Other accumulated non-consensus amino acid changes (38/120) were predicted to weaken the peptide-HLA binding affinity of known HIV T cell epitopes, suggesting that the previously published list of HLA-associated viral adaptations used in our study was not exhaustive. Only two Pol reverse transcriptase non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance mutations showed a significant change in proportion over time (K256Q [K101Q in reverse transcriptase region]; 22.9%, P-adjusted <0.001 and K258N [K103N in reverse transcriptase region]; 7.7%, P-adjusted = 0.020). Notably, we highlight the significant accumulation of adaptations (Gag: R76K, 40.8%, P-adjusted <0.001; H219Q, 25.8%, P-adjusted = 0.020 and R286K, 24.4%, P-adjusted = 0.036) that confer adaptation to both HLA-restricted T cell immune responses and antiretroviral therapy. There was a significant increase in baseline viral load between the two time periods examined (P ⟨0.001, OR = 2.4).
These findings provide evidence of ongoing HIV-1 adaptation to human immune responses at the population level, with a likely increase in virulence, as captured by viral load. The enrichment of viral adaptations within circulating strains may lead to loss of immune targets for prevalent immune responses and has important implications for vaccine development and cure strategies.

Background
Co-trimoxazole is a leading global cause of severe cutaneous adverse drug reactions (SCAR) including Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN) and drug reaction with eosinophilia and systemic symptoms (DRESS). Co-trimoxazole-induced SCAR are associated with HLA class I alleles including HLA-B*13:01 and HLA-B*38:02 in Southeast Asian (SEA) populations. However, the global generalizability of these associations is unknown but critical for population-appropriate risk stratification and diagnosis.

Objective
To determine HLA risk factors associated with co-trimoxazole-induced SJS/TEN and DRESS in populations from the United States (US) and South Africa (SA).

Methods
We performed high-resolution HLA typing on dermatologist-adjudicated co-trimoxazole-induced SCAR patients in the US (n=63) and SA (n=26) compared to population controls. Peptide binding and docking analyses were performed using MHCcluster2.0 and CB-Dock2.

Results
In a multiple logistic regression model, HLA-B*44:03 (Pc<0.001, OR: 4.08), HLA-B*38:01 (Pc<0.001, OR: 5.66), and HLA-C*04:01 (Pc=0.003, OR: 2.50) were independently associated with co-trimoxazole-induced SJS/TEN in the US. HLA-B* 44:03 was also associated with co-trimoxazole-induced DRESS in SA (Pc=0.019, OR: 10.69). Distinct HLA-B variants with shared peptide binding specificities (SPBS) and HLA-C*04:01 identified 94% and 78% of co-trimoxazole-induced SJS/TEN and DRESS in the US, respectively. The SEA risk allele HLA-B*13:01, with SPBS to HLA-B*44:03, was identified in just 1/63 US SCAR patient.

Conclusion
HLA alleles with SPBS to SEA-related risk alleles including HLA-B*44:03 (SPBS with HLA-B*13:01) and HLA-B*38:01 (SPBS with HLA-B*38:02) but also HLA-C*04:01 predisposed to co-trimoxazole-induced SCAR in the US and SA. These findings provide biological plausibility and strategies for global risk prediction and diagnosis of co-trimoxazole-induced SCAR.

Autoreactive B cell activity defines the earliest detectable stage (Stage 1) of type 1 diabetes (T1D) but is incompletely understood, particularly for B cells reactive against the key T1D autoantigen, insulin. To test whether Stage 1 T1D B cells are transcriptionally rewired compared to healthy individuals, we performed single-cell transcriptional, phenotypic, and immune repertoire profiling of CD19+ cells isolated from the peripheral blood of Stage 1 T1D individuals, identified via Type 1 Diabetes TrialNet as being positive for ≥ 2/5 islet autoantibodies, and healthy controls. Stage 1 T1D memory B cells upregulated n = 122 genes compared to healthy controls, including genes involved in actin cytoskeleton rearrangement, B cell receptor (BCR) signaling, and antigen presentation, and exhibited reduced BCR somatic hypermutation, particularly in atypical-like memory B cells. Clonally expanded B cells in the atypical-like memory subset of Stage 1 T1D individuals exhibited avidity driven insulin-binding specificities, without polyreactivity to HEp-2 cell autoantigens. Insulin-binding B cells showed non-significant upregulation of genes involved in key B cell functions. Our findings highlight transcriptional and BCR-repertoire differences in Stage 1 T1D B cells with potential for optimization as future screening tools to identify rare, autoreactive B cells and biomarkers of T1D progression.

Cytomegalovirus (CMV) establishes lifelong latency and is linked to immunosenescence in older and immunocompromised individuals. We hypothesize that CMV drives systemic and tissue-specific immune changes that may contribute to cardiovascular disease (CVD). Thoracic aorta, blood and perivascular mediastinal adipose tissue from cardiac surgery patients (n = 11) were processed within 30–60 min of excision. CMV IgG titres were quantified through ELISA to determine CMV status: CMV(−) (n = 4) and CMV(+) (n = 7). Immune profiling was performed using flow cytometry and single-cell RNA sequencing. Analyses included MiloR and differential gene expression. Participants (mean age 69.7 ± 8.4 years) were 80% male and 70% Caucasian. CMV(−) and CMV(+) participants had mean IgG titres of 0.038 and 13.55 IU ml−1, respectively. CD8+ T-cells expressing CD57+, GPR56+ and CX3CR1+ (CGC) were increased in the blood of CMV(+) participants. In the aorta of CMV(+) participants, CD8+ T cells and CD4+ T cells had decreased HLA-C expression and suppressed interferon-α pathways. In contrast, the TNF-α signalling pathway was increased. CMV infection shapes immune responses and in this pilot, we observed suppression of interferon-α signalling and increased TNF-α-associated pathways in the aorta. Larger studies are needed to define how CMV-driven immune remodelling contributes to CVD.

This article is part of the discussion meeting issue ‘The indirect effects of cytomegalovirus infection: mechanisms and consequences.’

The COVID-19 pandemic highlighted the critical need for vaccine strategies capable of addressing emerging viral threats. Betacoronaviruses, including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome (MERS), and SARS-CoV-2, present significant pandemic risks due to their zoonotic potential and genetic diversity. T cell-mediated immunity has demonstrated durable responses and strong cross-reactivity, offering a promising avenue for achieving broad immunity within a viral family. In this study, we combined comprehensive epitope mapping with sequence conservation analyses to identify conserved T cell epitope regions (CTERs), which constitute 12% of the complete SARS-CoV-2 proteome. We showed that SARS-CoV-2 CTER-specific T cells cross-reactively recognize sequences from multiple Betacoronavirus subgenera. Importantly, incorporating CTERs from non-spike proteins significantly enhanced T cell cross-reactivity potential and human leukocyte antigen (HLA) coverage compared with T cells targeting only spike proteins. Our findings lay the groundwork for a multi-antigen vaccine strategy that includes non-spike proteins to expand cross-reactive immunity across a broader spectrum of Betacoronaviruses.

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by a progressive loss of motor neurons. Neuroinflammation is apparent in affected tissues, including increased T cell infiltration and activation of microglia, particularly in the spinal cord
. Autoimmune responses are thought to have a key role in ALS pathology, and it is hypothesized that T cells contribute to the rapid loss of neurons during disease progression
. However, until now there has been no reported target for such an autoimmune response. Here we show that ALS is associated with recognition of the C9orf72 antigen, and we map the specific epitopes that are recognized. We show that these responses are mediated by CD4
T cells that preferentially release IL-5 and IL-10, and that IL-10-mediated T cell responses are significantly greater in donors who have a longer predicted survival time. Our results reinforce the previous hypothesis that neuroinflammation has an important role in ALS disease progression, possibly because of a disrupted balance of inflammatory and counter-inflammatory T cell responses
. These findings highlight the potential of therapeutic strategies aimed at enhancing regulatory T cells
, and identify a key target for antigen-specific T cell responses that could enable precision therapeutics in ALS.

Chikungunya virus (CHIKV), a mosquito-borne alphavirus, causes acute febrile illness that can progress into chronic arthritis-like disease (CHIKVD) in humans. CD4
T cells have important functions in CHIKV infection, yet the CHIKV target proteins for these CD4 + T cells are poorly characterized. Here, by stimulating PBMCs collected from individuals with chronic CHIKVD with peptides spanning the entire CHIKV proteome, we provide a comprehensive landscape of CHIKV CD4
T cell epitopes. We identify three immunodominant regions and associated core motifs in CHIKV E1, nsP1 and CP proteins. In addition, by in silico assessment of the sequence conservation of CHIKV proteome with closely related alphaviruses, we define CHIKV epitopes conserved across arthritogenic and encephalitic viruses. Overall, our work describes CD4
T cell targets of CHIKV in humans, thereby assisting in studying the functions of CD4
T cells in CHIKV pathogenesis and vaccine design.

Persistent systemic inflammation is associated with an elevated risk of cardiometabolic diseases. However, the characteristics of the innate and adaptive immune systems in individuals who develop these conditions remain poorly defined. Doublets, or cell-cell complexes, are routinely eliminated from flow cytometric and other immune phenotyping analyses, which limits our understanding of their relationship to disease states. Using well-characterized clinical cohorts, including participants with controlled human immunodeficiency virus (HIV) as a model for chronic inflammation and increased immune cell interactions, we show that circulating CD14+ monocytes complexed to CD3+ T cells are dynamic, biologically relevant, and increased in individuals with diabetes after adjusting for confounding factors. The complexes form functional immune synapses with increased expression of proinflammatory cytokines and greater glucose utilization. Furthermore, in persons with HIV, the CD3+ T cell: CD14+ monocyte complexes had more HIV copies compared to matched CD14+ monocytes or CD4+ T cells alone. Our results demonstrate that circulating CD3+ T-cell: CD14+ monocyte pairs represent dynamic cellular interactions that may contribute to inflammation and cardiometabolic disease pathogenesis. CD3+ T-cell: CD14+ monocyte complexes may originate or be maintained, in part, by chronic viral infections. These findings provide a foundation for future studies investigating mechanisms linking T cell-monocyte cell-cell complexes to developing immune-mediated diseases, including HIV and diabetes.

Developing an effective HIV-1 vaccine is a global health priority, but HIV-1 mutational escape from T cells poses a challenge. While escape from human leukocyte antigen class I (HLA-I)–restricted CD8+ T cells is well characterized, less is known about HLA-II–restricted T cell escape. We used computational methods to identify 149 sites across the HIV-1 clade B genome under HLA-II–associated selection. Functional assays, including activation-induced intracellular cytokine staining and enzyme-linked immunospot for interferon-γ, revealed diverse mechanisms of HIV-1 adaptation to HLA-II–associated immune pressure, ranging from loss to sustained antigen recognition. T cell receptor and RNA sequencing demonstrated variable clonotype overlap of T cell clones to recognize adapted versus non-adapted peptides, with cells targeting adapted peptides exhibiting a dysfunctional transcriptomic state. Moreover, incorporating HLA-II–associated adaptation strengthened the correlation between Gag-specific viral adaptation and poor disease outcomes. Last, we mapped viral regions prone to HLA-II–associated adaptation and found that these adaptations can increase in frequency within populations.