Characterization of Symbiodinium-associated viruses and implications for coral health

<p>Coral reefs are in decline worldwide. Much of this decline is attributable to mass coral bleaching events and disease outbreaks, both of which are linked to anthropogenic climate change. Despite increased research effort, much remains unknown about these phenomena, especially the causative agents of many coral diseases. In particular, coral-associated viruses have received little attention, and their potential roles in coral diseases are largely unknown. This study aimed to address this lack of information by characterising the viruses associated with reef-building corals and Symbiodinium (dinoflagellates that can form symbioses with corals). Symbiodinium virus screening experiments revealed the presence of numerous and varied virus-like particles (VLPs) inside cells. Of the 49 Symbiodinium cultures screened, approximately one third contained putative latent viral infections that could be induced to enter their lytic cycle by UV irradiation. Electron microscope examination revealed VLPs closely resembling viruses previously found in dinoflagellates and other microalgae. Three cultures that showed evidence of latent viral infections were chosen for whole transcriptome sequencing, which revealed the presence of viral genes that were expressed in several different types of Symbiodinium. The relationship between the detected genes and known viral gene sequences suggested that the cells were infected with double-stranded DNA (dsDNA) viruses. In order to determine how the host cell responds to stress-induced viral infection, the expression levels of genes associated with stress response and viral infection were measured. The expression levels of many genes were unchanged following UV stress, and expression of genes that were predicted to be upregulated following stress, such as those encoding antioxidant enzymes, in fact showed lower expression levels. Despite this, several groups of genes involved in viral infection and host cell response were upregulated following stress, providing further evidence for stress-induced latent or chronic viral infections. In addition to the research carried out on Symbiodinium cell cultures, viruses associated with three coral diseases were studied using electron microscopy. Virus-like particles were present in coral and Symbiodinium cells from all three diseases, but viral abundance was correlated with disease state in only one: white patch syndrome (WPS) of Porites australiensis. The locations and morphologies of the VLPs associated with WPS suggested the presence of dsDNA and single-stranded RNA (ssRNA) viruses infecting both the coral animal and Symbiodinium cells. DNA sequences obtained from WPS-affected corals matched closely with sequences obtained from VLP-containing Symbiodinium cells. Based on the evidence gathered from Symbiodinium cell cultures and coral tissues, I propose a theoretical model of viral infection in WPS. In this model, the coral animal cells are routinely subject to chronic viral infections, and Symbiodinium cells harbour two types of chronic or latent infections – a dsDNA and an ssRNA virus – that can be induced via stress, resulting in cell lysis or loss of the cells from the coral host. In addition to detection and rudimentary identification of viruses infecting Symbiodinium cells, this study generated the largest dinoflagellate transcriptomic dataset to date. These data will prove valuable for future research into Symbiodinium, both in terms of viral infections and more generally.</p>

Characterization of Symbiodinium-associated viruses and implications for coral health

<p>Coral reefs are in decline worldwide. Much of this decline is attributable to mass coral bleaching events and disease outbreaks, both of which are linked to anthropogenic climate change. Despite increased research effort, much remains unknown about these phenomena, especially the causative agents of many coral diseases. In particular, coral-associated viruses have received little attention, and their potential roles in coral diseases are largely unknown. This study aimed to address this lack of information by characterising the viruses associated with reef-building corals and Symbiodinium (dinoflagellates that can form symbioses with corals). Symbiodinium virus screening experiments revealed the presence of numerous and varied virus-like particles (VLPs) inside cells. Of the 49 Symbiodinium cultures screened, approximately one third contained putative latent viral infections that could be induced to enter their lytic cycle by UV irradiation. Electron microscope examination revealed VLPs closely resembling viruses previously found in dinoflagellates and other microalgae. Three cultures that showed evidence of latent viral infections were chosen for whole transcriptome sequencing, which revealed the presence of viral genes that were expressed in several different types of Symbiodinium. The relationship between the detected genes and known viral gene sequences suggested that the cells were infected with double-stranded DNA (dsDNA) viruses. In order to determine how the host cell responds to stress-induced viral infection, the expression levels of genes associated with stress response and viral infection were measured. The expression levels of many genes were unchanged following UV stress, and expression of genes that were predicted to be upregulated following stress, such as those encoding antioxidant enzymes, in fact showed lower expression levels. Despite this, several groups of genes involved in viral infection and host cell response were upregulated following stress, providing further evidence for stress-induced latent or chronic viral infections. In addition to the research carried out on Symbiodinium cell cultures, viruses associated with three coral diseases were studied using electron microscopy. Virus-like particles were present in coral and Symbiodinium cells from all three diseases, but viral abundance was correlated with disease state in only one: white patch syndrome (WPS) of Porites australiensis. The locations and morphologies of the VLPs associated with WPS suggested the presence of dsDNA and single-stranded RNA (ssRNA) viruses infecting both the coral animal and Symbiodinium cells. DNA sequences obtained from WPS-affected corals matched closely with sequences obtained from VLP-containing Symbiodinium cells. Based on the evidence gathered from Symbiodinium cell cultures and coral tissues, I propose a theoretical model of viral infection in WPS. In this model, the coral animal cells are routinely subject to chronic viral infections, and Symbiodinium cells harbour two types of chronic or latent infections – a dsDNA and an ssRNA virus – that can be induced via stress, resulting in cell lysis or loss of the cells from the coral host. In addition to detection and rudimentary identification of viruses infecting Symbiodinium cells, this study generated the largest dinoflagellate transcriptomic dataset to date. These data will prove valuable for future research into Symbiodinium, both in terms of viral infections and more generally.</p>

Chronic viral infections persistently alter marrow stroma and impair hematopoietic stem cell fitness

Chronic viral infections are associated with hematopoietic suppression, bone marrow (BM) failure, and hematopoietic stem cell (HSC) exhaustion. However, how persistent viral challenge and inflammatory responses target BM tissues and perturb hematopoietic competence remains poorly understood. Here, we combine functional analyses with advanced 3D microscopy to demonstrate that chronic infection with lymphocytic choriomeningitis virus leads to (1) long-lasting decimation of the BM stromal network of mesenchymal CXCL12-abundant reticular cells, (2) proinflammatory transcriptional remodeling of remaining components of this key niche subset, and (3) durable functional defects and decreased competitive fitness in HSCs. Mechanistically, BM immunopathology is elicited by virus-specific, activated CD8 T cells, which accumulate in the BM via interferon-dependent mechanisms. Combined antibody-mediated inhibition of type I and II IFN pathways completely preempts degeneration of CARc and protects HSCs from chronic dysfunction. Hence, viral infections and ensuing immune reactions durably impact BM homeostasis by persistently decreasing the competitive fitness of HSCs and disrupting essential stromal-derived, hematopoietic-supporting cues.

A single-cell reference atlas delineates CD4+ T cell subtype-specific adaptation during acute and chronic viral infections

CD4+ T cells are critical orchestrators of immune responses against a large variety of pathogens, including viruses. The multifaceted roles of CD4+ T cells, including their help to innate cells, CD8+ T and B cells and their support for long-lived immunity rely on a profound functional heterogeneity. While multiple CD4+ T cell subtypes and their key transcriptional regulators have been identified, there is a lack of consistent definition for CD4+ T cell transcriptional states. In addition, the progressive changes affecting CD4+ T cell subtypes during and after immune responses remain poorly defined. Taking advantage of single-cell transcriptomics, efficient computational methods, and robust animal models, we characterize the transcriptional landscape of CD4+ T cells responding to self-resolving and chronic viral infections. We build a comprehensive atlas of virus-specific CD4+ T cells and their evolution over time, and identify six major distinct cell states that are consistently observed in acute and chronic infections. During the course of acute infection, T cell composition progressively changes from effector to memory states, with subtype-specific gene modules and kinetics. Conversely, T cells in persistent infections fail to transition from effector to memory states, and acquire distinct, chronicity-associated transcriptional programs. By single-cell T cell receptor (TCR) sequencing analysis, we characterize the clonal structure of virus-specific CD4+ T cells across individuals and T cell subtypes. We find that virus-specific CD4+ T cell responses are mainly private across individuals and that most T cells differentiate into all subtypes independently of their TCR, in both acute and chronic infections. Finally, we show that our CD4+ T cell atlas can be used as a reference to accurately interpret cell states in external single-cell datasets. Overall, this study describes a previously unappreciated level of adaptation of the transcriptional states of CD4+ T cells responding to viruses and provides a new computational resource for CD4+ T cell analysis, available online at https://spica.unil.ch.

Single cell multi-omics reveals early elevated function and multiple fates within human progenitor exhausted CD8+ T cells

T-cell exhaustion is a hallmark of hepatitis C virus (HCV) infection and limits protective immunity in chronic viral infections and cancer. Limited knowledge exists of the initial viral and immune dynamics that characterise exhaustion in humans. We studied longitudinal blood samples from a unique cohort of subjects with primary infection using single cell multi-omics to identify the functions and phenotypes of HCV-specific CD8+ T cells. Early elevated IFN-γ response against the transmitted virus was associated with the rate of immune escape, larger clonal expansion, and early onset of exhaustion. Irrespective of disease outcome we discovered progenitors of early-exhaustion with intermediate expression of PD-1. Intra clonal analysis revealed distinct trajectories with multiple fates suggesting evolutionary plasticity of precursor cells. These findings challenge current paradigm on the contribution of CD8+ T cells to HCV disease outcome and provide data for future studies on T-cell differentiation in human infections.

Interleukin-21 in Viral Infections

Interleukin (IL)-21 is a cytokine that affects the differentiation and function of lymphoid and myeloid cells and regulates both innate and adaptive immune responses. In addition to regulating the immune response to tumor and viral infections, IL-21 also has a profound effect on the development of autoimmune and inflammatory diseases. IL-21 is produced mainly from CD4+ T cells—in particular, follicular helper T (Tfh) cells—which have a great influence on the regulation of antibody production. It is also an important cytokine for the activation of CD8+ T cells, and its role in recovering the function of CD8+ T cells exhausted by chronic microbial infections and cancer has been clarified. Thus, IL-21 plays an extremely important role in viral infections, especially chronic viral infections. In this review, I will introduce the findings to date on how IL-21 is involved in some typical viral infections and the potential of treating viral diseases with IL-21.

Antibody-independent functions of B cells during viral infections

The humoral immune response and antibody-mediated functions of B cells during viral infections are well described. However, we have limited understanding of antibody-independent B cell functions, such as cytokine production and antigen presentation, in acute and chronic viral infections and their role in protection and/or immunopathogenesis. Here, we summarize the current literature on these antibody-independent B cell functions and identify remaining knowledge gaps. B cell subsets produce anti- and pro-inflammatory cytokines, which can have both beneficial and detrimental effects during viral clearance. As professional antigen presenting cells, B cells also play an important role in immune regulation/shaping of the developing adaptive immune responses. Since B cells primarily express TLR7 and TLR9, we specifically discuss the role of Toll-like receptor (TLR)-mediated B cell responses to viral infections and their role in augmenting adaptive immunity through enhanced cytokine production and antigen presentation. However, viruses have evolved strategies to subvert TLR signaling and additional stimulation via B cell receptor (BCR) may be required to overcome the defective TLR response in B cells. To conclude, antibody-independent B cell functions seem to have an important role in regulating both acute and chronic viral infections and may form the basis for novel therapeutic approaches in treatment of viral infections in the future.

The transmembrane serine protease hepsin suppresses type I interferon induction by cleaving STING

Many viral proteases mediate the evasion of antiviral innate immunity by cleaving adapter proteins in the interferon (IFN) induction pathway. Host proteases are also involved in innate immunity and inflammation. Here, we report that the transmembrane protease hepsin (also known as TMPRSS1), which is predominantly present in hepatocytes, inhibited the induction of type I IFN during viral infections. Knocking out hepsin in mouse embryonic fibroblasts (MEFs) increased the viral infection–induced expression of Ifnb1, an Ifnb1 promoter reporter, and an IFN-sensitive response element promoter reporter. Ectopic expression of hepsin in cultured human hepatocytes and HEK293T cells suppressed the induction of IFNβ during viral infections by reducing the abundance of STING. These effects depended on the protease activity of hepsin. We identified a putative hepsin target site in STING and showed that mutating this site protected STING from hepsin-mediated cleavage. In addition to hepatocytes, several hepsin-producing prostate cancer cell lines showed reduced STING-mediated type I IFN induction and responses. These results reveal a role for hepsin in suppressing STING-mediated type I IFN induction, which may contribute to the vulnerability of hepatocytes to chronic viral infections.

COVID-19 Vaccination in Patients with Classic Kaposi’s Sarcoma

The novel coronavirus disease 2019 (COVID-19) has represented an overwhelming challenge for worldwide health systems. Patients with cancer are considered at higher risk for severe COVID-19 and increased mortality in case of infection. Although data on the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination in patients with cancer are limited, there is enough evidence supporting anti-infective vaccination in general in patients with active cancer, or with history of previous malignancy. Subjects with classic Kaposi’s sarcoma (KS) represent a small subset of cancer patients, which should be considered at heightened risk for infections due to several factors including age, and impaired immune function status. Several cases of human herpesviruses reactivation among critically ill COVID-19 patients have been described. Moreover, in case of severe infection and treatment with immunomodulating agents, patients with CKS are exposed at significant risk of viral reactivation and disease progression. Considering the baseline clinical risk factors of patients with CKS, and the complex interplay of the two viral agents, SARS-CoV-2 vaccination should be strongly recommended among patients with KS. KS represents an interesting field to study the interactions among chronic viral infections, SARS-CoV-2 and the host’s immune system. Prospective observational studies are needed to provide more insights on vaccine activity and safety among patients with cancer, optimal vaccine schedules, potential interactions with antineoplastic therapies, and other comorbidities including chronic viral infections.