niryuu/sni-each-converted huggingface dataset:
Ebolaviruses are non-segmented, negative-sense RNA viruses (NNSVs) within the order 19 Mononegavirales that possess the multifunctional virion protein 35 (VP35), a major determinant 20 of virulence and pathogenesis that is indispensable for viral replication and host innate immune 21 evasion. VP35 is functionally equivalent to the phosphoprotein (P) of other mononegaviruses 22 such as rhabdoviruses and paramyxoviruses. Phosphorylation of the P protein is universally 23 regarded as functionally important however, a regulatory role(s) of phosphorylation on VP35 24 function remains unexplored. Here, we identified a highly conserved Ser129 residue near the 25 homo-oligomerization coiled coil motif, which is essential for VP35 functions. Affinity-purification 26 MS followed by post-translational modification (PTM) analysis predicted phosphorylation of 27 Ser129. Co-immunoprecipitation, cross-linking, and biochemical characterization studies 28 revealed a moderately decreased capacity of VP35-S129A to oligomerize. Functional analysis 29 showed that Ser-to-Ala substitution of Ebola virus (EBOV) VP35 did not affect IFN inhibitory 30 activity but nearly abolished EBOV minigenome activity. Further coimmunoprecipitation studies 31 demonstrated a lost interaction between VP35-S129A and the amino terminus of the viral 32 polymerase but not between viral nucleoprotein (NP) or VP35-WT. Taken together, our findings 33 provide evidence that phosphorylation modulates VP35 function, supporting VP35 as a NNSV P 34 protein and providing a potentially valuable therapeutic target. 35 Importance 36 Ebola virus (EBOV) can cause severe disease in humans. The 2013-2016 West African 37 epidemic and the two recent outbreaks in the Democratic Republic of the Congo underscore the 38 urgent need for effective countermeasures, which remain lacking. A better understanding of 39 EBOV biology and the modulation of multifunctional viral proteins is desperately needed to 40 develop improved therapeutics. We provide evidence here that function of virion protein 35 41 (VP35) is modulated by phosphorylation of Ser129, a conserved residue among other 42 ebolavirus species. These findings shed light on EBOV biology and present a potential target for 43 broad acting anti-ebolavirus therapeutics. 44 45 46 47 48 49
Output: Mutation of Ebola virus VP35 Ser129 uncouples interferon antagonist and replication functions
Traditional vaccines such as inactivated or live attenuated vaccines, are gradually giving way to more biochemically de fi ned vaccines that are most often based on a recombinant antigen known to possess neutralizing epitopes. Such vaccines can offer improvements in speed, safety and manufacturing process but an inevitable consequence of their high degree of puri fi cation is that immunogenicity is reduced through the lack of the innate triggering molecules present in more complex preparations. Targeting recombinant vaccines to antigen presenting cells (APCs) such as dendritic cells however can improve immunogenicity by ensuring that antigen processing is as ef fi cient as possible. Immune complexes, one of a number of routes of APC targeting, are mimicked by a recombinant approach, crystallizable fragment (Fc) fusion proteins, in which the target immunogen is linked directly to an antibody effector domain capable of interaction with receptors, FcR, on the APC cell surface. A number of virus Fc fusion proteins have been expressed in insect cells using the baculovirus expression system and shown to be ef fi ciently produced and puri fi ed. Their use for immunization next to non-Fc tagged equivalents shows that they are powerfully immunogenic in the absence of added adjuvant and that immune stimulation is the result of the Fc-FcR interaction.
Output: Virus Glycoproteins Tagged with the Human Fc Domain as Second Generation Vaccine Candidates
Viral zoonoses have represented a significant public health problem throughout history, affecting all continents. Furthermore, many viral zoonoses have emerged or reemerged in recent years, highlighting the importance of such diseases. Emerging viral zoonoses encompass a vast number of different viruses and many different transmission modes. There are many factors influencing the epidemiology of the various zoonoses, such as ecological changes, changes in agriculture and food production, the movement of pathogens, including via travel and trade, human behavior and demographical factors, and microbial changes and adaptation. Costeffective prevention and control of emerging viral zoonoses necessitates an interdisciplinary and holistic approach and international cooperation. Surveillance, laboratory capability, research, training and education, and last but not least, information and communication are key elements.
Output: Zoonoses in the Emergence of Human Viral Diseases
The spike (S) protein is a key structural protein of coronaviruses including, the porcine transmissible gastroenteritis virus (TGEV). The S protein is a type I membrane glycoprotein located in the viral envelope and is responsible for mediating the binding of viral particles to specific cell receptors and therefore specific cell types. It is also an important immune target for the host in neutralizing the virus. Four antigenic sites A, B, C, and D that reside near the N-terminal domain have been defined in the S protein. Of these, the region encoding antigenic sites A and to a lesser extent D, herein defined as S-AD, are most critical in eliciting host neutralizing antibodies. Herein, we enzymatically amplified, cloned, and expressed the S-AD fragment from TGEV in the prokaryotic expression vector, pET-30a. Maximum protein expression was achieved at 30°C over a 5-h period post-induction. Rabbit polyclonal antiserum was generated using recombinant S-AD (rS-AD) protein. In contrast to prior studies showing no activity with bacterially produced S protein, results indicated that polyclonal serum recognized TGEV-infected cells and reduced infection by 100%. Furthermore, the truncated rS-AD peptide was able to bind to the surface of cells from swine testes in a competitive manner and completely inhibit viral infection.
Output: Bacterial expression of antigenic sites A and D in the spike protein of transmissible gastroenteritis virus and evaluation of their inhibitory effects on viral infection
Using sequence data to infer population dynamics is playing an increasing role in the analysis of outbreaks. The most common methods in use, based on coalescent inference, have been widely used but not extensively tested against simulated epidemics. Here, we use simulated data to test the ability of both parametric and non-parametric methods for inference of effective population size (coded in the popular BEAST package) to reconstruct epidemic dynamics. We consider a range of simulations centred on scenarios considered plausible for pandemic influenza, but our conclusions are generic for any exponentially growing epidemic. We highlight systematic biases in non-parametric effective population size estimation. The most prominent such bias leads to the false inference of slowing of epidemic spread in the recent past even when the real epidemic is growing exponentially. We suggest some sampling strategies that could reduce (but not eliminate) some of the biases. Parametric methods can correct for these biases if the infected population size is large. We also explore how some poor sampling strategies (e.g. that over-represent epidemiologically linked clusters of cases) could dramatically exacerbate bias in an uncontrolled manner. Finally, we present a simple diagnostic indicator, based on coalescent density and which can easily be applied to reconstructed phylogenies, that identifies time-periods for which effective population size estimates are less likely to be biased. We illustrate this with an application to the 2009 H1N1 pandemic. Pandemic growth rates from sequences E. de Silva et al. 1799 Pandemic growth rates from sequences E. de Silva et al. 1807 
Output: Inferring pandemic growth rates from sequence data
To test the methodology presented in our paper, we performed various sequence clusterings using different datasets previously tested in the literature (Hoang et al., 2015) . These include five genome datasets, i.e. mammal mitochondrion, influenza A virus, human rhinovirus, coronavirus and bacteria. Clustering results are shown below. In the case of 31 mammal mitochondrial genomes (dataset A), a K7 clustering resulted in the classification of mammal families C1 Ursidae, C2 Bovidae and Cetacean, C3 Cercopithecidae, C4 Hominidae, C6 Canidae and C7 Felidae. Cluster 5 contains the Rodentia and Lagomorpha with the Erinaceidae outgroup. This is the result of the early divergence between carnivores, which breaks them in the three tight families, leaving one cluster for the three furthest groups.
Output: Supplementary file of Mendizabal-Ruiz, et al. Genetic Signal Processing for DNA Sequence Clustering
A new disease, severe atypical respiratory syndrome (SARS), emerged in China in late 2002 and developed into the first epidemic of the 21st century. The disease was caused by an unknown animal coronavirus (CoV) that had crossed the species barrier through close contact of humans with infected animals, and was identified as the etiological agent for SARS. This new CoV not only became readily transmissible between humans but also was also more pathogenic. The disease spread across the world rapidly due to the air travel, and infected 8096 people and caused 774 deaths in 26 countries on 5 continents. The disease is characterized by flu-like symptoms, including high fever, malaise, cough, diarrhea, and infiltrates visible on chest radiography. The overall mortality was about 10%, but varied profoundly with age; the course of disease seemed to be milder in the pediatric age group and resulted rarely in a fatal outcome, but the mortality in the elderly was as high as 50%. Aggressive quarantine measures taken by the health authorities have successfully contained and terminated the disease transmission. As a result there are no SARS cases recorded recently. Nevertheless there is a possibility that the disease may emerge in the population with high vigor. Significant progress has been made in understanding the disease biology, pathogenesis, development of animal models, and design and evaluation of different vaccines, and these are the focus of this chapter.
Output: Structure, Immunopathogenesis and Vaccines Against SARS Coronavirus
There is little information on the role of nitric oxide ( • NO) in innate immunity to respiratory coronavirus (CoV) infections. We examined • NO levels by Greiss assay in bronchoalveolar lavage (BAL) of pigs infected with either porcine respiratory coronavirus (PRCV) or porcine reproductive and respiratory syndrome virus (PRRSV), a member of Nidovirales, like CoV. The antiviral effects of • NO on these two viruses were tested in an in vitro system using a • NO donor, S-nitroso-N-acetylpenicillamine (SNAP). We detected a large increase in • NO levels in BAL fluids of PRCV-infected pigs, but not in PRRSV-infected pigs. Pulmonary epithelial cell necrosis induced by PRCV coincided with increased • NO. Moreover, • NO levels in cell culture medium of PRRSV-infected alveolar macrophages (AMs) did not differ from that of mockinfected AMs. Antiviral assays showed that • NO significantly inhibited PRCV replication in swine testicular (ST) cells, whereas PRRSV was not susceptible to • NO based on the conditions tested. Our study suggests that unlike PRRSV which induces apoptosis in AMs, respiratory CoVs such as PRCV that infect pulmonary epithelial cells and cause cytolysis, induce • NO production in the respiratory tract. Thus, • NO may play a role in innate immunity to respiratory CoV infections by inhibiting viral replication.
Output: Nitric oxide is elicited and inhibits viral replication in pigs infected with porcine respiratory coronavirus but not porcine reproductive and respiratory syndrome virus
We would like to dedicate the article to Dr. Linda Brodsky (1952e2014) who spent her entire professional life at the Women and Children's Hospital of Buffalo working to improve the lives of children with airway disease. We would also like to acknowledge Dr. Brodsky's contribution to the standardization of tonsil size in airway obstruction. Respiratory virus Tonsil Adenoid Sleep-disordered breathing Obstructive sleep apnea Tonsil and adenoid hypertrophy Airway obstruction Recombinant adenovirus a b s t r a c t Background: Airway obstruction due to enlargement of tonsils and adenoids is a common pediatric problem resulting in sleep disordered breathing. The cause for the relatively abnormal growth of tonsils and adenoids is poorly understood. Methods: Non-acutely ill children undergoing tonsillectomy and adenoidectomy (T&A) for various reasons were enrolled prospectively in a study to determine the frequency of asymptomatic respiratory viral infections in each lymphoid tissue and to relate the number and types of virus to the degree of airway obstruction. Molecular techniques were used to detect 9 respiratory viruses while Brodsky scores and measurements of percentages airway obstruction were used to estimate the degree of airway compromise due to the tonsil and adenoid, respectively. Results: Viruses were detected in 70.9% of tonsils and 94.7% of adenoids, p < 0.001. Adenovirus was the most common virus detected at 71.1%. Adenoids had an average of 2.4 viruses compared to 0.92 for tonsils, p < 0.001. Higher Brodsky scores were only associated with EBV in tonsils, p ¼ 0.03, while greater percentages of airway obstruction in the adenoids were associated with adenovirus, EBV, corona virus, parainfluenza virus and rhinovirus, p 0.005. Conclusions: Asymptomatic viral infections are common and directly related to the degree of airway obstruction significantly more often in adenoids than tonsils.
Output: The ubiquity of asymptomatic respiratory viral infections in the tonsils and adenoids of children and their impact on airway obstruction
Co-infections by multiple pathogens have important implications in many aspects of health, epidemiology and evolution. However, how to disentangle the non-linear dynamics of the immune response when two infections take place at the same time is largely unexplored. Using data sets of the immune response during influenza-pneumococcal coinfection in mice, we employ here topological data analysis to simplify and visualise high dimensional data sets. We identified persistent shapes of the simplicial complexes of the data in the three infection scenarios: single viral infection, single bacterial infection, and co-infection. The immune response was found to be distinct for each of the infection scenarios and we uncovered that the immune response during the co-infection has three phases and two transition points. During the first phase, its dynamics is inherited from its response to the primary (viral) infection. The immune response has an early shift (few hours post coinfection) and then modulates its response to react against the secondary (bacterial) infection. Between 18 and 26 h post co-infection the nature of the immune response changes again and does no longer resembles either of the single infection scenarios.
Output: Topological data analysis to model the shape of immune responses during co-infections
Hemophagocytic lymphohistiocytosis is a frequently fatal clinicopathologic syndrome in which an uncontrolled and ineffective immune response leads to severe hyperinflammation. It may occur as either a familial disorder or a sporadic condition in association with a variety of triggers: infections, malignancies, autoimmune diseases, and acquired immune deficiencies. However, the most consistent association is with viral infections, especially Epstein---Barr virus. The main clinical features are fever, liver dysfunction, coagulation abnormalities and pancytopenia. Early diagnosis and treatment are important to reducing mortality, but the diagnosis is difficult because of the rarity of the syndrome and the lack of specificity of the clinical findings. Treatment should be directed toward treating the underlying disease and to suppressing the exaggerated inflammatory response through the use of immunosuppressive agents. Resumen La linfohistiocitosis hemofagocítica es un síndrome clinicopatológico de evolución potencialmente fatal, en el que una respuesta inmune no controlada e ineficaz conduce a hiperinflamación. Puede aparecer como una enfermedad familiar o esporádica, asociado a diferentes factores desencadenantes: infecciones, neoplasias, enfermedades autoinmunes o inmunodeficiencias adquiridas, pero la asociación más consistente es con infecciones virales, ଝ Please cite this article as: Mostaza-Fernández JL, Guerra Laso J, Carriedo Ule D, Ruiz de Morales JMG. Linfohistiocitosis hemofagocítica asociada a infecciones virales: reto diagnóstico y dilema terapéutico. Rev Clin Esp. 2014;214:320---327.
Output: Revista Clínica Española Hemophagocytic lymphohistiocytosis associated with viral infections: Diagnostic challenge and therapeutic dilemma ଝ
Atypical" pneumonia was described as a distinct and mild form of community-acquired pneumonia (CAP) already before Mycoplasma pneumoniae had been discovered and recognized as its cause. M. pneumoniae is detected in CAP patients most frequently among school-aged children from 5 to 15 years of age, with a decline after adolescence and tapering off in adulthood. Detection rates by polymerase chain reaction (PCR) or serology in children with CAP admitted to the hospital amount 4-39%. Although the infection is generally mild and self-limiting, patients of every age can develop severe or extrapulmonary disease. Recent studies indicate that high rates of healthy children carry M. pneumoniae in the upper respiratory tract and that current diagnostic PCR or serology cannot discriminate between M. pneumoniae infection and carriage. Further, symptoms and radiologic features are not specific for M. pneumoniae infection. Thus, patients may be unnecessarily treated with antimicrobials against M. pneumoniae. Macrolides are the first-line antibiotics for this entity in children younger than 8 years of age. Overall macrolides are extensively used worldwide, and this has led to the emergence of macrolide-resistant M. pneumoniae, which may be associated with severe clinical features and more extrapulmonary complications. This review focuses on the characteristics of M. pneumoniae infections in children, and exemplifies that simple clinical decision rules may help identifying children at high risk for CAP due to M. pneumoniae. This may aid physicians in prescribing appropriate first-line antibiotics, since current diagnostic tests for M. pneumoniae infection are not reliably predictive.
Output: Infection with and Carriage of Mycoplasma pneumoniae in Children
Background: Infrared thermography (IRT) is used to screen febrile passengers at international airports, but it suffers from low sensitivity. This study explored the application of a combined visible and thermal image processing approach that uses a CMOS camera equipped with IRT to remotely sense multiple vital signs and screen patients with suspected infectious diseases. Methods: An IRT system that produced visible and thermal images was used for image acquisition. The subjects' respiration rates were measured by monitoring temperature changes around the nasal areas on thermal images; facial skin temperatures were measured simultaneously. Facial blood circulation causes tiny color changes in visible facial images that enable the determination of the heart rate. A logistic regression discriminant function predicted the likelihood of infection within 10 s, based on the measured vital signs. Sixteen patients with an influenza-like illness and 22 control subjects participated in a clinical test at a clinic in Fukushima, Japan. Results: The vital-sign-based IRT screening system had a sensitivity of 87.5% and a negative predictive value of 91.7%; these values are higher than those of conventional fever-based screening approaches. Conclusions: Multiple vital-sign-based screening efficiently detected patients with suspected infectious diseases. It offers a promising alternative to conventional fever-based screening.
Output: Remote sensing of multiple vital signs using a CMOS camera-equipped infrared thermography system and its clinical application in rapidly screening patients with suspected infectious diseases
The formation of antibodies to interferon-beta (IFN-b), a protein-based disease-modifying agent for multiple sclerosis (MS), is a problem in clinical practice. These antibodies may neutralize the biological effects of the protein drug, potentially decreasing its therapeutic effects. By high-resolution HLA class I and II typing we identified two HLA class II alleles associated with the development of antibodies to IFN-b. In two independent continuous and binary-trait association studies, HLA-DRB1*0401 and HLA-DRB1*0408 (odds ratio: 5.15)-but not other HLA alleles-were strongly associated with the development of binding and neutralizing antibodies to IFN-b. The associated HLA-DRB1*04 alleles differ from nonassociated HLA-DRB1*04 alleles by a glycine-to-valine substitution in position 86 of the epitope-binding alpha-helix of the HLA class II molecule. The peptide-binding motif of HLA-DRB1*0401 and *0408 might promote binding and presentation of an immunogenic peptide, which may eventually break Tcell tolerance and facilitate antibody development to IFN-b. In summary, we identified genetic factors determining the immunogenicity of IFN-b, a protein-based disease-modifying agent for the treatment of MS.
Output: ARTICLE HLA-DRB1*0401 and HLA-DRB1*0408 Are Strongly Associated with the Development of Antibodies against Interferon-b Therapy in Multiple Sclerosis
Viral infections are an important and often unrecognized component of disease in immunocompromised patients. The diagnosis and management of viral infections have expanded largely because of new quantitative molecular diagnostic assays. Well-recognized pathogens such as herpes simplex virus (HSV), cytomegalovirus (CMV), and respiratory viruses have been joined by newly recognized pathogens such as BK virus, human herpesvirus-6 (HHV-6), and human metapneumovirus in this highly susceptible patient population. The role of Epstein-Barr virus (EBV) and Human herpesvirus-8 (HHV-8) in lymphoproliferative diseases also continue to be clarified. As a result, the management of viral infections in patients with hematologic malignancies continues to be a growing challenge for the clinician.
Output: Pathogens Chapter 2 Viruses
Genetic engineering of cytomegalovirus (CMV) currently relies on generating a bacterial artificial chromosome (BAC) by introducing a bacterial origin of replication into the viral genome using in vivo recombination in virally infected tissue culture cells. However, this process is inefficient, results in adaptive mutations, and involves deletion of viral genes to avoid oversized genomes when inserting the BAC cassette. Moreover, BAC technology does not permit the simultaneous manipulation of multiple genome loci and cannot be used to construct synthetic genomes. To overcome these limitations, we adapted synthetic biology tools to clone CMV genomes in Saccharomyces cerevisiae. Using an early passage of the human CMV isolate Toledo, we first applied transformation-associated recombination (TAR) to clone 16 overlapping fragments covering the entire Toledo genome in Saccharomyces cerevisiae. Then, we assembled these fragments by TAR in a stepwise process until the entire genome was reconstituted in yeast. Since next-generation sequence analysis revealed that the low-passage-number isolate represented a mixture of parental and fibroblast-adapted genomes, we selectively modified individual DNA fragments of fibroblast-adapted Toledo (Toledo-F) and again used TAR assembly to recreate parental Toledo (Toledo-P). Linear, full-length HCMV genomes were transfected into human fibroblasts to recover virus. Unlike Toledo-F, Toledo-P displayed characteristics of primary isolates, including broad cellular tropism in vitro and the ability to establish latency and reactivation in humanized mice. Our novel strategy thus enables de novo cloning of CMV genomes, more-efficient genome-wide engineering, and the generation of viral genomes that are partially or completely derived from synthetic DNA.
Output: Cloning, Assembly, and Modification of the Primary Human Cytomegalovirus Isolate Toledo by Yeast-Based Transformation-Associated Recombination
In transmissible gastroenteritis (TGE) of piglets, an infection closely resembling human rotavirus enteritis, we studied the timing and extent of epithelial viral invasion along the small intestine after a single oral inoculum of virus; we related these findings to measured alterations in mucosal structure, kinetics, and differentiation, and to previously documented abnormalities of ion transport that occurred at the height of diarrhea. Six and twelve hours after inoculation, before diarrhea, extensive specific viral immunofluorescence and viral particles on electron microscopy were seen in villus but not crypt enterocytes in jejunum, mid-intestine, and ileum. At 24 and 40 hr, when diarrhea was most severe, immunofluorescence was patchy; villus blunting (P < 0.001) and increased crypt depth (P < 0.001) were observed by light microscopy in all segments; radioautographically labeled enterocytes showed accelerated migration and shortened life span; and cells on villi were deficient in sucrase activity (P < 0.001) and
Output: The Mucosal Lesion in Viral Enteritis Extent and Dynamics of the Epithelial Response to Virus Invasion in Transmissible Gastroenteritis of Piglets
The severe acute respiratory syndrome-coronavirus (SARS-CoV) caused an outbreak of atypical pneumonia in 2003. The SARS-CoV viral genome encodes several proteins which have no homology to proteins in any other coronaviruses, and a number of these proteins have been implicated in viral cytopathies. One such protein is 3a, which is also known as X1, ORF3 and U274. 3a expression is detected in both SARS-CoV infected cultured cells and patients. Among the different functions identified, 3a is a capable of inducing apoptosis. We previously showed that caspase pathways are involved in 3a-induced apoptosis. In this study, we attempted to find out protein domains on 3a that are essential for its pro-apoptotic function. Protein sequence analysis reveals that 3a possesses three major protein signatures, the cysteine-rich, Yxx and diacidic domains. We showed that 3a proteins carrying respective mutations in these protein domains exhibit reduced pro-apoptotic activities, indicating the importance of these domains on 3a's pro-apoptotic function. It was previously reported that 3a possesses potassium ion channel activity. We further demonstrated that the blockade of 3a's potassium channel activity abolished caspase-dependent apoptosis. This report provides the first evidence that ion channel activity of 3a is required for its proapoptotic function. As ion channel activity has been reported to regulate apoptosis in different pathologic conditions, finding ways to modulate the ion channel activity may offer a new direction toward the inhibition of apoptosis triggered by SARS-CoV.
Output: The ion channel activity of the SARS-coronavirus 3a protein is linked to its pro-apoptotic function
The synthesis of racemic substituted 7-amino-5,7,8,9-tetrahydrobenzocyclohepten-6-one hydrochlorides was optimized to enhance reproducibility and increase the overall yield. In order to investigate their specificity, series of enzyme inhibition assays were carried out against a diversity of proteases, covering representative members of aspartic, cysteine, metallo and serine endopeptidases and including eight members of the monometallic M1 family of aminopeptidases as well as two members of the bimetallic M17 and M28 aminopeptidase families. This aminobenzosuberone scaffold indeed demonstrated selective inhibition of M1 aminopeptidases to the exclusion of other tested protease families; it was particularly potent against mammalian APN and its bacterial/parasitic orthologues EcPepN and Pf AM1.
Output: molecules Aminobenzosuberone Scaffold as a Modular Chemical Tool for the Inhibition of Therapeutically Relevant M1 Aminopeptidases
The well-known immunosuppressive drug cyclosporin A inhibits replication of various viruses including coronaviruses by binding to cellular cyclophilins thus inactivating their cis-trans peptidyl-prolyl isomerase function. Viral nucleocapsid proteins are inevitable for genome encapsidation and replication. Here we demonstrate the interaction between the N protein of HCoV-229E and cyclophilin A, not cyclophilin B. Cyclophilin inhibitors abolish this interaction. Upon infection, cyclophilin A stays evenly distributed throughout the cell, whereas cyclophilin B concentrates at ER-bleb-like structures. We further show the inhibitory potential of non-immunosuppressive CsA derivatives Alisporivir, NIM811, compound 3 on HCoV-229E-GFP and -Luciferase replication in human Huh-7.5 hepatoma cells at 18 and 48 h time points post infection with EC 50 s at low micromolar ranges. Thus, non-immunosuppressive CsA derivatives effectively inhibit HCoV-229E replication suggesting them as possible candidates for the treatment of HCoV infection. The interruption of interaction between CypA and N protein by CsA and its derivatives suggest a mechanism how CypA inhibitors suppress viral replication.
Output: Influences of cyclosporin A and non-immunosuppressive derivatives on cellular cyclophilins and viral nucleocapsid protein during human coronavirus 229E replication
In an investigation of blood-sucking insects and arboviruses, a virus (YN12243) was isolated from Culicoides samples collected in the Sino-Burmese border region of Yunnan Province, China. The virus caused cytopathic effect (CPE) in C6/36 cells and passaged stably. Polyacrylamide gel analysis showed that the genome of YN12243 was composed of 12 segments of double-stranded RNA (dsRNA), with a distribution pattern of 6-6. The nucleotide and amino acid sequences of the coding region (1-12 segments) were 17,803 bp and 5,925 amino acids in length, respectively. The phylogenetic analysis of VP1 protein (RdRp) revealed that YN12243 belonged to genus Seadornavirus of family Reoviridae, and further analysis indicated that YN12243 belongs to the Banna virus (BAV) genotype A2. Additionally, YN12243 was located in the same evolutionary cluster as BAV strains isolated from different mosquito species, suggesting that the BAV isolated from Culicoides does not have species barriers. These results indicate that Culicoides can also be a vector for BAV. In view of the hematophagous habits of Culicoides on cattle, horses, deer, and other large animals, as well as the possibility of spreading and causing a variety of animal arboviral diseases, it is important to improve infection detection and monitor the BAV in large livestock.
Output: SCIENCE CHINA Genome sequencing and phylogenetic analysis of Banna virus (genus Seadornavirus, family Reoviridae) isolated from Culicoides
Bats and rodents are being increasingly recognized as reservoirs of emerging zoonotic viruses. Various studies have investigated bat viruses in tropical regions, but to date there are no data regarding viruses with zoonotic potential that circulate in bat and rat populations in Viet Nam. To address this paucity of data, we sampled three bat farms and three wet markets trading in rat meat in the Mekong Delta region of southern Viet Nam. Faecal and urine samples were screened for the presence of RNA from paramyxoviruses, coronaviruses and filoviruses. Paramyxovirus RNA was detected in 4 of 248 (1%) and 11 of 222 (4.9%) bat faecal and urine samples, respectively. Coronavirus RNA was detected in 55 of 248 (22%) of bat faecal samples; filovirus RNA was not detected in any of the bat samples. Further, coronavirus RNA was detected in 12 of 270 (4.4%) of rat faecal samples; all samples tested negative for paramyxovirus. Phylogenetic analysis revealed that the bat paramyxoviruses and bat and rat coronaviruses were related to viruses circulating in bat and rodent populations globally, but showed no cross-species mixing of viruses between bat and rat populations within Viet Nam. Our study shows that potentially novel variants of paramyxoviruses and coronaviruses commonly circulate in bat and rat populations in Viet Nam. Further characterization of the viruses and additional human and animal surveillance is required to evaluate the likelihood of viral spillover and to assess whether these viruses pose a risk to human health. bats, coronavirus, paramyxovirus, rats, Viet Nam, zoonotic viruses *VIZIONS consortium group members are present in Appendix 1. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Output: Detection of potentially novel paramyxovirus and coronavirus viral RNA in bats and rats in the Mekong Delta region of southern Viet Nam
BackgroundDetection and characterization of viral RNA pathogens from fieldwork are challenging due to the instability of the RNA molecule. FTA cards® have proved useful for sample storage and latter identification of pathogens with importance for agricultural, animal and human health: however, for optimal handling, processing, and biosafety measures are not well-established. ObjectiveThis systematic review aims to summarize the reported effectiveness of FTA cards® for storage and transport of viral RNA, as well as the conditions for their handling and use in downstream processes. Finally, the biosafety measures required to protect researchers and clinical lab workers are considered. MethodsWe performed a systematic review following the PRISMA statement. We searched MEDLINE (PubMed), Scopus and Web of Science using the keywords "FTA cards" AND "RNA". Articles were screened by title and abstract, and after examination of inclusion and exclusion criteria, relevant information was extracted. The quality of the studies was assessed, and the evidence was qualitatively summarized. ResultsA total of 175 records were retrieved, and 11 additional documents were found by checking references of the eligible articles. A total of 47 articles were included. Samples from animals accounted for 38.3% of the publications, which identified viruses that cause disease in poultry, wild birds, suids, or bovids. Three different methods for RNA extraction were reported. Other factors that vary across reports include the size of RNA amplicon, storage temperature, and duration of storage. Only fourteen articles tested the inactivation of the virus on the FTA card®, and in one case, the virus remained infective. ConclusionFTA cards® could be a suitable option for RNA virus storage and transport for fieldwork in areas where proper conditions for RNA preservation are difficult to achieve. Three different protocols have been used for RNA detection from this matrix. Biospecimens in the form of dried blood spots should be considered potentially infectious unless specifically treated to inactivate viral pathogens. technology consists of filter paper impregnated with a patented chemical mixture that contains chemical denaturants and a free radical scavenger. The chemical mixture lyses cells and organelles, prevents overgrowth of bacteria, and denatures proteins. The DNA is captured in the matrix and remains tightly bound while proteins and inhibitors are washed. This keeps DNA stable during long-term storage at room temperature (GE Healthcare, 2019).
Output: A systematic review of FTA cards® as a tool for viral RNA preservation in fieldwork: Are they safe and effective?
This study aimed to determine the aetiology of community-acquired pneumonia (CAP) by adding polymerase chain reaction (PCR) to conventional methods and to describe the clinical and laboratory features between patients with bacterial pneumonia (BP) and viral pneumonia (VP). Adults with CAP admitted from November 2009 to October 2010 were included. Demographics, comorbidities, severity and clinical features were recorded. Conventional microbiological methods included blood and sputum cultures, acute and convalescent serologic samples, and antigen urinary detection. New methods included multiplex PCR for Mycoplasma pneumoniae, Legionella pneumophila, Chlamydophila pneumoniae, Bordetella pertussis and 15 respiratory viruses. A total of 169 patients were included. Using conventional methods, we identified a pathogen in 51 % of cases. With PCR, up to 70 % of cases had an aetiological diagnosis. Fortyfive patients had BP (34 %), 22 had VP (17 %) and 25 (19 %) had co-infection (BP and VP). Pneumococci and respiratory syncytial virus (RSV) were the most frequently identified pathogens. Procalcitonin (PCT) and C-reactive protein (CRP) median values were significantly higher in BP than in VP patients. Shaking chills, higher CURB score and shock were significantly more frequent in BP. A viral infection was identified in more than one-third of patients with CAP. Clinical and laboratory features could help to differentiate between VP and BP and to guide empirical therapy. A. Sangil : E. Calbo : S. Benet : M. E. Viladot : V. Pascual :
Output: Aetiology of community-acquired pneumonia among adults in an H1N1 pandemic year: the role of respiratory viruses
Previously described polyclonal or monoclonal antibodies (mAb) to rabbit CD5, raised against expressed recombinant protein or peptides, recognize CD5 on most rabbit B cells. The mAb KEN-5 was originally reported to recognize rabbit CD5. However, KEN-5 binds almost exclusively to T cells and only to a minor population of B cells. We show here that by Enzyme-linked Immunosorbent Assay (ELISA), KEN-5 binds to recombinant rabbit CD5. This interaction is partially inhibited by polyclonal goat anti-CD5 antibody. In addition, immunoprecipitations from lysates of surface biotinylated rabbit lymphocytes with KEN-5 or our anti-CD5 mAb isolate molecules that migrate identically on gels with the same approximate relative molecular mass of 67,000 M r . By flow cytometric analyses of individual cells from spleen, thymus and appendix, KEN-5 recognizes CD5like molecules mainly on T cells and on 3-6% of IgM + B cells. Immunohistochemical staining of splenic and appendix tissues and confocal immunofluorescent imaging confirm and extend results from flow cytometric analyses. Quantitation of fluorescent colocalization indicates that staining by KEN-5 colocalizes with staining by anti-CD5 on small percentages lymphocytes in splenic tissue sections. As CD5 has both N-and O-linked glycosylation, we hypothesised that differential binding of KEN-5 to T cells and B-cells may be explained by different glycan structures on the CD5 present on T compared to B cells. This hypothesis is supported by ELISA data that show that deglycosylation diminishes the binding of KEN-5 to recombinant rabbit CD5. Screening KEN-5 on an array with 406 glycans was inconclusive. Although we did not identify a strongly binding glycan structure, the data are suggestive that the epitope recognized by KEN-5 may be influenced by glycan structures. The epitope this mAb recognizes may either be the glycan itself, or more likely, is influenced by neighboring glycan structure. Our findings suggest that development, selection and function of different B-and T-cell subsets or their preferential survival may be directly or indirectly dependent on different glycan structures associated with CD5 or CD5-like molecules expressed on T cells compared to B cells.
Output: Characterization of Rabbit CD5 Isoforms NIH Public Access Author Manuscript
Antibodies are the principal immune effectors that mediate protection against reinfection following viral infection or vaccination. Robust techniques for human mAb isolation have been developed in the last decade. The study of human mAbs isolated from subjects with prior immunity has become a mainstay for rational structure-based, next-generation vaccine development. The plethora of detailed molecular and genetic studies coupling the structure of antigen-antibody complexes with their antiviral function has begun to reveal common principles of critical interactions on which we can build better vaccines and therapeutic antibodies. This review outlines the approaches to isolating and studying human antiviral mAbs and discusses the common principles underlying the basis for their activity. This review also examines progress toward the goal of achieving a comprehensive understanding of the chemical and physical basis for molecular recognition of viral surface proteins in order to build predictive molecular models that can be used for vaccine design.
Output: Cell Host & Microbe Review Principles of Broad and Potent Antiviral Human Antibodies: Insights for Vaccine Design
Case summary This work describes the diagnosis and successful treatment of a 2-year-old domestic cat infected with Leishmania species and presenting fever, and ulcerative and nodular skin lesions after being treated for pyodermatitis for 1 year without clinical improvement. After anamnesis the cat was submitted to a complete clinical examination. Blood was collected for determination of haematological and biochemical parameters, detection of feline leukaemia virus (FeLV), feline immunodeficiency virus (FIV), feline coronavirus (FCoV) and Leishmania amastigotes. Fine-needle aspiration puncture from the skin nodules was also performed. After definitive diagnosis the animal was treated and followed up over a 2 year period. The animal tested negative for FIV-specific antibodies, FeLV antigen and feline coronavirus RNA. Leishmania amastigotes in the skin nodules were confirmed by cytology and molecular diagnosis. Treatment was initiated with allopurinol, resulting in a slight clinical improvement. Thus, N-methyl-glucamine antimoniate was added and administered for 30 days, with complete closure of the ulcerative lesions in the hindlimbs requiring a surgical approach. Close monitoring of the patient in the following 24 months indicated that combined therapy was safe and clinical cure was achieved without further relapses or side effects. Relevance and novel information Considering the increasing number of feline leishmaniosis cases and the inconsistent results of most therapeutic protocols described in the literature, the use of new approaches, especially in refractory cases, is essential. Although the use of allopurinol and N-methyl-glucamine antimoniate is off-label in cats, in this case the combination treatment was followed by an extensive analytical monitoring, supporting their safety and effectiveness.
Output: Successful treatment of feline leishmaniosis using a combination of allopurinol and N-methyl- glucamine antimoniate
Middle East respiratory syndrome coronavirus infection control health facilities symptom assessment Background: Transmission of Middle East respiratory syndrome (MERS) to health care personnel (HCP) is a major concern. This study aimed to review cases of MERS-related events, such as development of MERS-like symptoms or exposure to patients. Methods: A MERS screening clinic (MSC) for HCP was setup in the National Medical Center during the MERS outbreak in 2015. Clinical and laboratory data from HCP who visited the MSC were retrospectively reviewed. Additionally, these data were compared with the results of postoutbreak questionnaire surveys and interviews about MERS-related symptoms and risk-related events. Results: Of the 333 HCP who participated in MERS patient care, 35 HCP (10.5%) visited the MSC for MERSlike symptoms. No one was infected with MERS, and the most common symptom was fever (68.6%) followed by cough (34.3%). However, 106 of 285 postoutbreak survey participants experienced at least 1 MERSrelated symptom and 26 reported exposure to patients without appropriate personal protective equipment, whereas only 4 HCP visited the MSC to report exposure events. Conclusions: Although a considerable number of HCP experienced MERS-related symptoms or unprotected exposure during MERS patient care, some did not take appropriate action. These findings imply that for infection control strategy to be properly performed, education should be strengthened so that HCP can accurately recognize the risk situation and properly notify the infection control officer.
Output: A Middle East respiratory syndrome screening clinic for health care personnel during the 2015 Middle East respiratory syndrome outbreak in South Korea: A single-center experience
Background: Healthcare-associated infections (HCAIs) cause significant morbidity and mortality worldwide, and outbreaks are often only identified after they reach high levels. A wide range of data is collected within healthcare settings; however, the extent to which this information is used to understand HCAI dynamics has not been quantified. Aim: To examine the use of spatiotemporal analyses to identify and prevent HCAI transmission in healthcare settings, and to provide recommendations for expanding the use of these techniques. Methods: A systematic review of the literature was undertaken, focusing on spatiotemporal examination of infectious diseases in healthcare settings. Abstracts and full-text articles were reviewed independently by two authors to determine inclusion. Findings: In total, 146 studies met the inclusion criteria. There was considerable variation in the use of data, with surprisingly few studies (N ¼ 22) using spatiotemporal-specific analyses to extend knowledge of HCAI transmission dynamics. The remaining 124 studies were descriptive. A modest increase in the application of statistical analyses has occurred in recent years. Conclusion: The incorporation of spatiotemporal analysis has been limited in healthcare settings, with only 15% of studies including any such analysis. Analytical studies provided greater data on transmission dynamics and effective control interventions than studies without spatiotemporal analyses. This indicates the need for greater integration of spatiotemporal techniques into HCAI investigations, as even simple analyses provide significant improvements in the understanding of prevention over simple descriptive summaries.
Output: Spatial and temporal analyses to investigate infectious disease transmission within healthcare settings
Microbial cultures and/or microbial associated diseases often have a characteristic smell. Volatile organic compounds (VOCs) are produced by all microorganisms as part of their normal metabolism. The types and classes of VOC produced is wide, including fatty acids and their derivatives (e.g. hydrocarbons, aliphatic alcohols and ketones), aromatic compounds, nitrogen containing compounds, and volatile sulfur compounds. A diversity of ecological niches exist in the human body which can support a polymicrobial community, with the exact VOC profile of a given anatomical site being dependent on that produced by both the host component and the microbial species present. The detection of VOCs is of interest to various disciplines, hence numerous analytical approaches have been developed to accurately characterize and measure VOCs in the laboratory, often from patient derived samples. Using these technological advancements it is evident that VOCs are indicative of both health and disease states. Many of these techniques are still largely confined to the research laboratory, but it is envisaged that in future bedside 'VOC profiling' will enable rapid characterization of microbial associated disease, providing vital information to healthcare practitioners.
Output: TOPICAL REVIEW Microbial volatile compounds in health and disease conditions