Background The study of non-hospitalised COVID-19 cases provides a context for improved understanding of the immune response to existing and new infections. Population-based cohorts provide a unique opportunity to do this in relation to rich longitudinal pre- and pan-pandemic data. The Avon Longitudinal Study of Parents and Children (ALSPAC) is a prospective population-based cohort study which recruited pregnant women in 1990–1992 and has subsequently followed participants for over 30 years. Methods A study comprising three clinic visits was implemented, in response to the COVID-19 pandemic, amongst ALSPAC participants to measure SARS-CoV-2 specific humoral and cellular responses longitudinally. Here we present data from the first clinic in December 2020 before the start of the UK vaccination campaign and examine associations with a set of exemplar pre- and pan-pandemic health factors. Results We observed humoral and cellular memory immune responses to SARS-CoV-2 infection in mild cases of COVID-19 up to 9 months post-infection. Symptomatic infection elicited a memory immune response of greater magnitude, though there was variation in response in both asymptomatic and symptomatic individuals. We examined health factors associated with severe COVID-19 and found that cardio-metabolomic, respiratory and immune-related health factors associate with a memory immune response of higher magnitude. For example, in older participants (mean age 58 years), higher BMI was associated with an immune memory response of greater magnitude, particularly with anti-S and anti-N binding antibodies. Conclusions We set out to illustrate the use of cohort studies to deliver detailed immunological data and to provide example analyses of how life course health factors can be examined in relation to the immune response following a widespread and novel infection. We expanded this assessment to include longitudinally assessed traits, opening up the potential for the more common use of longitudinal population studies for the better understanding the aetiology of infection outcome.

Viral vaccine development has mostly relied on measuring neutralizing antibody responses to evaluate vaccine immunogenicity. Yet, a compelling body of evidence has now demonstrated that T cell immunity, an integral component of the adaptive immune response, also plays a critical role in controlling acute viral infection. T cell responses however, are not routinely measured in clinical trials to assess vaccine potency. If neutralizing antibody titers were indeed statistically associated with the magnitude of vaccine-induced antigen-specific T cell responses induced by a vaccine, then arguably T cell response could be inferred directly from antibody titers, without the need for independent measurement. To test this assumption, we examined, in a cohort of adult vaccinees, both neutralizing antibody titers and T cell responses induced by the live-attenuated yellow fever vaccine (YF17D). Crucially, we found no correlation between neutralizing antibody titers and the magnitude of antigen-specific T cell responses. Consistent with this observation, transcriptional profiling revealed distinct innate immune signatures that independently correlated with B and T cell immunity, suggesting that dichotomous pathways shape humoral and cellular immune responses separately. Protein-level analysis further supported this dichotomy, showing that discrete cytokine and chemokine profiles were selectively associated with neutralizing antibody production or T cell responses. Our findings suggest that neutralizing antibody titers may not always be a reliable proxy for vaccine-induced T cell response, and highlight the need for the independent measurement of T cell immunity in vaccine studies, particularly for viral infections where the protective role of T cells has been clearly demonstrated.

Dengue is spreading globally, and there is urgent need to define immune correlates of protection for this disease. Dengue infection first occurs in the skin following the bite of an infected mosquito; however, knowledge of host immune responses within this site remains sparse. We investigated the phenotypic, functional, and transcriptional profiles of skin and blood T cells in 73 patients with dengue and 10 healthy volunteers. We show that the skin T cell compartment undergoes marked reshaping and is strongly enriched with proliferating CD4+ and CD8+ T cells compared with the blood of patients. Activated skin CD8+ T cells expressed a core transcriptional signature of tissue-resident memory T (TRM) cells, supporting their differentiation to the TRM cell lineage during infection. The magnitude of skin and blood CD8+ T cell responses were associated with protection from hospitalization in this cohort. These data support a protective role of skin-resident and circulating CD8+ T cells in dengue and warrant evaluation of vaccination strategies inducing skin TRM cells to enhance protective immunity.

Background:The study of non-hospitalised COVID-19 cases provides a context for improved understanding of the immune response to existing and new infections. Population-based cohorts provide a unique opportunity to do this in relation to rich longitudinal pre- and pan-pandemic data. The Avon Longitudinal Study of Parents and Children (ALSPAC) is a prospective population-based cohort study which recruited pregnant women in 1990-1992 and has subsequently followed participants for over 30 years. Methods:A study comprising three clinic visits was implemented, in response to the COVID-19 pandemic, amongst ALSPAC participants to measure SARS-CoV-2 specific humoral and cellular responses longitudinally. Here we present data from the first clinic in December 2020 before the start of the UK vaccination campaign and examine associations with a set of exemplar pre- and pan-pandemic health factors. Results:We observed humoral and cellular memory immune responses to SARS-CoV-2 infection in mild cases of COVID-19 up to 9 months post-infection. Symptomatic infection elicited a memory immune response of greater magnitude, though there was variation in response in both asymptomatic and symptomatic individuals. We examined health factors associated with severe COVID-19 and found that cardio-metabolomic, respiratory and immune-related health factors associate with a memory immune response of higher magnitude. For example, in older participants (mean age 58 years), higher BMI was associated with an immune memory response of greater magnitude, particularly with anti-S and anti-N binding antibodies. Conclusions:We set out to illustrate the use of cohort studies to deliver detailed immunological data and to provide example analyses of how life course health factors can be examined in relation to the immune response following a widespread and novel infection. We expanded this assessment to include longitudinally assessed traits, opening up the potential for the more common use of longitudinal population studies for the better understanding the aetiology of infection outcome.

BACKGROUND:Immunological memory to vaccination and viral infection involves the coordinated action of B and T cells; thus, integrated analysis of these 2 components is critical for understanding their respective contributions to protection against breakthrough infections (BIs) after vaccination. METHODS:We investigated cellular and humoral immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and/or vaccination in 300 adult participants from the Avon Longitudinal Study of Parents and Children (ALSPAC). Participants were grouped by those with (cases) and without (controls) a history of SARS-CoV-2 infection. To provide a quantitative correlate for protection against BI in the 8-month period after the study, Youden index thresholds were calculated for all immune measures analyzed. RESULTS:The magnitude of antibody and T-cell responses following the second vaccine dose was associated with protection against BI in participants with a history of SARS-CoV-2 infection (cases), but not in infection-naive controls. Over 8 months of follow-up, 2 threshold combinations provided the best performance for protection against BI in cases: (i) anti-spike immunoglobulin G (IgG) (≥666.4 binding antibody units [BAU]/mL) combined with anti-nucleocapsid pan-immunoglobulin (pan-Ig) (≥0.1332 BAU/mL) and (ii) spike 1-specific T cells (≥195.6 spot-forming units/106 peripheral blood mononuclear cells) combined with anti-N pan-Ig (≥0.1332 BAU/mL). Both combinations offered 100% specificity for detecting cases without BI, with sensitivities of 83.3% and 72.2%, respectively. CONCLUSIONS:Collectively, these results suggest that hybrid B- and T-cell immunity offers superior protection from BI after coronavirus disease 2019 (COVID-19) vaccination, and this finding has implications for designing next-generation COVID-19 vaccines that are capable of eliciting immunity to a broader repertoire of SARS-CoV-2 proteins.

Dengue is a mosquito-borne virus infection affecting half of the world's population for which therapies are lacking. The role of T and NK-cells in protection/immunopathogenesis remains unclear for dengue. We performed a longitudinal phenotypic, functional and transcriptional analyses of T and NK-cells in 124 dengue patients using flow cytometry and single-cell RNA-sequencing. We show that T/NK-cell signatures early in infection discriminate patients who develop severe dengue (SD) from those who do not. These signatures are exacerbated in patients with overweight/obesity compared to healthy weight patients, supporting their increased susceptibility to SD. In SD, CD4+/CD8+ T-cells and NK-cells display increased co-inhibitory receptor expression and decreased cytotoxic potential compared to non-SD. Using transcriptional and proteomics approaches we show decreased type-I Interferon responses in SD, suggesting defective innate immunity may underlie NK/T-cell dysfunction. We propose that dysfunctional T and NK-cell signatures underpin dengue pathogenesis and may represent novel targets for immunomodulatory therapy in dengue.

Obesity is a risk factor for severe dengue, but underlying mechanisms remain unclear. This study compared clinical features, outcomes, and biomarkers between overweight/obese and healthy-weight patients with dengue infection. We conducted an observational matched cohort study (2019-2022) including 75 overweight/obese patients and 75 matched healthy-weight patients with dengue (by age, sex, illness phase, and inpatient ward). The primary clinical outcome was overall severity per WHO 2009 classification. Secondary outcomes included warning signs, ICU admission, fever clearance, and hospital stay. Laboratory outcomes comprised trajectories of hematology, biochemistry, and endothelial, inflammatory, and lipid biomarkers. The majority of patients were enrolled on day 2-3 of illness, with DENV-2 (63.3%) as the predominant serotype and secondary infections in 93.4%. Clinical signs and symptoms at enrolment and severe dengue development (6.3% vs. 9.2%) were comparable between groups. However, the overweight/obese group developed fluid accumulation more frequently (64.1% vs. 41.5%). Laboratory profiles showed consistently higher leukocyte (∼0.55-1 K/μL), neutrophil (∼0.19-0.84 K/μL), and lymphocyte counts (∼0.04-0.28 K/μL), total cholesterol (∼0.39-0.46 mmol/L), low-density lipoprotein cholesterol (∼0.36-0.48 mmol/L), triglycerides (∼0.21-0.44 log2-mmol/L), C-reactive protein (∼0.21-0.43 log10-mg/L), ferritin (∼0.12-0.15 log10-ng/mL), and leptin (∼0.89-1 log10-ng/mL) in the overweight/obese group, alongside lower high-density lipoprotein cholesterol (∼0.06-0.23 mmol/L) and adiponectin (∼0.05-0.24 log10-ng/mL). Liver transaminases were initially higher (days 1-5) in the overweight/obese group. Overweight/obese patients with dengue infection display distinct clinical and immunometabolic profiles, particularly greater fluid accumulation, higher inflammatory markers and liver injury. These findings suggest obesity modifies the host response to dengue, and this patient group should be prioritized for upcoming immunomodulatory and other host-directed therapeutic trials. Dengue is a major global health problem, and people with obesity appear to have a higher risk of developing severe disease. However, the reasons for this increased vulnerability are still poorly understood. In this study, we compared 75 overweight or obese patients with dengue to 75 patients of healthy weight who were carefully matched by age, sex, disease stage, and hospital ward. Although both groups had similar symptoms at enrollment and similar rates of severe dengue, the overweight/obese group developed fluid accumulation more often-a key sign of clinical deterioration. They also showed distinct laboratory patterns throughout their illness. Overweight/obese patients consistently had higher levels of white blood cells, inflammatory markers, liver enzymes, and lipid measures, as well as higher leptin and lower adiponectin, two hormones linked to metabolic health. These findings suggest that excess body weight alters the body’s immune and metabolic response to dengue infection, even when outward symptoms appear comparable. Understanding these differences is important because it can help clinicians identify patients at higher risk and guide the development of new treatments. Our results support prioritizing overweight and obese individuals for future trials of immunomodulatory or other host-directed therapies for dengue.

The dynamic functioning of immune cells is regulated by cellular metabolic processes, and there is growing interest in the study of immunometabolic correlates of dysfunctional immune responses. SCENITH is a novel flow cytometry-based technique that allows for ex vivo metabolic profiling of immune cells within heterogeneous samples. Cryopreservation of clinical samples is frequently undertaken to facilitate high throughput processing and longitudinal analyses of immune responses, but is thought to lead to cellular metabolic dysfunction. We aimed to investigate the impact of cryopreservation on immune cell metabolism, harnessing SCENITH's unique ability to describe the divergent bioenergetic characteristics of distinct immune cell subsets. We demonstrate that upon activation, T cells are unable to sufficiently/readily undergo metabolic reprogramming. Additionally, we find that cryopreservation introduces a time-dependent metabolic artefact that favours glycolysis and impairs oxidative phosphorylation, suggesting that cryopreservation results in mitochondrial dysfunction. Despite this artefact, SCENITH was still able to reveal the distinct bioenergetic profiles of contrasting immune cells populations following cryopreservation. Whilst SCENITH can provide valuable information about immune cell metabolism even in cryopreserved samples, our findings have important implications for the design of future studies. Investigators should carefully consider how to process and store clinical samples to ensure that cryopreservation does not confound analyses, particularly where longitudinal sampling is required.

Immunological memory to vaccination and viral infection involves coordinated action of B and T-cells, thus integrated analysis of these two components is critical for understanding their contributions to protection against breakthrough infections (BI). We investigated cellular and humoral immune responses to SARS-CoV-2 infection and/or COVID-19 vaccination in participants from the Avon Longitudinal Study of Parents and Children (ALSPAC). The magnitude of antibody and T-cell responses following the second vaccine dose was associated with protection against BI in participants with a history of SARS-CoV-2 infection (cases), but not in infection-naive controls. Youdens index thresholds for protection against BI were calculated for all immune measures. Anti-Spike IgG (>666.4 BAU/mL) and anti-nucleocapsid N pan Ig (>0.1332 BAU/mL) thresholds combined were 100% sensitive and 83% specific for cases without BI over 8-months follow-up. Collectively these results point to the superior protective effect of hybrid immunity and have implications for the design of next-generation COVID-19 vaccines. ### Competing Interest Statement AF was a lead investigator on trials of COVID-19 vaccines funded by Oxford/Astra-Zeneca, Valneva and Sanofi and the UK government. He also leads a University of Bristol sponsored epidemiological study of adult respiratory disease funded by Pfizer which has evaluated COVID-19 vaccine effectiveness. During the pandemic he was a member of the Joint Committee on Vaccination and Immunisation which advised the UK government on COVID-19 vaccine policy and of the WHO Specialist Advisory Group of Experts COVID-19 vaccine working group. No other authors declare competing interests. ### Funding Statement This work was funded by UK Research and Innovation (UKRI) and the National Institute of Health Research (NIHR) through the UK COVID-19 Immunology Consortium (UK CIC). This work was supported by the Elizabeth Blackwell Institute, University of Bristol, with funding from the Wellcome Trust ISSF3 grant 204813/Z/16/Z, and the University Alumni and Friends (LW, LR, AH, AD, AF and OF). NJT is the PI of the Avon Longitudinal Study of Parents and Children (MRC & WT 217065/Z/19/Z), is supported by the University of Bristol NIHR Biomedical Research Centre (BRC-1215-2001), the MRC Integrative Epidemiology Unit (MC\_UU\_00011/1) and works within the CRUK Integrative Cancer Epidemiology Programme (C18281/A29019). MK is supported by the Medical Research Council (MR/W021315/1). MS is supported by the Academy of Medical Sciences (Springboard Award SB007\100173). The UK Medical Research Council and the Wellcome Trust (Grant ref: 217065/Z/19/Z) and the University of Bristol provide core support for ALSPAC. This publication is the work of the authors; LR, AH, LW, HEB and MS will serve as guarantors for the contents of this paper. A comprehensive list of grant funding is available on the ALSPAC website (http://www.bristol.ac.uk/alspac/external/documents/grant-acknowledgements.pdf). This research was specifically funded by Wellcome Trust and MRC grant 102215/2/13/2. The funders had no role in the study design, data collection, data analysis nor preparation of the manuscript or decision to publish. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The ALSPAC Ethics and Law Committee at the University of Bristol gave ethical approval for this work (NHS REC 20/HRA/4854). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors.

Introduction:Dengue virus infection is a global health problem lacking specific therapy, requiring an improved understanding of DENV immunity and vaccine responses. Considering the recent emerging of new dengue vaccines, here we performed an integrative systems vaccinology characterization of molecular signatures triggered by the natural DENV infection (NDI) and attenuated dengue virus infection models (DVTs).Methods and results:We analyzed 955 samples of transcriptomic datasets of patients with NDI and attenuated dengue virus infection trials (DVT1, DVT2, and DVT3) using a systems vaccinology approach. Differential expression analysis identified 237 common differentially expressed genes (DEGs) between DVTs and NDI. Among them, 28 and 60 DEGs were up or downregulated by dengue vaccination during DVT2 and DVT3, respectively, with 20 DEGs intersecting across all three DVTs. Enriched biological processes of these genes included type I/II interferon signaling, cytokine regulation, apoptosis, and T-cell differentiation. Principal component analysis based on 20 common DEGs (overlapping between DVTs and our NDI validation dataset) distinguished dengue patients by disease severity, particularly in the late acute phase. Machine learning analysis ranked the ten most critical predictors of disease severity in NDI, crucial for the anti-viral immune response.Conclusion:This work provides insights into the NDI and vaccine-induced overlapping immune response and suggests molecular markers (e.g., IFIT5, ISG15, and HERC5) for anti-dengue-specific therapies and effective vaccination development.

BACKGROUND:Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can lead to severe disease with increased morbidity and mortality among certain risk groups. The presence of autoantibodies against type I interferons (aIFN-Abs) is one mechanism that contributes to severe coronavirus disease 2019 (COVID-19). METHODS:This study aimed to investigate the presence of aIFN-Abs in relation to the soluble proteome, circulating immune cell numbers, and cellular phenotypes, as well as development of adaptive immunity. RESULTS:aIFN-Abs were more prevalent in critical compared to severe COVID-19 but largely absent in the other viral and bacterial infections studied here. The antibody and T-cell response to SARS-CoV-2 remained largely unaffected by the presence aIFN-Abs. Similarly, the inflammatory response in COVID-19 was comparable in individuals with and without aIFN-Abs. Instead, presence of aIFN-Abs had an impact on cellular immune system composition and skewing of cellular immune pathways. CONCLUSIONS:Our data suggest that aIFN-Abs do not significantly influence development of adaptive immunity but covary with alterations in immune cell numbers.

Coronavirus disease-19 (COVID-19) causes immune perturbations which may persist long term, and patients frequently report ongoing symptoms for months after recovery. We assessed immune activation at 3–12 months post hospital admission in 187 samples from 63 patients with mild, moderate, or severe disease and investigated whether it associates with long COVID. At 3 months, patients with severe disease displayed persistent activation of CD4+ and CD8+ T-cells, based on expression of HLA-DR, CD38, Ki67, and granzyme B, and elevated plasma levels of interleukin-4 (IL-4), IL-7, IL-17, and tumor necrosis factor-alpha (TNF-α) compared to mild and/or moderate patients. Plasma from severe patients at 3 months caused T-cells from healthy donors to upregulate IL-15Rα, suggesting that plasma factors in severe patients may increase T-cell responsiveness to IL-15-driven bystander activation. Patients with severe disease reported a higher number of long COVID symptoms which did not however correlate with cellular immune activation/pro-inflammatory cytokines after adjusting for age, sex, and disease severity. Our data suggests that long COVID and persistent immune activation may correlate independently with severe disease.

Some T cells that have been activated by a herpesvirus can also respond to SARS-CoV-2, even if the original herpesvirus infection happened before the COVID-19 pandemic.

COVID-19 causes immune perturbations which may persist long-term, and patients frequently report ongoing symptoms for months after recovery. We assessed the extent and nature of immune activation at 3 months post hospital admission in patients with mild, moderate or severe COVID-19 and investigated whether immune activation associates with disease severity and long COVID. Patients with severe disease displayed persistent activation of CD4+ and CD8+ T-cells, based on expression of HLA-DR, CD38, Ki67 and granzyme B, but they lacked activation of other immune subsets. Elevated plasma levels of IL-4, IL-7, IL- 17 and TNF- were present in patients with severe compared to mild and/or moderate disease. Plasma from severe patients caused T-cells from healthy donors to upregulate IL-15R, suggesting that factors in the plasma of severe patients may increase T-cell responsiveness to IL-15-driven bystander" activation, which may drive persistent T-cell activation after severe COVID-19. Patients with severe disease reported a higher number of long COVID symptoms which correlated with the frequency of two subsets of activated CD4+ and CD8+ T cells (CD4+ T-cell population 2 and CD8+ T-cell population 4; FDR p<0.05), however these associations were lost after adjusting for age, sex and disease severity. Our data suggests that persistent immune activation and long COVID correlate independently with severe disease.

Low-volume antibody assays can be used to track SARS-CoV-2 infection rates in settings where active testing for virus is limited and remote sampling is optimal. We developed 12 ELISAs detecting total or antibody isotypes to SARS-CoV-2 nucleocapsid, spike protein or its receptor binding domain (RBD), 3 anti-RBD isotype specific luciferase immunoprecipitation system (LIPS) assays and a novel Spike-RBD bridging LIPS total-antibody assay. We utilized pre-pandemic (n=984) and confirmed/suspected recent COVID-19 sera taken pre-vaccination rollout in 2020 (n=269). Assays measuring total antibody discriminated best between pre-pandemic and COVID-19 sera and were selected for diagnostic evaluation. In the blind evaluation, two of these assays (Spike Pan ELISA and Spike-RBD Bridging LIPS assay) demonstrated >97% specificity and >92% sensitivity for samples from COVID-19 patients taken >21 days post symptom onset or PCR test. These assays offered better sensitivity for the detection of COVID-19 cases than a commercial assay which requires 100-fold larger serum volumes. This study demonstrates that low-volume in-house antibody assays can provide good diagnostic performance, and highlights the importance of using well-characterized samples and controls for all stages of assay development and evaluation. These cost-effective assays may be particularly useful for seroprevalence studies in low and middle-income countries.

Neutrophils are vital in defence against pathogens but excessive neutrophil activity can lead to tissue damage and promote acute respiratory distress syndrome (ARDS). COVID-19 is associated with systemic expansion of immature neutrophils but the functional consequences of this shift to immaturity are not understood. We used flow cytometry to investigate activity and phenotypic diversity of circulating neutrophils in COVID-19. First, we demonstrate hyperactivation of immature CD10- subpopulations in severe disease, with elevated degranulation of secondary granule markers. Partially activated immature neutrophils are detectable three months post symptom onset, indication long term myeloid dysregulation in convalescent COVID-19 patients. Second, we demonstrate that neutrophils from moderately ill patients downregulate the chemokine receptor CXCR2, while neutrophils from severely ill individuals failed to do so, suggesting altered ability for organ trafficking. CD10- and CXCR2hi neutrophil subpopulations were enriched in severe disease and may represent biomarkers for early identification of individuals at high risk of progressing to severe COVID-19.

Abstract Background Severe dengue, characterized by shock and organ dysfunction, is driven by an excessive host immune response. We investigated the role of hyperinflammation in dengue pathogenesis. Methods Patients recruited into an observational study were divided into 3 plasma leak severity grades. Hyperinflammatory biomarkers were measured at 4 time points. Frequencies, activation, and cytotoxic potential of natural killer (NK) cells were analyzed by flow cytometry. RNA was extracted from sorted CD56+ NK cells and libraries were prepared using SMART-Seq and sequenced using HiSeq3000 (Illumina). Results Sixty-nine patients were included (grade 0, 42 patients; grade 1, 19 patients; grade 2, 8 patients). Patients with grade 2 leakage had higher biomarkers than grade 0, including higher peak ferritin levels (83.3% vs 45.2%) and H-scores (median, 148.5 vs 105.5). NK cells from grade 2 patients exhibited decreased expression of perforin and granzyme B and activation markers. RNA sequencing revealed 3 single-nucleotide polymorphisms in NK cell functional genes associated with more severe leakage—NK cell lectin-like receptor K1 gene (KLRK1) and perforin 1 (PRF1). Conclusions Features of hyperinflammation are associated with dengue severity, including higher biomarkers, impaired NK cell function, and polymorphisms in NK cell cytolytic function genes (KLRK1 and PRF1). Trials of immunomodulatory therapy in these patients is now warranted.

Severe COVID-19 is associated with alterations to the neutrophil compartment with circulating hyperactive immature neutrophils and a maintenance of CXCR2 expression. Neutrophils are vital in defence against pathogens, but excessive neutrophil activity can lead to tissue damage and promote acute respiratory distress syndrome. COVID-19 is associated with systemic expansion of immature neutrophils, but the functional consequences of this shift to immaturity are not understood. We used flow cytometry to investigate activity and phenotypic diversity of circulating neutrophils in acute and convalescent COVID-19 patients. First, we demonstrate hyperactivation of immature CD10 − subpopulations in severe disease, with elevated markers of secondary granule release. Partially activated immature neutrophils were detectable 12 wk post-hospitalisation, indicating long term myeloid dysregulation in convalescent COVID-19 patients. Second, we demonstrate that neutrophils from moderately ill patients down-regulate the chemokine receptor CXCR2, whereas neutrophils from severely ill individuals fail to do so, suggesting an altered ability for organ trafficking and a potential mechanism for induction of disease tolerance. CD10 − and CXCR2 hi neutrophil subpopulations were enriched in severe disease and may represent prognostic biomarkers for the identification of individuals at high risk of progressing to severe COVID-19.

Abstract Dengue virus (DENV) infection is a global health problem with no specific therapy or vaccine currently available to combat it. Here we performed a comprehensive analysis of publicly available transcriptome data of patients with natural DENV infection (NDI) and DENV vaccine trials (DVT1, DVT2, and DVT3), identifying common transcriptional signatures according to the time of infection in NDI and DVTs, and disease severity in NDI. We identified 237 common differentially expressed genes (DEGs) between NDI and DVT1. Of those, 20 were commonly affected by dengue vaccination during DVT2 and DVT3. Machine learn analysis ranked the 10 NDI's most critical predictors for disease severity, e.g., IFIT5, ISG15, and HERC5, which play an essential role in the anti-viral immune response. Hence, this work provides new insight into the NDI and vaccine-induced overlapping immune response and suggests novel targets for developing anti-dengue-specific therapies and monitoring the effectiveness of vaccination.