Strategies and mechanisms for host and pathogen survival in acute and persistent viral infections

Disinfection and post-disinfection conditions drive bacterial and viral evolution across the environment and host

Water disinfection practices have long been established as a critical engineering intervention for controlling pathogen transmission and safeguarding individual and public health. However, recent discoveries have unveiled the significant role disinfection and post-disinfection play in accelerating the development of resistance to disinfectants and antimicrobial drugs within bacterial and viral communities in the environment. This phenomenon, in turn, may facilitate the emergence of persistent microbes and those with new genetic characteristics. These microbes may thrive in host environments with increased infectivity and resistance, posing challenges to current medical treatments and jeopardizing human health. In this perspective, we illuminate the intricate interplay between aquatic environments, microbes, and hosts and how microbial virulence evolves across the environment and host under the pressure of disinfection and post-disinfection conditions. We aim to draw attention to the previously overlooked potential risks associated with disinfection in driving the virulence evolution of bacteria and viruses, establish connections between pathogens in diverse environments and hosts within the overarching framework of the One Health concept, and ultimately provide guidelines for advancing future water disinfection technologies to effectively curb the spread of infectious diseases.

Metabolic changes in Toxoplasma gondii-infected host cells measured by autofluorescence imaging

Toxoplasma gondii, the causative agent of toxoplasmosis, is an obligate intracellular parasite that infects warm-blooded vertebrates across the world. In humans, seropositivity rates of T. gondii range from 10% to 90% across communities. Despite its prevalence, few studies address how T. gondii infection changes the metabolism of host cells. In this study, we investigate how T. gondii manipulates the host cell metabolic environment by monitoring the metabolic response over time using noninvasive autofluorescence lifetime imaging of single cells, metabolite analysis, extracellular flux analysis, and reactive oxygen species (ROS) production. Autofluorescence lifetime imaging indicates that infected host cells become more oxidized and have an increased proportion of bound NAD(P)H compared to uninfected controls. Over time, infected cells also show decreases in levels of intracellular glucose and lactate, increases in oxygen consumption, and variability in ROS production. We further examined changes associated with the pre-invasion "kiss and spit" process using autofluorescence lifetime imaging, which also showed a more oxidized host cell with an increased proportion of bound NAD(P)H over 48 hours compared to uninfected controls, suggesting that metabolic changes in host cells are induced by T. gondii kiss and spit even without invasion.IMPORTANCEThis study sheds light on previously unexplored changes in host cell metabolism induced by T. gondii infection using noninvasive, label-free autofluorescence imaging. In this study, we use optical metabolic imaging (OMI) to measure the optical redox ratio (ORR) in conjunction with fluorescence lifetime imaging microscopy (FLIM) to noninvasively monitor single host cell response to T. gondii infection over 48 hours. Collectively, our results affirm the value of using autofluorescence lifetime imaging to noninvasively monitor metabolic changes in host cells over the time course of a microbial infection. Understanding this metabolic relationship between the host cell and the parasite could uncover new treatment and prevention options for T. gondii infections worldwide.

Herd immunity to endemic diseases: Historical concepts and implications for public health policy

BACKGROUND

"Herd immunity" became a contested term during the COVID-19 pandemic. Although the term "herd immunity" is often used to refer to thresholds at which some diseases can be eliminated (e.g., due to mass vaccination), the term has multiple referents. Different concepts of herd immunity have been relevant throughout the history of immunology and infectious disease epidemiology. For some diseases, herd immunity plays a role in the development of an endemic equilibrium, rather than elimination via threshold effects.

METHODS

We reviewed academic literature from 1920 to 2022, using historical and philosophical analysis to identify and develop relevant concepts of herd immunity.

RESULTS

This paper analyses the ambiguity surrounding the concept of herd immunity during the pandemic. We argue for the need to recapture a long-standing interpretation of this concept as one of the factors that leads to a dynamic endemic equilibrium between a host population and a mutating respiratory pathogen.

CONCLUSIONS

Informed by the history of infectious disease epidemiology, we argue that understanding the concept in this way will help us manage both SARS-CoV-2 and hundreds of other seasonal respiratory pathogens with which we live but which have been disrupted due to sustained public health measures/non-pharmaceutical interventions targeting SARS-CoV-2.

A historical perspective on arboviruses of public health interest in Southern Africa

Arboviruses are an existing and expanding threat globally, with the potential for causing devastating health and socioeconomic impacts. Mitigating this threat necessitates a One Health approach that integrates vector surveillance, rapid disease detection, and innovative prevention and control measures. In Southern Africa, limited data on the epidemiology of arboviruses, their vectors, and their hosts prevent an effective response. We reviewed the current knowledge on arboviruses in Southern Africa and identified opportunities for further research. A literature search was conducted to identify studies published on arboviruses in 10 tropical and temperate countries of the Southern African Development Community (SADC) from 1900 onward. We identified 280 studies, half (51.1%) originating from South Africa, that described 31 arboviral species, their vectors, and their clinical effects on hosts reported in the region. Arboviral research flourished in the SADC in the mid-20th century but then declined, before reemerging in the last two decades. Recent research consists largely of case reports describing outbreaks. Historical vector surveillance and serosurveys from the mid-20th century suggest that arboviruses are plentiful across Southern Africa, but large gaps remain in the current understanding of arboviral distribution, transmission dynamics, and public health impact.

Arboviruses: Transmission and Host Resistance

In this review, there is a complete description of the classes of arboviruses, their evolutionary process, virus characterization, disease transmission methods; it also describes about the vectors involved in transmission and their mood of transmission, both biologically as well as non-biologically and, about host, the resistance mechanism in host, and artificial methods of preventing those viral transmissions. Arboviruses transmitted to hosts by some vectors such as mosquitoes, ticks, etc. The virus replicates in the host can be prevented by some host resistance mechanisms like RNA interference (RNAi), which degrade virus RNA by its antiviral activity, insect repellents, IGRs, and PI technology.

VirusHound-I: prediction of viral proteins involved in the evasion of host adaptive immune response using the random forest algorithm and generative adversarial network for data augmentation

Throughout evolution, pathogenic viruses have developed different strategies to evade the response of the adaptive immune system. To carry out successful replication, some pathogenic viruses encode different proteins that manipulate the molecular mechanisms of host cells. Currently, there are different bioinformatics tools for virus research; however, none of them focus on predicting viral proteins that evade the adaptive system. In this work, we have developed a novel tool based on machine and deep learning for predicting this type of viral protein named VirusHound-I. This tool is based on a model developed with the multilayer perceptron algorithm using the dipeptide composition molecular descriptor. In this study, we have also demonstrated the robustness of our strategy for data augmentation of the positive dataset based on generative antagonistic networks. During the 10-fold cross-validation step in the training dataset, the predictive model showed 0.947 accuracy, 0.994 precision, 0.943 F1 score, 0.995 specificity, 0.896 sensitivity, 0.894 kappa, 0.898 Matthew's correlation coefficient and 0.989 AUC. On the other hand, during the testing step, the model showed 0.964 accuracy, 1.0 precision, 0.967 F1 score, 1.0 specificity, 0.936 sensitivity, 0.929 kappa, 0.931 Matthew's correlation coefficient and 1.0 AUC. Taking this model into account, we have developed a tool called VirusHound-I that makes it possible to predict viral proteins that evade the host's adaptive immune system. We believe that VirusHound-I can be very useful in accelerating studies on the molecular mechanisms of evasion of pathogenic viruses, as well as in the discovery of therapeutic targets.

cGAS-STING Pathway Activation during Trypanosoma cruzi Infection Leads to Tissue-Dependent Parasite Control

Host cell invasion by Trypanosoma cruzi is a markedly silent process, with limited host transcriptional changes indicative of innate immune recognition, except for a modest type I IFN (IFN-I) response. In this study, we show that T. cruzi-induced IFN-β production was nearly abolished in primary murine cGAS-/- or stimulator of IFN genes (STING)-deficient (STINGGt) macrophages and fibroblasts. T. cruzi infection did not impact the ability of IFN-regulatory factor reporter macrophages to respond to classical cGAS-STING agonists, indicating that the limited IFN-β induction is not due to active parasite suppression. cGAS-/-, STINGGt, and IFN-α/β receptor-/- (IFNAR-/-) macrophages infected with T. cruzi yielded significantly higher numbers of amastigotes compared with wild-type macrophages; however, the impact of the STING pathway during infection in vivo is more complex. Despite an initial increase in parasite growth, STINGGt and IFNAR-/- mice ultimately had lower parasite burden in footpads as compared with wild-type mice, demonstrating a role for IFN-I expression in potentiating parasite growth at the infection site. STING pathway activation had little impact on parasite levels in the skeletal muscle; however, in the heart, cGAS-/- and STINGGt mice, but not IFNAR-/- mice, accumulated higher acute parasite loads, suggesting a protective role of STING sensing of T. cruzi in this organ that was independent of IFN-I. Together, these results demonstrate that host cGAS-STING senses T. cruzi infection, enhancing parasite growth at the site of entry, and contributes to acute-phase parasite restriction in the heart, a major site of tissue damage in chronic T. cruzi infection.

Contribution of viral and bacterial infections to senescence and immunosenescence

Cellular senescence is a key biological process characterized by irreversible cell cycle arrest. The accumulation of senescent cells creates a pro-inflammatory environment that can negatively affect tissue functions and may promote the development of aging-related diseases. Typical biomarkers related to senescence include senescence-associated β-galactosidase activity, histone H2A.X phosphorylation at serine139 (γH2A.X), and senescence-associated heterochromatin foci (SAHF) with heterochromatin protein 1γ (HP-1γ protein) Moreover, immune cells undergoing senescence, which is known as immunosenescence, can affect innate and adaptative immune functions and may elicit detrimental effects over the host's susceptibility to infectious diseases. Although associations between senescence and pathogens have been reported, clear links between both, and the related molecular mechanisms involved remain to be determined. Furthermore, it remains to be determined whether infections effectively induce senescence, the impact of senescence and immunosenescence over infections, or if both events coincidently share common molecular markers, such as γH2A.X and p53. Here, we review and discuss the most recent reports that describe cellular hallmarks and biomarkers related to senescence in immune and non-immune cells in the context of infections, seeking to better understand their relationships. Related literature was searched in Pubmed and Google Scholar databases with search terms related to the sections and subsections of this review.

Metabolic changes to host cells with Toxoplasma gondii infection

Toxoplasma gondii, the causative agent of toxoplasmosis, is an obligate intracellular parasite that infects warm-blooded vertebrates across the world. In humans, seropositivity rates of T. gondii range from 10% to 90%. Despite its prevalence, few studies address how T. gondii infection changes the metabolism of host cells. Here, we investigate how T. gondii manipulates the host cell metabolic environment by monitoring metabolic response over time using non-invasive autofluorescence lifetime imaging of single cells, seahorse metabolic flux analysis, reactive oxygen species (ROS) production, and metabolomics. Autofluorescence lifetime imaging indicates that infected host cells become more oxidized and have an increased proportion of bound NAD(P)H with infection. These findings are consistent with changes in mitochondrial and glycolytic function, decrease of intracellular glucose, fluctuations in lactate and ROS production in infected cells over time. We also examined changes associated with the pre-invasion "kiss and spit" process using autofluorescence lifetime imaging, which similarly showed a more oxidized host cell with an increased proportion of bound NAD(P)H over 48 hours. Glucose metabolic flux analysis indicated that these changes are driven by NADH and NADP+ in T. gondii infection. In sum, metabolic changes in host cells with T. gondii infection were similar during full infection, and kiss and spit. Autofluorescence lifetime imaging can non-invasively monitor metabolic changes in host cells over a microbial infection time-course.

An Overview of the Use of Nanoparticles in Vaccine Development

Vaccines represent one of the most significant advancements in public health since they prevented morbidity and mortality in millions of people every year. Conventionally, vaccine technology focused on either live attenuated or inactivated vaccines. However, the application of nanotechnology to vaccine development revolutionized the field. Nanoparticles emerged in both academia and the pharmaceutical industry as promising vectors to develop future vaccines. Regardless of the striking development of nanoparticles vaccines research and the variety of conceptually and structurally different formulations proposed, only a few of them advanced to clinical investigation and usage in the clinic so far. This review covered some of the most important developments of nanotechnology applied to vaccine technologies in the last few years, focusing on the successful race for the preparation of lipid nanoparticles employed in the successful anti-SARS-CoV-2 vaccines.

The evolution of SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths and substantial morbidity worldwide. Intense scientific effort to understand the biology of SARS-CoV-2 has resulted in daunting numbers of genomic sequences. We witnessed evolutionary events that could mostly be inferred indirectly before, such as the emergence of variants with distinct phenotypes, for example transmissibility, severity and immune evasion. This Review explores the mechanisms that generate genetic variation in SARS-CoV-2, underlying the within-host and population-level processes that underpin these events. We examine the selective forces that likely drove the evolution of higher transmissibility and, in some cases, higher severity during the first year of the pandemic and the role of antigenic evolution during the second and third years, together with the implications of immune escape and reinfections, and the increasing evidence for and potential relevance of recombination. In order to understand how major lineages, such as variants of concern (VOCs), are generated, we contrast the evidence for the chronic infection model underlying the emergence of VOCs with the possibility of an animal reservoir playing a role in SARS-CoV-2 evolution, and conclude that the former is more likely. We evaluate uncertainties and outline scenarios for the possible future evolutionary trajectories of SARS-CoV-2.

Cherax quadricarinatus Resistant to Chequa iflavirus: A Pilot Study

High mortalities of redclaw crayfish (Cherax quadricarinatus) were reported from northern Queensland farms, mainly attributed to two viruses, Chequa iflavirus and Athtab bunyavirus. From a research population of redclaw crayfish with these pre-existing viral infections, five individuals were found uninfected by Chequa iflavirus but infected with Athtab bunyavirus. A pilot study was designed to examine if progeny crayfish from this cohort were resistant to infections by Chequa iflavirus. Two experiments measured changes in viral load with RT-qPCR. Seven donors, four negative controls and six crayfish injected with a purified virus or saline were used. In Experiment 1, the purified viral inoculum was injected into the crayfish, and they were bled 14 days post-injection (dpi). In Experiment 2, haemolymph containing the viruses was injected into the same crayfish and they were bled at 24 hpi, 48 hpi, 7 dpi and 14 dpi. In Exp. 1, the crayfish cleared Chequa iflavirus infections within 14 dpi, while in Exp. 2, it was within 24 hpi. One mortality was observed, but that crayfish had cleared the virus before dying. The number of copies of Athtab bunyavirus and the weights of the crayfish did not differ significantly (p > 0.05) between the control and injected crayfish. Histology of crayfish all showed that the haemolymph vessels were clear of granulomas, suggesting no bacterial involvement. There was no melanisation in the gill tissue of control crayfish, but it was prominent in virus-injected crayfish. Neither group had haemocytic infiltration of the muscle fibres. Anti-viral immune mechanisms of RNA interference and Cherax quadricarinatus Down Syndrome Cell Adhesion Molecule (DSCAM) are hypothesised to be involved in viral clearance. We conclude that these crayfish were resistant to Chequa iflavirus infections and could be commercially exploited by aquaculturists as a nuclear breeding stock if numbers are increased over time.

Sleep and Neuroimmunomodulation for Maintenance of Optimum Brain Function: Role of Noradrenaline

Immune function and sleep are two normal physiological processes to protect the living organism from falling sick. There is hardly any disease in which they remain unaffected, though the quantum of effect may differ. Therefore, we propose the existence of a strong correlation between sleep (quality or quantity) and immune response. This may be supported by the fact that sleep loss modulates many of the immunological molecules, which includes interferons; however, not much is known about their mechanism of action. Sleep is divided into rapid eye movement sleep (REMS) and non-REMS. For practical reasons, experimental studies have been conducted mostly by inducing loss of REMS. It has been shown that withdrawal of noradrenaline (NA) is a necessity for generation of REMS. Moreover, NA level increases in the brain upon REMS loss and the elevated NA is responsible for many of the sleep loss-associated symptoms. In this review, we describe how sleep (and its disturbance/loss) modulates the immune system by modulating the NA level in the brain or vice versa to maintain immune functions, physiological homeostasis, and normal healthy living. The increased levels of NA during REMS loss may cause neuroinflammation possibly by glial activation (as NA is a key modulator of microglia). Therefore, maintaining sleep hygiene plays a crucial role for a normal healthy living.

Midgut membrane protein BmSUH facilitates Bombyx mori nucleopolyhedrovirus oral infection

Baculoviruses are virulent pathogens that infect a wide range of insects. They initiate infections via specific interactions between the structural proteins on the envelopes of occlusion-derived virions (ODVs) and the midgut cell surface receptors in hosts. However, host factors that are hijacked by baculoviruses for efficient infection remain largely unknown. In this study, we identified a membrane-associated protein sucrose hydrolase (BmSUH) as an ODV binding factor during Bombyx mori nucleopolyhedrovirus (BmNPV) primary infection. BmSUH was specifically expressed in the midgut microvilli where the ODV-midgut fusion happened. Knockout of BmSUH by CRISPR/Cas9 resulted in a significantly higher survival rate after BmNPV orally infection. Liquid chromatography-tandem mass spectrometry analysis and co-immunoprecipitation analysis demonstrated that PIF protein complex required for ODV binding could interact with BmSUH. Furthermore, fluorescence dequenching assay showed that the amount of ODV binding and fusion to the midgut decreased in BmSUH mutants compared to wild-type silkworm, suggesting the role of BmSUH as an ODV binding factor that mediates the ODV entry process. Based on a multilevel survey, the data showed that BmSUH acted as a host factor that facilitates BmNPV oral infection. More generally, this study indicated that disrupting essential protein-protein interactions required for baculovirus efficient entry may be broadly applicable to against viral infection.

Baculoviridae is a large family of pathogens that infect insects and frequently cause fatal diseases. Bombyx mori nucleopolyhedrovirus (BmNPV) is a major threat to the sericulture industry. Although we have learned a lot about baculoviruses over the past several decades, the detailed interaction patterns between host proteins and viral proteins that lead to infection remain underexplored. Here, we determined that BmSUH, a midgut microvilli protein, was required for the efficient oral infection of BmNPV. Our research suggests that BmSUH mediates the entry of occlusion-derived virions into the midgut epithelia by interacting with per os infectivity factors. According to the findings, inhibition of viral binding to host cells is an attractive strategy to prevent infection. This study provides an approach for preventing BmNPV infection through developing genetic resistance to viruses by using CRISPR/Cas9 system to abolish the host factors that are essential for viral entry.

SARS-CoV-2 infection produces chronic pulmonary epithelial and immune cell dysfunction with fibrosis in mice

A subset of individuals who recover from coronavirus disease 2019 (COVID-19) develop post-acute sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (PASC), but the mechanistic basis of PASC-associated lung abnormalities suffers from a lack of longitudinal tissue samples. The mouse-adapted SARS-CoV-2 strain MA10 produces an acute respiratory distress syndrome in mice similar to humans. To investigate PASC pathogenesis, studies of MA10-infected mice were extended from acute to clinical recovery phases. At 15 to 120 days after virus clearance, pulmonary histologic findings included subpleural lesions composed of collagen, proliferative fibroblasts, and chronic inflammation, including tertiary lymphoid structures. Longitudinal spatial transcriptional profiling identified global reparative and fibrotic pathways dysregulated in diseased regions, similar to human COVID-19. Populations of alveolar intermediate cells, coupled with focal up-regulation of profibrotic markers, were identified in persistently diseased regions. Early intervention with antiviral EIDD-2801 reduced chronic disease, and early antifibrotic agent (nintedanib) intervention modified early disease severity. This murine model provides opportunities to identify pathways associated with persistent SARS-CoV-2 pulmonary disease and test countermeasures to ameliorate PASC.

Interaction analysis of FADS2 gene variants with chronic hepatitis B infection in Chinese patients

The risk of chronic hepatitis B (CHB) infection is often affected by polyunsaturated fatty acids (PUFAs) metabolism which is strongly influenced by single nucleotide polymorphisms (SNPs) within the PUFA metabolic pathway. Given this, we designed this study to determine the relationship between specific polymorphisms within fatty acid desaturase 2 (FADS2), a key enzyme in PUFA metabolism, and CHB infection. We completed this evaluation using a case-control study comprising 230 CHB patients and 234 unrelated healthy controls in which the genetic relationships between three previously identified SNPs, isolated via mass spectrometry, and CHB infection. Our data revealed that none of these three SNPs (rs174568, rs174601, and rs2727270) were significantly associated with susceptibility to CHB infection when compared to healthy controls. However, when we stratified our cohort by sex, male subjects with the TC genotype for FADS2 exhibited a decreased risk for CHB infection (OR = 0.62, 95%CI = 0.39-0.96; OR = 0.64, 95%CI = 0.41-1.00; OR = 0.57, 95%CI = 0.36-0.90). Furthermore, age stratification revealed that both the T allele and the TC genotypes for each of the three target SNPs were less common in Chinese CHB cases in people younger than 50 years old. Correlation analysis also revealed that there was no statistically significant relationship between these three SNPs and HBV-DNA replication or hepatitis B surface antigen (HBsAg) levels. Thus, our data suggests that rs174568, rs174601, and rs2727270 may affect the CHB outcomes in various age or sex subgroups, suggesting that they may be useful predictive or diagnostic biomarkers of CHB infection in some populations.

A model of persistent post SARS-CoV-2 induced lung disease for target identification and testing of therapeutic strategies

COVID-19 survivors develop post-acute sequelae of SARS-CoV-2 (PASC), but the mechanistic basis of PASC-associated lung abnormalities suffers from a lack of longitudinal samples. Mouse-adapted SARS-CoV-2 MA10 produces an acute respiratory distress syndrome (ARDS) in mice similar to humans. To investigate PASC pathogenesis, studies of MA10-infected mice were extended from acute disease through clinical recovery. At 15-120 days post-virus clearance, histologic evaluation identified subpleural lesions containing collagen, proliferative fibroblasts, and chronic inflammation with tertiary lymphoid structures. Longitudinal spatial transcriptional profiling identified global reparative and fibrotic pathways dysregulated in diseased regions, similar to human COVID-19. Populations of alveolar intermediate cells, coupled with focal upregulation of pro-fibrotic markers, were identified in persistently diseased regions. Early intervention with antiviral EIDD-2801 reduced chronic disease, and early anti-fibrotic agent (nintedanib) intervention modified early disease severity. This murine model provides opportunities to identify pathways associated with persistent SARS-CoV-2 pulmonary disease and test countermeasures to ameliorate PASC.

Host Defenses to Viruses: Lessons from Inborn Errors of Immunity

The constant battle between viruses and their hosts leads to their reciprocal evolution. Viruses regularly develop survival strategies against host immunity, while their ability to replicate and disseminate is countered by the antiviral defense mechanisms that host mount. Although most viral infections are generally controlled by the host’s immune system, some viruses do cause overt damage to the host. The outcome can vary widely depending on the properties of the infecting virus and the circumstances of infection but also depends on several factors controlled by the host, including host genetic susceptibility to viral infections. In this narrative review, we provide a brief overview of host immunity to viruses and immune-evasion strategies developed by viruses. Moreover, we focus on inborn errors of immunity, these being considered a model for studying host response mechanisms to viruses. We finally report exemplary inborn errors of both the innate and adaptive immune systems that highlight the role of proteins involved in the control of viral infections.

SARS-CoV-2-Specific Immune Response and the Pathogenesis of COVID-19

The review aims to consolidate research findings on the molecular mechanisms and virulence and pathogenicity characteristics of coronavirus disease (COVID-19) causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and their relevance to four typical stages in the development of acute viral infection. These four stages are invasion; primary blockade of antiviral innate immunity; engagement of the virus's protection mechanisms against the factors of adaptive immunity; and acute, long-term complications of COVID-19. The invasion stage entails the recognition of the spike protein (S) of SARS-CoV-2 target cell receptors, namely, the main receptor (angiotensin-converting enzyme 2, ACE2), its coreceptors, and potential alternative receptors. The presence of a diverse repertoire of receptors allows SARS-CoV-2 to infect various types of cells, including those not expressing ACE2. During the second stage, the majority of the polyfunctional structural, non-structural, and extra proteins SARS-CoV-2 synthesizes in infected cells are involved in the primary blockage of antiviral innate immunity. A high degree of redundancy and systemic action characterizing these pathogenic factors allows SARS-CoV-2 to overcome antiviral mechanisms at the initial stages of invasion. The third stage includes passive and active protection of the virus from factors of adaptive immunity, overcoming of the barrier function at the focus of inflammation, and generalization of SARS-CoV-2 in the body. The fourth stage is associated with the deployment of variants of acute and long-term complications of COVID-19. SARS-CoV-2's ability to induce autoimmune and autoinflammatory pathways of tissue invasion and development of both immunosuppressive and hyperergic mechanisms of systemic inflammation is critical at this stage of infection.

Genome-Wide Analysis of Alternative Splicing during Host-Virus Interactions in Chicken

The chicken is a model animal for the study of evolution, immunity and development. In addition to their use as a model organism, chickens also represent an important agricultural product. Pathogen invasion has already been shown to modulate the expression of hundreds of genes, but the role of alternative splicing in avian virus infection remains unclear. We used RNA-seq data to analyze virus-induced changes in the alternative splicing of Gallus gallus, and found that a large number of alternative splicing events were induced by virus infection both in vivo and in vitro. Virus-responsive alternative splicing events preferentially occurred in genes involved in metabolism and transport. Many of the alternatively spliced transcripts were also expressed from genes with a function relating to splicing or immune response, suggesting a potential impact of virus infection on pre-mRNA splicing and immune gene regulation. Moreover, exon skipping was the most frequent AS event in chickens during virus infection. This is the first report describing a genome-wide analysis of alternative splicing in chicken and contributes to the genomic resources available for studying host-virus interaction in this species. Our analysis fills an important knowledge gap in understanding the extent of genome-wide alternative splicing dynamics occurring during avian virus infection and provides the impetus for the further exploration of AS in chicken defense signaling and homeostasis.

Eradication of Bovine Viral Diarrhoea (BVD) in Cattle in Switzerland: Lessons Taught by the Complex Biology of the Virus

Bovine viral diarrhoea virus (BVDV) and related ruminant pestiviruses occur worldwide and cause considerable economic losses in livestock and severely impair animal welfare. Switzerland started a national mandatory control programme in 2008 aiming to eradicate BVD from the Swiss cattle population. The peculiar biology of pestiviruses with the birth of persistently infected (PI) animals upon in utero infection in addition to transient infection of naïve animals requires vertical and horizontal transmission to be taken into account. Initially, every animal was tested for PI within the first year, followed by testing for the presence of virus in all newborn calves for the next four years. Prevalence of calves being born PI thus diminished substantially from around 1.4% to <0.02%, which enabled broad testing for the virus to be abandoned and switching to economically more favourable serological surveillance with vaccination being prohibited. By the end of 2020, more than 99.5% of all cattle farms in Switzerland were free of BVDV but eliminating the last remaining PI animals turned out to be a tougher nut to crack. In this review, we describe the Swiss BVD eradication scheme and the hurdles that were encountered and still remain during the implementation of the programme. The main challenge is to rapidly identify the source of infection in case of a positive result during antibody surveillance, and to efficiently protect the cattle population from re-infection, particularly in light of the endemic presence of the related pestivirus border disease virus (BDV) in sheep. As a consequence of these measures, complete eradication will (hopefully) soon be achieved, and the final step will then be the continuous documentation of freedom of disease.

Of Mice and Schoolchildren: A Conceptual History of Herd Immunity

This article explores a tension at the core of the concept of herd immunity that has been overlooked in public and scientific discussions-namely: how can immunity, a phenomenon of individual biological defenses, be made relevant to populations? How can collectives be considered "immune"? Over the course of more than a century of use of the term, scientists have developed many different understandings of the concept in response to this inherent tension. Originating among veterinary scientists in the United States in the late 19th century, the concept was adopted by British scientists researching human infectious disease by the early 1920s. It soon became a staple concept for epidemiologists interested in disease ecology, helping to articulate the population dynamics of diseases such as diphtheria and influenza. Finally, though more traditional understandings of the concept remained in scientific use, in the era after World War II, it increasingly came to signal the objective and outcome of mass vaccination. Recognizing the complexity of scientific efforts to resolve the paradox of herd immunity may help us consider the best distribution of immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Interaction analysis of gene variants related to one-carbon metabolism with chronic hepatitis B infection in Chinese patients

BACKGROUND

The risk of chronic hepatitis B (CHB) infection is influenced by aberrant DNA methylation and altered nucleotide synthesis and repair, possibly caused by polymorphic variants in one-carbon metabolism genes. In the present study, we investigated the relationship between polymorphisms belonging to the one-carbon metabolic pathway and CHB infection.

METHODS

A case-control study using 230 CHB patients and 234 unrelated healthy controls was carried out to assess the genetic association of 24 single nucleotide polymorphisins (SNPs) determined by mass spectrometry.

RESULTS

Three SNPs, comprising rs10717122 and rs2229717 in serine hydroxymethyltransferase1/2 (SHMT2) and rs585800 in betaine-homocysteine S-methyltransferase (BHMT), were associated with the risk of CHB. Patients with DEL allele, DEL.DEL and DEL.T genotypes of rs10717122 had a 1.40-, 2.00- and 1.83-fold increased risk for CHB, respectively. Cases inheriting TA genotype of rs585800 had a 2.19-fold risk for CHB infection. The T allele of rs2229717 was less represented in the CHB cases (odds ratio = 0.66, 95% confidence interval = 0.48-0.92). The T allele of rs2229717 was less in patients with a low hepatitis B virus-DNA level compared to the control group (odds ratio = 0.49, 95% confidence interval = 0.25-0.97) and TT genotype of rs2229717 had a significant correlation with hepatitis B surface antigen level (p = 0.0195). Further gene-gene interaction analysis showed that subjects carrying the rs10717122 DEL.DEL/DEL.T and rs585800 TT/TA genotypes had a 2.74-fold increased risk of CHB.

CONCLUSIONS

The results of the present study suggest that rs10717122, rs585800 and rs2229717 and gene-gene interactions of rs10717122 and rs585800 affect the outcome of CHB infection, at the same time as indicating their usefulness as a predictive and diagnostic biomarker of CHB infection.

Antimicrobial resistance of ocular microbes and the role of antimicrobial peptides

Isolation of antimicrobial-resistant microbes from ocular infections may be becoming more frequent. Infections caused by these microbes can be difficult to treat and lead to poor outcomes. However, new therapies are being developed which may help improve clinical outcomes. This review examines recent reports on the isolation of antibiotic-resistant microbes from ocular infections. In addition, an overview of the development of some new antibiotic therapies is given. The recent literature regarding antibiotic use and resistance, isolation of antibiotic-resistant microbes from ocular infections and the development of potential new antibiotics that can be used to treat these infections was reviewed. Ocular microbial infections are a global public health issue as they can result in vision loss which compromises quality of life. Approximately 70 per cent of ocular infections are caused by bacteria including Chlamydia trachomatis, Staphylococcus aureus, and Pseudomonas aeruginosa and fungi such as Candida albicans, Aspergillus spp. and Fusarium spp. Resistance to first-line antibiotics such as fluoroquinolones and azoles has increased, with resistance of S. aureus isolates from the USA to fluoroquinolones reaching 32 per cent of isolates and 35 per cent being methicillin-resistant (MRSA). Lower levels of MRSA (seven per cent) were isolated by an Australian study. Antimicrobial peptides, which are broad-spectrum alternatives to antibiotics, have been tested as possible new drugs. Several have shown promise in animal models of keratitis, especially treating P. aeruginosa, S. aureus or C. albicans infections. Reports of increasing resistance of ocular isolates to mainstay antibiotics are a concern, and there is evidence that for ocular surface disease this resistance translates into worse clinical outcomes. New antibiotics are being developed, but not by large pharmaceutical companies and mostly in university research laboratories and smaller biotech companies. Antimicrobial peptides show promise in treating keratitis.

An immune epigenetic insight to COVID-19 infection

Severe acute respiratory syndrome coronavirus-2 is a positive-sense RNA virus, a causal agent of ongoing COVID-19 pandemic. ACE2R methylation across three CpG sites (cg04013915, cg08559914, cg03536816) determines the host cell's entry. It regulates ACE2 expression by controlling the SIRT1 and KDM5B activity. Further, it regulates Type I and III IFN response by modulating H3K27me3 and H3K4me3 histone mark. SARS-CoV-2 protein with bromodomain and protein E mimics bromodomain histones and evades from host immune response. The 2'-O MTases mimics the host's cap1 structure and plays a vital role in immune evasion through Hsp90-mediated epigenetic process to hijack the infected cells. Although the current review highlighted the critical epigenetic events associated with SARS-CoV-2 immune evasion, the detailed mechanism is yet to be elucidated.

A comparative genomics-based study of positive strand RNA viruses emphasizing on SARS-CoV-2 utilizing dinucleotide signature, codon usage and codon context analyses

The novel corona virus disease or COVID-19 caused by a positive strand RNA virus (PRV) called SARS-CoV-2 is plaguing the entire planet as we conduct this study. In this study a multifaceted analysis was carried out employing dinucleotide signature, codon usage and codon context to compare and unravel the genomic as well as genic characteristics of the SARS-CoV-2 isolates and how they compare to other PRVs which represents some of the most pathogenic human viruses. The main emphasis of this study was to comprehend the codon biology of the SARS-CoV-2 in the backdrop of the other PRVs like Poliovirus, Japanese encephalitis virus, Hepatitis C virus, Norovirus, Rubella virus, Semliki Forest virus, Zika virus, Dengue virus, Human rhinoviruses and the Betacoronaviruses since codon usage pattern along with the nucleotide composition prevalent within the viral genome helps to understand the biology and evolution of viruses. Our results suggest discrete genomic dinucleotide signature within the PRVs. Some of the genes from the different SARS-CoV-2 isolates were also found to demonstrate heterogeneity in terms of their dinucleotide signature. The SARS-CoV-2 isolates also demonstrated a codon context trend characteristically dissimilar to the other PRVs. The findings of this study are expected to contribute to the developing global knowledge base in countering COVID-19.

Cell-Mediated Responses to Human Metapneumovirus Infection

Viruses are the most common cause of acute respiratory tract infections (ARTI). Human metapneumovirus (hMPV) frequently causes viral pneumonia which can become life-threatening if the virus spreads to the lungs. Even though hMPV was only isolated in 2001, this negative-stranded RNA virus has probably been circulating in the human population for many decades. Interestingly, almost all adults have serologic evidence of hMPV infection. A well-established host immune response is evoked when hMPV infection occurs. However, the virus has evolved to circumvent and even exploit the host immune response. Further, infection with hMPV induces a weak memory response, and re-infections during life are common. In this review, we provide a comprehensive overview of the different cell types involved in the immune response in order to better understand the immunopathology induced by hMPV. Such knowledge may contribute to the development of vaccines and therapeutics directed against hMPV.

Cell-Mediated Responses to Human Metapneumovirus Infection

Viruses are the most common cause of acute respiratory tract infections (ARTI). Human metapneumovirus (hMPV) frequently causes viral pneumonia which can become life-threatening if the virus spreads to the lungs. Even though hMPV was only isolated in 2001, this negative-stranded RNA virus has probably been circulating in the human population for many decades. Interestingly, almost all adults have serologic evidence of hMPV infection. A well-established host immune response is evoked when hMPV infection occurs. However, the virus has evolved to circumvent and even exploit the host immune response. Further, infection with hMPV induces a weak memory response, and re-infections during life are common. In this review, we provide a comprehensive overview of the different cell types involved in the immune response in order to better understand the immunopathology induced by hMPV. Such knowledge may contribute to the development of vaccines and therapeutics directed against hMPV.

Cell-Mediated Responses to Human Metapneumovirus Infection

Viruses are the most common cause of acute respiratory tract infections (ARTI). Human metapneumovirus (hMPV) frequently causes viral pneumonia which can become life-threatening if the virus spreads to the lungs. Even though hMPV was only isolated in 2001, this negative-stranded RNA virus has probably been circulating in the human population for many decades. Interestingly, almost all adults have serologic evidence of hMPV infection. A well-established host immune response is evoked when hMPV infection occurs. However, the virus has evolved to circumvent and even exploit the host immune response. Further, infection with hMPV induces a weak memory response, and re-infections during life are common. In this review, we provide a comprehensive overview of the different cell types involved in the immune response in order to better understand the immunopathology induced by hMPV. Such knowledge may contribute to the development of vaccines and therapeutics directed against hMPV.

Exosomal miRNAs: novel players in viral infection

Exosomes are secreted nanovesicles that are able to transfer their cargo (such as miRNAs) between cells. To determine to what extent exosomes and exosomal miRNAs are involved in the pathogenesis, progression and diagnosis of viral infections. The scientific literature (PubMed and Google Scholar) was searched from 1970 to 2019. The complex biogenesis of exosomes and miRNAs was reviewed. Exosomes contain both viral and host miRNAs that can be used as diagnostic biomarkers for viral diseases. Viral proteins can alter miRNAs, and conversely miRNAs can alter the host response to viral infections in a positive or negative manner. It is expected that exosomal miRNAs will be increasingly used for diagnosis, monitoring and even treatment of viral infections.

Viral Innate Immune Evasion and the Pathogenesis of Emerging RNA Virus Infections

Positive-sense single-stranded RNA (+ssRNA) viruses comprise many (re-)emerging human pathogens that pose a public health problem. Our innate immune system and, in particular, the interferon response form the important first line of defence against these viruses. Given their genetic flexibility, these viruses have therefore developed multiple strategies to evade the innate immune response in order to optimize their replication capacity. Already many molecular mechanisms of innate immune evasion by +ssRNA viruses have been identified. However, research addressing the effect of host innate immune evasion on the pathology caused by viral infections is less prevalent in the literature, though very relevant and interesting. Since interferons have been implicated in inflammatory diseases and immunopathology in addition to their protective role in infection, antagonizing the immune response may have an ambiguous effect on the clinical outcome of the viral disease. Therefore, this review discusses what is currently known about the role of interferons and host immune evasion in the pathogenesis of emerging coronaviruses, alphaviruses and flaviviruses.

Exploitation of glycosylation in enveloped virus pathobiology

Glycosylation is a ubiquitous post-translational modification responsible for a multitude of crucial biological roles. As obligate parasites, viruses exploit host-cell machinery to glycosylate their own proteins during replication. Viral envelope proteins from a variety of human pathogens including HIV-1, influenza virus, Lassa virus, SARS, Zika virus, dengue virus, and Ebola virus have evolved to be extensively glycosylated. These host-cell derived glycans facilitate diverse structural and functional roles during the viral life-cycle, ranging from immune evasion by glycan shielding to enhancement of immune cell infection. In this review, we highlight the imperative and auxiliary roles glycans play, and how specific oligosaccharide structures facilitate these functions during viral pathogenesis. We discuss the growing efforts to exploit viral glycobiology in the development of anti-viral vaccines and therapies.

Balancing sensitivity and specificity in distinguishing TCR groups by CDR sequence similarity

Background

Repertoire sequencing is enabling deep explorations into the cellular immune response, including the characterization of commonalities and differences among T cell receptor (TCR) repertoires from different individuals, pathologies, and antigen specificities. In seeking to understand the generality of patterns observed in different groups of TCRs, it is necessary to balance how well each pattern represents the diversity among TCRs from one group (sensitivity) vs. how many TCRs from other groups it also represents (specificity). The variable complementarity determining regions (CDRs), particularly the third CDRs (CDR3s) interact with major histocompatibility complex (MHC)-presented epitopes from putative antigens, and thus encode the determinants of recognition.

Results

We here systematically characterize the predictive power that can be obtained from CDR3 sequences, using representative, readily interpretable methods for evaluating CDR sequence similarity and then clustering and classifying sequences based on similarity. An initial analysis of CDR3s of known structure, clustered by structural similarity, helps calibrate the limits of sequence diversity among CDRs that might have a common mode of interaction with presented epitopes. Subsequent analyses demonstrate that this same range of sequence similarity strikes a favorable specificity/sensitivity balance in distinguishing twins from non-twins based on overall CDR3 repertoires, classifying CDR3 repertoires by antigen specificity, and distinguishing general pathologies.

Conclusion

We conclude that within a fairly broad range of sequence similarity, matching CDR3 sequences are likely to share specificities.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2864-8) contains supplementary material, which is available to authorized users.

Antiviral defense in salmonids - Mission made possible?

Viral diseases represent one of the major threats for salmonid aquaculture. Survival from viral infections are highly dependent on host innate antiviral immune defense, where interferons are of crucial importance. Neutralizing antibodies and T cell effector mechanisms mediate long-term antiviral protection. Despite an immune cell repertoire comparable to higher vertebrates, farmed fish often fail to mount optimal antiviral protection. In the quest to multiply and spread, viruses utilize a variety of strategies to evade or escape the host immune system. Understanding the specific interplay between viruses and host immunity at depth is crucial for developing successful vaccination and treatment strategies in mammals. However, this knowledge base is still limited for pathogenic fish viruses. Here, we have focused on five RNA viruses with major impact on salmonid aquaculture: Salmonid alphavirus, Infectious salmon anemia virus, Infectious pancreatic necrosis virus, Piscine orthoreovirus and Piscine myocarditis virus. This review explore the protective immune responses that salmonids mount to these viruses and the existing knowledge on how the viruses counteract and/or bypass the immune response, including their IFN antagonizing effects and their mechanisms to establish persisting infections.

What if protective immunity is antigen-driven and not due to so-called "memory" B and T cells?

Vaccines or early childhood exposure to infection mediate immunity, that is, improved resistance against disease and death caused by a second infection with the same agent. This has been explained by and equaled to immunological memory, that is, an "altered immune system behavior" that is maintained in a presumably antigen-independent fashion. This review summarizes epidemiological and experimental data, that largely falsify this idea and that show that periodic re-exposure to antigen either, artificially as vaccines or naturally as low-level persisting antigens or infections, or immune complexes on follicular dendritic cells or endemic re-exposure is necessary for protection. Both, the huge success of vaccines in controlling childhood infections, the reduction in clinical disease and the chance of endemically re-exposure, have gradually reduced periodical re-exposure to infections and thereby endangered protective herd immunity. In parallel, vaccine deniers have created susceptibility islands even in an otherwise well vaccinated population, thereby creating a very new situation when compared to the later parts of the 20th century. If protective Immunity is-as emphasized here-antigen driven, then increasingly frequent revaccinations will be necessary (even more so with too much attenuated vaccines) to maintain both herd immunity and individual resistance to acute infections. Of course, this rule also applies to tumor vaccines.

Persistence and Sexual Transmission of Filoviruses

There is an increasing frequency of reports regarding the persistence of the Ebola virus (EBOV) in Ebola virus disease (EVD) survivors. During the 2014⁻2016 West African EVD epidemic, sporadic transmission events resulted in the initiation of new chains of human-to-human transmission. Multiple reports strongly suggest that these re-emergences were linked to persistent EBOV infections and included sexual transmission from EVD survivors. Asymptomatic infection and long-term viral persistence in EVD survivors could result in incidental introductions of the Ebola virus in new geographic regions and raise important national and local public health concerns. Alarmingly, although the persistence of filoviruses and their potential for sexual transmission have been documented since the emergence of such viruses in 1967, there is limited knowledge regarding the events that result in filovirus transmission to, and persistence within, the male reproductive tract. Asymptomatic infection and long-term viral persistence in male EVD survivors could lead to incidental transfer of EBOV to new geographic regions, thereby generating widespread outbreaks that constitute a significant threat to national and global public health. Here, we review filovirus testicular persistence and discuss the current state of knowledge regarding the rates of persistence in male survivors, and mechanisms underlying reproductive tract localization and sexual transmission.

The role of myeloid-derived suppressor cells in chronic infectious diseases and the current methodology available for their study

An effective pathogen has the ability to evade the immune response. The strategies used to achieve this may be based on the direct action of virulence factors or on the induction of host factors. Myeloid-derived suppressor cells (MDSCs) are immune cells with an incredible ability to suppress the inflammatory response, which makes them excellent targets to be exploited by pathogenic bacteria, viruses, or parasites. In this review, we describe the origin and suppressive mechanisms of MDSCs, as well as their role in chronic bacterial, viral, and parasitic infections, where their expansion seems to be essential in the chronicity of the disease. We also analyze the disadvantages of current MDSC depletion strategies and the different in vitro generation methods, which can be useful tools for the deeper study of these cells in the context of microbial infections.

Human lung epithelial cells support human metapneumovirus persistence by overcoming apoptosis

Human metapneumovirus (hMPV) has been identified as a major cause of lower respiratory tract infection in children. Epidemiological and molecular evidence has highlighted an association between severe childhood respiratory viral infection and chronic lung diseases, such as asthma and chronic obstructive pulmonary disease. Currently, animal models have demonstrated the ability of hMPV to persist in vivo suggesting a role of the virus in asthma development in children. However, mechanisms involved in hMPV persistence in the respiratory tract are not yet understood. In the present study we monitored hMPV infection in human alveolar epithelial A549 cells in order to understand if the virus is able to persist in these cells upon acute infection. Our data show that hMPV initially induces an apoptotic process in A549 cells through poly (ADP-ribose) polymerase 1 cleavage, caspase-3/7 activation and Wee1 activity. The hMPV-infected cells were then able to overcome the apoptotic pathway and cell cycle arrest in G2/M by expressing B-cell lymphoma 2 and to acquire a reservoir cell phenotype with constant production of infectious virus. These findings provide evidence of the ability of hMPV to persist in alveolar epithelial cells and help in understanding the mechanisms responsible for hMPV persistence in the human respiratory tract.

Exploitation of Interleukin-10 (IL-10) Signaling Pathways: Alternate Roles of Viral and Cellular IL-10 in Rhesus Cytomegalovirus Infection

There is accumulating evidence that the viral interleukin-10 (vIL-10) ortholog of both human and rhesus cytomegalovirus (HCMV and RhCMV, respectively) suppresses the functionality of cell types that are critical to contain virus dissemination and help shape long-term immunity during the earliest virus-host interactions. In particular, exposure of macrophages, peripheral blood mononuclear cells, monocyte-derived dendritic cells, and plasmacytoid dendritic cells to vIL-10 suppresses multiple effector functions including, notably, those that link innate and adaptive immune responses. Further, vaccination of RhCMV-uninfected rhesus macaques with nonfunctional forms of RhCMV vIL-10 greatly restricted parameters of RhCMV infection following RhCMV challenge of the vaccinees. Vaccinees exhibited significantly reduced shedding of RhCMV in saliva and urine following RhCMV challenge compared to shedding in unvaccinated controls. Based on the evidence that vIL-10 is critical during acute infection, the role of vIL-10 during persistent infection was analyzed in rhesus macaques infected long term with RhCMV to determine whether postinfection vaccination against vIL-10 could change the virus-host balance. RhCMV-seropositive macaques, which shed RhCMV in saliva, were vaccinated with nonfunctional RhCMV vIL-10, and shedding levels of RhCMV in saliva were evaluated. Following robust increases in vIL-10-binding and vIL-10-neutralizing antibodies, shedding levels of RhCMV modestly declined, consistent with the interpretation that vIL-10 may play a functional role during persistent infection. However, a more significant association was observed between the levels of cellular IL-10 secreted in peripheral blood mononuclear cells exposed to RhCMV antigens and shedding of RhCMV in saliva. This result implies that RhCMV persistence is associated with the induction of cellular IL-10 receptor-mediated signaling pathways.

IMPORTANCE

Human health is adversely impacted by viruses that establish lifelong infections that are often accompanied with increased morbidity and mortality (e.g., infections with HIV, hepatitis C virus, or human cytomegalovirus). A longstanding but unfulfilled goal has been to develop postinfection vaccine strategies that could "reboot" the immune system of an infected individual in ways that would enable the infected host to develop immune responses that clear reservoirs of persistent virus infection, effectively curing the host of infection. This concept was evaluated in rhesus macaques infected long term with rhesus cytomegalovirus by repeatedly immunizing infected animals with nonfunctional versions of the rhesus cytomegalovirus-encoded viral interleukin-10 immune-modulating protein. Following vaccine-mediated boosting of antibody titers to viral interleukin-10, there was modest evidence for increased immunological control of the virus following vaccination. More significantly, data were also obtained that indicated that rhesus cytomegalovirus is able to persist due to upregulation of the cellular interleukin-10 signaling pathway.

Hit-and-run, hit-and-stay, and commensal bacteria present different peptide content when viewed from the perspective of the T cell

Different types of bacteria face different pressures from the immune system, with those that persist ("hit-and-stay") potentially having to adapt more in order to escape than those prone to short-lived infection ("hit-and-run"), and with commensal bacteria potentially different from both due to additional physical mechanisms for avoiding immune detection. The Janus Immunogenicity Score (JIS) was recently developed to assess the likelihood of T cell recognition of an antigen, using an analysis that considers both binding of a peptide within the antigen by major histocompatability complex (MHC) and recognition of the peptide:MHC complex by cognate T cell receptor (TCR). This score was shown to be predictive of T effector vs. T regulatory or null responses in experimental data, as well as to distinguish viruses representative of the hit-and-stay vs. hit-and-run phenotypes. Here, JIS-based analyses were conducted in order to characterize the extent to which the pressure to avoid T cell recognition is manifested in genomic differences among representative hit-and-run, hit-and-stay, and commensal bacteria. Overall, extracellular proteins were found to have different JIS profiles from cytoplasmic ones. Contrasting the bacterial groups, extracellular proteins were shown to be quite different across the groups, much more so than intracellular proteins. The differences were evident even at the level of corresponding peptides in homologous protein pairs from hit-and-run and hit-and-stay bacteria. The multi-level analysis of patterns of immunogenicity across different groups of bacteria provides a new way to approach questions of bacterial immune camouflage or escape, as well as to approach the selection and optimization of candidates for vaccine design.

RSV P-protein impairs extrinsic apoptosis pathway in a macrophage-like cell line persistently infected with respiratory syncytial virus

Disabling apoptosis is practically a mandatory step for establishing and maintaining viral persistence in host cells. Thus, persisting viruses have evolved strategies to impair apoptosis mechanisms. Apoptosis can be induced through either the intrinsic or the extrinsic pathway. Previously, we reported that staurosporine-induced intrinsic apoptotic pathway was down-regulated in a macrophage cell line persistently infected with respiratory syncytial virus (RSV, MΦP). In the present study, our results showed that the extrinsic apoptotic pathway was also impaired in this cell line and that RSV P-protein interfered with the onset of the extrinsic apoptotic process. In this work, we analyzed and compared the expression of several components of the DISC complex (i.e., TNF-α, TNFR1, caspase-8, and cIAP2) in MΦP cells with that in mock-infected macrophages. Additionally, by using DNA sequence analysis in silico, we searched for an RSV protein putatively interfering with the triggering of the extrinsic apoptotic process. The analysis showed that viral P-protein shared a 52% homology with the caspase-8 death domain. Subsequently, the nucleic acid sequence of the viral P-protein was cloned and transfected into the macrophage cell line; the effect of this transfection on staurosporine-induced apoptosis was evaluated by assaying for cell viability and caspases-8 and -9 activity. The results revealed that although caspase-9 was activated, the activity of the caspase-8 was impaired in the RSV P-protein transfected cells; more of these cells survived than did mock-transfected cells. These findings suggest that P-protein impaired the extrinsic pathway of apoptosis. Our findings contribute to the understanding of the mechanism by which viral proteins subvert the extrinsic apoptosis process in cells persistently infected with RSV.

DNA methylation at hepatitis B viral integrants is associated with methylation at flanking human genomic sequences

Integration of DNA viruses into the human genome plays an important role in various types of tumors, including hepatitis B virus (HBV)–related hepatocellular carcinoma. However, the molecular details and clinical impact of HBV integration on either human or HBV epigenomes are unknown. Here, we show that methylation of the integrated HBV DNA is related to the methylation status of the flanking human genome. We developed a next-generation sequencing-based method for structural methylation analysis of integrated viral genomes (denoted G-NaVI). This method is a novel approach that enables enrichment of viral fragments for sequencing using unique baits based on the sequence of the HBV genome. We detected integrated HBV sequences in the genome of the PLC/PRF/5 cell line and found variable levels of methylation within the integrated HBV genomes. Allele-specific methylation analysis revealed that the HBV genome often became significantly methylated when integrated into highly methylated host sites. After integration into unmethylated human genome regions such as promoters, however, the HBV DNA remains unmethylated and may eventually play an important role in tumorigenesis. The observed dynamic changes in DNA methylation of the host and viral genomes may functionally affect the biological behavior of HBV. These findings may impact public health given that millions of people worldwide are carriers of HBV. We also believe our assay will be a powerful tool to increase our understanding of the various types of DNA virus-associated tumorigenesis.

mRNA Structural constraints on EBNA1 synthesis impact on in vivo antigen presentation and early priming of CD8+ T cells

Recent studies have shown that virally encoded mRNA sequences of genome maintenance proteins from herpesviruses contain clusters of unusual structural elements, G-quadruplexes, which modulate viral protein synthesis. Destabilization of these G-quadruplexes can override the inhibitory effect on self-synthesis of these proteins. Here we show that the purine-rich repetitive mRNA sequence of Epstein-Barr virus encoded nuclear antigen 1 (EBNA1) comprising G-quadruplex structures, limits both the presentation of MHC class I-restricted CD8⁺ T cell epitopes by CD11c⁺ dendritic cells in draining lymph nodes and early priming of antigen-specific CD8⁺ T-cells. Destabilization of the G-quadruplex structures through codon-modification significantly enhanced in vivo antigen presentation and activation of virus-specific T cells. Ex vivo imaging of draining lymph nodes by confocal microscopy revealed enhanced antigen-specific T-cell trafficking and APC-CD8⁺ T-cell interactions in mice primed with viral vectors encoding a codon-modified EBNA1 protein. More importantly, these antigen-specific T cells displayed enhanced expression of the T-box transcription factor and superior polyfunctionality consistent with the qualitative impact of translation efficiency. These results provide an important insight into how viruses exploit mRNA structure to down regulate synthesis of their viral maintenance proteins and delay priming of antigen-specific T cells, thereby establishing a successful latent infection in vivo. Furthermore, targeting EBNA1 mRNA rather than protein by small molecules or antisense oligonucleotides will enhance EBNA1 synthesis and the early priming of effector T cells, to establish a more rapid immune response and prevent persistent infection.

Maintenance proteins of viruses establishing latent infections regulate their synthesis to levels sufficient for maintaining persistent infection but below threshold levels for host immune detection. The Epstein-Barr virus maintenance protein, EBNA1, has recently been shown to contain unusual G-quadruplex structures within its repeat mRNA that reduces its translational efficiency. In this study we assess how modification of the EBNA1 mRNA repeat sequence to destabilize the native G-quadruplex structures and thereby increase translation, impacts on the activation of EBNA1-specific T cells in vivo. Mice primed with viral vectors encoding a more efficiently translated EBNA1 mRNA revealed increased trafficking of EBNA1-specific T cells, an enhanced functional profile and increased expression of transcription factors providing evidence for a potential link between mRNA translational efficiency and antigen presentation in vivo and the resultant impact on the functional programming of effector T cells. These findings suggest a novel approach to therapeutic development through the use of antisense strategies or small molecules targeting EBNA1 mRNA structure.

Immunogenicity evaluation of a DNA vaccine expressing the hepatitis C virus non-structural protein 2 gene in C57BL/6 mice

BACKGROUNDS

Most of the hepatitis C virus (HCV) infections elicit poor immune responses and 75% to 85% of cases become chronic; therefore, the development of an effective vaccine against HCV is of paramount importance. In this study, we aimed to evaluate co-administration of HCV non-Structural Protein 2 and IL-12 DNA vaccines in C57BL/6 mice.

METHODS

A plasmid encoding full-length HCV NS2 protein (non-structural protein 2) was generated and used to vaccinate mice. Negative control (an empty expression vector) was also employed to evaluate the background response. To investigate immune responses against vaccine, C57BL/6 mice received three doses of the vaccine with a two-week interval. Cellular immunity was assessed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide assay for lymphocyte proliferation, lactate dehydrogenase release for cytotoxic T lymphocyte (CTL) activity and cytokine assay.

RESULTS

The findings demonstrated that immunization of mice with plasmid expressing HCV NS2 induced CTL response, interferon gamma production, and lymphocyte proliferation compared to negative control. The results also demonstrated that co-administration of IL-12 with the HCV NS2 plasmid induced significantly better immune response in C57BL/6 mice.

CONCLUSION

DNA vaccine encoding HCV NS2 is an effective candidate that can trigger CTL-based immune response against HCV. In addition, the results suggested that combining the DNA vaccine approach with immune stimulatory cytokines may significantly enhance antigen-specific immune responses.

Adjustable locks and flexible keys: plasticity of epitope-paratope interactions in germline antibodies

Ag recognition by independent primary Abs against a small flexible Ag with overlapping epitopes was analyzed to address the determinants of Ag specificity during the initial encounter. Crystal structures of two distinct dodecapeptide Ags, GDPRPSYISHLL and PPYPAWHAPGNI, in complex with the germline mAb 36-65 were determined and compared with the structures of the same Ags bound to another independent germline mAb, BBE6.12H3. For each peptide Ag, the two germline mAbs recognized overlapping epitopes, but in different topologies. The peptide structures differed, and the two paratopes attained discrete conformations, leading to different surface topologies, in a mode that can be described as adjustable locks and flexible keys. This is in contrast to mature mAbs, in which conformational convergence of different paratopes while binding to a common epitope in a similar conformation has been reported. These results suggest that the primary immune receptor repertoire is highly versatile as compared with its mature counterpart. Germline and mature mAbs adopt distinct mechanisms for recognizing a flexible epitope. Whereas conservation of conformational repertoire is a key characteristic of mature mAbs achieved through affinity maturation, the germline mAbs, at the initial stages of Ag encounter, maintain substantial plasticity, accommodating a broad specificity repertoire.

Integrated assessment of predicted MHC binding and cross-conservation with self reveals patterns of viral camouflage

Background

Immune recognition of foreign proteins by T cells hinges on the formation of a ternary complex sandwiching a constituent peptide of the protein between a major histocompatibility complex (MHC) molecule and a T cell receptor (TCR). Viruses have evolved means of "camouflaging" themselves, avoiding immune recognition by reducing the MHC and/or TCR binding of their constituent peptides. Computer-driven T cell epitope mapping tools have been used to evaluate the degree to which particular viruses have used this means of avoiding immune response, but most such analyses focus on MHC-facing 'agretopes'. Here we set out a new means of evaluating the TCR faces of viral peptides in addition to their agretopes, integrating evaluations of both sides of the ternary complex in a single analysis.

Methods

This paper develops what we call the Janus Immunogenicity Score (JIS), bringing together a well-established method for predicting MHC binding, with a novel assessment of the potential for TCR binding based on similarity with self. Intuitively, both good MHC binding and poor self-similarity are required for high immunogenicity (i.e., a robust T effector response).

Results

Focusing on the class II antigen-processing pathway, we show that the JIS of T effector epitopes and null or regulatory epitopes deposited in a large database of epitopes (Immune Epitope Database) are significantly different. We then show that different types of viruses display significantly different patterns of scores over their constituent peptides, with viruses causing chronic infection (Epstein-Barr and cytomegalovirus) strongly shifted to lower scores relative to those causing acute infection (Ebola and Marburg). Similarly we find distinct patterns among influenza proteins in H1N1 (a strain against which human populations rapidly developed immunity) and H5N1 and H7N9 (highly pathogenic avian flu strains, with significantly greater case mortality rates).

Conclusion

The Janus Immunogenicity Score, which integrates MHC binding and TCR cross-reactivity, provides a new tool for studying immunogenicity of pathogens and may improve the selection and optimization of antigenic elements for vaccine design.