niryuu/sni-each-converted huggingface dataset:
Background: Coxsackievirus A4 (CV-A4) is classified as human enterovirus A according to its serotype. CV-A4, an etiological agent of hand, foot, and mouth disease, affects children worldwide and can circulate in closed environments such as schools and hospitals for long periods. Findings: An outbreak of febrile illness at a nursery school in Beijing, China, was confirmed to be caused by CV-A4. Phylogenetic analysis of the complete genome of the isolated strain showed that the virus belongs to the same cluster as the predominant CV-A4 strain in China. This outbreak was controlled by effective measures. Conclusions: The early identification of the pathogen and timely intervention may be the most critical factors in controlling an outbreak caused by CV-A4 in a preschool.
Output: Outbreak of febrile illness caused by coxsackievirus A4 in a nursery school in Beijing, China
Plant-made or "biofarmed" viral vaccines are some of the earliest products of the technology of plant molecular farming, and remain some of the brightest prospects for the success of this field. Proofs of principle and of efficacy exist for many candidate viral veterinary vaccines; the use of plant-made viral antigens and of monoclonal antibodies for therapy of animal and even human viral disease is also well established. This review explores some of the more prominent recent advances in the biofarming of viral vaccines and therapies, including the recent use of ZMapp for Ebolavirus infection, and explores some possible future applications of the technology. Recent candidate viral vaccines produced in plants Hepatitis B virus (HBV) vaccines are one of the blockbuster vaccine success stories of modern times: since identification of the virus in the 1960s, it took less than
Output: Plant-based vaccines against viruses
The Cystatins constitute a large group of evolutionary related proteins with diverse biological activities. They have been recently realized as instrumental in myriad of pathophysiological conditions. They have been implicated in various pathological conditions. The degree of malignancy of various types of cancer cells has been found to be inversely associated with the expression of cystatins. Cystatins have been found to have various antimicrobial, antiviral and immunomodulatory properties. Keeping in view as their being prospective drug targets and anti-disease options this review explores the role of cytoplasmic and cell secreted cystatins in various human diseases.
Output: Cystatins in Health and Diseases
The infl ammatory response in community-acquired pneumonia (CAP) depends on the host and on the challenge of the causal microorganism. Here, we analyze the patterns of inflammatory cytokines, procalcitonin (PCT), and C-reactive protein (CRP) in order to determine fl their diagnostic value. Methods: This was a prospective study of 658 patients admitted with CAP. PCT and CRP were analyzed by immunoluminometric and immunoturbidimetric assays. Cytokines (tumor necrosis factor-a [TNF-a ], IL-1 b, IL-6, IL-8, and IL-10) were measured using enzyme immunoassay. Results: The lowest medians of CRP, PCT, TNF-a, and IL-6 were found in CAP of unknown cause, and the highest were found in patients with positive blood cultures. Different cytokine profiles fi and biomarkers were found depending on cause: atypical bacteria (lower PCT and IL-6), viruses (lower PCT and higher IL-10), Enterobacteriaceae (higher IL-8), Streptococcus pneumoniae (high PCT), and Legionella pneumophila (higher CRP and TNF-a). PCT Ն 0.36 mg/dL to predict positive blood cultures showed sensitivity of 85%, specifi city of 42%, and negative predictive value (NPV) of 98%, whereas a cutoff of Յ 0.5 mg/dL to predict viruses or atypicals vs bacteria showed sensitivity of 89%/81%, specifi city of 68%/68%, positive predictive value of 12%/22%, and NPV of 99%/97%. In a multivariate Euclidean distance model, the lowest infl ammatory expression fl was found in unknown cause and the highest was found in L pneumophila, S pneumoniae , and Enterobacteriaceae. Atypical bacteria exhibit an infl ammatory pattern closer to that of viruses. Conclusions: Different infl ammatory patterns elicited by different microorganisms may provide a useful tool for diagnosis. Recognizing these patterns provides additional information that may facilitate a broader understanding of host infl ammatory response to microorganisms. Abbreviations: CAP 5 community-acquired pneumonia; CRP 5 C-reactive protein; GNB 5 gram-negative bacilli; GPC 5 gram-positive cocci; NPV 5 negative predictive value; PCT 5 procalcitonin; TNF-a 5 tumor necrosis factor-a
Output: Cytokine Activation Patterns and Biomarkers Are Infl uenced by fl Microorganisms in Community-Acquired Pneumonia Downloaded from 12 (5-24) NS
China's public health surveillance system for HIV was established in late 1980s and has evolved significantly during the past three decades. With the gradually changing mode of HIV transmission from sharing of intravenous injecting equipment to sexual exposure and the rapid spread of HIV infection among Chinese homosexual men in recent years, an efficient and comprehensive population-level surveillance system for describing epidemics trends and risk behaviours associated with HIV acquisition are essential for effective public health interventions for HIV. The current review describes the overall strength of the Chinese HIV surveillance system and its structural weaknesses from a political and social perspective. The HIV surveillance system in China has undergone substantial revamping leading to a comprehensive, timely and efficient reporting system. However, large data gaps and lack of quality control and sharing of information obstruct the full performance of the system. This is largely due to fragmented authoritarianism brought about by the underlying political structure. Social stigma and discrimination in health institutes are also key barriers for further improvements of HIV diagnosis and surveillance in China. © Zhang et al.; Licensee Bentham Open. This is an open access article licensed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/ 3.0/) which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited.
Output: Describing the Chinese HIV Surveillance System and the Influences of Political Structures and Social Stigma
During an epidemic outbreak in a human population, susceptibility to infection can be reduced by raising awareness of the disease. In this paper, we investigate the effects of three forms of awareness (i.e., contact, local, and global) on the spread of a disease in a random network. Connectivity-correlated transmission rates are assumed. By using the mean-field theory and numerical simulation, we show that both local and contact awareness can raise the epidemic thresholds while the global awareness cannot, which mirrors the recent results of Wu et al. The obtained results point out that individual behaviors in the presence of an infectious disease has a great influence on the epidemic dynamics. Our method enriches mean-field analysis in epidemic models.
Output: Modeling epidemic spread with awareness and heterogeneous transmission rates in networks
RNA-protein interactions (RPIs) play a very important role in a wide range of post-transcriptional regulations, and identifying whether a given RNA-protein pair can form interactions or not is a vital prerequisite for dissecting the regulatory mechanisms of functional RNAs. Currently, expensive and time-consuming biological assays can only determine a very small portion of all RPIs, which calls for computational approaches to help biologists efficiently and correctly find candidate RPIs. Here, we integrated a successful computing algorithm, conjoint triad feature (CTF), and another method, chaos game representation (CGR), for representing RNA-protein pairs and by doing so developed a prediction model based on these representations and random forest (RF) classifiers. When testing two benchmark datasets, RPI369 and RPI2241, the combined method (CTF+CGR) showed some superiority compared with four existing tools. Especially on RPI2241, the CTF+CGR method improved prediction accuracy (ACC) from 0.91 (the best record of all published works) to 0.95. When independently testing a newly constructed dataset, RPI1449, which only contained experimentally validated RPIs released between 2014 and 2016, our method still showed some generalization capability with an ACC of 0.75. Accordingly, we believe that our hybrid CTF+CGR method will be an important tool for predicting RPIs in the future.
Output: Prediction of RNA-protein interactions using conjoint triad feature and chaos game representation
Background: Despite recent discovery of the novel human rhinovirus species, HRV-C, little is known about the association of HRV-C in diseases other than respiratory tract infections. Objectives: To investigate the presence of HRV-C in fecal samples of children with gastroenteritis. Study design: 734 fecal samples from hospitalized children with gastroenteritis were subject to picornavirus detection by RT-PCR of the conserved 5 -NCR. Positive samples were subject to VP4 and 3D pol gene analysis for species determination. The clinical and molecular epidemiology of HRV-C and other picornaviruses was analyzed. Results: Picornaviruses were detected in 113 (15.4%) of 734 fecal samples from children with gastroenteritis by RT-PCR of 5 -NCR, with 58 containing potential HRVs and 55 containing other enteroviruses. PCR of the VP4 and 3D pol regions was positive in 21 and 19 samples respectively (both regions positive in 8 samples). Sequencing analysis showed the presence of HRV-C in four samples, and diverse picornaviruses including HRV-A (n = 2), HEV-A (n = 2), HEV-B (n = 2), HEV-C (n = 21) and HPeV (n = 2) in other samples, with co-detection of HRV-C and HPeV in one sample. Of the four children with HRV-C detected in fecal samples, three presented with diarrhea in the absence of respiratory symptoms, while one also had acute bronchiolitis. The four HRV-C strains from fecal samples belonged to the existing clade of diverse HRV-C genotypes, indistinguishable from previous respiratory strains. Conclusions: HRV-C can be detected in fecal samples of children with gastroenteritis, in the absence of respiratory symptoms. This study also represented the first to detect HPeV in our population.
Output: Detection of human rhinovirus C in fecal samples of children with gastroenteritis
Standard precautions should be applied to prevent health care-associated infections during every nursing activity. However, adherence to standard precautions was reported to be inadequate. Therefore, this study aimed to identify the rates of standard precaution adherence and the association between perception of patient safety management and standard precaution adherence. In this cross-sectional descriptive study, a convenience sample of nurses was recruited from a university-affiliated teaching hospital in Seoul, Korea. Data were collected using a structured self-report questionnaire. Among the 332 questionnaires returned (response rate: 94.9%), a total of 329 nurses were analyzed. In the present study, the overall standard precaution adherence rate was approximately 53.5%. The multiple linear regression results revealed that participants' perceptions of patient safety management were only significantly associated with standard precaution adherence after adjusting other covariates (β = 0.412, p < 0.001). Nurse supervisors should focus more on raising awareness about nurses' perception of patient safety management based on the specific work environment, such as the total number of nurses working together and the nurse-to-patient ratio. Nurse educators should develop integrated curricula to help graduate nurses transition smoothly into professional practice and enhance adherence to standard precautions in diverse health care settings.
Output: Association between Hospital Nurses' Perception of Patient Safety Management and Standard Precaution Adherence: A Cross-Sectional Study
M iniaturized integrated DNA analysis systems offer the potential to provide unprecedented advances in cost and speed relative to current benchtop-scale instrumentation by allowing rapid bioanalysis assaysto be performed in a portable self contained device format that can be inexpensively mass-produced. The polymerase chain reaction (PCR) has been a natural focus of many of these miniaturization efforts, owing to its capability to efficiently replicate target regions ofinterest from small quantities template DNA. Scale-down ofPCR has proven to be particularly challenging, however, due to an unfavorable combination of relatively severe temperature extremes (resulting in the need to repeatedly heat minute aqueous sample volumes to temperatures in the vicinity of95'C with minimal evaporation) and high surface area to volume conditions imposed by nanoliter reactor geometries (often leading to inhibition ofthe reaction by nonspecific adsorption ofreagents at the reactor walls). Despite these daunting challenges, considerable progress has been made in the development of microfluidic devices capable ofperforming increasingly sophisticated PCR-based bioassays.This chapter reviews the progress that has been made to date and assessesthe outlook for future advances.
Output: peR in Integrated Microfluidic Systems
During the prevention of coronavirus disease 2019 , epidemiological data is essential for controlling the source of infection, cutting off the route of transmission, and protecting vulnerable populations. Following Law of the People's Republic of China on Prevention and Treatment of Infectious Diseases and other related regulations, medical institutions have been authorized to collect the detailed information of patients, while it is still a formidable task in megacities because of the significant patient mobility and the existing information sharing barrier. As a smart city which strengthens precise epidemic prevention and control, Shanghai has established a multi-department platform named "one-net management" on dynamic information monitoring. By sharing epidemiological data with medical institutions under a safe environment, we believe that the ability to prevent and control epidemics among medical institutions will be effectively and comprehensively improved.
Output: Feature Demand Analysis and Management Suggestion: Sharing Epidemiological Data Among Medical Institutions in Megacities for Epidemic Prevention and Control
Several nucleic acid amplification techniques (NAATs), particularly PCR and real-time PCR, are currently used in the routine clinical laboratories. Such approaches have allowed rapid diagnosis with a high degree of sensitivity and specificity. However, conventional PCR methods have several intrinsic disadvantages such as the requirement for temperature cycling apparatus, and sophisticated and costly analytical equipments. Therefore, amplification at a constant temperature is an attractive alternative method to avoid these requirements. A new generation of isothermal amplification techniques are gaining a wide popularity as diagnostic tools due to their simple operation, rapid reaction and easy detection. The main isothermal methods reviewed here include loopmediated isothermal amplification, nucleic acid sequencebased amplification, and helicase-dependent amplification. In this review, design criteria, potential of amplification, and application of these alternative molecular tests will be discussed and compared to conventional NAATs.
Output: Alternative Molecular Tests for Virological Diagnosis
Canine infectious respiratory disease (CIRD) is a syndrome where multiple viral and bacterial pathogens are involved sequentially or synergistically to cause illness. There is limited information regarding the prevalence of pathogens related to CIRD in the United States as well as the role of co-infections in the pathogenesis of the syndrome. We aimed to conduct a comprehensive etiologic and epidemiologic study of multiple CIRD agents in a diverse dog population using molecular methods and statistical modeling analyses. In addition, a novel probe-based multiplex real-time PCR was developed to simultaneously detect and differentiate two species of Mycoplasma (M. canis and M. cynos). Canine adenovirus, canine distemper virus, canine parainfluenza virus, coronavirus, influenza A virus (H3N2 and H3N8), Bordetella bronchiseptica, M. canis, M. cynos and Streptococcus equi subsp. zooepidemicus were investigated in specimens from clinically ill and asymptomatic dogs received at the Athens Veterinary Diagnostic Laboratory. Results showed low occurrence of classical CIRD agents such as B. bronchiseptica, canine adenovirus and distemper virus, while highlighting the potential role of emerging bacteria such as M. canis and M. cynos. Statistical modeling analyses of CIRD pathogens emphasized the impact of co-infections on the severity of clinical presentation, and showed that host factors, such as animal age, are the most important predictors of disease severity. This study provides new insights into the current understanding of the prevalence and role of co-infections with selected viruses and bacteria in the etiology of CIRD, while underscoring the importance of molecular diagnosis and vaccination against this disease.
Output: Canine infectious respiratory disease: New insights into the etiology and epidemiology of associated pathogens
The dog is considered the main domestic reservoir for Trypanosoma cruzi infection and a suitable experimental animal model to study the pathological changes during the course of Chagas disease (CD). Vaccine development is one of CD prevention methods to protect people at risk. Two plasmids containing genes encoding a trans-sialidase protein (TcSP) and an amastigote-specific glycoprotein (TcSSP4) were used as DNA vaccines in a canine model. Splenomegaly was not found in either of the recombinant plasmid-immunized groups; however, cardiomegaly was absent in animals immunized only with the plasmid containing the TcSSP4 gene. The inflammation of subendocardial and myocardial tissues was prevented only with the immunization with TcSSP4 gene. In conclusion, the vaccination with these genes has a partial protective effect on the enlargement of splenic and cardiac tissues during the chronic CD and on microscopic hearth damage, since both plasmids prevented splenomegaly but only one avoided cardiomegaly, and the lesions in heart tissue of dog immunized with plasmid containing the TcSSP4 gene covered only subepicardial tissue.
Output: Effect of the Plasmid-DNA Vaccination on Macroscopic and Microscopic Damage Caused by the Experimental Chronic Trypanosoma cruzi Infection in the Canine Model
Field epidemiology involves the implementation of quick and targeted public health interventions with the aid of epidemiological methods. In this article, we share our practical experiences in outbreak management and in safeguarding the population against novel diseases. Given that cities represent the financial nexuses of the global economy, global health security necessitates the safeguard of cities against epidemic diseases. Singapore's public health landscape has undergone a systemic and irreversible shift with global connectivity, rapid urbanization, ecological change, increased affluence, as well as shifting demographic patterns over the past two decades. Concomitantly, the threat of epidemics, ranging from severe acute respiratory syndrome and influenza A (H1N1) to the resurgence of vector-borne diseases as well as the rise of modern lifestyle-related outbreaks, have worsened difficulties in safeguarding public health amidst much elusiveness and unpredictability. One critical factor that has helped the country overcome these innate and man-made public health vulnerabilities is the development of a resilient field epidemiology service, which includes our enhancement of surveillance and response capacities for outbreak management, and investment in public health leadership. We offer herein the Singapore story as a case study in meeting the challenges of disease control in our modern built environment.
Output: The Singapore Field Epidemiology Service: Insights Into Outbreak Management
is paper provides a review of the past, present, and future of public health surveillance-the ongoing systematic collection, analysis, interpretation, and dissemination of health data for the planning, implementation, and evaluation of public health action. Public health surveillance dates back to the �rst recorded epidemic in 3180 B.C. in Egypt. Hippocrates (460 B.C.-370 B.C.) coined the terms endemic and epidemic, John Graunt (1620-1674) introduced systematic data analysis, Samuel Pepys (1633-1703) started epidemic �eld investigation, �illiam Farr (1807-1883) founded the modern concept of surveillance, John Snow (1813-1858) linked data to intervention, and Alexander Langmuir gave the �rst comprehensive de�nition of surveillance. Current theories, principles, and practice of public health surveillance are summarized. A number of surveillance dichotomies, such as epidemiologic surveillance versus public health surveillance, are described. Some future scenarios are presented, while current activities that can affect the future are summarized: exploring new frontiers; enhancing computer technology; improving epidemic investigations; improving data collection, analysis, dissemination, and use; building on lessons from the past; building capacity; enhancing global surveillance. It is concluded that learning from the past, re�ecting on the present, and planning for the future can further enhance public health surveillance.
Output: The Past, Present, and Future of Public Health Surveillance
The rapid discovery of novel viruses using next generation sequencing (NGS) technologies including DNA-Seq and RNA-Seq, has greatly expanded our understanding of viral diversity in recent years. The timely identification of novel viruses using NGS technologies is also important for us to control emerging infectious diseases caused by novel viruses. In this study, we identified a novel duck coronavirus (CoV), distinct with chicken infectious bronchitis virus (IBV), using RNA-Seq. The novel duck-specific CoV was a potential novel species within the genus Gammacoronavirus, as indicated by sequences of three regions in the viral 1b gene. We also performed a survey of CoVs in domestic fowls in China using reverse-transcription polymerase chain reaction (RT-PCR), targeting the viral nucleocapsid (N) gene. A total of 102 CoV positives were identified through the survey. Phylogenetic analysis of the viral N sequences suggested that CoVs in domestic fowls have diverged into several region-specific or host-specific clades or subclades in the world, and IBVs can infect ducks, geese and pigeons, although they mainly circulate in chickens. Moreover, this study provided novel data supporting the notion that some hostspecific CoVs other than IBVs circulate in ducks, geese and pigeons, and indicated that the novel duck-specific CoV identified through RNA-Seq in this study is genetically closer to some CoVs circulating in wild water fowls. Taken together, this study shed new insight into the diversity, distribution, evolution and control of avian CoVs.
Output: Identification and Survey of a Novel Avian Coronavirus in Ducks
In commercial poultry production there are a number of diseases which are of particular importance due to the heavy economic losses that can arise if a flock becomes infected. The development of an automated and rapid disease detection system would therefore be of considerable benefit to both production and animal welfare. This study represents an intelligence device for diagnosing avian diseases by using Data-mining methods and Dempster-Shafer evidence theory (D-S). 14-day-old chickens were divided into four groups. Each group was deliberately infected with a disease: Newcastle Disease (ND), Bronchitis Virus (BV), Avian Influenenza (AI), and the last group was considered as control samples. Fast Fourier Transform (FFT) and Discrete Wavelet Transform (DWT) were used to process the chicken's sound signals in frequency and time-frequency domains, respectively. In order to achieve information, 25 statistical features from frequency domains, and 75 statistical features from time-frequency domains were extracted. During dimensionality reduction stage, the best features of the sound signals were selected, using improved distance evaluation (IDE) method. The chicken's sound signals were analyzed in two consecutive days after virus infection. Support vector machine (SVM) was used as the classifier in this study. The first classification was done with SVM and based on sound features in frequency and time-frequency domains with accuracy of 41.35 and 83.33%, respectively. The accuracy of the method based on D-S infusion of sound data reached 91.15%. The developed model based on achievement result could diagnose Newcastle Disease, Bronchitis Virus and Avian Influenza from sound signals.
Output: Original papers
Background: Meeting the UN Sustainable Development Goals requires a relatively rapid transition towards a circular economy. Therefore, a multidisciplinary perspective is required to sketch why a transition from diets based primarily on animal proteins towards diets based primarily on plant proteins products is extremely urgent for both food security and sustainability. Scope and approach: This review starts out by identifying ecological, economic and social aspects of sustainable food consumption. Subsequently, it is argued how protein supply is underlying and linking the top-3 of anthropogenic impacts based on the planetary boundaries concept, i.e. 1) biodiversity loss, 2) nitrogen cycle acceleration, and 3) carbon cycle acceleration (resulting in climate change). These environmental impacts associated with current Western food consumption need to be reduced urgently. In order to address the inefficiencies inherent to current dietary patterns, therefore, a ranked list of more sustainable options is proposed, based on their order of magnitude. Addressing consumers, industry, and governmental stakeholders plus cultural aspects, challenges and options are sketched. Key findings and conclusions: Clearly, a dietary transition from primarily animal towards plant protein products is required. Fortunately, new dietary guidelines are increasingly taking sustainability into account and the contours of a diet transition are slowly emerging.
Output: The next protein transition ☆
The existence of coronaviruses in bats is unknown until the recent discovery of bat-SARS-CoV in Chinese horseshoe bats and a novel group 1 coronavirus in other bat species. Among 309 bats of 13 species captured from 20 different locations in rural areas of Hong Kong over a 16-month period, coronaviruses were amplified from anal swabs of 37 (12%) bats by RT-PCR. Phylogenetic analysis of RNA-dependent-RNA-polymerase (pol) and helicase genes revealed six novel coronaviruses from six different bat species, in addition to the two previously described coronaviruses. Among the six novel coronaviruses, four were group 1 coronaviruses (bat-CoV HKU2 from Chinese horseshoe bat, bat-CoV HKU6 from rickett's big-footed bat, bat-CoV HKU7 from greater bent-winged bat and bat-CoV HKU8 from lesser bent-winged bat) and two were group 2 coronaviruses (bat-CoV HKU4 from lesser bamboo bats and bat-CoV HKU5 from Japanese pipistrelles). An astonishing diversity of coronaviruses was observed in bats.
Output: Molecular diversity of coronaviruses in bats
Porcine epidemic diarrhea virus emerged in North America in April 2013 and has since been identified in 30 U.S. States, Canada and Mexico. The rapid spread of PEDV has raised concerns about the role of feed and particularly pork-by-product components such as spray-dried porcine plasma (SDPP) in PEDV transmission. The aim of this study was to determine the infectivity of PEDV RNA present in commercial SDPP. Specifically, 40 3-week-old PEDV naïve pigs were randomly assigned to one of five treatment groups. At day post inoculation (dpi) 0, NEG-CONTROL pigs were sham-inoculated, PEDV-CONTROL pigs received cell culture propagated PEDV, and SDPP-CONTROL pigs were switched to a diet with 5% SDPP containing 5.160.1 log 10 PEDV RNA copies/g. To evaluate a potential positive effect of anti-PEDV antibodies in SDPP on PEDV challenge, four days prior to PEDV challenge the pigs in the SDPP-PEDV group were switched to and remained on a 5% SDPP diet through dpi 28. Another group, EGG-PEDV, was orally administered a commercial egg-derived liquid PEDV globulin product from dpi -4 through 6. All PEDV-CONTROL pigs began shedding PEDV in feces by dpi 3 and seroconverted between dpi 7 and 14, whereas pigs in NEG-CONTROL and SDPP-CONTROL groups remained PEDV RNA negative and did not seroconvert to PEDV for the study duration. This indicates no evidence of infectivity of the PEDV RNA in the SDPP lot utilized. Furthermore, under the study conditions SDPP or egg-derived liquid PEDV globulin addition did not significantly alter PEDV-shedding or overall disease course after experimental challenge.
Output: Porcine Epidemic Diarrhea Virus RNA Present in Commercial Spray-Dried Porcine Plasma Is Not Infectious to Naïve Pigs
With the emergence of highly pathogenic variant strains, porcine epidemic diarrhea virus (PEDV) has led to significant economic loss in the global swine industry. Many studies have described how coronaviruses enter cells, but information on PEDV invasion strategies remains insufficient. Given that the differences in gene sequences and pathogenicity between classical and mutant strains of PEDV may lead to diverse invasion mechanisms, this study focused on the cellular entry pathways and cellular transport of the PEDV GI and GII subtype strains in Vero cells and IPEC-J2 cells. We first characterized the kinetics of PEDV entry into cells and found that the highest invasion rate of PEDV was approximately 33% in the IPEC-J2 cells and approximately 100% in the Vero cells. To clarify the specific endocytic pathways, systematic research methods were used and showed that PEDV enters cells via the clathrin-and caveolae-mediated endocytosis pathways, in which dynamin II, clathrin heavy chain, Eps15, cholesterol, and caveolin-1 were indispensably involved. In addition, lipid raft extraction assay showed that PEDV can also enter cells through lipid raft-mediated endocytosis. To investigate the trafficking of internalized PEDV, we found that PEDV entry into cells relied on low pH and internalized virions reached lysosomes through the early endosome-late endosome-lysosome pathway. The results concretely revealed the entry mechanisms of PEDV and provided an insightful theoretical basis for the further understanding of PEDV pathogenesis and guidance for new targets of antiviral drugs. © The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article' s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article'
Output: PEDV enters cells through clathrin-, caveolae-, and lipid raft-mediated endocytosis and traffics via the endo-/lysosome pathway
Because of its essential role in gas exchange and oxygen delivery, the lung has evolved a variety of strategies to control inflammation and maintain homeostasis. Invasion of the lung by pathogens (and in some instances exposure to certain noninfectious particulates) disrupts this equilibrium and triggers a cascade of events aimed at preventing or limiting colonization (and more importantly infection) by pathogenic microorganisms. In this review we focus on viral infection of the lung and summarize recent advances in our understanding of the triggering of innate and adaptive immune responses to viral respiratory tract infection, mechanisms of viral clearance, and the wellrecognized consequences of acute viral infection complicating underlying lung diseases, such as asthma.
Output: Viral infection of the lung: Host response and sequelae
A capsid protein of porcine circovirus 2 (PCV 2) serves as a diagnostic antigen for the detection of PCV 2-associated disease known as a postweaning multisystemic wasting syndrome (PMWS). In this report, a bacterial expression system was developed for the expression and purification of the full-length PCV 2 capsid (Cap) protein from a codon-optimized cap gene. Replacement of rare arginine codons located at the 5 end of the cap reading frame with codons optimal for E. coli was found to overcome the poor expression of the viral protein in the prokaryotic system. The Cap protein was purified to greater than 95% homogeneity by using a single cation-exchange chromatography at a yield of 10 mg per litre of bacterial culture. Despite the failure of the E. coli-expressed Cap protein to self-assemble into virus-like particles (VLPs), the immunization of mice with recombinant Cap yielded antibodies with the same specificity as those raised against native PCV 2 virions. In addition, the antigenic properties of the purified Cap protein were employed in a subunit-based indirect ELISA to monitor the levels of PCV 2 specific antibodies in piglets originating from a herd which was experiencing PCV 2 infection. These results pave the way for a straightforward large-scale production of the recombinant PCV 2 capsid protein and its use as a diagnostic antigen or a PCV 2 subunit vaccine.
Output: Heterologous expression of full-length capsid protein of porcine circovirus 2 in Escherichia coli and its potential use for detection of antibodies
Infectious bronchitis virus (IBV) infection is highly infectious respiratory disease in poultry industry with significant economic importance. The prevalence of IBV in quail industry in Malaysia was not well documented; therefore, its actual role in the epidemiology of the disease is relatively unknown. This study was to determine the susceptibility of Japanese quail, as one of the species in commercial poultry industry, toward IBV. In addition, it will also give a potential impact on the overall health management in the quail industry even though it had been established that quail are resistant to diseases affecting poultry. Moreover, to the best of our knowledge, it is the first experimental study on IBV inoculation in quail. In this experimental study, 20 quails were divided into 4 groups (n 5 5 for group A, B, and C, n 5 5 for control group). The quails in group A, B, and C were infected via intraocular and intranasal routes with 0.2 mL of 10 ! 5 EID 50 of the virus. Clinical signs, gross lesions, positive detection of virus, and trachea histopathological scoring were used to assess the susceptibility of these Japanese quails. The results have indicated mild ruffled feathers and watery feces in these inoculated birds. Trachea, lung, and kidney were subjected to onestep reverse transcription polymerase chain reaction for virus detection. The virus was found from trachea and lung samples, whereas it was absent from all kidney samples. Only 3 quails were found with gross lesions. There was a significant difference of tracheal lesion by 0.009 6 0.845 (P , 0.05) within the treatment groups. In summary, Japanese quails might be susceptible to IBV.
Output: Molecular and pathogenicity of infectious bronchitis virus (Gammacoronavirus) in Japanese quail (Coturnix japonica)
Background: The novel H7N9 virus causes severe illness, including pneumonia and acute respiratory distress syndrome, with high rates of mortality. We investigated the association of initial radiologic characteristics obtained at admission with clinical outcomes in patients with avian influenza H7N9 pneumonia. Methods: Demographics, comorbidities, clinical findings, radiologic appearance and scores of the affected lung parenchyma were compared between survivor group (n = 15) and mortality group (n = 7). Two radiologic scores were calculated, one using chest radiography and one using CT. Follow-up CT scans at discharge were analyzed in 12 patients of the survival group. Results: All the patients in mortality group developed acute respiratory distress syndrome and required mechanical ventilation, while in the survival group 33% (5/15) developed acute respiratory distress syndrome (P,0.05) and 27% (4/15) required mechanical ventilation (P,0.05). The mean radiographic and CT scores of the mortality group were 50% higher compared to the survival group (P,0.05). ROC analysis revealed an area under curve of 0.738 for the radiographic score with an optimal cutoff value of a score of 19 for prediction of mortality, with a sensitivity of 71% and a specificity of 67%, and an area under curve of 0.833 for the CT score with an optimal cutoff value of a CT score of 21 for prediction of mortality, with a sensitivity of 86% and a specificity of 73%. The mean CT score of the affected lung parenchyma at discharge was 30% lower than the initial CT examination (P,0.05). Conclusion: High initial radiologic score is associated with mortality in patients with avian influenza H7N9 pneumonia.
Output: Association of Radiologic Findings with Mortality in Patients with Avian Influenza H7N9 Pneumonia
Japanese encephalitis virus (JEV), one of the causes for epidemic encephalitis, belongs to the family of Flaviviridae. In this study, we demonstrated that cellular DEAD-box RNA helicase DDX5 plays an important role in JEV replication. The knockdown of DDX5 was able to decrease JEV replication, and overexpression of DDX5 mutants lacking the helicase activity also reduced JEV replication, suggesting the helicase activity is essential for JEV replication. DDX5 knockdown did not affect virus assembly and release. GST-pulldown and co-immunoprecipitation experiments demonstrated that DDX5 could interact with JEV core protein, non-structural protein 3 (NS3) and 5 (NS5-MTase and NS5-RdRp domains). Meanwhile, we also confirmed that DDX5 interacts with these viral proteins during JEV infection. Confocal microscopy analysis showed that endogenous DDX5 is recruited to the cytoplasm and colocalizes with these viral proteins and viral RNA. RNA-pulldown experiment showed that DDX5 only binds to the JEV 3 0 untranslated region (UTR). Finally, we confirmed the role of DDX5 in JEV RNA replication using JEV-replicon system. In conclusion, we identified DDX5 as a positive regulator for JEV replication.
Output: The DEAD-box RNA helicase DDX5 acts as a positive regulator of Japanese encephalitis virus replication by binding to viral 3 0 UTR
Lycorine potently inhibits flaviviruses in cell culture. At 1.2-μM concentration, lycorine reduced viral titers of West Nile (WNV), dengue, and yellow fever viruses by 10 2 -to 10 4 -fold. However, the compound did not inhibit an alphavirus (Western equine encephalitis virus) or a rhabdovirus (vesicular stomatitis virus), indicating a selective antiviral spectrum. The compound exerts its antiviral activity mainly through suppression of viral RNA replication. A Val→Met substitution at the 9th amino acid position of the viral 2K peptide (spanning the endoplasmic reticulum membrane between NS4A and NS4B proteins) confers WNV resistance to lycorine, through enhancement of viral RNA replication. Initial chemistry synthesis demonstrated that modifications of the two hydroxyl groups of lycorine can increase the compound's potency, while reducing its cytotoxicity. Taken together, the results have established lycorine as a flavivirus inhibitor for antiviral development. The lycorine-resistance results demonstrate a direct role of the 2K peptide in flavivirus RNA synthesis.
Output: A single-amino acid substitution in West Nile virus 2K peptide between NS4A and NS4B confers resistance to lycorine, a flavivirus inhibitor HHS Public Access
Glycyrrhetic acid polyglycosides were synthesized in one-pot via cationic ring-opening condensation polymerization of cyclic sulfite (4) initiated by glycyrrhetic acid as an aglycon. Sulfite 4 worked as a practical monomer for the preparation of (1 ? 2)-linked polysaccharide skeletons. The chemical stability of 4 was evaluated by the comparison of thermodynamic parameters with those of conventional epoxide (2). The grafting reaction of 4 from glycyrrhetic acid (5) was performed in the presence of TfOH and MS 3A in CH 2 Cl 2 at room temperature. The polymerization degree was moderately controllable by the change of feed ratio of initiator.
Output: One-pot synthesis of glycyrrhetic acid polyglycosides based on grafting-from method using cyclic sulfite
Often, when modeling infectious disease spread, the complex network through which the disease propagates is approximated by simplified spatial information. Here, we simulate epidemic spread through various contact networks and fit spatial-based models in a Bayesian framework using Markov chain Monte Carlo methods. These spatial models are individual-level models which account for the spatio-temporal dynamics of infectious disease. The focus here is on choosing a spatial model which best predicts the true probabilities of infection, as well as determining under which conditions such spatial models fail. Spatial models tend to predict infection probability reasonably well when disease spread is propagated through contact networks in which contacts are only within a certain distance of each other. If contacts exist over long distances, the spatial models tend to perform worse when compared to the network model. Crown
Output: Spatial approximations of network-based individual level infectious disease models
The black beetle virus (BBV) is an isometric insect virus whose genome consists of two messenger-active RNA molecules encapsidated in a single virion. The nucleotide sequence of BBV RNA1 (3105 bases) has been determined, and this, together with the sequence of BBV RNA2 (1399 bases) provides the complete primary structure of the BBV genome. The RNA1 sequence encompasses a 5' non-coding region of 38 nucleotides, a coding region for a protein of predicted molecular weight 101,873 (protein A, implicated in viral RNA synthesis) and a 3' proximal region encoding RNA3 (389 bases), a subgenomic messenger RNA made in infected cells but not encapsidated into virions. The RNA3 sequence starts 16 bases inside the coding region of protein A and contains two overlapping open reading frames for proteins of molecular weight 10,760 and 11,633, one of which is believed to be protein B, made in BBV-infected cells. A limited homology exists between the sequences of RNA1 and RNAB. Sequence regions have been identified that provide energetically favorable bonding between RNA2 and RNA1 possibly to facilitate their common encapsidation, and between RNA2 and negative strand RNA1 possibly to regulate the production of RNA3.
Output: Structure of the Black Beetle Virus Genome and its Functional Implications
Objective: In order to investigate the clinical and epidemiological rules of severe acute respiratory syndrome (sArs), rates and levels sArs coronavirus (sArs-coV) IgG antibodies of the patients and community populations from several areas were detected. Methods: Indirect immunofluorescent assay (IFA) and double-antigen sandwich enzyme-linked immunosorbent assay (ELIsA) were used to detect the sArs coronavirus-specific IgG antibodies in sera of 1700, including 1453 general populations from Hongkong, Marco, Guangzhou and Peking and 257 SARS patients from Guangzhou and Peking. The dynamics of the serum antibodies of SARS patients were observed from 3 to 360 days after onset of symptoms. Results: 90% of 257 patient serum specimens after 20 days of disease onset showed positive SARS-CoV IgG either using ELISA or IFA . 257 SARS patients, antibodies titers increased steadily in early 4 to 6 months after onset of SARS. The titers of most cases came to the peak in the 6th month. Then antibodies titers declined rapidly in some cases. However, all specimens still were positive for SARS-CoV IgG in the 48th month. Conclusions: this study suggest that few inapparent infectious patients exist during sArs epidemic. serum IgG antibodies has diagnostic value for SARS in the late course of disease and the antibodies present more than 48 months. (Int J Biomed Sci 2005; 1: 72-75) 
Output: Seroepidemiological Study on SARS-CoV IgG Antibodies of Different Populations from Several Areas
Staphylococcus aureus is a common cause of infections in humans. The emergence of virulent, antibiotic-resistant strains of S. aureus is a significant public health concern. Most virulence and resistance factors in S. aureus are encoded by mobile genetic elements, and transduction by bacteriophages represents the main mechanism for horizontal gene transfer. The baseplate is a specialized structure at the tip of bacteriophage tails that plays key roles in host recognition, cell wall penetration, and DNA ejection. We have used high-resolution cryo-electron microscopy to determine the structure of the S. aureus bacteriophage 80α baseplate at 3.75 Å resolution, allowing atomic models to be built for most of the major tail and baseplate proteins, including two tail fibers, the receptor binding protein, and part of the tape measure protein. Our structure provides a structural basis for understanding host recognition, cell wall penetration and DNA ejection in viruses infecting Gram-positive bacteria. Comparison to other phages demonstrates the modular design of baseplate proteins, and the adaptations to the host that take place during the evolution of staphylococci and other pathogens. The emergence of virulent strains of Staphylococcus aureus that are resistant to most antibiotics has become a major public health concern. Virulence and resistance determinants in S. aureus are usually carried on mobile genetic elements (MGEs). Transduction by bacteriophages provides the main means by which MGEs are disseminated horizontally through the bacterial population, and is therefore essential to the evolution of pathogenicity of S. aureus and other pathogens. The baseplate is a complex structure at the tip of bacteriophage tails that serves multiple roles, including host recognition and binding, cell wall penetration, and ejection of the phage DNA. We have determined the structure of the baseplate from bacteriophage 80α, a representative of phages involved in host pathogenicity and in the mobilization of MGEs in S. aureus. Our structure provides a basis for understanding host recognition and infection by phages infecting Gram-positive hosts, and the PLOS Pathogens | https://doi.
Output: Structure of the host cell recognition and penetration machinery of a Staphylococcus aureus bacteriophage
Porcine reproductive and respiratory syndrome virus (PRRSV) is a pathogen of great economic significance that impacts the swine industry globally. Since the first report of a porcine reproductive and respiratory syndrome (PRRS) outbreak, tremendous efforts to control this disease, including various national policies and plans incorporating the use of multiple modified live-virus vaccines, have been made. However, PRRSV is still a significant threat to the swine industry, and new variants continually emerge as a result of PRRSV evolution. Several studies have shown that pandemic PRRSV strains have enormous genetic diversity and that commercial vaccines can only provide partial protection against these strains. Therefore, effective anti-PRRSV drugs may be more suitable and reliable for PRRSV control. In this study, we observed that isobavachalcone (IBC), which was first isolated from Psoralea corylifolia, had potent anti-PRRSV activity in vitro. Although many biological activities of IBC have been reported, this is the first report describing the antiviral activity of IBC. Furthermore, after a systematic investigation, we demonstrated that IBC inhibits PRRSV replication at the post-entry stage of PRRSV infection. Thus, IBC may be a candidate for further evaluation as a therapeutic agent against PRRSV infection of swine in vivo.
Output: Isobavachalcone inhibits post-entry stages of the porcine reproductive and respiratory syndrome virus life cycle