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The high-risk α-type papillomaviruses have a C-terminal PDZ-binding motif (PBM) on one of the two major oncoproteins E6 or E7; the vast majority on E6. The PBM is essential for the high-risk HPV life cycle, for episomal maintenance of the virus genome, and for maintaining the mitotic stability of the infected cell. The question is why only these viruses have PBMs - are there specific constraints imposed by the mucosal epithelium in which these viruses replicate? However the low-risk α-HPVs, such as HPV-6 and HPV-11 replicate extremely efficiently without a PBM, while viruses of the alpha8 group, such as HPV-40, replicate well with a very primitive PBM. So what does PDZ-binding capacity contribute to the fitness of the virus?

Despite the success of antiretroviral therapy (ART) for people living with HIV, lifelong treatment is required and there is no cure. HIV can integrate in the host genome and persist for the life span of the infected cell. These latently infected cells are not recognized as foreign because they are largely transcriptionally silent, but contain replication-competent virus that drives resurgence of the infection once ART is stopped. With a combination of immune activators, neutralizing antibodies, and therapeutic vaccines, some nonhuman primate models have been cured, providing optimism for these approaches now being evaluated in human clinical trials. In vivo delivery of gene-editing tools to either target the virus, boost immunity or protect cells from infection, also holds promise for future HIV cure strategies. In this Review, we discuss advances related to HIV cure in the last 5 years, highlight remaining knowledge gaps and identify priority areas for research for the next 5 years. An effective and scalable cure strategy is a top priority for the HIV research field; this Review discusses recent advances, knowledge gaps, and priority research areas for the next 5 years.

The stability analysis in this mathematical model was related to the infection of the Coronavirus Disease 2019 (Covid-19). In this mathematical model there were two balance points, namely the point of balance free from Covid-19 and the one infected with Covid-19. The stability of the equilibrium point was influenced by all parameters, i.e. target cells die during each cycle, number of target cells at  = 0, target cells infected during each cycle based on virion unit density, effective surface area of the network, the ratio of the number of virus particles to the number of virions, infected cells die during each cycle, the number of virus particles produced by each infected cell during each cycle, and virus particles die during each cycle. In the simulation model, immunity is divided into high, medium and low immunity. For high, moderate and low immunity, respectively, the highest number of target cells is in high, medium and low immunity, whereas for the number of infected cells and the number of Covid-19, it is in the opposite sequence of the number of target cells.

The field of cellular microbiology, rooted in the co-evolution of microbes and their hosts, studies intracellular pathogens and their manipulation of host cell machinery. In this review, we highlight emerging technologies and infection models that recently promoted opportunities in cellular microbiology. We overview the explosion of microscopy techniques and how they reveal unprecedented detail at the host-pathogen interface. We discuss the incorporation of robotics and artificial intelligence to image-based screening modalities, biochemical mapping approaches, as well as dual RNA-sequencing techniques. Finally, we describe chips, organoids and animal models used to dissect biophysical and in vivo aspects of the infection process. As our knowledge of the infected cell improves, cellular microbiology holds great promise for development of anti-infective strategies with translational applications in human health., Cellular microbiology is a field that combines the study of infection and cell biology. In this review, we highlight emerging technologies and infection models that recently transformed our understanding of the infected cell and may inspire future medicine.

У статті на підставі літературних даних продемонстровано роль клітинних реакцій у розвитку імунної відповіді при пневмонії, спричиненої Staphylococcus aureus. Описано механізми взаємодії Staphylococcus aureus із вродженими лімфоїдними клітинами, Т-лімфоцитами. Наведена порівняльна характеристика рецепторного апарату NK-клітин, описано механізми кiлинга інфікованих клітин iмуноцитами вродженої імунної системи.

Viroporins are involved in viral pathogenesis, play an important role in the morphogenesis of virions and ensure their release from the infected cell. These proteins are potentially promising as possible targets for the regulation of virus reproduction. The literature data on the current understanding of coronavirus viroporins functioning are summarized in the review. Special attention is focused on specific structural features that determine the functional ability of these proteins. The basic principles of viroporins localization in the cell and their influence on the coronavirus life cycle are considered. Keywords: coronavirus, pore formation, protein 3a, protein 8a, protein E, SARS, viroporins

An interesting finding that emerged from the study was the difference in potency between inactivated rabies vaccines prepared in liquid and lyophilized forms. Inactivated rabies vaccine prepared from BHK21 infected cell culture in the two forms revealed that its immunogenicity was completely preserved on lyophilization. The two vaccine formulae were found to be free from foreign contaminants, safe in both inoculated mice and puppies and potent inducing high levels of specific rabies antibodies in vaccinated puppies. Such antibodies were increased gradually from the first-week post-vaccination to the same extent in the blood of immunized puppies with the lyophilized vaccine as in that of puppies immunized with liquid vaccine. These results confirmed the claim that inactivated rabies vaccines could be lyophilized with retention of potency. Considering the possible value of a stable, freeze-dried rabies vaccine that could be stored and transported with ease, it was considered desirable to confirm the above findings.

A fines de diciembre de 2019, un nuevo coronavirus (SARS-CoV-2) fue identificado como el agente causal de una nueva enfermedad respiratoria llamada COVID-19 por la OMS Sus sintomas incluyen fiebre, tos seca y dificultad respiratoria Estos sintomas en general son leves, aunque, pueden ser fatales en adultos mayores y pacientes con comorbilidades Se realizo busqueda bibliografica en Pubmed y Clinical Key donde se seleccionaron 22 articulos de acuerdo con los criterios de inclusion SARS-CoV-2 pertenece al genero de los Betacoronavirus y tiene similitudes genomicas con SARS-CoV y MERS-CoV El virion de SARS-CoV-2 consta de una nucleocapside y de una envoltura externa compuesta por proteinas estructurales principales y accesorias Su material genetico consiste en una cadena de RNA monocatenario de polaridad positiva, en el que, se codifican proteinas importantes para su transcripcion y replicacion El mecanismo de infeccion de SARS-CoV-2 comienza con la union del virion a un receptor (ACE2) de la celula huesped y su posterior entrada por endocitosis El genoma RNA viral se libera al citoplasma donde se transcriben y se traducen las proteinas necesarias para la produccion de las proteinas estructurales y para la replicacion de su material genetico Posteriormente, el RNA replicado se asocia con la nucleocapside y se ensambla junto con las proteinas estructurales para conformar las particulas viricas que seran liberadas de la celula infectada El sistema inmune hace frente a la infeccion viral mediante el reconocimiento de patrones moleculares asociados a patogenos (PAMPs) por parte de la inmunidad innata y por la accion de los linfocitos T y B por parte de la inmunidad humoral El conocimiento de las bases geneticas y moleculares de SARS-CoV-2 permite visualizar la posibilidad de establecer tratamientos farmacologicos o desarrollo de vacunas para controlar y disminuir los efectos patogenicos de la enfermedad In late December 2019, a new coronavirus (SARS-CoV-2) was identified as a causative agent of a new respiratory disease called COVID-19 by WHO Its symptoms include fever, dry cough, and shortness of breath Generally, these symptoms are mild, although, can be fatal in older adults and patients with comorbidities A bibliographic search was carried out in Pubmed and Clinical Key 22 articles were selected according to inclusion criteria SARS-CoV-2 belongs to the genus of Betacoronaviruses and has genomic similarities to SARS-CoV and MERS-CoV SARS-CoV-2 virion is made up of a nucleocapsid and external envelope composed of main structural and accesory proteins Its genetic is a positive sense single stranded RNA in which important proteins are encoded for their transcription and replication The mechanism of SARS-CoV-2 infection begins with the binding of the virion to (ACE2) receptor of the host cell and subsequent entry by endocytosis This RNA genome is released into cytoplasm and the necessary proteins for the production of structural proteins and the replication of genetic material are transcribed and translated Then, the replicated RNA associates with the nucleocapsid and assembles together with the structural proteins to form the viral particles that will be released from the infected cell The immune system faces viral infection through the recognition of molecular patterns associated with pathogens (PAMPs) by innate immunity and the action of T cells and B cells by humoral immunity Knowledge of the genetic and molecular basis of SARS-CoV-2 allows us to visualize the possibility of establishing pharmacological or vaccine treatments to control and reduce the pathogenic effects of the disease

The purpose of this study was aimed to isolate a Salmonella Typhimurium-specific phage (KFS-ST) from washing water in a poultry processing facility and to investigate the feasibility of the KFS-ST as a novel bio-receptor for the magnetoelastic (ME) biosensor method. KFS-ST against S. Typhimurium was isolated, propagated, and purified using a CsCl-gradient ultracentrifugation. Morphological characteristics of KFS-ST were analyzed using transmission electron microscopy (TEM). Its specificity and efficiency of plating analysis were conducted against 39 foodborne pathogens. The temperature and pH stabilities of KFS-ST were investigated by the exposure of the phage to various temperatures (−70°C–70°C) and pHs (1–12) for 1 h. A one-step growth curve analysis was performed to determine the eclipse time, latent time and burst size of phage. The storage stability of KFS-ST was studied by exposing KFS-ST to various storage temperatures (−70°C, −20°C, 4°C, and 22°C) for 12 weeks. KFS-ST was isolated and purified with a high concentration of (11.47 ± 0.25) Log PFU/mL. It had an icosahedral head (56.91 ± 2.90 nm) and a non-contractile tail (225.49 ± 2.67 nm), which was classified into the family of Siphoviridae in the order of Caudovirales. KFS-ST exhibited an excellent specificity against only S. Typhimurium and S. Enteritidis, which are considered two of the most problematic Salmonella strains in the meat and poultry. However, KFS-ST did not exhibit any specificity against six other Salmonella and 27 non-Salmonella strains. KFS-ST was stable at temperature of 4°C to 50°C and at pH of 4 to 12. The eclipse time, latent time, and burst size of KFS-ST were determined to be 10 min, 25 min and 26 PFU/ infected cell, respectively. KFS-ST was relatively stable during the 12-week storage period at all tested temperatures. Therefore, this study demonstrated the feasibility of KFS-ST as a novel bio-receptor for the detection of S. Typhimurium and S. Enteritidis in meat and poultry products using the ME biosensor method.

The outbreaks of viruses with wide spread and mortality in the world population have motivated the research for new therapeutic approaches. There are several viruses that cause a biochemical imbalance in the infected cell resulting in oxidative stress. These effects may be associated with the development of pathologies and worsening of symptoms. Therefore, this review is aimed at discussing natural compounds with both antioxidant and antiviral activities, specifically against coronavirus infection, in an attempt to contribute to global researches for discovering effective therapeutic agents in the treatment of coronavirus infection and its severe clinical complications. The contribution of the possible action of these compounds on metabolic modulation associated with antiviral properties, in addition to other mechanisms of action, is presented.

Oncolytic viruses are designed to replicate in and kill cancer cells, and have shown tremendous promise in preclinical and clinical studies. Indeed, several oncolytic viruses are available to patients in a number of different countries around the world. However, most oncolytic viruses show a poor ability to spread throughout the tumor mass, frequently leading to only a partial response and regrowth of the tumor. One approach to improve spread of the viral effect throughout the tumor mass is to arm the oncolytic virus with a fusogenic protein. In this manner, a single infected cell can fuse with many adjacent uninfected cells, essentially amplifying the anti-tumor effects. In this review, we discuss the development and use of fusogenic proteins to enhance the efficacy of human adenovirus-based vectors for cancer therapy.

This paper proposes and analyzes a CTL-mediated HIV infection model. The model describes the interaction between healthy CD4+T cells, silent infected cells, active infected cells, free HIV particles, and cytotoxic T lymphocytes (CTLs). The healthy CD4+T cells can be infected when contacted by one of the following: (i) free HIV particles, (ii) silent infected cells, and (iii) active infected cells. The incidence rates of the healthy CD4+T cells with free HIV particles, silent infected cells, and active infected cells are given by general functions. Moreover, the production/proliferation and removal/death rates of all compartments are represented by general functions. The model is an improvement of the existing HIV infection models which have neglected the incidence between the silent infected cells and healthy CD4+T cells. We first show that the model is well posed. The proposed model has three equilibria and their existence is governed by derived two threshold parameters: the basic HIV reproduction number $\Re _{0}$ ℜ 0 and the HIV-specific CTL-mediated immunity reproduction number $\Re _{1}$ ℜ 1 . Under a set of conditions on the general functions and the parameters $\Re _{0}$ ℜ 0 and $\Re _{1}$ ℜ 1 , we have proven the global asymptotic stability of all equilibria by using Lyapunov method. We have illustrated the theoretical results via numerical simulations. We have studied the effect of cell-to-cell (CTC) transmission on the dynamical behavior of the system. We have shown that inclusion of CTC transmission decreases the concentration of healthy CD4+T cells and increases the concentrations of infected cells and free HIV particles.

Hepatitis D virus (HDV) requires hepatitis B surface antigen (HBsAg) for its assembly and release. Current HBV treatments are only marginally effective against HDV because they fail to inhibit HBsAg production/secretion. However, monotherapy with the nucleic acid polymer REP 2139-Ca is accompanied by rapid declines in both HBsAg and HDV RNA. We used mathematical modeling to estimate HDV-HBsAg-host parameters and to elucidate the mode of action and efficacy of REP 2139-Ca against HDV in 12 treatment-naive HBV/HDV co-infected patients. The model accurately reproduced the observed decline of HBsAg and HDV, which was simultaneous. Median serum HBsAg half-life (t1/2) was estimated as 1.3 [0.9–1.8] days corresponding to a pretreatment production and clearance of ~108 [107.7–108.3] IU/day. The HDV-infected cell loss was estimated to be 0.052 [0.035–0.074] days−1 corresponding to an infected cell t1/2 = 13.3 days. The efficacy of blocking HBsAg and HDV production were 98.2 [94.5–99.9]% and 99.7 [96.0–99.8]%, respectively. In conclusion, both HBsAg production and HDV replication are effectively inhibited by REP 2139-Ca. Modeling HBsAg kinetics during REP 2139-Ca monotherapy indicates a short HBsAg half-life (1.3 days) suggesting a rapid turnover of HBsAg in HBV/HDV co-infection.

Adherent-invasive Escherichia coli (AIEC) strains have been extensively related to Crohn's disease (CD) etiopathogenesis. Higher AIEC prevalence in CD patients versus controls has been reported, and its mechanisms of pathogenicity have been linked to CD physiopathology. In CD, the therapeutic armamentarium remains limited and non-curative; hence, the necessity to better understand AIEC as a putative instigator or propagator of the disease is certain. Nonetheless, AIEC identification is currently challenging because it relies on phenotypic assays based on infected cell cultures which are highly time-consuming, laborious and non-standardizable. To address this issue, AIEC molecular mechanisms and virulence genes have been studied; however, a specific and widely distributed genetic AIEC marker is still missing. The finding of molecular tools to easily identify AIEC could be useful in the identification of AIEC carriers who could profit from personalized treatment. Also, it would significantly promote AIEC epidemiological studies. Here, we reviewed the existing data regarding AIEC genetics and presented those molecular markers that could assist with AIEC identification. Finally, we highlighted the problems behind the discovery of exclusive AIEC biomarkers and proposed strategies to facilitate the search of AIEC signature sequences.

Significance Quantifying the kinetics of SARS-CoV-2 infection and individual infectiousness is important for understanding SARS-CoV-2 transmission and evaluating intervention strategies. Here, we developed within-host models of SARS-CoV-2 infection, and by fitting them to clinical data, we estimated key within-host viral dynamic parameters. We also developed a mechanistic model for viral transmission and show that the logarithm of the viral load in the upper respiratory tract serves as an appropriate surrogate for a person’s infectiousness. Using data on how viral load changes during infection, we further evaluated the effectiveness of PCR and antigen-based testing strategies for averting transmission and identifying infected individuals., The within-host viral kinetics of SARS-CoV-2 infection and how they relate to a person’s infectiousness are not well understood. This limits our ability to quantify the impact of interventions on viral transmission. Here, we develop viral dynamic models of SARS-CoV-2 infection and fit them to data to estimate key within-host parameters such as the infected cell half-life and the within-host reproductive number. We then develop a model linking viral load (VL) to infectiousness and show a person’s infectiousness increases sublinearly with VL and that the logarithm of the VL in the upper respiratory tract is a better surrogate of infectiousness than the VL itself. Using data on VL and the predicted infectiousness, we further incorporated data on antigen and RT-PCR tests and compared their usefulness in detecting infection and preventing transmission. We found that RT-PCR tests perform better than antigen tests assuming equal testing frequency; however, more frequent antigen testing may perform equally well with RT-PCR tests at a lower cost but with many more false-negative tests. Overall, our models provide a quantitative framework for inferring the impact of therapeutics and vaccines that lower VL on the infectiousness of individuals and for evaluating rapid testing strategies.

The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV, and HIV-1, endogenous retroviruses, and human papillomavirus., SCOPUS: ar.j, info:eu-repo/semantics/published

Dengue infection affects more than half of the world’s population, with 1 billion symptomatic cases identified per year and several distinct genetic serotypes: DENV 1–4. Transmitted via the mosquito bite, the dengue virus infects Langerhans cells. Monocytes, B lymphocytes, and mast cells infected with dengue virus produce various cytokines although it is not clear which ones are predominant during DHF disease. A mathematical model of the Dengue virus infection is developed according to complex dynamics determined by many factors. Starting from a state of equilibrium that we could define as “virus-free” asymptotically stable with a viral reproduction number lower than one which means a very effective action of the innate immune system: it stops the infectious process, the mathematical analysis of stability in the presence of the virus demonstrates that the proposed model is dynamically influenced. Dengue fever affects more than half of the world’s population, with 1 billion symptomatic cases and multiple genetic serotypes confirmed each year, which simulates a network of interactions between the various populations involved without considering the speeds of the processes in question which are indicated in a separate computation. In this research, a hybrid approach of petri nets is utilized to connect the discrete models of dengue.

In this paper, we study possibilities of eradication of populations at an early stage of a patient’s infection in the framework of the seven-order Stengel model with 11 model parameters and four treatment parameters describing the interactions of wild-type and mutant HIV particles with various immune cells. We compute ultimate upper bounds for all model variables that define a polytope containing the attracting set. The theoretical possibility of eradicating HIV-infected populations has been investigated in the case of a therapy aimed only at eliminating wild-type HIV particles. Eradication conditions are expressed via algebraic inequalities imposed on parameters. Under these conditions, the concentrations of wild-type HIV particles, mutant HIV particles, and infected cells asymptotically tend to zero with increasing time. Our study covers the scope of acceptable therapies with constant concentrations and values of model parameters where eradication of infected particles/cells populations is observed. Sets of parameter values for which Stengel performed his research do not satisfy our local asymptotic stability conditions. Therefore, our exploration develops the Stengel results where he investigated using the optimal control theory and numerical dynamics of his model and came to a negative health prognosis for a patient. The biological interpretation of these results is that after a sufficiently long time, the concentrations of wild-type and mutant HIV particles, as well as infected cells will be maintained at a sufficiently low level, which means that the viral load and the concentration of infected cells will be minimized. Thus, our study theoretically confirms the possibility of efficient treatment beginning at the earliest stage of infection. Our approach is based on a combination of the localization method of compact invariant sets and the LaSalle theorem.

International audience; The search for inhibitors of SARS-CoV-2 viral replication depends on the understanding of the events taking place at different molecular levels during the viral infection. The macro-molecular level focuses on the interactions among viral and host proteins, while the micro-molecular level focuses on the different biochemical modifications that occur to one or more amino acids on proteins. A hybrid approach for modeling the SARS-CoV-2 viral replication in the micro-and macro-molecular levels is presented in this paper. The proposed approach combines two domains which complement one another, ontology engineering and discrete event system specification (DEVS) modeling.In this approach, biological knowledge at the micro-level of the viral system is capitalized and inferred by ontological models, while the dynamic behavior of SARS-CoV-2 molecular mechanisms and their different state changes in time are modeled by DEVS models. We illustrate the proposed approach through the modeling and simulation of the ribosome, a key molecule of the host cell that all viruses compete for, including the SARS-CoV-2.

Biophysical separation promises label-free, less-invasive methods to manipulate the diverse properties of live cells, such as density, magnetic susceptibility, and morphological characteristics. However, some cellular changes are so minute that they are undetectable by current methods. We developed a multiparametric cell-separation approach to profile cells with simultaneously changing density and magnetic susceptibility. We demonstrated this approach with the natural biophysical phenomenon of Plasmodium falciparum infection, which modifies its host erythrocyte by simultaneously decreasing density and increasing magnetic susceptibility. Current approaches have used these properties separately to isolate later-stage infected cells, but not in combination. We present biophysical separation of infected erythrocytes by balancing gravitational and magnetic forces to differentiate infected cell stages, including early stages for the first time, using magnetic levitation. We quantified height distributions of erythrocyte populations—27 ring-stage synchronized samples and 35 uninfected controls—and quantified their unique biophysical signatures. This platform can thus enable multidimensional biophysical measurements on unique cell types., Deshmukh et al. combine microscale magnetic levitation with minute density and magnetic susceptibility differences to enhance biophysical separation of cells. They demonstrate the feasibility of this approach on cells infected with malaria parasites, which simultaneously decrease host cell density and increase its magnetic susceptibility.

International audience; Benefiting from the recent advances of synchrotron X-ray nanoprobes, we demonstrate three-dimensional (3D) correlative nano-imaging on malaria-infected human red blood cells. By combining X-ray fluorescence to-mography and phase contrast nanotomography on the same cell with sub-100 nm pixel size, we establish a routine workflow from the data acquisition, data processing to tomographic reconstruction. We quantitatively compare the elemental volumes obtained with different reconstruction methods, the total variation minimization giving the most satisfactory results. We reveal elemental correlations in different cell compartments more reliably on reconstructions as opposed to 2D projections. Finally, we determine for the first time the 3D mass fraction maps of multiple elements at sub-cellular level. The estimated total number of Fe atoms and the total mass of the red blood cell show very good agreement with previously reported values.

We used a combination of DOP-PCR with high throughput sequencing (HTS) to study infected cell cultures over time to assess the feasibility of using this technique to provide a read-out other than cytopathic effect in cell culture infectivity assays. Because DOP-PCR primers feature a short constant sequence at their 3' terminus, the procedure yields a reproducible representational library of products from a given PCR template, including viral nucleic acids. Using SV40- and MVM-infected cultures harvested at different times, we show that the number of viral matches among DOP-PCR products parallels the quantity of virus as shown by real-time PCR, and further show that HTS analysis of specific DOP-PCR products that increase in quantity over time could be used to identify the infecting virus with a sensitivity similar to that of typical cell-culture assays that rely on cytopathic effect.

Hematological diseases are blood-related diseases which include leukemia, leucopenia, hemophilia, etc. In which leukemia is severe hematological disease and death rate is very high and hence need proper and faster diagnosis. Leukemia is the formation of giant nuclei or immature increase of leukocytes or WBCs; hence, the need of extracting the shape features and other symptoms must be investigated. This paper suggested and experimented a technique for separating or segmenting white blood cell stain images of leukemia-affected patients. The successful segmentation of an infected cell divides the images into nucleus and outer fluid part cytoplasm, since these two regions contain features that correlate to different forms of leukemia. The algorithm checks and experiments 250 images, and the performance validation using cross-validation techniques shows the nucleus segmentation accuracy as 94% and cytoplasm segmentation accuracy as 78%, respectively.

Malaria is still an infectious disease that causes high mortality in endemic regions. It is thought that it will maintain importance in the future, especially due to people travelling from African countries where malaria is endemic to its eradicated regions. Therefore, rapid and accurate diagnosis is a critical step in the effective treatment of malaria and reducing mortality rates. This paper provides a malaria diagnosis system using an artificial neural network approach with SURF (Speeded Up Robust Features) method that helps the clinicians to predict and locate infected cell with malaria on the sample thin blood smear image. The performance of the proposed neural network and local image feature extraction technique SURF were analyzed statistically and presented in this paper. The network was trained using only 45 infected thin blood smear images and was then tested with 200 (100 infected and 100 non-infected) unseen images. The experimental results showed that the proposed system identified the malaria parasite with 93% accuracy, 86% sensitivity and 100% specificity.

Sequencing individual HIV-proviruses and their adjacent cellular junctions can elucidate mechanisms of infected cell persistence in vivo. Here, we present a high throughput microfluidic method to sequence entire proviruses in their native integration site context. We used the method to analyze infected cells from people with HIV on suppressive antiretroviral therapy, demonstrating >90% capture and sequencing of paired proviral genomes and integration sites. This method should enable comprehensive genetic analysis of persistent HIV-infected cell reservoirs, providing important insights into the barriers to HIV cure.

To make new infectious particles, all viruses must manipulate host cell metabolism to secure sufficient availability of biomolecules and energy-a phenomenon now known as metabolic reprogramming. Numerous observations of this has already been made for a range of viruses with each type of virus seemingly applying its own unique tactics to accomplish this unifying goal. In this light, metabolic reprogramming of the infected cell is largely beneficial to the virus and not to the host. On the other hand, virus-induced metabolic reprogramming represents a transformed self with distorted cellular and extracellular levels of distinct metabolites and metabolic by-products. This review briefly outlines current knowledge of virus-induced metabolic reprogramming, discusses how this could be sensed by the infected host to initiate anti-viral programs, and presents examples of innate anti-viral mechanisms of the host that target the availability of biomolecules to block viral replication.

Mycoplasma contamination of cell line cultures is a common, yet often undetected problem in research laboratories. Many of the existing techniques to detect mycoplasma contamination of cultured cells are time-consuming, expensive, and have significant drawbacks. Here, we describe a mycoplasma detection system that is useful for detecting multiple species of mycoplasma in infected cell lines. The system contains three dye-labeled detection aptamers that can specifically bind to mycoplasma-infected cells and a dye-labeled control aptamer that minimally binds to cells. With this system, mycoplasma-contaminated cells can be detected within 30 min by using a flow cytometer, fluorescence microscope, or microplate reader. Further, this system may be used to detect mycoplasma-contaminated culture medium. This study presents an novel mycoplasma detection model that is simple, rapid, inexpensive, and sensitive.

This article examines three aspects of antivirals, such as hydroxychloroquine, chloroquine, and remdesvir, as they might relate to the treatment of a viral infection such as COVID-19: (i) the use of vaporization for the delivery of antivirals, with the bulk constituents having mild antiviral efficacy; (ii) the application of a marine natural product extract as opposed to a single molecule as an antiviral agent; and (iii) a counter intuitive approach to formulation that is, in part, based on delivering multiple species that fall into three categories: building blocks for the virus to accelerate replication; an energy source for the infected cell to boost its immune response; and the species that antagonize or provide toxicity to the virus.

A critical step in the life cycle of a virus is spread to a new target cell, which generally involves the release of new viral particles from the infected cell which can then initiate infection in the next target cell. While cell-free viral particles released into the extracellular environment are necessary for long distance spread, there are disadvantages to this mechanism. These include the presence of immune system components, the low success rate of infection by single particles, and the relative fragility of viral particles in the environment. Several mechanisms of direct cell-to-cell spread have been reported for animal viruses which would avoid the issues associated with cell-free particles. A number of viruses can utilize several different mechanisms of direct cell-to-cell spread, but our understanding of the differential usage by these pathogens is modest. Although the mechanisms of cell-to-cell spread differ among viruses, there is a common exploitation of key pathways and components of the cellular cytoskeleton. Remarkably, some of the viral mechanisms of cell-to-cell spread are surprisingly similar to those used by bacteria. Here we summarize the current knowledge of the conventional and non-conventional mechanisms of viral spread, the common methods used to detect viral spread, and the impact that these mechanisms can have on viral pathogenesis.

Malaria causes a serious health problem in the tropical and subtropical regions of the globe. In many cases, the consequences of this disease are fatal. Therefore, a simple, fast, accurate and affordable diagnostic system for the early detection of this disease is necessary for the timely administration of antimalarial drugs.The malarial parasite, during its intra-erythrocyte development, processes a significant amount of hemoglobin, which in this case turns into a hem form called hemozoin. Hemozoin and hemoglobin have different molar extinction coefficients at certain optical wavelengths, hence, light absorption and an optoacoustic signal (OAS) from the infected cell will be different from that of a healthy cell. The paper describes the developed theoretical model intended for studying the influence of intra-erythrocyte malarial parasite development on optoacoustic signals. The OAS were calculated based on the models of healthy and infected blood modeled on the basis of a 3D model.The simulated OAS were analyzed in the temporal and frequency domains to obtain signs of infection at various stages. The calculated OAS spectra have different amplitude levels, which indicates that the optoacoustic method can be useful for differentiating various intraerythrocyte stages of the malarial parasite. The carried out modeling and the results obtained allow us to continue working on the creation of an optoacoustic flow cytometer.

The presence of cells latently infected with HIV is currently considered to be a major barrier to viral eradication within a patient. Here, we consider birth-death-immigration models for the latent cell population in a single patient, and present analytical results for the size of this population in the absence of treatment. We provide results both at steady state (viral set point), and during the non-equilibrium setting of early infection. We obtain semi-analytic results showing how latency-reversing drugs might be expected to affect the size of the latent pool over time. We also analyze the probability of rare mutant viral strains joining the latent cell population, allowing for steady-state and dynamic viral populations within the host.

Transmissible spongiform encephalopathies (TSEs) are a group of lethal neurodegenerative diseases involving the structural conversion of cellular prion protein (PrP(C)) into the pathogenic isoform (PrP(Sc)) for which no effective treatment is currently available. Previous studies have implicated that a polymeric molecule with a repeating unit, such as pentosane polysulfate and polyamidoamide dendrimers, exhibits a potent anti-prion activity, suggesting that poly-(amino acid)s could be a candidate molecule for inhibiting prion propagation. Here, by screening a series of poly-(amino acid)s in a prion-infected neuroblastoma cell line (GT(FK)), we identified poly-L-His as a novel anti-prion compound with an IC(50) value of 1.8 µg/mL (0.18 µM). This potent anti-prion activity was specific to a high-molecular-weight poly-L-His and absent in monomeric histidine or low-molecular-weight poly-L-His. Solution NMR data indicated that poly-L-His directly binds to the loop region connecting Helix 2 and Helix 3 of PrP(C) and sterically blocks the structural conversion toward PrP(Sc). Poly-L-His, however, did not inhibit prion propagation in a prion-infected mouse when administered intraperitoneally, suggesting that the penetration of blood-brain barrier and/or the chemical stability of this polypeptide must be addressed before its application in vivo. Taken together, this study revealed the potential use of poly-L-His as a novel treatment against TSEs. (203 words)

In this paper we propose and analyze an HCV dynamics model taking into consideration the cure of infected hepatocytes and antibody immune response. We incorporate both virus-to-cell and cell-to-cell transmissions into the model. We incorporate a distributed-time delay to describe the time between the HCV or infected cell contacts an uninfected hepatocyte and the emission of new active HCV. We show that the solutions of the proposed model are nonnegative and ultimately bounded. We derive two threshold parameters which fully determine the existence and stability of the three steady states of the model. Using Lyapunov functionals, we established the global stability of the steady states. The theoretical results are confirmed by numerical simulations.

This paper proposes and analyzes an adaptive immunity HIV infection model. The model describes the interaction between healthy CD 4 + T cells, silent (latent) infected cells, active infected cells, free HIV particles, Cytotoxic T lymphocytes (CTLs) and antibodies. The healthy CD 4 + T cells can be infected when they are contacted by one of the following: (i) free HIV particles, and this is known as virus-to-cell (VTC) transmission (ii) silent infected cells, and we call this mode of infection as silent HIV-infected cell-to-cell (CTC) transmission, and (iii) active infected cells, and we call this mechanism active HIV-infected CTC transmission. The incidence rates of the healthy CD 4 + T cells with free HIV particles, silent infected cells, and active infected cells are given by general functions. Moreover, the production/proliferation and removal/death rates of all compartments are represented by general functions. The model is an improvement of the existing HIV infection models which have neglected the incidence between the silent infected cells and healthy CD 4 + T cells. We first show that the model is well-posed. Then, we show that the model has five equilibria and their existence are governed by five threshold parameters. Under a set of conditions on the general functions and the threshold parameters, we have proven the global asymptotic stability of all equilibria by using Lyapunov’s method. We have illustrated the theoretical results via numerical simulations. We have studied the effect of CTC transmission on the dynamical behavior of the system. We have shown that inclusion of CTC transmission decreases the concentration of the healthy CD4 + T cells and increases the concentrations of the infected cells and free HIV particles.

Efforts to cure HIV-1 infection require better quantification of the HIV-1 reservoir, particularly the clones of cells harboring replication-competent (intact) proviruses, termed repliclones. The digital droplet PCR assays commonly used to quantify intact proviruses do not differentiate among specific repliclones, thus the dynamics of repliclones are not well defined. The major challenge in tracking repliclones is the relative rarity of the cells carrying specific intact proviruses. To date, detection and accurate quantification of repliclones requires in-depth integration site sequencing. Here, we describe a simplified workflow using integration site-specific qPCR (IS-qPCR) to determine the frequencies of the proviruses integrated in individual repliclones. We designed IS-qPCR to determine the frequencies of repliclones and clones of cells that carry defective proviruses in samples from three donors. Comparing the results of IS-qPCR with deep integration site sequencing data showed that the two methods yielded concordant estimates of clone frequencies (r = 0.838). IS-qPCR is a potentially valuable tool that can be applied to multiple samples and cell types over time to measure the dynamics of individual repliclones and the efficacy of treatments designed to eliminate them.

Characteristics of E. coli O157:H7-specific infection bacteriophages (O157 coliphages) and broad-host-range bacteriophages for other E. coli serotypes (broad-host coliphages) were compared. The burst sizes of the two groups ranged from 40 to 176 PFU/infected cell. Distributions of the virulence factors stx1, stx2, ehxA, and saa between the two groups were not differentiated. Broad-host-range coliphages showed lower stability at 70°C, in relation to O157 coliphages. However, O157 coliphages showed high acid and ethanol tolerance by reduction of only 22% and 11% phages, respectively, under pH 3 and 70% ethanol for 1 h exposure. Therefore, these results revealed that the O157 coliphages might be more stable under harsh environments, which might explain their effective infection of the acid-tolerant E. coli O157:H7.

Background and Hypothesis: High-risk human papillomavirus type-16 and -18 cause approximately 70% of cervical and 60% of oropharyngeal cancers. While the majority of HPV infections are transient and resolve on their own, some infections persist and progress to cancer. The in vivo and in vitro high-risk HPV transformation ability works to immortalize primary human keratinocytes resulting from the activities of the viral oncoproteins E6 and E7. A well-studied effect of E6 is the degradation of tumor suppressor gene p53 via binding to the ubiquitin ligase E6AP. Additionally, E6 interacts with the cellular calcium-binding protein E6BP, but the functional significance remains unknown. Here we studied the effects of E6BP knockout in normal human and HPV-infected cell lines. Experimental Design or Project Methods: CRISPR-Cas9 system was used to knockout E6BP in HPV-human cervical cancer cell lines: HeLa (high-copy HPV18) and SiHa (low-copy HPV16) as well as human keratinocyte HaCaT (mutant p53) and p53-null lung carcinoma H1299 cell lines. Cells were transfected with a puromycin-resistant CRISPR*Cas9 control plasmid (pLentiv2) and one that carries a guide RNA against E6BP (pLentiv2-E6BP) and selected with puromycin. RFP-GFP, which does not carry a puromycin resistance, was transfected into cells to establish transfection efficiency and to serve as the control for the puromycin. After successful selection, polyclonal populations of pLentiv2 control and pLentiv2-E6BP cells were screened for E6BP protein levels. pLentiv2-E6BP cell populations with reduced E6BP protein were serial diluted to generate monoclonal cell lines. Clones were then screened E6BP protein expression, and low expression clones were further processed for DNA sequencing of the E6BP gene editing site. Additionally, the effects of E6BP knockout in Siha and HeLa cells on p53, p21, and E6AP protein expression was studied by immunoblot. Results: Monoclonal pLentiv2-E6BP cell lines for H1299 and HaCaT cells were established and as well as polyclonal pLentiv2-E6BP HeLa and SiHa cell populations. Preliminary results indicate that E6BP knockout in HeLa and Siha cells reduces the p53 and p21 levels compared to pLentiv2 control cells. Additionally, E6AP protein expression was not affected by E6BP knockout in the polyclonal SiHa cells. Conclusion and Potential Impact: These preliminary results suggest that E6BP levels may influence p53 and p21 levels in HPV cells. It is of particular importance to further investigate if low levels of E6BP contribute to a worse outcome during HPV induced carcinogenesis.

It has been isolated a lytic bacteriophage specific toEscherichia coli, which can infect at least one different bacterial group. Phage ФGF1 was isolated from a wastewater treatment plant. It is resistant to the effect of chloroform and is stable at 40 and 50 °C. In addition, it is stable in the range of pH 5-8. Its host range is wide, infecting even strains from another genus such asShigella. The one-step growth curve yielded a short latent period of 15 minutes and a burst size of 85 PFU per infected cell. Under the electron microscope, this phage presents the C3 morphotype, extremely rare among members of the Podoviridae family. Phage ФGF1 shows some characteristics that could be considered useful in biocontrol applications againstE. coli. Keywords: Bacteriophage,Escherichia coli, morphotype C3,Podoviridae.IMPORTANCEWastewater throughout the world is a heavy carrier of potential pathogens that live in their environment along with other biological agents, such as bacteriophages, which play a controlling role of the bacterial populations there, as in soil. The description of the diversity of such bacteriophages is of paramount importance since they could be used to intentionally reduce or remove those pathogens from that environment. Our work describes a bacteriophage that lives primarily in this type of water.

Persistent infection with human papillomavirus (HPV) initiates ~5% of all human cancers, and particularly cervical and oropharyngeal cancers. HPV vaccines prevent HPV infection, but do not eliminate existing HPV infections. Papillomaviruses induce hyperproliferation of epithelial cells. In this review we discuss how hyperproliferation renders epithelial cells less sensitive to immune attack, and impacts upon the efficiency of the local immune system. These observations have significance for the design of therapeutic HPV cancer immunotherapies.

Growing evidence suggests the outcome of Mycobacterium tuberculosis (Mtb) infection is established rapidly after exposure, but how the current tuberculosis vaccine, BCG, impacts early immunity is poorly understood. Here we found that murine BCG immunization promotes a dramatic shift in infected cell types. While alveolar macrophages (AM) are the major infected cell for the first two weeks in unimmunized animals, BCG promotes the accelerated recruitment and infection of lung infiltrating phagocytes. Interestingly, this shift is dependent on CD4 T cells, yet does not require intrinsic recognition of antigen presented by infected AM. Mtb-specific T cells are first activated in lung regions devoid of infected cells, and these events precede vaccine-induced reduction of the bacterial burden, which occurs only after the co-localization of T cells and infected cells. Understanding how BCG alters early immune responses to Mtb provides new avenues to improve upon the immunity it confers.