title: Epidemic curves made easy using the R package incidence

text: The epidemiological curve (epicurve) is one of the simplest yet most useful tools used by field epidemiologists, modellers, and decision makers for assessing the dynamics of infectious disease epidemics. Here, we present the free, open-source package incidence for the R programming language, which allows users to easily compute, handle, and visualise epicurves from unaggregated linelist data. This package was built in accordance with the development guidelines of the R Epidemics Consortium (RECON), which aim to ensure robustness and reliability through extensive automated testing, documentation, and good coding practices. As such, it fills an important gap in the toolbox for outbreak analytics using the R software, and provides a solid building block for further developments in infectious disease modelling. incidence is available from https://www.repidemicsconsortium.org/incidence.


title: Letter to the Editor Re: Coronavirus disease 2019: The harms of exaggerated information and non‐evidence‐based measures

text: Letter to the Editor Re: Coronavirus disease 2019: The harms of exaggerated information and non-evidence-based measures Prof. Ioannidis clearly and correctly identifies a real issue of the current emergency, namely that related to misinformation. This misinformation led to an erroneous perception of risk in some cases with the consequent lack of adoption of preventive interventions and in others to unmotivated and irrational behavior (e.g. panic shopping, shortage of supplies for personal protection such as face masks, etc).


title: Cricket paralysis virus internal ribosome entry site-derived RNA promotes conventional vaccine efficacy by enhancing a balanced Th1/Th2 response

text: Abstract An ideal adjuvant should increase vaccine efficacy through balanced Th1/Th2 responses and be safe to use. Recombinant protein-based vaccines are usually formulated with aluminum (alum)-based adjuvants to ensure an adequate immune response. However, use of alum triggers a Th2-biased immune induction, and hence is not optimal. Although the adjuvanticity of RNA has been reported, a systematic and overall investigation on its efficacy is lacking. We found that single strand RNA (termed RNA adjuvant) derived from cricket paralysis virus intergenic region internal ribosome entry site induced the expression of various adjuvant-function-related genes, such as type 1 and 2 interferon (IFN) and toll-like receptor (TLR), T cell activation, and leukocyte chemotaxis in human peripheral blood mononuclear cells; furthermore, its innate and IFN transcriptome profile patterns were similar to those of a live-attenuated yellow fever vaccine. This suggests that protein-based vaccines formulated using RNA adjuvant function as live-attenuated vaccines. Application of the RNA adjuvant in mouse enhanced the efficacy of Middle East respiratory syndrome spike protein, a protein-subunit vaccine and human papillomavirus L1 protein, a virus-like particle vaccine, by activating innate immune response through TLR7 and enhancing pAPC chemotaxis, leading to a balanced Th1/Th2 responses. Moreover, the combination of alum and the RNA adjuvant synergistically induced humoral and cellular immune responses and endowed long-term immunity. Therefore, RNA adjuvants have broad applicability and can be used with all conventional vaccines to improve vaccine efficacy qualitatively and quantitively.


title: Anti‐influenza virus agents: Synthesis and mode of action

text: Annual epidemics of influenza virus infection are responsible for considerable morbidity and mortality, and pandemics are much more devastating. Considerable knowledge of viral infectivity and replication has been acquired, but many details still have to be elucidated and the virus remains a challenging target for drug design and development. This review provides an overview of the antiviral drugs targeting the influenza viral replicative cycle. Included are a brief description of their chemical syntheses and biological activities. For other reviews, see References.1, 2, 3, 4, 5, 6, 7, 8, 9 © 2006 Wiley Periodicals, Inc. Med Res Rev, 28, No. 1, 1–38, 2008


Not the 2020 we asked for


COVID-19: Its Eventual Defeat.


The impact of the COVID-19 pandemic and Italian lockdown measures on clinical presentation and management of acute heart failure


title: Zoonotic Diseases and Phytochemical Medicines for Microbial Infections in Veterinary Science: Current State and Future Perspective

text: Diseases caused by bacterial infections in small-scale and industrial livestock are becoming serious global health concern in veterinary science. Zoonotic bacteria, including Staphylococcus, Campylobacter, and Bartonella species, that infect animals and humans cause various illnesses, such as fever, diarrhea, and related complications. Bacterial diseases in animals can be treated with various classes of antibiotics, including fluoroquinolones, beta-lactams, aminoglycosides, and macrolides. However, the overuse and misuse of antibiotics have led to drug resistance in infectious agents, e.g., methicillin-resistant Staphylococcus; this hampers the treatment of infections in livestock, and such problems are increasing worldwide. Dietary phytochemicals and herbal medicines are useful and viable alternatives to pharmaceuticals because they are economical, effective, non-resistance-forming, renewable, and environmentally friendly. They are small molecules with high structural diversity that cause selective stress to or stimulation of resident microbiota, consequently causing an abundance of such microorganisms; thus, they can be used in preventing various diseases, ranging from metabolic and inflammatory diseases to cancer. In addition, the antioxidant effects of phytochemicals prevent substantial losses in the livestock industry by increasing animal fertility and preventing diseases. Potentially effective plant extracts could be used in combination with antibiotics to decrease the required dose of antibiotics and increase their effectiveness. This strategy can help avoid the side effects of chemical antimicrobials and allow the effective use of phytochemicals for treating diseases. Furthermore, phytochemicals are considered as potential alternatives to antibiotics because of their economical, non-resistance-forming and environmentally friendly properties. Flavonoids such as resveratrol, epigallocatechin gallate, and phenols such as galangin, puerarin, and ursolic acid are proven to be effective as antimicrobial agents. This review provides invaluable information about the types of microbial infections in animals and the current knowledge on phytotherapeutic agents classified by their mode of actions. It also provides insights into potential strategies for effectively treating animal infections using phytochemicals.


title: Development of an efficient viral aerosol collector for higher sampling flow rate

text: Viral aerosol infection through cough generates large amounts of viral aerosol and can result in many adverse health effects such as influenza flu and severe acute respiratory syndrome (SARS). To characterize the coughed viral aerosol, the sampler needs to sample at higher flow rate and possess high physical collection efficiency as well as high viral preservation. However, most current inertia-based high flow bioaerosol samplers are not suited for viral aerosol sampling since the viability will be lost doing the sampling process. Current condensation growth methods only have good physical collection efficiency and viral preservation at low flow rate (< 10 LPM). In this study, we developed a viral aerosol sampling system using a cooler and steam-jet aerosol collector (SJAC) for bioaerosol collection for the first time. The system is based on mixing condensation growth method and has high viral preservation at a higher flow rate (12.5 LPM). We control the inlet aerosol flow temperature and the SJAC mixing reservoir temperature to improve the physical collection efficiency and viability preservation of the viral aerosol. Results indicate that the physical collection efficiency is 70–99% for aerosol 30–100 nm when the aerosol flow and mixing reservoir temperature was 19 and 50 °C, respectively. In addition, the system was 7 and 22 times more efficient for viability preservation of MS2 bacteriophage than the commonly used All Glass Impinger 30 (AGI-30) and BioSampler®, respectively. Finally, the system can be applied to sample at a lower concentration (10(5) PFU/m(3)), and results shows the system was 4.7 times more efficient for viability preservation than using AGI-30 alone. The developed viral collection system will improve our understanding of the characteristics of coughed aerosol and can be used for future evaluation of respiratory protective equipment and environmental sampling.


title: Microparticle encoding technologies for high-throughput multiplexed suspension assays

text: The requirement for analysis of large numbers of biomolecules for drug discovery and clinical diagnostics has driven the development of low-cost, flexible and high-throughput methods for simultaneous detection of multiple molecular targets in a single sample (multiplexed analysis). The technique that seems most likely to satisfy all of these requirements is the multiplexed suspension (bead-based) assay, which offers a number of advantages over alternative approaches such as ELISAs and microarrays. In a bead based assay, different probe molecules are attached to different beads (of a few tens of microns in size), which are then reacted in suspension with the target sample. After reaction, the beads must be identifiable in order to determine the attached probe molecule, and thus each bead must be labelled (encoded) with a unique identifier. A large number of techniques have been proposed for encoding beads. This critical review analyses each technology on the basis of its ability to fulfil the practical requirements of assays, whilst being compatible with low-cost, high-throughput manufacturing processes and high-throughput detection methods. As a result, we identify the most likely candidates to be used for future integrated device development for practical applications.


title: Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5‐day‐old neonatal piglets from virulent challenge

text: In this study, the pathogenicity of porcine deltacoronavirus (PDCoV) strain NH (passage 10, P10) was evaluated. We found that PDCoV strain NH is enteropathogenic in 5‐day‐old pigs. Pathogenicity experiments provided a challenge model for studying the protection efficiency of passive immunity. In order to investigate the protective efficacy of passive immunity in newborn piglets, pregnant sows were vaccinated with either a PDCoV‐inactivated vaccine at the Houhai acupoint (n = 5) or DMEM as a negative control (n = 2) using a prime/boost strategy 20 and 40 days before delivery. PDCoV spike (S)‐specific IgG and neutralizing antibody (NA) responses were detected in immunized sows and piglets born to immunized sows. PDCoV spike (S)‐specific sIgA was also detected in the colostrum and milk of immunized sows. Five days post‐farrowing, piglets were orally challenged with PDCoV strain NH (10(5) TCID(50)/piglet). Severe diarrhoea, high levels of viral RNA copies and substantial intestinal villus atrophy were detected in piglets born to unimmunized sows. Only 4 of 31 piglets (12.9%) born to immunized sows in the challenge group displayed mild to moderate diarrhoea, lower viral RNA copies and minor intestinal villi damage compared to piglets born to unimmunized sows post‐challenge. Mock piglets exhibited no typical clinical symptoms. The challenge experiment results indicated that the inactivated PDCoV vaccine exhibited 87.1% protective efficacy in the piglets. These findings suggest that the inactivated PDCoV vaccine has the potential to be an effective vaccine, providing protection against virulent PDCoV.


title: Thoracic Anesthesia of Patients with Suspected or Confirmed 2019 Novel Coronavirus Infection: Preliminary Recommendations for Airway Management by the EACTA Thoracic Subspecialty Committee

text: Abstract The novel coronavirus has caused a pandemic around the world. Management of patients with suspected or confirmed coronavirus infection who have to undergo thoracic surgery will be a challenge for the anesthesiologists. infection who have to undergo thoracic surgery will be a challenge for the anesthesiologists. The thoracic subspecialty committee of European Association of Cardiothoracic Anaesthesiology (EACTA) has conducted a survey of opinion in order to create recommendations for the anesthetic approach to these challenging patients. It should be emphasized that both the management of the infected patient with COVID-19 and the self-protection of the anesthesia team constitute a complicated challenge. The text focuses therefore on both important topics.


title: A Nationwide Survey of UK cardiac surgeons’ view on clinical decision making during the COVID-19 pandemic

text: Abstract Background No firm recommendations are currently available to guide decision making for patients requiring cardiac surgery during the COVID-19 pandemic. Systematic appraisal of senior surgeons’ consensus can be used to generate interim recommendations until data from clinical observations will become available. Hence, we aimed to collect and quantitatively appraise nationwide UK consultants’ opinion on clinical decision making for patients requiring cardiac surgery during the COVID-19 pandemic. Methods We mailed a web-based questionnaire to all consultant cardiac surgeons through the Society for Cardiothoracic Surgery in Great Britain and Ireland (SCTS) mailing list on the 17th April 2020 and we pre-determined to close the survey on the 21st April 2020. This survey was primarily designed to gather information on UK surgeons’ opinion using 12 items. Strong consensus was predefined as an opinion shared by at least 60% of responding consultants. Results A total of 86 consultant surgeons undertook the survey. All UK cardiac units were represented by at least one consultant. Strong consensus was achieved for the following key questions:1) before any hospital admission for cardiac surgery, nasopharyngeal swab, r-PCR and chest CT should be performed; 2) the use of full PPE should to be adopted in every case by the theatre team regardless patient’s COVID-19 status; 3) the risk of COVID-19 exposure for patients undergoing heart surgery should be considered moderate to high and likely to increase mortality if it occurs; 4) cardiac procedure should be decided based on a rapidly convened multidisciplinary team discussion for every patient. The majority believed that both aortic and mitral surgery should be considered in selected cases. The role of coronary artery bypass graft surgery during the pandemic was controversial. Conclusions In this unprecedented pandemic period, this survey provides information for generating interim recommendations until data from clinical observations will become available.


title: Pharmacokinetics, toxicity of nasal cilia and immunomodulating effects in Sprague–Dawley rats following intranasal delivery of thymopentin with or without absorption enhancers

text: Thymopentin (TP 5), a synthetic pentapeptide, has been used in clinic as a modulator for immnuodeficiencies through intramuscular administration. The objectives of this study was to investigate the pharmacokinetics using normal rats and toxicity of nasal cilia as well as immunomodulating effects using immunosuppression rats after intranasal delivery of thymopentin with or without an absorption enhancer. The absorption extent of fluorescein isothiocyanate (FITC) labeled TP 5 via nasal delivery at a single dose is significantly improved by incorporating sodium deoxycholate, Brij 35 and chitosan, respectively. FITC-TP 5 can also be absorbed to such an extent ranging from 15 to 28% after intranasal administration of FITC-TP 5 alone, FITC-TP 5 with sodium caprylate, or with bacitracin, respectively. After seven consecutive days multiple dosing, TP 5 formulation with sodium deoxycholate or Brij 35 caused apparently injury to nasal cilia, indicating these two enhancers would not be appropriate for nasal delivery. Results from superoxide dismutase activity, maleic dialdehyde, T-lymphocyte subsets (CD3+, CD4+, CD8+ and CD4+/CD8+ ratio) analyses suggest that all the selected enhancers improve the modulating effects of TP 5 in the immunosuppression rats. On an overall evaluation, intranasal TP 5 alone, TP 5 with chitosan, or TP 5 with bacitracin formulation may be suitable for the future clinical application.


title: Modelling the Distributional impact of the Covid‐19 Crisis(1)

text: The COVID‐19 emergency has had a dramatic impact on market incomes and income support policies. The lack of timely available data constrains the estimation of the scale and direction of recent changes in the income distribution, which in turn constrain policymakers seeking to monitor such developments. We overcome the lack of data by proposing a dynamic calibrated microsimulation approach to generate counterfactual income distributions as a function of more timely external data than is available in dated income surveys. We combine nowcasting methods using publicly available data and a household income generation model to perform the first calibrated simulation based upon actual data aiming to assess the distributional implications of the COVID‐19 crisis in Ireland. Overall, we find that the crisis had an equalizing real‐time effect for both gross and disposable incomes, notwithstanding the significant hardship experienced by many households. This article is protected by copyright. All rights reserved


title: Minimizing transmission of COVID-19 while delivering optimal cancer care in a National Cancer Centre

text: The COVID-19 pandemic has disrupted current models of healthcare and adaptations will likely continue. With the gradual easing of lockdown measures worldwide, cancer centres must be prepared to implement novel means to prevent repeated waves of infection. There are two limitations unique to oncology – a higher susceptibility of patients to COVID-19 and the multidisciplinary approach required of cancer management. We describe the measures implemented in the largest cancer centre in Singapore to continue optimal cancer care in spite of the ongoing pandemic, with no nosocomial infections reported in our centre to date. We adopted a multipronged approach, with an overall committee supervising the entire COVID-19 management effort. A screening clinic was setup to triage patients prior to entry to the centre. Each Oncology Division within the cancer centre designed solutions tailored to the specific needs of their discipline. We explore in detail the screening criteria and workflow of the screening clinic, as well as modifications by individual divisions to reduce infection risk to patients and healthcare professionals. This approach can be modelled by other cancer centres during this prolonged COVID-19 pandemic.


title: Psychological Distress and Its Correlates Among COVID-19 Survivors During Early Convalescence Across Age Groups

text: OBJECTIVE: To examine the psychological distress and the associated predictor factors of the 2019 corona-virus disease (COVID-19) on survivors in the early recovery stage across their ages in Shenzhen. METHOD: A survey questionnaire consisting of post-traumatic stress disorder self-rating scale (PTSD-SS), self-rating depression scale (SDS) and self-rating anxiety scale (SAS) was presented to COVID-19 survivors still in quarantine. Demographic variables, sociopsychological variables, medical history, and overall parameters of COVID-19 were collected by telephone interviews and by checking medical records. Scores of each scale and subscale were dependent variables in the statistical analysis using the Mann-Whitney test and stepwise regression analysis. RESULTS: A total of 126 subjects were included in the study, the mean scores of PTSD-SS, SDS and SAS were 45.5±18.9, 47.3±13.1 and 43.2±10.2 respectively, meanwhile, 9(31.0%), 28 (22.2%), and 48(38.1%) of the survivors met the cut-score for clinical significant symptoms of stress response, anxiety and depression, respectively. Infected family members, and post-infection physical discomforts were significantly associated with scores on all three scales. Social support, retirement, and being female had significant associations with the PTSD-SS score. The survivors aged 60 or above experienced less severe stress response symptoms, fewer emotional symptoms of depression, and fewer anxiety symptoms than younger survivors. CONCLUSION: The occurrence rate of psychological distress among the COVID-19 survivors in early convalescence was high, which may improve after the quarantine or may persist and even deteriorate with time as reported in SARS survivors, highlighting the need for all COVID-19 survivors to be screened for psychological distress regularly for timely intervention. The predictors indicated by the current study may help to identify those at high-risk. The current study also contributes to geriatric psychiatry by indicating that the older survivors suffered less emotional reactivity and fewer stress response symptoms from infectious diseases than the younger ones.


title: Development of selected bacterial groups of the rectal microbiota of healthy calves during the first week postpartum

text: AIMS: The intestinal microbiota of newborn calves is largely unexplored even if it is of great significance for their future health. Therefore, the aim of the study was to gain a better insight into the development dynamics of certain bacterial groups during the first week of life. METHODS AND RESULTS: Faecal samples of healthy Simmental calves (dual‐purpose breed; n = 80), bottle fed and raised in a dairy farm were taken immediately after birth and at 6/12/24/48/72/168 h (h) after birth. Samples were analysed using cultural, biochemical and molecular–biological methods. The aerobe, anaerobe, Enterobacteriaceae and Enterococcus counts of healthy calves increased significantly between 6 and 24 h postpartum (P <0·05). Apart from the anaerobes, bacterial counts decreased after reaching a plateau at 24–48 h. Enterococcus faecalis was detected in significantly higher counts compared to E. faecium (P <0·05). Lactobacilli developed more slowly and increased until day 7 after birth to a mean value of 6·8 × 10(7) CFU per g. MALDI‐TOF analysis of 2338 lactobacilli isolates resulted in 36 different species. CONCLUSIONS: Lactobacillus reuteri became the most common Lactobacillus sp. during the first week of life. SIGNIFICANCE AND IMPACT OF THE STUDY: This fact seems to be very important for the calf’s intestinal health because L. reuteri is known to show in vitro bactericidal effects against bacterial pathogens and anti‐infective activities against rotaviruses and Cryptosporidium parvum.


title: Plasminogen improves lung lesions and hypoxemia in patients with COVID-19

text: BACKGROUND: Lungs from patients with coronavirus disease 2019 (COVID-19) have shown typical signs of acute respiratory distress syndrome (ARDS), formation of hyaline membrane mainly composed of fibrin, and ‘ground-glass’ opacity. Previously, we showed plasminogen itself is a key regulator in fibrin degradation, wound healing and infection. AIM: We aimed to investigate whether plasminogen can improve lung lesions and hypoxemia of COVID-19. DESIGN: Thirteen clinically moderate, severe or critical COVID-19 patients were treated with atomization inhalation of freeze-dried plasminogen. METHODS: Levels of their lung lesions, oxygen saturation and heart rates were compared before and after treatment by CT scanning images and patient monitor. RESULTS: After plasminogen inhalation, conditions of lung lesions in 5 clinically moderate patients have quickly improved, shown as the decreased range and density of ‘ground glass’ opacity. Improvements of oxygen saturation were observed in 6 clinically severe patients. In the 2 patients with critical conditions, the oxygen levels have significantly increased from 79-82% to 91% just about 1 hour after the first inhalation. In 8 of 13 patients the heart rates had slowed down. For the 5 clinically moderate patients, the difference is even statistically significant. Furthermore, a general relief of chest tightness was observed. CONCLUSION: Whereas it is reported that plasminogen is dramatically increased in adults with ARDS, this study suggests that additional plasminogen may be effective and efficient in treating lung lesions and hypoxemia during COVID-19 infections. Although further studies are needed, this study highlights a possible hope of efficiently combating this rapid epidemic emergency.


title: Update on different aspects of HCV variability: focus on NS5B polymerase

text: The study of hepatitis C virus (HCV) genotypes/subtypes, quasispecies and recombinants obtained by virus genome sequencing are important for epidemiological studies, to trace the source of infection, for development of new direct acting antivirals (DAAs) therapy and for understanding antiviral selection pressures. The HCV NS5B gene encodes a polymerase, which is responsible for virus replication and is a potential target for the development of antiviral agents. Many studies for classification of HCV use a particular segment of the NS5B gene, in addition to other specific regions, and phylogenetic analysis. Actually, some nucleoside/nucleotide analogues and non-nucleoside inhibitors target NS5B protein. This review focuses on HCV variability, phylogenetic analysis and the role of NS5B in the virus-host interactions.


title: Modelling the Effect of Area-deprivation on COVID-19 Incidences: A Study of Chennai Megacity, India

text: Abstract Objectives Socioeconomic inequalities may affect COVID-19 incidence. The goal of the research was to explore the association between deprivation of socioeconomic status (SES) and spatial patterns of COVID-19 incidence in Chennai megacity for unfolding the disease epidemiology. Study design Ecological (or contextual) study for electoral wards (sub-cities) of Chennai megacity. Methods Using data of confirmed COVID-19 cases from May 15, 2020, to May 21, 2020, for 155 electoral wards obtained from the official website of the Chennai municipal corporation, we examined the incidence of COVID-19 diseases using two count regression models namely, Poisson Regression (PR) and Negative Binomial Regression (NBR). As explanatory factors, we considered area-deprivation that represented the deprivation of socioeconomic status (SES). An index of multiple deprivations (IMD) developed to measure the area-deprivation using an advanced local statistic, Geographically Weighted Principal Component Analysis (GWPCA). Based on the availability of appropriately scaled data, five domains (i.e. poor housing condition, low asset possession, poor availability of WaSH services, lack of household amenities and services, and gender disparity) were selected as components of the IMD in this study. Results The Hot-spot analysis revealed that area-deprivation was significantly associated with higher incidences of COVID-19 in Chennai megacity. The high variations (adj. R2: 72.2%) with the lower BIC (124.34) and AIC (112.12) for the NBR compared to PR suggests that the NBR model better explains the relationship between area-deprivation and COVID-19 incidences in Chennai megacity. NBR with two-sided tests, and p<0.05 was considered statistically significant. The outcome of the PR and NBR suggests that when all other variables were constant, according to NBR, the relative risk (RR) of COVID-19 incidences was 2.19 for the wards with high housing deprivation or in other words, the wards with high housing deprivation having 119% higher probability (RR= e0.786=2.19, 95% CI=1.98 to 2.40) compared to areas with low deprivation. Similarly, in the wards with poor availability of WaSH services, chances of having COVID-19 incidence was 90% higher compared to the wards with good WaSH services (RR= e0.642=1.90, 95% CI=1.79 to 2.00). Spatial risks of COVID-19 infections were predominantly concentrated in the wards with higher levels of area-deprivation which were mostly located in the north-eastern parts of Chennai megacity. Conclusions We formulated an area-based IMD, which was substantially related to COVID-19 incidences in the Chennai megacity. This study highlights that the risks of COVID-19 infections tend to be higher in more deprived areas of SES and the north-eastern part of Chennai megacity was predominantly high-risk areas. Our results can guide measures of COVID-19 control and prevention by considering spatial risks and area-deprivation.


title: Feline calicivirus strain differentiation using monoclonal antibody analysis in an enzyme-linked immuno-flow-assay

text: Abstract Six monoclonal antibodies raised against feline calicivirus (FCV) strain F9 were used in an enzyme-linked immuno-flow-assay (ELIFA) to analyse 55 isolates of FCV. Forty seven field isolates were obtained from cats with acute oral/respiratory disease, chronic oral lesions, and from cats showing vaccine reactions, i.e. clinical signs of FCV infection shortly after vaccination. Eight reference strains including F9 and three vaccine strains based on F9 were also examined. All of the strains of F9, derived from various sources, reacted with all six of the monoclonal antibodies, whereas some of the field isolates did not react with any. In general, the field isolates showed a spectrum of reactivities and selected isolates could be distinguished. However, there were no clear cut differences between the clinical groups. Overall, the oral/respiratory group showed less reactivity with the monoclonals, suggesting they were less related to F9. Although the other groups appeared to be more closely related to F9, none of the isolates reacted with all six monoclonal antibodies.


title: Structural efficiency to manipulate public research institution networks

text: Abstract With the rising use of network analysis in the public sector, researchers have recently begun paying more attention to the management of entities from a network perspective. However, guiding elements in a network is difficult because of their complex and dynamic states. In a bid to address the issues involved in achieving network-wide outcomes, our work here sheds new light on quantifying structural efficiency to control inter-organizational networks maintained by public research institutions. In doing so, we draw attention to the set of subordinates suitable as change initiators to influence the entire research profiles of subordinates from three major public research institutions: the Government-funded Research Institutes (GRIs) in Korea, the Max-Planck-Gesellschaft (MPG) in Germany, and the National Laboratories (NLs) in the United States. Building networks on research similarities in portfolios, we investigate these networks with respect to their structural efficiency and topological properties. According to our estimation, only less than 30% of nodes are sufficient to initiate a cascade of changes throughout the network across institutions. The subunits that drive the network exhibit an inclination neither toward retaining a large number of connections nor toward having a long academic history. Our findings suggest that this structural efficiency indicator helps assess structural development or improvement plans for networks inside a multiunit public research institution.


Why is hyperglycemia worsening COVID‐19 and its prognosis?


title: Managing Bioterrorism Mass Casualties in an Emergency Department: Lessons Learned From a Rural Community Hospital Disaster Drill

text: Bioterrorism represents a threat for which most emergency departments (EDs) are ill prepared. In order to develop an evidence-based plan for ED and hospital management of contaminated patients, a review was conducted of the most effective strategies developed during the severe acute respiratory syndrome (SARS) epidemic, as well as Centers for Disease Control and Prevention and military guidelines on biowarfare. Six basic steps were identified: 1) lock down the hospital and control access to the ED; 2) protect emergency care personnel with appropriate personal protective equipment; 3) decontaminate and triage patients; 4) isolate patients; 5) treat patients with appropriate medications or measures, including decontamination of wounds; and 6) use restrictive admission and transfer guidelines. By emphasizing these six basic concepts, a rural ED passed an annual state-run bioterrorism mass-casualty drill. The drill provided health care personnel with the knowledge and skills necessary to prepare for future bioterrorism casualties. These same concepts could also be used to manage highly virulent viral or bacterial outbreaks.


title: Emerging viruses set to soar

text: The emergence rate of novel viruses, such as the coronavirus that sparked SARS, could well be on the rise.Researchers now think that the SARS virus split from group 2 coronaviruses, and that this happened relatively recently on the scale of coronavirus evolution.


title: Evaluation of the neutrophil:lymphocyte ratio as an indicator of chronic distress in the laboratory mouse

text: When evaluating the effect of husbandry and biomethodologies on the well-being of laboratory mice, it is critical to utilize measurements that allow the distinguishing of acute stress from chronic stress. One of the most common measurements of stress in laboratory animals is the corticosterone assessment. However, while this measurement provides a highly accurate reflection of the animal's response to acute stressors, its interpretation is more prone to error when evaluating the effect of chronic stress. This study evaluated the use of the neutrophil:lymphocyte (NE:LY) ratio as an assessment of chronic stress in male and female C57Bl/6N mice as compared to serum corticosterone. One group of mice was exposed to mild daily stressors for 7 days, while the control group was handled with normal husbandry. The NE:LY ratio and serum corticosterone levels were significantly elevated in the chronically stressed mice, though a significant increase in corticosterone was only significant in males when compared by sex. The chronically stressed mice also demonstrated significantly fewer entries into the open arms and less time spent in the open arms of the elevated plus maze, suggesting that the mild daily stressors had induced a state of distress. The findings of this study confirm that the NE:LY ratio is a valid measurement for chronic stress in the laboratory mouse. However, these assays do not distinguish between distress or eustress, so behavioral and physiological assessments should always be included to determine a complete assessment of the well-being of the mouse. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/laban.1298) contains supplementary material, which is available to authorized users.


title: The ‘Heart Kuznets Curve’? Understanding the relations between economic development and cardiac conditions

text: As countries turn wealthier, some health indicators, such as child mortality, seem to have well-defined trends. However, others, including cardiovascular conditions, do not follow clear linear patterns of change with economic development. Abnormal blood pressure is a serious health risk factor with consequences for population growth and longevity as well as public and private expenditure in health care and labor productivity. This also increases the risk of the population in certain pandemics, such as COVID-19. To determine the correlation of income and blood pressure, we analyzed time-series for the mean systolic blood pressure (SBP) of men’s population (mmHg) and nominal Gross Domestic Product per capita (GDPPC) for 136 countries from 1980 to 2008 using regression and statistical analysis by Pearson’s correlation (r). Our study finds a trend similar to an inverted-U shaped curve, or a ‘Heart Kuznets Curve’. There is a positive correlation (increase GDPPC, increase SBP) in low-income countries, and a negative correlation in high-income countries (increase GDPPC, decrease SBP). As country income rises people tend to change their diets and habits and have better access to health services and education, which affects blood pressure. However, the latter two may not offset the rise in blood pressure until countries reach a certain income. Investing early in health education and preventive health care could avoid the sharp increase in blood pressure as countries develop, and therefore, avoiding the ‘Heart Kuznets Curve’ and its economic and human impacts.


title: HSD11B1 is upregulated synergistically by IFNγ and TNFα and mediates TSG-6 expression in human UC-MSCs

text: Inflammatory factors such as IFNγ and TNFα could endow mesenchymal stem cells (MSCs) a potent immunomodulatory property, a process called licensing, but the mechanisms are not fully understood. We here found that glucocorticoid-activating enzyme 11β-hydroxysteroid dehydrogenase type 1 (HSD11B1), which converts inactive cortisone to the active cortisol and thereby regulates tissue glucocorticoid (GC) levels, was greatly upregulated by IFNγ and TNFα in human umbilical cord-derived MSCs (UC-MSCs) in a synergistic manner. While IFNγ alone was not able to induce HSD11B1, it could increase the activity of NF-kB and thus augment the upregulation of HSD11B1 by TNFα. Interestingly, the upregulation of HSD11B1 by IFNγ and TNFα also required glucocorticoid receptor. Furthermore, HSD11B1 was shown to be required for the expression of TNF-stimulated gene 6 (TSG-6), an important anti-inflammatory effector molecule of MSCs. Therefore, the inflammatory factors IFNγ and TNFα can promote GC metabolism and thereby drive the expression of anti-inflammatory factor TSG-6 in human UC-MSCs, forming a potential negative feedback loop. These findings help to understand the relationship between inflammation and GC metabolism.


title: Inactivated or damaged? Comparing the effect of inactivation methods on influenza virions to optimize vaccine production

text: The vast majority of commercially available inactivated influenza vaccines are produced from egg-grown or cell-grown live influenza virus. The first step in the production process is virus inactivation with β-propiolactone (BPL) or formaldehyde (FA). Recommendations for production of inactivated vaccines merely define the maximal concentration for both reagents, leaving the optimization of the process to the manufacturers. We assessed the effect of inactivation with BPL and FA on 5 different influenza virus strains. The properties of the viral formulation, such as successful inactivation, preservation of hemagglutinin (HA) binding ability, fusion capacity and the potential to stimulate a Toll-like receptor 7 (TLR7) reporter cell line were then assessed and compared to the properties of the untreated virus. Inactivation with BPL resulted in undetectable infectivity levels, while FA-treated virus retained very low infectious titers. Hemagglutination and fusion ability were highly affected by those treatments that conferred higher inactivation, with BPL-treated virus binding and fusing at a lower degree compared to FA-inactivated samples. On the other hand, BPL-inactivated virus induced higher levels of activation of TLR7 than FA-inactivated virus. The alterations caused by BPL or FA treatments were virus strain dependent. This data shows that the inactivation procedures should be tailored on the virus strain, and that many other elements beside the concentration of the inactivating agent, such as incubation time and temperature, buffer and virus concentration, have to be defined to achieve a functional product.


title: Development of Monoclonal Antibody and Diagnostic Test for Middle East Respiratory Syndrome Coronavirus Using Cell-Free Synthesized Nucleocapsid Antigen

text: Protein nativity is one of the most critical factors for the quality of antigens used as immunogens and the reactivities of the resultant antibodies. The preparation and purification of native viral antigens in conventional cell-based protein expression systems are often accompanied by technical hardships. These challenges are attributable mainly to protein aggregation and insolubility during expression and purification, as well as to very low expression levels associated with the toxicity of some viral proteins. Here, we describe a novel approach for the production of monoclonal antibodies (mAbs) against nucleocapsid protein (NP) of the Middle East respiratory syndrome coronavirus (MERS-CoV). Using a wheat germ cell-free protein synthesis system, we successfully prepared large amounts of MERS-CoV NP antigen in a state that was highly soluble and intact for immunization. Following mouse immunization and hybridoma generation, we selected seven hybridoma clones that produced mAbs with exclusive reactivity against MERS-CoV NP. Epitope mapping and subsequent bioinformatic analysis revealed that these mAbs recognized epitopes located within relatively highly conserved regions of the MERS-CoV amino-acid sequence. Consistently, the mAbs exhibited no obvious cross-reactivity with NPs derived from other related viruses, including SARS coronavirus. After determining the optimal combinations of these mAbs, we developed an enzyme-linked immunosorbent assay and a rapid immunochromatographic antigen detection test that can be reliably used for laboratory diagnosis of MERS-CoV. Thus, this study provides strong evidence that the wheat germ cell-free system is useful for the production of diagnostic mAbs against emerging pathogens.


Reply to D.G. Barten et al “Re: Non-COVID-19 visits to emergency departments during the pandemic: the impact of fear”


title: Animal models for highly pathogenic emerging viruses

text: Exotic and emerging viral pathogens associated with high morbidity and mortality in humans are being identified annually with recent examples including Lujo virus in southern Africa, Severe fever with Thrombocytopenia virus in China and a SARS-like coronavirus in the Middle East. The sporadic nature of these infections hampers our understanding of these diseases and limits the opportunities to design appropriate medical countermeasures against them. Due to this, animal models are utilized to gain insight into the pathogenesis of disease with the overall goal of identifying potential targets for intervention and evaluating specific therapeutics and vaccines. For these reasons it is imperative that animal models of disease recapitulate the human condition as closely as possible in order to provide the best predictive data with respect to the potential efficacy in humans. In this article we review the current status of disease models for highly pathogenic and emerging viral pathogens.


title: Rapid viral diagnosis and ambulatory management of suspected COVID-19 cases presenting at the infectious diseases referral hospital in Marseille, France, - January 31st to March 1st, 2020: A respiratory virus snapshot

text: Abstract Background Rapid virological diagnosis is needed to limit the length of isolation for suspected COVID-19 cases. Method We managed the first 280 patients suspected to have COVID-19 through a rapid care circuit and virological diagnosis in our infectious disease reference hospital in Marseille, France. Rapid viral detection was performed on sputum and nasopharyngeal samples. Results Over our study period, no SARS-CoV-2 was detected. Results were obtained within approximately 3 h of the arrival of patient samples at the laboratory. Other viral infections were identified in 49% of the patients, with most common pathogens being influenza A and B viruses, rhinovirus, metapneumovirus and common coronaviruses, notably HKU1 and NL63. Conclusion Early recognition of COVID-19 is critical to isolate confirmed cases and prevent further transmission. Early rule-out of COVID-19 allows public health containment measures to be adjusted by reducing the time spent in isolation.


title: Chapter 9 Trends in Antiviral Strategies

text: Abstract Viral populations are true moving targets regarding the genomic sequences to be targeted in antiviral designs. Experts from different fields have expressed the need of new paradigms for antiviral interventions and viral disease control. This chapter reviews several strategies that aim at counteracting the adaptive capacity of viral quasispecies. The proposed designs are based on combinations of different antiviral drugs and immune modulators, or in the administration of virus-specific mutagenic agents, in an approach termed lethal mutagenesis of viruses. It consists of decreasing viral fitness by an excess of mutations that render viral proteins sub-optimal or non-functional. Viral extinction by lethal mutagenesis involves several sequential, overlapping steps that recapitulate the major concepts of intra-population interactions and genetic information stability discussed in preceding chapters. Despite the magnitude of the challenge, the chapter closes with some optimistic prospects for an effective control of viruses displaying error-prone replication, based on the combined targeting of replication fidelity and the induction of the innate immune response.


title: Cardiac biomarker-based risk stratification algorithm in patients with severe COVID-19

text: BACKGROUND AND AIMS: Cardiac biomarkers like cardiac troponins and natriuretic peptides are elevated in a substantial proportion of patients with coronavirus disease 2019 (COVID-19). We propose an algorithmic approach using cardiac biomarkers to triage, risk-stratify and prognosticate patients with severe COVID-19. METHODS: We systematically searched the PubMed and Google Scholar databases until May 31st, 2020, and accessed the available data on the role of cardiac biomarkers in patients with COVID-19. RESULTS: COVID-19 is associated with acute cardiac injury in around 7–28% of patients, significantly increasing its associated complications and mortality. Patients with underlying cardiovascular disease are more prone to develop acute cardiac injury as a result of COVID-19. The use of cardiac biomarkers may aid in differentiating the cardiac cause of dyspnea in patients with severe COVID-19. Cardiac biomarkers may also aid in triaging, risk-stratification, clinical decision-making, and prognostication of patients with COVID-19. However, there are concerns that routine testing in all patients with COVID-19 irrespective of severity, may result in unnecessary downstream investigations which may be misleading. In this brief review, using an algorithmic approach, we have tried to rationalize the use of cardiac biomarkers among patients with severe COVID-19. This approach is also likely to lessen the infection exposure risk to the cardiovascular team attending patients with severe COVID-19. CONCLUSION: It appears beneficial to triage, risk-stratify, and prognosticate patients with COVID-19 based on the evidence of myocardial injury and the presence of underlying cardiovascular disease. Future research studies are, however, needed to validate these proposed benefits.


Fecal Calprotectin and RT-PCR from both nasopharyngeal swab and stool samples prior to treatment decision in IBD patients during CoVID-19 outbreak.


title: Virus membrane-fusion proteins: more than one way to make a hairpin

text: Structure–function studies have defined two classes of viral membrane-fusion proteins that have radically different architectures but adopt a similar overall 'hairpin' conformation to induce fusion of the viral and cellular membranes and therefore initiate infection. In both classes, the hairpin conformation is achieved after a conformational change is triggered by interaction with the target cell. This review will focus in particular on the properties of the more recently described class II proteins.


title: Ebola virus (EBOV) infection: Therapeutic strategies

text: Abstract Within less than a year after its epidemic started (in December 2013) in Guinea, Ebola virus (EBOV), a member of the filoviridae, has spread over a number of West-African countries (Guinea, Sierra Leone and Liberia) and gained allures that have been unprecedented except by human immunodeficiency virus (HIV). Although EBOV is highly contagious and transmitted by direct contact with body fluids, it could be counteracted by the adequate chemoprophylactic and -therapeutic interventions: vaccines, antibodies, siRNAs (small interfering RNAs), interferons and chemical substances, i.e. neplanocin A derivatives (i.e. 3-deazaneplanocin A), BCX4430, favipiravir (T-705), endoplasmic reticulum (ER) α-glucosidase inhibitors and a variety of compounds that have been found to inhibit EBOV infection blocking viral entry or by a mode of action that still has to be resolved. Much has to be learned from the mechanism of action of the compounds active against VSV (vesicular stomatitis virus), a virus belonging to the rhabdoviridae, that in its mode of replication could be exemplary for the replication of filoviridae.


title: Automated cell-based luminescence assay for profiling antiviral compound activity against enteroviruses

text: We describe the development, optimisation, and validation of an automated, cell-based and high-throughput screening assay using existing luminescence-based ATPlite reagents for identifying antiviral compounds that inhibit enterovirus replication. Antiviral efficacy was determined by measuring the ATP levels in cells that were protected from the viral cytopathic effect (CPE) by the antiviral compounds pleconaril and rupintrivir. CPE-based assay conditions were optimised at a cell density of 5000 cells/well and a viral infection dose of 100 CCID(50) in 384-well plates. The assay exhibited excellent robustness, with Z′-factor values between 0.75 and 0.82, coefficients of variation between 0.33% and 1.45%, and signal-to-background ratios ranging from 6.92 to 22.6 when testing three enterovirus A71 isolates circulating in China. The assay was also suitable for screening other picornaviruses, such as poliovirus, coxsackievirus, echovirus, and parechovirus.


title: Hospital and community acquired infection and the built environment – design and testing of infection control rooms

text: Summary Negative-pressure isolation rooms are required to house patients infected with agents transmissible by the aerosol route in order to minimise exposure of healthcare workers and other patients. Housing patients in a separate room provides a barrier which minimises any physical contact with other patients. An isolation room held at negative pressure to reduce aerosol escape and a high air-change rate to allow rapid removal of aerosols can eliminate transmission of infectious aerosols to those outside the room. However, badly designed and/or incorrectly operating isolation rooms have been shown to place healthcare workers and other patients at risk from airborne diseases such as tuberculosis. Few standards are available for the design of isolation rooms and no pressure differential or air-change rates are specified. Techniques such as aerosol particle tracer sampling and computational fluid dynamics can be applied to study the performance of negative-pressure rooms and to assess how design variables can affect their performance. This should allow cost-effective designs for isolation rooms to be developed. Healthcare staff should be trained to understand how these rooms operate and there should be systems in place to ensure they are functioning correctly.


title: Exchange of amino acids in the H1-haemagglutinin to H3 residues is required for efficient influenza A virus replication and pathology in Tmprss2 knock-out mice

text: The haemagglutinin (HA) of H1N1 and H3N2 influenza A virus (IAV) subtypes has to be activated by host proteases. Previous studies showed that H1N1 virus cannot replicate efficiently in Tmprss2(−/−) knock-out mice whereas H3N2 viruses are able to replicate to the same levels in Tmprss2(−/−) as in wild type (WT) mice. Here, we investigated the sequence requirements for the HA molecule that allow IAV to replicate efficiently in the absence of TMPRSS2. We showed that replacement of the H3 for the H1-loop sequence (amino acids 320 to 329, at the C-terminus of HA(1)) was not sufficient for equal levels of virus replication or severe pathology in Tmprss2(−/−) knock-out mice compared to WT mice. However, exchange of a distant amino acid from H1 to H3 sequence (E31D) in addition to the HA-loop substitution resulted in virus replication in Tmprss2(−/−) knock-out mice that was comparable to WT mice. The higher virus replication and lung damage was associated with increased epithelial damage and higher mortality. Our results provide further evidence and insights into host proteases as a promising target for therapeutic intervention of IAV infections.


title: Effect of acetate Ringer(’)s solution with or without 5% dextrose administered intravenously to diarrheic calves

text: The objectives of this study were to evaluate the effects of intravenous acetate Ringer’s solution, with or without dextrose, on diarrheic calves with either experimentally induced or spontaneous diarrhea. In the experimental model, diarrhea was induced in nine healthy calves by administering cold milk (below 4°C) twice a day for 2 days. The calves were randomly assigned to the isotonic saline (ISS), acetated Ringer’s (AR) or acetated Ringer’s with 5% dextrose (ARD) groups, with three calves assigned to each group. The calves received 80 ml/kg of their designated solution, at a flow rate of 20 ml/kg/hr. Infusion of ISS, AR and ARD were all found to be safe and effective in increasing plasma volume. Intravenous (IV) infusion of ISS resulted in the acidification secondary to dilution, while AR and ARD infusion inhibited acidification. In addition, prevention of catabolism was observed only with IV infusion of ARD. Sixteen calves with spontaneous diarrhea were enrolled in the clinical study. The calves were randomly assigned to the AR or ARD groups, with eight calves being assigned to each group. The calves received 100 ml/kg of their designated solution, at a flow rate of 25 ml/kg/hr. Intravenous infusion of AR and ARD was found to be effective in increasing plasma volume and inhibiting acidification. Only infusion of ARD prevented catabolism, but it also led to hyperglycemia. Our results suggest that a solution containing dextrose may be beneficial for wasting diarrheic calves.


title: Acute aorto‐iliac and mesenteric arterial thromboses as presenting features of COVID‐19

text: SARS-CoV-2 infection has been reported to induce a hypercoagulable state1 which is associated with disease severity and poor outcomes.2,3 Rates of thromboembolic events and use of augmented thromboprophylaxis in patients with COVID-19 are therefore the subject of significant interest. However, the clinical manifestations of this procoagulant tendency are poorly defined. In this report we describe two cases of major occlusive arterial events in previously asymptomatic individuals with confirmed COVID-19.


title: COVID‐19, internists and resilience: the north‐south Italy outbreak.

text: According to data from the World Health Organization, Italy has been particularly affected by the ongoing COVID‐19 pandemic. On April 1(st) 2020, Italy gained, at a world level, the highest number of total confirmed cases (n=110,574) and deaths (n=13,155) since the beginning of the outbreak. The number of cases raised exponentially, reaching a total of 227,364 infected subjects and 32,330 deaths on May, 20. The distribution of infected subjects and deaths, however, was not homogeneous, being respectively about 7‐times and 12‐times higher in northern‐ than in southern regions


title: Genomic legacy of the African cheetah, Acinonyx jubatus

text: BACKGROUND: Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations. RESULTS: Here the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DNA SNVs. Cheetah genomes are on average 95 % homozygous compared to the genomes of the outbred domestic cat (24.08 % homozygous), Virunga Mountain Gorilla (78.12 %), inbred Abyssinian cat (62.63 %), Tasmanian devil, domestic dog and other mammalian species. Demographic estimators impute two ancestral population bottlenecks: one >100,000 years ago coincident with cheetah migrations out of the Americas and into Eurasia and Africa, and a second 11,084–12,589 years ago in Africa coincident with late Pleistocene large mammal extinctions. MHC class I gene loss and dramatic reduction in functional diversity of MHC genes would explain why cheetahs ablate skin graft rejection among unrelated individuals. Significant excess of non-synonymous mutations in AKAP4 (p<0.02), a gene mediating spermatozoon development, indicates cheetah fixation of five function-damaging amino acid variants distinct from AKAP4 homologues of other Felidae or mammals; AKAP4 dysfunction may cause the cheetah’s extremely high (>80 %) pleiomorphic sperm. CONCLUSIONS: The study provides an unprecedented genomic perspective for the rare cheetah, with potential relevance to the species’ natural history, physiological adaptations and unique reproductive disposition. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0837-4) contains supplementary material, which is available to authorized users.


title: Cell membrane proteins with high N-glycosylation, high expression and multiple interaction partners are preferred by mammalian viruses as receptors

text: MOTIVATION: Receptor mediated entry is the first step for viral infection. However, the question of how viruses select receptors remains unanswered. RESULTS: Here, by manually curating a high-quality database of 268 pairs of mammalian virus–host receptor interaction, which included 128 unique viral species or sub-species and 119 virus receptors, we found the viral receptors are structurally and functionally diverse, yet they had several common features when compared to other cell membrane proteins: more protein domains, higher level of N-glycosylation, higher ratio of self-interaction and more interaction partners, and higher expression in most tissues of the host. This study could deepen our understanding of virus–receptor interaction. AVAILABILITY AND IMPLEMENTATION: The database of mammalian virus–host receptor interaction is available at http://www.computationalbiology.cn: 5000/viralReceptor. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


title: 12 Pseudo-obstruction syndromes

text: Abstract Chronic intestinal pseudo-obstruction (CIP) is a clinical syndrome characterized by symptoms and signs of intestinal occlusion, in absence of any mechanical obstruction of the gut lumen. It causes impaired transit of intestinal contents and is determined by abnormalities of motor activity. The term CIP is used to indicate a heterogeneous group of disorders with many different pathogenic mechanisms. The defect in the regulation of intestinal transit can be at any level of motility control. Two main types of CIP are recognized, termed respectively myogenic (when smooth muscle cells are affected) and neurogenic (caused by abnormalities of extrinsic and/or intrinsic nervous supplies). Both types may be secondary to a variety of recognizable diseases or idiopathic. In myogenic CIP, intestinal transit is impaired because of lack of propulsive strength; in the neurogenic form, contractions are powerful but not sufficiently co-ordinated to propel intestinal contents aborally in an organized fashion. CIP belongs to the large and loosely defined group of digestive functional disorders. These disorders probably share common pathogenic mechanisms but with different expressiveness. The reasons why only some patients present recurrent symptomatological bouts resembling mechanical occlusion has not been clarified. This aspect is of great clinical relevance and deserves attention, as CIP patients, unlike other patients with severe functional disorders, may undergo repeated, useless and potentially dangerous operations. The diagnosis of CIP may be suggested by clinical features and is based on radiological, endoscopic, manometric, and histological findings. Recent technological improvements facilitate the recognition of this intriguing syndrome. In particular, manometric recording of the small bowel motility, which has long been considered an important research technique, can now also be regarded as a useful diagnostic tool.


Living through a pandemic – A time for clarity, courage and truth


title: COVID-19: the vasculature unleashed

text: On the basis of emerging evidence from patients with COVID-19, we postulate that endothelial cells are essential contributors to the initiation and propagation of severe COVID-19. Here, we discuss current insights into the link between endothelial cells, viral infection and inflammatory changes and propose novel therapeutic strategies.


title: Large-scale purification and crystallization of the endoribonuclease XendoU: troubleshooting with His-tagged proteins

text: XendoU is the first endoribonuclease described in higher eukaryotes as being involved in the endonucleolytic processing of intron-encoded small nucleolar RNAs. It is conserved among eukaryotes and its viral homologue is essential in SARS replication and transcription. The large-scale purification and crystallization of recombinant XendoU are reported. The tendency of the recombinant enzyme to aggregate could be reversed upon the addition of chelating agents (EDTA, imidazole): aggregation is a potential drawback when purifying and crystallizing His-tagged proteins, which are widely used, especially in high-throughput structural studies. Purified monodisperse XendoU crystallized in two different space groups: trigonal P3(1)21, diffracting to low resolution, and monoclinic C2, diffracting to higher resolution.


title: Measurement of dairy calf behavior prior to onset of clinical disease and in response to disbudding using automated calf feeders and accelerometers

text: ABSTRACT We determined if feeding and lying behavior, recorded by automatic calf feeding systems (ACFS) and accelerometers, could be used to detect changes in behavior before onset of neonatal calf diarrhea (NCD) or in response to disbudding pain in dairy calves. At 4 d of age, 112 calves had accelerometers attached to their hind leg and were housed in pens with ACFS. Calves were examined daily for signs of illness or injury. Of the 112 calves monitored, 18 were diagnosed with NCD; activities of calves with NCD were then compared with those of 18 healthy controls (calves that had no symptoms of NCD, other illnesses, or injury). Feeding (milk consumption and the number of rewarded and unrewarded visits to the feeder) and lying behavior during the 5 d leading up to calves displaying clinical signs of NCD were analyzed. Calves with NCD performed fewer unrewarded visits and consumed less milk than healthy calves during the 2- and 4-d periods before diagnosis with NCD, respectively. Calves with NCD tended to perform fewer lying bouts than healthy calves over the 5-d period before diagnosis with NCD. At 3 wk of age, a subset of 51 healthy calves were allocated to 1 of 5 treatment groups: (1) sham handling (SHAM, n = 10), (2) cautery disbudding (DB, n = 11), (3) administration of local anesthetic (LA) and DB (LA+DB, n = 11), 4) administration of a nonsteroidal anti-inflammatory drug (NSAID) and DB (NSAID+DB, n = 9), and (5) administration of LA, NSAID and DB (LA+NSAID+DB, n = 10). Feeding and lying behavior were recorded continuously for 24 h pre- and postdisbudding. We found no effect of treatment on the number of rewarded or unrewarded visits to the feeder and milk volume consumed 24 h before administration of treatments. During the 24-h postdisbudding period, SHAM calves performed more unrewarded visits than DB, LA+DB, and NSAID+DB calves, but the number of unrewarded visits did not differ between SHAM and LA+NSAID+DB calves. During the first hour of the posttreatment period we noted a difference in lying times among treatments, with DB and NSAID+DB calves spending less time lying than SHAM calves and lying times being similar between SHAM, LA+DB, and LA+NSAID+DB calves. The ACFS and accelerometers have the potential to automatically gather valuable information regarding health status and pain in calves. Therefore, it may be advantageous to combine both of these measures (ACFS and accelerometers) when evaluating NCD on farm or pain in calves in future research.


title: Use of the informational spectrum methodology for rapid biological analysis of the novel coronavirus 2019-nCoV: prediction of potential receptor, natural reservoir, tropism and therapeutic/vaccine target

text: A novel coronavirus recently identified in Wuhan, China (SARS-CoV-2) has expanded the number of highly pathogenic coronaviruses affecting humans. The SARS-CoV-2 represents a potential epidemic or pandemic threat, which requires a quick response for preparedness against this infection. The present report uses the informational spectrum methodology to identify the possible origin and natural host of the new virus, as well as putative therapeutic and vaccine targets. The performed in silico analysis indicates that the newly emerging SARS-CoV-2 is closely related to severe acute respiratory syndrome (SARS)-CoV and, to a lesser degree, Middle East respiratory syndrome (MERS)-CoV. Moreover, the well-known SARS-CoV receptor (ACE2) might be a putative receptor for the novel virus as well. Actin protein was also suggested as a host factor that participates in cell entry and pathogenesis of SARS-CoV-2; therefore, drugs modulating biological activity of this protein (e.g. ibuprofen) were suggested as potential candidates for treatment of this viral infection. Additional results indicated that civets and poultry are potential candidates for the natural reservoir of the SARS-CoV-2, and that domain 288-330 of S1 protein from the SARS-CoV-2 represents promising therapeutic and/or vaccine target.


title: Blue Ribbon Abstract Award: Assessment of Education and Communication Resources for Public Health Emergencies in U.S. Hospitals

text: Abstract BACKGROUND: Established systems for education and rapid dissemination of information are essential to a healthcare facility's ability to respond to emerging public health threats. We assessed the education activities and communication resources available for this purpose in a representative sample of U.S. hospitals. METHODS: We selected a 20% (n=1236) random sample of hospitals from the 2000 American Hospital Association database, stratified by bed size, service, metropolitan statistical sampling area (MSSA), and region to ensure representativeness. Infection control professionals (ICPs) at the hospitals were asked to complete a Web-based questionnaire during October 21–December 22, 2003. RESULTS: ICPs at 556 (45%) hospitals completed the survey, including 518 (93%) general medical-surgical, 20 (4%) other specialty (including oncology), and 18 (3%) children's hospitals; 352 (63%) were in urban (<100,000 population) areas and 224 (40%) had <100 beds. Most hospitals had provided educational programs about infection control issues related to smallpox (87%), smallpox vaccine-related adverse events (76%), severe acute respiratory syndrome (SARS) (75%); and anthrax (73%). Fewer offered programs on monkeypox (27%). Hospitals reported that the best ways to disseminate information to them were via e-mail (97%), Web sites or group e-mail lists (72%), videoconference (40%), or teleconference (35%). Urban hospitals were more likely than rural to identify Web sites (p=0.001) and videoconference (p=0.03) as the best ways to receive information. Hospitals used e-mail (94%), teleconferencing (72%), Web-based training (61%), computer-based tools (50%), and videoconferencing (46%) to reach hospital-based clinical personnel. Urban hospitals were more likely than rural to use e-mail (p=0.01) to reach personnel. Hospitals identified model preparedness plans (61%), educational materials for personnel (54%) or patients/public (40%), and tabletop exercises/drills (46%) as being most helpful to preparedness efforts. CONCLUSIONS: Hospitals may differ substantially in preparedness and response readiness. These findings will assist in determining the best strategies for communicating with hospitals and providing information to assist them in preparedness efforts.


Other emerging viral pathogens


title: Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses

text: Abstract Current technologies with next generation sequencing have revolutionized metagenomics analysis of clinical samples. To achieve the non-selective amplification and recovery of low abundance genetic sequences, a simplified Sequence-Independent, Single-Primer Amplification (SISPA) technique in combination with MiSeq platform was applied to target negative- and positive-sense single-stranded RNA viral sequences. This method allowed successful sequence assembly of full or near full length avian influenza virus (AIV), infectious bronchitis virus (IBV), and Newcastle disease virus (NDV) viral genome. Moreover, SISPA analysis applied to unknown clinical cases of mixed viral infections produced genome assemblies comprising 98% NDV and 99% of IBV genomes. Complete or near complete virus genome sequence was obtained with titers at or above 104.5 EID50/ml (50% embryo infectious dose), and virus identification could be detected with titers at or above 103 EID50/ml. Taken together, these studies demonstrate a simple template enrichment protocol for rapid detection and accurate characterization of avian RNA viruses.


title: Comparative Seasonal Respiratory Virus Epidemic Timing in Utah

text: Previous studies have found evidence of viral interference between seasonal respiratory viruses. Using laboratory-confirmed data from a Utah-based healthcare provider, Intermountain Health Care, we analyzed the time-specific patterns of respiratory syncytial virus (RSV), influenza A, influenza B, human metapneumovirus, rhinovirus, and enterovirus circulation from 2004 to 2018, using descriptive methods and wavelet analysis (n = 89,462) on a local level. The results showed that RSV virus dynamics in Utah were the most consistent of any of the viruses studied, and that the other seasonal viruses were generally in synchrony with RSV, except for enterovirus (which mostly occurs late summer to early fall) and influenza A and B during pandemic years.


title: AVOIDING HEALTH WORKER INFECTION AND CONTAINING THE CORONAVIRUS DISEASE 2019 PANDEMIC: Perspectives from the frontline in Wuhan

text: Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused great public concern worldwide due to its high rates of infectivity and pathogenicity. The Chinese government responded in a timely manner, alleviated the dilemma, achieved a huge victory and lockdown has now been lifted in Wuhan. However, the outbreak has occurred in more than 200 other countries. Globally, as of 9:56 am CEST on 19 May 2020, there have been 4,696,849 confirmed cases of COVID-19, including 315,131 deaths, reported to Word Health Organization (WHO). The spread of COVID-19 overwhelmed the healthcare systems of many countries and even crashed the fragile healthcare systems of some. Although the situation in each country is different, health workers play a critical role in the fight against COVID-19. In this review, we highlight the status of health worker infections in China and other countries, especially the causes of infection in China and the standardised protocol to protect health workers from the perspective of an anaesthesiologist, in the hope of providing references to reduce medical infections and contain the COVID-19 epidemic.


title: Do slit lamp shields and face masks protect ophthalmologists amidst COVID-19?

text: Unlike face masks which provided some protection against both aerosols and droplets, slit lamp shields conferred protection only against direct large droplet transmission, with a limited role in reducing aerosol transmission risk.


title: Impact of COVID-19 outbreak on clinical practice and training of young gastroenterologists: a European Survey

text: ABSTRACT Background: SARS-CoV-2 disease (COVID-19) is a major challenge for the healthcare system and physicians, imposing changes in daily clinical activity. Aims: we aimed to describe what European trainees and young gastroenterologists know about COVID-19 and identify training gaps to implement educational programs. Methods: A prospective web-based electronic survey was developed and distributed via e-mail to all members of the Italian Young Gastroenterologist and Endoscopist Association and to European representatives. Results: One hundred and ninety-seven subjects participated in the survey, of whom 14 (7.1%) were excluded. The majority were gastroenterologists in training (123, 67.7%) working in institutions with COVID-19 inpatients (159, 86.9%), aged ≤30 years (113, 61.8%). The activity of Gastroenterology Units was restricted to emergency visits and endoscopy, with reductions of activities of up to 90%. 84.5% of participants felt that the COVID-19 outbreak impacted on their training, due to unavailability of mentors (52.6%) and interruption of trainee's involvement (66.4%). Most participants referred absence of training on the use of personal protective equipment, oxygen ventilation systems and COVID-19 therapies. Conclusion: COVID-19 outbreak significantly impacted on gastroenterologists’ clinical activity. The resources currently deployed are inadequate, and therefore educational interventions to address this gap are warranted in the next future.


A Case of In-flight Transmission of Severe Acute Respiratory Syndrome (SARS): SARS Serology Positive


title: Intestinal replication of a porcine respiratory coronavirus closely related antigenically to the enteric transmissible gastroenteritis virus

text: Abstract One-week-old piglets were inoculated with the porcine respiratory coronavirus (PRCV) either intravenously or directly into the lumen of the gastrointestinal tract. Both inoculation routes resulted in the isolation of virus from the caudal small intestine. Viral replication, however, was only observed upon inoculation into the digestive tract in quantities of ≥ 103 TCID50. Replication remained limited to a few unidentified cells located in or underneath the epithelial layer at villus- or crypt-sites. Virus was excreted in the faeces for several days but infection of the respiratory tract occured rarely in the same pigs. The results of this study indicate that small changes in molecular structure between PRCV and transmissible gastroenteritis virus have resulted in important changes in host cell tropism.


title: Viral antibody titers, immunogenetic markers, and their interrelations in multiple sclerosis patients and controls

text: Abstract Our purpose was to investigate possible interrelations between antibody titers against seven viruses (measles, rubella, herpes simplex, mumps, varicella-zoster, coronavirus, cytomegalovirus), HLA-class II antigens, and immunoglobulin Gm allotypes in multiple sclerosis (MS). We studied 57 MS patients and 59 controls with similar age and sex distributions. In MS patients, we found the classical increased frequency of HLA-DR2, HLA-DQw1 and also an excess of Gm (3; ±23; 5*). Mumps antibody levels were higher in MS patients than in controls; elevation was not significant for measles antibodies. Analysis suggests that an association between HLA-DQwl and antibody titers against various viruses exists in controls but is absent in MS patients. In particular, we found that mumps antibody titers were higher in DQwl-positive than in DQwl-negative controls, while there was no significant difference among MS cases. Accordingly, we found that the overall difference between patients and controls was due to the fact that DQwl-positive patients had higher titers than controls, while DQwl-negative cases had similar titers as controls. These findings suggest that biological and molecular characteristics of DQwl might differ in MS patients.


title: CD8(+) T Cells: Foot Soldiers of the Immune System

text: Resting naive CD8(+) T cells have an astounding capacity to react to pathogens by massive expansion and differentiation into cytotoxic effector cells that migrate to all corners of the body to clear the infection. The initial interaction with antigen-presenting cells in the central lymphoid organs drives an orchestrated program of differentiation aimed at producing sufficient numbers of effectors to get the job done without resulting in clonal exhaustion. Interactions with antigen-presenting cells and other immune cells continue at the site of infection to regulate further on-site expansion and differentiation, all with the goal of protecting the host with minimal bystander tissue damage. Here we review recent advances in CD8(+) T cell recognition of antigen in lymphoid as well as in nonlymphoid tissues in the periphery, and how CD8(+) T cell expansion and differentiation are controlled in these contexts.


title: Nanofabrication of a gold fiducial array on specimen support for electron tomography

text: Abstract Here we describe the production, using lithography and micro-engineering technologies, of patterned arrays of nanofabricated gold dots on a thin Si3N4 electron transparent layer, supported by silicon. We illustrate that the support with a patterned structure of nanosized gold can be exploited for (cryo) electron tomography application as a specimen support with predefined alignment markers. This nanogold patterned support has several advantages. The Si3N4 window provides a 50nm thin, strong and flat support with a ∼0.7mm2 large electron-beam transparent window. The nanogold pattern has a user-defined size and density, is highly regular and stable. This facilitates accurate tracking during tilt series acquisition, provides sufficient contrast for accurate alignment during the image reconstruction step and avoids an uneven lateral distribution and movement of individual fiducials. We showed that the support is suitable for electron tomography on plastic sections.


title: Effects on lung, immune function offer warning for drinking in crisis

text: While it remains much too early to determine precisely how alcohol use might affect risk for or progression of COVID‐19, any efforts to connect the dots from past alcohol research would suggest it wise for nondrinkers and low‐risk drinkers to maintain that status during this public health crisis. It's already known that disaster can result in increased alcohol consumption based on the work of Deborah Hasin, Ph.D., after 9/11 (see “Alcohol and isolation: Experts comment on drinking behavior during COVID‐19,” ADAW March 30; https://onlinelibrary.wiley.com/doi/10.1002/adaw.32670).


title: Network analysis of host–virus communities in bats and rodents reveals determinants of cross‐species transmission

text: Bats are natural reservoirs of several important emerging viruses. Cross‐species transmission appears to be quite common among bats, which may contribute to their unique reservoir potential. Therefore, understanding the importance of bats as reservoirs requires examining them in a community context rather than concentrating on individual species. Here, we use a network approach to identify ecological and biological correlates of cross‐species virus transmission in bats and rodents, another important host group. We show that given our current knowledge the bat viral sharing network is more connected than the rodent network, suggesting viruses may pass more easily between bat species. We identify host traits associated with important reservoir species: gregarious bats are more likely to share more viruses and bats which migrate regionally are important for spreading viruses through the network. We identify multiple communities of viral sharing within bats and rodents and highlight potential species traits that can help guide studies of novel pathogen emergence.


title: A newly isolated Chinese virulent genotype GIIb porcine epidemic diarrhea virus strain: Biological characteristics, pathogenicity and immune protective effects as an inactivated vaccine candidate

text: Abstract Since October 2010, severe porcine epidemic diarrhea (PED) outbreaks caused by highly virulent PED virus (PEDV) strains have occurred continuously in the Chinese pig population and caused considerable economic losses. Although PEDV vaccines based on classical PEDV strains have been widely used in China in recent years, the morbidity and mortality in piglets remain high. Therefore, virulent genotype GII PEDV strains that are prevalent in the field should be isolated and used to develop next-generation vaccines. In the present study, a Chinese virulent genotype GIIb PEDV strain, CH/HNPJ/2017, was serially propagated in Vero cells for up to 90 passages. The S genes contained typical insertions and deletions that were also found in other recently isolated highly virulent PEDV strains from China and other countries and had two neighboring unique insertion mutations, which resulted in four amino acid changes in the S1 region of passages P10 and P60. Pig infection studies revealed that the CH/HNPJ/2017 strain was highly virulent in piglets, and the median pig diarrhea dose (PDD50) was 7.68 log10PDD50/3 mL. Furthermore, the cell-adapted CH/HNPJ/2017 strain elicited potent serum IgG and neutralizing antibody responses in immunized pigs when it was used as an inactivated vaccine candidate. In addition, the pigs that received the experimental inactivated vaccines were partially protected (3/5) against subsequent viral challenge. In brief, these data indicate that the CH/HNPJ/2017 strain is a promising candidate for developing a safe and effective PEDV vaccine in the future.


Identification and Characterization of a Unique Ribosomal Frameshifting Signal in SARS-CoV ORF3A


title: α4-integrins control viral meningoencephalitis through differential recruitment of T helper cell subsets

text: INTRODUCTION: Natalizumab blocks α4-integrins and is a prototypic agent for a series of anti-inflammatory drugs that impair trafficking of immune cells into the CNS. However, modulation of the access of immune cells to the CNS is associated with impaired immune surveillance and detrimental viral infections of the CNS. Here, we explored the potency of cellular immune responses within the CNS to protect against viral encephalitis in mice with T cell conditional disruption of VLA-4 integrin (α4β1) expression. RESULTS: While VLA-4 expression in virus specific Th1 cells is non-redundant for their ability to access the CNS, α4-integrin deficient Th17 cells enter the CNS compartment and generate an inflammatory milieu upon intrathecal vaccinia virus (VV) infection. However, in contrast to Th1 cells that can adopt direct cytotoxic properties, Th17 cells fail to clear the virus due to insufficient Eomes induced perforin-1 expression. CONCLUSION: The quality of the intrathecal cellular antiviral response under conditions of impaired VLA-4 function jeopardizes host protection. Our functional in vivo data extend our mechanistic understanding of anti-viral immunity in the CNS and help to estimate the risk potential of upcoming therapeutic agents that target the trafficking of immune cells into distinct anatomical compartments.


title: Viral infections in children's wards—how well do we manage them?

text: Abstract Children are frequently admitted to hospital wards with viral infections. Many are not life-threatening to the index case, but the spread to vulnerable patients who are already at higher risk should be avoided. To do so requires active awareness and availability of rapid diagnosis (i.e. the same day). Cohorting and handwashing have been found to be the best measures to prevent spread of respiratory syncytial virus (responsible for considerable morbidity every winter) in hospital wards.


title: Evaluation of ViroCyt(®) Virus Counter for Rapid Filovirus Quantitation

text: Development and evaluation of medical countermeasures for diagnostics, vaccines, and therapeutics requires production of standardized, reproducible, and well characterized virus preparations. For filoviruses this includes plaque assay for quantitation of infectious virus, transmission electron microscopy (TEM) for morphology and quantitation of virus particles, and real-time reverse transcription PCR for quantitation of viral RNA (qRT-PCR). The ViroCyt(®) Virus Counter (VC) 2100 (ViroCyt, Boulder, CO, USA) is a flow-based instrument capable of quantifying virus particles in solution. Using a proprietary combination of fluorescent dyes that stain both nucleic acid and protein in a single 30 min step, rapid, reproducible, and cost-effective quantification of filovirus particles was demonstrated. Using a seed stock of Ebola virus variant Kikwit, the linear range of the instrument was determined to be 2.8E+06 to 1.0E+09 virus particles per mL with coefficient of variation ranging from 9.4% to 31.5% for samples tested in triplicate. VC particle counts for various filovirus stocks were within one log of TEM particle counts. A linear relationship was established between the plaque assay, qRT-PCR, and the VC. VC results significantly correlated with both plaque assay and qRT-PCR. These results demonstrated that the VC is an easy, fast, and consistent method to quantify filoviruses in stock preparations.


title: Biological Activities of Rhamnan Sulfate Extract from the Green Algae Monostroma nitidum (Hitoegusa)

text: Monostroma nitidum is a green single-cell layered algae that grows on the southwest coast of Japan. It is often used for salad ingredients, boiled tsukudani, soups, etc., due to its health benefits. M. nitidum is composed of many cell aggregates, and the various substances that fill the intercellular space are dietary fibers, vitamins, and minerals. Rhamnan sulfate (RS), a sulfated polysaccharide, is main the component of the fiber extracted from M. nitidum. Recently, some biological properties of RS have been demonstrated by in vitro and in vivo studies that probably protect human subjects from viruses and ameliorate vascular dysfunction caused by metabolic disorders, especially lifestyle-related diseases. In this review, we focus on the antithrombotic effects of RS and introduce its antiviral and other biological activities.


The Impact of COVID-19 on Vascular Training


Lopinavir/ritonavir/ribavirin: Various toxicities following off-label treatment: case report


title: No evidence of increased risk for COVID‐19 infection in patients treated with Dupilumab for atopic dermatitis in a high‐epidemic area ‐ Bergamo, Lombardy, Italy

text: Atopic dermatitis (AD) is a chronic inflammatory skin disease. Patients with AD have increased infection risk, including skin infections and systemic infections. Dupilumab, a fully human monoclonal antibody, blocks the shared receptor component for interleukin‐4 (IL‐4) and IL‐13. Dupilumab is approved for inadequately controlled moderate‐to‐severe AD.(1)


title: Detection of new respiratory viruses in hospitalized infants with bronchiolitis: a three‐year prospective study

text: Aim: We have designed a study with the objective of describing the clinical impact of other viruses different from the respiratory syncytial virus (RSV) in hospitalized infants with bronchiolitis. Methods: A 3 year prospective study was conducted on infants admitted to the Paediatrics Department of the Severo Ochoa Hospital (Spain). We studied the frequency of 16 respiratory viruses. Clinical characteristics of RSV‐only infections were compared with other single agent viral infections. Results: Positive results were confirmed in 275 (86.5%) of the 318 children studied. A single virus was detected in 196 patients and 79 were dual or multiple viral infections. RSV was detected in 61.3% of total bronchiolitis. Rhinovirus (RV) was 17.4% of the identified virus, followed by human bocavirus (HBoV), adenovirus and metapneumovirus (hMPV). Only RV, HBoV and hMPV were significant as single infections. RSV patients were younger than HBoV (p > 0.0001) and hMPV (p = 0.025). Seasonality was clearly different between them. Children with RSV infection needed treatment in the intensive care unit more frequently than others. Conclusions: In hospitalized infants, RSV was the most frequent agent in bronchiolitis in winter, but other viruses were present in 47% of the patients. RV, HBoV and hMPV had a significant proportion of single infections. Clinical characteristics were similar amongst them, but seasonality was clearly different.


title: The metagenomic approach and causality in virology

text: Nowadays, the metagenomic approach has been a very important tool in the discovery of new viruses in environmental and biological samples. Here we discuss how these discoveries may help to elucidate the etiology of diseases and the criteria necessary to establish a causal association between a virus and a disease.


title: The VIZIER project: Overview; expectations; and achievements

text: Abstract VIZIER is an acronym for a research project entitled “Comparative Structural Genomics of Viral Enzymes Involved in Replication” funded by the European Commission between November 1st, 2004 and April 30th, 2009. It involved 25 partners from 12 countries. In this paper, we describe the organization of the project and the culture created by its multidisciplinary essence. We discuss the main thematic sections of the project and the strategy adopted to optimize the integration of various scientific fields into a common objective: to obtain crystal structures of the widest variety of RNA virus replication enzymes documented and validated as potential drug targets. We discuss the thematic sections and their overall organization, their successes and bottlenecks around the protein production pipeline, the “low hanging fruit” strategy, and measures directed to problem solving. We discuss possible future options for such large-scale projects in the area of antiviral drug design. In a series of accompanying papers in Antiviral Research, the project and its achievements are presented for each virus family.


title: Analysis of genomic and intracellular viral RNAs of small plaque mutants of mouse hepatitis virus, JHM strain

text: Abstract The genomic RNA and intracellular RNA of mouse hepatitis virus, strain JHM (MHV-JHM) and two plaque mutants (la and 2c), which have been isolated from a persistently infected culture (JHM-CC), have been analyzed by T1-resistant oligonucleotide finger-printing. The genomic RNA of the virus population (JHM-CC virus) released from different passage levels of the same persistent infection has also been analyzed. The analysis shows the locations within the genomic and intracellular RNAs of more than 45 T1-resistant oligonucleotides and confirm earlier studies (J. L. Leibowitz, K. C. Wilhelmsen, and C. W. Bond (1981), Virology 114, 39–51), showing that the six subgenomic RNAs of MHV-JHM form a 3′ coterminal nested set which extends for different lengths in a 5′ direction. The analysis also identifies in each subgenomic RNA those large T1 oligonucleotides derived from noncontiguous regions of the genome during mRNA synthesis. Two important conclusions can be reached from analysis of the mutant viruses. First, the virus population released from the persistent infection represents a fairly constant mixture of viruses, and the fluctuating emergence of variants as predominant species in the culture does not occur. Second, the data indicate that for particular intracellular RNAs of mutant viruses the sequence rearrangements occurring during subgenomic mRNA synthesis are different from those in the corresponding intracellular RNA of wild-type virus. The result may indicate a potential flexibility in the leader/body fusion process that has not been previously recognized.


title: Glucocorticoids in osteonecrosis of the femoral head: A new understanding of the mechanisms of action

text: Abstract Glucocorticoid (GC) usage is the most common non-traumatic cause of osteonecrosis of the femoral head (ON). Despite the strong association of GC with ON, the underlying mechanisms have been unclear. Investigators have proposed both direct and indirect effects of GC on cells. Indirect and direct mechanisms remain intimately related and often result in positive feedback loops to potentiate the disease processes. However, the direct effects, in particular apoptosis, have recently been shown to be increasingly important. Suppression of osteoblast and osteoclast precursor production, increased apoptosis of osteoblasts and osteocytes, prolongation of the lifespan of osteoclasts and apoptosis of endothelial cells (EC) are all direct effects of GC usage. Elevated blood pressure through several pathways may raise the risk of clot formation. High-dose GC also decreases tissue plasminogen activator activity (t-PA) and increases plasma plasminogen activator inhibitor-1 (PAI-1) antigen levels increasing the procoagulant potential of GC. Inhibited angiogenesis, altered bone repair and nitric oxide metabolism can also result. Also, GC treatment modulates other vasoactive mediators such as endothelin-1, noradrenalin and bradykinin. Thus, GCs act as a regulator of local blood flow by modulating vascular responsiveness to vasoactive substances. Vasoconstriction induced in intraosseous femoral head arteries causes femoral head ischemia. GCs also cause ischemia through increased intraosseous pressure, which subsequently decreases the blood flow to the femoral head by apoptosis of ECs as well as elevating the level of adipogenesis and fat hypertrophy in the bone marrow. It is difficult to predict which patients receiving a specific dose of GC will develop ON, indicating individual differences in steroid sensitivity and the potential of additional mechanisms. The textbook model of ON is a multiple hit theory in which, with a greater number of risk factors, the risk of ON increases. While more effort is needed to better comprehend the role of GC in ON, newer data on GC action upon the endothelial cell and the regional endothelial bed dysfunction theory sheds new light on particular GC mechanisms. Better understanding of GC pathomechanisms can lead to better treatment options.


title: Epidemiology of Severe Acute Respiratory Illness and Risk Factors for Influenza Infection and Clinical Severity among Adults in Malawi, 2011–2013

text: Data on the epidemiology of severe acute respiratory illness (SARI) in adults from low-income, high human immunodeficiency virus (HIV) prevalence African settings are scarce. We conducted adult SARI surveillance in Blantyre, Malawi. From January 2011 to December 2013, individuals aged ≥ 15 years with SARI (both inpatients and outpatients) were enrolled at a large teaching hospital in Blantyre, Malawi. Nasopharyngeal aspirates were tested for influenza and other respiratory viruses by polymerase chain reaction. We estimated hospital-attended influenza-positive SARI incidence rates and assessed factors associated with influenza positivity and clinical severity (Modified Early Warning Score > 4). We enrolled 1,126 SARI cases; 163 (14.5%) were positive for influenza. Human immunodeficiency virus prevalence was 50.3%. Annual incidence of hospital-attended influenza-associated SARI was 9.7–16.8 cases per 100,000 population. Human immunodeficiency virus was associated with a 5-fold greater incidence (incidence rate ratio 4.91, 95% confidence interval [CI]: 3.83–6.32). On multivariable analysis, female gender, as well as recruitment in hot, rainy season (December to March; adjusted odds ratios (aOR): 2.82, 95% CI: 1.57–5.06) and cool, dry season (April to August; aOR: 2.47, 95% CI: 1.35–4.15), was associated with influenza positivity, whereas influenza-positive patients were less likely to be HIV-infected (aOR: 0.59, 95% CI: 0.43–0.80) or have viral coinfection (aOR: 0.51, 95% CI: 0.36–0.73). Human immunodeficiency virus infection (aOR: 1.86; 95% CI: 1.35–2.56) and recruitment in hot, rainy season (aOR: 4.98, 95% CI: 3.17–7.81) were independently associated with clinical severity. In this high HIV prevalence population, influenza was associated with nearly 15% of hospital-attended SARI. Human immunodeficiency virus infection is an important risk factor for clinical severity in all-cause and influenza-associated SARI. Expanded access to HIV testing and antiretroviral treatment, as well as targeted influenza vaccination, may reduce the burden of SARI in Malawi and other high HIV prevalence settings.


title: Full genome analysis of a novel adenovirus from the South Polar skua (Catharacta maccormicki) in Antarctica

text: Abstract Adenoviruses have been identified in humans and a wide range of vertebrate animals, but not previously from the polar region. Here, we report the entire 26,340-bp genome of a novel adenovirus, detected by PCR, in tissues of six of nine South Polar skuas (Catharacta maccormicki), collected in Lake King Sejong, King George Island, Antarctica, from 2007 to 2009. The DNA polymerase, penton base, hexon and fiber genes of the South Polar skua adenovirus (SPSAdV) exhibited 68.3%, 75.4%, 74.9% and 48.0% nucleotide sequence similarity with their counterparts in turkey hemorrhagic enteritis virus. Phylogenetic analysis based on the entire genome revealed that SPSAdV belonged to the genus Siadenovirus, family Adenoviridae. This is the first evidence of a novel adenovirus, SPSAdV, from a large polar seabird (family Stercorariidae) in Antarctica.