title: Diseases associated with spontaneous feline leukemia virus (FeLV) infection in cats

text: Abstract More than 2000 cats sent for necropsy in order to provide a diagnosis were investigated immunohistologically using paraffin sections for the presence of a persistent infection with feline leukemia virus (FeLV). The spectrum of neoplastic and non-neoplastic diseases associated significantly with FeLV infection was determined statistically. Three-quarters of the cats with persistent FeLV infections died of non-neoplastic diseases and about 23% died of tumors, nearly exclusively those of the leukemia/lymphoma disease complex. A strong association with liver degeneration, icterus and a FeLV-associated enteritis was found in addition to the known association with non-neoplastic diseases and conditions such as anemia, bacterial secondary infections and respiratory tract inflammations due to the immunosuppressive effect of FeLV, hemorrhages and feline infectious peritonitis. Surprisingly, diseases and conditions like feline infectious panleukopenia, enteritis (of other types than FeLV-associated enteritis and feline infectious panleukopenia), glomerulonephritis, uremia and hemorrhagic cystitis were not associated with persistent FeLV infection. Another unexpected finding was that most pathogenic infectious agents demonstrated in the cats were not FeLV-associated either. Thus, immunosuppression due to FeLV infection seems to make the animals susceptible to certain pathogenic infectious agents, but not to the majority.


title: Human Rhinovirus Proteinase 2A Induces Th1 and Th2 Immunity in COPD

text: BACKGROUND: Tobacco related lung diseases including chronic obstructive pulmonary disease (COPD), are major causes of lung-related disability and death worldwide. Acute exacerbation of COPD (AE-COPD) is commonly associated with upper and lower respiratory viral infections and may result in respiratory failure in those with advanced lung disease. OBJECTIVE: We sought to determine the mechanism underlying COPD exacerbation, and host response to pathogen-derived factors. METHODS: Over a 24 months period, we assessed the viral causes for upper and lower respiratory infections in COPD (n=155) and control (n=103) subjects. We collected nasal and bronchoalveolar lavage (BAL) fluid and peripheral blood under baseline and exacerbated condition. We determined the effect of human rhinovirus (HRV) proteinases on T cell activation in humans, and in mice. RESULTS: HRVs are isolated from nasal and lung fluid from subjects with AE-COPD. BAL fluid, and CD4 T cells from COPD patients exhibited a type 1 T helper (Th1), and Th2 cell cytokine phenotype during acute infection. HRV-encoded proteinase 2A activated monocyte-derived dendritic cells in vitro, and induced strong Th1, and Th2 immune responses from CD4 T cells. Intranasal administration of recombinant rhinovirus proteinase 2A in mice resulted in an increase in airway hyperreactivity, lung inflammation, and IL-4 and IFN-γ production from CD4 T cells. CONCLUSION: Our findings suggest that patients with severe COPD show Th1 and Th2 bias responses during AE-COPD. HRV-encoded proteinase 2A, like other microbial proteinases, could provide a Th1 and Th2-biasing adjuvant factor during upper and lower respiratory infection in patients with severe COPD. Alteration of the immune response to secreted viral proteinases may contribute to worsening of dyspnea and respiratory failure in COPD.


SARS, lay epidemiology, and fear


title: QSAR Models for Predicting Cathepsin B Inhibition by Small Molecules: Continuous and Binary QSAR Models to Classify Cathepsin B Inhibition Activities of Small Molecules

text: Cathepsin B is a potential target for the development of drugs to treat several important human diseases. A number of inhibitors targeting this protein have been developed in the past several years. Recently, a group of small molecules were identified to have inhibitory activity against cathepsin B through high throughput screening (HTS) tests. In this study, traditional continuous and binary QSAR models were built to classify the biological activities of previously identified compounds and to distinguish active compounds from inactive compounds for drug development based on the calculated molecular and physicochemical properties. Strong correlations were obtained for the continuous QSAR models with regression correlation coefficients (r(2)) and cross-validated correlation coefficients (q(2)) of 0.77 and 0.61 for all compounds, and 0.82 and 0.68 for the compound set excluding 3 outliers, respectively. The models were further validated through the leave-one-out (LOO) method and the training-test set method. The binary models demonstrated a strong level of predictability in distinguishing the active compounds from inactive compounds with accuracies of 0.89 and 0.94 for active and inactive compounds, respectively, in non-cross-validated models. Similar results were obtained for the cross-validated models. Collectively, these results demonstrate the models’ ability to discriminate between active and inactive compounds, suggesting that the models may be used to pre-screen compounds to facilitate compound optimization and to design novel inhibitors for drug development.


title: Chaperna-Mediated Assembly of Ferritin-Based Middle East Respiratory Syndrome-Coronavirus Nanoparticles

text: The folding of monomeric antigens and their subsequent assembly into higher ordered structures are crucial for robust and effective production of nanoparticle (NP) vaccines in a timely and reproducible manner. Despite significant advances in in silico design and structure-based assembly, most engineered NPs are refractory to soluble expression and fail to assemble as designed, presenting major challenges in the manufacturing process. The failure is due to a lack of understanding of the kinetic pathways and enabling technical platforms to ensure successful folding of the monomer antigens into regular assemblages. Capitalizing on a novel function of RNA as a molecular chaperone (chaperna: chaperone + RNA), we provide a robust protein-folding vehicle that may be implemented to NP assembly in bacterial hosts. The receptor-binding domain (RBD) of Middle East respiratory syndrome-coronavirus (MERS-CoV) was fused with the RNA-interaction domain (RID) and bacterioferritin, and expressed in Escherichia coli in a soluble form. Site-specific proteolytic removal of the RID prompted the assemblage of monomers into NPs, which was confirmed by electron microscopy and dynamic light scattering. The mutations that affected the RNA binding to RBD significantly increased the soluble aggregation into amorphous structures, reducing the overall yield of NPs of a defined size. This underscored the RNA-antigen interactions during NP assembly. The sera after mouse immunization effectively interfered with the binding of MERS-CoV RBD to the cellular receptor hDPP4. The results suggest that RNA-binding controls the overall kinetic network of the antigen folding pathway in favor of enhanced assemblage of NPs into highly regular and immunologically relevant conformations. The concentration of the ion Fe(2+), salt, and fusion linker also contributed to the assembly in vitro, and the stability of the NPs. The kinetic “pace-keeping” role of chaperna in the super molecular assembly of antigen monomers holds promise for the development and delivery of NPs and virus-like particles as recombinant vaccines and for serological detection of viral infections.


title: Immunohistochemistry analysis of pulmonary infiltrates in necropsy samples of children with non-pandemic lethal respiratory infections (RSV; ADV; PIV1; PIV2; PIV3; FLU A; FLU B)

text: Abstract Background Acute viral respiratory infections represent a globally important cause of morbidity and mortality in childhood. An individual's cellular response appears to play a critical role in recovery from infections, given that individuals with impaired cellular immunity, congenital or acquired, have more severe diseases and secrete the virus for longer periods. Objectives The aim of this study was to immunohistochemically evaluate the expression of the cell surface antigens CD4, CD8, CD25, CD14 and CD74, in pneumonic infiltrates in the alveolar septa using paraffin-embedded lung samples from autopsies of immunocompetent children who died of lethal, non-pandemic, severe acute respiratory infections. Study design From 794 cases of pediatric autopsies of patients with severe respiratory disease (between 1960 and 2004), 193 cases were selected for this study. To identify subpopulations of inflammatory cells in the alveolar septa, cell surface antigen expression was assessed by immunohistochemistry using the following primary antibodies: anti-CD4, anti-CD8, anti-CD14, anti-CD25 and anti-CD74. Results The TCD8+ lymphocyte count was higher in the virus-positive group (p =0.04) and was also much higher among cases that were positive for more than three viral types (p =0.016). There were fewer CD14+ cells in cases of AdV (adenovirus) infection (p =0.002), and there was a predominance of CD74+ cells in the histopathological pattern defined as interstitial pneumonitis (p =0.037). Conclusions The results of this study demonstrate that TCD8+ lymphocytes present in the alveolar septa participate to a greater extent in the response toward viral pneumonia, while CD14+ cell numbers are often reduced in cases of AdV.


title: Comparative analysis of coronavirus genomic RNA structure reveals conservation in SARS-like coronaviruses

text: Coronaviruses, including SARS-CoV-2 the etiological agent of COVID-19 disease, have caused multiple epidemic and pandemic outbreaks in the past 20 years(1–3). With no vaccines, and only recently developed antiviral therapeutics, we are ill equipped to handle coronavirus outbreaks(4). A better understanding of the molecular mechanisms that regulate coronavirus replication and pathogenesis is needed to guide the development of new antiviral therapeutics and vaccines. RNA secondary structures play critical roles in multiple aspects of coronavirus replication, but the extent and conservation of RNA secondary structure across coronavirus genomes is unknown(5). Here, we define highly structured RNA regions throughout the MERS-CoV, SARS-CoV, and SARS-CoV-2 genomes. We find that highly stable RNA structures are pervasive throughout coronavirus genomes, and are conserved between the SARS-like CoV. Our data suggests that selective pressure helps preserve RNA secondary structure in coronavirus genomes, suggesting that these structures may play important roles in virus replication and pathogenesis. Thus, disruption of conserved RNA secondary structures could be a novel strategy for the generation of attenuated SARS-CoV-2 vaccines for use against the current COVID-19 pandemic.


title: Comparison of reverse transcription loop-mediated isothermal amplification, conventional PCR and real-time PCR assays for Japanese encephalitis virus

text: We developed and evaluated a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detecting Japanese encephalitis virus (JEV). The sensitivity of the JEV RT-LAMP assay was in concordance with that of real-time RT-PCR and 10-fold more sensitive than that of conventional RT-PCR, which the detection limit was 24 copies/μl. The JEV RT-LAMP was highly specific, which no cross-reactivity was found with dengue-2 virus, rabies virus, norovirus, astrovirus and human enterovirus 71. The JEV RT-LAMP assay was more simple and less time-consuming compared to the conventional RT-PCR and real-time RT-PCR, which the amplification could be completed in a single tube within 1 h under isothermal conditions at temperature of 63°C. The results suggest that the RT-LAMP assay can be applied as a practical molecular diagnostic tool for JEV infection and surveillance.


title: Cellular DNA quantification in respiratory samples for the normalization of viral load: a real need?

text: Abstract Background Respiratory tract infections have an enormous social economic impact, with high incidence of hospitalization and high costs. Adequate specimen collection is the first crucial step for the correct diagnosis of viral respiratory infections. Objectives The present retrospective study aimed: i) to verify the cell yield obtained from sampling the nasal respiratory tract using mid-turbinate flocked swabs; ii) to evaluate the normalization of viral load, based on cell number; and iii) to compare the kinetics of viral infection obtained with normalized vs non-normalized viral load. Study design The number of cells were quantified by real-time PCR in residual extract of nasal swabs tested for respiratory viruses detection and stored at −80 °C in a universal transport medium (UTM™). Results A total of 513 virus-positive and 226 virus-negative samples were analyzed. Overall, a median of 4.42 log10 β2-microgolubin DNA copy number/ml of UTM™ (range 1.17–7.26) was detected. A significantly higher number of cells was observed in virus-positive as compared to virus-negative samples (4.75 vs 3.76; p < 0.001). Viral loads expressed as log10 RNA copies/ml of UTM™ and log10 RNA copies/median number of cells were compared in virus-positive samples and a strict correlation (r = 0.89, p < 0.001) and agreement (R2 = 0.82) were observed. In addition, infection kinetics were compared using the two methods with a follow-up series of eight episodes of viral infection and the mean difference was -0.57 log10 (range −1.99 to 0.40). Conclusions The normalization of viral load using cellular load compliments the validation of real-time PCR results in the diagnosis of respiratory viruses but is not strictly needed.


title: Development of a triplex real-time RT-PCR assay for detection and differentiation of three US genotypes of porcine hemagglutinating encephalomyelitis virus

text: Abstract Porcine hemagglutinating encephalomyelitis virus (PHEV) is a single-stranded, positive-sense RNA virus. PHEV mainly causes two types of clinical manifestations representing vomiting and wasting and encephalomyelitis in piglets. However, our recent findings provide strong evidence that PHEV can also cause respiratory disease in older pigs. Genomic analysis of new PHEV strains identified in our former study further classifies PHEV into three genotypes. Detection and differentiation of these new mutants are critical in monitoring PHEV evolution in the field. In the present study, we report the development of a triplex real-time RT-PCR assay for detection and differentiation of three PHEV genotypes, 1, 2, and 3. Three sets of primers and probes were designed; one set of primers and probe targeting the conserved regions of the 3′ end nucleocapsid for detection of all three genotypes and another two sets of primers and probes targeting the regions of NS2 with different patterns of deletions for detection of both genotypes 1 and 3, or genotype 3 only. Genotype 1 was positive when two probe dyes showed signals, genotype 2 was positive when only one probe dye showed a signal, and genotype 3 was positive when all three probes showed signals. The detection limit of the developed triplex real-time RT-PCR was as low as 8 or 9 DNA copies for three sets of primers and probes. The specificity test showed no cross reaction with other porcine viruses. Positive field-samples were correctly typed by this new assay, which was further confirmed by DNA sequencing. The triplex real-time RT-PCR provides a rapid and sensitive method to detect and differentiate all three US genotypes of PHEV from clinical samples.


title: Coronavirus SARS‐CoV‐2: filtering fact from fiction in the infodemic: Q&A with virologist Professor Urs Greber

text: As the severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) continues to spread across the world, and the associated lung disease COVID-19 remains difficult to treat, information from media and private communication flows at high speed, often through unfiltered channels. Much of this information is speculative, as it derives from preliminary and inconclusive studies, and creates confusion as well as anxiety. This phenomenon was recently labelled as "infodemic" by the World Health Organization.


title: Nucleolin interacts with influenza A nucleoprotein and contributes to viral ribonucleoprotein complexes nuclear trafficking and efficient influenza viral replication

text: Influenza viruses replicate their single-stranded RNA genomes in the nucleus of infected cells and these replicated genomes (vRNPs) are then exported from the nucleus to the cytoplasm and plasma membrane before budding. To achieve this export, influenza viruses hijack the host cell export machinery. However, the complete mechanisms underlying this hijacking remain not fully understood. We have previously shown that influenza viruses induce a marked alteration of the nucleus during the time-course of infection and notably in the nucleolar compartment. In this study, we discovered that a major nucleolar component, called nucleolin, is required for an efficient export of vRNPs and viral replication. We have notably shown that nucleolin interacts with the viral nucleoprotein (NP) that mainly constitutes vRNPs. Our results suggest that this interaction could allow vRNPs to “catch” the host cell export machinery, a necessary step for viral replication.


title: Validation and Psychometric Evaluation of the Italian Version of the Fear of COVID-19 Scale

text: BACKGROUND: The advent of COVID-19 worldwide has led to consequences for people’s health, both physical and psychological, such as fear and anxiety. This is the case in Italy, one of the countries most affected by the pandemic. Given the heightened fear concerning COVID-19 in Italy., the present study analyzed the psychometric properties of the Italian version of the Fear of COVID-19 Scale (FCV-19S). METHODS: The sample comprised 250 Italian participants who were administered Italian versions of the FCV-19S, the Hospital Anxiety and Depression Scale (HADS), and the Severity Measure for Specific Phobia–Adult (SMSP-A). Several psychometric tests were performed to investigate the validity and reliability of the test including confirmatory factor analysis. RESULTS: Analysis of the data showed satisfactory psychometric characteristics and confirmed the scale’s unidimensional properties. The seven FCV-19S items had acceptable correlations with the test total (from .443 to .784). Furthermore, the loadings on the factor were significant and strong (from .684 to .897). The internal consistency was very good (α = .871). Construct validity for the FCV-19S was supported by significant and positive correlations with the HADS (r=.649) and SMSP-A (r=.703). CONCLUSIONS: The Italian version of the Fear of COVID-19 Scale is valid and reliable in assessing fear of COVID-19 among the general Italian population.


title: A Systematic Review of Cases of Acute Respiratory Distress Syndrome in the Coronavirus Disease 2019 Pandemic

text: The outbreak of coronavirus disease 2019 (COVID-19) was declared a global pandemic after it spread to 213 countries and has the highest total number of cases worldwide. About 80% of COVID-19 infections are mild or asymptomatic and never require hospitalization but about 5% of patients become critically ill and develop acute respiratory distress syndrome (ARDS). The widely used management for ARDS in COVID-19 has been in line with the standard approach, but the need to adjust the treatment protocols has been questioned based on the reports of higher mortality risk among those requiring mechanical ventilation. Treatment options for this widespread disease are limited and there are no definitive therapies or vaccines until now. Although some antimalarial and antiviral drugs may prove effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), their safety and efficacy are still under clinical trials. We conducted a systematic review of case reports on ARDS in SARS-CoV-2 infection to summarize the clinical presentation, laboratory and chest imaging findings, management protocols, and outcome of ARDS in COVID-19-positive patients. We need more data and established studies for the effective management of the novel SARS-CoV-2 and to reduce mortality in high-risk patients.


title: A real-time reporting system of causes of death or reasons for euthanasia: A model for monitoring mortality in domesticated cats in Taiwan

text: Abstract A novel, real-time mortality recording system was designed to collect mortality data in companion animals from veterinary hospitals in Taiwan. This retrospective study aims to introduce the system, and to utilize the data collected for further investigation of the lifespan and mortality of the domesticated cat population stratified by demographic variables. Our data revealed that 1325 domesticated cats were acquired between 2012 and 2014. The median age of the study population was 8.0 years (IQR 3.0–13.0; range 0.0–22.7). Neutered and purebred cats lived longer. The most common causes of death were renal and urologic disorders, followed by neoplasia, infection, cardiovascular disorders, and trauma. Independent factors for common causes were surveyed. Advanced age and neutering was found to be associated with death due to renal and urologic disorders as well as with neoplasia. In contrast, younger age was found to be associated with death due to trauma and infection; being unneutered and living in the capital city were found to be associated with death due to trauma. Being male or purebred was found to be associated with death due to cardiovascular disorders.


title: Improved microarray gene expression profiling of virus-infected cells after removal of viral RNA

text: BACKGROUND: Sensitivity and accuracy are key points when using microarrays to detect alterations in gene expression under different conditions. Critical to the acquisition of reliable results is the preparation of the RNA. In the field of virology, when analyzing the host cell's reaction to infection, the often high representation of viral RNA (vRNA) within total RNA preparations from infected cells is likely to interfere with microarray analysis. Yet, this effect has not been investigated despite the many reports that describe gene expression profiling of virus-infected cells using microarrays. RESULTS: In this study we used coronaviruses as a model to show that vRNA indeed interferes with microarray analysis, decreasing both sensitivity and accuracy. We also demonstrate that the removal of vRNA from total RNA samples, by means of virus-specific oligonucleotide capturing, significantly reduced the number of false-positive hits and increased the sensitivity of the method as tested on different array platforms. CONCLUSION: We therefore recommend the specific removal of vRNA, or of any other abundant 'contaminating' RNAs, from total RNA samples to improve the quality and reliability of microarray analyses.


title: Environmental Epigenetics and Genome Flexibility: Focus on 5-Hydroxymethylcytosine

text: Convincing evidence accumulated over the last decades demonstrates the crucial role of epigenetic modifications for mammalian genome regulation and its flexibility. DNA methylation and demethylation is a key mechanism of genome programming and reprogramming. During ontogenesis, the DNA methylome undergoes both programmed changes and those induced by environmental and endogenous factors. The former enable accurate activation of developmental programs; the latter drive epigenetic responses to factors that directly or indirectly affect epigenetic biochemistry leading to alterations in genome regulation and mediating organism response to environmental transformations. Adverse environmental exposure can induce aberrant DNA methylation changes conducive to genetic dysfunction and, eventually, various pathologies. In recent years, evidence was derived that apart from 5-methylcytosine, the DNA methylation/demethylation cycle includes three other oxidative derivatives of cytosine—5-hydroxymethylcytosine (5hmC), 5-formylcytosine, and 5-carboxylcytosine. 5hmC is a predominantly stable form and serves as both an intermediate product of active DNA demethylation and an essential hallmark of epigenetic gene regulation. This makes 5hmC a potential contributor to epigenetically mediated responses to environmental factors. In this state-of-the-art review, we consolidate the latest findings on environmentally induced adverse effects on 5hmC patterns in mammalian genomes. Types of environmental exposure under consideration include hypnotic drugs and medicines (i.e., phenobarbital, diethylstilbestrol, cocaine, methamphetamine, ethanol, dimethyl sulfoxide), as well as anthropogenic pollutants (i.e., heavy metals, particulate air pollution, bisphenol A, hydroquinone, and pentachlorophenol metabolites). We put a special focus on the discussion of molecular mechanisms underlying environmentally induced alterations in DNA hydroxymethylation patterns and their impact on genetic dysfunction. We conclude that DNA hydroxymethylation is a sensitive biosensor for many harmful environmental factors each of which specifically targets 5hmC in different organs, cell types, and DNA sequences and induces its changes through a specific metabolic pathway. The associated transcriptional changes suggest that environmentally induced 5hmC alterations play a role in epigenetically mediated genome flexibility. We believe that knowledge accumulated in this review together with further studies will provide a solid basis for new approaches to epigenetic therapy and chemoprevention of environmentally induced epigenetic toxicity involving 5hmC patterns.


title: The Cellular and Physiological Basis for Lung Repair and Regeneration: Past, Present, and Future

text: The respiratory system, which includes the trachea, airways, and distal alveoli, is a complex multi-cellular organ that intimately links with the cardiovascular system to accomplish gas exchange. In this review and as members of the NIH/NHLBI-supported Progenitor Cell Translational Consortium, we discuss key aspects of lung repair and regeneration. We focus on the cellular compositions within functional niches, cell-cell signaling in homeostatic health, the responses to injury, and new methods to study lung repair and regeneration. We also provide future directions for an improved understanding of the cell biology of the respiratory system, as well as new therapeutic avenues.


title: Diffuse Alveolar Damage (DAD) from Coronavirus Disease 2019 Infection is Morphologically Indistinguishable from Other Causes of DAD

text: AIMS: Diffuse alveolar damage (DAD) is a ubiquitous finding in inpatient coronavirus disease 2019 (COVID‐19)‐related deaths, but recent reports also describe additional atypical findings, including vascular changes. Here, we assess lung autopsy findings in COVID‐19 inpatients and untreated, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2)‐positive individuals who died in the community to understand the relative impact of medical intervention on lung histology. Additionally, we investigate if COVID‐19 represents a unique histologic variant of DAD by comparing the pathologic findings to uninfected control patients. METHODS AND RESULTS: Lung sections from autopsy cases were reviewed by three pulmonary pathologists, including two who were blinded to patient cohort. The cohorts included 4 COVID‐19 inpatients, 4 cases with post‐mortem SARS‐CoV‐2 diagnoses who died in the community, and 8 SARS‐CoV‐2‐negative control cases. DAD was present in all but one SARS‐CoV‐2‐positive patient who was asymptomatic and died in the community. Although SARS‐CoV‐2‐positive patients were noted to have more focal perivascular inflammation/endothelialitis than control patients, there were no significant differences in the presence of hyaline membranes, fibrin thrombi, airspace organization, and “acute fibrinous and organizing pneumonia”‐like intraalveolar fibrin deposition between the cohorts. Fibrinoid vessel wall necrosis, hemorrhage, and capillaritis were not features of COVID‐19‐related DAD. CONCLUSIONS: DAD is the primary histologic manifestation of severe lung disease in COVID‐19 patients who die both in the hospital and in the community, suggesting no contribution of hyperoxemic mechanical ventilation to the histologic changes. There are no distinctive morphologic features to confidently differentiate COVID‐19‐related DAD from DAD due to other causes.


An Example of Employing the Principles of Bioethics to Medical Decision Making in the COVID‐19 Era


title: Sustainability appraisal in infrastructure projects (SUSAIP) Part 1. Development of indicators and computational methods

text: Abstract The process of translating strategic sustainability objectives into concrete action at project-specific levels is a difficult task. The multi-dimensional perspectives of sustainability such as economy, society, environment, combined with a lack of structured methodology and information at various hierarchical levels, further exacerbate the problem. This paper (Part 1 of a two-part series) proposes an analytical decision model and a structured methodology for sustainability appraisal in infrastructure projects. The paper uses the ‘weighted sum model’ technique in multi-criteria decision analysis (MCDA) and the ‘additive utility model’ in analytical hierarchical process (AHP) for multi-criteria decision making, to develop the model from first principles. It discusses the development of key performance indicators encapsulated within the analytical model. It concludes by discussing other potential applications of the proposed model and methodology for process automation as part of integrated sustainability appraisal in infrastructure design and construction. Part 2 uses a case study to demonstrate the model application in infrastructure sustainability appraisal at design stages. The paper also discusses the challenges for sustainability research, and gives recommendations.


title: Big city, small world: density, contact rates, and transmission of dengue across Pakistan

text: Macroscopic descriptions of populations commonly assume that encounters between individuals are well mixed; i.e. each individual has an equal chance of coming into contact with any other individual. Relaxing this assumption can be challenging though, due to the difficulty of acquiring detailed knowledge about the non-random nature of encounters. Here, we fitted a mathematical model of dengue virus transmission to spatial time-series data from Pakistan and compared maximum-likelihood estimates of ‘mixing parameters’ when disaggregating data across an urban–rural gradient. We show that dynamics across this gradient are subject not only to differing transmission intensities but also to differing strengths of nonlinearity due to differences in mixing. Accounting for differences in mobility by incorporating two fine-scale, density-dependent covariate layers eliminates differences in mixing but results in a doubling of the estimated transmission potential of the large urban district of Lahore. We furthermore show that neglecting spatial variation in mixing can lead to substantial underestimates of the level of effort needed to control a pathogen with vaccines or other interventions. We complement this analysis with estimates of the relationships between dengue transmission intensity and other putative environmental drivers thereof.


title: A distance learning enzyme assay and kinetics laboratory in the time of COVID‐19

text: This article describes a straightforward approach to deliver an enzyme assay and kinetics laboratory via online delivery methods in the time of COVID‐19.


title: The role of IL-29 in immunity and cancer

text: Abstract Interleukin-29 (IL-29) is a new member of the recently discovered interferon λ (IFNλ) family. It is produced predominantly by maturing dendritic cells and macrophages. It has been implicated in numerous immunological responses and has shown antiviral activity similar to the Type I interferons, although its target cell population is more limited than the Type I interferons. In recent years, the role of IL-29 in the pathogenesis of various cancers has also been extensively studied. In this review, we will discuss the recent advances of IL-29 in immunological processes and the pathogenesis of various cancer.


Does a cell protein explain covid-19 severity?


Feline models of viral pathogenesis: Opportunity knocks


title: Influenza epidemiology among hospitalized children in Stockholm, Sweden 1998–2014

text: BACKGROUND: Influenza remains a common reason for the hospitalization of children. There is a need for long term studies that are also population based. We describe the epidemiology of severe influenza in a defined population 1998–2014. METHOD: Retrospective study of annually collected data of virologically confirmed influenza in hospitalized children 0–17 years living in the catchment area (230,000 children). We gathered information about comorbidity and complications from case records, and compared Influenza A, B and A(H1N1)pdm09 with respect to these factors. RESULTS: A total of 922 children with influenza were hospitalized. The mean rate remained unchanged at 22.5–24.2 per 100,000 children per year. There were two major outbreaks: influenza A(H3N2) in 2003–2004 and the A(H1N1) pandemic in 2009–2010. The proportion of children with influenza B increased from 8% during the first half of the study period to 28% during the second half. The highest admission rate was found in children <3 months of age, 169 per 100,000. Children with influenza B were older than those with influenza A. Comorbidity was found in 34%, complications in 41%, and 11% needed intensive care management. The mortality rate was 0.17/100,000 children. CONCLUSION: Influenza remains an important reason for the hospitalization of children, especially during the first years of life. The increasing proportion of influenza B may have to be considered when recommending influenza vaccines.


title: Kinetics of the in vitro antibody response to transmissible gastroenteritis (TGE) virus from pig mesenteric lymph node cells, using the ELISASPOT and ELISA tests

text: Abstract A method is described for in vitro studies of viral humoral immune responses in the pig. After oral immunization with transmissible gastroenteritis (TGE) coronavirus, antibody production from primed mesenteric lymph node cells was revealed by an in vitro boost with viral antigen. For the latter the leukocytes were co-cultured with UV-inactivated virus using a variety of different methods of antigenic stimulation. Enumeration of specific antibody-secreting cells (ASC) and titration of secreted anti-virus antibodies were performed with ELISASPOT (using 3-amino 9-ethyl carbazole as the peroxidase chromogen) and ELISA tests respectively, according to the Ig isotype. The results showed a close relationship between ASC numbers and secreted antibody titres. The best in vitro antibody synthesis was observed when the sensitized cells were maintained in contact with virus during the whole culture period. Antibody responses were defined by a kinetic profile characterized by a narrow peak, with a maximum occuring after 4 and 6 days of culture and with the IgA response appearing earlier than the IgG. This methodology, which analyses specific antibody responses at the cellular level, may permit studies on the mechanisms of Ig isotype regulation. Extended to leukocytes from other organs of the immune system, it may also constitute an in vitro model to study antibody responses expressed in different lymphoid tissues of the pig.


Letter to the Editor in Response to article: “Clinical considerations for patients with diabetes in times of COVID-19 epidemic (Gupta et al.)


title: Using Problem-based Learning for Pandemic Preparedness

text: To test the hypothesis that PBL is an effective method for preparing multidisciplinary learner groups at community health centers (CHCs) for pandemics, quantitative and qualitative methods were utilized to evaluate the conduct of a PBL case of a hypothetical outbreak of severe acute respiratory syndrome (SARS) at two CHCs in Hawaii, with multidisciplinary health professional and student participants. It was found that: (1) there was an overall increase in knowledge of bioevent preparedness; (2) participants gave high ratings for the effectiveness of the PBL process; (3) participants found value in the multidisciplinary group process; and (4) participants strongly agreed that they preferred the PBL process to the traditional lecture format for learning about bioevent preparedness. The PBL approach is useful in educating community-based health professionals from different disciplines about issues related to pandemic preparedness.


title: Detection of antibodies against SARS‐CoV‐2 in patients with COVID‐19

text: Detection of IgM and IgG against SARS-CoV-2 is a fast and simple screening method. As an effective supplement to RNA testing, antibody detection is of epidemiological significance and an important means to understand the occurrence, development, prognosis, and outcome of COVID-19. However, more medical research is needed on the expression level of antibodies against SARS-CoV-2 and the prognosis of COVID-19. This article is protected by copyright. All rights reserved.


title: PEDV ORF3 Independently Regulates IκB Kinase β-Mediated NF-κB and IFN-β Promoter Activities

text: The Open Reading Frame 3 (ORF3), an accessory protein of porcine epidemic diarrhea virus (PEDV), has been shown to interact with a myriad of cellular proteins, among which include the IκB kinase β (IKBKB). Here, specific IKBKB domains responsible for ORF3–IKBKB interaction were identified. Dysregulation of NF-κB and Type I interferon (IFN) in the presence of ORF3 was also demonstrated. We showed that while ORF3 was capable of up-regulating IKBKB-meditated NF-κB promoter activity, it surprisingly down-regulated the activation of IKBKB-meditated IFN-β promoter and expression of IFN-β mRNA. When overexpressed, ORF3 could suppress Poly I:C mediated type I IFN production and induction. Finally, we demonstrated that IKBKB- and RIG-I-mediated type I IFN induction by ORF3 resulted in different outcomes. Our study is the first to demonstrate the potential and complex roles of ORF3 in the involvement of aberrant immune signaling as well as in the virus–host interaction.


Prise en charge des cancers oculaires en période épidémique de Covid-19[[[en]]]Management of ocular cancer during COVID-19 pandemic


Albert Camus’ ‘The COVID-19 Plague’ Revisited


title: Let’s emerge from the pandemic lockdown into a fairer academic world

text: King et al. argue that academic institutions need to better support employees who have faced disproportionate consequences of the pandemic and lockdown.


title: Chapter 8 Bioactive Coumarins and Xanthones From Calophyllum Genus and Analysis of Their Druglikeness and Toxicological Properties

text: Abstract Calophyllum spp. (Calophyllaceae) is a genus of tropical trees valued in the chemopharmacological industry as an important source of biogenetically related coumarins and xanthones, which can lead to the development of new drugs due to their relevant pharmacological activities and diversity of molecular structural. These compounds have relevant pharmacological activities, such as: cytotoxicity against human tumor cell lines (especially leukemia), parasites (Plasmodium, Leshmania, and Trypanosoma), retroviruses (e.g., HIV), and Mycobacterium tuberculosis. Chemoinformatic and toxicoinformatic tools were used here to perform a computational analysis of 70 coumarins and 70 xanthones isolated from this genus in order to explore their potential as new drugs. Most coumarins from this genus possess similar patterns of druglikeness with differences in its physicochemical properties. Xanthones, on the other hand, show quite similar physicochemical properties and druglikeness. It is interesting to note that the vast majority of these compounds (57 coumarins and 59 xanthones) are in compliance with Lipinski´s Rule of Five. Remarkably, two xanthones (2-hydroxyxanthone and caledonixanthone-B) have leadlikeness potential that accordingly with chemoinformatic analysis may target MAO A and B, respectively, and therefore may exhibit antidepressant potential. These compounds also target tyrosine-phosphorilation-regulated kinase 1A (DYRK1A) which is over-expressed in a variety of hematological and brain cancers, therefore they could act as anticancer compounds. Several toxicological predictions were also depicted. Coumarins could be an irritant and may affect the reproductive system, while xanthones may have mutagenic results. To our knowledge, this is the first chemoinformatic report on the main active compounds of this genus and its potential for drug development.


title: First detection of bovine coronavirus in Yak (Bos grunniens) and a bovine coronavirus genome with a recombinant HE gene

text: The yak (Bosgrunniens) is a unique domestic bovine species that plays an indispensable role for herdsmen in the Qinghai–Tibet Plateau. Here, 336 diarrhoeic samples were collected from yaks on 29 farms in the Qinghai–Tibet Plateau from 2015 to 2017. Approximately 69.05 % (232/336) of the diarrhoeic samples were assessed as bovine coronavirus (BCoV)-positive by RT-PCR assay, and most of the detected strains showed a unique evolution based on 40 spike (S), nucleocapsid (N) and haemagglutinin-esterase (HE) gene fragments. Notably, the 12 complete S genes detected shared 1 identical amino acid mutation (E121V) in the S1 subunit compared with the other 150 complete S genes in the GenBank database. Furthermore, a BCoV strain (designated YAK/HY24/CH/2017) was isolated from one diarrhoeic sample (virus titre : 10(8.17)TCID(50) ml(−1)), and a phylogenetic analysis based on complete genome sequences revealed that strain YAK/HY24/CH/2017 has the closest genetic relationship with the BCoV prototype strain Mebus. Interestingly, 2 significant characteristics were observed in the genome of strain YAK/HY24/CH/2017 : (1) the strain had 26 unique amino acid variations in the S gene compared with the other 150 BCoV S genes in the GenBank database and (2) a recombination event was identified between the esterase and lectin domains of the HE gene. In conclusion, this study revealed the high prevalence of BCoV in yaks in the Qinghai–Tibet Plateau. To the best of our knowledge, this is the first description of the molecular prevalence of BCoV in yaks and of a BCoV genome with an HE gene recombination.


title: Multicenter evaluation of the QIAstat Respiratory Panel—A new rapid highly multiplexed PCR based assay for diagnosis of acute respiratory tract infections

text: Acute respiratory tract infections (ARTI), including the common cold, pharyngitis, sinusitis, otitis media, bronchiolitis and pneumonia are the most common diagnoses among patients seeking medical care in western countries, and account for most antibiotic prescriptions. While a confirmed and fast ARTI diagnosis is key for antibiotic prescribing, empiric antimicrobial treatment remains common, because viral symptoms are often clinically similar and difficult to distinguish from those caused by bacteria. As a result, inappropriate antibiotic prescriptions are high and in certain settings likely higher than the commonly estimated 30%. The QIAstat Respiratory Panel(®) assay (QIAstat RP) is a multiplexed in vitro diagnostics test for the rapid simultaneous detection of 21 pathogens directly from respiratory samples, including human mastadenovirus A-G, primate bocaparvovirus 1+2, human coronavirus (HKU1, NL63, OC43, 229E), human metapneumovirus A/B, rhinovirus/enterovirus, influenza A virus (no subtype, subtype H1, H1N1/2009, H3), influenza B virus, human respirovirus 1+3, human orthorubulavirus 2+4, human orthopneumovirus, Bordetella pertussis, Chlamydia pneumoniae, Mycoplasma pneumoniae and Legionella pneumophila. We describe the first multicenter study of 445 respiratory samples, collected through the 2016–2017 and 2018 respiratory seasons, with performance compared against BioFire FilmArray RP v1.7 and discrepancy testing by Seegene Allplex RP. The QIAstat RP demonstrated a positive percentage of agreement of 98.0% (95% CI: 96.0–99.1%) and a negative percentage agreement of 99.8% (95% CI: 99.6–99.9%). With use of this comprehensive and rapid test, improved patient outcomes and antimicrobial stewardship may potentially be achieved.


title: COVID-19 : caractéristiques cliniques, biologiques et radiologiques chez l’adulte, la femme enceinte et l’enfant. Une mise au point au cœur de la pandémie

text: The spread of the new coronavirus SARS-CoV-2, discovered in China in January 2020, led to a pandemic as early as March 2020, forcing every health care system in the affected countries to adapt quickly. In order to better address this major health crisis, which has given rise to numerous scientific publications, we have synthesized the main original clinical studies to facilitate the day-to-day management of patients with COVID-19. We detail the early signs and progression of the disease as well as the different clinical forms, including extra-pulmonary, as known at the beginning of this pandemic. We focus on clinical, biological and CT markers predictive of severity or mortality. Finally, we discuss the impact of SARS-CoV-2 infection in populations suspected to be at high risk of severe forms.


title: Identification of a metabolic gene panel to predict the prognosis of myelodysplastic syndrome

text: Myelodysplastic syndrome (MDS) is clonal disease featured by ineffective haematopoiesis and potential progression into acute myeloid leukaemia (AML). At present, the risk stratification and prognosis of MDS need to be further optimized. A prognostic model was constructed by the least absolute shrinkage and selection operator (LASSO) regression analysis for MDS patients based on the identified metabolic gene panel in training cohort, followed by external validation in an independent cohort. The patients with lower risk had better prognosis than patients with higher risk. The constructed model was verified as an independent prognostic factor for MDS patients with hazard ratios of 3.721 (1.814‐7.630) and 2.047 (1.013‐4.138) in the training cohort and validation cohort, respectively. The AUC of 3‐year overall survival was 0.846 and 0.743 in the training cohort and validation cohort, respectively. The high‐risk score was significantly related to other clinical prognostic characteristics, including higher bone marrow blast cells and lower absolute neutrophil count. Moreover, gene set enrichment analyses (GSEA) showed several significantly enriched pathways, with potential indication of the pathogenesis. In this study, we identified a novel stable metabolic panel, which might not only reveal the dysregulated metabolic microenvironment, but can be used to predict the prognosis of MDS.


title: COVID‐19 infections and deaths among Connecticut nursing home residents: facility correlates

text: OBJECTIVE: To determine the associations of nursing home registered nurse (RN) staffing, overall quality of care, and concentration of Medicaid or racial and ethnic minority residents with COVID‐19 confirmed cases and deaths by April 16, 2020 among Connecticut nursing home residents. DESIGN: Cross‐sectional analysis on Connecticut nursing home (n=215) COVID‐19 report, linked to other nursing home files and county counts of confirmed cases and deaths. Multivariable two‐part models determined the associations of key nursing home characteristics with the likelihood of at least 1 confirmed case (or death) in the facility, and with the count of cases (deaths) among facilities with at least 1 confirmed case (death). RESULTS: The average number of confirmed cases was 8 per nursing home (zero in 107 facilities), and the average number of confirmed deaths was 1.7 per nursing home (zero in 131 facilities). Among facilities with at least 1 confirmed case, every 20 minutes (per resident day) increase in RN staffing was associated with 22% fewer confirmed cases (incidence rate ratio [IRR]=0.78, 95% confidence interval [CI] 0.68‐0.89, p<0.001); compared to 1‐ to 3‐star facilities, 4‐ or 5‐star facilities had 13% fewer confirmed cases (IRR=0.87, 95% CI 0.78‐0.97, p<0.015); and facilities with high concentration of Medicaid residents (IRR=1.16, 95% CI 1.02‐1.32, p=0.025) or racial/ethnic minority residents (IRR=1.15, 95% CI 1.03‐1.29, p=0.026) had 16% and 15% more confirmed cases, respectively, than their counterparts. Among facilities with at least 1 death, every 20 minutes increase in RN staffing significantly predicted 26% fewer COVID‐19 deaths (IRR=0.74, 95% CI 0.55‐1.00, p=0.047). Other focused characteristics did not show statistically significant associations with deaths. CONCLUSIONS: Nursing homes with higher RN staffing and quality ratings have the potential to better control the spread of the novel coronavirus and reduce deaths. Nursing homes caring predominantly for Medicaid or racial and ethnic minority residents tend to have more confirmed cases.


title: Target Virus or Target Ourselves for COVID-19 Drugs Discovery?-Lessons learned from anti-influenzas virus therapies

text: Abstract The COVID-19 pandemic, after it was reported in December 2019, is a highly contagious and now spreading to over 190 countries, causing a severe public health burden. Currently, there is no vaccine or specific drug to treat COVID-19, which is caused by a novel coronavirus, SARS-2-CoV. For this emergency, the FDA has approved Remdesivir and Hydroxychloroquine for treatment of COVID-19 as Emergency Use Authorization. However, even after this pandemic, COVID-19 may still have a chance to come back. Therefore, we need to come out with new strategies for drug discovery for combating COVID-19 in the future.


title: Application of deep learning technique to manage COVID-19 in routine clinical practice using CT images: Results of 10 convolutional neural networks

text: Abstract Fast diagnostic methods can control and prevent the spread of pandemic diseases like coronavirus disease 2019 (COVID-19) and assist physicians to better manage patients in high workload conditions. Although a laboratory test is the current routine diagnostic tool, it is time-consuming, imposing a high cost and requiring a well-equipped laboratory for analysis. Computed tomography (CT) has thus far become a fast method to diagnose patients with COVID-19. However, the performance of radiologists in diagnosis of COVID-19 was moderate. Accordingly, additional investigations are needed to improve the performance in diagnosing COVID-19. In this study is suggested a rapid and valid method for COVID-19 diagnosis using an artificial intelligence technique based. 1020 CT slices from 108 patients with laboratory proven COVID-19 (the COVID-19 group) and 86 patients with other atypical and viral pneumonia diseases (the non-COVID-19 group) were included. Ten well-known convolutional neural networks were used to distinguish infection of COVID-19 from non-COVID-19 groups: AlexNet, VGG-16, VGG-19, SqueezeNet, GoogleNet, MobileNet-V2, ResNet-18, ResNet-50, ResNet-101, and Xception. Among all networks, the best performance was achieved by ResNet-101 and Xception. ResNet-101 could distinguish COVID-19 from non-COVID-19 cases with an AUC of 0.994 (sensitivity, 100%; specificity, 99.02%; accuracy, 99.51%). Xception achieved an AUC of 0.994 (sensitivity, 98.04%; specificity, 100%; accuracy, 99.02%). However, the performance of the radiologist was moderate with an AUC of 0.873 (sensitivity, 89.21%; specificity, 83.33%; accuracy, 86.27%). ResNet-101 can be considered as a high sensitivity model to characterize and diagnose COVID-19 infections, and can be used as an adjuvant tool in radiology departments.


title: Viral antibodies in bovine fetuses in Argentina

text: Abstract In order to establish the prevalence of viral infections of the bovine fetus in Argentina, a serological survey for antibodies against viral agents currently affecting cattle in this country was conducted. Antibodies against foot-and-mouth disease virus (FMDV), bovine herpesvirus-1 (BHV-1), bovine leukaemia virus (BLV), bovine rotavirus (BRV), bovine coronavirus (BCV), bovine viral diarrhoea virus (BVDV) and parainfluenza-3 (PI-3) were investigated in a total of 315 fetal serum samples. Conventional techniques were used: indirect immunofluorescence (FMDV, BHV-1, BVDv and BCV), radial immunodiffusion (BLV), ELISA (BRV) and haemagglutination inhibition (PI-3). Antibodies against BHV-1, BVDV and PI-3 were detected in samples from fetuses in the second and third trimester of gestation, with a prevalence of 1·21 per cent (two of 165), 2·03 per cent (four of 197) and 5·08 per cent (nine of 177), respectively. Either antibodies or non-antibody factors able to bind to BRV and Bcv antigens were detected with a prevalence of 2·44 per cent (five of 205) and 4·54 per cent (five of 110), respectively. In addition, 14·68 per cent of non-specific inhibitors of PI-3 mediated haemagglutination were found. No seropositives against FMDV and BLV were detected.


title: Epidemiology, genome, and clinical features of the pandemic SARS-CoV-2: a recent view

text: Since the emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China, the number of globally confirmed cases according to World Health Organization statistics reached 292 124 in 189 countries by 22 March 2020. The number of deaths reached 12 784, with estimated case-fatality rates ranging from 0.5% to 5.7%. Children population seems to be the least affected by the disease, while the highest rate of death is among the elderly and people with comorbidities. Most infected individuals are asymptomatic or only exhibit mild symptoms. After the incubation period, the most common symptoms are fever, cough and fatigue. Asymptomatic carrier state is of paramount importance because of carriers' ability to spread the infection and to shed the virus into the air and surroundings. Although much is still unknown about SARS-CoV-2, the scientific research is moving at an unprecedented pace towards understanding the nature, effective control, prevention and treatment of SARS-CoV-2. Various reports have suggested an in vivo evolution of the virus, which may explain the rapid spread and changing epidemiology of SARS-CoV-2, but further evidence is needed. Unfortunately, no effective treatment or therapeutic drug is available for the disease; only supportive treatment and classical intervention measures are available for confronting the SARS-CoV-2 pandemic.


title: Evaluation of Two Dry Commercial Therapeutic Diets for the Management of Feline Chronic Gastroenteropathy

text: Management of feline chronic gastroenteropathies has included intervention with both veterinary therapeutic formulas designed to manage non-specific gastrointestinal disorders and those designed with limited novel or hydrolyzed ingredients for management of food-responsive enteropathies and steroid-responsive enteropathies (inflammatory bowel disease). There have been few studies evaluating the use of dietary intervention for the management of feline chronic gastroenteropathy. This prospective, multi-center study evaluated the use of two commercially available feline veterinary therapeutic dry diets designed to manage non-specific gastrointestinal disorders in 28 cats with a history of chronic vomiting and/or diarrhea. The majority of cats enrolled in the study had a history of vomiting (n = 25), with a smaller number having a history of concurrent diarrhea (n = 2) or diarrhea alone (n = 3). Cats were excluded if diagnostic tests identified any systemic or infectious disease that could be associated with the clinical signs of vomiting or diarrhea, and if they were panhypoproteinemic, hypoalbuminemic, hypocobalaminemic, or had a Spec fPL ≥5.4 µg/L. Cats were randomized to one of two veterinary therapeutic diets for 4 weeks. Feeding of both therapeutic diets resulted in a numeric reduction in the number of vomiting episodes over the 4-week period, but no significant differences were seen between dietary interventions. When looking within dietary groups, significant differences were seen in cats fed Diet A with reductions of 69.1, 73.3, and 63.2% (p values of 0.008, 0.003, and 0.029) in weeks 2, 3, and 4, respectively, when compared to week 0. The probability of vomiting also showed significant reductions in cats fed Diet A between weeks 0 and 2, 3, and 4, with odds ratios of 0.008, 0.005, and 0.005, respectively (p values of 0.038, 0.23, and 0.23). Results of this study demonstrate that a veterinary therapeutic gastrointestinal formula can be effective in the management of feline chronic vomiting. Cats that fail to respond to this dietary approach after a 2- to 4-week trial may benefit from a limited novel or hydrolyzed ingredient formula and may require additional diagnostics to better characterize the underlying disease.


title: Traffic-driven SIR epidemic spreading in networks

text: Abstract We study SIR epidemic spreading in networks driven by traffic dynamics, which are further governed by static routing protocols. We obtain the maximum instantaneous population of infected nodes and the maximum population of ever infected nodes through simulation. We find that generally more balanced load distribution leads to more intense and wide spread of an epidemic in networks. Increasing either average node degree or homogeneity of degree distribution will facilitate epidemic spreading. When packet generation rate ρ is small, increasing ρ favors epidemic spreading. However, when ρ is large enough, traffic congestion appears which inhibits epidemic spreading.


title: Sorting of progeny coronavirus from condensed secretory proteins at the exit from the trans-Golgi network of AtT20 cells

text: Murine hepatitis virus (strain A59), (MHV-A59) is a coronavirus that buds into pre-Golgi compartments and then exploits the exocytic pathway of the host cell to reach the exterior. The fibroblastic cells in which replication of this virus is usually studied have only a constitutive exocytic pathway that the virus uses. MHV-A59 also infects, albeit inefficiently, AtT20 cells, murine pituitary tumor cells with a regulated as well as a constitutive exocytic pathway. Here we examine AtT20 cells at early times after the infection, when the Golgi apparatus retains its morphological and biochemical integrity. We observe that progeny coronavirus and secretory protein destined for the secretory granules of the regulated exocytic pathway traverse the same Golgi stacks and accumulate in the trans-Golgi network. Their pathways diverge at this site, the condensed secretory proteins including the ACTH going to the secretory granules and the coronavirus to post-Golgi transport vesicles devoid of ACTH. On very rare occasions there is missorting such that aggregates of condensed secretory proteins and viruses occur together in post-Golgi vesicles. We conclude that the constitutive and regulated exocytic pathways, identified respectively by the progeny virions and the secretory protein ACTH, diverge at the exit from the trans-Golgi network.


title: Emerging Highly Virulent Porcine Epidemic Diarrhea Virus: Molecular Mechanisms of Attenuation and Rational Design of Live Attenuated Vaccines

text: The highly virulent porcine epidemic diarrhea virus (PEDV) emerged in China in 2010. It infects pigs of all ages, and causes severe diarrhea and high mortality rates in newborn pigs, leading to devastating economic losses in the pork industry worldwide. Effective and safe vaccines against highly virulent PEDV strains are still unavailable, hampering the further prevention, control and eradication of the disease in herds. Vaccination of pregnant sows with live attenuated vaccines (LAVs) is the most effective strategy to induce lactogenic immunity in the sows, which provides A passive protection of suckling piglets against PEDV via the colostrum (beestings, or first milk) and milk. Several LAV candidates have been developed via serially passaging the highly virulent PEDV isolates in non-porcine Vero cells. However, their efficacies in the induction of sufficient protection against virulent PEDV challenge vary in vivo. In this review, we summarize the current knowledge of the virulence-related mutations of PEDV and their potential roles in PEDV attenuation in vivo. With the successful development of reverse genetics systems for PEDV, we also discuss how to use them to generate promising LAV candidates that are safe, effective and genetically stable. This article provides timely insight into the rational design of effective and safe PEDV LAV candidates.


title: Multipurpose Instantaneous Microarray Detection of Acute Encephalitis Causing Viruses and Their Expression Profiles

text: Detection of multiple viruses is important for global analysis of gene or protein content and expression, opening up new prospects in terms of molecular and physiological systems for pathogenic diagnosis. Early diagnosis is crucial for disease treatment and control as it reduces inappropriate use of antiviral therapy and focuses surveillance activity. This requires the ability to detect and accurately diagnose infection at or close to the source/outbreak with minimum delay and the need for specific, accessible point-of-care diagnosis able to distinguish causative viruses and their subtypes. None of the available viral diagnostic assays combine a point-of-care format with the complex capability to identify a large range of human and animal viruses. Microarray detection provides a useful, labor-saving tool for detection of multiple viruses with several advantages, such as convenience and prevention of cross-contamination of polymerase chain reaction (PCR) products, which is of foremost importance in such applications. Recently, real-time PCR assays with the ability to confirm the amplification product and quantitate the target concentration have been developed. Furthermore, nucleotide sequence analysis of amplification products has facilitated epidemiological studies of infectious disease outbreaks and monitoring of treatment outcomes for infections, in particular for viruses that mutate at high frequency. This review discusses applications of microarray technology as a potential new tool for detection and identification of acute encephalitis-causing viruses in human serum, plasma, and cell cultures.


title: Community Mental Health Care Delivery During the COVID-19 Pandemic: Practical Strategies for Improving Care for People with Serious Mental Illness

text: The COVID-19 pandemic has presented a formidable challenge to care continuity for community mental health clients with serious mental illness and for providers who have had to quickly pivot the modes of delivering critical services. Despite these challenges, many of the changes implemented during the pandemic can and should be maintained. These include offering a spectrum of options for remote and in-person care, greater integration of behavioral and physical healthcare, prevention of viral exposure, increased collaborative decision-making related to long-acting injectable and clozapine use, modifying safety plans and psychiatric advance directives to include new technologies and broader support systems, leveraging natural supports, and integration of digital health interventions. This paper represents the authors’ collaborative attempt to both reflect the changes to clinical practice we have observed in CMHCs across the US during this pandemic and to suggest how these changes can align with best practices identified in the empirical literature.


title: Ability of device to collect bacteria from cough aerosols generated by adults with cystic fibrosis

text: Background: Identifying lung pathogens and acute spikes in lung counts remain a challenge in the treatment of patients with cystic fibrosis (CF). Bacteria from the deep lung may be sampled from aerosols produced during coughing. Methods: A new device was used to collect and measure bacteria levels from cough aerosols of patients with CF. Sputum and oral specimens were also collected and measured for comparison. Pseudomonas aeruginosa, Staphylococcus aureus, Klebsiella pneumoniae, and Streptococcus mitis were detected in specimens using Real-Time Polymerase Chain Reaction (RT-PCR) molecular assays. Results: Twenty adult patients with CF and 10 healthy controls participated. CF related bacteria (CFRB) were detected in 13/20 (65%) cough specimens versus 15/15 (100%) sputum specimens. Commensal S. mitis was present in 0/17 (0%, p=0.0002) cough specimens and 13/14 (93%) sputum samples. In normal controls, no bacteria were collected in cough specimens but 4/10 (40%) oral specimens were positive for CFRB. Conclusions: Non-invasive cough aerosol collection may detect lower respiratory pathogens in CF patients, with similar specificity and sensitivity to rates detected by BAL, without contamination by oral CFRB or commensal bacteria.


title: Mental health in elderly Spanish people in times of COVID-19 outbreak

text: BACKGROUND: We aim to assess COVID-19 outbreak-related emotional symptoms, identify gender differences, and study the relationship between the emotional state and environmental features in the elderly. METHODS: We conducted a cross-sectional study starting on March 29 to April 5, 2020 based on a national online survey using snowball sampling techniques. Symptoms of anxiety (Hamilton Anxiety Scale), depression (Beck Depression Inventory) and acute stress (Acute Stress Disorder Inventory) were compared between people over and under 60 years old. Gender differences and the relationship of loneliness, regular exercise, economic losses and use of anxiolytics on the mental state were evaluated. RESULTS: 1639 [150 (9.2%) aged ≥60] participants completed the survey. The ≥60 group showed lower mean (SD) BDI levels than the <60 group [3.02 (3.28) vs. 4.30 (4.93)]; and lower mean (SD) ASDI scores than the <60 group [3.68 (3.20) vs. 4.45 (3.06)]. There were no gender differences in any of the clinical measures. The presence of economic losses as well as the increase in the use of anxiolytics was significantly associated with higher emotional distress in the elderly compared to the younger group. CONCLUSIONS: Older people has shown less emotional distress, with no differences between men and women. Economic loss and substance use should be monitored to guarantee the emotional well-being of the elderly.


title: Mathematical Modeling of COVID-19 Transmission Dynamics with a Case Study of Wuhan

text: Abstract We propose a compartmental mathematical model for the spread of the COVID-19 disease with special focus on the transmissibility of super-spreaders individuals. We compute the basic reproduction number threshold, we study the local stability of the disease free equilibrium in terms of the basic reproduction number, and we investigate the sensitivity of the model with respect to the variation of each one of its parameters. Numerical simulations show the suitability of the proposed COVID-19 model for the outbreak that occurred in Wuhan, China.


title: The amino-terminal signal peptide on the porcine transmissible gastroenteritis coronavirus matrix protein is not an absolute requirement for membrane translocation and glycosylation

text: Abstract cDNA clones mapping within the first 2601 bases of the 3′ end of the porcine transmissible gastroenteritis coronavirus (TGEV) genome were sequenced by the method of Maxam and Gilbert and an open reading frame yielding a protein having properties of the matrix (M or E1) protein was identified. It is positioned at the 5′ side of the nucleocapsid (N) gene from which it is separated by an intergenic stretch of 12 bases. The deduced M protein comprises 262 amino acids, has a molecular weight of 29,544, is moderately hydrophobic, and has a net charge of +7 at neutral pH. Thirty-four percent of its amino acid sequence is homologous with the M protein of the bovine coronavirus (BCV), 32% with that of the mouse hepatitis coronavirus (MHV), and 19% with that of the avian infectious bronchitis coronavirus (IBV). Judging from alignment with the BCV, MHV, and IBV M proteins, the amino terminus of the TGEV M protein extends 54 amino acids from the virion envelope which compares with only 28 for BCV, 26 for MHV, and 21 for IBV. Eleven of the sixteen amino-terminal amino acids are hydrophobic and the positions of charged amino acids around this sequence suggest that the first 16 amino acids comprise a potentially cleavable signal peptide for membrane insertion. A similar sequence is not found in the M proteins of BCV, MHV, or IBV. When mRNA from infected cells, or RNA prepared by in vitro transcription of the reconstructed M gene, was translated in vitro in the presence of microsomes, the M protein became translocated and glycosylated. When a protein without the amino-terminal signal peptide was made by translating a truncated version of the M gene transcript, some translocation and glycosylation also occurred suggesting that the amino-terminal signal peptide on the TGEV M protein is not an absolute requirement for membrane translocation. Interestingly, the amino-terminal peptide did not appear to be cleaved during in vitro translation in the presence of microsomes suggesting that a step in virion assembly may be required for proper exposure of the cleavage site to the signal peptidase.


title: Risques viraux émergents en transfusion sanguine

text: During the last 20 years, the safety of blood products increased dramatically with regard to the infectious risk and notably to that represented by retroviruses (HIV and HTLV) and hepatitis B and C viruses. The aim of this review is to identify the residual and emergent viral threats that could be responsible for the occurring of new contaminations in the receivers of blood products. Beside many other viruses (HHV-8, erythrovirus B19, hepatitis A and E viruses…), a special attention has been paid to emerging arbovirus diseases (West Nile virus infection, dengue, chikungunya) that threaten to occur in the French metropolitan area following the implantation in Europe of the mosquito Aedes albopictus, the main vector of dengue and chikungunya in temperate regions. Another blood-linked risk, notably in United Kingdom and France, is the prion agent responsible for the variant form of the Creutzfeldt-Jakob disease. The review is concluded by a brief overview of the measures aimed to control these emergences, including the exclusion of at-risk donors, the diagnostic tests able to detect a specific agent, the leukocyte reduction of labile blood products, and the physical or chemical treatments aiming the nonspecific inactivation of infectious agents potentially present in blood without impairing significantly the physiological properties of blood compounds. The ability to control prospectively the new viral risks linked to blood products is a challenge for the preservation of the confidence of both clinicians and receivers in the safety of blood transfusion.


Propiedades antivirales y antiinflamatorias de ivermectina y su potencial uso en COVID-19


title: Globalization and advances in information and communication technologies: The impact on nursing and health

text: Globalization and information and communication technology (ICT) continue to change us and the world we live in. Nursing stands at an opportunity intersection where challenging global health issues, an international workforce shortage, and massive growth of ICT combine to create a very unique space for nursing leadership and nursing intervention. Learning from prior successes in the field can assist nurse leaders in planning and advancing strategies for global health using ICT. Attention to lessons learned will assist in combating the technological apartheid that is already present in many areas of the globe and will highlight opportunities for innovative applications in health. ICT has opened new channels of communication, creating the beginnings of a global information society that will facilitate access to isolated areas where health needs are extreme and where nursing can contribute significantly to the achievement of “Health for All.” The purpose of this article is to discuss the relationships between globalization, health, and ICT, and to illuminate opportunities for nursing in this flattening and increasingly interconnected world.


title: Prospective evaluation of a new automated nucleic acid extraction system using routine clinical respiratory specimens

text: The aim of the study was to evaluate the MagNA Pure 96™ nucleic acid extraction system using clinical respiratory specimens for identifying viruses by qualitative real‐time PCR assays. Three extraction methods were tested, that is, the MagNA Pure LC™, the COBAS Ampliprep™, and the MagNA Pure 96™ with 10‐fold dilutions of an influenza A(H1N1)pdm09 sample. Two hundred thirty‐nine respiratory specimens, 35 throat swabs, 164 nasopharyngeal specimens, and 40 broncho‐alveolar fluids, were extracted with the MagNA Pure 96™ and the COBAS Ampliprep™ instruments. Forty COBAS Ampliprep™ positive samples were also tested. Real‐time PCRs were used to identify influenza A and influenza A(H1N1)pdm09, rhinovirus, enterovirus, adenovirus, varicella zoster virus, cytomegalovirus, and herpes simplex virus. Similar results were obtained on RNA extracted from dilutions of influenza A(H1N1)pdm09 with the three systems: the MagNA Pure LC™, the COBAS Ampliprep™, and the MagNA Pure 96™. Data from clinical respiratory specimens extracted with the MagNA Pure 96™ and COBAS Ampliprep™ instruments were in 98.5% in agreement (P < 0.0001) for influenza A and influenza A(H1N1)pdm09. Data for rhinovirus were in 97.3% agreement (P < 0.0001) and in 96.8% agreement for enterovirus. They were in 100% agreement for adenovirus. Data for cytomegalovirus and HSV1‐2 were in 95.2% agreement (P < 0.0001). The MagNA Pure 96™ instrument is easy‐to‐use, reliable, and has a high throughput for extracting total nucleic acid from respiratory specimens. These extracts are suitable for molecular diagnosis with any type of real‐time PCR assay. J. Med. Virol. 84:906–911, 2012. © 2012 Wiley Periodicals, Inc.


title: Modeling the Heterogeneity of Dengue Transmission in a City

text: Dengue fever is one of the most important vector-borne diseases in the world, and modeling its transmission dynamics allows for determining the key influence factors and helps to perform interventions. The heterogeneity of mosquito bites of humans during the spread of dengue virus is an important factor that should be considered when modeling the dynamics. However, traditional models generally assumed homogeneous mixing between humans and vectors, which is inconsistent with reality. In this study, we proposed a compartmental model with negative binomial distribution transmission terms to model this heterogeneity at the population level. By including the aquatic stage of mosquitoes and incorporating the impacts of the environment and climate factors, an extended model was used to simulate the 2014 dengue outbreak in Guangzhou, China, and to simulate the spread of dengue in different scenarios. The results showed that a high level of heterogeneity can result in a small peak size in an outbreak. As the level of heterogeneity decreases, the transmission dynamics approximate the dynamics predicted by the corresponding homogeneous mixing model. The simulation results from different scenarios showed that performing interventions early and decreasing the carrying capacity for mosquitoes are necessary for preventing and controlling dengue epidemics. This study contributes to a better understanding of the impact of heterogeneity during the spread of dengue virus.


title: Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases

text: OBJECTIVES: To report methods and findings of 2 autopsies with molecular evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive individuals. METHODS: Postmortem examination was completed following Centers for Disease Control and Prevention public guidelines. Numerous formalin-fixed paraffin-embedded (FFPE) tissue types from each case were surveyed for SARS-CoV-2 RNA by quantitative reverse transcription polymerase chain reaction (qRT-PCR). SARS-CoV-2 viral genome was sequenced by next-generation sequencing (NGS) from FFPE lung tissue blocks. RESULTS: Postmortem examinations revealed diffuse alveolar damage, while no viral-associated hepatic, cardiac, or renal damage was observed. Viral RNA was detected in lungs, bronchi, lymph nodes, and spleen in both cases using qRT-PCR method. RNA sequencing using NGS in case 1 revealed mutations most consistent with Western European Clade A2a with ORF1a L3606F mutation. CONCLUSIONS: SARS-CoV-2 testing and viral sequencing can be performed from FFPE tissue. Detection and sequencing of SARS-CoV-2 in combination with morphological findings from postmortem tissue examination can aid in gaining a better understanding of the virus’s pathophysiologic effects on human health.


title: Effect of inhaled azodicarbonamide on F344 N rats and B6C3F1 mice with 2-week and 13-week inhalation exposures

text: Abstract Azodicarbonamide (ADA), a compound used in the baking and plastics industries, has been reported to cause pulmonary sensitization and dermatitis in people. Two-week repeated and 13-week subchronic inhalation exposures of F344 N rats and B6C3F1 mice to ADA were conducted to determine the toxicity of inhaled ADA. The mean air concentrations of ADA in the 2-week studies were 207, 102, 52, 9.4, or 2.0 mg/m3. No exposure-related mortality nor abnormal clinical signs were observed in rats or mice during or after exposure. The terminal body weights were slightly depressed in the highest exposure group. Liver weights were lower in male rats exposed to 200 mg ADA/m3. No significant lesions were noted on either gross or histologic evaluation of rats or mice. In the 13-week subchronic study, the mean air concentrations of ADA were 204, 100, or 50 mg/m3. No mortality or clinical signs related to exposure were observed. The terminal body weights of exposed rats were not significantly different from those of control rats but were significantly depressed in mice exposed to 100 or 200 mg ADA/m3. No histopathological lesions were noted in mice. Lung weights were increased and enlarged mediastinal and/or tracheobronchial lymph nodes were noted in rats exposed to 50 mg ADA/m3. No exposure-related lesions were observed microscopically in rats exposed to 100 or 200 mg ADA/m3. All rats in the 50 mg DNA/m3 exposure group only had lung lesions that consisted of perivascular cuffing with lymphocytes and a multifocal type II cell hyperplasia, suggesting a possible immune reaction to an antigen in the lung. Viral titers for rats exposed to 50 mg ADA/m3 were negative for Sendai virus and pneumonia virus of mice, which produce similar lesions. The possibility of an unknown viral antigen causing this lesion cannot be eliminated. Lung tissue from male rats was analyzed for ADA and biurea, the major metabolite of ADA. No ADA was detected. The amount of biurea in the lungs increased nonlinearly with increasing exposure concentration, suggesting that clearance was somewhat impaired with repeated exposures. However, even at the highest exposure concentration, this amount of biurea was less than 1% of the estimated total ADA deposited over the exposure period. In summary, ADA is rapidly cleared from the lungs, even when inhaled at concentrations up to 200 mg/m3. Exposure to ADA for up to 13 weeks did not appear to be toxic to rodents.


title: Mathematical model of infection kinetics and its analysis for COVID-19, SARS and MERS

text: Abstract The purpose of this paper is to reveal the spread rules of the three pneumonia: COVID-19, SARS and MERS. We compare the new spread characteristics of COVID-19 with those of SARS and MERS. By considering the growth rate and inhibition constant of infectious diseases, their propagation growth model is established. The parameters of the three coronavirus transmission growth models are obtained by nonlinear fitting. Parametric analysis shows that the growth rate of COVID-19 is about twice that of the SARS and MERS, and the COVID-19 doubling cycle is two to three days, suggesting that the number of COVID-19 patients would double in two to three days without human intervention. The infection inhibition constant in Hubei is two orders of magnitude lower than in other regions, which reasonably explains the situation of the COVID-19 outbreak in Hubei.


title: Comparative analysis of perceived stress in dermatologists and other physicians during home‐quarantine and COVID‐19 pandemic with exploration of possible risk factors‐ A web‐based cross‐sectional study from Eastern India

text: Since the declaration of COVID‐19 as global pandemic, several countries including India have enforced a national quarantine.We aimed to compare the perceived stress of Dermatologists and non‐dermatologists, due to quarantine and COVID‐19 pandemic and analyze the role of possible risk‐factors. We conducted a web‐based cross‐sectional study to determine the perceived stress of doctors using the Perceived stress scale‐10 and evaluate possible risk‐factors. Among 384 valid responders,we had 37.5% dermatologists and 62.5% non‐dermatologists. Perceived stress was more in non‐dermatologists compared to dermatologists, but not statistically significant (P = 0.1). Degree of stress was also comparable (P = 0.5). Higher stress was significantly associated with females and unmarried individuals in both groups. Risk of infecting self or colleagues or family members and lack of protective gear at work‐place were top causes of stress. Perceived stress is increased in all doctors due to COVID‐19 pandemic and quarantine. Even dermatologists have developed high‐stress due to current situation, comparable to non‐dermatologists, despite being traditionally considered an out‐patient speciality with minimum stress. Thus, proper mental health care policies should be adopted for all doctors, including dermatologists. This article is protected by copyright. All rights reserved.


nBreastfeeding Risk from Detectable Severe Acute Respiratory Syndrome Coronavirus 2 in Breastmilk


title: Oncological Surgery During the COVID‐19 Pandemic: The Need for Deep and Lasting Measures

text: The COVID‐19 pandemic has overwhelmed health system capacity and affected cancer centers worldwide. This letter to the editor proposes the need to prepare for a long‐lasting battle.


title: Regulation of aminopeptidase N (EC 3.4.11.2; APN; CD13) by interferon-γ on the HL-60 cell line

text: Abstract Membrane-bound peptidases play important roles in the regulation of local concentrations of various signalling peptides such as the growth factors, hormones, chemokines and cytokines. That is accomplished by means of their enzyme activity. Recently, membrane-bound peptidases have also been shown to act as receptors, receiving signals from as yet undefined ligands and transducing them into the cell interior. By using either or both of these mechanisms, peptidases interact with fundamental cellular functions: growth, differentiation, activation and death. This study addressed the effects of a T-cell derived cytokine, interferon-gamma (IFN-γ) on the activity of aminopeptidase N (APN), an ectoenzyme processing several signal peptides. Cells of a myelo-monocytic cell line HL-60 were used as a model system, and APN was assayed at the levels of mRNA, its membrane marker CD13, and the enzyme activity. Regulation of CD13/APN by IFN-γ was found at all three levels. The direction of regulation was time-dependent: an initial down-regulation seen 24 and 48 hrs after the onset of treatment with IFN-γ was replaced by an up-regulation after 72 and/or 96 hrs. Up-regulation of CD13/APN observed after 96 hrs was preceded by an up-regulation of APN mRNA reaching its maximum after 72 hrs. The IFN-γ-induced regulation of APN was due to membrane aminopeptidase N, since it could be completely abrogated by an APN blocking antibody WM-15. The delayed up-regulation of CD13/APN (observed after 72 and/or 96 hrs), required de novo protein synthesis as it could be abrogated by cycloheximide, an inhibitor of protein synthesis. Possible role of endogenous (IFN-γ-induced) TGF-β in mediating CD13/APN up-regulation could be excluded, since no TGF-β was found in supernatants of IFN-γ treated HL-60 cells. Thus, our data show regulation of CD13/APN on cells of myelo-monocytic origin by a T-cell derived cytokine, IFN-γ. A similar mechanism might play a role in inflammation.


title: Le syndrome respiratoire aigu sévère (SRAS) existe aussi chez l’enfant et semble d’autant moins agressif que l’enfant est plus jeune K.L.E. Hon

text: Unknown


title: The SARS-CoV-2 cytopathic effect is blocked with autophagy modulators

text: SARS-CoV-02 is a new type of coronavirus capable of rapid transmission and causing severe clinical symptoms; much of which has unknown biological etiology. It has prompted researchers to rapidly mobilize their efforts towards identifying and developing anti-viral therapeutics and vaccines. Discovering and understanding the virus’ pathways of infection, host-protein interactions, and cytopathic effects will greatly aid in the design of new therapeutics to treat COVID-19. While it is known that chloroquine and hydroxychloroquine, extensively explored as clinical agents for COVID-19, have multiple cellular effects including inhibiting autophagy, there are also dose-limiting toxicities in patients that make clearly establishing their potential mechanisms-of-action problematic. Therefore, we evaluated a range of other autophagy modulators to identify an alternative autophagy-based drug repurposing opportunity. In this work, we found that 6 of these compounds blocked the cytopathic effect of SARS-CoV-2 in Vero-E6 cells with EC(50) values ranging from 2.0 to 13 μM and selectivity indices ranging from 1.5 to >10-fold. Immunofluorescence staining for LC3B and LysoTracker dye staining assays in several cell lines indicated their potency and efficacy for inhibiting autophagy correlated with the measurements in the SARS-CoV-2 cytopathic effect assay. Our data suggest that autophagy pathways could be targeted to combat SARS-CoV-2 infections and become an important component of drug combination therapies to improve the treatment outcomes for COVID-19.


title: Origination and consequences of bovine viral diarrhea virus diversity

text: The potential consequences of BVDV genetic and antigenic diversity are far ranging. The complexity of clinical presentations associated with BVDV likely arises from factors encoded by the virus genome. More importantly,prevention and control of BVDV may be complicated by diagnostic and immunization failure resulting from virus diversity. Evolutionary pressures will continue to drive further diversity, making control of BVDV challenging. Current and the potential for future BVDV strain diversity should be considered when designing BVDV control programs both at the individual farm and national herd level.


title: Containment measures for emerging and re-emerging vector-borne and other infectious diseases of poverty in urban settings: a scoping review

text: BACKGROUND: The emergence and re-emergence of vector-borne and other infectious diseases of poverty pose a threat to the health of populations living in urban and low-income settings. A detailed understanding of intervention strategies, including effectiveness of past outbreak containment, is necessary to improve future practices. The objective was to determine what is known about the effectiveness of containment measures for emerging and re-emerging vector-borne and other infectious diseases of poverty in urban settings and identify research gaps and implications for public health practice. MAIN BODY: We conducted a scoping review and systematically searched peer-reviewed and grey literature published between 2000 and 2016. Different data extraction tools were used for data coding and extraction, and data on implementation process and transferability were extracted from all studies. A quality assessment was conducted for each included study. We screened 205 full-text articles and reports for a total of 31 articles included in the review. The quality of the studies was generally low to moderate. The largest body of evidence concerned control activities for Ebola virus and dengue fever. The majority of interventions (87%) relied on multiple types of measures, which were grouped into four categories: 1) healthcare provision; 2) epidemiological investigation and/or surveillance; 3) environmental or sanitary interventions; and 4) community-based interventions. The quality of the majority of studies (90%) was poor or moderate, and one-third of the studies did not provide a clear description of the outcomes and of the procedures and/or tools used for the intervention. CONCLUSIONS: Our results highlight the difficulty of establishing causation when assessing the effect of containment measures. Studies that extend beyond solely reporting on effectiveness and take into account the complexity of real-world settings are urgently needed. We recommend the allocation of research efforts to the evaluation of the implementation processes of interventions as well as their comprehensive and systematic description using validated checklists. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s40249-018-0478-4) contains supplementary material, which is available to authorized users.


title: Use of early corticosteroid therapy on ICU admission in patients affected by severe pandemic (H1N1)v influenza A infection

text: INTRODUCTION: Early use of corticosteroids in patients affected by pandemic (H1N1)v influenza A infection, although relatively common, remains controversial. METHODS: Prospective, observational, multicenter study from 23 June 2009 through 11 February 2010, reported in the European Society of Intensive Care Medicine (ESICM) H1N1 registry. RESULTS: Two hundred twenty patients admitted to an intensive care unit (ICU) with completed outcome data were analyzed. Invasive mechanical ventilation was used in 155 (70.5%). Sixty-seven (30.5%) of the patients died in ICU and 75 (34.1%) whilst in hospital. One hundred twenty-six (57.3%) patients received corticosteroid therapy on admission to ICU. Patients who received corticosteroids were significantly older and were more likely to have coexisting asthma, chronic obstructive pulmonary disease (COPD), and chronic steroid use. These patients receiving corticosteroids had increased likelihood of developing hospital-acquired pneumonia (HAP) [26.2% versus 13.8%, p < 0.05; odds ratio (OR) 2.2, confidence interval (CI) 1.1–4.5]. Patients who received corticosteroids had significantly higher ICU mortality than patients who did not (46.0% versus 18.1%, p < 0.01; OR 3.8, CI 2.1–7.2). Cox regression analysis adjusted for severity and potential confounding factors identified that early use of corticosteroids was not significantly associated with mortality [hazard ratio (HR) 1.3, 95% CI 0.7–2.4, p = 0.4] but was still associated with an increased rate of HAP (OR 2.2, 95% CI 1.0–4.8, p < 0.05). When only patients developing acute respiratory distress syndrome (ARDS) were analyzed, similar results were observed. CONCLUSIONS: Early use of corticosteroids in patients affected by pandemic (H1N1)v influenza A infection did not result in better outcomes and was associated with increased risk of superinfections.


title: MultiBac: from protein complex structures to synthetic viral nanosystems

text: The MultiBac baculovirus/insect cell expression vector system was conceived as a user-friendly, modular tool-kit for producing multiprotein complexes for structural biology applications. MultiBac has allowed the structure and function of many molecular machines to be elucidated, including previously inaccessible high-value drug targets. More recently, MultiBac developments have shifted to customized baculoviral genomes that are tailored for a range of applications, including synthesizing artificial proteins by genetic code expansion. We review some of these developments, including the ongoing rewiring of the MultiBac system for mammalian applications, notably CRISPR/Cas9-mediated gene editing.


title: Contributions of pediatrics and pediatric pathology to the body of knowledge regarding human disease

text: Summary A century or so ago, pediatrics and pediatric pathology did not exist. Then, many fetuses/newborns died in utero or shortly after birth. With time, the issue of sepsis was addressed, and a greater number of newborns survived. Gradually, in this soil, the disciplines of pediatrics and pediatric nursing arose, as some recognized that infants were not merely small adults but were, in fact, quite different. Years later, pediatric pathology developed as a field of exploration. Today, pediatric pathology is a specialty, as witnessed by training programs, societies devoted to research and education, an expanding number of textbooks and innovative research. Pediatric pathology is distinct from adult pathology, as seen by the diversity of malformations and metabolic diseases stemming from mutations, the immaturity of the newborn's immune system, and the types of neoplasms germane to infants and children. Much of the progress in these areas was facilitated by the simultaneous emergence of cytogenetics and molecular biology and their powerful tools of investigation. The latter were applied in a synergistic fashion to a major extent in maternity clinics and children's hospitals by, among others, molecular biologists, clinical geneticists, cytogeneticists, pediatricians, and pediatric pathologists. This article describes a select but small number of the many contributions of pediatrics and pediatric pathology to the current body of medical knowledge.


title: SARS‐CoV‐2 Testing and Outcomes in the First 30 Days after the First Case of COVID‐19 at an Australian Children’s Hospital

text: OBJECTIVE: International studies describing COVID‐19 in children have shown low proportions of paediatric cases and generally a mild clinical course. We aimed to present early data on children tested for SARS‐CoV‐2 at a large Australian tertiary children’s hospital according to the state health department guidelines, which varied over time. METHODS: We conducted a retrospective cohort study at The Royal Children’s Hospital, Melbourne, Australia. It included all paediatric patients (aged 0–18 years) who presented to the Emergency Department (ED) or the Respiratory Infection Clinic (RIC) and were tested for SARS‐CoV‐2. The 30‐day study period commenced after the first confirmed positive case was detected at the hospital on 21(st) March 2020, until 19(th) April 2020. We recorded epidemiological and clinical data. RESULTS: There were 433 patients in whom SARS‐CoV‐2 testing was performed in ED (331 (76%)) or RIC (102 (24%)). There were 4 (0.9%) who had positive SARS‐CoV‐2 detected, none of whom were admitted to hospital or developed severe disease. Of these SARS‐CoV‐2 positive patients, 1/4 (25%) had a comorbidity, which was asthma. Of the SARS‐CoV‐2 negative patients, 196/429 (46%) had comorbidities. Risk factors for COVID‐19 were identified in 4/4 SARS‐CoV‐2 positive patients and 47/429 (11%) SARS‐CoV‐2 negative patients. CONCLUSIONS: Our study identified a very low rate of SARS‐CoV‐2 positive cases in children presenting to a tertiary ED or RIC, none of whom were admitted to hospital. A high proportion of patients who were SARS‐CoV‐2 negative had comorbidities.


Can concomitant use of zinc and curcumin with other immunity‐boosting nutraceuticals be the arsenal against COVID‐19?


title: Intragastric immunization with recombinant Lactobacillus casei expressing flagellar antigen confers antibody-independent protective immunity against Salmonella enterica serovar Enteritidis

text: A recombinant Lactobacillus casei expressing a flagellar antigen from Salmonella enterica serovar Enteritidis was constructed and evaluated as a mucosal vaccine. Intragastric immunization of the recombinant strain conferred protective immunity against Salmonella infection in mice. This immunization did not result in antigen-specific antibody in either feces or sera but induced the release of IFN-γ on restimulation of primed lymphocytes ex vivo. The results suggested that the protective efficacy provided by flagellin-expressing L. casei is mainly attributable to cell-mediated immune responses. In addition, an adjuvant-type effect of the antigen delivery system with L. casei was also observed.


title: Inferring super-spreading from transmission clusters of COVID-19 in Hong Kong, Japan and Singapore

text: Super-spreading events in an outbreak can change the nature of an epidemic. Therefore, it is useful for public health teams to determine if an ongoing outbreak has any contribution from such events, which may be amenable to interventions. We estimated the basic reproductive number (R(0)) and the dispersion factor (k) from empirical data on clusters of epidemiologically-linked COVID-19 cases in Hong Kong, Japan and Singapore. This allowed us to infer the presence or absence of super-spreading events during the early phase of these outbreaks. The relatively large values of k implied that large cluster sizes, compatible with super-spreading, were unlikely.


title: A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike

text: SARS-CoV-2 has emerged as a global pathogen(1,2), sparking urgent vaccine development efforts with the trimeric spike(3,4). However, the inability of antibodies like CR3022(5), which binds a cryptic spike epitope with nanomolar affinity(6), to neutralize virus, suggests a spike-based means of neutralization escape. Here, we show the SARS-CoV-2 spike to have 10% the unfolding enthalpy of a globular protein at physiological pH, where it is recognized by antibodies like CR3022, and up to 10-times more unfolding enthalpy at endosomal pH, where it sheds such antibodies, suggesting that the spike evades potentially neutralizing antibody through a pH-dependent mechanism of conformational masking. To understand the compatibility of this mechanism with ACE2-receptor interactions, we carried out binding measurements and determined cryo-EM structures of the spike recognizing up to three ACE2 molecules at both physiological and endosomal pH. In the absence of ACE2, cryo-EM analyses indicated lower pH to reduce conformational heterogeneity. Single-receptor binding domain (RBD)-up conformations dominated at pH 5.5, resolving into a locked all-down conformation at lower pH through lowering of RBD and refolding of a pH-dependent switch. Notably, the emerging Asp614Gly strain(7) partially destabilizes the switch that locks RBD down, thereby enhancing functional interactions with ACE2 while reducing evasion by conformational masking.