Prediction and analysis of multi epitope based vaccine against Newcastle disease virus based on haemagglutinin neuraminidase protein

Newcastle disease virus (NDV), an avian orthoavulavirus, is a causative agent of Newcastle disease named (NDV), and can cause even the epidemics when disease is not treated. Previously several vaccines based on attenuated and inactivated viruses have been reported which are rendered useless with the passage of time due to versatile changes in viral genome. Therefore, we aimed to develop an effective multi-epitope vaccine against the haemagglutinin neuraminidase (HN) protein of 26 NDV strains from Pakistan through a modern immunoinformatic approaches. As a result, a vaccine chimaera was constructed by combining T-cell and B-cell epitopes with the appropriate linkers and adjuvant. The designed vaccine was highly immunogenic, non-allergen and antigenic; therefore, the potential 3D-structureof multi epitope vaccine was constructed, refined and validated. A molecular docking study of a multiepitope vaccine candidate with the chicken Toll-like receptor-4 indicated successful binding. An In silico immunological simulation was used to evaluate the candidate vaccine''s ability to elicit an effective immune response. According to the computational studies, the proposed multiepitope vaccine is physically stable and may induce immune responses whichsuggested it a strong candidate against 26 Newcastle disease virus strains from Pakistan.     

Spread of Pathogens Causing Respiratory Viral Diseases Before and During CoVID-19 Pandemic in Kazakhstan

Analyze clinical samples collected and determine the etiology of viral pathogens and the dynamics of their spread. Acute respiratory viral infections remain one of the key health problems worldwide. They constitute etiologically independent diseases, with similar clinical infection manifestations and a single mechanism for the transmission of pathogens. 4712 nasopharyngeal swabs were collected from people before and during the COVID-19 pandemic with acute respiratory infections that tested negative for COVID-19 and were examined in this study. The collected samples were screened by a real-time polymerase chain reaction on a Rotor-Gene Q6 plex instrument. Statistical processing of the results, tabular, and graphical data were analyzed in the MS Excel. The largest number of the nasopharyngeal swabs were collected from children under 17 years of age (60.75%). In 702 samples (9.85%) pathogens of respiratory infections of non-influenza etiology were detected, including adenovirus, bocavirus, coronavirus, metapneumovirus, paramyxovirus types I–IV, respiratory syncytial virus, and rhinovirus. At the same time, both before and during the COVID-19 pandemic, different influenza virus variants co-circulation (A/H1N1, A/H3N2, and type B) were discovered, with a predominance of viruses with the antigenic formula A/H1N1. The results of the study indicate the need for continuous monitoring of the viral pathogens spread, which will expand the existing knowledge of the viral etiology of respiratory diseases and highlight the importance of viruses in the respiratory infections occurrence.     

Do viruses use vectors to penetrate mucus barriers?

I propose a mechanism by which viruses successfully infect new individuals, despite being immotile particles with no ability for directed movement. Within cells, viral particle movements are directed by motors and elements of the cytoskeleton, but how viruses cross extracellular barriers, like mucus, remains a mystery. I propose that viruses cross these barriers by hitch-hiking on bacteria or sperm cells which can transport themselves across mucosal layers designed to protect the underlying cells from pathogen attack. An important implication of this hypothesis is that agents that block interactions between viruses and bacteria or sperm may be new tools for disease prevention.     

Adaptive modeling of viral diseases in bats with a focus on rabies

Many emerging and reemerging viruses, such as rabies, SARS, Marburg, and Ebola have bat populations as disease reservoirs. Understanding the spillover from bats to humans and other animals, and the associated health risks requires an analysis of the disease dynamics in bat populations. Traditional compartmental epizootic models, which are relatively easy to implement and analyze, usually impose unrealistic aggregation assumptions about disease-related structure and depend on parameters that frequently are not measurable in field conditions. We propose a novel combination of computational and adaptive modeling approaches that address the maintenance of emerging diseases in bat colonies through individual (intra-host) models of the response of the host to a viral challenge. The dynamics of the individual models are used to define survival, susceptibility and transmission conditions relevant to epizootics as well as to develop and parametrize models of the disease evolution into uniform and diverse populations. Applications of the proposed approach to modeling the effects of immunological heterogeneity on the dynamics of bat rabies are presented.     

Occurrence and distribution of viruses infecting potato in Russia

Potato viral disease has been a major problem in potato production worldwide including Russia. Here, we detected Potato Virus M (PVM), P (PVP), S (PVS), Y (PVY), and X (PVX) and Potato Leaf Roll Virus (PLRV) by RT-PCR on potato leaves and tubers from the Northwestern (NW), Volga (VF), and Far Eastern (FE) federal districts of Russia. Each sample was co-infected with up to five viruses. RT-PCR disclosed all six viruses in NW, three in VF, and five in FE. Phylogenetic analyses of PVM and PVS strains resolved all PVM isolates in Group O (ordinary) and all PVS isolates in Group O. Seven PVY strains were detected, and they included only recombinants. PVY recombinants were thus the dominant potato virus strains in Russia, although they widely varied among the regions. Our research provides insights into the geographical distribution and genetic variability of potato viruses in Russia.     

Efficacy of a Carrageenan nasal spray in patients with common cold: a randomized controlled trial

Background

The common cold is the most widespread viral infection in humans. Iota-carrageenan has previously shown antiviral effectiveness against cold viruses in clinical trials. This study investigated the efficacy of a carrageenan-containing nasal spray on the duration of the common cold and nasal fluid viral load in adult patients.

Methods

In a randomized, double-blind, placebo-controlled trial, 211 patients suffering from early symptoms of the common cold were treated for seven days. Application was performed three times daily with either a carrageenan-supplemented nasal spray or saline solution as placebo with an overall observation period of 21 days. The primary endpoint was the duration of disease defined as the time until the last day with symptoms followed by all other days in the study period without symptoms. During the study, but prior unblinding, the definition of disease duration was adapted from the original protocol that defines disease duration as the time period of symptoms followed by 48 hours without symptoms.

Results

In patients showing a laboratory-confirmed cold virus infection and adherence to the protocol, alleviation of symptoms was 2.1 days faster in the carrageenan group in comparison to placebo (p = 0.037). The primary endpoint that had been prespecified but was changed before unblinding was not met. Viral titers in nasal fluids showed a significantly greater decrease in carrageenan patients in the intention-to-treat population (p = 0.024) and in the per protocol population (p = 0.018) between days 1 and 3/4.

Conclusions

In adults with common cold virus infections, direct local administration of carrageenan with nasal sprays reduced the duration of cold symptoms. A significant reduction of viral load in the nasal wash fluids of patients confirmed similar findings from earlier trials in children and adults.

Trial registration

Current Controlled Trials ISRCTN80148028     

广东省烟草花叶病病原病毒的鉴定

烟草花叶病是广东省产烟区的主要病害之一。我们在南雄等八个县进行调查,1983年至1984年的一般发病率为2～20％。根据血清学反应、病毒粒体形态、鉴别寄主反应及寄主范围、媒介昆虫种类、物理性质、交互保护反应等各项检验结果,鉴定广东省烟草花叶病病原是:三个黄瓜花叶病毒可能株系(普通株系CMV-C,烟草坏死株系CMV-TN,烟草黄色坏死株系(CMV-TYN),烟草花叶病毒(TMV),马铃薯病毒Y(PVY),烟草脉带花叶病毒(TVBMV)和烟草褪绿斑驳病毒(TCMV)(暂定)。     

Organelle dynamics and viral infections: at cross roads

Viruses are obligate intracellular parasites of the host cells. A commonly accepted view is the requirement of internal membranous structures for various aspects of viral life cycle. Organelles enable favourable intracellular environment for several viruses. However, studies reporting organelle dynamics upon viral infections are scant. In this review, we aim to summarize and highlight modulations caused to various organelles upon viral infection or expression of its proteins.     

Bats and Viruses： a Brief Review

Bats, probably the most abundant, diverse and geographically dispersed vertebrates on earth, have recently been shown to be the reservoir hosts of a number of emerging viruses responsible for severe human and livestock disease outbreaks. Flying foxes have been demonstrated to be the natural reservoir for Hendra and Nipah viruses. Evidence supporting the possibility of bats as potential reservoirs for SARS coronavirus (SARS-CoV) and Ebola virus has also been reported. The recent discovery of these viruses and other viruses occurring naturally in the bat population provides a unique insight into a diverse pool of potentially emergent and pathogenic viruses. The factors which influence the ability of zoonotic viruses to effectively cross the species barrier from bats to other animal populations are poorly understood. A brief review is provided here on the recently emerged bat viruses and on current and future strategies for research in this area.     

龙眼鬼帚病的研究 Ⅲ．病毒病原的确认

应用５００、１５００单位人体注射用的盐酸四环素和青霉素Ｇ钾浸渍处理龙眼鬼帚病苗,均无抑制病状表现,表明本病不是由ＭＬＯ和ＢＬＯ引起的;电镜观察仅在病叶组织筛管细胞内见到成束分布在细胞质内的线状病毒粒体;通过Ａ蛋白。免疫电镜检测,亦可在龙眼鬼帚病介体昆虫荔枝蝽（ＴｅｓｓａｒａｔｏｍａｐａｐｉｌｌｏｓａＤｒｕｒｙ）、龙眼角颊木虱（ＣａｒｎｅｇｅｎａｐｓｙｌｌａｓｉｎｉｃａＹａｎｇｅｔＬｉ）唾液腺内捕获到与病叶组织相同的病毒粒体,从而进一步肯定本病病原的病毒性质。     

Early molecular events during the interaction of enveloped riboviruses with cells

A kinetic model was constructed and partly solved to describe the migration of the fluorescence label 1,6-diphenylhexatriene (DPH) in both directions when enveloped viruses, labelled with DPH in their envelopes are in contact with unlabelled cells or cell labelled in their membranes are in contact with unlabelled enveloped viruses. The central assumption is that two types of receptor sites exist on the cell surface, i.e., physical adsorption sites (P-sites), available to all the viruses studied in these papers and binding sites (B-sites) available only to the viruses which penetrate into the specific cells.The differential equations for the label migration, for different values of the ratio number of viruses number of sites were numerically solved, assuming different fractions of P- and B-sites.The equations also describe, appropriately the mechanism of rapid label migration in the system and substantiate the magnitude time of residence of the nonpenetrating viruses adsorbed on the cell surface. The resulting curves match satisfactorily those for the label release by the viruses and account well for the steady state values of the kinetics of label migration in the virus-cell system.     

On the relative fitness of early and late stage Simian immunodeficiency virus isolates

Simian immunodeficiency virus (SIV) has been shown to evolve from a relatively slowly replicating and mildly cytopathic virus early in the infection (SIVMneCL8) to a faster replicating and more cytopathic virus at later stages of the infection (SIVMne170). It has recently been demonstrated that the early and mildly cytopathic variant SIVMneCL8 out-competed the late and highly cytopathic strain SIVMne170 in cell culture experiments, because the fitness disadvantage derived from the higher cytopathicity was not matched by a sufficient increase in the viral replication rate. However, in another set of experiments where the life span of cells in culture was artificially limited, the late and more cytopathic virus won the competition, because under this condition cytopahticity was not an important determinant of viral fitness. It was hypothesized that the limited life span experiment reflected the immune-mediated high turnover environment in vivo more accurately, and that the presence of immune responses accounts for the selection of the cytopathic strain SIVmne170 during later stages of the infection. This paper investigates the effect of immune responses, in particular cytotoxic T lymphocyte (CTL) responses, on the competition dynamics between these two SIV strains with the help of mathematical models. Model analysis and parameter estimates derived from previously published data on SIV growth kinetics suggest that the SIV-specific CTL response might not be the driving force that leads to the selection of the cytopathic strain SIVMne170 during later stages of the infection. This implies that more complex evolutionary mechanisms might have to be invoked in order to explain the emergence of these strains in vivo. One possibility is that the ability of multiple virus particles to infect the same cell (coinfection) might be a pre-requisite for the emergence of the cytopathic strain SIVMne170 as the disease progresses.     

CRISPR/Cas9在人病毒感染相关疾病治疗研究中的应用*

病毒感染相关疾病严重威胁人类的健康,目前的抗病毒疗法难以治愈慢性病毒性感染引起的一些疾病,如获得性免疫缺陷综合征和乙型肝炎等,因此迫切需要新的治疗方法。可直接靶向遗传物质的基因编辑技术或将成为对抗病毒的有力工具。作为一种可编程的核酸酶介导的新型基因编辑技术,CRISPR/Cas9系统因其具有编辑效率高、操作简单、成本低、适用范围广等优点,而成功应用于多种人类相关疾病的研究中,也为病毒感染相关疾病的研究以及开发新的治疗方法提供了新的技术手段。主要对CRISPR/Cas9系统的作用机制以及在人类常见的病毒感染相关疾病治疗研究中的最新进展进行综述。     

两种鳜病毒的共感染现象及引起感染细胞的超微变化

借助细胞培养和电镜技术,揭示了鳜球形病毒(Siniperca chuatsi spherical virus,SCSV)与鳜弹状病毒(Siniperca chuatsi rhabdovirus,SCRV)在草鱼鳍细胞(Grass carp fins,GCF)中共感染的现象。在筛选到敏感鱼类细胞系和建立了 鳜病毒体外增殖系统的基础上,取息典型病毒感染出血症的鳜组织,制备组织悬液,接种到GCF细胞中传代培养, 在攻毒后间隔不同时间收集细胞,对攻毒细胞的超薄切片进行电镜观察。揭示两种形态的鳜病毒可在同一个GCF 细胞中增殖,并描述和分析了病毒复制引起感染细胞的超微病变。本研究结果有助于阐明鱼类重要病毒病害的发 生过程及致病机理。     

Structural Dynamics as a Contributor to Error-prone Replication by an RNA-dependent RNA Polymerase

RNA viruses encoding high- or low-fidelity RNA-dependent RNA polymerases (RdRp) are attenuated. The ability to predict residues of the RdRp required for faithful incorporation of nucleotides represents an essential step in any pipeline intended to exploit perturbed fidelity as the basis for rational design of vaccine candidates. We used x-ray crystallography, molecular dynamics simulations, NMR spectroscopy, and pre-steady-state kinetics to compare a mutator (H273R) RdRp from poliovirus to the wild-type (WT) enzyme. We show that the nucleotide-binding site toggles between the nucleotide binding-occluded and nucleotide binding-competent states. The conformational dynamics between these states were enhanced by binding to primed template RNA. For the WT, the occluded conformation was favored; for H273R, the competent conformation was favored. The resonance for Met-187 in our NMR spectra reported on the ability of the enzyme to check the correctness of the bound nucleotide. Kinetic experiments were consistent with the conformational dynamics contributing to the established pre-incorporation conformational change and fidelity checkpoint. For H273R, residues comprising the active site spent more time in the catalytically competent conformation and were more positively correlated than the WT. We propose that by linking the equilibrium between the binding-occluded and binding-competent conformations of the nucleotide-binding pocket and other active-site dynamics to the correctness of the bound nucleotide, faithful nucleotide incorporation is achieved. These studies underscore the need to apply multiple biophysical and biochemical approaches to the elucidation of the physical basis for polymerase fidelity.     

Partitioning and inactivation of viruses by the caprylic acid precipitation followed by a terminal pasteurization in the manufacturing process of horse immunoglobulins

Caprylic acid (octanoic acid), has been used for over 50 years as a stabilizer of human albumin during pasteurization. In addition caprylic acid is of great interest, by providing the advantage of purifying mammalian immunoglobulins and clearing viruses infectivity in a single step. Exploiting these two properties, we sequentially used the caprylic acid precipitation and the pasteurization to purify horse hyperimmune globulins used in the manufacturing of Sérocytol. To evaluate the effectiveness of the process for the removal/inactivation of viruses, spiking studies were carried out for each dedicated step. Bovine viral diarrhoea virus (BVDV), pseudorabies virus (PRV), encephalomyocarditis virus (EMCV) and minute virus of mice (MVM) were used for the virological validation. Our data show that the treatment with caprylic acid 5% (v/v) can effectively be used as well to purify or to ensure viral safety of immunoglobulins. Caprylic acid precipitation was very efficient in removing and/or inactivating enveloped viruses (PRV, BVDV) and moderately efficient against non-enveloped viruses (MVM, ECMV). However the combination with the pasteurization ensured an efficient protection against both enveloped and non-enveloped viruses. So that viruses surviving to the caprylic acid precipitation will be neutralized by pasteurization. Significant log reduction were achieved > or =9 log(10) for enveloped viruses and 4 log(10) for non-enveloped viruses, providing the evidence of a margin of viral safety achieved by our manufacturing process. Its a simple and non-expensive manufacturing process of immunoglobulins easily validated that we have adapted to a large production scale with a programmable operating system.     

Viral population dynamics and virulence thresholds

Viral factors and host barriers influence virally induced disease, and asymptomatic versus symptomatic infection is governed by a 'virulence threshold'. Understanding modulation of virulence thresholds could lend insight into disease outcome and aid in rational therapeutic and vaccine design. RNA viruses are an excellent system to study virulence thresholds in the context of quasispecies population dynamics. RNA viruses have high error frequencies and our understanding of viral population dynamics has been shaped by quasispecies evolutionary theory. In turn, research using RNA viruses as replicons with short generation times and high mutation rates has been an invaluable tool to test models of quasispecies theory. The challenge and new frontier of RNA virus population dynamics research is to combine multiple theoretical models and experimental data to describe viral population behavior as it changes, moving within and between hosts, to predict disease and pathogen emergence. Several excellent studies have begun to undertake this challenge using novel approaches.     

Potential effects of HMGB1 on viral replication and virus infection-induced inflammatory responses: A promising therapeutic target for virus infection-induced inflammatory diseases

Inflammatory responses, characterized by the overproduction of numerous proinflammatory mediators by immune cells, is essential to protect the host against invading pathogens. Excessive production of proinflammatory cytokines is a key pathogenic factor accounting for severe tissue injury and disease progression during the infection of multiple viruses, which are therefore termed as “cytokine storm”. High mobility group box 1 (HMGB1), a ubiquitous DNA-binding protein released either over virus-infected cells or activated immune cells, may act as a proinflammatory cytokine with a robust capacity to potentiate inflammatory response and disease severity. Moreover, HMGB1 is a host factor that potentially participates in the regulation of viral replication cycles with complicated mechanisms. Currently, HMGB1 is regarded as a promising therapeutic target against virus infection. Here, we provide an overview of the updated studies on how HMGB1 is differentially manipulated by distinct viruses to regulate viral diseases.     

嵌合O/GSLX/CHN/2010株S片段的基因工程口蹄疫病毒的生物学特性

【目的】研究嵌合口蹄疫病毒(Foot-and-mouth disease virus,FMDV) O/GSLX/CHN/2010株S片段的基因工程病毒的生物学特性。【方法】运用反向遗传操作技术,将FMDV O/GSLX/CHN/2010的S片段嵌合进2株同谱系FMDV的感染性克隆骨架,拯救得到两株基因工程嵌合病毒rGDexc、rGZexc;进而从病毒复制和病毒对乳鼠的致病力方面,对嵌合病毒、亲本基因工程病毒以及FMDV O/GSLX/CHN/2010株进行了评价。【结果】FMDV O/GSLX/CHN/2010株复制较慢,对乳鼠致病力较差。嵌合病毒和亲本基因工程病毒的复制能力、对乳鼠的致病力明显高于FMDV O/GSLX/CHN/2010株。【结论】研究表明FMDV O/GSLX/CHN/2010的S片段不能独自决定该病毒较差的复制能力和较弱的乳鼠致病力。这一发现为进一步研究O/GSLX/CHN/2010的致弱机制以及S片段对病毒生物学特性的影响奠定了基础。