niryuu/sni-each-converted huggingface dataset:
A novel porcine deltacoronavirus (PdCV) was first discovered in Ohio and Indiana in February 2014, rapidly spread to other states in the United States and Canada, and caused significant economic loss in the swine industry. The origin and virulence of this novel porcine coronavirus are not known. Here, we characterized U.S. PdCV isolates and determined their virulence in gnotobiotic and conventional piglets. Genome analyses revealed that U.S. PdCV isolates possess unique genetic characteristics and share a close relationship with Hong Kong and South Korean PdCV strains and coronaviruses (CoVs) of Asian leopard cats and Chinese ferret-badgers. The PdCV-positive intestinal content (Ohio CVM1) and the cell culture-adapted PdCV Michigan (MI) strain were orally inoculated into gnotobiotic and/or conventional piglets. Within 1 to 3 days postinfection, profuse watery diarrhea, vomiting, and dehydration were observed. Clinical signs were associated with epithelial necrosis in the gastric pits and small intestine, the latter resulting in severe villous atrophy. Mild interstitial pneumonia was identified in the lungs of PdCVinfected piglets. High levels of viral RNA (8 to 11 log RNA copies/g) were detected in intestinal tissues/luminal contents and feces of infected piglets, whereas moderate RNA levels (2 to 5 log RNA copies/g) were detected in blood, lung, liver, and kidney, indicating multisystemic dissemination of the virus. Polyclonal immune serum against PdCV but not immune serum against porcine epidemic diarrhea virus (PEDV) reacted with PdCV-infected small-intestinal epithelial cells, indicating that PdCV is antigenically distinct from PEDV. Collectively, we demonstrate for the first time that PdCV caused severe gastrointestinal diseases in swine. Indiana and subsequently spread rapidly across the United States and Canada, causing significant economic losses. Here, we report the detailed genetic characterization, phylogeny, and virulence of emergent PdCV strains in the United States. We found that PdCV caused severe diarrhea, vomiting, and dehydration in gnotobiotic and conventional piglets, signs that were clinically indistinguishable from those caused by PEDV and TGEV. In addition to extensive intestinal lesions, PdCV caused significant lesions in the stomach and mild pulmonary lesions that have not been reported for TGEV and PEDV. The finding that PdCV is a significant enteric disease of swine highlights the need to develop effective measures to control this disease. . 2015. Origin, evolution, and virulence of porcine deltacoronaviruses in the United States. mBio 6(2): e00064-15.
Output: Origin, Evolution, and Virulence of Porcine Deltacoronaviruses in the United States
In a field trial on a farm in Turkey, we tested whether specific egg-yolk antibodies had a prophylactic effect on neonatal diarrhea. Owing to its antibody spectrum, this egg powder was very suitable for this farm since mainly rotavirus was identified. Regardless of the dosage (2 g, 4 g, or 8 g egg powder), the calves (n = 164) which received specific egg-yolk antibodies via the whole egg during the first 14 days of life showed significant improvements in risk and duration of diarrhea and in body weight gain compared with calves of the control group (n = 80) which had not received any egg powder. These significant differences in body weight still persisted after 3 months of life. The mortality risk in the control group amounted to 8.8%, while in all egg powder groups (n = 164) only one calf died as a result of diarrhea. Breed-dependent differences in the parameters were not observed.
Output: PREVENTIVE VETERINARY MEDICINE Dose-dependent effects of specific egg-yolk antibodies on diarrhea of newborn calves
A Western immunoblot assay for confirmatory serodiagnosis of severe acute respiratory syndrome (SARS) was developed utilizing viral lysate antigens combined with a recombinant nucleocapsid protein, GST-N (glutathione S-transferase-nucleocapsid) of the SARS coronavirus (SARS-CoV). The viral lysate antigens were separated by electrophoresis and transblotted onto nitrocellulose membranes. The resultant membrane was subsequently added with the GST-N recombinant protein at a specific location. The positions of bands corresponding to some of the structural proteins immobilized on the membrane were then located and verified with mouse or rabbit antisera specific to the respective proteins. The Western immunoblot assay was able to detect antibodies to SARS-CoV in all 40 serum specimens from SARS patients and differentiate the SARSpositive samples from those of the healthy donor or non-SARS patient controls (150 samples) when set criteria were followed. In addition, when the immunoblot was used to test samples considered falsely positive by an in-house-developed SARS-specific enzyme-linked immunosorbent assay, band patterns different from those with samples from SARS patients were obtained.
Output: Use of Viral Lysate Antigen Combined with Recombinant Protein in Western Immunoblot Assay as Confirmatory Test for Serodiagnosis of Severe Acute Respiratory Syndrome
Recent whole genome sequence analyses revealed that a high degree of proteomic complexity is achieved with a limited number of genes. This surprising fi nding underscores the importance of alternative splicing through which a single gene can generate structurally and functionally distinct protein isoforms [ 1 ] . Based on genome-wide analysis, 75% of human genes are thought to encode at least two alternatively spliced isoforms [ 2, 3 ] . The regulation of splice site usage provides a versatile mechanism for controlling gene expression and for the generation of proteome diversity, playing essential roles in many biological processes, such as embryonic development, cell growth, and apoptosis. The splice sites are generally recognized by the splicing machinery, a ribonuclear protein complex known as the spliceosome. Spliceosome binding is determined by competing activities of various auxiliary regulatory proteins, such as members of SR protein or heterogeneous nuclear ribonucleoprotein (hnRNP) families, which bind speci fi c regulatory sequences and alter the binding of the spliceosome to a particular splice site [ 1, 4 ] . Pre-mRNA splicing is regulated in a tissue-speci fi c or developmental stage-speci fi c manner [ 5 ] . The selection of splice site can be altered by numerous extracellular stimuli such as hormones, immune response, neuronal depolarization, and cellular stress, through changes in synthesis/degradation, complex formation, and intracellular localization of regulatory proteins. SR proteins are heavily phosphorylated in cells and involved in constitutive and alternative splicing, and the phosphorylation states of SR proteins are altered in response to these extracellular stimuli [ 6 ] . Splicing mutations located in either intronic or exonic regions frequently cause hereditary diseases, and more than 15% of mutations that cause genetic disease
Output: Introduction Modulation of Pre-mRNA Splicing Patterns with Synthetic Chemicals and Their Clinical Applications
Background: A novel coronavirus (2019-nCoV) causing an outbreak of pneumonia in Wuhan, Hubei province of China was isolated in January 2020. This study aims to investigate its epidemiologic history, and analyze the clinical characteristics, treatment regimens, and prognosis of patients infected with 2019-nCoV during this outbreak. Methods: Clinical data from 137 2019-nCoV-infected patients admitted to the respiratory departments of the respiratory departments of nine tertiary hospitals in Hubei province from December 30, 2019 to January 24, 2020 were retrospectively collected, including general status, clinical manifestations, laboratory test results, imaging characteristics, and treatment regimens. Results: None of the 137 patients (61 males, 76 females, aged 20-83 years, median age 57 years) had a definite history of exposure to Huanan Seafood Wholesale Market. Major initial symptoms included fever (112/137, 81.8%), coughing (66/137, 48.2%), and muscle pain or fatigue (44/137, 32.1%), with other, less typical initial symptoms observed at low frequency, including heart palpitations, diarrhea, and headache. Nearly 80% of the patients had normal or decreased white blood cell counts, and 72.3% (99/137) had lymphocytopenia. Lung involvement was present in all cases, with most chest computed tomography scans showing lesions in multiple lung lobes, some of which were dense; ground-glass opacity co-existed with consolidation shadows or cordlike shadows. Given the lack of effective drugs, treatment focused on symptomatic and respiratory support. Immunoglobulin G was delivered to some critically ill patients according to their conditions. Systemic corticosteroid treatment did not show significant benefits. Notably, early respiratory support facilitated disease recovery and improved prognosis. The risk of death was primarily associated with age, underlying chronic diseases, and median interval from the appearance of initial symptoms to dyspnea. Conclusions: The majority of patients with 2019-nCoV pneumonia present with fever as the first symptom, and most of them still showed typical manifestations of viral pneumonia on chest imaging. Middle-aged and elderly patients with underlying comorbidities are susceptible to respiratory failure and may have a poorer prognosis.
Output: Clinical characteristics of novel coronavirus cases in tertiary hospitals in Hubei Province
Whether influenza vaccination influences the severity of illness in cases of clinical failure in solid organ transplant (SOT) recipients receiving influenza vaccine has not been extensively studied. Our goal was to evaluate the frequency of influenza vaccination among SOT recipients with influenza disease and its impact on the illness severity during the 2010-2011 season. Adult SOT recipients with confirmed influenza infection were included from December 2010 to April 2011. Follow-up data were recorded and antibody titres were determined using a microneutralization assay. Sixty-four SOT recipients were included in the study, ten (15.6%) with severe disease, requiring admission to intensive care units, of whom four (6.3%) died. In all, 34 (53.1%) received the 2010-2011 seasonal influenza vaccine and 32 (50.0%) received the 2009-H1N1 pandemic vaccine, and none had detectable antibodies against influenza at the time of diagnosis of influenza infection. Twenty-three (67.6%) of the patients that received the vaccine required hospital admission and presented less dyspnoea (10, 29.4% versus 14 (50.0%), p 0.09) and pneumonia (8, 23.8% versus 15, 50.0%, p 0.03, relative risk 0.3, 95% CI 0.1-0.9) than unvaccinated patients, with relative risk reductions of 60% and 70%, respectively. Although influenza vaccination confers protection on SOT recipients against developing influenza pneumonia, the rate of clinical failure is still high. New strategies to improve influenza immunization are needed for this group of patients.
Output: Reduced incidence of pneumonia in influenza-vaccinated solid organ transplant recipients with influenza disease
Molecular infectious disease diagnostic tests have undergone major advances in the past decade and will continue to rapidly evolve. Assays have become extraordinarily simple to perform, eliminating the need for pre-analytic sample preparation and post-amplification analysis. This allows these tests to be performed in settings without sophisticated expertise in molecular biology, including locations with limited resources. Additionally, the sensitivity and specificity of these assays is superb and many offer extremely fast turn-around times. These tests have major impacts on patient care, but also have some limitations. ARTICLE HISTORY
Output: Sample-to-result molecular infectious disease assays: clinical implications, limitations and potential
An extremely affordable virus concentration method based on adsorption-elution to glass wool and subsequent reconcentration through polyethylene glycol 6000 (PEG) precipitation was optimized to recover not only non-enveloped viruses but also enveloped viruses. Hepatitis A virus (HAV) and transmissible gastroenteritis virus (TGEV) were employed as surrogates for naked and enveloped viruses, respectively, to set up the methodology. Initial experimentation in small-volume samples showed that both types of particles readily adsorbed to the positively charged glass wool but were poorly detached from it through standard elution with 0.05 M glycine with 3% of beef extract buffer, pH 9.5, with elution efficiencies of 7.2% and 2.6%, for HAV and TGEV, respectively. To improve the recovery of enveloped viruses, several modifications in the elution were assayed: increasing the elution pH, extending glass wool and eluent contact time, adding a detergent, or performing the elution by recirculation or under agitation. Considering practicability and performance, recircularization of the eluent at pH 11.0 for 20 min was the elution procedure of choice, with efficiencies of 25.7% and 18.8% for HAV and TGEV in 50 L of water. Additionally, employing 20% PEG instead of 10% for virus reconcentration improved recoveries up to 47% and 51%, respectively. The optimized procedure was applied to detect naturally occurring HAV and coronaviruses in surface water of Wadi Hanifa, Riyadh. HAV was detected in 38% of the samples, while one sample was positive for an alphacoronavirus. This cheap virus detection system enables the comprehensive surveillance of viruses present in water samples.
Output: Glass Wool Concentration Optimization for the Detection of Enveloped and Non-enveloped Waterborne Viruses
The present study was performed to elucidate the clinical outcome, and etiology of acute otitis media (AOM) in children based on virologic and bacteriologic tests. The study group consisted of 120 children aged 6 to 144 months with AOM. Middle ear fluid (MEF) was tested for viral pathogens by reverse transcriptase polymerase chain reaction (RT-PCR) and for bacteria by gram-staining and culture. Clinical response was assessed on day 2 to 4, 11 to 13, 26 to 28. Respiratory viruses were isolated in 39 patients (32.5%). Respiratory syncytial virus (RSV) (46.5%) was the most common virus identified in MEF samples, followed by human rhinovirus (HRV) (25.6%), human coronavirus (HCV) (11.6%), influenza (IV) type A (9.3%), adenovirus type sub type A (AV) (4%), and parainfluenza (PIV) type -3 (2%) by RT-PCR. In total 69 bacterial species were isolated from 65 (54.8%) of 120 patients. Streptococcus pneumoniae (S. pneumoniae) was the most frequently isolated bacteria. Viral RNA was detected in 31 (56.3%) of 55 bacteria-negative specimens and in 8 (12.3%) of 65 bacteria-positive MEF samples. No significant differences were found between children representing viral infection alone, combined viral and bacterial infection, bacterial infection alone, and neither viral nor bacterial infection, regarding clinical cure, relapse and reinfection rates. A significantly higher rate of secretory otitis media (SOM) was observed in alone or combined RSV infection with S. pneumonia or Haemophilus influenzae (H. influenzae) than in other viruses infection. Conclusion. This study provides information about etiologic agents and diagnosis of AOM in Turkish children. The findings highlight the importance of common respiratory viruses and bacterial pathogens, particularly RSV, HRV, S. pneumoniae and H. influenzae, in predisposing to and causing AOM in children.
Output: Acute otitis media and respiratory viruses
A divergent rotavirus I was detected using viral metagenomics in the feces of a cat with diarrhea. The eleven segments of rotavirus I strain Felis catus encoded non-structural and structural proteins with amino acid identities ranging from 25 to 79% to the only two currently sequenced members of that viral species both derived from canine feces. No other eukaryotic viral sequences nor bacterial and protozoan pathogens were detected in this fecal sample suggesting the involvement of rotavirus I in feline diarrhea.
Output: Rotavirus I in feces of a cat with diarrhea
The diagnostics of respiratory viral infections has improved markedly during the last 15 years with the development of PCR techniques. Since 1997, several new respiratory viruses and their subgroups have been discovered: influenza A viruses H5N1 and H1N1, human metapneumovirus, coronaviruses SARS, NL63 and HKU1, human bocavirus, human rhinoviruses C and D and potential respiratory pathogens, the KI and WU polyomaviruses and the torque teno virus. The detection of previously known viruses has also improved. Currently, a viral cause of respiratory illness is almost exclusively identifiable in children, but in the elderly, the detection rates of a viral etiology are below 40%, and this holds also true for exacerbations of chronic respiratory illnesses. The new viruses cause respiratory symptoms like the common cold, cough, bronchitis, bronchiolitis, exacerbations of asthma and chronic obstructive pulmonary disease and pneumonia. Acute respiratory failure may occur. These viruses are distributed throughout the globe and affect people of all ages. Data regarding these viruses and the elderly are scarce. This review introduces these new viruses and reviews their clinical significance, especially with regard to the elderly population.
Output: New Respiratory Viruses and the Elderly
Cut-off Cut-off Supplementary Figure 1 | Setting cut-off to identify links and hidden source. (a) Coarse-grained distribution of element values ln(1 − λ i )a ij times −1 in the reconstructed vector X of all nodes in a Newman-Watts small-world network (NW), where bin accumulation is implemented for the original distribution. The peak centered at zero corresponds to null connections and the other corresponds to actual links. A cut-off value can be set within the gap between the two peaks. (b) The values of ln(1 − λ i )a ij times -1 in the reconstructed vector X for Erdös-Rényi random networks (ER), Watts-Strogatz small-world networks (WS), NW and Barabási-Albert scale-free networks (BA), where green and yellow points correspond to existent links and null connections, respectively. All the networks share the same cut-off value of about 0.13. (c) Coarse-grained distribution of the structural variance σ in the NW network, where bin accumulation is exercised on the original distribution. The largest peak centered close zero corresponds to nodes of indirect neighbors of the hidden source and the large positive values of σ are associated with the immediate neighbors of the hidden source. A cut-off can be set within the largest gap. (d) The variance σ * i of element values in the reconstructed vector x of all nodes in the presence of a hidden source for ER, WS, NW and BA networks, where green and yellow points correspond to immediate neighbors and indirect neighbors of the hidden source, respectively. All the networks share the same cut-off values of about σ * i = 0.9. The network size in a,b is 200 and in c,d is 50, Θ = 0.25, ∆ = 0.45, λ i and δ i are uniformly distributed in the ranges (0.2, 0.4) and (0.4, 0.6), respectively. SIS dynamics are used for the illustration. Panels a and c correspond to Fig. 2a with nt = 0.4 and Fig. 5 in the main text, respectively.
Output: Supplementary Figures
Background: Members of the Baculoviridae encode two types of proteins that mediate virus:cell membrane fusion and penetration into the host cell. Alignments of primary amino acid sequences indicate that baculovirus fusion proteins of group I nucleopolyhedroviruses (NPV) form the GP64 superfamily. The structure of these viral penetrenes has not been determined. The GP64 superfamily includes the glycoprotein (GP) encoded by members of the Thogotovirus genus of the Orthomyxoviridae. The entry proteins of other baculoviruses, group II NPV and granuloviruses, are class I penetrenes. Results: Class III penetrenes encoded by members of the Rhabdoviridae and Herpesviridae have an internal fusion domain comprised of beta sheets, other beta sheet domains, an extended alpha helical domain, a membrane proximal stem domain and a carboxyl terminal anchor. Similar sequences and structural/functional motifs that characterize class III penetrenes are located collinearly in GP64 of group I baculoviruses and related glycoproteins encoded by thogotoviruses. Structural models based on a prototypic class III penetrene, vesicular stomatitis virus glycoprotein (VSV G), were established for Thogoto virus (THOV) GP and Autographa california multiple NPV (AcMNPV) GP64 demonstrating feasible cysteine linkages. Glycosylation sites in THOV GP and AcMNPV GP64 appear in similar model locations to the two glycosylation sites of VSV G. These results suggest that proteins in the GP64 superfamily are class III penetrenes.
Output: Virology Journal Proteomics computational analyses suggest that baculovirus GP64 superfamily proteins are class III penetrenes
Objective: The objective of this study was to assess epidemiological and clinical features of human bocavirus (HBoV) coinfection with other viruses. Method: Children coinfected with HBoV between January 2012 and December 2014 were enrolled and retrospectively reviewed. Result: A total of 984 patients were stratified into five groups: HBoV infection alone (n ¼ 249), respiratory syncytial virus (RSV) infection alone (n ¼ 649), HBoV coinfection with RSV (n ¼ 28), with human rhinovirus (HRV) (n ¼ 39) and with other virus (n ¼ 19). Length of hospitalization was longer in HBoV coinfection with RSV group than HBoV (9.0 days vs. 7.0 days, p ¼ 0.001), RSV (9.0 days vs. 8.0 days, p ¼ 0.016) infection alone group. Pneumonia was more common in the HBoV coinfection with RSV group compared with the HBoV, RSV infection alone group, respectively (75.0% vs. 44.2%, 31.3%, p < 0.001). HBoV DNA copy numbers (383 000 copies/ml) were positively correlated with the length of hospitalization (r ¼ 0.334, p < 0.001). K E Y W O R D S : coinfection, human bocavirus, respiratory syncytial virus, disease severity, acute respiratory infections Human bocavirus (HBoV) was first identified in 2005 in nasopharyngeal aspirates collected from children with respiratory diseases [1]. Since then, HBoV has been detected worldwide, with prevalence rates between 1. 5% and 19% [2-4]. The recent widespread use of molecular methods has markedly increased the ability to identify respiratory V C The Author(s) [
Output: Impact of RSV Coinfection on Human Bocavirus in Children with Acute Respiratory Infections
Acid dependent infection of Hela and Vero cells by BTV-10 occurs from within early-endosomes following virus uptake by clathrin-mediated endocytosis (Forzan et al., 2007: J Virol 81: 4819-4827). Here we report that BTV-1 infection of BHK cells is also dependent on a low endosomal pH; however, virus entry and infection were not inhibited by dominant-negative mutants of Eps15, AP180 or the 'aa' splice variant of dynamin-2, which were shown to inhibit clathrin-mediated endocytosis. In addition, infection was not inhibited by depletion of cellular cholesterol, which suggests that virus entry is not mediated by a lipid-raft dependent process such as caveolae-mediated endocytosis. Although virus entry and infection were not inhibited by the dominant-negative dynamin-2 mutant, entry was inhibited by the general dynamin inhibitor, dynasore, indicating that virus entry is dynamin dependent. During entry, BTV-1 co-localised with LAMP-1 but not with transferrin, suggesting that virus is delivered to late-endosomal compartments without first passing through early-endosomes. BTV-1 entry and infection were inhibited by EIPA and cytochalasin-D, known macropinocytosis inhibitors, and during entry virus co-localised with dextran, a known marker for macropinocytosis/fluid-phase uptake. Our results extend earlier observations with BTV-10, and show that BTV-1 can infect BHK cells via an entry mechanism that is clathrin and cholesterol-independent, but requires dynamin, and shares certain characteristics in common with macropinocytosis. Citation: Gold S, Monaghan P, Mertens P, Jackson T (2010) A Clathrin Independent Macropinocytosis-Like Entry Mechanism Used by Bluetongue Virus-1 during Infection of BHK Cells. PLoS ONE 5(6): e11360.
Output: A Clathrin Independent Macropinocytosis-Like Entry Mechanism Used by Bluetongue Virus-1 during Infection of BHK Cells
The membrane (M) proteins of murine coronavirus (MHV) strains have been reported to contain only O-linked oligosaccharides. The predicted O-glycosylation site consisting of four amino acid residues of Ser -Ser -Thr -Thr is located immediately adjacent to the initiator Met and is well conserved among MHV strains investigated so far. We analyzed the nucleotide sequence of a highly virulent strain MHV-2 M-coding region and demonstrated that MHV-2 had a unique amino acid, Asn, at position 2 at the conserved O-glycosylation site. We also demonstrated that this substitution added N-linked glycans to MHV-2 M protein resulting in increment of molecular mass of MHV-2 M protein compared with JHM strain having only O-linked glycans.
Output: Unique N-linked glycosylation of murine coronavirus MHV-2 membrane protein at the conserved O-linked glycosylation site
Endogenous retroviruses have traditionally been defined as descendants of extinct retroviruses that infected and integrated into the chromosomes of host germ-line cells and were thereafter transmitted vertically as part of host genomes. Most retain at least the vestiges of genes once required for infectious horizontal transfer, namely envelope genes. In contrast, the long evolutionary histories of retrotransposons are presumed not to have included infectious ancestors. With the characterization of the Gypsy retrotransposon in Drosophila melanogaster as an infectious, endogenous retrovirus, these distinctions have blurred. A number of plant LTR retroelements possess coding regions whose conceptual translations produce hypothetical proteins with predicted structural elements found in viral envelope proteins, and the term endogenous retrovirus began to be applied to these elements. The question of whether any of the many plant retroelement genes now annotated as "env-like" generate proteins that have or had envelope functions remains unanswered. This review reevaluates the available data.
Output: Plant Endogenous Retroviruses? A Case of Mysterious ORFs
Background: The impact of the severe acute respiratory syndrome (SARS) outbreak in 2003 on the emergency department (ED) medical needs of adult patients has not been elucidated. The purpose of this study was to investigate the demographic and clinical characteristics of ED adult patients before, during and after the SARS epidemic in a SARS-dedicated hospital. Methods: A retrospective, ED chart review was conducted, and demographic data were obtained from a computer database, for a total of 17,586 patients. Patient information, including age, gender, mode of arrival, triage category, time of visit, main diagnosis, use of ED services, and status after the ED visit, were collected and compared for pre-, early-, peak-, late-, and post-SARS epidemic stages. Results: Demographic data demonstrated a significant decrease in patient attendances per day, with a mean reduction of 92.5 8.3 patients (43.7 3.9% reduction in rate; p < 0.01) during peak-versus pre-epidemic stages, but revealed no differences in patient age and gender. The numbers of patients with ambulance transport, inter-hospital referral, and critical illnesses, including DOA, categorized as triage 1, or admitted to a ward or intensive care unit after the ED visit, were not influenced by the SARS epidemic. The number of patients with upper airway infections and suicide attempts from drug overdoses increased, but not statistically significantly. The number of patients with other diagnoses decreased progressively from early-to peak-epidemic stages, but returned to their earlier levels at the post-epidemic stage. Statistically significant decreases (p < 0.05) were noted in mean attendance at peakversus pre-and early-epidemic stages for patients with cardiovascular disease, inflammatory or functional bowel disease, endocrine disease, dizziness or vertigo, or trauma. Conclusion: The SARS outbreak did not eliminate the need of critically ill patients for advanced medical support. However, besides an overall decrease in patient numbers, the SARS epidemic markedly altered demographic information, clinical characteristics, and the use of medical services by adult patients in the ED of a SARS-dedicated hospital. [J Chin Med Assoc 2005;68(6):254-259] 
Output: Impact of Severe Acute Respiratory Syndrome (SARS) Outbreaks on the Use of Emergency Department Medical Resources
Two fragments, S66 and S55, of the S glycoprotein of the newly identified canine coronavirus type I (CCoV type I), were expressed in a procariotic system. The purified recombinant proteins of 350 and 366 amino acids in length, respectively, were employed to develop an enzyme-linked immunosorbent assay (ELISA) for the detection of CCoV type I antibodies in dog sera. Four canine sera-positive for CCoV type II, four sera-positive for CCoV type I and 10 negative control sera were examined. Only the sera-positive for CCoV type I strongly reacted with both the proteins, whereas the sera-positive for CCoV type II showed low reactivity in the ELISA test. As CCoV type I seems to be not cultivable in cell cultures, the recombinant fragments of the S protein represent a unique method to study, preliminarily, the immunological and the pathogenetic characteristics of this new virus.
Output: Cloning and expression of two fragments of the S gene of canine coronavirus type I
The introduction of the Individual Visit Scheme (IVS), which allows Mainland Chinese travelers (hereafter called Chinese travelers) to visit Hong Kong on an individual basis, has been beneficial to the fast recovery of the local economy in Hong Kong from severe acute respiratory syndrome (SARS). The IVS travelers, together with the packaged travelers who visited Hong Kong by joining packaged tours, are presently forming the largest segment of inbound travelers to Hong Kong. Despite the significant economic contributions of Chinese travelers to Hong Kong in general, and to the foodservice sector in particular, there has been an absence of prior studies on IVS travelers' behavior of selecting restaurants in the existing hospitality and tourism literature. This paper reports on an exploratory study that investigated the perceived importance of attributes that pertain to the selection of restaurants from the perspective of IVS and packaged travelers from Mainland China. Empirical findings of a questionnaire survey with 230 Chinese travelers, including 127 IVS travelers and 103 packaged travelers, showed that the respondents in general viewed the included attributes as relatively important. In addition, only two attributes exhibited significant differences between IVS and packaged travelers. Findings of this research would be useful for hospitality and tourism practitioners to better prepare for receiving the growing number of Chinese travelers. r
Output: How do Mainland Chinese travelers choose restaurants in Hong Kong? An exploratory study of individual visit scheme travelers and packaged travelers
In 2012, a novel human coronavirus emerged and was tentatively named ''Middle East respiratory syndrome coronavirus'' (MERS-CoV). The high mortality rate of MERS-CoV focused attention on the ecology of the virus. It has been found that MERS-CoV belongs to the group C lineage of the genus Betacoronavirus. Coronavirus surveillance studies in different populations of bats have suggested that they are probable reservoirs for this novel virus, and phylogenetic analysis of both the spike (S1) and RNA-dependent RNA polymerase proteins of MERS-CoV have revealed that it is related to bat viruses. Recently, the MERS-CoV and its neutralizing antibodies were detected in dromedary camels. Despite the limited number of reported cases of person-to-person transmission, the rapid evolution of the virus poses a continuous threat to humans worldwide. This paper reviews the current state of knowledge regarding the virology, clinical spectrum, evolution, diagnosis and treatment of MERS-CoV infections.
Output: Middle East respiratory syndrome coronavirus (MERS-CoV): evidence and speculations
Benchmarks and metrics related to laboratory test utilization are based on evidence-based medical literature that may suffer from a positive publication bias. Guidelines are only as good as the data reviewed to create them. Disruptive technologies require time for appropriate use to be established before utilization review will be meaningful. Metrics include monitoring the use of obsolete tests and the inappropriate use of lab tests. Test utilization by clients in a hospital outreach program can be used to monitor the impact of new clients on lab workload. A multi-disciplinary laboratory utilization committee is the most effective tool for modifying bad habits, and reviewing and approving new tests for the lab formulary or by sending them out to a reference lab.
Output: Establishing benchmarks and metrics for disruptive technologies, inappropriate and obsolete tests in the clinical laboratory
Multiprotein complexes catalyze vital biological functions in the cell. A paramount objective of the SPINE2 project was to address the structural molecular biology of these multiprotein complexes, by enlisting and developing enabling technologies for their study. An emerging key prerequisite for studying complex biological specimens is their recombinant overproduction. Novel reagents and streamlined protocols for rapidly assembling co-expression constructs for this purpose have been designed and validated. The high-throughput pipeline implemented at IGBMC Strasbourg and the ACEMBL platform at the EMBL Grenoble utilize recombinant overexpression systems for heterologous expression of proteins and their complexes. Extension of the ACEMBL platform technology to include eukaryotic hosts such as insect and mammalian cells has been achieved. Efficient production of large multicomponent protein complexes for structural studies using the baculovirus/insect cell system can be hampered by a stoichiometric imbalance of the subunits produced. A polyprotein strategy has been developed to overcome this bottleneck and has been successfully implemented in our MultiBac baculovirus expression system for producing multiprotein complexes. Abbreviations: BEVS, baculovirus expression vector system; CFP, cyan florescent protein; CMV, cytomegalovirus; dpa, day of proliferation arrest; dsRed, red fluorescent protein; E. coli, Escherichia coli; EGFP, enhanced green fluorescent protein; EM, electron microscopy; FRET, fluorescence resonance energy transfer; HT, high throughput; kb, kilo base; kDa, kilo dalton; MOI, multiplicity of infection; NMR, nuclear magnetic resonance (spectroscopy); ORF, open reading frame; Ori, origin of replication; p10, p10 baculoviral late promoter; polh, polyhedrin baculoviral very late promoter; R6Kc, bacteriophage R6Kc; SDS-PAGE, sodium dodecylsulfate-polyacryamide gel electrophoresis; Sf9, Sf21, Spodoptera frugiperda cell lines 9 or 21, respectively; SLIC, sequence and ligation independent cloning; tcs, TEV protease cleavage site; TEV, tobacco etch virus, resp. a protease (N1A) from this virus; YFP, yellow fluorescent protein.
Output: Robots, pipelines, polyproteins: Enabling multiprotein expression in prokaryotic and eukaryotic cells
Background: Acute Respiratory Infections (ARI) are common causes of febrile illnesses in many settings in Senegal. These infections are usually managed presumptively due to lack of appropriate diagnostic tools. This situation, can lead to poor management of febrile illness or antibiotic misuse. In addition, there are limited data on the spectrum of pathogens commonly responsible for these ARI. This study was conducted to explore the pathogens community among patients with acute respiratory infection in a rural area in Senegal. Methods: A cross sectional study was conducted from August to December 2015. Children and adult patients attending Keur Socé health post for signs suggestive of acute respiratory infection were enrolled after providing inform consent. Eligible participants were recruited using a consecutive sampling method. Paired nose and throat swabs were collected for pathogen detection. Samples were processed using a multiplex PCR designed to identify 21 pathogens including both virus and bacteria. Results: Two hundred and fifty patients participated in the study. Samples positivity rate was evaluated at 95.2% (238/250). Streptococcus pneumoniae was the predominant pathogen (74%) and was present in all months and all age-groups, followed by Staphylococcus aureus (28,8%) and rhinovirus (28,4%). Respiratory syncytial virus (RSV) was detected only among children under 5 years old in August and September while coronavirus was present in all age groups, during the months of October and December. Conclusion: This pilot study revealed a diversity of pathogens over the time and across all age groups, highlighting the need for further exploration. A pathogen community approach including both virus and bacteria at a larger scale becomes crucial for a better understanding of transmission dynamics at population level in order to help shape ARI control strategies.
Output: Upper respiratory infections in a rural area with reduced malaria transmission in Senegal: a pathogens community study
is the etiologic agent of the febrile respiratory illness, commonly referred to as 'flu'. The lysosomal protease cathepsin B (CTSB) has shown to be involved in the lifecycle of various viruses. Here, we examined the role of CTSB in the IAV lifecycle. Methods-CTSB-deficient (CTSB −/− ) macrophages and the human lung epithelial cell line A549 cells treated with CA-074Me were infected with the A/Puerto Rico/8/34 strain of IAV (IAV-PR8). Viral entry and propagation were measured through quantitative real-time RT-PCR; production and localization of hemagglutinin (HA) protein in the infected host cells were analysed by Western blots, flow cytometry and confocal microscopy; production of progeny viruses were measured by a hemagglutination assay. Results-CTSB −/− macrophages and CA-074Me-treated A549 cells had no defects in incorporating IAV-PR8 virions and permitting viral RNA synthesis. However, these cells produced significantly lower amounts of HA protein and progeny virions than wild-type or untreated cells. Conclusion-These data indicate that CTSB is involved in the expression of IAV-PR8 HA protein and subsequent optimal production of IAV-PR8 progeny virions. Targeting CTSB can be a novel therapeutic strategy for treating IAV infection.
Output: Cathepsin B plays a key role in optimal production of the influenza A virus
Macroautophagy/autophagy has been shown to mediate the selective lysosomal degradation of pathogenic bacteria and viruses (xenophagy), and to contribute to the activation of innate and adaptative immune responses. Autophagy can serve as an antiviral defense mechanism but also as a proviral process during infection. Atg8-family proteins play a central role in the autophagy process due to their ability to interact with components of the autophagy machinery as well as selective autophagy receptors and adaptor proteins. Such interactions are usually mediated through LC3-interacting region (LIR) motifs. So far, only one viral protein has been experimentally shown to have a functional LIR motif, leaving open a vast field for investigation. Here, we have developed the iLIR@viral database (http://ilir.uk/virus/) as a freely accessible web resource listing all the putative canonical LIR motifs identified in viral proteins. Additionally, we used a curated text-mining analysis of the literature to identify novel putative LIR motif-containing proteins (LIRCPs) in viruses. We anticipate that iLIR@viral will assist with elucidating the full complement of LIRCPs in viruses.
Output: iLIR@viral: A web resource for LIR motif-containing proteins in viruses
Bats are being increasingly recognized as reservoir hosts of highly pathogenic and zoonotic emerging viruses (Marburg virus, Nipah virus, Hendra virus, Rabies virus, and coronaviruses). While numerous studies have focused on the mentioned highly human-pathogenic bat viruses in tropical regions, little is known on similar human-pathogenic viruses that may be present in European bats. Although novel viruses are being detected, their zoonotic potential remains unclear unless further studies are conducted. At present, it is assumed that the risk posed by bats to the general public is rather low. In this review, selected viruses detected and isolated in Europe are discussed from our point of view in regard to their human-pathogenic potential. All European bat species and their roosts are legally protected and some European species are even endangered. Nevertheless, the increasing public fear of bats and their viruses is an obstacle to their protection. Educating the public regarding bat lyssaviruses might result in reduced threats to both the public and the bats.
Output: European Bats as Carriers of Viruses with Zoonotic Potential
Patrick Manson, a clinician-scientist serving in China (1866±1889), discovered that many tropical infectious diseases require a vector peculiar to warm climate for person to person transmission. He demonstrated the nocturnal periodicity of microfilariae in the blood of patients with elephantiasis. These microfilariae undergo metamorphosis when ingested by the mosquito acting as the vector for the completion of their life cycle. Furthermore, he demonstrated the linkage between the lung fluke and endemic haemoptysis by finding operculated eggs in patients' sputa. He predicted that the miracidium from hatched eggs uses crustaceans, such as fresh-water snails found at tropical conditions, as the intermediate hosts in the life cycle of many trematodes. His vector hypothesis leads to vector control which is now the cornerstone for the World Health Organization's programme for the elimination/control of lymphatic filariasis, dracunculiasis and malaria. Before leaving China, he established the Alice Memorial Hospital, the Hong Kong College of Medicine for Chinese (the forerunner of the University of Hong Kong), and the Hong Kong Medical Society for medical service and education. He also incepted the Hong Kong Dairy Farm for supplying hygienic milk affordable by pregnant women, children and patients.
Output: Emerging Microbes and Infections (2012) 1, e31
MicroRNAs (miRNAs) are a class of noncoding RNAs involved in posttranscriptional regulation of gene expression and many critical roles in numerous biological processes. Porcine epidemic diarrhea virus (PEDV), the etiological agent of porcine epidemic diarrhea, causes substantial economic loss in the swine industry worldwide. Previous studies reported miRNA involvement in viral infection; however, their role in regulating PEDV infection remains unknown. In this study, we investigated the regulatory relationship between miRNA-221-5p and PEDV infection, finding that miR-221-5p overexpression inhibited PEDV replication in a dose-dependent manner, and that silencing endogenous miR-221-5p enhanced viral replication. Our results showed that miR-221-5p directly targets the 3 untranslated region (UTR) of PEDV genomic RNA to inhibit PEDV replication, and that miR-221-5p overexpression activates nuclear factor (NF)-κB signaling via p65 nuclear translocation, thereby upregulating interferon (IFN)-β, IFN-stimulated gene 15, and MX1 expression during CH/HBTS/2017 infection. We subsequently identified NF-κB-inhibitor α and suppressor of cytokine signaling 1, negative regulators of the NF-κB pathway, as miR-221-5p targets. These results demonstrated the ability of miR-221-5p to inhibit PEDV replication by targeting the 3' UTR of the viral genome and activating the NF-κB-signaling pathway. Our findings will aid the development of preventive and therapeutic strategies for PEDV infection.
Output: MicroRNA-221-5p Inhibits Porcine Epidemic Diarrhea Virus Replication by Targeting Genomic Viral RNA and Activating the NF-κB Pathway
In this paper, we present an RFID-enabled platform for hospital ward management. Active RFID tags are attached to individuals and assets in the wards. Active RFID readers communicate with the tags continuously and automatically to keep track of the real-time information about the locations of the tagged objects. The data regarding the locations and other transmitted information are stored in the ward management system. This platform enables capabilities of real-time monitoring and tracking of individuals and assets, reporting of ward statistics, and providing intelligence and analytics for hospital ward management. All of these capabilities benefit hospital ward management by enhanced patient safety, increased operational efficiency and throughput, and mitigation of risk of infectious disease widespread. A prototype developed based on our proposed architecture of the platform was tested in a pilot study, which was conducted in two medical wards of the intensive care unit of one of the largest public general hospitals in Hong Kong. This pilot study demonstrates the feasibility of the implementation of this RFIDenabled platform for practical use in hospital wards. Furthermore, the data collected from the pilot study are used to provide data analytics for hospital ward management.
Output: RFID analytics for hospital ward management
In response to the severe acute respiratory syndrome (SARS) pandemic of 2003 and the influenza pandemic of 2009, many countries instituted border measures as a means of stopping or slowing the spread of disease. The measures, usually consisting of a combination of border entry/exit screening, quarantine, isolation, and communications, were resource intensive, and modeling and observational studies indicate that border screening is not effective at detecting infectious persons. Moreover, border screening has high opportunity costs, financially and in terms of the use of scarce public health staff resources during a time of high need. We discuss the border-screening experiences with SARS and influenza and propose an approach to decision-making for future pandemics. We conclude that outbreak-associated communications for travelers at border entry points, together with effective communication with clinicians and more effective disease control measures in the community, may be a more effective approach to the international control of communicable diseases.
Output: Entry Screening for Infectious Diseases in Humans PERSPECTIVE Find emerging infectious disease information on
Middle East respiratory syndrome coronavirus (MERS-CoV) has recently emerged in the Middle East. Since 2012, there have been approximately 2,100 confirmed cases, with a 35% case fatality rate. Disease severity has been linked to patient health status, as people with chronic diseases or an immunocompromised status fare worse, although the mechanisms of disease have yet to be elucidated. We used the rhesus macaque model of mild MERS to investigate whether the immune response plays a role in the pathogenicity in relation to MERS-CoV shedding. Immunosuppressed macaques were inoculated with MERS-CoV and sampled daily for 6 days to assess their immune statues and to measure viral shedding and replication. Immunosuppressed macaques supported significantly higher levels of MERS-CoV replication in respiratory tissues and shed more virus, and virus disseminated to tissues outside of the respiratory tract, whereas viral RNA was confined to respiratory tissues in non-immunosuppressed animals. Despite increased viral replication, pathology in the lungs was significantly lower in immunosuppressed animals. The observation that the virus was less pathogenic in these animals suggests that disease has an immunopathogenic component and shows that inflammatory responses elicited by the virus contribute to disease.
Output: Pathogenicity and Viral shedding of Mers-coV in immunocompromised rhesus Macaques