title: Modification of SARS-CoV S1 gene render expression in Pichia pastoris

text: S1 gene fragment containing receptor-binding region was amplified by several sets of primers using Over-Lap PCR. The native S1 gene was modified at A + T abundant regions; n.t.777–1683, n.t.1041–1050, n.t.1236–1248, n.t.1317–1335, n.t.1590–1605; based on the same amino acid sequences. The modified gene was cloned into a yeast expression vector pPIC9K. The resultant plasmid pPIC9K- S1 was transformed into Pichia pastoris GS 115 and the protein expression was induced with methanol. SDS-PAGE confirmed that the recombinant SI was secreted in the supernatant of induced GS 115. The protein yield reached 69 mg/l. ELISA and Western blot demonstrated that the S1 could react with the convalescent sera of people infected by SARS-CoV. Furthermore, ligand blot assay showed that the recombinant S1 could react with ACE2, the receptor of SARS-CoV. The molecular mass of expressed S1 was about 70 kDa, which was higher than that of the 30 kDa expected. PNGase F deglycosylation resulted in a protein band of 30 kDa. In conclusion, the S1 gene modification rendered the high-level expression of S1 in P. pastoris GS 115 and the protein was secreted as a biologically active form which was hyperglycosylated.


title: Chicken mannose binding lectin has antiviral activity towards infectious bronchitis virus

text: Abstract Mannose binding lectin (MBL) is a collagenous C-type lectin, which plays an important role in innate immunity. It can bind to carbohydrates on the surface of a wide range of pathogens, including viruses. Here we studied the antiviral effect of recombinant chicken (rc)MBL against Infectious Bronchitis Virus (IBV), a highly contagious coronavirus of chicken. rcMBL inhibited in a dose-dependent manner the infection of BHK-21 cells by IBV-Beaudette, as detected by immunofluorescence staining of viral proteins and qPCR. ELISA and negative staining electron microscopy showed that rcMBL bound directly to IBV, resulting in the aggregation of viral particles. Furthermore, we demonstrated that MBL bound specifically to the spike S1 protein of IBV which mediates viral attachment. This subsequently blocked the attachment of S1 to IBV-susceptible cells in chicken tracheal tissues as shown in protein histochemistry. Taken together, rcMBL exhibits antiviral activity against IBV, based on a direct interaction with IBV virions.


title: VIRUSES | Introduction

text: Abstract Several virus types can contaminate food, with the consequent possibility of human infection. The most common foodborne virus is norovirus, with hepatitis A and hepatitis E viruses also being prominent. Food can be directly contaminated with viruses by infected handlers, and also indirectly by, for example, polluted water used for irrigation or washing. Routine screening of foodstuffs for virus contamination is seldom performed, and may not be wholly cost-effective. Prevention of contamination through risk management of critical control points is more realistic, but physical means of virus elimination will always be required in case of failure of procedural controls. Much research remains necessary before the global challenge of foodborne viruses will be met.


title: Increase in cardiovascular pathology in female sprague-dawley rats following chronic treatment with 2,3,7,8-tetrachlorodibenzo-p-dioxin and 3,3′,4,4′,5-pentachlorobiphenyl

text: The effects of chronic exposure to dioxin (2,3,7,8,-tetrachlorodibenzo-p-dioxin [TCDD]) and a dioxin-like compound (3,3′,4,4′,5-pentachlorobiphenyl [PCB126]) on the cardiovascular system were evaluated in female Harlan Sprague-Dawley rats as part of an ongoing National Toxicology Program investigation. The animals were gavage treated 5 d per week with up to 1000 ng of PCB126 per kilogram of body weight per day or up to 100 ng of TCDD per kilogram of body weight per day for up to 2 yr. The control animals received only a corn oil/acetone vehicle (99:1 mixture). The corresponding stop-study groups received the highest doses for 31 wk and then received only the vehicle for the remainder of the study. After a full necropsy of all animals, a complete set of tissues was examined microscopically. Administration of each compound was associated with treatment-related increases in the incidences of degenerative cardiovascular lesions. Cardiomyopathy and chronic active arteritis increased in a dose-related manner in all groups treated with PCB126 or with TCDD. Increased incidences were also observed in the stop-study groups, indicating that a shorter term exposure may produce some effects. The average severity of cardiomyopathy was minimal or slightly greater in all dose groups, including the controls. Chronic active arteritis occurred primarily in the mesentery and pancreas, although the rectum, liver, heart, ovary, uterus, and glandular stomach in the PCB126 study and the liver and ovary in the TCDD study were affected in a few of the dosed animals. The authors’ investigations indicate that the rat cardiovascular system is a target for dioxin toxicity, which increases the incidence of spontaneous cardiomyopathy and arteritis.


title: Innovations in modeling influenza virus infections in the laboratory

text: Respiratory viruses represent one of the most substantial infectious disease burdens to the human population today, and in particular, seasonal and pandemic influenza viruses pose a persistent threat to public health worldwide. In recent years, advances in techniques used in experimental research have provided the means to better understand the mechanisms of pathogenesis and transmission of respiratory viruses, and thus more accurately model these infections in the laboratory. Here, we briefly review the model systems used to study influenza virus infections, and focus particularly on recent advances that have increased our knowledge of these formidable respiratory pathogens.


title: Hematopoietic Stem Cell Transplantation in an Infant with Immunodeficiency, Centromeric Instability, and Facial Anomaly Syndrome

text: Immunodeficiency, centromeric instability, and facial anomaly (ICF) syndrome is a rare autosomal recessive genetic condition with severe immunodeficiency, which leads to lethal infections if not recognized and treated in early childhood. Up-to-date treatment regimens consist of prophylactic and supportive treatment of the recurrent infections. Here, we report the case of a 1-year-old boy of Moroccan consanguineous parents, who was diagnosed at 4 months of age with ICF syndrome with a homozygous missense mutation in the DNMT3B gene. He was initially admitted to the hospital with recurrent pulmonary infections from the opportunistic pathogen Pneumocystis jirovecii (PJ). Further immunological workup revealed agammaglobulinemia in the presence of B cells. After successful recovery from the PJ pneumonia, he underwent hematopoietic stem cell transplantation (HSCT) from the HLA-matched healthy sister using a chemotherapeutic conditioning regimen consisting of treosulfan, fludarabine, and thiotepa. Other than acute chemotherapy-associated side effects, no serious adverse events occurred. Six months after HSCT immune-reconstitution, he had a stable chimerism with 2.9% autologous portion in the peripheral blood and a normal differential blood cell count, including all immunoglobulin subtypes. This is one of the first cases of successful HSCT in ICF syndrome. Early diagnosis and subsequent HSCT can prevent severe opportunistic infections and cure the immunodeficiency. Centromeric instability and facial anomaly remain unaffected. Although the long-term patient outcome and the neurological development remain to be seen, this curative therapy for immunodeficiency improves life expectancy and quality of life. This case is meant to raise physicians awareness for ICF syndrome and highlight the consideration for HSCT in ICF syndrome early on.


title: Rotavirus infections in calves: efficacy of oral vaccination in endemically infected herds

text: A commercially available modified live reovirus-like (rotavirus) vaccine proved innocuous in calves deprived of colostrum and protected one out of three calves against challenge 72 h after vaccination. The vaccine was evaluated in two dairy herds in the 1977 calf season. No significant differences were observed in the incidence rates or severity of undifferentiated neonatal calf diarrhoea or rotavirus-associated late diarrhoea between calves given a placebo (76) and vaccinated (74) calves in these herds. Samples of colostrum contained specific antibodies against rotavirus and neutralisation of the vaccine virus by colostral antibody in the intestinal tract was considered the major reason for the failure of the vaccine to reduce the incidence of neonatal diarrhoea in these herds.


title: Viral diarrhea of young animals: A review

text: Abstract A brief presentation is given of the enteric viral infections of young animals. The general characteristics of rotaviruses, coronaviruses and parvoviruses are reported, and the different aspects of the diseases associated with these viruses are discussed. Certain suggestions are made regarding the prevention of these diseases.


title: Aviation and global climate change in the 21st century

text: Abstract Aviation emissions contribute to the radiative forcing (RF) of climate. Of importance are emissions of carbon dioxide (CO2), nitrogen oxides (NO x ), aerosols and their precursors (soot and sulphate), and increased cloudiness in the form of persistent linear contrails and induced-cirrus cloudiness. The recent Fourth Assessment Report (AR4) of the Intergovernmental Panel on Climate Change (IPCC) quantified aviation's RF contribution for 2005 based upon 2000 operations data. Aviation has grown strongly over the past years, despite world-changing events in the early 2000s; the average annual passenger traffic growth rate was 5.3% yr−1 between 2000 and 2007, resulting in an increase of passenger traffic of 38%. Presented here are updated values of aviation RF for 2005 based upon new operations data that show an increase in traffic of 22.5%, fuel use of 8.4% and total aviation RF of 14% (excluding induced-cirrus enhancement) over the period 2000–2005. The lack of physical process models and adequate observational data for aviation-induced cirrus effects limit confidence in quantifying their RF contribution. Total aviation RF (excluding induced cirrus) in 2005 was ∼55 mW m−2 (23–87 mW m−2, 90% likelihood range), which was 3.5% (range 1.3–10%, 90% likelihood range) of total anthropogenic forcing. Including estimates for aviation-induced cirrus RF increases the total aviation RF in 2005–78 mW m−2 (38–139 mW m−2, 90% likelihood range), which represents 4.9% of total anthropogenic forcing (2–14%, 90% likelihood range). Future scenarios of aviation emissions for 2050 that are consistent with IPCC SRES A1 and B2 scenario assumptions have been presented that show an increase of fuel usage by factors of 2.7–3.9 over 2000. Simplified calculations of total aviation RF in 2050 indicate increases by factors of 3.0–4.0 over the 2000 value, representing 4–4.7% of total RF (excluding induced cirrus). An examination of a range of future technological options shows that substantive reductions in aviation fuel usage are possible only with the introduction of radical technologies. Incorporation of aviation into an emissions trading system offers the potential for overall (i.e., beyond the aviation sector) CO2 emissions reductions. Proposals exist for introduction of such a system at a European level, but no agreement has been reached at a global level.


title: Direct diagnosis of human respiratory coronaviruses 229E and OC43 by the polymerase chain reaction

text: Abstract An RT-PCR-hybridization was developed that amplified genetic material from the M protein gene of HCoV-229E and HCoV-OC43. The analytic sensitivity of these original primers were compared with primers defined in the N gene and described previously. The results show that 0.05 TCID50 of HCoV-229E and 0.01 TCID50 of HCoV-OC43 can be detected by this molecular method using the original method. Detection of HCoV-229E and HCoV-OC43 in clinical specimens is possible using this method: 348 respiratory specimens (202 sputum and 146 nasal aspirates) were tested with this RT-PCR-hybridization and 12 human coronavirus are detected (3%). The method could provide a useful tool for demonstrating the role of human coronavirus in infections of the respiratory tract.


title: Updated insights into the mechanism of action and clinical profile of the immunoadjuvant QS-21: A review

text: Abstract Background Vaccine adjuvants are compounds that significantly enhance/prolong the immune response to a co-administered antigen. The limitations of the use of aluminium salts that are unable to elicite cell responses against intracellular pathogens such as those causing malaria, tuberculosis, or AIDS, have driven the development of new alternative adjuvants such as QS-21, a triterpene saponin purified from Quillaja saponaria. Purpose The aim of this review is to attempt to clarify the mechanism of action of QS-21 through either receptors or signaling pathways in vitro and in vivo with special emphasis on the co-administration with other immunostimulants in new adjuvant formulations, called adjuvant systems (AS). Furthermore, the most relevant clinical applications will be presented. Methods A literature search covering the period 2014–2018 was performed using electronic databases from Sci finder, Science direct, Medline/Pubmed, Scopus, Google scholar. Results Insights into the mechanism of action of QS-21 can be summarized as follows: 1) in vivo stimulation of Th2 humoral and Th1 cell-mediated immune responses through action on antigen presenting cells (APCs) and T cells, leading to release of Th1 cytokines participating in the elimination of intracellular pathogens. 2) activation of the NLRP3 inflammasome in mouse APCs with subsequent release of caspase-1 dependent cytokines, Il-1β and Il-18, important for Th1 responses. 3) synthesis of nearly 50 QS-21 analogs, allowing structure/activity relationships and mechanistic studies. 4) unique synergy mechanism between monophosphoryl lipid A (MPL A) and QS-21, formulated in a liposome (AS01) in the early IFN-γ response, promoting vaccine immunogenicity. The second part of the review is related to phase I-III clinical trials of QS-21, mostly formulated in ASs, to evaluate efficacy, immunogenicity and safety of adjuvanted prophylactic vaccines against infectious diseases, e.g. malaria, herpes zoster, tuberculosis, AIDS and therapeutic vaccines against cancer and Alzheimer's disease. Conclusion The most advanced phase III clinical applications led to the development of two vaccines containing QS-21 as part of the AS, the Herpes Zoster vaccine (HZ/su) (Shingrix™) which received a license in 2017 from the FDA and a marketing authorization in the EU in 2018 and the RTS,S/AS01 vaccine (Mosquirix™) against malaria, which was approved by the EMA in 2015 for further implementation in Sub-Saharan countries for routine use.


title: Radiographic and Clinical Features of Children With Coronavirus Disease (COVID-19) Pneumonia

text: Objective: The purpose of this study was to investigate chest computed tomography (CT) findings in children with coronavirus disease-19 (COVID-19) pneumonia in our hospital. Methods: This study included 22 pediatric patients with confirmed COVID-19 from January to March, 2020. The chest CT images and clinical data were reviewed. Results: The most prevalent presenting symptoms were fever (64%) and cough (59%), and a mildly elevated mean (SD) C-reactive protein (CRP) level of 11.22(11.06) and erythrocyte sedimentation rateof 18.8(15.17) were detected. The major CT abnormalities observed were mixed ground-glass opacity and consolidation lesions (36%), consolidations (32%), and groundglass opacities (14%). Peripheral distribution (45%) of lung lesions was predominant. Most of the lesions were multilobar(68%), with an average of three lung segments involved. Conclusion: Children with COVID-19 had relatively milder symptoms and less severe lung inflammation than adults.Chest CT plays an important role in the management of children with COVID-19 pneumonia.


title: From “A”IV to “Z”IKV: Attacks from Emerging and Re-emerging Pathogens

text: 100 years after the infamous “Spanish flu” pandemic, the 2017–2018 flu season has been severe, with numerous infections worldwide. In between, there have been continuous, relentless attacks from (re-)emerging viruses. To fully understand viral pathogenesis and develop effective medical countermeasures, we must strengthen current surveillance and basic research efforts.


Indirect casualties of COVID‐19: perspectives from an American vascular surgery practice at a tertiary care centre


title: Survival of the Enveloped Virus Phi6 in Droplets as a Function of Relative Humidity, Absolute Humidity, and Temperature

text: Infectious diseases caused by enveloped viruses, such as influenza, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS), cause thousands of deaths and billions of dollars of economic losses per year. Studies have found a relationship among temperature, humidity, and influenza virus incidence, transmission, or survival; however, there are contradictory claims about whether absolute humidity (AH) or relative humidity (RH) is most important in mediating virus infectivity. Using the enveloped bacteriophage Phi6, which has been suggested as a surrogate for influenza viruses and coronaviruses, we designed a study to discern whether AH, RH, or temperature is a better predictor of virus survival in droplets. Our results show that Phi6 survived best at high (>85%) and low (<60%) RHs, with a significant decrease in infectivity at mid-range RHs (∼60 to 85%). At an AH of less than 22 g · m(−3), the loss in infectivity was less than 2 orders of magnitude; however, when the AH was greater than 22 g · m(−3), the loss in infectivity was typically greater than 6 orders of magnitude. At a fixed RH of 75%, infectivity was very sensitive to temperature, decreasing two orders of magnitude between 19°C and 25°C. We used random forest modeling to identify the best environmental predictors for modulating virus infectivity. The model explained 83% of variation in Phi6 infectivity and suggested that RH is the most important factor in controlling virus infectivity in droplets. This research provides novel information about the complex interplay between temperature, humidity, and the survival of viruses in droplets. IMPORTANCE Enveloped viruses are responsible for a number of infectious diseases resulting in thousands of deaths and billions of dollars of economic losses per year in the United States. There has been a lively debate in the literature over whether absolute humidity (AH) or relative humidity (RH) modulates virus infectivity. We designed a controlled study and used advanced statistical modeling techniques specifically to address this question. By providing an improved understanding of the relationship between environmental conditions and virus infectivity, our work will ultimately lead to improved strategies for predicting and controlling disease transmission.


title: Pneumonia in Normal and Immunocompromised Children: An Overview and Update

text: Pneumonia is an infection of the lung parenchyma caused by a wide variety of organisms in pediatric patients. The role of imaging is to detect the presence of pneumonia, and determine its location and extent, exclude other thoracic causes of respiratory symptoms, and show complications such as effusion/empyema and suppurative lung changes. The overarching goal of this article is to review cause, role of imaging, imaging techniques, and the spectrum of acute and chronic pneumonias in children. Pneumonia in the neonate and immunocompromised host is also discussed.


title: Determining the spatial effects of COVID-19 using the spatial panel data model

text: Abstract This study investigates the propagation power and effects of the coronavirus disease 2019 (COVID-19) in light of published data. We examine the factors affecting COVID-19 together with the spatial effects, and use spatial panel data models to determine the relationship among the variables including their spatial effects. Using spatial panel models, we analyse the relationship between confirmed cases of COVID-19, deaths thereof, and recovered cases due to treatment. We accordingly determine and include the spatial effects in this examination after establishing the appropriate model for COVID-19. The most efficient and consistent model is interpreted with direct and indirect spatial effects.


Meticillin-resistant Staphylococcus aureus


title: Control dynamics of severe acute respiratory syndrome transmission

text: Severe acute respiratory syndrome (SARS) is a serious disease with many puzzling features. We present a simple, dynamic model to assess the epidemic potential of SARS and the effectiveness of control measures. With this model, we analysed the SARS epidemic data in Beijing. The data fitting gives the basic case reproduction number of 2.16 leading to the outbreak, and the variation of the effective reproduction number reflecting the control effect. Noticeably, our study shows that the response time and the strength of control measures have significant effects on the scale of the outbreak and the lasting time of the epidemic.


title: Development of Vaccine Delivery Vehicles Based on Lactic Acid Bacteria

text: Live recombinant bacteria represent attractive antigen delivery systems able to induce both mucosal and systemic immune responses against heterologous antigens. The first live recombinant bacterial vectors developed were derived from attenuated pathogenic microorganisms. In addition to the difficulties often encountered in the construction of stable attenuated mutants of pathogenic organisms, attenuated pathogens may retain a residual virulence level that renders them unsuitable for the vaccination of partially immunocompetent individuals such as infants, the elderly or immunocompromised patients. As an alternative to this strategy, non-pathogenic food-grade lactic acid bacteria (LAB) maybe used as live antigen carriers. This article reviews LAB vaccines constructed using antigens other than tetanus toxin fragment C, against bacterial, viral, and parasitic infective agents, for which protection studies have been performed. The antigens utilized for the development of LAB vaccines are briefly described, along with the efficiency of these systems in protection studies. Moreover, the key factors affecting the performance of these systems are highlighted.


title: Chapter 20 Discovery of Zinc for Human Health and Biomarkers of Zinc Deficiency

text: Abstract Zinc deficiency in humans was recognized for the first time in 1963, and a recommended dietary allowance (RDA) for zinc was established by the US National Academy of Sciences in 1974. The present World Health Organization (WHO) estimate is that nearly 2billion subjects living in the developing world may have zinc deficiency. This is mainly because they subsist on cereal proteins which contain high quantities of organic phosphate compounds, which combine with zinc making it unavailable for absorption. The major adverse clinical effects of zinc deficiency are growth retardation, decreased cell-mediated immunity, impairment of cognitive functions, increased oxidative stress, and upregulation of inflammatory cytokines. Our studies have shown that nearly 30% of healthy, well-to-do elderly subjects living in developed countries may also be zinc deficient due to an increased phytate to zinc molar ratio in their diet. Over 300 enzymes and 2000 transcription factors are now known to require zinc for their functions and stability of their structures, and several studies have now shown that zinc may be a molecular signal for neuronal and immune cells. Fourteen ZIP and 10 ZNT zinc transporters are known to maintain intracellular zinc homeostasis. Therapeutic impacts of zinc on human health are also being investigated. Zinc is being used for the treatment of acute diarrhea in infants and children in developing countries globally, and this has resulted in saving millions of lives. Zinc is now an approved drug for the treatment and maintenance therapy of Wilson's disease, a serious fatal genetic disorder. According to a recent Cochrane Review, zinc is the only treatment which is effective in decreasing the incidence of infections and pain crises in patients with sickle cell disease. Zinc acetate lozenges have been shown to decrease the duration of the common cold by 50%, provided the treatment is started within 24h of the onset of symptoms, the solution chemistry of the zinc preparation is proper, and the zinc dosages are adequate. Age-related macular degeneration (AMD) accounts for a large proportion of legal blindness in elderly subjects throughout the world. The Age-Related Eye Disease Study Group (AREDS) was supported by National Eye Institute. The National Institutes of Health (NIH) has now reported the results of their 10-year zinc supplementation study in patients with AMD. Zinc was effective in decreasing the incidences of blindness and progression of AMD in elderly subjects. Most importantly, zinc-supplemented subjects showed increased longevity and this was due to a decrease in cardiovascular events. No other micronutrient has shown this dramatic effect on decreasing mortality in the elderly. Our placebo-controlled, zinc supplementation trial in the elderly has shown that zinc supplementation decreased the incidence of infections by 66% and improved cell-mediated immunity. Also, we showed that oxidative stress markers and gene expression of inflammatory cytokines were decreased in elderly subjects who received zinc supplementation. These studies suggest that zinc supplementation in the elderly may have a preventive role in atherosclerosis. Plasma zinc is widely used as a biomarker of zinc deficiency in humans. This test is, however, neither specific nor sensitive. Assays of immunological markers such as plasma active thymulin and gene expression of IL-2 in PHA-stimulated lymphocytes are very sensitive and specific for the diagnosis of human zinc deficiency. The assay of zinc in cells such as lymphocytes and granulocytes are better than plasma zinc; however, even these assays are less sensitive than immunological biomarkers.


title: The effect of social distance measures on COVID-19 epidemics in Europe: an interrupted time series analysis

text: Following the introduction of unprecedented “stay-at-home” national policies, the COVID-19 pandemic recently started declining in Europe. Our research aims were to characterize the changepoint in the flow of the COVID-19 epidemic in each European country and to evaluate the association of the level of social distancing with the observed decline in the national epidemics. Interrupted time series analyses were conducted in 28 European countries. Social distance index was calculated based on Google Community Mobility Reports. Changepoints were estimated by threshold regression, national findings were analyzed by Poisson regression, and the effect of social distancing in mixed effects Poisson regression model. Our findings identified the most probable changepoints in 28 European countries. Before changepoint, incidence of new COVID-19 cases grew by 24% per day on average. From the changepoint, this growth rate was reduced to 0.9%, 0.3% increase, and to 0.7% and 1.7% decrease by increasing social distancing quartiles. The beneficial effect of higher social distance quartiles (i.e., turning the increase into decline) was statistically significant for the fourth quartile. Notably, many countries in lower quartiles also achieved a flat epidemic curve. In these countries, other plausible COVID-19 containment measures could contribute to controlling the first wave of the disease. The association of social distance quartiles with viral spread could also be hindered by local bottlenecks in infection control. Our results allow for moderate optimism related to the gradual lifting of social distance measures in the general population, and call for specific attention to the protection of focal micro-societies enriching high-risk elderly subjects, including nursing homes and chronic care facilities.


title: Trends in the chemical and pharmacological research on the tropical trees Calophyllum brasiliense and Calophyllum inophyllum, a global context

text: Tropical trees of Calophyllum genus (Calophyllaceae) have chemical and biological importance as potential source of secondary active metabolites which can lead to the development of new drugs. Research on this species has been rising since 1992 due to the discovering of anti-HIV properties of Calanolide A found in Calophyllum inophyllum leaves. This compound is the most important natural product for potential development of new anti-HIV drugs and phytomedicines. The scientometric analysis (1953–2014) here performed revealed that the most studied species of Calophyllum genus are: C. inophyllum and C. brasiliense, distributed in the Asian, and American continents, respectively. Current research on these species is carried out mainly in India and Brazil, respectively, where these species grow. Research on C. brasiliense is focused mainly on ecological, antiparasitic, cytotoxic properties, and isolation of new compounds. Chemical studies and biodiesel development are the main topics in the case of C. inophyllum. Text mining analysis revealed that coumarins, and xanthones are the main secondary active metabolites responsible for most of the reported pharmacological properties, and are potential compounds for the treatment of leukemia and against intracellular parasites causing American Trypanosomiasis and Leshmaniasis. On the other hand, C. inophyllum represents an important source for the development of 2nd generation biodiesel. Medicinal and industrial applications of these species may impulse sustainable forest plantations. To our knowledge this is the first scientometric and text mining analysis of chemical and biomedical research on Calophyllum genus, C. brasiliense and C. inophyllum.


title: Characteristics of seminal plasma proteins and their correlation with canine semen analysis

text: Abstract The objectives were to separate canine seminal plasma proteins (with SDS-PAGE) and to determine the correlation between specific proteins and semen characteristics. Three ejaculates from 20 mixed-breed dogs, of unknown fertility, were collected by digital manipulation. Ejaculate volume and color, sperm motility, sperm vigor, percentage of morphologically normal spermatozoa, and membrane integrity (hypoosmotic swelling test and fluorescent staining) were assessed. For each dog, seminal plasma was pooled from all three ejaculates and proteins were separated with SDS-PAGE, using polyacrylamide concentrations of 13% and 22% in the separation gels. After staining, gel images were digitized to estimate molecular weights (MW) and integrated optical density (IOD) of each lane and of individual bands. Total seminal plasma protein concentration was 2.19±1.56g/dL (mean±SD; range 1.12–5.19g/dL). A total of 37 protein bands were identified (although no dog had all 37 bands). In the 13% gel, molecular weights ranged from 100.6 to 17.1kDa, with four bands (49.7, 33.2, 26.4, and 19.5kDa) present in samples from all dogs. In the 22% gel, molecular weights ranged from 15.6 to 3.6kDa, with nine bands (15.6, 13.5, 12.7, 11.7, 10.5, 8.7, 7.8, 5.6, and 4.9kDa) present in samples from all dogs. Combined for both gels, the majority of bands (85%) had molecular weights <17kDa, with B20 (15.6kDa) in high concentrations in samples from all dogs. There were positive correlations (P ≤0.01) between two bands, B4 (67kDa) and B5 (58.6kDa), and sperm motility (r =0.66 and r =0.46), sperm vigor (r =0.56 and r =0.66), percentage of morphologically normal spermatozoa (r =0.55 and r =0.59), the hypoosmotic swelling test (r =0.76 and r =0.68), and fluorescent staining (r =0.56 and r =0.59), respectively. In conclusion, 37 proteins were identified in seminal plasma; two were significantly correlated with semen characteristics.


title: Global change of surgical and oncological clinical practice in urology during early COVID-19 pandemic

text: OBJECTIVES: While the coronavirus disease 2019 (COVID-19) pandemic captures healthcare resources worldwide, data on the impact of prioritization strategies in urology during pandemic are absent. We aimed to quantitatively assess the global change in surgical and oncological clinical practice in the early COVID-19 pandemic. METHODS: In this cross-sectional observational study, we designed a 12-item online survey on the global effects of the COVID-19 pandemic on clinical practice in urology. Demographic survey data, change of clinical practice, current performance of procedures, and current commencement of treatment for 5 conditions in medical urological oncology were evaluated. RESULTS: 235 urologists from 44 countries responded. Out of them, 93% indicated a change of clinical practice due to COVID-19. In a 4-tiered surgery down-escalation scheme, 44% reported to make first cancellations, 23% secondary cancellations, 20% last cancellations and 13% emergency cases only. Oncological surgeries had low cancellation rates (%): transurethral resection of bladder tumor (27%), radical cystectomy (21–24%), nephroureterectomy (21%), radical nephrectomy (18%), and radical orchiectomy (8%). (Neo)adjuvant/palliative treatment is currently not started by more than half of the urologists. COVID-19 high-risk-countries had higher total cancellation rates for non-oncological procedures (78% vs. 68%, p = 0.01) and were performing oncological treatment for metastatic diseases at a lower rate (35% vs. 48%, p = 0.02). CONCLUSION: The COVID-19 pandemic has affected clinical practice of 93% of urologists worldwide. The impact of implementing surgical prioritization protocols with moderate cancellation rates for oncological surgeries and delay or reduction in (neo)adjuvant/palliative treatment will have to be evaluated after the pandemic. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00345-020-03333-6) contains supplementary material, which is available to authorized users.


title: Activation of CD8 T Lymphocytes during Viral Infections

text: Abstract CD8 T lymphocytes are a major cell population of the adaptive immune system. A fundamental characteristic of the CD8 T lymphocyte pool is that it is composed of millions of clones; each with a unique T cell receptor capable of recognizing a limited number of peptides displayed at the cell surface bound to the grooves of major histocompatibility complex class I (MHC I) molecules. Naïve CD8 T lymphocytes are normally resting and circulate between the blood and secondary lymphoid organs in search of their cognate peptide–MHC complexes. During viral infections, bone marrow–derived professional antigen-presenting cells (pAPCs) in secondary lymphoid organs display viral peptides on their MHC I molecules. Specific CD8 T lymphocytes that recognize these peptide–MHC adducts become activated (primed), proliferate extensively, and develop into effectors capable of killing infected cells, identified by the presence at their surface of the pertinent viral peptide–MHC complexes. This article describes how the process of priming naïve CD8 T lymphocytes occurs.


title: The War on Severe Acute Respiratory Syndrome: United States Forces Korea’s Campaign Plan

text: A mysterious new respiratory illness known as severe acute respiratory syndrome (SARS) has become the most perplexing infectious disease to emerge in the 21st century. From March to May 2003, it competed daily with the war in Iraq as the most sensational media event of the moment. U.S. personnel serving in the Republic of Korea represented the largest U.S. military population at risk for SARS. With tensions growing between Pyongyang and Washington, the United States/Republic of Korea alliance could not afford to be rendered combat ineffective by SARS. To remain mission ready, the U.S. Forces Korea (USFK) commander declared a “War on SARS” and directed his medical staff to develop a plan to prevent a SARS outbreak among USFK personnel. This article outlines the USFK campaign plan for the SARS epidemic and documents lessons learned for future outbreaks of highly infectious diseases.


title: Theiler’s murine encephalomyelitis virus infection of astrocytes induces the expression of chemokines which attract activated but not resting T lymphocytes

text: In this article, we studied the production of the chemokine CXCL9, also termed Mig (monokine induced by gamma interferon) by cultured SJL/J mouse astrocytes infected with the BeAn strain of Theiler’s murine encephalomyelitis virus (TMEV). This picornavirus induces demyelination in the SJL/J genetically susceptible strain of mice through an immune process mediated by CD4(+) Th1 T cells. Those cells were chemoattracted by chemokines inside the central nervous system (CNS) after blood-brain barrier (BBB) disruption. cRNAs from TMEV- and mock-infected astrocytes cells were hybridized to the Affymetrix murine genome U74v2 DNA microarray. Hybridization data analysis revealed the upregulation of six sequences potentially coding for Mig. We confirmed post infection Mig mRNA increase by quantitative (qPCR) and RT-PCR. The presence of Mig in the supernatants of infected astrocytes was quantified using a specific ELISA. Secreted Mig was biologically active, inducing chemoattraction of mouse activated CD4(+) T lymphocytes. Conversely, attracting activity on CD3(+) resting T cells that can be attributed to chemokines as CXCL12/SDF-1α could not be demonstrated in these supernatants. No overinduction of the gene coding for this chemokine was assessed by DNA hybridization either. Both recombinant IFN-γ and TNF-α inflammatory cytokines were also strong inducers of Mig in SJL/J astrocyte cultures.


title: The influence of collagen film nanostructure on pulmonary stem cells and collagen–stromal cell interactions

text: Abstract We have recently identified a rare subpopulation of lung colony cells with the characteristics of pulmonary stem cells, and discovered that stem cell colonies grew preferentially on type I collagen films in a serum-free medium. In order to further optimize culture conditions and determine stem cell growth in relation to microenvironments (including the stroma, medium and nanostructures of type I collagen films), both primary and pre-sorted stem cells were cultured on the type I collagen films with controllable degree of polymerization and film thickness, as confirmed by an atomic force microscope and surface profiler. We found that in a primary culture, the spreading of stromal cells is greatly restrained and both the size and number of colonies are significantly reduced on highly polymerized collagen films. In contrast, in a pre-sorted stem cell culture without stromal cells, the intrinsic stem cell properties and cell number are independent of the degree of collagen polymerization. Our results indicate that the nanostructures of type I collagen films primarily affect stem colony formation through the collagen–stroma interactions. In those cases, collagen film thickness shows no effect on colony formation.


title: Enhancing the Antiviral Efficacy of RNA-Dependent RNA Polymerase Inhibition by Combination with Modulators of Pyrimidine Metabolism

text: Genome-wide analysis of the mode of action of GSK983, a potent antiviral agent, led to the identification of dihydroorotate dehydrogenase as its target along with the discovery that genetic knockdown of pyrimidine salvage sensitized cells to GSK983. Because GSK983 is an ineffective antiviral in the presence of physiological uridine concentrations, we explored combining GSK983 with pyrimidine salvage inhibitors. We synthesized and evaluated analogs of cyclopentenyl uracil (CPU), an inhibitor of uridine salvage. We found that CPU was converted into its triphosphate in cells. When combined with GSK983, CPU resulted in large drops in cellular UTP and CTP pools. Consequently, CPU-GSK983 suppressed dengue virus replication in the presence of physiological concentrations of uridine. In addition, the CPU-GSK983 combination markedly enhanced the effect of RNA-dependent RNA polymerase (RdRp) inhibition on viral infection. Our findings highlight a new host-targeting strategy for potentiating the antiviral activity of RdRp inhibitors.


title: Viral diseases of fish in Japan

text: Abstract Viruses causing infectious pancreatic necrosis (IPN) and infectious hematopoietic necrosis (IHN) were first isolated in Japan during the 1970s and these two diseases remain among the most serious problems affecting cultured salmonids in Japan. In addition to IHN and IPN, four other viral diseases cause major economic losses among cultured fishes in Japan. These include viral pancreatic hepatic necrosis of yellowtail, rhabdovirus infection of Japanese flounder and black rock fish, Kuchishiro-sho of tiger puffer fish, and epidermal hyperplasia or necrosis of Japanese flounder. Over the years, a number of other viruses have been isolated from, or have been observed by electron microscopy, in moribund fish. Members of 10 of the existing families of animal viruses are represented in this group. Their importance to the aquaculture industry in Japan is reviewed here.


title: A newly established bovine intestinal epithelial cell line is effective for in vitro screening of potential antiviral immunobiotic microorganisms for cattle

text: Abstract We evaluated whether a bovine intestinal epithelial (BIE) cell line could serve as a useful in vitro model system for studying antiviral immune responses in bovine intestinal epithelial cells (IECs) and for the primary screening of immunobiotic microorganisms with antiviral protective capabilities. Immunofluorescent analyses revealed that toll-like receptor 3 (TLR3) was expressed in BIE cells, and the results of real-time quantitative PCR showed that these cells respond to stimulation with poly(I:C) by up-regulating pro-inflammatory cytokines and type I interferons. In addition, we demonstrated that BIE cells are useful for the primary screening of immunobiotic lactic acid bacteria strains which are able to beneficially modulate antiviral immune responses triggered by TLR3 activation in bovine IECs. The characterization of BIE cells performed in the present study represents an important step towards the establishment of a valuable bovine in vitro system that could be used for the development of immunomodulatory feed for bovine hosts.


title: Global shifts in mammalian population trends reveal key predictors of virus spillover risk

text: Emerging infectious diseases in humans are frequently caused by pathogens originating from animal hosts, and zoonotic disease outbreaks present a major challenge to global health. To investigate drivers of virus spillover, we evaluated the number of viruses mammalian species have shared with humans. We discovered that the number of zoonotic viruses detected in mammalian species scales positively with global species abundance, suggesting that virus transmission risk has been highest from animal species that have increased in abundance and even expanded their range by adapting to human-dominated landscapes. Domesticated species, primates and bats were identified as having more zoonotic viruses than other species. Among threatened wildlife species, those with population reductions owing to exploitation and loss of habitat shared more viruses with humans. Exploitation of wildlife through hunting and trade facilitates close contact between wildlife and humans, and our findings provide further evidence that exploitation, as well as anthropogenic activities that have caused losses in wildlife habitat quality, have increased opportunities for animal–human interactions and facilitated zoonotic disease transmission. Our study provides new evidence for assessing spillover risk from mammalian species and highlights convergent processes whereby the causes of wildlife population declines have facilitated the transmission of animal viruses to humans.


title: An efficient lattice Boltzmann model for indoor airflow and particle transport

text: Abstract The three-dimensional multiple-relaxation-time LB (MRT-LB) and Lagrangian particle tracking methods were applied to simulate turbulent airflow and particle dispersion in a ventilated room with a partition. The turbulent airflow was simulated by large eddy simulation (LES) using the MRT-LB method with the Smagorinsky model. This method was verified by comparing it with experimental and other numerical results. Good agreement was observed between airflow simulation and experimental data. It is also demonstrated that the LES carried out by the MRT-LB method can produce airflow results very similar to the RNG LES and provide better prediction than the standard and RNG k–ε models. In order to further improve the efficiency of the MRT-LB method, the multi-block grid refinement (MBGR) technique was used. The accuracy and efficiency of the MBGR and the consistency of physical quantities across the interface were investigated. In simulation of particle dispersion in the model room, particles with diameters of 1 and 10 µm were considered. It is shown that this model can successfully capture dispersion characteristics of particles.


title: Exosome Biogenesis, Regulation, and Function in Viral Infection

text: Exosomes are extracellular vesicles released upon fusion of multivesicular bodies (MVBs) with the cellular plasma membrane. They originate as intraluminal vesicles (ILVs) during the process of MVB formation. Exosomes were shown to contain selectively sorted functional proteins, lipids, and RNAs, mediating cell-to-cell communications and hence playing a role in the physiology of the healthy and diseased organism. Challenges in the field include the identification of mechanisms sustaining packaging of membrane-bound and soluble material to these vesicles and the understanding of the underlying processes directing MVBs for degradation or fusion with the plasma membrane. The investigation into the formation and roles of exosomes in viral infection is in its early years. Although still controversial, exosomes can, in principle, incorporate any functional factor, provided they have an appropriate sorting signal, and thus are prone to viral exploitation. This review initially focuses on the composition and biogenesis of exosomes. It then explores the regulatory mechanisms underlying their biogenesis. Exosomes are part of the endocytic system, which is tightly regulated and able to respond to several stimuli that lead to alterations in the composition of its sub-compartments. We discuss the current knowledge of how these changes affect exosomal release. We then summarize how different viruses exploit specific proteins of endocytic sub-compartments and speculate that it could interfere with exosome function, although no direct link between viral usage of the endocytic system and exosome release has yet been reported. Many recent reports have ascribed functions to exosomes released from cells infected with a variety of animal viruses, including viral spread, host immunity, and manipulation of the microenvironment, which are discussed. Given the ever-growing roles and importance of exosomes in viral infections, understanding what regulates their composition and levels, and defining their functions will ultimately provide additional insights into the virulence and persistence of infections.


title: Parent-collected respiratory specimens—A novel method for respiratory virus and vaccine efficacy research

text: Population-based respiratory research and vaccine efficacy studies have previously required clinic or home visits when a subject had an acute respiratory illness. This method may mean parents are unwilling to enrol their child or report an illness of interest. We conducted a community-based cohort study into respiratory illnesses in 234 pre-school aged children using parent-collected specimens. Between January 2003 and January 2004 there were 563 specimens collected from 730 identified illnesses and these were tested using a panel of respiratory virus polymerase chain reaction (PCR) assays; 409 (73%) were positive for any virus. Specimens were not more likely to be positive when collected by a healthcare worker parent, when they included a throat swab, or when a very good collection technique was reported. A delay from illness onset to specimen collection of up to 5 days did not appear to impact on sensitivity of virus identification, but a delay of six or more days with minor delays in testing saw positivity fall. Combined with daily symptom diary completion and PCR testing, parent-collected specimens are an efficient and acceptable method for the conduct of future vaccine efficacy studies and other community-based respiratory virus research.


title: Generalized lattice graphs for 2D-visualization of biological information

text: Abstract Several graph representations have been introduced for different data in theoretical biology. For instance, complex networks based on Graph theory are used to represent the structure and/or dynamics of different large biological systems such as protein–protein interaction networks. In addition, Randic, Liao, Nandy, Basak, and many others developed some special types of graph-based representations. This special type of graph includes geometrical constrains to node positioning in space and adopts final geometrical shapes that resemble lattice-like patterns. Lattice networks have been used to visually depict DNA and protein sequences but they are very flexible. However, despite the proved efficacy of new lattice-like graph/networks to represent diverse systems, most works focus on only one specific type of biological data. This work proposes a generalized type of lattice and illustrates how to use it in order to represent and compare biological data from different sources. We exemplify the following cases: protein sequence; mass spectra (MS) of protein peptide mass fingerprints (PMF); molecular dynamic trajectory (MDTs) from structural studies; mRNA microarray data; single nucleotide polymorphisms (SNPs); 1D or 2D-Electrophoresis study of protein polymorphisms and protein-research patent and/or copyright information. We used data available from public sources for some examples but for other, we used experimental results reported herein for the first time. This work may break new ground for the application of Graph theory in theoretical biology and other areas of biomedical sciences.


title: COVID-19 pandemic preparedness: A practical guide from clinical pharmacists’ perspective

text: DISCLAIMER: In an effort to expedite the publication of articles related to the COVID-19 pandemic, AJHP is posting these manuscripts online as soon as possible after acceptance. Accepted manuscripts have been peer-reviewed and copyedited, but are posted online before technical formatting and author proofing. These manuscripts are not the final version of record and will be replaced with the final article (formatted per AJHP style and proofed by the authors) at a later time. PURPOSE: To describe our hospital pharmacy department’s preparation for an influx of critically ill patients during the coronavirus disease 2019 (COVID-19) pandemic and offer guidance on clinical pharmacy services preparedness for similar crisis situations. SUMMARY: Personnel within the department of pharmacy at a medical center at the US epicenter of the COVID-19 pandemic proactively prepared a staffing and pharmacotherapeutic action plan in anticipation of an expected surge in admissions of critically ill patients with COVID-19 and expansion of acute care and intensive care unit (ICU) capacity. Guidance documents focusing on supportive care and pharmacotherapeutic treatment options were developed. Repurposing of non–ICU-trained clinical pharmacotherapy specialists to work collaboratively with clinician teams in ICUs was quickly implemented; staff were prepared for these duties through use of shared tools to facilitate education and practice standardization. CONCLUSION: As challenges were encountered at the peak of the pandemic, interdisciplinary collaboration and teamwork was crucial to ensure that all patients were proactively assessed and that their respective pharmacotherapeutic regimens were optimized.


title: Spatio-temporal spread of infectious pathogens of humans

text: Spatio-temporal aspects in the propagation of infectious pathogens of humans are reviewed. Mathematical modelling of these issues using metapopulation models is presented.


title: Coronavirus impacts on post-pandemic planned travel behaviours

text: • Provides a prompt understanding of a real time pandemic (coronavirus Covid-19); • Analyses the intra-pandemic perception and post-pandemic planned behaviours; • Evaluates planned changes to travel behaviours; • Discusses intra-pandemic effects on perceptions towards tourist destinations.


title: Immunopathology of highly virulent pathogens: insights from Ebola virus

text: Ebola virus is a highly virulent pathogen capable of inducing a frequently lethal hemorrhagic fever syndrome. Accumulating evidence indicates that the virus actively subverts both innate and adaptive immune responses and triggers harmful inflammatory responses as it inflicts direct tissue damage. The host immune system is ultimately overwhelmed by a combination of inflammatory factors and virus-induced cell damage, particularly in the liver and vasculature, often leading to death from septic shock. We summarize the mechanisms of immune dysregulation and virus-mediated cell damage in Ebola virus–infected patients. Future approaches to prevention and treatment of infection will be guided by answers to unresolved questions about interspecies transmission, molecular mechanisms of pathogenesis, and protective adaptive and innate immune responses to Ebola virus.


title: Crisis Standard of Care: Management of Infantile Spasms during COVID‐19

text: The Child Neurology Society collaborated with the Pediatric Epilepsy Research Consortium to issue an online statement April 6, 2020 of immediate recommendations to streamline diagnosis, treatment, and follow up of infantile spasms. The recommendations encourage use of telemedicine, outpatient over inpatient studies, and oral therapies as initial treatment. Each recommendation is earmarked as enduring if intended to outlast the pandemic, and limited if intended only during the duration of the pandemic. This article is protected by copyright. All rights reserved.


title: Hydroxychloroquine and the treatment of Sjogren's Syndrome, Chronic Ulcerative Stomatitis, and Oral Lichen Planus in the age of COVID-19

text: The Federal Drug Administration has recently approved the off-label use of Hydroxychloroquine (HCQ) for the treatment of COVID-19 infections. However, a recent study has not only failed to demonstrate HCQ efficacy but has documented an HCQ COVID-19 therapy serious side-effect of QT prolongation and secondary arrhythmia. HCQ has been utilized as an off-label drug and deemed safe and effective for such oral lesions as Sjogren's syndrome (SS), Chronic Ulcerative Stomatitis (CUS), and Oral Lichen Planus (OLP). As HCQ may be appropriately utilized for the off-label treatment of SS, CUS, and OLP, the relevant HCQ safety concerns such as dosage, drug-drug interactions, and QT prolongation and secondary arrhythmia are discussed. Due to the possibility of decreased pharmacy HCQ supplies, replacement drugs with respect to SS, CUS, and OLP patients being successfully treated with HCQ are also discussed.


title: The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents

text: BACKGROUND: Thousands of different microorganisms affect the health, safety, and economic stability of populations. Many different medical and governmental organizations have created lists of the pathogenic microorganisms relevant to their missions; however, the nomenclature for biological agents on these lists and pathogens described in the literature is inexact. This ambiguity can be a significant block to effective communication among the diverse communities that must deal with epidemics or bioterrorist attacks. RESULTS: We have developed a database known as the Microbial Rosetta Stone. The database relates microorganism names, taxonomic classifications, diseases, specific detection and treatment protocols, and relevant literature. The database structure facilitates linkage to public genomic databases. This paper focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. CONCLUSION: The Microbial Rosetta Stone is available at . The database provides public access to up-to-date taxonomic classifications of organisms that cause human diseases, improves the consistency of nomenclature in disease reporting, and provides useful links between different public genomic and public health databases.


title: Porcine Epidemic Diarrhoea Virus in Italy: Disease spread and the role of transportation

text: Porcine Epidemic Diarrhoea Virus (PEDV) causes watery diarrhoea, dehydration, and a high mortality rate among suckling pigs. Recently, PEDV had a large negative economic impact on the swine industries in Asia and North America. In 2014, PEDV re‐emerged in many European countries, but most countries only reported a few sporadic cases. Here, we report the epidemic wave that occurred in Italy from 2015 to 2017. During this time, PEDV was detected by real‐time PCR in 438 farms located mainly in the high‐density pig production area in Northern Italy. Most of the outbreaks were in farrow‐to‐finish, farrow‐to‐wean and finisher farms. Clinical signs were observed mainly in suckling and fattening animals, while mortality rates were higher in piglets, reaching 50%. A sequence analysis showed that a PEDV strain, similar to the OH851 S‐INDEL strain isolated in the USA in January 2014, was responsible for the outbreaks in Italy in 2015 and 2016. However, from January 2017, a recombinant variant strain, containing a portion of the Swine Enteric Coronavirus in the S1 gene, spread and almost completely outcompeted the previous nonrecombinant strain. In total, 14.1% of the environmental swabs collected from trucks at slaughterhouses after animals were unloaded tested positive for PEDV before the trucks were cleaned and disinfected, and 46% remained positive after cleaning and disinfection processes were performed. Moreover, environmental swabs indicated that 17.3% of the empty trucks arriving at the farms to load animals were PEDV‐positive. This study indicates that trucks can have an important role in the spread of PEDV in Italy.


PCR detection and new therapies for COVID-19


title: Altered Gut Microbiota Profiles in Sows and Neonatal Piglets Associated with Porcine Epidemic Diarrhea Virus Infection

text: Porcine epidemic diarrhea virus (PEDV) is a devastating cause of diarrhea in pigs worldwide. Most of studies have focused on molecular and pathogenic characterization of PEDV, whereas there were limited studies in understanding the role of gut microbiota (GM) in viral-associated diarrhea. Here, using the Illumina MiSeq platform, we examined and compared the impact of PEDV infection on the GM of sows and their piglets less than 10 days old. Our results showed that PEDV caused alternations in the structure and abundance of GM from levels of phylum to genus, and even species. For sows, a significant decrease of observed species was found in diarrheal sows than that in healthy sows (p < 0.05). The unweighted and weighted UniFrac distances also revealed considerable segregations of GM structure among healthy, asymptomatic, and diarrheal sows. For piglets, Bacteroidetes, the dominant bacteria in healthy piglets, were replaced by Firmicutes in asymptomatic and diarrheal piglets. The abundances of Fusobacteria and Proteobacteria were also remarkably increased in asymptomatic piglets and diarrheal piglets when compared to those of the healthy piglets. Our findings demonstrated that PEDV infection caused severe perturbations of GM, reduced probiotic bacteria, and enriched pathogenic bacteria.


title: The Membrane Protein of Severe Acute Respiratory Syndrome Coronavirus Functions as a Novel Cytosolic Pathogen-Associated Molecular Pattern To Promote Beta Interferon Induction via a Toll-Like-Receptor-Related TRAF3-Independent Mechanism

text: Most of the intracellular pattern recognition receptors (PRRs) reside in either the endolysosome or the cytoplasm to sense pathogen-derived RNAs, DNAs, or synthetic analogs of double-stranded RNA (dsRNA), such as poly(I:C). However, it remains elusive whether or not a pathogen-derived protein can function as a cytosolic pathogen-associated molecular pattern (PAMP). In this study, we demonstrate that delivering the membrane gene of severe acute respiratory syndrome coronavirus (SARS-CoV) into HEK293T, HEK293ET, and immobilized murine bone marrow-derived macrophage (J2-Mφ) cells significantly upregulates beta interferon (IFN-β) production. Both NF-κB and TBK1-IRF3 signaling cascades are activated by M gene products. M protein rather than M mRNA is responsible for M-mediated IFN-β induction that is preferentially associated with the activation of the Toll-like receptor (TLR) adaptor proteins MyD88, TIRAP, and TICAM2 but not the RIG-I signaling cascade. Blocking the secretion of M protein by brefeldin A (BFA) failed to reverse the M-mediated IFN-β induction. The antagonist of both TLR2 and TLR4 did not impede M-mediated IFN-β induction, indicating that the driving force for the activation of IFN-β production was generated from inside the cells. Inhibition of TRAF3 expression by specific small interfering RNA (siRNA) did not prevent M-mediated IFN-β induction. SARS-CoV pseudovirus could induce IFN-β production in an M rather than M(V68A) dependent manner, since the valine-to-alanine alteration at residue 68 in M protein markedly inhibited IFN-β production. Overall, our study indicates for the first time that a pathogen-derived protein is able to function as a cytosolic PAMP to stimulate type I interferon production by activating a noncanonical TLR signaling cascade in a TRAF3-independent manner.


title: Inactivation of influenza A viruses in the environment and modes of transmission: A critical review

text: Summary Objectives The relative importance of airborne, droplet and contact transmission of influenza A virus and the efficiency of control measures depends among other factors on the inactivation of viruses in different environmental media. Methods We systematically review available information on the environmental inactivation of influenza A viruses and employ information on infectious dose and results from mathematical models to assess transmission modes. Results Daily inactivation rate constants differ by several orders of magnitude: on inanimate surfaces and in aerosols daily inactivation rates are in the order of 1–102, on hands in the order of 103. Influenza virus can survive in aerosols for several hours, on hands for a few minutes. Nasal infectious dose of influenza A is several orders of magnitude larger than airborne infectious dose. Conclusions The airborne route is a potentially important transmission pathway for influenza in indoor environments. The importance of droplet transmission has to be reassessed. Contact transmission can be limited by fast inactivation of influenza virus on hands and is more so than airborne transmission dependent on behavioral parameters. However, the potentially large inocula deposited in the environment through sneezing and the protective effect of nasal mucus on virus survival could make contact transmission a key transmission mode.


title: Different host cell proteases activate the SARS-coronavirus spike-protein for cell–cell and virus–cell fusion

text: Abstract Severe acute respiratory syndrome coronavirus (SARS-CoV) poses a considerable threat to human health. Activation of the viral spike (S)-protein by host cell proteases is essential for viral infectivity. However, the cleavage sites in SARS-S and the protease(s) activating SARS-S are incompletely defined. We found that R667 was dispensable for SARS-S-driven virus–cell fusion and for SARS-S-activation by trypsin and cathepsin L in a virus–virus fusion assay. Mutation T760R, which optimizes the minimal furin consensus motif 758-RXXR-762, and furin overexpression augmented SARS-S activity, but did not result in detectable SARS-S cleavage. Finally, SARS-S-driven cell–cell fusion was independent of cathepsin L, a protease essential for virus–cell fusion. Instead, a so far unknown leupeptin-sensitive host cell protease activated cellular SARS-S for fusion with target cells expressing high levels of ACE2. Thus, different host cell proteases activate SARS-S for virus–cell and cell–cell fusion and SARS-S cleavage at R667 and 758-RXXR-762 can be dispensable for SARS-S activation.


title: Urgent Guidance for Navigating and Circumventing the QTc-Prolonging and Torsadogenic Potential of Possible Pharmacotherapies for Coronavirus Disease 19 (COVID-19)

text: Abstract As the coronavirus disease 19 (COVID-19) global pandemic rages across the globe, the race to prevent and treat this deadly disease has led to the “off-label” repurposing of drugs such as hydroxychloroquine and lopinavir/ritonavir, which has the potential for unwanted QT-interval prolongation and a risk of drug-induced sudden cardiac death. With the possibility that a considerable proportion of the world’s population soon could receive COVID-19 pharmacotherapies with torsadogenic potential for therapy or postexposure prophylaxis, this document serves to help health care professionals mitigate the risk of drug-induced ventricular arrhythmias while minimizing risk of COVID-19 exposure to personnel and conserving the limited supply of personal protective equipment.


title: Ninety-day inhalation study in rats, comparing smoke from cigarettes that heat tobacco with those that burn tobacco

text: Abstract Eight groups of 30 male and 30 female rats were exposed 1 hr per day, 5 days per week for 13 weeks, to smoke from reference (tobacco burned) or test (tobacco only heated) cigarettes, at nicotine concentrations of 5, 15, or 30 μg/liter of air. Similar smoke concentrations of wet total particulate matter and carbon monoxide were produced in each of the test/reference comparisons. There was a pronounced depression of minute ventilation of animals in the reference groups, but not in the test animals. Blood carboxyhemoglobin concentrations were similar in animals exposed to smoke from test and reference cigarettes. Plasma concentrations of nicotine and cotinine in the test groups were higher than in the reference groups. There were no differences between the smoke-exposed groups in terms of body weight or feed consumption. At necropsy, an increase in heart weight was noted in both high exposure groups. There were notable differences in histopathology, with fewer and less-pronounced changes in the test groups than in the reference groups. Many of the histopathological responses induced in the reference groups were absent in the test groups. Overall, the study demonstrated a substantial reduction in the biological activity of smoke from the test cigarette when compared with the reference.


High expression of ACE2 on the keratinocytes reveals skin as a potential target for SARS-CoV-2


title: SCHIZOPHRENIA AND COVID-19 DELIRIUM.

text: Since its outbreak, coronavirus disease 2019 has been producing atypical manifestations aside from fever, coughing and dysnea. One of the most common is delirium, which, however, is highly overlooked. This has consequences in the treatment of patients and also may lead to underdiagnosing the infection. In this work, we present the case of a man diagnosed with schizophrenia, who had been stable for more than 20 years and that presented with an atypical picture of psychotic and confusional symptoms related to COVID-19 infection.


title: Prevalence and clinical characteristics of human metapneumovirus infections in hospitalized infants in Spain

text: Human metapneumovirus (hMPV), a condition recently described in the Netherlands, causes lower respiratory infections, particularly in young children and among the elderly. The objective of this study was to describe the characteristics of hMPV infections in hospitalized infants <2 years of age and to compare them to those of infections caused by respiratory syncytial virus (RSV). A prospective study was conducted on the clinical characteristics of infants admitted to hospital for respiratory infection through 5 years. Simultaneous detection of influenza A, B, and C viruses, RSV, and adenoviruses was performed in clinical samples by multiple reverse transcription nested‐PCR assay. The presence of hMPV was tested in all samples using two separate RT‐PCR tests. Some respiratory virus was detected in 70.5% of the 1,322 children included in the study. hMPV was found in 101 of the positive nasopharyngeal aspirates (10.8%), and was the most common virus after RSV and rhinovirus. Peak incidence was found in March. Over 80% of children were <12 months. The more common diagnoses were bronchiolitis (49.5%) and recurrent wheezing (45.5%). Fifty‐four percent of cases required oxygen therapy and, one percent, assisted ventilation. Thirty percent were co‐infections, with clinical characteristics indistinguishable from single infections. Seventy‐one hMPV single infections were compared to 88 RSV single infections. hMPV infections were significantly more frequent than RSV in infants older than 6 months (P = 0.04). Recurrent wheezing was diagnosed more frequently in hMPV patients (P = 0.001). All other variables tested were similar, in both groups. hMPV was the third most frequent virus after RSV and rhinovirus in infants <2 years of age, hospitalized for respiratory infection, and was associated with bronchiolitis and recurrent wheezing. hMPV predominantly occurred in spring. Co‐infections were frequent and clinically similar to single infections and RSV infections. Pediatr Pulmonol. © 2006 Wiley‐Liss, Inc.


title: The ventilation of multiple-bed hospital wards in the tropics: A review

text: Abstract Hospital and healthcare facilities have diverse indoor environment due to the different comfort and health needs of its occupants. Currently, most ventilation studies revolve around specialised areas such as operating rooms and isolation rooms. This paper focuses on the ventilation of multiple-bed hospital wards in the tropical climate, taking into account the design, indoor conditions and engineering controls. General ward layouts are described briefly. The required indoor conditions such as temperature, humidity, air movements and indoor air quality in the ward spaces are summarized based on the current guidelines and practices. Also, recent studies and engineering practices in the hospital indoor environment are elaborated. Usage of computational fluid dynamics tools for the ventilation studies is discussed as well. As identified during the review, there is an apparent knowledge gap for ventilation studies in the tropics compared with temperate climates, as fact studies have only been published for hospital wards in countries with a temperate climate. Therefore, it is highlighted that specific tropical studies along with novel engineering controls are required in addressing the ventilation requirements for the tropics.


title: Identification of Candidate COVID-19 Therapeutics using hPSC-derived Lung Organoids

text: The SARS-CoV-2 virus has caused already over 3.5 million COVID-19 cases and 250,000 deaths globally. There is an urgent need to create novel models to study SARS-CoV-2 using human disease-relevant cells to understand key features of virus biology and facilitate drug screening. As primary SARS-CoV-2 infection is respiratory-based, we developed a lung organoid model using human pluripotent stem cells (hPSCs) that could be adapted for drug screens. The lung organoids, particularly aveolar type II cells, express ACE2 and are permissive to SARS-CoV-2 infection. Transcriptomic analysis following SARS-CoV-2 infection revealed a robust induction of chemokines and cytokines with little type I/III interferon signaling, similar to that observed amongst human COVID-19 pulmonary infections. We performed a high throughput screen using hPSC-derived lung organoids and identified FDA-approved drug candidates, including imatinib and mycophenolic acid, as inhibitors of SARS-CoV-2 entry. Pre- or post-treatment with these drugs at physiologically relevant levels decreased SARS-CoV-2 infection of hPSC-derived lung organoids. Together, these data demonstrate that hPSC-derived lung cells infected by SARS-CoV-2 can model human COVID-19 disease and provide a valuable resource to screen for FDA-approved drugs that might be repurposed and should be considered for COVID-19 clinical trials.


title: Evaluation of an incubation instrument-free reverse transcription recombinase polymerase amplification assay for rapid and point-of-need detection of canine distemper virus

text: Abstract Canine distemper, caused by Canine distemper virus (CDV), is a highly contagious and fatal systemic disease in free-living and captive carnivores worldwide. Accurate, rapid and simple detection of CDV is critical to improve disease management and prevent outbreaks. In this study, a visible and incubation instrument-free reverse-transcription recombinase polymerase amplification assay combined with lateral flow strip (LFS RT-RPA) was developed to detect CDV using primers and lateral flow (LF) probe specific for the nucleocapsid (N) protein gene. The CDV LFS RT-RPA assay was performed in a closed fist using body heat for 15 min, and the products were visible to the naked eyes on the LFS within 5 min. The assay could detect CDV, and there was no cross-reaction with the other viruses tested. Using the in vitro transcribed CDV RNA as template, the analytical sensitivity was 9.4 × 101 copies per reaction, which was the same result as that of a real-time RT-PCR. The assay performance was further evaluated by testing 32 nasal/oropharyngeal swab samples, and CDV RNA positive rate was 62.0% (20/32) by LFS RT-RPA, which was the same result as that of the real-time RT-PCR assay. The performance of the LFS RT-RPA was comparable to real-time RT-PCR, while the LFS RT-RPA assay was much faster and easier to perform. The novel CDV LFS RT-RPA assay provides an attractive and promising tool for rapid and reliable detection of CDV in the underequipped laboratory and point-of-need facility, which is of great significance in CD control in low resource settings.


title: Associations Between Media Exposure and Mental Distress Among U.S. Adults at the Beginning of the COVID-19 Pandemic

text: Introduction Exposure to disaster-related media may be a risk factor for mental distress, but this has not been examined in the context of the coronavirus disease 2019 (COVID-19 pandemic. This study assesses if exposure to social and traditional media during the rise of the COVID-19 pandemic was associated with mental distress among U.S. adults. Methods Data came from the Understanding America Study, a cross-sectional, nationally representative sample of adults who completed surveys online. Participants included 6,329 adults surveyed between March 10 and March 31, 2020. Regression analyses examined associations of: (1) self-reported average time spent on social media in a day (hours) and (2) number of traditional media sources (radio, TV, and newspaper) consulted to learn about COVID-19 with self-reported mental distress (4-item Patient Health Questionnaire). Data were analyzed in April 2020. Results Participants responding at later survey dates reported more time spent on social media (β=0.02, 95% CI=0.01, 0.03), a greater number of traditional media sources consulted to learn about COVID-19 (β=0.01, 95% CI=0.01, 0.02), and greater mental distress (β=0.07, 95% CI=0.04, 0.09). Increased time spent on social media and consulting a greater number of traditional media sources to learn about COVID-19 were independently associated with increased mental distress, even after adjusting for potential confounders (social media: β=0.14, 95% CI=0.05, 0.23; traditional media: β=0.14, 95% CI=0.08, 0.20). Conclusions Exposure to a greater number of traditional media sources and more hours of social media was modestly associated with mental distress during the rise of the COVID-19 pandemic in the U.S.


title: Enhancement of the vaccinia virus/phage T7 RNA polymerase expression system using encephalomyocarditis virus 5'-untranslated region sequences

text: Abstract A recombinant vaccinia virus producing the bacteriophage T7 RNA polymerase was used to express foreign genes in eukaryotic cells. Translation efficiency in this expression system was enhanced significantly by employing the encephalomyocarditis virus (EMCV) 5'-untranslated region (UTR) which confers cap-independent translation by directing internal initiation of translation. The enhancement was accomplished by fusing open reading frames (ORFs) to the N terminus of the EMCV polyprotein coding region, thus utilizing its highly efficient translation initiation site. Expression vectors were constructed to allow cloning in all three reading frames. As reporter genes, we used the lacZ gene and a number of genes encoding coronavirus structural proteins: among others the genes encoding glycoproteins with N-terminal signal sequences. The signal sequences of these glycoproteins are located internally in the primary translation product. We demonstrated that this did not interfere with translocation and glycosylation and yields biologically active proteins. The usefulness of sequences that direct internal initiation was extended by using EMCV UTR s to express two and three ORFs from polycistronic mRNAs.


title: Host-Encoded Reporters for the Detection and Purification of Multiple Enveloped Viruses

text: The identification of host cell factors for virus replication holds great promise for the development of new anti-viral therapies. Recently, high-throughput screening methods have emerged as powerful tools to identify candidate host factors for therapeutic intervention. The development of assay systems suitable for large-scale automated screening is of particular importance for novel viruses with high pathogenic potential for which limited biological information can be developed in a short period of time. This report presents a general enzymatic reporter system for the detection and characterization of multiple enveloped viruses that does not rely on engineering of the virus. Instead, reporter enzymes are incorporated into virus particles by targeting to lipid microdomains in producer cells. The approach allows a variety of human pathogenic enveloped viruses to be detected by sensitive, inexpensive and automatable enzymatic assays. Tagged viruses can be purified quickly and efficiently by a magnetic bead-based capture method. The method allows general detection of enveloped viruses without prior reference to their sequence.


title: Ebola virus outbreak, updates on current therapeutic strategies

text: Filoviruses are enveloped negative‐sense single‐stranded RNA viruses, which include Ebola and Marburg viruses, known to cause hemorrhagic fever in humans with a case fatality of up to 90%. There have been several Ebola virus outbreaks since the first outbreak in the Democratic Republic of Congo in 1976 of which, the recent 2013–2015 epidemic in Guinea, Liberia, and Sierra Leone is the largest in recorded history. Within a few months of the start of the outbreak in December 2013, thousands of infected cases were reported with a significant number of deaths. As of March 2015, according to the Centers for Disease Control and Prevention, there have been nearly 25 000 suspected cases, with 15 000 confirmed by laboratory testing, and over 10 000 deaths. The large number of cases and the high mortality rate, combined with the lack of effective Food and Drug Administration‐approved treatments, necessitate the development of potent and safe therapeutic measures to combat the current and future outbreaks. Since the beginning of the outbreak, there have been considerable efforts to develop and characterize protective measures including vaccines and antiviral small molecules, and some have proven effective in vitro and in animal models. Most recently, a cocktail of monoclonal antibodies has been shown to be highly effective in protecting non‐human primates from Ebola virus infection. In this review, we will discuss what is known about the nature of the virus, phylogenetic classification, genomic organization and replication, disease transmission, and viral entry and highlight the current approaches and efforts, in the development of therapeutics, to control the outbreak. Copyright © 2015 John Wiley & Sons, Ltd.


title: CASE STUDY: Effects of a blend of prebiotics, probiotics, and hyperimmune dried egg protein on the performance, health, and innate immune responses of Holstein calves

text: ABSTRACT The objectives of this study were to evaluate the effects of supplementing a blend of prebiotics, probiotics, and hyperimmune dried egg protein on the performance, health, and innate immune responses of Holstein calves during the first 21 d of age. Ninety, day-old Holstein bull calves were completely randomized to 1 of 2 treatment groups: prophylactic or control. Prophylactic calves had a proprietary blend of prebiotics, probiotics, and hyperimmune egg protein (Calf-Pro Plus and Calf Life, C and E Agri Products, Baldwin, ND) added directly to the milk replacer at each feeding. Control calves were fed the milk replacer only. Treatment did not influence the performance of Holstein calves. Among calves that voluntarily refused milk replacer, prophylactic calves refused less (P = 0.005) than control calves over the first 4 d of life. Prophylactic treatment reduced the incidence of enteric morbidity (25.0 vs. 51.1% for prophylactic and control calves, respectively; P = 0.011). However, treatment did not influence either total peripheral leukocyte or differential counts. Furthermore, hematocrit and plasma concentrations of haptoglobin, cortisol, glucose, and urea nitrogen were not different between treatments. Last, ex vivo innate immune responses evaluated at 21 d of age were not different between treatments. Calves fed the combination of prebiotics, probiotics, and hyperimmune egg protein rejected less milk replacer during the first 4 d of the experiment and had fewer days with enteric morbidity than did the control calves.


title: Prior and Novel Coronaviruses, COVID-19, and Human Reproduction: What Is Known?

text: Structured Abstract Objective To summarize current understanding of the effects of novel and prior coronaviruses on human reproduction, specifically male and female gametes, and in pregnancy. Design Review of English publications in PubMed and Embase to April 6, 2020. Methods Manuscripts were screened for reports including coronavirus, reproduction, including pathophysiology and pregnancy. Intervention(s) None. Main Outcome Measure(s) Reproductive outcomes; effects on gametes; pregnancy outcomes; neonatal complications. Results Seventy-nine reports formed the basis of the review. Coronavirus binding to cells involves the S1 domain of the spike protein to receptors present in reproductive tissues, including angiotensin converting enzyme-2 (ACE2), CD26, Ezrin, and cyclophilins. SARS-CoV-1 may cause severe orchitis leading to germ cell destruction in males. Reports indicate decreased sperm concentration and motility for 72-90 days following COVID-19 infection. Gonadotropin-dependent expression of ACE2 was found in human ovaries, but it is unclear whether SARS-CoV-2 adversely affects female gametogenesis. Evidence suggests that COVID-19 infection has a lower maternal case fatality rate than SARS or MERS, but anecdotal reports suggest that infected, asymptomatic women may develop respiratory symptoms postpartum. COVID-19 infections in pregnancy are associated with preterm delivery. Postpartum neonatal transmission from mother to child has been reported. Conclusion COVID-19 infection may adversely affect some pregnant women and their offspring. Additional studies are needed to assess effects of SARS-CoV-2 infection on male and female fertility.


title: Expression, purification and crystallization of the SARS-CoV macro domain

text: Macro domains or X domains are found as modules of multidomain proteins, but can also constitute a protein on their own. Recently, biochemical and structural studies of cellular macro domains have been performed, showing that they are active as ADP-ribose-1′′-phosphatases. Macro domains are also present in a number of positive-stranded RNA viruses, but their precise function in viral replication is still unknown. The major human pathogen severe acute respiratory syndrome coronavirus (SARS-CoV) encodes 16 non-structural proteins (nsps), one of which (nsp3) encompasses a macro domain. The SARS-CoV nsp3 gene region corresponding to amino acids 182–355 has been cloned, expressed in Escherichia coli, purified and crystallized. The crystals belong to space group P2(1), with unit-cell parameters a = 37.5, b = 55.6, c = 108.9 Å, β = 91.4°, and the asymmetric unit contains either two or three molecules. Both native and selenomethionine-labelled crystals diffract to 1.8 Å.


title: Diagnostic Investigation of Emerging Viruses of Companion Animals

text: In this article, the authors are specifically concerned with the timely and accurate detection of emerging diseases of small animals that are viral in origin. Veterinarians are bound to encounter emerging viruses in their practice. The problem is unavoidable, because viruses are highly mutagenic. Even the immune response dictates the nature of virus that evolves in a host. If the clinical signs and diagnostic methods fail to correlate, the veterinarian should work with the diagnostic laboratory to solve the diagnostic puzzle.


Triumphs, trials, and tribulations of the global response to MERS coronavirus


title: Imprint Cytology for Intra-operative Assessment of Surgical Margins for Skeletal Tumours in COVID-19 Pandemic

text: In the current COVID-19 pandemic, tremendous pressure is been exerted on the existing health infrastructure of many developing nations. Limb salvage surgeries in bone and soft tissue sarcomas cannot be delayed beyond a certain time-period and constitute an orthopaedic emergency in certain situations. Evaluation of intra-operative surgical margins forms an important step especially in cases with planned close margins or intercalary resections. Techniques such as imprint cytology can be preferred over frozen sections for evaluation of the surgical margins especially in COVID-19 positive patients. The advantages it offers such as completion of the procedure within the operation room complex, no generation of aerosols, and almost equal sensitivity and specificity when compared with frozen section method do warrant a modification of current surgical practice in the current health crisis especially in resource-constrained nations. Awareness and better communication regarding the same from the pathologist to the surgical team will go a long way in conserving resources and avoid unnecessary exposure to potentially infected aerosols.


title: Childhood cervical lymphadenopathy

text: Abstract Cervical lymphadenopathy is a common problem in children. The condition most commonly represents a transient response to a benign local or generalized infection, but occasionally it might herald the presence of a more serious disorder. Acute bilateral cervical lymphadenopathy usually is caused by a viral upper respiratory tract infection or streptococcal pharyngitis. Acute unilateral cervical lymphadenitis is caused by streptococcal or staphylococcal infection in 40% to 80% of cases. The most common causes of subacute or chronic lymphadenitis are cat scratch disease, mycobacterial infection, and toxoplasmosis. Supraclavicular or posterior cervical lymphadenopathy carries a much higher risk for malignancies than does anterior cervical lymphadenopathy. Generalized lymphadenopathy is often caused by a viral infection, and less frequently by malignancies, collagen vascular diseases, and medications. Laboratory tests are not necessary in the majority of children with cervical lymphadenopathy. Most cases of lymphadenopathy are self-limited and require no treatment. The treatment of acute bacterial cervical lymphadenitis without a known primary source should provide adequate coverage for both Staphylococcus aureus and group A beta hemolytic streptococci.


title: Human Coronavirus NL63 Molecular Epidemiology and Evolutionary Patterns in Rural Coastal Kenya

text: BACKGROUND: Human coronavirus NL63 (HCoV-NL63) is a globally endemic pathogen causing mild and severe respiratory tract infections with reinfections occurring repeatedly throughout a lifetime. METHODS: Nasal samples were collected in coastal Kenya through community-based and hospital-based surveillance. HCoV-NL63 was detected with multiplex real-time reverse transcription PCR, and positive samples were targeted for nucleotide sequencing of the spike (S) protein. Additionally, paired samples from 25 individuals with evidence of repeat HCoV-NL63 infection were selected for whole-genome virus sequencing. RESULTS: HCoV-NL63 was detected in 1.3% (75/5573) of child pneumonia admissions. Two HCoV-NL63 genotypes circulated in Kilifi between 2008 and 2014. Full genome sequences formed a monophyletic clade closely related to contemporary HCoV-NL63 from other global locations. An unexpected pattern of repeat infections was observed with some individuals showing higher viral titers during their second infection. Similar patterns for 2 other endemic coronaviruses, HCoV-229E and HCoV-OC43, were observed. Repeat infections by HCoV-NL63 were not accompanied by detectable genotype switching. CONCLUSIONS: In this coastal Kenya setting, HCoV-NL63 exhibited low prevalence in hospital pediatric pneumonia admissions. Clade persistence with low genetic diversity suggest limited immune selection, and absence of detectable clade switching in reinfections indicates initial exposure was insufficient to elicit a protective immune response.


title: A SARS-CoV-2 infection model in mice demonstrates protection by neutralizing antibodies

text: Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic with millions of human infections. One limitation to the evaluation of potential therapies and vaccines to inhibit SARS-CoV-2 infection and ameliorate disease is the lack of susceptible small animals in large numbers. Commercially available laboratory strains of mice are not readily infected by SARS-CoV-2 because of species-specific differences in their angiotensin-converting enzyme 2 (ACE2) receptors. Here, we transduced replication-defective adenoviruses encoding human ACE2 via intranasal administration into BALB/c mice and established receptor expression in lung tissues. hACE2-transduced mice were productively infected with SARS-CoV-2, and this resulted in high viral titers in the lung, lung pathology, and weight loss. Passive transfer of a neutralizing monoclonal antibody reduced viral burden in the lung and mitigated inflammation and weight loss. The development of an accessible mouse model of SARS-CoV-2 infection and pathogenesis will expedite the testing and deployment of therapeutics and vaccines.


title: Radiographic follow‐up of pneumonia in children

text: This study assessed the clinical value of routine follow‐up chest radiographs in hospitalized children with community‐acquired pneumonia. The study population consisted of 196 children hospitalized for community‐acquired pneumonia diagnosed between 1993–1995. Seventeen infective agents (10 viruses and 7 bacteria) were sought. Chest radiographs were taken on admission and 3–7 weeks later. All children were treated with antibiotics. Data on the course of illness over the following 8–10 years were obtained from patient files and questionnaires sent to parents. A potential causative agent was found in 165 (84%) of 196 cases. On follow‐up chest radiographs, residual or new changes were seen in 30% of cases. The residual changes tended to be more common after mixed viral‐bacterial infection (43%) than after sole viral (25%) or sole bacterial (20%) infection. Interstitial infiltrates (66%), atelectasis (46%), and enlarged lymph nodes were the most common sequelae seen on follow‐up. Residual findings on follow‐up radiographs did not affect the treatment of the children. No further chest radiographs were taken. During the 8–10‐year follow‐up of 194 children, no illnesses appeared that were associated with previous pneumonia. Twenty‐six children had a new episode of pneumonia, 7 of them had asthma, and 6 had different underlying illnesses. In conclusion, routine follow‐up chest radiographs are not needed in childhood community‐acquired pneumonia if the child has a clinically uneventful recovery. Pediatr Pulmonol. © 2005 Wiley‐Liss, Inc.


title: Safety of snake antivenom immunoglobulins: Efficacy of viral inactivation in a complete downstream process

text: Viral safety remains a challenge when processing a plasma‐derived product. A variety of pathogens might be present in the starting material, which requires a downstream process capable of broad viral reduction. In this article, we used a wide panel of viruses to assess viral removal/inactivation of our downstream process for Snake Antivenom Immunoglobulin (SAI). First, we screened and excluded equine plasma that cross‐reacted with any model virus, a procedure not published before for antivenoms. In addition, we evaluated for the first time the virucidal capacity of phenol applied to SAI products. Among the steps analyzed in the process, phenol addition was the most effective one, followed by heat, caprylic acid, and pepsin. All viruses were fully inactivated only by phenol treatment; heat, the second most effective step, did not inactivate the rotavirus and the adenovirus used. We therefore present a SAI downstream method that is cost‐effective and eliminates viruses to the extent required by WHO for a safe product. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:972–979, 2013


title: Exploration of the metal coordination region of concanavalin A for its interaction with human norovirus

text: Abstract Rapid methods for the detection and clinical treatment of human norovirus (HuNoV) are needed to control foodborne disease outbreaks, but reliable techniques that are fast and sensitive enough to detect small amounts of HuNoV in food and aquatic environments are not yet available. We explore the interactions between HuNoV and concanavalin A (Con A), which could facilitate the development of a sensitive detection tool for HuNoV. Biophysical studies including hydrogen/deuterium exchange (HDX) mass spectrometry and surface plasmon resonance (SPR) revealed that when the metal coordinated region of Con A, which spans Asp16 to His24, is converted to nine alanine residues (mCon AMCR), the affinity for HuNoV (GII.4) diminishes, demonstrating that this Ca2+ and Mn2+ coordinated region is responsible for the observed virus-protein interaction. The mutated carbohydrate binding region of Con A (mCon ACBR) does not affect binding affinity significantly, indicating that MCR of Con A is a major region of interaction to HuNoV (GII.4). The results further contribute to the development of a HuNoV concentration tool, Con A-immobilized polyacrylate beads (Con A-PAB), for rapid detection of genotypes from genogroups I and II (GI and GII). This method offers many advantages over currently available methods, including a short concentration time. HuNov (GI and GII) can be detected in just 15 min with 90% recovery through Con A-PAB application. In addition, this method can be used over a wide range of pH values (pH 3.0 – 10.0). Overall, this rapid and sensitive detection of HuNoV (GI and GII) will aid in the prevention of virus transmission pathways, and the method developed here may have applicability for other foodborne viral infections.


title: Molecular detection of gastrointestinal viral infections in hospitalized patients

text: Abstract Gastrointestinal viral syndromes are a common cause of morbidity and mortality in humans worldwide. Etiological agents include a large number of viruses encompassing several orders, families, and genera. During the period April 2011 to April 2012, 689 stool samples from as many patients hospitalized at the Fondazione IRCCS Policlinico San Matteo of Pavia exhibiting gastrointestinal syndromes were examined for the presence of rotavirus, norovirus, astrovirus, adenovirus, rhinovirus, enterovirus, parechovirus, bocavirus, coronavirus, sapovirus, cosavirus, and aichi virus using polymerase chain reaction assays. Gastrointestinal viral agents were detected in 246 (36%) patients of the 689 analyzed. Adenovirus and norovirus were the most common viruses in this cohort, while aichi virus was the only gastrointestinal agent not detected. Surprisingly, rhinovirus was one of the most frequently detected viruses. However, a potential association with gastroenteritis remains to be confirmed.


title: Neurological diseases as mortality predictive factors for patients with COVID-19: a retrospective cohort study

text: INTRODUCTION: In the current study, we evaluated factors that increase the coronavirus disease (COVID-19) patient death rate by analyzing the data from two cohort hospitals. In addition, we studied whether underlying neurological diseases are risk factors for death. METHODS: In this retrospective cohort study, we included 103 adult inpatients (aged ≥ 18 years). We evaluated differences in demographic data between surviving and non-surviving COVID-19 patients. RESULTS: In a multivariate logistic analysis, age and the presence of chronic lung disease and Alzheimer’s dementia (AD) were the only significant parameters for predicting COVID-19 non-survival (p < 0.05). However, hypertension, coronary vascular disease, dyslipidemia, chronic kidney disease, diabetes, and history of taking angiotensin II receptor blockers (ARBs) or angiotensin-converting enzyme (ACE) inhibitors, as well as nonsteroidal anti-inflammatory drugs (NSAIDs), were not significantly associated with the death of COVID-19 patients. The optimal cutoff value obtained from the maximum Youden index was 70 (sensitivity, 80.77%; specificity, 61.04%), and the odds ratio of non-survival increased 1.055 fold for every year of age. CONCLUSIONS: Clinicians should closely monitor and manage the symptoms of COVID-19 patients who are over the age of 70 years or have chronic lung disease or AD.