Herpes Simplex Virus 1 (HSV-1) is a neurotropic virus causing encephalitis and post-infectious complications. Infections can induce a range of acute, subacute, and progressing brain disease, and in recent years it has emerged that immune responses are involved in the pathogenesis of these diseases.

Mice were infected with HSV-1 through corneal infection, and the brain stem was analyzed using single-cell and GeoMx spatial transcriptomics. Through these technologies we profiled temporal transcriptomic changes in cell populations, pathways, and cell-cell communication associated with antiviral activity and inflammation-induced disturbance of physiological brain structures and activities.

We found that microglia proportions increased early after HSV-1 infection, followed by monocyte influx and later by T cells. The blood-brain barrier was disrupted, and transcriptomic profiles associated with homeostatic brain transcriptional activities were altered. Early transcriptional responses were dominated by antiviral and inflammatory activities. A microglia subpopulation with high type I interferon and chemokine expression localized to infection sites, likely mediating antiviral defense and immune recruitment. Monocyte subpopulations displayed a broader activation profile than microglia and was a central mediator of crosstalk between immune cells. Cytokines from microglia, monocytes, and T cells reprogrammed brain cells, notably endothelial cells and oligodendrocytes, disrupting brain functions. Comparing datasets from various brain diseases revealed the identified microglia subpopulation as specific to viral infections.

This study identifies a unique population of virus-activated microglia with antiviral and proinflammatory properties and reveals monocytes to be a key driver of interactions driving pathology in the virus-infected brain.

Chronic HBV infection is a major risk factor for hepatocellular carcinoma, posing a significant global health burden. However, predictive models for HBV clearance based on immune biomarkers remain limited.

We systematically developed a predictive tool by quantifying mRNA expression levels of CD4⁺ T-cell subset transcription factors, cytokines, and immune checkpoints in PBMCs from chronic HBV patients and resolved HBV individuals using RT-qPCR. A binary logistic regression model was constructed in the training cohort, with performance evaluated by ROC and calibration curves, followed by internal and external validation in independent cohorts. For in vivo validation, an HBV-transfected mouse model was established via rapid tail vein injection of pGL3-CP-Fluc-HBV1.2C2 plasmid. Outcomes included body weight, HBsAg/HBV DNA levels, and luciferase activity. Kaplan-Meier analysis assessed cumulative clearance rates, while RT-qPCR tracked model-related mRNA dynamics in PBMCs.

The model identified GATA3, FOXP3, IFNG, TNF, and HAVCR2 as key genes, demonstrating robust predictive accuracy for HBV clearance. Dose-specific temporal patterns of immune gene regulation were observed, revealing distinct immunomodulatory mechanisms between groups.

This study establishes a reliable immune-based predictive model for HBV clearance and highlights divergent immune responses in chronic versus resolved infection.

Intramuscular injection of seasonal influenza vaccines provides strain-specific neutralizing antibodies, but not against variants, and no effective mucosal immunity. Here, we report that multi-subtype neuraminidase (NA) and M2 ectodomain repeat (5xM2e) virus-like particle vaccine (NA-M2e) conferred higher efficacy of broad cross-protection after two doses of intranasal delivery than intramuscular injection. The intranasally vaccinated mice displayed high levels of IgA antibodies, IFN-γ+ CD4 and CD8 T cells, germinal center B cells, plasma cells, and early innate immune cells locally in the lungs. In contrast, intramuscular vaccination systemically induced innate and adaptive immune responses in the spleen. Our findings demonstrate that the intranasal delivery of NA-M2e vaccine induces enhanced mucosal immunity and comparable serum IgG antibodies, offering improved efficacy of cross-protection against diverse influenza virus strains compared to the intramuscular injection in a mouse model.

This study investigates the infectivity of SARS-CoV-2 and its immune evasion mechanisms, particularly through mutations in the spike protein that enable the virus to escape host immune responses. As global vaccination efforts continue, understanding viral evolution and immune evasion strategies remains critical. This analysis focuses on fourteen key mutations (Arg346Lys, Lys417Asp, Leu452Glu, Leu452Arg, Phe456Leu, Ser477Asp, Thr478Lys, Glu484Ala, Glu484Lys, Glu484Gln, Gln493Arg, Gly496Ser, Glu498Arg, and His655Y) within the receptor-binding domain (RBD) of the spike protein. The results reveal consistent patterns of immune escape across various SARS-CoV-2 variants, with specific mutations influencing protein stability, binding affinity to the hACE2 receptor, and antibody recognition. These findings demonstrate how single-point mutations can destabilize the spike protein and reduce the efficacy of the immune response. By correlating expression levels and thermodynamic stability with immune evasion, this study provides valuable insights into the functional characteristics of the spike protein. The findings contribute to the understanding of immune escape variants and identify potential targets for enhancing vaccine efficacy and developing therapeutic approaches in response to the evolving SARS-CoV-2 landscape. SHORT SUMMARY: The study investigates the infectivity of SARS-CoV-2 and its implications for immune evasion. It focuses on fourteen key mutations within the spike protein's Receptor-Binding Domain (S-RBD) and reveals consistent patterns associated with immune escape in various SARS-CoV-2 variants. The research highlights the influence of factors such as protein fold stability, hACE2 binding, and antibody evasion on spike protein evolution. Single-point immune escape variants alter virus stability, impacting antibody response success. The study provides valuable insights into immune escape variants and suggests avenues for enhancing vaccine efficacy. It also opens the way for novel therapeutic approaches in the context of SARS-CoV-2 variants.

The spike glycoprotein is a key factor in the infection cycle of SARS-CoV-2, as it mediates both receptor recognition and membrane fusion by the virus. Therefore, in this study, we aimed to design a multi-peptide conjugate vaccine against SARS-CoV-2, targeting the early stages of the virus's life cycle. We used iBoost technology, which is designed to induce immune responses against low- or non-immunogenic epitopes. We selected six peptide sequences, each representing a key domain of the spike protein (i.e., receptor binding domain (RBM), subdomain 1 (SD1), subdomain 2 (SD2), S1/S2, fusion peptide and the S2' sequences (FP + S2'), heptad repeat 1 (HR1)). Immunization studies in mice displayed targeted humoral and cellular immune responses against specific peptides of the spike protein simultaneously, while inducing cross-protection against the Delta and Omicron coronavirus variants. Moreover, vaccinated hamsters challenged with SARS-CoV-2 elicited high antibody levels against key peptides, induced early neutralizing antibody responses and resulted in less weight loss compared to controls. This highlights the potential for improving viral control and disease outcomes when utilizing this strategy. Therefore, by using iBoost technology in conjunction with our peptide design strategy, we were able to successfully target non-immunodominant regions in the spike protein while activating both arms of the adaptive immune system.

Overt immune activation by viral infections can lead to cytokine storm syndromes, such as hemophagocytic lymphohistiocytosis (HLH) and macrophage activation syndrome (MAS).

We aimed to compare the immune response to different viral pathogens to understand the connection between infections and cytokine storm syndromes.

We recruited children who sought care at the emergency department with fever for ≥3 days. We performed immune profiling using Olink proximity extension assay and flow cytometry. We compared the findings with cases of HLH, MAS, Kawasaki disease (KD), and multisystem inflammatory syndrome in children (MIS-C).

We enrolled 352 febrile patients and studied 110 cases of confirmed common viral infections. We found that Epstein-Barr virus (EBV) uniquely triggered high levels of multiple cytokines (IL-18, IL-27, TNF, FLT3 ligand, and lymphotoxin alpha) and IFN-γ-induced chemokines (CXCL9/10/11 and CCL19). These patterns are similar to the hyperinflammatory response associated with HLH/MAS but are less consistent with the findings in KD and MIS-C. Flow cytometry analysis revealed that CD38+HLA-DR+ T lymphocytes, which are pathogenic cells responsible for IFN-γ production in HLH/MAS, are vastly expanded in patients with acute EBV infection. Cell sorting identified CD38+HLA-DR+ T cells as atypical lymphocytes that are classically associated with acute EBV infection.

This work broadens our understanding of common viral infections in children and provides an immunologic basis for the link between EBV infection and HLH/MAS.

The study aims to assess baseline immune parameters that predict infection risk in autoimmune rheumatic disease (ARD) patients, with the goal of identifying high-risk individuals requiring immunosuppressive therapy escalation, based on infection rates during a one-year follow-up.

The independent cohort study was conducted at a tertiary rheumatology center in India from December 2019 to March 2022. It included adult participants with ARDs undergoing immunosuppression. Ethics approval and informed consent were obtained. Patients underwent detailed history, clinical examination, and baseline investigations, which included complete hemogram, inflammatory parameters, immunoglobulin levels, cellular levels of the immune system, complement levels, and viral markers. Descriptive statistics, ANOVA, chi-squared tests, t-tests, and Fisher's exact tests were used. OLS regression analyses identified significant predictors of infection risk. They were followed up for a period of 1 year for any infection episodes.

Of the 106 participants recruited, 4 were excluded due to disease-related complications during the 3-month period of follow-up. The mean age of the participants was 38.21 ± 12.73 years, with an average follow-up duration of 13.1 ± 8.35 months. Among the remaining 102 participants, younger age was associated with a lower infection risk (OR 1.047). Protective factors against infection included lower levels of immunoglobulin E (IgE) (OR 0.379), methotrexate (MTX) use (OR 0.247), and biologics (OR 0.543). Conversely, lower Immunoglobulin G (IgG), elevated neutrophil counts (OR 3.588), higher neutrophil-to-lymphocyte ratios (NLR) (OR 2.577), low platelet counts (OR 0.546), and steroid use, which increased the risk fivefold (OR 5.686), were identified as risk factors. Ordinary Least Squares (OLS) regression analysis highlighted age, IgG levels, CD19 lymphocyte counts, WBC counts, and ESR as significant predictors of infection risk between the groups.

Older age, low IgG, low B cell count (CD19) predict susceptibility to infections; high neutrophil counts, low platelets, and elevated NLR are key predictors of developing infection in ARDs patients. Careful monitoring and tailored treatment strategies are essential to reduce infection risks. Further research is needed in this direction to develop predictive algorithms.

Allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients are severely immunocompromised and susceptible to bacterial, viral, and fungal infections. Despite improved anti-microbial prophylaxis and preemptive strategies, bacterial bloodstream infections (BSIs) occur frequently in allo-HSCT recipients and are associated with increased morbidity and mortality. Cytomegalovirus (CMV) and Epstein Barr virus (EBV) are the most relevant viruses following allo-HSCT and remain major concerns. Fungal infections, including those caused by Candida and Aspergillus species, are persistent and feared complications.

We aim to provide clinicians caring for allo-HSCT recipients with a comprehensive overview of the risk factors that predispose patients to common bacterial, fungal, and viral infections during the first years post-transplant. The focus is on the value of noninvasive diagnostic biomarkers and serological assays in enhancing the early detection and management of these infections.

Effective management of infectious complications following allo-HSCT relies on continuous immune recovery monitoring and the implementation of advanced diagnostic methods. Utilizing noninvasive diagnostic methods is crucial for early detection and different intervention strategies. The development and integration of reliable microbiological markers into clinical practice is essential for enhancing patient outcomes and mitigating infection-related risks. Emphasizing diagnostic innovation will be pivotal in advancing patient care post-allo-HSCT.

The discovery of long non-coding RNAs (lncRNAs) has provided a new perspective on the centrality of RNA in gene regulation and genome organization. Here, we screened for lncRNAs with putative functions in the host response to single-stranded RNA respiratory viruses. We identify CARINH as a conserved cis-acting lncRNA up-regulated in three respiratory diseases to control the expression of its antisense gene IRF1, a key transcriptional regulator of the antiviral response. CARINH and IRF1 are coordinately increased in the circulation of patients infected with human metapneumovirus, influenza A virus, or SARS-CoV-2, and in macrophages in response to viral infection or TLR3 agonist treatment. Targeted depletion of CARINH or its mouse ortholog Carinh in macrophages reduces the expression of IRF1/Irf1 and their associated target gene networks, increasing susceptibility to viral infection. Accordingly, CRISPR-mediated deletion of Carinh in mice reduces antiviral immunity, increasing viral burden upon sublethal challenge with influenza A virus. Together, these findings identify a conserved role of lncRNA CARINH in coordinating interferon-stimulated genes and antiviral immune responses.

Vesiculovirus carajas (CARV) is a pathogen with neuroinvasive potential, yet its impact on neuroinflammation and sickness behavior remains poorly understood. In this study, we investigated the neuropathological and immunological responses to CARV encephalitis in adult BALB/c mice. Mice were intranasally inoculated with either infected or uninfected brain homogenates, and clinical, histopathological, and cytokine profiles were analyzed. CARV antigens were primarily detected in necrotic neurons, with prominent microglial activation near the ventricles and blood vessels. By day 10 post-infection, infected mice exhibited significantly elevated levels of MCP-1, IFN-γ, IL-12 p70, TNF-α, IL-6, and IL-10 in the brain, indicating a strong inflammatory response. These findings highlight the inflammatory modulation associated with CARV infection and suggest a hematogenous route of neuroinvasion, distinguishing CARV from other vesiculovirus species. This study provides new insights into the pathogenesis of CARV encephalitis and its potential impact on neuroimmune dynamics.

(1) Background: We aimed to analyze the epidemiological characteristics of hemorrhagic fever with renal syndrome (HFRS) in Longyou County and to provide a basis for the future response to this disease. (2) Methods: Data on hemorrhagic fever and host animals were collected from 2011 to 2023. Descriptive methods were used to analyze the epidemic. The R4.4.1 software was used to show how the host density relates to the virus levels, temperature, and rainfall and to predict the host density. (3) Results: We observed 58 cases of hemorrhagic fever, the majority of which occurred in farmers. There were two incidence peaks each year during the spring and winter seasons, accounting for 22.41% and 43.10% of the total cases, respectively. The outdoor rodent population density was significantly and positively correlated with the outdoor rodent virus prevalence (R2 = 0.9411), serving as a robust predictor of the outdoor rodent virus prevalence. Additionally, the density of outdoor rodents exhibited a strong nonlinear relationship with the temperature and precipitation. (4) Conclusions: After hemorrhagic fever vaccination, rodent population density control, and rodent carrier rodent control from 1995 to 2000, the hemorrhagic fever epidemic was generally stable, and the epidemiological characteristics remained stable. In the future, we should continue to take active and effective comprehensive measures to intervene, further realize the effective control of HFRS, and prevent the recurrence of hemorrhagic fever epidemics.

The replication and mortality caused by the viral hemorrhagic septicemia virus (VHSV) in fish vary depending on temperature. VHSV causes mortality at the temperatures below 15 °C, while infection is not established in olive flounder at temperatures above 25 °C. However, how VHSV infection manifests at the cellular level under different temperature conditions is not understood. In this study, we aimed to elucidate the mechanism by which VHSV infection is controlled by comparing viral replication and immune responses in vitro and in vivo. In the in vitro experiment, viral mRNA levels on day 5 post-challenge differed more than 10-fold between temperatures, highest at 15 °C, followed by 20 °C, and lowest at 25 °C, with replication gradually increasing over 5 days. In vivo, replication peaked by day 2 and then declined at all temperatures. VHSV infection showed a controlled tendency in the fish, whereas the virus exhibited a continuously increasing infection pattern for up to 5 days in olive flounder spleen cell cultures at a temperature of 25 °C. The level of viral infection within the cells (25 °C) was lower compared to conditions below 20 °C; however, the expression levels of interferon-related genes and pro-inflammatory cytokine genes were relatively low. The expression of ISG15 and Mx genes in spleen (25 °C) was significantly high at 24 h post challenge in the in vivo experiment.

Tumor necrosis factor-alpha (TNF-α) is a pleiotropic cytokine with critical roles in inflammation, cell survival, and defense. As a member of the TNF superfamily, it exerts its effects by binding to transmembrane receptors and triggering various downstream signaling pathways. Although TNF-α's involvement in antiviral responses in mammals is well-established, its role in teleost remains poorly understood. This study investigated the contribution of TNF-α1 to antiviral immunity in zebrafish using a tnf-α1(-/-) knockout (KO) line. We challenged both wild-type and tnf-α1(-/-) zebrafish with viral hemorrhagic septicemia virus (VHSV) at both embryonic and adult stages. Mortality was observed at 4 days post-infection (dpi) in tnf-α1-deficient adult fish challenged with 5 × 106 TCID50 (VHSV) and at 5 dpi in adult wild fish challenged with the same concentration. In addition, tnf-α1(-/-) KO adult fish reached the maximum mortality of 100 % at 20 dpi, whereas wild adult fish reached 54 % mortality at the same time point. This increased susceptibility to early mortality was associated with a higher viral burden and altered expression of key immune genes, including the pro-inflammatory cytokines il-6 and il-1β, the anti-inflammatory cytokine il-10, and interferon-related genes such as irf1 and ifn-γ. Our findings demonstrate the crucial role of TNF-α1 in antiviral defense mechanisms in zebrafish and provide valuable insights into the functional conservation of TNF-α signaling across vertebrate species. This knowledge may contribute to the development of strategies to combat viral diseases in fish.

Neurological disorders, some of which are associated with viral infections, are growing due to the aging and expanding population. Despite strong defenses of the central nervous system, some viruses have evolved ways to breach them, which often result in dire consequences. In this review, we recount the various ways by which different viruses can enter the CNS, and we describe the consequences of such invasions. Consequences may manifest as acute disease, such as encephalitis, meningitis, or result in long-term effects, such as neuromuscular dysfunction, as occurs in poliomyelitis. We discuss evidence for viral involvement in the causation of well-known chronic neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, multiple sclerosis, as well as vascular dementia in the elderly. We also describe the approaches currently available to control a few of the neural viral infections. These include antivirals that are effective against human immunodeficiency virus and herpes simplex virus, as well as vaccines valuable for controlling rabies virus, poliomyelitis virus, and some flavivirus infections. There is an urgent need to better understand, at a molecular level, how viruses contribute to acute and, especially, chronic neurological diseases and to develop more precise and effective vaccines and therapies.

The canine distemper virus (CDV) could infect various wildlife species worldwide. The viral infection in large felids directly impacts wildlife conservation. This study aimed to understand better the burden of CDV outbreaks in captive tiger populations in Thailand and a novel discovery of their clinical signs with a history of CDV exposure. We followed up on their infection from May 2016 to October 2020 with laboratory testing and veterinary medical records. The cumulative morbidity and mortality rates were relatively high. Moreover, 50% of the tigers survived at 2 years after infection. All suspected and confirmed cases of CDV infections were significantly associated with laryngeal inflammation, which developed into paralysis in almost 50% of cases. Altogether, 50% of all tiger cases with chronic infection developed stridor at 314 days after virus infection [95% CI: 302-320]. Therefore, laryngeal paralysis may result from CDV infection and degeneration, potentially affecting the peripheral and central nervous systems. This condition could pose a life-threatening risk to tigers. The virus could spread quickly by contact with bodily excretion among tigers and fomite contamination once it affects a specific population. Implementation of biosecurity measures and vaccination is essential to mitigate the risk of disease spread and infection rates in tiger populations.

The within-host environment changes over circadian time and influences the replication and severity of viruses. Genetic knockout of the circadian transcription factors CRYPTOCHROME 1 and CRYPTOCHROME 2 (CRY1-/-/CRY2-/-; CKO) leads to altered protein homeostasis and chronic activation of the integrated stress response (ISR). The adaptive ISR signalling pathways help restore cellular homeostasis by downregulating protein synthesis in response to endoplasmic reticulum overloading or viral infections. By quantitative mass spectrometry analysis, we reveal that many viral recognition proteins and type I interferon (IFN) effectors are significantly upregulated in lung fibroblast cells from CKO mice compared with wild-type (WT) mice. This basal 'antiviral state' restricts the growth of influenza A virus and is governed by the interaction between proteotoxic stress response pathways and constitutive type I IFN signalling. CKO proteome composition and type I IFN signature were partially phenocopied upon sustained depletion of CRYPTOCHROME (CRY) proteins using a small-molecule CRY degrader, with modest differential gene expression consistent with differences seen between CKO and WT cells. Our results highlight the crosstalk between circadian rhythms, cell-intrinsic antiviral defences and protein homeostasis, providing a tractable molecular model to investigate the interface of these key contributors to human health and disease.This article is part of the Theo Murphy meeting issue 'Circadian rhythms in infection and immunity'.

Viral lower respiratory tract infection (vLRTI) is a leading cause of hospitalization and death in children worldwide. Despite this, no studies have employed proteomics to characterize host immune responses to severe pediatric vLRTI in both the lower airway and systemic circulation. To address this gap, gain insights into vLRTI pathophysiology, and test a novel diagnostic approach, we assayed 1,305 proteins in tracheal aspirate (TA) and plasma from 62 critically ill children using SomaScan. We performed differential expression (DE) and pathway analyses comparing vLRTI (n = 40) to controls with non-infectious acute respiratory failure (n = 22), developed a diagnostic classifier using LASSO regression, and analyzed matched TA and plasma samples. We further investigated the impact of viral load and bacterial coinfection on the proteome. The TA signature of vLRTI was characterized by 200 DE proteins (Padj <0.05) with upregulation of interferons and T cell responses and downregulation of inflammation-modulating proteins including FABP and MIP-5. A nine-protein TA classifier achieved an area under the receiver operator curve (AUC) of 0.96 (95% CI: 0.90-1.00) for identifying vLRTI. In plasma, the host response to vLRTI was more muted with 56 DE proteins. Correlation between TA and plasma was limited, although ISG15 was elevated in both compartments. In bacterial coinfection, we observed increases in the TNF-stimulated protein TSG-6, as well as CRP, and interferon-related proteins. Viral load correlated positively with interferon signaling and negatively with neutrophil-activation pathways. Taken together, our study provides fresh insights into the lower airway and systemic proteome of severe pediatric vLRTI and identifies novel protein biomarkers with diagnostic potential.IMPORTANCEWe describe the first proteomic profiling of the lower airway and blood in critically ill children with severe viral lower respiratory tract infection (vLRTI). From tracheal aspirate (TA), we defined a proteomic signature of vLRTI characterized by increased expression of interferon signaling proteins and decreased expression of proteins involved in immune modulation including FABP and MIP-5. Using machine learning, we developed a parsimonious diagnostic classifier that distinguished vLRTI from non-infectious respiratory failure with high accuracy. Comparative analysis of paired TA and plasma specimens demonstrated limited concordance, although the interferon-stimulated protein ISG15 was significantly upregulated with vLRTI in both compartments. We further identified TSG-6 and CRP as airway biomarkers of bacterial-viral coinfection, and viral load analyses demonstrated a positive correlation with interferon-related protein expression and a negative correlation with the expression of neutrophil activation proteins. Taken together, our study provides new insights into the lower airway and systemic proteome of severe pediatric vLRTI.

Equine herpesvirus type 1 (EHV1) is a ubiquitous viral pathogen infecting the equine population worldwide. EHV1 infection causes respiratory illness, abortion, neonatal foal mortality, and myeloencephalopathy. The currently available modified live EHV1 vaccines have safety and efficacy limitations. The two mutant EHV1 viruses (vToH-DMV (∆IR6/gE) and vToH-QMV (∆IR6/UL43/gE/UL56)), generated by the deletion of genes responsible for virulence (gE and IR6) and immunosuppression (uL43 and uL56), have been previously characterized by our group and found to generate good immune responses. The present study aimed to determine the safety and protective efficacy of the above mutants against a virulent EHV1 challenge in a murine model.

BALB/c mice were intranasally immunized with a live vToH-QMV or vToH-DMV vaccine. Intranasal booster immunization was given at 14 days post-vaccination (dpv). Both mutants induced an optimal level of EHV1-specific humoral and cell-mediated immune responses, as determined by virus neutralization assay, ELISA, and immunophenotyping. At 35 dpv, the mice were intranasally challenged with wild-type EHV1 (vRaj strain).

Amongst the two mutants, vToH-QMV induced a better immune response than the vToH-DMV vaccine. Furthermore, vToH-QMV provided good protection in mice against the virulent challenge. It specifically exhibited less severe clinical disease in terms of clinical signs, body weight reduction, and gross and histopathological lung lesions accompanied by early virus clearance.

These studies are suggestive of vToH-QMV EHV1 being a potential vaccine candidate against EHV1 infection, which needs to be finally tested in the main host, i.e., horses.

Despite advances in medicine and antimicrobial research, viral infections continue to pose a major threat to human health. While major strides have been made in generating vaccines and small molecules to combat emerging pathogens, new modalities of treatment are warranted in diseases where there is a lack of treatment options, or where treatment cannot fully eradicate pathogens, as in HIV infection. Cellular therapies, some of which are FDA approved for treating cancer, take advantage of our developing understanding of the immune system, and harness this knowledge to enhance, or direct, immune responses toward infectious agents. As with cancer, viruses that evade immunity, do so by avoiding immune recognition or by redirecting the cellular responses that would eradicate them. As such, infusing virus specific immune cells has the potential to improve patient outcomes and should be investigated as a potential tool in the arsenal to fight infection. The present manuscript summarizes key findings made using cellular therapies for the treatment of viral infections, focusing on the potential that these strategies might have in controlling disease.

Persistence is a strategy used by many viruses to evade eradication by the immune system, ensuring their permanence and transmission within the host and optimizing viral fitness. During persistence, viruses can trigger various phenomena, including target organ damage, mainly due to an inflammatory state induced by infection, as well as cell proliferation and/or immortalization. In addition to immune evasion and chronic inflammation, factors contributing to viral persistence include low-level viral replication, the accumulation of viral mutants, and, most importantly, maintenance of the viral genome and reliance on viral oncoprotein production. This review focuses on the process of genome integration, which may occur at different stages of infection (e.g., HBV), during the chronic phase of infection (e.g., HPV, EBV), or as an essential part of the viral life cycle, as seen in retroviruses (HIV, HTLV-1). It also explores the close relationship between integration, persistence, and oncogenesis. Several models have been proposed to describe the genome integration process, including non-homologous recombination, looping, and microhomology models. Integration can occur either randomly or at specific genomic sites, often leading to genome destabilization. In some cases, integration results in the loss of genomic regions or impairs the regulation of oncogene and/or oncosuppressor expression, contributing to tumor development.

Feline herpesvirus type 1 (FHV) and feline calicivirus (FCV) are significant pathogens causing upper respiratory tract disease in cats. Existing inactivated or modified live vaccines against FCV and FHV face limitations in safety and efficacy. To overcome these challenges, a recombinant strain FHV ΔgI/gE-FCV VP1 was developed by deleting the gI/gE gene and concurrently expressing FCV VP1, using the FHV WX19 strain as the parental virus. Results indicated the presence of FCV VP1 in FHV ΔgI/gE-FCV VP1-infected CRFK cells, confirmed through protein blotting and immunofluorescence assays and virus-like particles (VLPs) of FCV were observed using transmission electron microscopy. For efficacy in cats, each animal received intranasal vaccination with 1 mL of FHV ΔgI/gE-FCV VP1 at 106 TCID50. Following completion of vaccination on day 28, animals were exposed to a potent FCV strain. Assessments included clinical signs, nasal shedding, virus neutralizing antibodies, cytokine expression and postmortem histological testing. All vaccinations with FHV ΔgI/gE-FCV VP1 were deemed safe, with significantly reduced clinical disease scores, pathological changes and viral nasal shedding following infection and robust immune responses were induced. These findings collectively suggest the effectiveness of FHV-based recombinant vaccines in preventing FCV infections.

There is a potential link between autoimmune diseases and Epstein-Barr virus (EBV) infections, with EBV playing a substantial role in the onset of Sjögren's syndrome (SjS). Some EBV proteins could mimic host self-antigens post-infection, leading to molecular mimicry. This similarity may cause the immune system to attack its tissues mistakenly. Among the various proteins associated with EBV, nuclear antigen 1 (EBNA-1) is essential for the latent replication of infected cells and is prevalent in all EBV-related diseases. In the study, single-chain variable fragment (scFv) antibodies targeting EBNA-1 were isolated using phage display technology from a primary SjS patient who also had a chronic active EBV infection. The specific clones were enriched after panning, and the binding activity of selected scFvs targeting EBNA-1 was confirmed. Sequence analysis indicated that the scFvs exhibiting positive signals could be grouped into five clones, all of which used homologous heavy chain V regions derived from germline Vh4-39, and two types of light chain V regions stemming from germline Vλ1-44 and Vλ3-15. These scFvs were found to exhibit a high degree of somatic mutations, likely indicative of antigen selection. Of the scFvs, P1-3 demonstrated the strongest binding affinity to EBNA-1, exhibiting a determined value of 7.3 x 10-8 M, and showed cross-reactivity to the SjS associated La/SSB self-antigen. The experimental results combined with AlphaFold 3 predictions revealed a potential epitope for scFv P1-3 binding to EBNA-1. Additionally, scFv P1-3 could also cross-bind to the modeled structure of La/SSB. We inferred a possible structural correlation between EBNA-1 and La/SSB involving an X2AX6PG epitope motif. This research contributes to our understanding of the structural basis of the interactions between antibodies and EBNA-1, shedding light on the VH and VL gene usage of anti-EBNA-1 antibodies in EBV-infected SjS patients and the potential origins of autoantibodies.

Viral proteins that evade the host's innate immune response play a crucial role in pathogenesis, significantly impacting viral infections and potential therapeutic strategies. Identifying these proteins through traditional methods is challenging and time-consuming due to the complexity of virus-host interactions. Leveraging advancements in computational biology, we present VirusHound-II, a novel tool that utilizes machine learning techniques to predict viral proteins evading the innate immune response with high accuracy. We evaluated a comprehensive range of machine learning models, including ensemble methods, neural networks, and support vector machines. Using a dataset of 1337 viral proteins known to evade the innate immune response (VPEINRs) and an equal number of non-VPEINRs, we employed pseudo amino acid composition as the molecular descriptor. Our methodology involved a tenfold cross-validation strategy on 80% of the data for training, followed by testing on an independent dataset comprising the remaining 20%. The random forest model demonstrated superior performance metrics, achieving 0.9290 accuracy, 0.9283 F1 score, 0.9354 precision, and 0.9213 sensitivity in the independent testing phase. These results establish VirusHound-II as an advancement in computational virology, accessible via a user-friendly web application. We anticipate that VirusHound-II will be a crucial resource for researchers, enabling the rapid and reliable prediction of viral proteins evading the innate immune response. This tool has the potential to accelerate the identification of therapeutic targets and enhance our understanding of viral evasion mechanisms, contributing to the development of more effective antiviral strategies and advancing our knowledge of virus-host interactions.

Diabetes mellitus (DM) is a metabolic syndrome characterized by hyperglycaemia, polydipsia, polyuria, and weight loss, among others. The pathophysiology for the disorders is complex and results in pancreatic abnormal function. Viruses have also been implicated in the metabolic syndrome. This study charted peptides to investigate and predict the autoimmune potential of shared sequences between 8 viral species proteins (which we termed 'diabetes-viruses') and the human pancreatic proteins. The structure and immunological relevance of shared sequences between viruses reported in DM onset and human pancreatic proteins were analysed. At nonapeptide mapping between human pancreatic protein and 'diabetic-viruses', reveal 1064 shared sequences distributed among 454 humans and 4288 viral protein sequences. The viral results showed herpesviruses, enterovirus (EV), human endogenous retrovirus, influenza A viruses, rotavirus, and rubivirus sequences are hosted by the human pancreatic protein. The most common shared nonapeptide was AAAAAAAAA, present in 30 human nonredundant sequences. Among the viral species, the shared sequence NSLEVLFQG occurred in 18 nonredundant EVs protein, while occurring merely in 1 human protein, whereas LGLDIEIAT occurred in 8 influenza A viruses overlapping to 1 human protein and KDELSEARE occurred in 2 rotaviruses. The prediction of the location of the shared sequences in the protein structures, showed most of the shared sequences are exposed and located either on the surface or cleft relative to the entire protein structure. Besides, the peptides in the viral protein shareome were predicted computationally for binding to MHC molecules. Here analyses showed that the entire 1064 shared sequences predicted 203 to be either HLA-A or B supertype-restricted epitopes. Fifty-one of the putative epitopes matched reported HLA ligands/T-cell epitopes majorly coming from EV B supertype representative allele restrictions. These data, shared sequences, and epitope charts provide important insight into the role of viruses on the onset of DM and its implications.

One of the worst zoonotic illnesses, avian influenza (AI), or commonly referred to as bird flu, is caused by viruses belonging to the genus Influenza viruses, which are members of the Orthomyxoviridae family. The harmful effects of AI illness can affect both human and animal health and cause financial losses. Globally, the AI virus lacks political purpose and is not limited by geographical limits. It has been isolated from poultry, wild birds, and captive birds in Asia, North America, Europe, Australia, and South America. Their virulence is divided into highly pathogenic AI (HPAI) and low pathogenic AI (LPAI). The AI virus can also be diagnosed in a laboratory setting using molecular tests like real-time polymerase chain reaction or serological tests like the hemagglutinin inhibition test, agar gel immunodiffusion, antigen detection enzyme-linked immunosorbent assay, and other immunoassays. The type of AI virus and host species determines the clinical manifestations, severity, and fatality rates of AI. Human infection with AI viruses typically results from direct transmission from infected birds to humans. AI outbreaks in domestic and wild birds are uncommon; however, an infection can pose a significant threat to public, veterinary, and medical health. Successful vaccination reduces the probability of AI H5N1 virus infection in meat and other poultry products and prevents systemic infection in chickens. This review will provide information that can be used as a reference for recognizing the dangers of AI and for preventing and controlling the disease, considering its potential to become a serious pandemic outbreak.

Virus spread at the single-cell level is largely uncharacterized. We have designed and constructed a microfluidic device in which each nanowell contains a single, infected cell (donor) and a single, uninfected cell (recipient). Using a GFP-expressing poliovirus as our model, we observed both lytic and non-lytic spread. Donor cells supporting lytic spread established infection earlier than those supporting non-lytic spread. However, non-lytic spread established infections in recipient cells substantially faster than lytic spread and yielded higher rates of genome replication. While lytic spread was sensitive to the presence of capsid entry/uncoating inhibitors, non-lytic spread was not. Consistent with emerging models for non-lytic spread of enteroviruses using autophagy, reduction in LC3 levels in cells impaired non-lytic spread and elevated the fraction of virus in donor cells spreading lytically. The ability to distinguish lytic and non-lytic spread unambiguously will enable discovery of viral and host factors and host pathways used for non-lytic spread of enteroviruses and other viruses as well.

Cancer patients are more susceptible to an aggressive course of COVID-19. Developing biomarkers identifying cancer patients at high risk of COVID-19-related death could help determine who needs early clinical intervention. The miRNAs hosted in the genomic regions associated with the risk of aggressive COVID-19 could represent potential biomarkers for clinical outcomes.

Plasma samples were collected at The University of Texas MD Anderson Cancer Center from cancer patients (N = 128) affected by COVID-19. Serum samples were collected from vaccinated healthy individuals (n = 23) at the Municipal Clinical Emergency Teaching Hospital in Timisoara, Romania. An in silico positional cloning approach was used to identify the presence of miRNAs at COVID-19 risk-associated genomic regions: CORSAIRs (COvid-19 RiSk AssocIated genomic Regions). The miRNA levels were measured by RT-qPCR.

We found that miRNAs were enriched in CORSAIR. Low plasma levels of hsa-miR-150-5p and hsa-miR-93-5p were associated with higher COVID-19-related death. The levels of hsa-miR-92b-3p were associated with SARS-CoV-2 test positivity. Peripheral blood mononuclear cells (PBMC) increased secretion of hsa-miR-150-5p, hsa-miR-93-5p, and hsa-miR-92b-3p after in vitro TLR7/8- and T cell receptor (TCR)-mediated activation. Increased levels of these three miRNAs were measured in the serum samples of healthy individuals between one and nine months after the second dose of the Pfizer-BioNTech COVID-19 vaccine. SARS-CoV-2 infection of human airway epithelial cells influenced the miRNA levels inside their secreted extracellular vesicles.

MiRNAs are enriched at CORSAIR. Plasma miRNA levels can represent a potential blood biomarker for predicting COVID-19-related death in cancer patients.

While the benefits of physical activity on mental health are well-known, systematic reviews and meta-analyses on its impact on mental illness in adults with COVID-19 are scarce. This study of 25 randomized controlled trials shows that physical activity significantly reduces anxiety (standardized mean difference [SMD] = -0.915; 95% confidence interval [CI] = -1.182 to -0.648; I2 = 82.0%; p < 0.001) and depression (SMD = -0.752; 95% CI = -1.034 to -0.470; I2 = 81.4%; p < 0.001). Traditional Chinese ethnic sports are notably effective. Interventions under 3 weeks best reduce depression, while 3 ≤ 7 weeks optimally reduce anxiety. Sessions ≤5 times weekly, with 30 ≤ 60 min for anxiety and >60 min for depression, yield the best outcomes. These results highlight the specific effectiveness of physical activity in alleviating anxiety and depression in COVID-19 patients.

BACKGROUNDMost humans have been infected with cytomegalovirus (CMV) by midlife without clinical signs of disease. However, in settings in which the immune system is undeveloped or compromised, the virus is not adequately controlled and consequently presents a major infectious cause of both congenital disease during pregnancy as well as opportunistic infection in children and adults. With clear evidence that risk to the fetus varies with gestational age at the time of primary maternal infection, further research on humoral responses to primary CMV infection during pregnancy is needed.METHODSHere, systems serology tools were applied to characterize antibody responses to CMV infection in pregnant and nonpregnant women experiencing either primary or chronic infection.RESULTSWhereas strikingly different antibody profiles were observed depending on infection status, limited differences were associated with pregnancy status. Beyond known differences in IgM responses used clinically for identification of primary infection, distinctions observed in IgA and FcγR-binding antibodies and among antigen specificities accurately predicted infection status. Machine learning was used to define the transition from primary to chronic states and predict time since infection with high accuracy. Humoral responses diverged over time in an antigen-specific manner, with IgG3 responses toward tegument decreasing over time as typical of viral infections, while those directed to pentamer and glycoprotein B were lower during acute and greatest during chronic infection.CONCLUSIONIn sum, this work provides insights into the antibody response associated with CMV infection status in the context of pregnancy, revealing aspects of humoral immunity that have the potential to improve CMV diagnostics.FUNDINGCYMAF consortium and NIH NIAID.

We demonstrate the role of signaling via the glucocorticoid receptor, NR3C1, in differentiation of CD8+ T cell memory. Pharmacological inhibition as well as the short hairpin RNA-mediated knockdown of the receptor hindered memory transition and limited the homeostatic turnover of the activated CD8+ T cells. Dexamethasone exposure of CD8+ T cells expanded during a resolving infection with influenza A virus or a γ-herpesvirus promoted conversion of effector cells into memory cells by modulating cellular metabolism and lowering the accumulation of reactive oxygen species. Reduced reactive oxygen species levels in the responding effector cells upregulated Bcl2 and enhanced survival. The generated virus-specific memory CD8+ T cells were efficiently recalled following challenge of animals with a secondary infection to control it better. The memory-enhancing effect was predominantly evident at low doses of dexamethasone. Therefore, controlled glucocorticoid signaling within the effector CD8+ T cells is crucial for optimal memory differentiation.

Interferon (IFN) induced activities are critical, early determinants of immune responses and infection outcomes. A key facet of IFN responses is the upregulation of hundreds of mRNAs termed interferon-stimulated genes (ISGs) that activate intrinsic and cell-mediated defenses. While primary interferon signaling is well-delineated, other layers of regulation are less explored but implied by aberrant ISG expression signatures in many diseases in the absence of infection. Consistently, our examination of tonic ISG levels across uninfected human tissues and individuals revealed three ISG subclasses. As tissue identity and many comorbidities with increased virus susceptibility are characterized by differences in metabolism, we characterized ISG responses in cells grown in media known to favor either aerobic glycolysis (glucose) or oxidative phosphorylation (galactose supplementation). While these conditions over time had a varying impact on the expression of ISG RNAs, the differences were typically greater between treatments than between glucose/galactose. Interestingly, extended interferon-priming led to divergent expression of two ISG proteins: upregulation of IRF1 in IFN-γ/glucose and increased IFITM3 in galactose by IFN-α and IFN-γ. In agreement with a hardwired response, glucose/galactose regulation of interferon-γ induced IRF1 is conserved in unrelated mouse and cat cell types. In galactose conditions, proteasome inhibition restored interferon-γ induced IRF1 levels to that of glucose/interferon-γ. Glucose/interferon-γ decreased replication of the model poxvirus vaccinia at low MOI and high MOIs. Vaccinia replication was restored by IRF1 KO. In contrast, but consistent with differential regulation of IRF1 protein by glucose/galactose, WT and IRF1 KO cells in galactose media supported similar levels of vaccinia replication regardless of IFN-γ priming. Also associated with glucose/galactose is a seemingly second block at a very late stage in viral replication which results in reductions in herpes- and poxvirus titers but not viral protein expression. Collectively, these data illustrate a novel layer of regulation for the key ISG protein, IRF1, mediated by glucose/galactose and imply unappreciated subprograms embedded in the interferon response. In principle, such cellular circuitry could rapidly adapt immune responses by sensing changing metabolite levels consumed during viral replication and cell proliferation.

Viral lower respiratory tract infection (vLRTI) is a leading cause of hospitalization and death in children worldwide. Despite this, no studies have employed proteomics to characterize host immune responses to severe pediatric vLRTI in both the lower airway and systemic circulation. To address this gap, gain insights into vLRTI pathophysiology, and test a novel diagnostic approach, we assayed 1,305 proteins in tracheal aspirate (TA) and plasma from 62 critically ill children using SomaScan. We performed differential expression (DE) and pathway analyses comparing vLRTI (n=40) to controls with non-infectious acute respiratory failure (n=22), developed a diagnostic classifier using LASSO regression, and analyzed matched TA and plasma samples. We further investigated the impact of viral load and bacterial coinfection on the proteome. The TA signature of vLRTI was characterized by 200 DE proteins (Padj<0.05) with upregulation of interferons and T cell responses and downregulation of inflammation-modulating proteins including FABP and MIP-5. A nine-protein TA classifier achieved an AUC of 0.96 (95% CI 0.90-1.00) for identifying vLRTI. In plasma, the host response to vLRTI was more muted with 56 DE proteins. Correlation between TA and plasma was limited, although ISG15 was elevated in both compartments. In bacterial coinfection, we observed increases in the TNF-stimulated protein TSG-6, as well as CRP, and interferon-related proteins. Viral load correlated positively with interferon signaling and negatively with neutrophil-activation pathways. Taken together, our study provides fresh insight into the lower airway and systemic proteome of severe pediatric vLRTI, and identifies novel protein biomarkers with diagnostic potential.

Interferon (IFN) induced activities are critical, early determinants of immune responses and infection outcomes. A key facet of IFN responses is the upregulation of hundreds of mRNAs termed interferon-stimulated genes (ISGs) that activate intrinsic and cell-mediated defenses. While primary interferon signaling is well-delineated, other layers of regulation are less explored but implied by aberrant ISG expression signatures in many diseases in the absence of infection. Consistently, our examination of tonic ISG levels across uninfected human tissues and individuals revealed three ISG subclasses. As tissue identity and many comorbidities with increased virus susceptibility are characterized by differences in metabolism, we characterized ISG responses in cells grown in media known to favor either aerobic glycolysis (glucose) or oxidative phosphorylation (galactose supplementation). While these conditions over time had a varying impact on the expression of ISG RNAs, the differences were typically greater between treatments than between glucose/galactose. Interestingly, extended interferon-priming led to divergent expression of two ISG proteins: upregulation of IRF1 in IFN-γ/glucose and increased IFITM3 in galactose by IFN-α and IFN-γ. In agreement with a hardwired response, glucose/galactose regulation of interferon-γ induced IRF1 is conserved in unrelated mouse and cat cell types. In galactose conditions, proteasome inhibition restored interferon-γ induced IRF1 levels to that of glucose/interferon-γ. Glucose/interferon-γ decreased replication of the model poxvirus vaccinia at low MOI and high MOIs. Vaccinia replication was restored by IRF1 KO. In contrast, but consistent with differential regulation of IRF1 protein by glucose/galactose, WT and IRF1 KO cells in galactose media supported similar levels of vaccinia replication regardless of IFN-γ priming. Also associated with glucose/galactose is a seemingly second block at a very late stage in viral replication which results in reductions in herpes- and poxvirus titers but not viral protein expression. Collectively, these data illustrate a novel layer of regulation for the key ISG protein, IRF1, mediated by glucose/galactose and imply unappreciated subprograms embedded in the interferon response. In principle, such cellular circuitry could rapidly adapt immune responses by sensing changing metabolite levels consumed during viral replication and cell proliferation.

Pain is often one of the initial indicators of a viral infection, yet our understanding of how viruses induce pain is limited. Immune cells typically recognize viral nucleic acids, which activate viral receptors and signaling, leading to immunity. Interestingly, these viral receptors and signals are also present in nociceptors and are associated with pain. Here, we investigate the response of nociceptors to nucleic acids during viral infections, specifically focusing on the role of the viral signal, Stimulator of Interferon Genes (STING). Our research shows that cytosolic double-stranded DNA (dsDNA) from viruses, like herpes simplex virus 1 (HSV-1), triggers pain responses through STING expression in nociceptors. In addition, STING agonists alone can elicit pain responses. Notably, these responses involve the direct activation of STING in nociceptors through TRPV1. We also provided a proof-of-concept showing that STING and TRPV1 significantly contribute to the mechanical hypersensitivity induced by HSV-1 infection. These findings suggest that STING could be a potential therapeutic target for relieving pain during viral infections.