docid: fjvoyaos

title: A Role for Protein Phosphatase 2A in Regulating p38 Mitogen Activated Protein Kinase Activation and Tumor Necrosis Factor-Alpha Expression during Influenza Virus Infection

text: Influenza viruses of avian origin continue to pose pandemic threats to human health. Some of the H5N1 and H9N2 virus subtypes induce markedly elevated cytokine levels when compared with the seasonal H1N1 virus. We previously showed that H5N1/97 hyperinduces tumor necrosis factor (TNF)-alpha through p38 mitogen activated protein kinase (MAPK). However, the detailed mechanisms of p38MAPK activation and TNF-alpha hyperinduction following influenza virus infections are not known. Negative feedback regulations of cytokine expression play important roles in avoiding overwhelming production of proinflammatory cytokines. Here we hypothesize that protein phosphatases are involved in the regulation of cytokine expressions during influenza virus infection. We investigated the roles of protein phosphatases including MAPK phosphatase-1 (MKP-1) and protein phosphatase type 2A (PP2A) in modulating p38MAPK activation and downstream TNF-alpha expressions in primary human monocyte-derived macrophages (PBMac) infected with H9N2/G1 or H1N1 influenza virus. We demonstrate that H9N2/G1 virus activated p38MAPK and hyperinduced TNF-alpha production in PBMac when compared with H1N1 virus. H9N2/G1 induced PP2A activity in PBMac and, with the treatment of a PP2A inhibitor, p38MAPK phosphorylation and TNF-alpha production were further increased in the virus-infected macrophages. However, H9N2/G1 did not induce the expression of PP2A indicating that the activation of PP2A is not mediated by p38MAPK in virus-infected PBMac. On the other hand, PP2A may not be the targets of H9N2/G1 in the upstream of p38MAPK signaling pathways since H1N1 also induced PP2A activation in primary macrophages. Our results may provide new insights into the control of cytokine dysregulation.


title: Effective inhibition of porcine transmissible gastroenteritis virus replication in ST cells by shRNAs targeting RNA-dependent RNA polymerase gene

text: Abstract Transmissible gastroenteritis virus (TGEV) is identified as one of the most important pathogenic agents during swine enteric infection, leading to high mortality in neonatal pigs and severe annual economic loss in swine-producing areas. Up to date, various vaccines developed against TGEV still need to be improved. To exploit the possibility of using RNA interference (RNAi) as a strategy against TGEV infection, two shRNA-expressing plasmids (pEGFP-U6/P1 and pEGFP-U6/P2) targeting the RNA-dependent RNA polymerase (RdRp) gene of TGEV were constructed and transfected into swine testicular (ST) cells. The cytopathic effect (CPE) and MTS assays demonstrated that both shRNAs were capable of protecting cells against TGEV invasion with very high specificity and efficiency. A real-time quantitative RT-PCR further confirmed that the amounts of viral RNAs in cell cultures pre-transfected with the two plasmids were reduced by 95.2% and up to 100%, respectively. Our results suggest that RNAi might be a promising new strategy against TGEV infection.


title: Angiotensin Converting Enzyme 2 May Mediate Disease Severity In COVID-19

text: Identification of vulnerability to severe coronavirus disease 2019 (COVID-19) is extremely important and might allow optimised shielding and easing of lockdown. The disease is attributed to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which enters host cells through binding to angiotensin converting enzyme 2 (ACE2) on the cell surface. Clinical syndromes such as hypertension that display reduced ACE2 expression tend to correlate with a more severe disease course, whereas treatments which upregulate ACE2 such as the use of angiotensin converting enzyme inhibitors (ACE-i) appear to have a protective effect against COVID-19. Pre-clinical studies have shown that plasma soluble ACE2 could render SARS-CoV-2 inactive in a dose-dependent manner. The association of clinical syndromes or treatments that impact ACE2 expression and clinical severity of COVID-19 infection combined with the reduction in viral load with human recombinant serum ACE2 shown in pre-clinical studies indicate a key role for ACE2 in determining COVID-19 severity. In conclusion, we propose that measurement of ACE2 level may help identify individuals at risk of severe infection where targeted shielding can be used and could provide a novel therapeutic target.


title: Genotype-specific fluorogenic RT-PCR assays for the detection and quantitation of canine coronavirus type I and type II RNA in faecal samples of dogs

text: Abstract Two genotype-specific fluorogenic RT-PCR assays were developed for the detection and quantitation of canine coronavirus (CCoV) type I and type II RNA in the faeces of dogs with diarrhoea. Both the fluorogenic assays showed high specificity, sensitivity and reproducibility, allowing a precise quantitation of CCoV type I and type II RNA over a linear range of about eight orders of magnitude (from 101 to 108 copies of standard RNA). Comparison with genotype-specific gel-based RT-PCR assays revealed that the fluorogenic assays were more sensitive and more rapid than conventional amplifications, with a large increase in throughput. The genotype-specific fluorogenic assays were then used to detect and measure viral loads in the faecal samples collected from dogs naturally or experimentally infected with type I, type II, or both genotypes. Of 174 samples collected from naturally infected dogs, 77 were positive for CCoV type I and 46 for CCoV type II. Thirty-eight dogs were found to be infected naturally by both genotypes, with viral RNA titres generally higher for type I in comparison to type II. At the same time, dogs infected experimentally shed type I RNA with higher titres with respect to type II.


docid: ryiuuyuz

title: A method for evaluating health care workers’ personal protective equipment technique

text: BACKGROUND: Given the potential for the transfer of infectious diseases among patients in isolation, health care workers (HCWs), and other patients in the hospital environment, the proper use of personal protective equipment (PPE) is paramount. The literature is limited regarding studies of HCWs’ use of PPE in patient care tasks. METHODS: A pilot study was conducted to examine the feasibility of using a simulated health care environment to assess HCWs’ technique when implementing standard airborne and contact isolation precautions. The participants (n = 10) were assigned patient care tasks based on their specific professional roles. The encounters were digitally recorded during donning and doffing of PPE, as well as during interactions with the simulated patient. Powdered fluorescent marker was used as a measure of contamination. RESULTS: The pilot data show various inconsistencies in the HCWs’ PPE technique. Each of the 10 participants committed at least one breach of standard airborne and contact isolation precautions. CONCLUSION: An expanded research study of HCW behaviors is needed to properly examine these contamination and exposure pathways. Training programs should be developed that emphasize the common errors in HCWs’ PPE technique.


title: Responses of three urban U.S. children’s hospitals to COVID-19: Seattle, new York and new orleans

text: Since January 2020, there has been a worldwide pandemic of COVID-19, caused by a novel coronavirus--severe acute respiratory syndrome coronavirus 2. The United States has been particularly affected, with the largest number of confirmed cases in a single country in the world. Healthcare systems for adults as well as children have dealt with challenges. This article will reflect on the experiences of selected children’s hospitals in Seattle, New York City, and New Orleans, three of the “hotspots” in the US and share common aspects and lessons learned from these experiences. This article discusses testing and cohorting of patients, personal protective equipment utilization, limiting workplace exposure, and information sharing.


title: A novel delivery system for supraglottic atomization allows increased lung deposition rates of pulmonary surfactant in newborn piglets

text: BACKGROUND: Earlier attempts to deliver effective lung doses of surfactant by aerosolization were unsuccessful, mostly because of technical shortcomings. We aimed at quantifying the lung deposition of poractant alfa with a new supraglottic delivery system for surfactant atomization in an experimental neonatal model. METHODS: The method involved six sedated 1-day-old piglets lying in the lateral decubitus, spontaneously breathing on nasal-mask continuous positive airway pressure (nCPAP). A pharyngeal cannula housing a multi-channel air-blasting atomization catheter was placed through the mouth with its tip above the glottis entrance. In all, 200 mg kg(−1) of a (99m)Tc-surfactant mixture was atomized through the catheter synchronously with inspiration. Six intubated control piglets received an equal amount of intratracheally instilled (99m)Tc-surfactant mixture. The percentage of the (99m)Tc-surfactant mixture deposited in the lungs was estimated by scintigraphy. RESULTS: Median (range) deposition in the lungs was 40% (24–68%) after atomization and 87% (55–95%) after instillation (p < 0.001). Overall, almost 80% of the deposited surfactant was in the dependent lung. Effective atomization time (atomizer on) was 28 (17–52) min, yielding an output rate of 0.1–0.2 mL min(−1). CONCLUSIONS: Without endotracheal intubation, in spontaneously breathing newborn piglets, this new supraglottic atomizer delivery system attained a median lung deposition of 40% of the nominal dose of surfactant.


The COVID-19 pandemic and its impact on addiction treatment


title: Who shares? Profiling consumers in the sharing economy

text: Abstract Sharing platforms are becoming increasingly common, transforming how organisations and customers interact across diverse categories. While there is clear demand for the sharing economy, less is known about heterogeneity of consumer preferences and the varying demand that exists for sharing experiences across different categories of consumption. In order to help brands better understand who shares, this research takes a step forward in the profiling of users of the sharing economy. Drawing on social psychology, this research investigates how social norms can be employed as a form of social influence and nudge consumers to engage in higher levels of shared consumption. We find three clear segments of sharing consumers, representing 86% of all consumers: the mobility-focused sharer, the diverse-platform sharer, and the power-platform sharer. The last segment (accounting for 14%) comprises consumers who do not engage with sharing platforms. Moreover, social norms influenced the future behaviours of only one segment of consumers: the diverse-platform sharer. We discuss how sharing platform providers can better understand, target, and convert consumers to engage in sharing.


title: Putting Synthesis into Biology: A Viral View of Genetic Engineering through De Novo Gene and Genome Synthesis

text: Summary The rapid improvements in DNA synthesis technology hold the potential to revolutionize biosciences in the near future. Traditional genetic engineering methods are template dependent and make extensive but laborious use of site-directed mutagenesis to explore the impact of small variations on an existing sequence “theme.” De novo gene and genome synthesis frees the investigator from the restrictions of the pre-existing template and allows for the rational design of any conceivable new sequence theme. Viruses, being among the simplest replicating entities, have been at the forefront of the advancing biosciences since the dawn of molecular biology. Viral genomes, especially those of RNA viruses, are relatively short, often less than 10,000 bases long, making them amenable to whole genome synthesis with the currently available technology. For this reason viruses are once again poised to lead the way in the budding field of synthetic biology—for better or worse.


title: A single vertebrate DNA virus protein disarms invertebrate immunity to RNA virus infection

text: Virus-host interactions drive a remarkable diversity of immune responses and countermeasures. We found that two RNA viruses with broad host ranges, vesicular stomatitis virus (VSV) and Sindbis virus (SINV), are completely restricted in their replication after entry into Lepidopteran cells. This restriction is overcome when cells are co-infected with vaccinia virus (VACV), a vertebrate DNA virus. Using RNAi screening, we show that Lepidopteran RNAi, Nuclear Factor-κB, and ubiquitin-proteasome pathways restrict RNA virus infection. Surprisingly, a highly conserved, uncharacterized VACV protein, A51R, can partially overcome this virus restriction. We show that A51R is also critical for VACV replication in vertebrate cells and for pathogenesis in mice. Interestingly, A51R colocalizes with, and stabilizes, host microtubules and also associates with ubiquitin. We show that A51R promotes viral protein stability, possibly by preventing ubiquitin-dependent targeting of viral proteins for destruction. Importantly, our studies reveal exciting new opportunities to study virus-host interactions in experimentally-tractable Lepidopteran systems. DOI: http://dx.doi.org/10.7554/eLife.02910.001


title: Antibody-mediated protection against MERS-CoV in the murine model

text: Abstract Murine antisera with neutralising activity for the coronavirus causative of Middle East respiratory syndrome (MERS) were induced by immunisation of Balb/c mice with the receptor binding domain (RBD) of the viral Spike protein. The murine antisera induced were fully-neutralising in vitro for two separate clinical strains of the MERS coronavirus (MERS-CoV). To test the neutralising capacity of these antisera in vivo, susceptibility to MERS-CoV was induced in naive recipient Balb/c mice by the administration of an adenovirus vector expressing the human DPP4 receptor (Ad5-hDPP4) for MERS-CoV, prior to the passive transfer of the RBD-specific murine antisera to the transduced mice. Subsequent challenge of the recipient transduced mice by the intra-nasal route with a clinical isolate of the MERS-CoV resulted in a significantly reduced viral load in their lungs, compared with transduced mice receiving a negative control antibody. The murine antisera used were derived from mice which had been primed sub-cutaneously with a recombinant fusion of RBD with a human IgG Fc tag (RBD-Fc), adsorbed to calcium phosphate microcrystals and then boosted by the oral route with the same fusion protein in reverse micelles. The data gained indicate that this dual-route vaccination with novel formulations of the RBD-Fc, induced systemic and mucosal anti-viral immunity with demonstrated in vitro and in vivo neutralisation capacity for clinical strains of MERS-CoV.


title: Newly emerging C group enteroviruses may elude diagnosis due to a divergent 5′-UTR

text: Summary Human enterovirus (HEV) 105 was first reported in 2012 in children from Peru and Congo. We report on the identification of a novel HEV-C105 strain in a pediatric patient in Cyprus with an upper respiratory tract infection. Sequence alignment and phylogenetic analysis of 5′-UTRs of all known HEVs revealed that our isolate belongs to a group of recently identified HEV-C viruses exhibiting a 5′-UTR distinct from all other previously known enteroviruses. This has important implications for diagnosis, as this region is the primary target for diagnostic assays. Increased awareness in laboratories may thus increase the rate of detection of enteroviruses belonging to this subspecies, or lead to the discovery of further genotypes.


title: Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene

text: Abstract The highly contagious and deadly porcine epidemic diarrhea virus (PEDV) first appeared in the US in April 2013. Since then the virus has spread rapidly nationwide and to Canada and Mexico causing high mortality among nursing piglets and significant economic losses. Currently there are no efficacious preventive measures or therapeutic tools to control PEDV in the US. The isolation of PEDV in cell culture is the first step toward the development of an attenuated vaccine, to study the biology of PEDV and to develop in vitro PEDV immunoassays, inactivation assays and screen for PEDV antivirals. In this study, nine of 88 US PEDV strains were isolated successfully on Vero cells with supplemental trypsin and subjected to genomic sequence analysis. They differed genetically mainly in the N-terminal S protein region as follows: (1) strains (n =7) similar to the highly virulent US PEDV strains; (2) one similar to the reportedly US S INDEL PEDV strain; and (3) one novel strain most closely related to highly virulent US PEDV strains, but with a large (197aa) deletion in the S protein. Representative strains of these three genetic groups were passaged serially and grew to titers of ∼5–6log10 plaque forming units/mL. To our knowledge, this is the first report of the isolation in cell culture of an S INDEL PEDV strain and a PEDV strain with a large (197aa) deletion in the S protein. We also designed primer sets to detect these genetically diverse US PEDV strains.


title: Prototype of a Smart Microfluidic Platform for the Evaluation of SARS-Cov-2 Pathogenesis, Along with Estimation of the Effectiveness of Potential Drug Candidates and Antigen–Antibody Interactions in Convalescent Plasma Therapy

text: Originating in China during December 2019, the novel corona-virus, SARS-CoV-2, has created mayhem worldwide in a very short time. The outbreak has been so rapid and widespread that the only option to treat the patients was administering drugs already available in the market like chloroquine/hydroxychloroquine (an antimalarial drug) and remedesivir. A large number of patients have been cured but the attribution to survival by these drugs has been controversial. Till date, we do not have any specific drug or vaccine available for COVID-19 and the pandemic seems to be far from over. To handle the current challenges posed by the outbreak effectively, we need to employ innovative interdisciplinary approaches. Organ-on-chip (OOC), particularly lung-on-chip, is one such approach which combines the potential of microfluidics, cell culture and molecular biology into a single miniaturised platform. The device is realized to be capable of simulating in-vivo physiological responses of an organ. In the current study, an OOC, which is a multichannel 3D cell culture microfluidic device, is made via soft lithography technique, using polydimethylsiloxane-polymer and diverse polymeric porous/semipermeable membranes. Several polymer membranes i.e. PDMS, polyvinylidene fluoride (PVDF), nitrocellulose, polyester etc., integrated into the microdevices, were efficiently explored to realize their better cell-adhesion and viability property. We also propose for the application of a simple, smart and cost-effective lung-on-chip platform to study the SARS-CoV-2 pathogenesis in humans, drug toxicity testing and provide insights into antigen–antibody interactions. This platform will enable us to study multiple phenomena at a micro-level generating more reliable data and a better understanding of the underlying mechanisms of SARS-CoV-2 infection and pathogenesis.


title: A Brief Review: The Z-curve Theory and its Application in Genome Analysis

text: In theoretical physics, there exist two basic mathematical approaches, algebraic and geometrical methods, which, in most cases, are complementary. In the area of genome sequence analysis, however, algebraic approaches have been widely used, while geometrical approaches have been less explored for a long time. The Z-curve theory is a geometrical approach to genome analysis. The Z-curve is a three-dimensional curve that represents a given DNA sequence in the sense that each can be uniquely reconstructed given the other. The Z-curve, therefore, contains all the information that the corresponding DNA sequence carries. The analysis of a DNA sequence can then be performed through studying the corresponding Z-curve. The Z-curve method has found applications in a wide range of areas in the past two decades, including the identifications of protein-coding genes, replication origins, horizontally-transferred genomic islands, promoters, translational start sides and isochores, as well as studies on phylogenetics, genome visualization and comparative genomics. Here, we review the progress of Z-curve studies from aspects of both theory and applications in genome analysis.


title: Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods

text: Abstract Virome (viral megagenomics) detection using next generation sequencing has been widely applied in virology, but its methods remain complicated and need optimization. In this study, we detected the viromes of RNA viruses of one mock sample, one pooled duck feces sample and one pooled mink feces sample on the Personal Genome Machine platform using the sequencing libraries prepared by three methods. The sequencing primers were added through random hybridization and ligation to fragmented viral RNA using a RNA-Seq kit in method 1, through random reverse transcription (RT) and polymerase chain reaction (PCR) in method 2 which was developed in our laboratory, and through hybridization and ligation to fragmented amplicons of random RT-PCR using a single primer in method 3. Although the results of these three samples (nine libraries) all showed that more classified viral families and genera were identified using methods 2 and 3 than using method 1, and more classified viral families and genera were identified using method 2 than using method 3, most of the differences were of no statistical significance. Moreover, 11 mammalian viral genera in minks were possibly identified for the first time through this study.


title: The major subunit ClpG of Escherichia coli CS31A fibrillae as an expression vector for different combinations of two TGEV coronavirus epitopes

text: Abstract Previously, two B-cell epitopes from the entero-pathogenic transmissible gastroenteritis virus (TGEV), namely the C epitope (TGEV-C) amino acids (aa) 363–371 and the A epitope (TGEV-A) aa 522–531 of the spike S protein (TGEV-S), have been separately expressed on the CS31A fibrillae at the surface of Escherichia coli following insertion into a same region of ClpG. However, the resulting chimeras induced a marginal TGEV-neutralizing antibody (Ab) response in mice. Here, with the view to improving this response, we introduced TGEV-C alone or in different tandem association with TGEV-A (A::C or C::A) in twelve putatively exposed regions of ClpG. Among the 28 resulting engineered proteins only 15, carrying up to 51 extra aa, had not essentially disturbed the correct CS31A fibrillae formation process. Six partially permissive sites accepting only TGEV-C and three highly permissive sites tolerating A::C or C::A tandem peptide, were identified throughout ClpG. Intact bacteria or extracted CS31A hybrid fibrillae expressing TGEV epitopes at any of the permissive sites, were recognized by Ab directed against the foreign parent protein, providing a direct argument for exposure of the corresponding ClpG region at the cell surface and for antigenicity of the epitopes in the polymeric CS31A fibrillae context. The potential of CS31A fibrillae as carriers of the TGEV peptides indicates that there may be three positions (N terminus, aa 202–204 and 202–218) in ClpG which may turn out to be important fusion sites and therefore be relevant for the eventual design of TGEV vaccines. Unexpectedly, TGEV-A, whatever its position in ClpG, mediated the partial proteolytic degradation of the hybrid proteins, suggesting that it functions as a substrate for a cellular protease, and thereby that its suitability as a vaccine antigen candidate is doubtful.


title: China’s ongoing battle against the coronavirus: a scholar-practitioner's experiences and reflections

text: In this communication essay, I respond to the three questions the journal editor Wei-Ning Xiang asked about my experiences in, and reflections on, the ongoing battle against the coronavirus pandemic in China. At this critical juncture when the people in China are progressing on the battleground, I dedicate the article to all the people fighting against the coronavirus around the world.


title: An explorative study on coping flexibility with behavioral approach system-activating stimuli: A comparison of people with and without bipolar disorder

text: Abstract Life events play a significant role in affecting mood symptoms of people with bipolar disorder (BD). However, we lack empirical data about the associations among disorder, mood state, behavioral activation system (BAS) sensitivity, and psychosocial functioning level. Thus, the present study aimed to identify the role of coping flexibility with BAS activating stimuli in relation to mood states among a sample of individuals with BD (n = 90) and a healthy control group (n = 90). Through multiple regressions, the moderating role of coping flexibility was determined. Findings showed that coping flexibility had an additional value in predicting mood states beyond BAS sensitivity and psychosocial functioning level. Specifically, perceived controllability was considerably important for the BD group, whereas fit index was crucial in the controls. In addition, a moderation analysis showed that perceived controllability alleviated the effects of BD diagnosis, BAS sensitivity, and psychosocial functioning level on mood states. Theoretically, this study helps integrate the concept of coping flexibility into the BAS dysregulation theory as it applies to BD. The practical implication for enhancing mindfulness practice is also discussed.


title: Autophagy in the regulation of pathogen replication and adaptive immunity

text: Autophagy is an evolutionary conserved homeostatic process by which cells deliver cytoplasmic material for degradation into lysosomes. Autophagy may have evolved as a nutrient-providing homeostatic pathway induced upon starvation, but with the acquisition of cargo-receptors autophagy has become an important cellular defence mechanism as well as a generator of antigenic peptides for MHC presentation. We propose that autophagy efficiently protects against microbes encountering the cytosolic environment accidentally, for example upon phagosomal damage, while pathogens routinely accessing the host cytosol have evolved to avoid or even benefit from autophagy.


title: Tropism and pathological findings associated with canine respiratory coronavirus (CRCoV)

text: Abstract Canine infectious respiratory disease (CIRD) occurs frequently in densely housed dog populations. One of the common pathogens involved is canine respiratory coronavirus (CRCoV), however little is known regarding its pathogenesis and the role it plays in the development of CIRD. The pathogenesis of five geographically unrelated canine respiratory coronavirus (CRCoV) isolates was investigated. Following experimental infection in dogs, all five CRCoV isolates gave rise to clinical signs of respiratory disease consistent with that observed during natural infection. The presence of CRCoV was associated with marked histopathological changes in the nares and trachea, with loss and damage to tracheal cilia, accompanied by inflammation. Viral shedding was readily detected from the oropharynx up to 10 days post infection, but there was little or no evidence of rectal shedding. The successful re-isolation of CRCoV from a wide range of respiratory and mucosal associated lymphoid tissues, and lung lavage fluids demonstrates a clear tropism of CRCoV for respiratory tissues and fulfils the final requirement for Koch's postulates. By study day 14 dogs had seroconverted to CRCoV and the antibodies raised were neutralising against both homologous and heterologous strains of CRCoV in vitro, thus demonstrating antigenic homogeneity among CRCoV strains from the two continents. Defining the role that CRCoV and other agents play in CIRD is a considerable, but important, challenge if the disease is to be managed, treated and prevented more successfully. Here we have successfully developed a model for studying the pathogenicity and the role of CRCoV in CIRD.


title: Features and drivers for energy-related carbon emissions in mega city: The case of Guangzhou, China based on an extended LMDI model

text: Based on the apparent energy consumption data, a systematic and comprehensive city-level total carbon accounting approach was established and applied in Guangzhou, China. A newly extended LMDI method based on the Kaya identity was adopted to examine the main drivers for the carbon emissions increments both at the industrial sector and the residential sector. Research results are listed as follow: (1) Carbon emissions embodied in the imported electricity played a significant important role in emissions mitigation in Guangzhou. (2) The influences and impacts of various driving factors on industrial and residential carbon emissions are different in the three different development periods, namely, the 10(th) five-year plan period (2003–2005), the 11(th) five-year plan period (2005–2010), and the 12(th) five-year plan period (2010–2013). The main reasons underlying these influencing mechanisms were different policy measures announced by the central and local government during the different five-year plan periods. (3) The affluence effect (g-effect) was the dominant positive effect in driving emissions increase, while the energy intensity effect of production (e-effect-Production), the economic structure effect (s-effect) and the carbon intensity effect of production (f-effect-Production) were the main contributing factors suppressing emissions growth at the industrial sector. (4) The affluence effect of urban (g-effect-AUI) was the most dominant positive driving factor on emissions increment, while the energy intensity effect of urban (e-effect-Urban) played the most important role in curbing emissions growth at the residential sector.


title: Fever with Rash in COVID‐19: Viral Exanthema or Secondary Lesions?

text: COVID‐19 originated in Wuhan, China and has developed into a pandemic since late 2019. The virus possesses powerful pathogenicity as well as transmissibility. Many open questions remain, including the description of potential involvement of other organs than the respiratory tract. Most patients have mild influenza‐like symptoms. A minority, especially patients with chronic lung disease, develops lethal disease including severe pneumonia, pulmonary edema, rapidly developing acute respiratory distress syndrome (ARDS), multiple organ failure and septic shock.


title: Diagnostic Testing for SARS-Coronavirus-2 in the Nursing Facility: Recommendations of a Delphi Panel of Long-Term Care Clinicians

text: With the COVID-19 pandemic progressing, guidance on strategies to mitigate its devastating effects in nursing facilities (NFs) is critical to preventing additional tragic outcomes. Asymptomatic spread of COVID-19 from nursing facility staff and residents is a major accelerator of infection. Facility-wide point-prevalence testing is an emerging strategy in disease mitigation. Because time is not available to await the results of randomized controlled trials before implementing strategies in this high-risk setting, an expert Delphi panel composed of experienced long-term care medicine professionals has now met to provide testing guidance for SARS-Coronavirus-2 to NFs. After many email and telephone discussions, the panel responded to a questionnaire that included six different scenarios, based on varying availability of Polymerase Chain Reaction (RT-PCR) testing and personal protective equipment (PPE). The panel endorsed facility-wide testing of staff and residents without dissent when diagnostic RT-PCR was available. While the panel recognized the limitations of RT-PCR testing, it strongly recommended this testing for both staff and residents in NFs that were either COVID-19 naive or had limited outbreaks. There was also consensus on testing residents with atypical symptoms in a scenario of limited testing capability. The panel favored testing every 1 to 2 weeks if testing was readily available, reducing the frequency to every month as community prevalence declined or as the collection of additional data further informed clinical critical thinking and decision-making. The panel recognized that frequent testing would have consequences in terms of potential staff shortages due to quarantine after positive tests and increased PPE use. However, the panel felt that not testing would allow new clusters of infection to form. The resulting high mortality rate would outweigh the potential negative consequences of testing. The panel also recognized the pandemic as a rapidly evolving crisis, and that new science and increasing experience might require an updating of its recommendations. The panel hopes that its recommendations will be of value to the long-term care industry and to policy makers as we work together to manage through this challenging and stressful time.


title: Telestroke in the Time of COVID-19: The Mayo Clinic Experience

text: Abstract On March 11, 2020, the World Health Organization declared the coronavirus disease 2019 (COVID-19) a pandemic, and in the weeks following, public health organizations, medical associations, and governing bodies throughout the world recommended limiting contact with others to “flatten the curve” of COVID-19. Although both ischemic and hemorrhagic strokes have been reported with COVID-19, there has been anecdotal suggestion of an overall decrease in stroke admissions. To date, the effects of any pandemic on telestroke service lines have not been described. The purpose of this cross-sectional analysis of telestroke activations in the 30 days before and after the declaration of the COVID-19 pandemic is to describe the difference in case volumes of telestroke activations, the characteristics of patients, and treatment recommendations between the two time frames. We found a 50% reduction in total telestroke activations between the pre- and post- groups, 142 and 71, respectively. There were no statistically significant differences in age, sex, diagnosis, or regional variations in activation volumes. The percentage of patients in whom we recommended acute stroke treatment with intravenous alteplase, mechanical thrombectomy, or both, decreased from 44% to 33%. The reasons for the significant decrease in telestroke activations and acute stroke treatment recommendations are likely multifactorial, regardless, underscoring the importance of continued public health measures to encourage patients and families to seek emergent medical care at the time of symptom onset.


title: Molecular Alterations Prompted by SARS-CoV-2 Infection: Induction of Hyaluronan, Glycosaminoglycan and Mucopolysaccharide Metabolism

text: Abstract Background The SARS-CoV-2 is the etiological agent causing COVID-19 which has infected more than 2 million people with more than 200000 deaths since its emergence in December 2019. In the majority of cases patients are either asymptomatic or show mild to moderate symptoms and signs of a common cold. A subset of patients, however, develop a severe atypical pneumonia, with the characteristic ground-glass appearance on chest x-ray and computerized tomography, which evolves into an acute respiratory distress syndrome, that requires mechanical ventilation and eventually results in multiple organ failure and death. The Molecular pathogenesis of COVID-19 is still unknown. Aim of the study In the present work we performed a stringent metanalysis from the publicly available RNAseq data from bronchoalveolar cells and peripheral blood mononuclear cells to elucidate molecular alterations and cellular deconvolution to identify immune cell profiles. Results Alterations in genes involved in hyaluronan, glycosaminoglycan and mucopolysaccharides metabolism were over-represented in bronchoalveolar cells infected by SARS-CoV-2, as well as potential lung infiltration with neutrophils, NK cells, T CD4+ cell and macrophages. The blood mononuclear cells presented a proliferative state. Dramatic reduction of neutrophils, NK and T lymphocytes, whereas an exacerbated increase in monocytes. Conclusions In summary our results revealed molecular pathogenesis of the SARS-CoV-2 infection to bronchoalveolar cells inducing the hyaluronan and glycosaminoglycan metabolism that could shape partially the components of the ground-glass opacities observed in CT. And the potential immune response profile in COVID-19.


title: Breaking the Enigma Code of Angiotensin II Type 2 Receptor Signaling

text: In this issue of Structure, Asada et al. (2019) present angiotensin receptor AT2R structure in complex with its main endogenous agonist, AngII peptide. Complementing the previous structural studies, the new complex structure sheds light on the AT2R activation mechanism and opens new avenues for drug discovery targeting this enigmatic receptor.


title: Murine coronaviruses: the histopathology of disease induced by intranasal inoculation

text: Mice inoculated intranasally with murine coronaviruses (mouse hepatitus viruses) were killed daily for seven days. Lung and liver sections stained by the immunopcroxidasc technique indicated that with three of the four strains examined viral localisation and replication in the lung preceded that found in (he liver. Thus, infection by the respiratory route may be of importance in the Iransmission of these viruses.


title: Heparanase, cell signaling, and viral infections

text: Heparanase (HPSE) is a multifunctional protein endowed with many non-enzymatic functions and a unique enzymatic activity as an endo-β-d-glucuronidase. The latter allows it to serve as a key modulator of extracellular matrix (ECM) via a well-regulated cleavage of heparan sulfate side chains of proteoglycans at cell surfaces. The cleavage and associated changes at the ECM cause release of multiple signaling molecules with important cellular and pathological functions. New and emerging data suggest that both enzymatic as well as non-enzymatic functions of HPSE are important for health and illnesses including viral infections and virally induced cancers. This review summarizes recent findings on the roles of HPSE in activation, inhibition, or bioavailability of key signaling molecules such as AKT, VEGF, MAPK–ERK, and EGFR, which are known regulators of common viral infections in immune and non-immune cell types. Altogether, our review provides a unique overview of HPSE in cell-survival signaling pathways and how they relate to viral infections.


Crops from U.S. food supply chains will never look nor taste the same again


title: Frontline nurses’ burnout, anxiety, depression, and fear statuses and their associated factors during the COVID-19 outbreak in Wuhan, China: A large-scale cross-sectional study

text: BACKGROUND: During the Coronavirus Disease 2019 (COVID-19) pandemic, frontline nurses face enormous mental health challenges. Epidemiological data on the mental health statuses of frontline nurses are still limited. The aim of this study was to examine mental health (burnout, anxiety, depression, and fear) and their associated factors among frontline nurses who were caring for COVID-19 patients in Wuhan, China. METHODS: A large-scale cross-sectional, descriptive, correlational study design was used. A total of 2,014 eligible frontline nurses from two hospitals in Wuhan, China, participated in the study. Besides sociodemographic and background data, a set of valid and reliable instruments were used to measure outcomes of burnout, anxiety, depression, fear, skin lesion, self-efficacy, resilience, and social support via the online survey in February 2020. FINDINGS: On average, the participants had a moderate level of burnout and a high level of fear. About half of the nurses reported moderate and high work burnout, as shown in emotional exhaustion (n = 1,218, 60.5%), depersonalization (n = 853, 42.3%), and personal accomplishment (n = 1,219, 60.6%). The findings showed that 288 (14.3%), 217 (10.7%), and 1,837 (91.2%) nurses reported moderate and high levels of anxiety, depression, and fear, respectively. The majority of the nurses (n = 1,910, 94.8%) had one or more skin lesions, and 1,950 (96.8%) nurses expressed their frontline work willingness. Mental health outcomes were statistically positively correlated with skin lesion and negatively correlated with self-efficacy, resilience, social support, and frontline work willingness. INTERPRETATION: The frontline nurses experienced a variety of mental health challenges, especially burnout and fear, which warrant attention and support from policymakers. Future interventions at the national and organisational levels are needed to improve mental health during this pandemic by preventing and managing skin lesions, building self-efficacy and resilience, providing sufficient social support, and ensuring frontline work willingness.


title: VII Digestive System 1

text: Publisher Summary This chapter deals with the digestive system. The major and minor salivary glands and their secretions also represent and integral part of the protective mechanism of the oral cavity, and derangement of saliva production may lead to loss of integrity of the oral mucosa. Drug-induced abnormalities of taste sensation are also well-described phenomena occurring in man although human studies are necessary for the detection of these effects. Inflammation of the oral cavity may involve the buccal mucosa, the gingiva (gingivitis), the tongue (glossitis), and the peridontal tissues (peridontitis). Therapeutic agents can induce inflammatory lesions in the tongue. Moreover, a protective layer of mucus, a visco-elastic material containing high molecular weight glycoproteins produced by the major and minor salivary glands, covers the stratified squamous mucosa of the oral cavity. Salivary secretions also possess digestive enzyme activity although in herbivores and carnivores, it is usually low in contrast to high digestive enzyme activity in omnivorous species.


title: Genome Signatures, Self-Organizing Maps and Higher Order Phylogenies: A Parametric Analysis

text: Genome signatures are data vectors derived from the compositional statistics of DNA. The self-organizing map (SOM) is a neural network method for the conceptualisation of relationships within complex data, such as genome signatures. The various parameters of the SOM training phase are investigated for their effect on the accuracy of the resulting output map. It is concluded that larger SOMs, as well as taking longer to train, are less sensitive in phylogenetic classification of unknown DNA sequences. However, where a classification can be made, a larger SOM is more accurate. Increasing the number of iterations in the training phase of the SOM only slightly increases accuracy, without improving sensitivity. The optimal length of the DNA sequence k-mer from which the genome signature should be derived is 4 or 5, but shorter values are almost as effective. In general, these results indicate that small, rapidly trained SOMs are generally as good as larger, longer trained ones for the analysis of genome signatures. These results may also be more generally applicable to the use of SOMs for other complex data sets, such as microarray data.


title: Development of a rapid test kit for SARS-CoV-2: an example of product design

text: We present an example of applying ‘need-driven’ product design principle to the development of a rapid test kit to detect SARS-COV-2 (COVID-19). The tests are intended for use in the field and, longer term, for home use. They detect whether a subject is currently infected with the virus and is infectious. The urgent need for large numbers of tests in field setting imposes constraints such as short test time and lack of access to specialist equipment, laboratories and skilled technicians to perform the test and interpret results. To meet these needs, an antigen test based on RT-LAMP with colorimetric readout was chosen. Direct use of swab sample with no RNA extraction was explored. After extensive experimental study (reported elsewhere), a rapid test kit has been fabricated to satisfy all design criteria.


title: A possible role for B cells in COVID-19?: Lesson from patients with Agammaglobulinemia

text: Summary COVID-19 had a mild clinical course in patients with Agammaglobulinemia lacking B lymphocytes, whereas it developed aggressively in Common Variable Immune Deficiency. Our data offer mechanisms for possible therapeutic targets.


docid: wllkumda

title: MHV-A59 Enters Polarized Murine Epithelial Cells through the Apical Surface but Is Released Basolaterally

text: Abstract Coronaviruses have a marked tropism for epithelial cells. Entry and release of the porcine transmissible gastroenteritis virus (TGEV) is restricted to apical surfaces of polarized epithelial cells, as we have recently shown (J. W. A. Rossen, C. P. J. Bekker, W. F. Voorhout, G. J. A. M. Strous, A. van der Ende, and P. J. M. Rottier, 1994, J. Virol. 68, 7966-7973). In this paper we analyze the interactions of mouse hepatitis coronavirus A59 (MHV-A59) with polarized murine kidney cells (mTAL) grown on permeable supports. After inoculation from the apical or basolateral side, virus entry was found to take place only through the apical membrane. The virus utilized a protein of the carcinoembryonic antigen family as its receptor. In contrast to TGEV, MHV-A59 was released preferentially from the basolateral plasma membrane domain, as evidenced by the accumulation of viral proteins and infectivity in the basolateral culture fluid as well as by electron microscopical observations in the mouse, MHV initially replicates in the nasal epithelium before being disseminated throughout the body; the basolateral release of MHV from epithelial cells into the animal's circulation may be the first step in the establishment of a systemic infection.


Virtual clinics: Need of the hour, a way forward in the future. Adapting practice during a healthcare crisis.


title: SARS-CoV-2 screening test for Japanese returnees from Wuhan, China, January 2020

text: BACKGROUND: Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) was found to be the causative microorganism of coronavirus disease 2019 (COVID-19), which started to spread in Wuhan, China. This study was to evaluate the effectiveness of questionnaire, symptoms-based screening, and PCR screening of returnees from COVID-19 endemic areas on a chartered flight, to examine the proportion of infected persons and the proportion of asymptomatic persons among infected persons who returned from Wuhan. METHODS: A retrospective cohort study was done in seven tertiary medical institutions in Japan. A total of 566 Japanese who returned from Wuhan participated in the study. RESULTS: Overall, 11 of the 566 passengers had a positive SARS-CoV-2 PCR result for pharyngeal swabs and six were asymptomatic. Only fever differed between SARS-CoV-2-positive and -negative individuals (p < 0.043). Six of the eleven PCR-positive individuals were asymptomatic and four remained positive on day 10 and One asymptomatic person tested positive up to day 27. Two of the eleven were negative on the first PCR test and positive on the second. CONCLUSIONS: Our results will be important insights on screening returnees from locked down cities, as well as important data on the proportion of asymptomatic individuals infected with SARS-CoV-2. A 13-day observation period and a second round of PCR may be effective to screen patients, including asymptomatic infections.


title: Knowledge, attitudes and practices towards pandemic influenza among cases, close contacts, and healthcare workers in tropical Singapore: a cross-sectional survey

text: BACKGROUND: Effective influenza pandemic management requires understanding of the factors influencing behavioral changes. We aim to determine the differences in knowledge, attitudes and practices in various different cohorts and explore the pertinent factors that influenced behavior in tropical Singapore. METHODS: We performed a cross-sectional knowledge, attitudes and practices survey in the Singapore military from mid-August to early-October 2009, among 3054 personnel in four exposure groups - laboratory-confirmed H1N1-2009 cases, close contacts of cases, healthcare workers, and general personnel. RESULTS: 1063 (34.8%) participants responded. The mean age was 21.4 (SE 0.2) years old. Close contacts had the highest knowledge score (71.7%, p = 0.004) while cases had the highest practice scores (58.8%, p < 0.001). There was a strong correlation between knowledge and practice scores (r = 0.27, p < 0.01) and knowledge and attitudes scores (r = 0.21, p < 0.01). The significant predictors of higher practice scores were higher knowledge scores (p < 0.001), Malay ethnicity (p < 0.001), exposure group (p < 0.05) and lower education level (p < 0.05). The significant predictors for higher attitudes scores were Malay ethnicity (p = 0.014) and higher knowledge scores (p < 0.001). The significant predictor for higher knowledge score was being a contact (p = 0.007). CONCLUSION: Knowledge is a significant influence on attitudes and practices in a pandemic, and personal experience influences practice behaviors. Efforts should be targeted at educating the general population to improve practices in the current pandemic, as well as for future epidemics.


title: Prophylactic efficacy of orally administered Bacillus poly-γ-glutamic acid, a non-LPS TLR4 ligand, against norovirus infection in mice

text: Poly-gamma-glutamic acid (γ-PGA), an extracellular biopolymer produced by Bacillus sp., is a non-canonical toll-like receptor 4 (TLR4) agonist. Here we show its antiviral efficacy against noroviruses. γ-PGA with a molecular mass of 2,000-kDa limited murine norovirus (MNV) replication in the macrophage cell line RAW264.7 by inducing interferon (IFN)-β and conferred resistance to viral infection-induced cell death. Additionally, γ-PGA interfered with viral entry into cells. The potent antiviral state mounted by γ-PGA was not attributed to the upregulation of TLR4 or TLR3, a sensor known to recognize norovirus RNA. γ-PGA sensing by TLR4 required the two TLR4-associated accessory factors MD2 and CD14. In ex vivo cultures of mouse ileum, γ-PGA selectively increased the expression of IFN-β in villi. In contrast, IFN-β induction was negligible in the ileal Peyer’s patches (PPs) where its expression was primarily induced by the replication of MNV. Oral administration of γ-PGA, which increased serum IFN-β levels without inducing proinflammatory cytokines, reduced MNV loads in the ileum with PPs and mesenteric lymph nodes in mice. Our results disclose a γ-PGA-mediated non-conventional TLR4 signaling in the ileum, highlighting the potential use of γ-PGA as a prophylactic antiviral agent against noroviruses.


title: Severe cytomegalovirus (CMV) community-acquired pneumonia (CAP) in a nonimmunocompromised host

text: Background Community-acquired pneumonia (CAP) in an immunocompetent host may be severe because of a variety or combination of host and microbial factors. In patients with severe cardiopulmonary dysfunction, even relatively avirulent pathogens, that is, Mycoplasma pneumoniae, Moraxella catarrhalis, may compromise borderline cardiac/heart function and present clinically as severe CAP. Alternately, patients with Streptococcus pneumoniae and impaired humoral immunity/splenic dysfunction may present as severe CAP. With the exception of Legionnaire's disease, influenza, and adenovirus, pathogen virulence is not a key determinant of CAP severity. Methods Diagnostically, patients with severe CAP may be approached based on the pattern of infiltrates on chest x-ray together with the severity of hypoxemia (ie, increased A-a gradient: >35). Results We present the case of an immunocompetent adult who presented with severe CAP during peak influenza season. Direct fluorescent antibody testing of his respiratory secretions was negative for influenza, adenovirus, and other respiratory viruses. Diagnostic bronchoscopy was negative for bacterial and fungal pathogens. The only clues to the cause of his severe CAP was the presence of relative lymphopenia, atypical lymphocytosis and elevated serum transaminases. After influenza and adenovirus were ruled out, cytomegalovirus (CMV) CAP was considered. The diagnosis of CMV CAP was made serologically by demonstrating highly elevated IgM CMV titers. Because the diagnosis was made during the patient's recovery late in hospitalization, he did not receive CMV antiviral therapy. Conclusion This case should remind clinicians that influenza and adenovirus are diagnostic considerations in patients presenting with severe CAP with diffuse bilateral interstitial infiltrates accompanied by severe hypoxemia in normal hosts. If influenza and adenovirus are ruled out, then CMV CAP, although rare, should be considered, particularly when viral CAP is accompanied by relative lymphopenia, atypical lymphocytosis and increased serum transaminases.


title: Novel One-Step Single-Tube Nested Quantitative Real-Time PCR Assay for Highly Sensitive Detection of SARS-CoV-2

text: [Image: see text] Coronavirus disease 2019 (COVID-19) has become a public health emergency. The reverse transcriptase real-time quantitative PCR (qRT-PCR) test is currently considered as the gold standard in the laboratory for the etiological detection of COVID-19. However, qRT-PCR results could be false-negative due to the inadequate sensitivity of qRT-PCR. In this study, we have developed and evaluated a novel one-step single-tube nested quantitative real-time PCR (OSN-qRT-PCR) assay for the highly sensitive detection of SARS-CoV-2 targeting the ORF1ab and N genes. The sensitivity of the OSN-qRT-PCR assay was 1 copy/reaction and 10-fold higher than that of the commercial qRT-PCR kit (10 copies/reaction). The clinical performance of the OSN-qRT-PCR assay was evaluated using 181 clinical samples. Among them, 14 qRT-PCR-negative samples (7 had no repetitive results and 7 had no cycle threshold (CT) values) were detected by OSN-qRT-PCR. Moreover, the 7 qRT-PCR-positives in the qRT-PCR gray zone (CT values of ORF1ab ranged from 37.48 to 39.07, and CT values of N ranged from 37.34 to 38.75) were out of the gray zone and thus were deemed to be positive by OSN-qRT-PCR, indicating that the positivity of these samples is confirmative. Compared to the qRT-PCR kit, the OSN-qRT-PCR assay revealed higher sensitivity and specificity, showing better suitability to clinical applications for the detection of SARS-CoV-2 in patients with low viral load.


title: Review article: prevention, diagnosis and management of COVID‐19 in the IBD patient

text: BACKGROUND: The current COVID‐19 pandemic, caused by SARS‐CoV‐2, has emerged as a public health emergency. All nations are seriously challenged as the virus spreads rapidly across the globe with no regard for borders. The primary management of IBD involves treating uncontrolled inflammation with most patients requiring immune‐based therapies. However, these therapies may weaken the immune system and potentially place IBD patients at increased risk of infections and infectious complications including those from COVID‐19. AIM: To summarise the scale of the COVID‐19 pandemic, review unique concerns regarding IBD management and infection risk during the pandemic and assess COVID‐19 management options and drug interactions in the IBD population. METHODS: A literature review on IBD, SARS‐CoV‐2 and COVID‐19 was undertaken and relevant literature was summarised and critically examined. RESULTS: IBD patients do not appear to be more susceptible to SARS‐CoV‐2 infection and there is no evidence of an association between IBD therapies and increased risk of COVID‐19. IBD medication adherence should be encouraged to prevent disease flare but where possible high‐dose systemic corticosteroids should be avoided. Patients should exercise social distancing, optimise co‐morbidities and be up to date with influenza and pneumococcal vaccines. If a patient develops COVID‐19, immune suppressing medications should be withheld until infection resolution and if trial medications for COVID‐19 are being considered, potential drug interactions should be checked. CONCLUSION: IBD patient management presents a challenge in the current COVID‐19 pandemic. The primary focus should remain on keeping bowel inflammation controlled and encouraging medication adherence.


The Solitary Confinement of Incarcerated American Youth During COVID-19


title: 9-[2-(R)-(Phosphonomethoxy)propyl]-2,6-diaminopurine (R)-PMPDAP and its prodrugs: Optimized preparation, including identification of by-products formed, and antiviral evaluation in vitro

text: Abstract New large-scale synthetic approach to antiretroviral agent 9-[2-(R)-(phosphonomethoxy)propyl]-2,6-diaminopurine, (R)-PMPDAP, was developed. Reaction of (R)-propanediol carbonate with 2,6-diaminopurine afforded exclusively (R)-9-(2-hydroxypropyl)-2,6-diaminopurine which was subsequently used for introduction of a phosphonomethyl residue using TsOCH2P(O)(OiPr)2 or BrCH2P(O)(OiPr)2 followed by deprotection of ester groups. All minor ingredients and by-products formed during the process were identified and further studied. The final product was obtained in high yield and its high enantiomeric purity (>99%) was confirmed by chiral capillary electrophoretic analysis using β-cyclodextrin as a chiral selector. Antiretroviral activity data of (R)-PMPDAP and its diverse prodrugs against HIV and FIV were investigated. Akin to (R)-PMPDAP, both prodrugs inhibit FIV replication in a selective manner. Compared to the parent molecule, the amidate prodrug was 10-fold less active against FIV in cell culture, whereas the alkoxyalkyl ester prodrug was 200-fold more potent in inhibiting FIV replication in vitro.


title: Experiences after Twenty Months with Pandemic Influenza A (H1N1) 2009 Infection in the Naïve Norwegian Pig Population

text: Pandemic (H1N1) 2009 influenza A virus was detected in Norwegian pigs in October 2009. Until then, Norway was regarded free of swine influenza. Intensified screening revealed 91 positive herds within three months. The virus was rapidly transmitted to the susceptible population, including closed breeding herds with high biosecurity. Humans were important for the introduction as well as spread of the virus to pigs. Mild or no clinical signs were observed in infected pigs. Surveillance of SIV in 2010 revealed that 41% of all the Norwegian pig herds had antibodies to pandemic (H1N1) 2009 virus. Furthermore, this surveillance indicated that pigs born in positive herds after the active phase did not seroconvert, suggesting no ongoing infection in the herds. However, results from surveillance in 2011 show a continuing spread of the infection in many herds, either caused by new introduction or by virus circulation since 2009.


title: Performance Evaluation of the PowerChek MERS (upE & ORF1a) Real-Time PCR Kit for the Detection of Middle East Respiratory Syndrome Coronavirus RNA

text: BACKGROUND: Molecular detection of Middle East respiratory syndrome coronavirus (MERS-CoV) using real-time reverse transcription (rRT)-PCR assays is the method of choice for diagnosis of MERS. We evaluated the performance of the PowerChek MERS (upE & ORF1a) real-time PCR Kit (PowerChek MERS assay; Kogene Biotech, Korea) a one-step rRT-PCR assay for the qualitative detection of MERS-CoV. METHODS: We evaluated PowerChek MERS assay performance in comparison with nested RT-PCR and sequencing of the RNA-dependent RNA polymerase (RdRp) and N genes. To evaluate diagnostic sensitivity and specificity, 100 clinical specimens (50 positive and 50 negative for MERS-CoV) were simultaneously tested by using the PowerChek MERS and sequencing assays. Assay performance, including limit of detection and precision, was evaluated in vitro by using MERS-CoV RNA transcripts. Analytical specificity was evaluated with a diverse collection of 16 respiratory virus–positive clinical specimens and 14 respiratory bacterial isolates. RESULTS: The 95% limits of detection of the PowerChek MERS assay for the upE and the open rading frame (ORF)1a were 16.2 copies/µL and 8.2 copies/µL, respectively. No cross-reactivity was observed. The diagnostic sensitivity and specificity of the PowerChek MERS assay were both 100% (95% confidence interval, 91.1–100%). CONCLUSIONS: The PowerChek MERS assay is a straightforward and accurate assay for detecting MERS-CoV RNA. The assay will be a useful tool for the rapid diagnosis of MERS and could prove especially important for MERS outbreak control.


title: Clinical Features and Outcomes of 105 Hospitalized patients with COVID-19 in Seattle, Washington

text: BACKGROUND: Washington State served as the initial epicenter of the SARS-CoV-2 pandemic in the United States. An understanding of the risk factors and clinical outcomes of hospitalized patients with COVID-19 may provide guidance for management. METHODS: All laboratory-confirmed COVID-19 cases in adults admitted to an academic medical center in Seattle, WA between March 2 and March 26, 2020 were included. We evaluated individuals with and without severe disease, defined as admission to the intensive care unit or death. RESULTS: One-hundred-five COVID-19 patients were hospitalized. Thirty-five percent were admitted from a senior home or skilled nursing facility. The median age was 69 years and half were women. Three or more comorbidities were present in 55% of patients, with hypertension (59%), obesity (47%), cardiovascular disease (38%) and diabetes (33%) being the most prevalent. Most (63%) had symptoms for 5 days or longer prior to admission. Only 39% had fever in the first 24 hours, whereas 41% had hypoxia at admission. Seventy-three percent of patients had lymphopenia. Of 50 samples available for additional testing, no viral coinfections were identified. Severe disease occurred in 49%. Eighteen percent of patients were placed on mechanical ventilation and the overall mortality rate was 33%. CONCLUSIONS: During the early days of the COVID-19 epidemic in Washington State, the disease had its greatest impact on elderly patients with medical comorbidities. We observed high rates of severe disease and mortality in our hospitalized patients.


title: Molecular detection and sequence characterization of diverse rhabdoviruses in bats, China

text: Abstract The Rhabdoviridae is among the most diverse families of RNA viruses and currently classified into 18 genera with some rhabdoviruses lethal to humans and other animals. Herein, we describe genetic characterization of three novel rhabdoviruses from bats in China. Of these, two viruses (Jinghong bat virus and Benxi bat virus) found in Rhinolophus bats showed a phylogenetic relationship with vesiculoviruses, and sequence analyses indicate that they represent two new species within the genus Vesiculovirus. The remaining Yangjiang bat virus found in Hipposideros larvatus bats were only distantly related to currently known rhabdoviruses.


docid: ftbjsoup

title: Attenuated live vaccine usage affects accurate measures of virus diversity and mutation rates in avian coronavirus infectious bronchitis virus

text: Abstract The full-length genomes of 11 infectious bronchitis virus (IBV) field isolates from three different types of the virus; Massachusetts (Mass), Connecticut (Conn) and California (CAL) isolated over a 41, 25 and 8 year period respectively, were sequenced and analyzed to determine the mutation rates and level of polymorphisms across the genome. Positive selection was not detected and mutation rates ranged from 10−4 to 10−6 substitutions/site/year for Mass and Conn IBV types where attenuated live vaccines are routinely used to control the disease. In contrast, for CAL type viruses, for which no vaccine exists, positive selection was detected and mutation rates were 10 fold higher ranging from 10−2 to 10−3 substitutions/site/year. Lower levels of genetic diversity among the Mass and Conn viruses as well as sequence similarities with vaccine virus genomes suggest that the origin of the Mass and all but one of the Conn viruses was likely vaccine virus that had been circulating in the field for an unknown but apparently short period of time. The genetic data also identified a recombinant IBV isolate with 7 breakpoints distributed across the entire genome suggesting that viruses within the same serotype can have a high degree of genetic variability outside of the spike gene. These data are important because inaccurate measures of genetic diversity and mutation rates could lead to underestimates of the ability of IBV to change and potentially emerge to cause disease.


title: Real-Time Fluorescence Loop Mediated Isothermal Amplification for the Diagnosis of Malaria

text: BACKGROUND: Molecular diagnostic methods can complement existing tools to improve the diagnosis of malaria. However, they require good laboratory infrastructure thereby restricting their use to reference laboratories and research studies. Therefore, adopting molecular tools for routine use in malaria endemic countries will require simpler molecular platforms. The recently developed loop-mediated isothermal amplification (LAMP) method is relatively simple and can be improved for better use in endemic countries. In this study, we attempted to improve this method for malaria diagnosis by using a simple and portable device capable of performing both the amplification and detection (by fluorescence) of LAMP in one platform. We refer to this as the RealAmp method. METHODOLOGY AND SIGNIFICANT FINDINGS: Published genus-specific primers were used to test the utility of this method. DNA derived from different species of malaria parasites was used for the initial characterization. Clinical samples of P. falciparum were used to determine the sensitivity and specificity of this system compared to microscopy and a nested PCR method. Additionally, directly boiled parasite preparations were compared with a conventional DNA isolation method. The RealAmp method was found to be simple and allowed real-time detection of DNA amplification. The time to amplification varied but was generally less than 60 minutes. All human-infecting Plasmodium species were detected. The sensitivity and specificity of RealAmp in detecting P. falciparum was 96.7% and 91.7% respectively, compared to microscopy and 98.9% and 100% respectively, compared to a standard nested PCR method. In addition, this method consistently detected P. falciparum from directly boiled blood samples. CONCLUSION: This RealAmp method has great potential as a field usable molecular tool for diagnosis of malaria. This tool can provide an alternative to conventional PCR based diagnostic methods for field use in clinical and operational programs.


title: Carving out a place for internal medicine during COVID‐19 epidemic in Italy

text: Internal medicine has been immediately involved in the coronavirus disease 2019 (COVID-19) epidemic in Italy, which started in late February 2020. The first few COVID-19 cases were suspected and diagnosed in internal medicine wards, including, among others, a young adult male from Codogno (referred to as "patient 1"), who was later transferred to the Intensive Care Unit of our hospital.


Post-surgical skin ulcers due to cytomegalovirus vasculopathy in a renal transplant recipient


title: Chapter Eight Prothymosin Alpha and Immune Responses Are We Close to Potential Clinical Applications?

text: Abstract The thymus gland produces soluble molecules, which mediate significant immune functions. The first biologically active thymic extract was thymosin fraction V, the fractionation of which led to the isolation of a series of immunoactive polypeptides, including prothymosin alpha (proTα). ProTα displays a dual role, intracellularly as a survival and proliferation mediator and extracellularly as a biological response modifier. Accordingly, inside the cell, proTα is implicated in crucial intracellular circuits and may serve as a surrogate tumor biomarker, but when found outside the cell, it could be used as a therapeutic agent for treating immune system deficiencies. In fact, proTα possesses pleiotropic adjuvant activity and a series of immunomodulatory effects (eg, anticancer, antiviral, neuroprotective, cardioprotective). Moreover, several reports suggest that the variable activity of proTα might be exerted through different parts of the molecule. We first reported that the main immunoactive region of proTα is the carboxy-terminal decapeptide proTα(100–109). In conjunction with data from others, we also revealed that proTα and proTα(100–109) signal through Toll-like receptor 4. Although their precise molecular mechanism of action is yet not fully elucidated, proTα and proTα(100–109) are viewed as candidate adjuvants for cancer immunotherapy. Here, we present a historical overview on the discovery and isolation of thymosins with emphasis on proTα and data on some immune-related new activities of the polypeptide and smaller immunostimulatory peptides thereof. Finally, we propose a compiled scenario on proTα’s mode of action, which could eventually contribute to its clinical application.


Virus ecology: a gap between detection and prediction


docid: prizmksg

title: New paradigm for protection:: The emergency ambulance services in the time of severe acute respiratory syndrome

text: Severe acute respiratory syndrome (SARS) is a newly emerging and highly infectious form of atypical pneumonia with a high rate of transmission, especially among health care workers. With SARS, certain policies had to be implemented rapidly by the emergency ambulance services and the Ministry of Health to support and protect all personnel adequately. The authors discuss the changes in policies and personnel behavior, the training and education that had to be disseminated widely, and certain alternatives in policies such as transportation. The authors hope to share their experience in the implementation of these strategies by the Singapore Civil Defence Force and stress the importance of the psychological preparedness of the paramedics and prehospital care providers worldwide in this era of SARS.


title: Molecular Detection of Respiratory Viruses

text: Over the past several years a wide variety of molecular assays for the detection of respiratory viruses has reached the market. The tests described herein range from kits containing primers and probes detecting specific groups of viruses, to self-contained systems requiring specialized instruments that extract nucleic acids and perform the polymerase chain reaction with little operator input. Some of the tests target just the viruses involved in large yearly epidemics such as influenza, or specific groups of viruses such as the adenoviruses or parainfluenza viruses; others can detect most of the known respiratory viruses and some bacterial agents.


title: Co-circulation of human metapneumovirus and SARS-associated coronavirus during a major nosocomial SARS outbreak in Hong Kong

text: Abstract Background The clinico-epidemiological significance of human metapneumovirus (hMPV) detected during the SARS outbreak is unknown. Objectives To characterize a nosocomial hMPV outbreak during the 2003 SARS epidemic. Study design and methods All available nasopharyngeal aspirate (NPA) collected from confirmed patients during the first 8 weeks of the SARS outbreak in 2003 were tested for hMPV by a nested RT-PCR assay targeting the F-gene. Clinico-epidemiological information was used to analyze the relationship of hMPV co-infection to specific risk factors (demographics/symptoms/outcomes; status as health-care workers (HCWs)/patients; history of exposure/contact; ward location). Multivariate logistic regression analysis was performed to determine independent risk factors. Results An hMPV outbreak occurred during 6–16 March 2003 (first week of the Hong Kong SARS epidemic). hMPV RNA was detected in 31 of 155 (20%) NPAs from SARS patients. HCW status (OR 2.72, 95% CI 1.11–6.68; p =0.029) or epidemiological linkage to the SARS outbreak ward (OR 3.59, 95% CI 1.42–9.05; p =0.007) were independent factors associated with hMPV infection. Symptoms of cough and coryza were more common in co-infected individuals (22.6% vs. 15.9%) but this was not statistically significant. Other clinical manifestations and outcomes were not different in co-infected patients. Conclusions A major nosocomial hMPV outbreak involving HCWs occurred during the early SARS epidemic. Patients with dual hMPV and SARS infection were not sicker than those with SARS infection only.


title: Understanding novel COVID-19: its impact on organ failure and risk assessment for diabetic and cancer patients

text: Abstract The current pandemic outbreak of COVID-19 originated from Wuhan, China. It is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with significant mortality and morbidity rate. The severe risk factors are commonly detected in patients of older age and with medical comorbidities like cancer and diabetes. Scientists and doctors have scrambled to gain knowledge about the novel virus and its pathophysiology in order to discover possible therapeutic regimens and vaccines for COVID-19. The therapeutic strategies like targeting the viral genome emphasize the promising approach to target COVID-19. Additionally, blocking the receptor, ACE2 via the neutralizing antibodies for viral escape that prevents it from entering into the cells provides another therapeutic regimen. In this review article, we have presented the effect of SARS-CoV-2 infection in comorbid patients and discussed organ failure caused by this virus. Based on the data available from the scientific literature and ongoing clinical trials, we have focused on therapeutic strategies. We hope that we would fill the gaps that puzzled the researchers and clinicians with the best of our knowledge collected for the betterment of the patients for the coming future.


title: Innate Immunity to H5N1 Influenza Viruses in Humans

text: Avian influenza virus infections in the human population are rare due to their inefficient direct human-to-human transmission. However, when humans are infected, a strong inflammatory response is usually induced, characterized by elevated levels of cytokines and chemokines in serum, believed to be important in the severe pathogenesis that develops in a high proportion of these patients. Extensive research has been performed to understand the molecular viral mechanisms involved in the H5N1 pathogenesis in humans, providing interesting insights about the virus-host interaction and the regulation of the innate immune response by these highly pathogenic viruses. In this review we summarize and discuss the most important findings in this field, focusing mainly on H5N1 virulence factors and their impact on the modulation of the innate immunity in humans.


title: Does infection of 2019 novel coronavirus cause acute and/or chronic sialadenitis?

text: Abstract 2019 novel coronavirus (2019-nCoV) is widespread in China and other countries. The target of 2019-nCoV and severe acute respiratory syndrome coronavirus (SARS-CoV) is angiotensin-converting enzyme 2 (ACE2) positive cells. ACE2 is present in the salivary gland duct epithelium, and thus it could be the target of 2019-nCoV and SARS-CoV. SARS-CoV-related animal model experiments show that it can infect the epithelial cells on the salivary gland duct in Chinese rhesus macaques by targeting ACE2. Clinical studies confirmed that 2019-nCoV and SARS-CoV could be detected in saliva of human patients. We hypothesize that the infection of 2019-nCoV and SARS-CoV will lead to inflammatory pathological lesions in patients’ target organs, and possibly inflammatory lesions in salivary glands. 2019-nCoV may cause acute sialoadenitis in the acute phase of infection. After the acute phase, chronic sialoadenitis may be caused by fibrosis repairment. Although there was no direct evidence to prove this, the available indirect evidence indicates a high probability of our hypothesis.


Lung Ultrasound During the COVID‐19 Pandemic: Building a Mobile Lung Ultrasound Unit


title: Influence of diabetes mellitus on the severity and fatality of SARS‐CoV‐2 infection

text: AIMS: Diabetes mellitus is one of the most common comorbidities in Coronavirus disease 2019 (COVID‐19) patients. The objective of this study was to evaluate the influences of diabetes mellitus on the severity and fatality of SARS‐CoV‐2 infection. MATERIALS AND METHODS: Medical records of 66 hospitalized COVID‐19 patients were collected and classified into non‐severe (mild/moderate cases) and severe (severe/critical cases) groups, respectively. Logistic regression analysis was used to estimate the risk of severe COVID‐19 (severe/critical infection). In addition, a meta‐analysis including published studies reported the impacts of diabetes mellitus on severity and fatality of COVID‐19, and our current study was conducted using fixed‐effects models. RESULTS: There were 22 diabetic and 44 non‐diabetic cases among the 66 hospitalized COVID‐19 patients. As the results shown, seven cases (31.82%) were diagnosed as severe COVID‐19 in diabetic patients, which was significantly higher than that in non‐diabetic group (4/44, 9.09%, P = 0.033). After adjustment for age and gender, the results showed that diabetes mellitus was significantly associated with COVID‐19 severity (OR: 5.29, 95% CI: 1.07–26.02). A meta‐analysis further confirmed the positive association between diabetes mellitus and COVID‐19 severity (pooled OR = 2.58, 95% CI: 1.93–3.45). Moreover, the diabetic patients infected with SARS‐CoV‐2 showed to have 2.95‐fold higher risk of fatality compared to those patients without diabetes mellitus (95% CI: 1.93–4.53). CONCLUSIONS: Our findings provide new evidences that diabetes mellitus is associated with a higher risk of severity and fatality of COVID‐19. Therefore, intensive monitoring and antidiabetic therapy should be considered in diabetic patients with SARS‐CoV‐2 infection. This article is protected by copyright. All rights reserved.


title: Solid supported lipid bilayers: From biophysical studies to sensor design

text: Abstract The lipid bilayer is one of the most eloquent and important self-assembled structures in nature. It not only provides a protective container for cells and sub-cellular compartments, but also hosts much of the machinery for cellular communication and transport across the cell membrane. Solid supported lipid bilayers provide an excellent model system for studying the surface chemistry of the cell. Moreover, they are accessible to a wide variety of surface-specific analytical techniques. This makes it possible to investigate processes such as cell signaling, ligand–receptor interactions, enzymatic reactions occurring at the cell surface, as well as pathogen attack. In this review, the following membrane systems are discussed: black lipid membranes, solid supported lipid bilayers, hybrid lipid bilayers, and polymer cushioned lipid bilayers. Examples of how supported lipid membrane technology is interfaced with array based systems by photolithographic patterning, spatial addressing, microcontact printing, and microfluidic patterning are explored. Also, the use of supported lipid bilayers in microfluidic devices for the development of lab-on-a-chip based platforms is examined. Finally, the utility of lipid bilayers in nanotechnology and future directions in this area are discussed.


title: A Modular Microarray Imaging System for Highly Specific COVID-19 Antibody Testing

text: To detect the presence of antibodies in blood against SARS-CoV-2 in a highly sensitive and specific manner, here we describe a robust, inexpensive ($200), 3D-printable portable imaging platform (TinyArray imager) that can be deployed immediately in areas with minimal infrastructure to read coronavirus antigen microarrays (CoVAMs) that contain a panel of antigens from SARS-CoV-2, SARS-1, MERS, and other respiratory viruses. Application includes basic laboratories and makeshift field clinics where a few drops of blood from a finger prick could be rapidly tested in parallel for the presence of antibodies to SARS-CoV-2 with a test turnaround time of only 2–4 h. To evaluate our imaging device, we probed and imaged coronavirus microarrays with COVID-19-positive and negative sera and achieved a performance on par with a commercial microarray reader 100x more expensive than our imaging device. This work will enable large scale serosurveillance, which can play an important role in the months and years to come to implement efficient containment and mitigation measures, as well as help develop therapeutics and vaccines to treat and prevent the spread of COVID-19.


title: Identification of the interaction between vimentin and nucleocapsid protein of transmissible gastroenteritis virus

text: Abstract Nucleocapsid (N) protein of transmissible gastroenteritis virus (TGEV) packages viral RNA genome to form a ribonucleoprotein complex. In addition to its function as a structural protein, N protein is involved in cell apoptosis or cell-cycle regulation. N protein possibly interacts with host factors to modulate cellular functions. To identify cellular proteins that interacted with N protein of TGEV, methods of GST pull-down and Co-IP were utilized to precipitate cellular proteins of swine testicular (ST). Bound cellular proteins were resolved by SDS-PAGE. Analysis of interacting proteins by mass spectrometry allowed identification of 15 cellular protein bands representative of 12 cellular proteins including vimentin that bound to N protein. Furthermore, the function of vimentin cytoskeleton in ST cells during TGEV infection was examined. Vimentin cytoskeleton was required for virus replication. The present study thus provides protein-related information about interaction of TGEV N protein with host cell that should be useful for understanding host cell response to coronavirus pathogenesis infection and the underlying mechanism of coronavirus replication.


Communiqué de l’Académie nationale de médecine


title: Consider TLR5 for new therapeutic development against COVID‐19

text: TLR5, a member of Toll-like receptors (TLRs), has a significant role to recognize the flagellin or same kind of molecule. After reorganization, it can modulate innate immune responses. In this article, we urge for the development of new therapeutic molecule by targeting TLR5 modulation against SARS-CoV-2. This article is protected by copyright. All rights reserved.


title: Fused-ring structure of decahydroisoquinolin as a novel scaffold for SARS 3CL protease inhibitors

text: Abstract The design and evaluation of a novel decahydroisoquinolin scaffold as an inhibitor for severe acute respiratory syndrome (SARS) chymotrypsin-like protease (3CLpro) are described. Focusing on hydrophobic interactions at the S2 site, the decahydroisoquinolin scaffold was designed by connecting the P2 site cyclohexyl group of the substrate-based inhibitor to the main-chain at the α-nitrogen atom of the P2 position via a methylene linker. Starting from a cyclohexene enantiomer obtained by salt resolution, trans-decahydroisoquinolin derivatives were synthesized. All decahydroisoquinolin inhibitors synthesized showed moderate but clear inhibitory activities for SARS 3CLpro, which confirmed the fused ring structure of the decahydroisoquinolin functions as a novel scaffold for SARS 3CLpro inhibitor. X-ray crystallographic analyses of the SARS 3CLpro in a complex with the decahydroisoquinolin inhibitor revealed the expected interactions at the S1 and S2 sites, as well as additional interactions at the N-substituent of the inhibitor.


title: Screening of Chloroquine, Hydroxychloroquine and its derivatives for their binding affinity to multiple SARS-CoV-2 protein drug targets

text: Recently Chloroquine and its derivative Hydroxychloroquine have garnered enormous interest amongst the clinicians and health authorities’ world over as a potential treatment to contain COVID-19 pandemic. The present research aims at investigating the therapeutic potential of Chloroquine and its potent derivative Hydroxychloroquine against SARS-CoV-2 viral proteins. At the same time screening was performed for some chemically synthesized derivatives of Chloroquine and compared their binding efficacy with chemically synthesized Chloroquine derivatives through in silico approaches. For the purpose of the study, some essential viral proteins and enzymes were selected that are implicated in SARS-CoV-2 replication and multiplication as putative drug targets. Chloroquine, Hydroxychloroquine, and some of their chemically synthesized derivatives, taken from earlier published studies were selected as drug molecules. We have conducted molecular docking and related studies between Chloroquine and its derivatives and SARS-CoV-2 viral proteins, and the findings show that both Chloroquine and Hydroxychloroquine can bind to specific structural and non-structural proteins implicated in the pathogenesis of SARS-CoV-2 infection with different efficiencies. Our current study also shows that some of the chemically synthesized Chloroquine derivatives can also potentially inhibit various SARS-CoV-2 viral proteins by binding to them and concomitantly effectively disrupting the active site of these proteins. These findings bring into light another possible mechanism of action of Chloroquine and Hydroxychloroquine and also pave the way for further drug repurposing and remodeling. Communicated by Ramaswamy H. Sarma


Avian Influenza: preparation not panic


title: Dpp4 inhibition as a therapeutic strategy in cardiometabolic disease: Incretin-dependent and -independent function

text: Abstract Cardiometabolic disorders including obesity, diabetes and cardiovascular disease are among the most severe health problems worldwide. DPP4 enzymatic inhibitors were first developed as anti-diabetic reagents which preserve incretin hormones and promote post-prandial insulin secretion. It's been shown in animal studies that incretin-based therapy has a beneficial effect on cardiovascular disease. Recent studies demonstrated novel non-catalytic functions of DPP4 that may play a role in cardiometabolic disease. Although the role of DPP4 inhibition-mediated incretin effects has been well-reviewed, little information of its incretin-independent actions was introduced in cardiometabolic disease. In the current review, we will summarize the catalytic dependent and independent effects of DPP4 inhibition on cardiometabolic disease.


title: Investigational use of ribavirin in the treatment of severe acute respiratory syndrome, Singapore, 2003

text: Objective Ribavirin is a broad spectrum nucleoside analogue efficacious in the treatment of several viral infections. In the recent severe acute respiratory syndrome (SARS) outbreak, ribavirin was used in various countries against this novel coronavirus. We conducted a retrospective analysis to assess the efficacy of ribavirin in the treatment of SARS in Singapore. Methods A total of 229 cases were analysed. Ninety‐seven (42.4%) patients received ribavirin at a mean of 6.4 days of illness. Clinical and laboratory parameters taken at the start of ribavirin treatment were compared with day 5, 6 or 7 parameters of those patients not on treatment. The two groups were compared using Fisher's exact test and Student's t‐test. Multivariate analysis was performed using Cox regression model with death as the outcome of interest. Results The treatment group had younger women with more symptoms of myalgia (P < 0.001). The crude death rate was 12.9% in the control and 10.3% (P = 0.679) in the treatment group. After correction for age, male sex, lactate dehydrogenase levels and steroid use, the hazard ratio was 1.03 (95% CI: 0.44–2.41, P = 0.939). Conclusion In this retrospective, uncontrolled cohort analysis, use of ribavirin did not appear to confer any benefit for patients with SARS.


title: Porcine epidemic diarrhea virus: An overview of current virological and serological diagnostic methods

text: Abstract Porcine epidemic diarrhea virus (PEDV) is the causative agent of an acute, highly contagious, and severe enteric disease that leads to high mortality rates in suckling piglets. Therefore, accurate diagnosis of PEDV infection is critical for the implementation of control measures for the virus. Many diagnostic tests have been recently developed and are currently available for the detection of PEDV, its proteins or nucleic acid, including virus isolation, immunofluorescence (IF) or immunohistochemistry (IHC), polymerase chain reaction (PCR) and isothermal amplification assays. Additionally, several serological assays have been developed and are currently used for the detection of antibodies against PEDV. Molecular assays such as real-time reverse transcriptase-PCR (rRT-PCR) became the methods of choice for the diagnosis of PEDV infection, providing sensitive, specific and rapid detection of the virus RNA in clinical samples. Whereas serological assays have been widely used to monitor prior exposure to the virus and to evaluate the efficacy of novel vaccine candidates or vaccination strategies. Here we discuss the properties of current PEDV diagnostic assays and prospects for improving diagnostic strategies in the future.


More PPE protects better against Ebola


title: The interaction between severe acute respiratory syndrome coronavirus 3C-like proteinase and a dimeric inhibitor by capillary electrophoresis

text: Abstract 3C-like proteinase of severe acute respiratory syndrome (SARS) coronavirus has been demonstrated to be a key target for drug design against SARS. The interaction between SARS coronavirus 3C-like (3CL) proteinase and an octapeptide interface inhibitor was studied by affinity capillary electrophoresis (ACE). The binding constants were estimated by the change of migration time of the analytes in the buffer solution containing different concentrations of SARS 3CL proteinase. The results showed that SARS 3CL proteinase was able to complex with the octapeptide competitively, with binding constants of 2.44×104 M−1 at 20°C and 2.11×104 M−1 at 37°C. In addition, the thermodynamic parameters deduced reveal that hydrophobic interaction might play major roles, along with electrostatic force, in the binding process. The ACE method used here could be developed to be an effective and simple way of applying large-scale drug screening and evaluation.


title: Evaluation of antigenic differences between wild and Sabin vaccine strains of poliovirus using the pseudovirus neutralization test

text: In the endgame of global polio eradication, serosurveillance is essential to monitor each country’s vulnerability to poliomyelitis outbreaks. Previously, we developed pseudovirus poliovirus (PV) neutralization test (pPNT) with type 1, 2, and 3 PV pseudovirus (PV(pv)), which possess a luciferase-encoding PV replicon in the capsids of wild-type strains (PV(pv)[WT]), showing that pPNT with type 2 and 3 PV(pv)(WT) but not type 1 shows high correlation with the conventional PV neutralization test (cPNT) performed with vaccine strains. Here, we analyse the antigenicity of PV(pv)(WT) and PV(pv) with capsid proteins of Sabin vaccine strains (PV(pv)[Sabin]) in human serum. Type 2 and 3 PV(pv)(WT) and PV(pv)(Sabin) show similar antigenicity in the analysed set of human sera in contrast to type 1 PV(pv). The levels of PV(pv)(Sabin) infection (%), including about 70% of PV(pv) infection (%) measured in the presence of human serum diluted to the cPNT titre, serve as the optimal threshold values for pPNT (5% for type 1 and 2, 10% for type 3) to show high correlation with cPNT results. Our results suggest that pPNT with PV(pv)(Sabin) could serve as an alternative to cPNT and provide a rationale for pPNT threshold values.


title: The SARS-CoV Fusion Peptide Forms an Extended Bipartite Fusion Platform that Perturbs Membrane Order in a Calcium-Dependent Manner

text: Abstract Coronaviruses (CoVs) are a major infectious disease threat and include the pathogenic human pathogens of zoonotic origin: severe acute respiratory syndrome CoV (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV). Entry of CoVs into host cells is mediated by the viral spike (S) protein, which is structurally categorized as a class I viral fusion protein, within the same group as influenza virus and HIV. However, S proteins have two distinct cleavage sites that can be activated by a much wider range of proteases. The exact location of the CoV fusion peptide (FP) has been disputed. However, most evidence suggests that the domain immediately downstream of the S2′ cleavage site is the FP (amino acids 798–818 SFIEDLLFNKVTLADAGFMKQY for SARS-CoV, FP1). In our previous electron spin resonance spectroscopic studies, the membrane-ordering effect of influenza virus, HIV, and Dengue virus FPs has been consistently observed. In this study, we used this effect as a criterion to identify and characterize the bona fide SARS-CoV FP. Our results indicate that both FP1 and the region immediately downstream (amino acids 816–835 KQYGECLGDINARDLICAQKF, FP2) induce significant membrane ordering. Furthermore, their effects are calcium dependent, which is consistent with in vivo data showing that calcium is required for SARS-CoV S-mediated fusion. Isothermal titration calorimetry showed a direct interaction between calcium cations and both FPs. This Ca2+-dependency membrane ordering was not observed with influenza FP, indicating that the CoV FP exhibits a mechanistically different behavior. Membrane-ordering effects are greater and penetrate deeper into membranes when FP1 and FP2 act in a concerted manner, suggesting that they form an extended fusion “platform.”


title: Measuring Similarity among Protein Sequences Using a New Descriptor

text: The comparison of protein sequences according to similarity is a fundamental aspect of today's biomedical research. With the developments of sequencing technologies, a large number of protein sequences increase exponentially in the public databases. Famous sequences' comparison methods are alignment based. They generally give excellent results when the sequences under study are closely related and they are time consuming. Herein, a new alignment-free method is introduced. Our technique depends on a new graphical representation and descriptor. The graphical representation of protein sequence is a simple way to visualize protein sequences. The descriptor compresses the primary sequence into a single vector composed of only two values. Our approach gives good results with both short and long sequences within a little computation time. It is applied on nine beta globin, nine ND5 (NADH dehydrogenase subunit 5), and 24 spike protein sequences. Correlation and significance analyses are also introduced to compare our similarity/dissimilarity results with others' approaches, results, and sequence homology.


title: Human Endogenous Retroviruses in Neurological Diseases

text: The causes of multiple sclerosis and amyotrophic lateral sclerosis have long remained elusive. A new category of pathogenic components, normally dormant within human genomes, has been identified: human endogenous retroviruses (HERVs). These represent ∼8% of the human genome, and environmental factors have reproducibly been shown to trigger their expression. The resulting production of envelope (Env) proteins from HERV-W and HERV-K appears to engage pathophysiological pathways leading to the pathognomonic features of MS and ALS, respectively. Pathogenic HERV elements may thus provide a missing link in understanding these complex diseases. Moreover, their neutralization may represent a promising strategy to establish novel and more powerful therapeutic approaches.


title: Respiratory viral infections within one year after pediatric lung transplant

text: Abstract: To characterize epidemiology and risk factors for respiratory viral infections (RVI) in pediatric lung transplant recipients within the first post‐transplant year, a retrospective multicenter study of pediatric lung transplant recipients from 1988 to 2005 was conducted at 14 centers in the United States and Europe. Data were recorded for 1 year post transplant. Associations between RVI and continuous and categorical risk factors were assessed using Wilcoxon's rank‐sum and χ(2) tests, respectively. Associations between time to RVI and risk factors or survival were assessed by multivariable Cox proportional hazards models. Of 576 subjects, 79 subjects (14%) had 101 RVI in the first year post transplant. Subjects with RVI were younger than those without RVI (median ages 9.7, 13; P<0.01). Viruses detected included adenovirus (n=25), influenza (n=9), respiratory syncytial virus (n=21), parainfluenza virus (n=19), enterovirus (n=4), and rhinovirus (n=22). In a multivariable model for time to first RVI, etiology other than cystic fibrosis (CF), younger age, and no induction therapy were independently associated with risk of RVI. Cytomegalovirus serostatus and acute rejection were not associated with RVI. RVI was independently associated with decreased 12‐month survival (hazard ratio 2.6, 95% confidence interval 1.6–4.4). RVI commonly occurs after pediatric lung transplantation with risk factors including younger age and non‐CF diagnosis. RVI is associated with decreased 1‐year survival.