title: Primary care physicians’ response to pandemic influenza in Hong Kong: a mixed quantitative and qualitative study

text: Summary Objectives The current study was conducted to use a developed framework to appraise the public primary care response to pandemic 2009 influenza A H1N1 virus in Hong Kong in 2009. Methods A cross-sectional survey was conducted of 300 doctors working in public primary care clinics. In addition, a qualitative study was conducted in two selected general outpatient clinics (GOPCs) with 10 doctors between September and December 2009. Results We found that there was an increase in clinical service demand for public primary care doctors and that there was lower compliance with hand washing as compared to the wearing of masks among GOPC doctors during the study period. Conclusions Since hand hygiene and influenza vaccination are effective methods to prevent the spread of influenza infection, future studies should explore the reasons for non-compliance with these preventive behaviors among doctors. More education and training in dealing with influenza A H1N1 infection may be needed.


title: Anatid herpesvirus 1 CH virulent strain induces syncytium and apoptosis in duck embryo fibroblast cultures

text: Abstract Anatid herpesvirus 1 (AHV-1) CH virulent strain was first isolated from an infected duck and it was found that this virus strain could induce cytopathic effect (CPE) in duck embryo fibroblast (DEF). Following AHV-1 infection, DEF showed morphological changes such as cell rounding, improved refractivity and detachment from the culture surface. However, its pathological characteristics were not adequately known. Related studies were performed and the results showed that syncytium formation could be observed as the other type of CPE in AHV-1 infection. Hematoxylin-eosin staining and 4’, 6-diamidino-2-phenylindole (DAPI) staining of infected DEF were each used to visualize the shape and distribution of chromatin within nuclei and nuclear fragmentation was observed. Chromatin condensation and margination, as well as formation of apoptotic bodies were observed by transmission electron microscopy (TEM). DNA ladder formation was detected in AHV-1 infected cells and apoptosis of the infected DEF was also detected by flow cytometry analysis of Annexin V-FITC/PI staining method. Therefore, it was suggested that AHV-1 virulent strain can induce syncytium and apoptosis in DEF. Syncytium formation and apoptosis observed in this study may contribute to the elucidation of AHV-1 pathogenesis.


title: Computational Design of High-Affinity Epitope Scaffolds by Backbone Grafting of a Linear Epitope

text: Abstract Computational grafting of functional motifs onto scaffold proteins is a promising way to engineer novel proteins with pre-specified functionalities. Typically, protein grafting involves the transplantation of protein side chains from a functional motif onto structurally homologous regions of scaffold proteins. Using this approach, we previously transplanted the human immunodeficiency virus 2F5 and 4E10 epitopes onto heterologous proteins to design novel “epitope-scaffold” antigens. However, side-chain grafting is limited by the availability of scaffolds with compatible backbone for a given epitope structure and offers no route to modify backbone structure to improve mimicry or binding affinity. To address this, we report here a new and more aggressive computational method—backbone grafting of linear motifs—that transplants the backbone and side chains of linear functional motifs onto scaffold proteins. To test this method, we first used side-chain grafting to design new 2F5 epitope scaffolds with improved biophysical characteristics. We then independently transplanted the 2F5 epitope onto three of the same parent scaffolds using the newly developed backbone grafting procedure. Crystal structures of side-chain and backbone grafting designs showed close agreement with both the computational models and the desired epitope structure. In two cases, backbone grafting scaffolds bound antibody 2F5 with 30- and 9-fold higher affinity than corresponding side-chain grafting designs. These results demonstrate that flexible backbone methods for epitope grafting can significantly improve binding affinities over those achieved by fixed backbone methods alone. Backbone grafting of linear motifs is a general method to transplant functional motifs when backbone remodeling of the target scaffold is necessary.


title: Oncology Treatment in the Era of COVID‐19: We Cannot Afford to Hit the Pause Button

text: The COVID‐19 pandemic has far‐reaching ramifications for patients undergoing cancer treatment. Oncologists and institutions have adjusted treatment practices and, in many cases, significantly curtailed clinical trial conduct. Whether these adjustments mitigate the risk of COVID‐19 complications without jeopardizing treatment of the cancer is unknown. Given the expected duration of the pandemic, it is imperative that treatment of the patient's cancer remain the priority and that advances in drug development continue through appropriately designed clinical trials.


title: Tumor‐associated macrophages secrete CC‐chemokine ligand 2 and induce tamoxifen resistance by activating PI3K/Akt/mTOR in breast cancer

text: Breast cancer is the most prevalent malignancy among women. Although endocrine therapy is effective, the development of endocrine resistance is a major clinical challenge. The tumor microenvironment (TME) promotes tumor malignancy, and tumor‐associated macrophages (TAM) within the TME play a crucial role in endocrine resistance. Herein, we aimed to elucidate the relationship between TAM and the endocrine‐resistant phenotype of breast cancer. Macrophages were cultured with conditioned medium (CM) from tamoxifen‐sensitive (MCF7‐S) or ‐resistant (MCF7‐R) MCF7 breast cancer cells. M2 polarization was detected by CD163 immunofluorescence. To determine the effect on endocrine resistance, MCF7 cells were cultured in the supernatant of different TAM, and then treated with tamoxifen. CC‐chemokine ligand 2 (CCL2) immunohistochemistry was carried out on pathological sections from 100 patients with invasive estrogen receptor‐positive breast cancer. We found that macrophages cultured in the CM of MCF7‐S and MCF7‐R cells were induced into TAM, with a more obvious M2 polarization in the latter. Tamoxifen resistance was increased by culture in TAM medium. TAM secreted CCL2, which increased endocrine resistance in breast cancer cells through activation of the PI3K/Akt/mTOR signaling pathway. High expression of CCL2 was correlated with infiltration of CD163+macrophages (r = 0.548, P < .001), and patients with high CCL2 expression presented shorter progression‐free survival than those with low CCL2 expression (P < .05). We conclude that CCL2 secreted by TAM activates PI3K/Akt/mTOR signaling and promotes an endocrine resistance feedback loop in the TME, suggesting that CCL2 and TAM may be novel therapeutic targets for patients with endocrine‐resistant breast cancer.


title: Antimicrobial and immunomodulatory activity induced by loperamide in mycobacterial infections

text: • Loperamide modulates macrophages immune responses towards mycobacteria. • Loperamide is an immunoregulator of inflammation during mycobacterial infection. • Loperamide induces immunomodulatory responses and bactericidal mechanisms. • The activation of opioid receptors by loperamide is involved in its immunomodulatory activity.


title: Autophagy protein ATG5 interacts transiently with the hepatitis C virus RNA polymerase (NS5B) early during infection

text: Abstract Autophagy is an important cellular process by which ATG5 initiates the formation of double membrane vesicles (DMVs). Upon infection, DMVs have been shown to harbor the replicase complex of positive-strand RNA viruses such as MHV, poliovirus, and equine arteritis virus. Recently, it has been shown that autophagy proteins are proviral factors that favor initiation of hepatitis C virus (HCV) infection. Here, we identified ATG5 as an interacting protein for the HCV NS5B. ATG5/NS5B interaction was confirmed by co-IP and metabolic labeling studies. Furthermore, ATG5 protein colocalizes with NS4B, a constituent of the membranous web. Importantly, immunofluorescence staining demonstrated a strong colocalization of ATG5 and NS5B within perinuclear regions of infected cells at 2days postinfection. However, colocalization was completely lacking at 5DPI, suggesting that HCV utilizes ATG5 as a proviral factor during the onset of viral infection. Finally, inhibition of autophagy through ATG5 silencing blocks HCV replication.


title: Early stage COVID-19 disease dynamics in Germany: models and parameter identification

text: Since the end of 2019 an outbreak of a new strain of coronavirus, called SARS-CoV-2, is reported from China and later other parts of the world. Since January 21, World Health Organization (WHO) reports daily data on confirmed cases and deaths from both China and other countries (www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports). The Johns Hopkins University (github.com/CSSEGISandData/COVID-19/blob/master/csse_COVID_19_data/csse_COVID_19_time_series/time_series_COVID19_confirmed_global.csv) collects those data from various sources worldwide on a daily basis. For Germany, the Robert-Koch-Institute (RKI) also issues daily reports on the current number of infections and infection related fatal cases (www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Situationsberichte/Gesamt.html). However, due to delays in the data collection, the data from RKI always lags behind those reported by Johns Hopkins. In this work we present an extended SEIRD-model to describe the disease dynamics in Germany. The parameter values are identified by matching the model output to the officially reported cases. An additional parameter to capture the influence of unidentified cases is also included in the model.


title: Clinical cystoisosporosis associated to porcine cytomegalovirus (PCMV, Suid herpesvirus 2) infection in fattening pigs

text: Abstract Cystoisospora (syn. Isospora) suis is the causative agent of neonatal porcine coccidiosis and one of the main causes of diarrhoea in suckling piglets worldwide. Infection with porcine cytomegalovirus (PCMV, Suid herpesvirus 2) causes inclusion body rhinitis in pigs. In a Swiss pig herd (n =2 boars, 7 sows, 2 gilts, 18 finishing pigs, 30 fattening pigs, 54 suckling piglets), an outbreak of PCMV infection with high morbidity in all age categories, characterized by fever, anorexia, reduced general condition, respiratory signs and increased piglet mortality, was diagnosed by histopathology and molecular methods. Five fattening pigs (age~17weeks) additionally showed diarrhoea, not typical for PCMV infections, and one fattener had to be euthanized due to poor condition. Histopathologically, severe fibrinopurulent jejunoileitis with extensive atrophy and fusion of intestinal villi, loss of goblet cells and crypt abscesses associated to C. suis infection were present. In the liver, herpesvirus intranuclear inclusion bodies were observed and PCMV was confirmed by PCR/sequencing. No further infectious causes of diarrhoea (i.e. Rotavirus A; TGEV; PEDV; PCV-2; enterotoxigenic Escherichia coli or Lawsonia intracellularis) were detected in the euthanized fattener. Coproscopically, C. suis oocysts were identified in the faeces from further fatteners with diarrhoea. While C. suis usually produces disease only in suckling piglets, its association with severe intestinal lesions and diarrhoea in ~17-week-old fatteners was surprising. It is supposed that the underlying PCMV infection might have contributed to the presentation of clinical cystoisosporosis in fattening pigs. The interaction mechanisms between these two pathogens are unknown.


title: Seasonal and interannual risks of dengue introduction from South-East Asia into China, 2005-2015

text: Due to worldwide increased human mobility, air-transportation data and mathematical models have been widely used to measure risks of global dispersal of pathogens. However, the seasonal and interannual risks of pathogens importation and onward transmission from endemic countries have rarely been quantified and validated. We constructed a modelling framework, integrating air travel, epidemiological, demographical, entomological and meteorological data, to measure the seasonal probability of dengue introduction from endemic countries. This framework has been applied retrospectively to elucidate spatiotemporal patterns and increasing seasonal risk of dengue importation from South-East Asia into China via air travel in multiple populations, Chinese travelers and local residents, over a decade of 2005–15. We found that the volume of airline travelers from South-East Asia into China has quadrupled from 2005 to 2015 with Chinese travelers increased rapidly. Following the growth of air traffic, the probability of dengue importation from South-East Asia into China has increased dramatically from 2005 to 2015. This study also revealed seasonal asymmetries of transmission routes: Sri Lanka and Maldives have emerged as origins; neglected cities at central and coastal China have been increasingly vulnerable to dengue importation and onward transmission. Compared to the monthly occurrence of dengue reported in China, our model performed robustly for importation and onward transmission risk estimates. The approach and evidence could facilitate to understand and mitigate the changing seasonal threat of arbovirus from endemic regions.


title: Inorganic Complexes and Metal-Based Nanomaterials for Infectious Disease Diagnostics

text: [Image: see text] Infectious diseases claim millions of lives each year. Robust and accurate diagnostics are essential tools for identifying those who are at risk and in need of treatment in low-resource settings. Inorganic complexes and metal-based nanomaterials continue to drive the development of diagnostic platforms and strategies that enable infectious disease detection in low-resource settings. In this review, we highlight works from the past 20 years in which inorganic chemistry and nanotechnology were implemented in each of the core components that make up a diagnostic test. First, we present how inorganic biomarkers and their properties are leveraged for infectious disease detection. In the following section, we detail metal-based technologies that have been employed for sample preparation and biomarker isolation from sample matrices. We then describe how inorganic- and nanomaterial-based probes have been utilized in point-of-care diagnostics for signal generation. The following section discusses instrumentation for signal readout in resource-limited settings. Next, we highlight the detection of nucleic acids at the point of care as an emerging application of inorganic chemistry. Lastly, we consider the challenges that remain for translation of the aforementioned diagnostic platforms to low-resource settings.


title: Evaluation of the effects of flushing feed manufacturing equipment with chemically treated rice hulls on porcine epidemic diarrhea virus cross-contamination during feed manufacturing

text: Various strategies have been proposed to mitigate potential risk of porcine epidemic diarrhea virus (PEDV) transmission via feed and feed ingredients. Wet disinfection has been found to be the most effective decontamination of feed mill surfaces; however, this is not practical on a commercial feed production scale. Another potential mitigation strategy would be using chemically treated rice hulls flushed through the feed manufacturing equipment. Therefore, the objective of this study was to determine the effects of medium-chain fatty acids (MCFA) or formaldehyde-treated rice hull flush batches as potential chemical mitigation strategies for PEDV during feed manufacturing. Feed without evidence of PEDV RNA contamination was inoculated with PEDV. Based on polymerase chain reaction analysis, this feed had a cycle threshold (Ct) = 30.2 and was confirmed infective in bioassay. After manufacturing the PEDV-positive feed, untreated rice hulls, formaldehyde-treated rice hulls, 2% MCFA- (a 1:1:1 blend of hexanoic, octanoic, and decanoic acid) treated rice hulls, or 10% MCFA-treated rice hulls were flushed through laboratory scale mixers. For the untreated rice hulls, 3 of 6 samples had detectable PEDV RNA, whereas 1 of 6 formaldehyde-treated rice hull flush samples and 2 of 6 of the 2% MCFA rice hull flush samples had detectable PEDV RNA. However, PEDV RNA was not detected in any of the 10% MCFA rice hull flush samples. Then, rice hulls treated with 10% MCFA were mixed and discharged through a production scale mixer and bucket elevator following PEDV-positive feed. No rice hull flush or feed samples from the mixer following chemically treated rice hull flush had detectible PEDV RNA. However, one 10% MCFA rice hull sample collected from the bucket elevator discharge spout had detectible PEDV RNA. Dust collected following mixing of PEDV contaminated feed had detectable PEDV RNA (Ct = 29.4) and was infectious. However, dust collected immediately after the 10% MCFA rice hull flush batch had a reduced quantity of PEDV RNA (Ct = 33.7) and did not cause infection. Overall, the use of rice hull flushes effectively reduced the quantity of detectible RNA present after mixing a batch of PEDV-positive feed. Chemical treatment of rice hulls with formaldehyde or 10% MCFA provided additional reduction in detectible RNA. Finally, dust collected after manufacturing PEDV-inoculated feed has the potential to serve as a vector for PEDV transmission.


title: Reduction of secondary transmission of SARS-CoV-2 in households by face mask use, disinfection and social distancing: a cohort study in Beijing, China

text: INTRODUCTION: Transmission of COVID-19 within families and close contacts accounts for the majority of epidemic growth. Community mask wearing, hand washing and social distancing are thought to be effective but there is little evidence to inform or support community members on COVID-19 risk reduction within families. METHODS: A retrospective cohort study of 335 people in 124 families and with at least one laboratory confirmed COVID-19 case was conducted from 28 February to 27 March 2020, in Beijing, China. The outcome of interest was secondary transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within the family. Characteristics and practices of primary cases, of well family contacts and household hygiene practices were analysed as predictors of secondary transmission. RESULTS: The secondary attack rate in families was 23.0% (77/335). Face mask use by the primary case and family contacts before the primary case developed symptoms was 79% effective in reducing transmission (OR=0.21, 95% CI 0.06 to 0.79). Daily use of chlorine or ethanol based disinfectant in households was 77% effective (OR=0.23, 95% CI 0.07 to 0.84). Wearing a mask after illness onset of the primary case was not significantly protective. The risk of household transmission was 18 times higher with frequent daily close contact with the primary case (OR=18.26, 95% CI 3.93 to 84.79), and four times higher if the primary case had diarrhoea (OR=4.10, 95% CI 1.08 to 15.60). Household crowding was not significant. CONCLUSION: The study confirms the highest risk of transmission prior to symptom onset, and provides the first evidence of the effectiveness of mask use, disinfection and social distancing in preventing COVID-19. We also found evidence of faecal transmission. This can inform guidelines for community prevention in settings of intense COVID-19 epidemics.


Post-infectious Guillain–Barré syndrome related to SARS-CoV-2 infection: a case report


title: Coronaviruses: emerging and re-emerging pathogens in humans and animals

text: The severe acute respiratory syndrome coronavirus (SARS-CoV) and recently emerged Middle East respiratory syndrome coronavirus (MERS-CoV) epidemics have proven the ability of coronaviruses to cross species barrier and emerge rapidly in humans. Other coronaviruses such as porcine epidemic diarrhea virus (PEDV) are also known to cause major disease epidemics in animals wiith huge economic loss. This special issue in Virology Journal aims to highlight the advances and key discoveries in the animal origin, viral evolution, epidemiology, diagnostics and pathogenesis of the emerging and re-emerging coronaviruses in both humans and animals.


title: Chinese hamster ovary cell lines selected for resistance to ebolavirus glycoprotein mediated infection are defective for NPC1 expression

text: Abstract Ebolavirus causes severe hemorrhagic fever in humans and non-human primates. Entry of ebolavirus is mediated by the viral glycoprotein, GP; however, the required host factors have not been fully elucidated. A screen utilizing a recombinant Vesicular Stomatitis Virus (VSV) encoding Zaire ebolavirus GP identified four Chinese Hamster Ovary (CHO) cell lines resistant to GP-mediated viral entry. Susceptibility to vectors carrying SARS coronavirus S or VSV-G glycoproteins suggests that endocytic and processing pathways utilized by other viruses are intact in these cells. A cathepsin-activated form of the ebolaviral glycoprotein did not overcome the entry restriction, nor did expression of several host factors previously described as important for ebolavirus entry. Conversely, expression of the recently described ebolavirus host entry factor Niemann–Pick Type C1 (NPC1) restored infection. Resistant cells encode distinct mutations in the NPC1 gene, resulting in loss of protein expression. These studies reinforce the importance of NPC1 for ebolavirus entry.


title: Colorectal surgery obesity-related morbidity during COVID-19

text: Tocilizumab, a monoclonal antiinterluekin-6 receptor antibody, has been empirically used in the treatment of cytokine release syndrome associated with severe coronavirus disease 2019 infections. The efficacy and safety of these medications for these patients is unknown. The purpose of this report was to present a case of acute large bowel perforation in a morbidly obese patient with coronavirus disease 2019 pneumonia who received empiric Tocilizumab. This case report analyzes the risks of acute large bowel perforation after using this medication empirically and discusses the appropriate management of this adverse event.


title: Insights into the Recent 2019 Novel Coronavirus (SARS-CoV-2) in Light of Past Human Coronavirus Outbreaks

text: Coronaviruses (CoVs) are RNA viruses that have become a major public health concern since the Severe Acute Respiratory Syndrome-CoV (SARS-CoV) outbreak in 2002. The continuous evolution of coronaviruses was further highlighted with the emergence of the Middle East Respiratory Syndrome-CoV (MERS-CoV) outbreak in 2012. Currently, the world is concerned about the 2019 novel CoV (SARS-CoV-2) that was initially identified in the city of Wuhan, China in December 2019. Patients presented with severe viral pneumonia and respiratory illness. The number of cases has been mounting since then. As of late February 2020, tens of thousands of cases and several thousand deaths have been reported in China alone, in addition to thousands of cases in other countries. Although the fatality rate of SARS-CoV-2 is currently lower than SARS-CoV, the virus seems to be highly contagious based on the number of infected cases to date. In this review, we discuss structure, genome organization, entry of CoVs into target cells, and provide insights into past and present outbreaks. The future of human CoV outbreaks will not only depend on how the viruses will evolve, but will also depend on how we develop efficient prevention and treatment strategies to deal with this continuous threat.


title: Effects of progressive muscle relaxation on anxiety and sleep quality in patients with COVID-19

text: Abstract Background Patients with Coronavirus Disease 2019(COVID-19) will experience high levels of anxiety and low sleep quality due to isolation treatment. Some sleep-improving drugs may inhibit the respiratory system and worsen the condition. Prolonged bedside instruction may increase the risk of medical infections. Objective To investigate the effect of progressive muscle relaxation on anxiety and sleep quality of COVID-19. Methods In this randomized controlled clinical trial, a total of 51 patients who entered the isolation ward were included in the study and randomly divided into experimental and control groups. The experimental group used progressive muscle relaxation (PMR) technology for 30 min per day for 5 consecutive days. During this period, the control group received only routine care and treatment. Before and after the intervention, the Spielberger State-Trait Anxiety Scale (STAI) and Sleep State Self-Rating Scale (SRSS) were used to measure and record patient anxiety and sleep quality. Finally, data analysis was performed using SPSS 25.0 software. Results The average anxiety score (STAI) before intervention was not statistically significant (P = 0.730), and the average anxiety score after intervention was statistically significant (P < 0.001). The average sleep quality score (SRSS) of the two groups before intervention was not statistically significant (P = 0.838), and it was statistically significant after intervention (P < 0.001). Conclusion Progressive muscle relaxation as an auxiliary method can reduce anxiety and improve sleep quality in patients with COVID-19.


Risk assessment of mixed and displacement ventilation (LAF) during orthopedic and trauma surgery on COVID-19 patients with increased release of infectious aerosols


title: Telepsychiatry coming into its own with COVID‐19

text: Among the other benefits of the CARES Act — the $2 trillion law signed by President Trump March 27 —is a big boost to telemedicine, including telepsychiatry. For so many years, psychiatrists have been hampered by the fact that, in general, they can't get paid for telemedicine. Insurance won't cover it, and, for the most part, patients assume that a phone call — or an email or text — should be free.


title: Middle East Respiratory Syndrome Coronavirus, Saudi Arabia, 2017–2018

text: We characterized exposures and demographics of Middle East respiratory syndrome coronavirus cases reported to the Saudi Arabia Ministry of Health during July 1–October 31, 2017, and June 1–September 16, 2018. Molecular characterization of available specimens showed that circulating viruses during these periods continued to cluster within lineage 5.


title: COVID-19 treatment with lopinavir–ritonavir resulting in sick sinus syndrome: a case report

text: BACKGROUND: COVID-19 infection is the most serious global public health crisis of the century. With no approved treatments against it, investigational treatments are being used despite limited safety data. Besides being at higher risk of complications of COVID-19 infection, patients with underlying cardiovascular disease are more likely to develop cardiac-related side effects of treatment. We present a case of sinus arrest with junctional escape related to lopinavir–ritonavir. CASE SUMMARY: A 67-year-old man, with underlying stable ischaemic heart disease, acquired COVID-19 infection. He had a prolonged duration of fever and cough. He subsequently developed acute respiratory distress and required intensive care unit (ICU) care. Given his severe infection, he was started on lopinavir–ritonavir. Hydroxychloroquine was not used as he had a prolonged QTc interval. During observation in the ICU, the patient developed recurrent episodes of sinus arrest with junctional escape. Initial concerns were of myocarditis, but he had no ST-segment changes on ECG, with mild elevations of highly sensitive troponin I and a normal transthoracic echocardiogram. A multidisciplinary team discussion involving the intensivist, infectious disease physicians, and cardiologist; the decision was made to stop treatment with lopinavir–ritonavir. Within 48 h, the bradyarrhythmia resolved. The patient did not require transvenous and permanent pacemaker insertion. CONCLUSION: Current efficacy and safety evidence of lopinavir–ritonavir as a treatment in COVID-19 patients is limited. Although uncommonly reported, those with underlying cardiovascular disease are at increased risk of bradyarrhythmia-related adverse effects of lopinavir–ritonavir. When initiating investigational therapies, especially in patients with cardiovascular conditions, adequate counselling and close monitoring are required.


title: Current treatment options and the role of peptides as potential therapeutic components for Middle East Respiratory Syndrome (MERS): A review

text: Abstract Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a highly pathogenic respiratory virus with mechanisms that may be driven by innate immune responses. Despite the effort of scientific studies related to this virus, Middle East Respiratory Syndrome (MERS) is still a public health concern. MERS-CoV infection has a high mortality rate, and to date, no therapeutic or vaccine has been discovered, that is effective in treating or preventing the disease. In this review, we summarize our understanding of the molecular and biological events of compounds acting as MERS-CoV inhibitors, the outcomes of existing therapeutic options and the various drugs undergoing clinical trials. Currently, several therapeutic options have been employed, such as convalescent plasma (CP), intravenous immunoglobulin (IVIG), monoclonal antibodies and repurposing of existing clinically approved drugs. However, these therapeutic options have drawbacks, thus the need for an alternative approach. The requirement for effective therapeutic treatment has brought the necessity for additional MERS treatments. We suggest that antimicrobial peptides (AMPs) may be used as alternative therapeutic agents against MERS-CoV infection. In addition, we propose the feasibility of developing effective agents by repurposing the existing and clinically approved anti-coronavirus and anti-viral peptide drugs.


Recommendations for Diagnosis and Treatment of Onychomycosis During the COVID‐19 Pandemic


title: T cell-derived interleukin-10 is an important regulator of the Th17 response during lethal alphavirus encephalomyelitis

text: Neuroadapted Sindbis virus infection of mice causes T cell-mediated fatal encephalomyelitis. In the absence of IL-10, pathogenic Th17 cells are increased and disease is accelerated. Lymphoid and myeloid cell contributions to IL-10 production were determined using VertX IL-10 transcriptional eGFP reporter mice. Effector and regulatory CD4(+) and CD8(+) T cells in the brain, but not the cervical lymph nodes, were the primary producers of IL-10. Th17 and Th1/Th17 cells were increased in mice that lacked T cell IL-10 production, although less than in the absence of IL-10. Morbidity and mortality were not affected suggesting an IL-10 threshold for disease exacerbation.


title: Comparison of the Effects of Air Pollution on Outpatient and Inpatient Visits for Asthma: A Population-Based Study in Taiwan

text: BACKGROUND: A nationwide asthma survey on the effects of air pollution is lacking in Taiwan. The purpose of this study was to evaluate the time trend and the relationship between air pollution and health care services for asthma in Taiwan. METHODS: Health care services for asthma and ambient air pollution data were obtained from the National Health Insurance Research database and Environmental Protection Administration from 2000 through 2009, respectively. Health care services, including those related to the outpatient and inpatient visits were compared according to the concentration of air pollutants. RESULTS: The number of asthma-patient visits to health-care facilities continue to increase in Taiwan. Relative to the respective lowest quartile of air pollutants, the adjusted relative risks (RRs) of the outpatient visits in the highest quartile were 1.10 (P-trend = 0.013) for carbon monoxide (CO), 1.10 (P-trend = 0.015) for nitrogen dioxide (NO(2)), and 1.20 (P-trend <0.0001) for particulate matter with an aerodynamic diameter ≦10µm (PM(10)) in the child group (aged 0–18). For adults aged 19–44, the RRs of outpatient visits were 1.13 (P-trend = 0.078) for CO, 1.17 (P-trend = 0.002) for NO(2,) and 1.13 (P-trend <0.0001) for PM(10). For adults aged 45–64, the RRs of outpatient visits were 1.15 (P-trend = 0.003) for CO, 1.19 (P-trend = 0.0002) for NO(2,) and 1.10 (P-trend = 0.001) for PM(10). For the elderly (aged≥ 65), the RRs of outpatient visits in were 1.12 (P-trend = 0.003) for NO(2) and 1.10 (P-trend = 0.006) for PM(10.) For inpatient visits, the RRs across quartiles of CO level were 1.00, 1.70, 1.92, and 1.86 (P-trend = 0.0001) in the child group. There were no significant linear associations between inpatient visits and air pollutants in other groups. CONCLUSIONS: There were positive associations between CO levels and childhood inpatient visits as well as NO(2), CO and PM(10) and outpatient visits.


title: Conséquences anormales des accidents médicaux non fautifs : Jurisprudence du Conseil d’État

text: Résumé L’indemnisation des accidents médicaux sans faute des professionnels ou des établissements est prévue par l’article L.1142-1 du code de la santé publique créé par la loi du 4 mars 2002 relative aux droits des malades et à la qualité du système de santé. Il indique les conditions d’imputabilité, de critères cliniques et de gravité. Parmi les critères cliniques « un accident médical (…) ouvre droit à la réparation des préjudices (…) au titre de la solidarité nationale, lorsqu’ils (…) qu’ils ont eu pour le patient des conséquences anormales au regard de son état de santé comme de l’évolution prévisible de celui-ci (…) ». Les ordres juridictionnels ont eu à caractériser cette « anormalité des conséquences ». Selon la jurisprudence du Conseil d’État du 12 décembre 2014 la condition d’anormalité est toujours « remplie lorsque l'acte médical a entraîné des conséquences notablement plus graves que celles auxquelles le patient était exposé de manière suffisamment probable en l’absence de traitement » et si tel n’est pas le cas, « elles ne peuvent être regardées comme anormales sauf si, dans les conditions où l’acte a été accompli, la survenance du dommage présentait une probabilité faible ; qu’ainsi, elles ne peuvent être regardées comme anormales au regard de l’état du patient lorsque la gravité de cet état a conduit à pratiquer un acte comportant des risques élevés dont la réalisation est à l’origine du dommage ». Le Conseil d’Etat a précisé, en 2019 qu’une probabilité de survenance de 3 % était une probabilité faible. Summary Compensation for no-fault medical accidents to professionals or establishments is provided for by article L.1142-1 of the public health code, created by the law of March 4, 2002 relating to the rights of patients and the quality of the health system. It indicates the conditions of accountability, clinical criteria and severity. Among the clinical criteria "a medical accident (...) gives the right to compensation for damages (...) in the name of national solidarity, when (...) they have had abnormal consequences for the patient in view of his condition as well as the foreseeable evolution of it (…)”. The jurisdictional orders have had to characterize this "abnormality of the consequences". According to the jurisprudence of the Conseil d’Etat of December 12, 2014 the condition of abnormality is always "satisfied when the medical act entailed consequences significantly more serious than those to which the patient was exposed in a sufficiently probable way in the absence of treatment ". And if this is not the case," they cannot be regarded as abnormal unless, under the conditions in which the act was performed, the occurrence of damage presented a low probability; that thus, they cannot be regarded as abnormal with regard to the state of the patient when the gravity of this state led to practicing an act involving high risks whose realization is at the origin of the damage ". The Conseil d’Etat specified in 2019 that a probability of occurrence of 3% was a low probability.


COVID-19: Exposing digital poverty in a pandemic (Correspondence)


title: Being a Public Manager in Times of Crisis The Art of Managing Stakeholders, Political Masters, and Collaborative Networks

text: The COVID‐19 pandemic is seen as the biggest crisis since World War II. What started out as a public health issue, has quickly morphed into a political, economic, and societal crisis of epic proportions. Administrative capacity is a major factor in determining whether societies will emerge from this unprecedented situation with resilience and optimism, or despair and disconnectedness, and whether trust in government will increase or decrease. Autonomous and competent public managers are key producers of such administrative capacity. This paper addresses those public managers, the unsung administrative heroes leading us through times of crisis from behind the scenes. Translating the state of the art in public administration literature, with a particular emphasis on publications in this journal, into accessible practitioner recommendations, it identifies three key competencies paramount to public managers in times of crisis: managing stakeholders, political masters, and collaborative networks. This article is protected by copyright. All rights reserved.


title: Canada, Health System of

text: This article describes how health care, including public health, is financed, organized, and delivered in Canada. Particular attention is paid to recent developments and reforms that have led to greater integration of public health into provincial and regional health-care systems as well as the establishment of the Public Health Agency of Canada (PHAC) at the national level.


title: Are China’s oldest-old living longer with less disability? A longitudinal modeling analysis of birth cohorts born 10 years apart

text: BACKGROUND: China has transitioned from being one of the fastest-growing populations to among the most rapidly aging countries worldwide. In particular, the population of oldest-old individuals, those aged 80+, is projected to quadruple by 2050. The oldest-old represent a uniquely important group—they have high demand for personal assistance and the highest healthcare costs of any age group. Understanding trends in disability and longevity among the oldest-old—that is, whether successive generations are living longer and with less disability—is of great importance for policy and planning purposes. METHODS: We utilized data from successive birth cohorts (n = 20,520) of the Chinese oldest-old born 10 years apart (the earlier cohort was interviewed in 1998 and the later cohort in 2008). Disability was defined as needing personal assistance in performing one or more of five essential activities (bathing, transferring, dressing, eating, and toileting) or being incontinent. Participants were followed for age-specific disability transitions and mortality (in 2000 and 2002 for the earlier cohort and 2011 and 2014 for the later cohort), which were then used to generate microsimulation-based multistate life tables to estimate partial life expectancy (LE) and disability-free LE (DFLE), stratified by sex and age groups (octogenarians, nonagenarians, and centenarians). We additionally explored sociodemographic heterogeneity in LE and DFLE by urban/rural residence and educational attainment. RESULTS: More recently born Chinese octogenarians (born 1919–1928) had a longer partial LE between ages 80 and 89 than octogenarians born 1909–1918, and octogenarian women experienced an increase in partial DFLE of 0.32 years (P = 0.004) across the two birth cohorts. Although no increases in partial LE were observed among nonagenarians or centenarians, partial DFLE increased across birth cohorts, with a gain of 0.41 years (P < 0.001) among nonagenarians and 0.07 years (P = 0.050) among centenarians. Subgroup analyses revealed that gains in partial LE and DFLE primarily occurred among the urban resident population. CONCLUSIONS: Successive generations of China’s oldest-old are living with less disability as a whole, and LE is expanding among octogenarians. However, we found a widening urban-rural disparity in longevity and disability, highlighting the need to improve policies to alleviate health inequality throughout the population. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12916-019-1259-z) contains supplementary material, which is available to authorized users.


title: Trilogy of ACE2: A peptidase in the renin–angiotensin system, a SARS receptor, and a partner for amino acid transporters

text: Abstract Angiotensin-converting enzyme (ACE) 2 is a homolog to the carboxypeptidase ACE, which generates angiotensin II, the main active peptide of renin–angiotensin system (RAS). After the cloning of ACE2 in 2000, three major ACE2 functions have been described so far. First ACE2 has emerged as a potent negative regulator of the RAS counterbalancing the multiple functions of ACE. By targeting angiotensin II ACE2 exhibits a protective role in the cardiovascular system and many other organs. Second ACE2 was identified as an essential receptor for the SARS coronavirus that causes severe acute lung failure. Downregulation of ACE2 strongly contributes to the pathogenesis of severe lung failure. Third, both ACE2 and its homologue Collectrin can associate with amino acid transporters and play essential role in the absorption of amino acids in the kidney and gut. In this review, we will discuss the multiple biological functions of ACE2.


title: Emerging Diseases: Overview

text: Emerging infectious diseases are diseases that are either new, are newly recognized, or are increasing in prevalence in new areas. Resurgent diseases are also usually grouped in this category, as is antimicrobial resistance. These diseases have been given formal recognition in the past two decades, although a historical outlook demonstrates that the phenomenon has probably been persistent, although largely undetected, through recorded history. Emergence has accelerated recently, driven by factors such as demographic change, land use change, increased rapidity and frequency of intercontinental transportation, and other mostly social trends. Continued infectious disease emergence poses, and will continue to pose, significant challenges for public health and for basic science.


title: Healthcare worker infected with Middle East Respiratory Syndrome during cardiopulmonary resuscitation in Korea, 2015

text: OBJECTIVES: During the outbreak of the Middle East Respiratory Syndrome (MERS) in Korea in 2015, the Korea Centers for Disease Control and Prevention (KCDC) confirmed a case of MERS in a healthcare worker in Daejeon, South Korea. To verify the precise route of infection for the case, we conducted an in-depth epidemiological investigation in cooperation with the KCDC. METHODS: We reviewed the MERS outbreak investigation report of the KCDC, and interviewed the healthcare worker who had recovered from MERS. Using the media interview data, we reaffirmed and supplemented the nature of the exposure. RESULTS: The healthcare worker, a nurse, was infected while performing cardiopulmonary resuscitation (CPR) for a MERS patient in an isolation room. During the CPR which lasted for an hour, a large amount of body fluid was splashed. The nurse was presumed to have touched the mask to adjust its position during the CPR. She suggested that she was contaminated with the MERS patient’s body fluids by wiping away the sweat from her face during the CPR. CONCLUSIONS: The possible routes of infection may include the following: respiratory invasion of aerosols contaminated with MERS-coronavirus (MERS-CoV) through a gap between the face and mask; mucosal exposure to sweat contaminated with MERS-CoV; and contamination during doffing of personal protective equipment. The MERS guidelines should reflect this case to decrease the risk of infection during CPR.


title: Reply to “Coronaviruses and immunosuppressed patients. The facts during the third epidemic”

text: We read with interest the letter by D’Antiga evaluating the early experience with Coronavirus‐19 disease (COVID‐19) in liver transplant (LT) recipients in Bergamo and suggesting the absence of correlation between immunosuppression and severity of disease. We report two cases of early liver transplant recipients infected by SARS‐CoV‐2 with only mild clinical manifestations. On the contrary, long‐term recipients with comorbities showed a more aggressive course and worse prognosis. Considering the emerging evidence of the contribution of immune activation in the severity of the COVID‐19, immunosuppression may in part prevent a more aggressive course of the disease.


title: Molecular Characterization of Porcine Reproductive and Respiratory Syndrome Virus, a Member of the Arterivirus Group

text: Abstract Porcine reproductive and respiratory syndrome virus (PRRSV)-specific cDNA clones spanning the 3′ terminal 5 kb of the genomic RNA were isolated, sequenced, and used as probes for identification of PRRSV-specific RNAs. The PRRSV genome is a positive-stranded polyadenylated RNA of about 15 kb. In infected cells, a 3′ coterminal nested set of six major subgenomic mRNAs could be demonstrated. Within the 3′ terminal 3.5 kb of the PRRSV genome, six overlapping reading frames (ORFs) were identified, each most likely expressed by one of the subgenomic mRNAs. Amino acid sequence comparisons revealed that the most 3′ terminal ORF (ORF7) encodes the PRRSV nucleocapsid protein with a calculated molecular weight of 14 kDa. It displays 44.8% amino acid identity with the capsid protein of lactate dehydrogenase-elevating virus (LDV) and 23.6% with that of equine arteritis virus (EAV). The product of ORF6, the second 3′ terminal ORF, represents a putative membrane protein and exhibits 53.2 and 27.2% amino acid identity with the corresponding LDV and EAV polypeptides, respectively. Similar to EAV, ORFs 2 through 5 might encode glycosylated viral proteins. The polypeptide deduced from the most 5′ ORF (ORF1b) contains two conserved domains common to EAV and coronavirus polymerases. Genome organization, strategy of gene expression, and the sequence of deduced proteins show that PRRSV belongs to the Arterivirus group of viruses.


Comment on “Smooth or Risky Revisit of an Old Malaria Drug for COVID-19?”


Redeployment DFT survey


Chapter 20 Feline Coronavirus Infection


title: Telemedicine for Diabetes Care in India during COVID19 Pandemic and National Lockdown Period: Guidelines for Physicians

text: Abstract Background and Aims In view of restrictions on mobility of patients because of COVID-19 pandemic, face-to-face consultations are difficult. We sought to study the feasibility of telemedicine in this scenario. Methods PubMed database and Google Scholar were searched using the key terms ‘telemedicine’, ‘diabetes’, ‘COVID-19’up to 31ST March 2020. In addition, existing guidelines including those by Ministry of Health and Family Welfare (MOHFW), Government of India were accessed. Results We discuss evidence and general guidelines regarding role of telemedicine in patients with diabetes along with its utility and limitations. Conclusions Telemedicine is a useful tool for managing patients of diabetes during this lockdown period. However, there is limited data and further research is required.


title: Identification of a Novel Afipia Species Isolated from an Indian Flying Fox

text: An old world fruit bat Pteropus giganteus, held in captivity and suffering from necrosis of its wing digits, failed to respond to antibiotic therapy and succumbed to the infection. Samples submitted to the National Centre for Foreign Animal Disease were tested for viral infection. Vero E6 cells exhibited minor but unique cytopathic effects on second blind passage, and full CPE by passage four. Utilizing an unbiased random amplification technique from cell culture supernatant, we identified a bacterium belonging to the Bradyrhizobiaceae. Purification of cell culture supernatant on TY media revealed a slow growing bacterial isolate. In this study using electron microscopy, 16S rRNA gene analysis and whole genome sequencing, we identify a novel bacterial species associated with the site of infection belonging to the genus Afipia. This genus of bacteria is very diverse, with only a limited number of species characterized. Afipia felis, previously described as the etiological agent to cause cat scratch disease, and Afipia septicemium, most recently shown to cause disease in humans, highlight the potential for members of this genus to form a branch of opportunistic pathogens within the Bradyrhizobiaceae. Increased utilization of next generation sequencing and genomics will aid in classifying additional members of this intriguing bacterial genera.


title: Coronaviridae ‐ old friends, new enemy!

text: Coronaviridae is a family of single‐stranded positive enveloped RNA viruses. This article aimed to review the history of these viruses in the last 60 years since their discovery to understand what lessons can be learned from the past. A review of the PubMed database was carried out, describing taxonomy, classification, virology, genetic recombination, host adaptation, and main symptoms related to each type of virus. SARS‐CoV‐2 is responsible for the ongoing global pandemic, SARS‐CoV and MERS‐CoV were responsible for causing severe respiratory illness and regional epidemics in the past while the four other strains of CoVs (229‐E OC43, NL63, and HKU1) circulate worldwide and normally only cause mild upper respiratory tract infections. Given the enormous diversity of coronavirus viruses in wildlife and their continuous evolution and adaptation to humans, future outbreaks would undoubtedly occur. Restricting or banning all trade in wild animals in wet markets would be a necessary measure to reduce future zoonotic infections.


title: Chapter 1 Introduction Discovering Issues and Challenges in Low- and Middle-Income Countries

text: Abstract There are gaps and challenges in pharmacy practice in developing countries and possible solutions for various pharmacy stakeholders. Health and public health are essentials for development. The weak global economy has hindered progress toward the sustainable development goals. Many people are still living in poverty with poor health status and inadequate healthcare. Poor health and pharmaceutical sectors in a country will increase the vulnerability of the country and leaves the society at risk. Effective public health interventions can save hundreds of millions of lives. Pharmacy system is one of the core components in a healthcare system, and pharmacists play a very important role. This book sheds light on various topics that individually and in combination determine the status of pharmacy practice in individual countries. This book incorporates multiple data sources and when outliers are discovered, that may be called to the attention of the reader. This book also provides knowledge and understanding about social and administrative aspects of pharmacy in healthcare in low- and middle-income countries.


title: Fatal Respiratory Infections Associated with Rhinovirus Outbreak, Vietnam

text: During an outbreak of severe acute respiratory infections in 2 orphanages, Vietnam, 7/12 hospitalized children died. All hospitalized children and 26/43 children from outbreak orphanages tested positive for rhinovirus versus 9/40 control children (p = 0.0005). Outbreak rhinoviruses formed a distinct genetic cluster. Human rhinovirus is an underappreciated cause of severe pneumonia in vulnerable groups.


title: Randomized controlled trial demonstrating the benefits of delta inulin adjuvanted immunotherapy in patients with bee venom allergy

text: Background Allergic reactions to Hymenoptera insect stings remain a major global clinical problem. Although effective, parenteral desensitization regimens require use of costly venom extracts and require frequent visits over extended periods of time. Objective Adjuvants are commonly used to enhance the efficacy of infectious disease vaccines, and this study asked whether Advax (Vaxine Pty Ltd, Adelaide, Australia), a novel noninflammatory polysaccharide adjuvant, might provide similar benefits for allergy desensitization. Methods A randomized, controlled phase 1/2 trial was undertaken in 27 adults with a history of rapid-onset systemic allergic reactions to honeybee stings and positive specific IgE levels to evaluate the safety and efficacy of honeybee venom immunotherapy (HBVIT) combined with Advax adjuvant. Venom immunotherapy (VIT) was administered monthly for 30 months after achievement of maintenance doses. Results Advax-adjuvanted HBVIT was well tolerated. Around week 14 of VIT, specific IgG4 responses peaked in both groups but increased earlier, peaked higher, and were better maintained through the end of the study in the Advax-adjuvanted arm. Several different patterns of serologic response to VIT were seen; some subjects had a dominant IgG4 response, some had a combined IgG4 and IgG1 response, and some had an exclusively IgG1 response. In some subjects specific IgE levels increased during the induction phase and then decreased, whereas in others specific IgE levels progressively decreased from the start of VIT. Conclusion Advax adjuvant favorably enhanced the immunogenicity of HBVIT, with an early and prolonged switch to specific IgG4 production. The ability of Advax adjuvant to enhance VIT efficacy warrants further study.


title: Evaluation of a molecular point-of-care testing for viral and atypical pathogens on intravenous antibiotic duration in hospitalized adults with lower respiratory tract infection: a randomized clinical trial

text: Abstract Objectives The primary objective was to evaluate whether a molecular point-of-care test (POCT) for viral and atypical pathogens added to routine real-time PCR could reduce duration of intravenous antibiotics in hospitalized patients with lower respiratory tract infection (LRTI) compared with routine real-time PCR. Methods In this single-centre, open-label, randomized controlled study, we enrolled hospitalized adults diagnosed with LRTI. Patients were randomized to an intervention group (POCT FilmArray Panel for 20 viruses, atypical pathogens and bacteria plus routine real-time PCR) or a control group (routine real-time PCR for ten pathogens). The primary outcome was duration of intravenous antibiotics during hospitalization. The secondary outcomes included length of stay, cost of hospitalization and de-escalation within 72 hours and between 72 hours and 7 days. Intention-to-treat analysis was used. Results Between October 2017 and July 2018, we enrolled 800 eligible patients (398 in the intervention group and 402 in the control group). Duration of intravenous antibiotics in the intervention group was shorter than in the control (7.0 days (interquartile range (IQR) 5.0–9.0) versus 8.0 days (IQR 6.0–11.0); p <0.001). Length of hospital stay in the intervention group was significantly shorter (8.0 days (IQR 7.0–11.0) versus 9.0 days (IQR 7.0–12.0; p <0.001) and the cost of hospitalization in the intervention group was significantly lower ($1804.7 (IQR 1298.4–2633.8) versus $2042.5 (IQR 1427.4–2926.2); p 0.002) than control group. More patients in the intervention group achieved de-escalation within 72 hours (7.9%, 29/367 versus 3.2%, 12/377; p 0.005) and between 72 hours and 7 days (29.7%, 109/367 versus 22.0%, 83/377; p 0.024). Conclusions Use of molecular POCT testing for respiratory viruses and atypical pathogens might help to reduce intravenous antibiotic use in hospitalized LRTI patients. Clinical Trial Registration clinicaltrials.gov Identifier: NCT03391076.


title: Genetic characterization and pathogenicity of Japanese porcine deltacoronavirus

text: Abstract Porcine deltacoronavirus (PDCoV) have recently emerged in several swine producing countries. Our survey found that in addition to porcine epidemic diarrhoea virus (PEDV), PDCoV has also been a causative enteric pathogen of diarrhoeic outbreaks occurring at swine farms around Japan since late 2013. Phylogenetic analysis using the complete genomes of PDCoVs detected in Japan in 2014 demonstrated that the PDCoVs from Japan may be closely related to the PDCoVs from the U.S. and Korea during 2013 to 2014 but not the PDCoVs from China and Hong Kong during 2004 to 2016 and from Thailand, Vietnam and Laos during 2015 to 2016. To investigate the pathogenicity of a representative Japanese PDCoV, we performed an experimental infection using hysterectomy-produced colostrum-deprived piglets. The PDCoV-inoculated piglets showed acute, watery diarrhoea, but all recovered and survived. In addition, all piglets inoculated with the Japanese PDCoV exhibited virus shedding at high level in faeces and viremia corresponding to their clinical symptoms. In the PDCoV-inoculated group, viruses were mainly detected from jejunums to colons by a quantitative PDCoV-specific PCR and microscopic observation. These findings would provide useful information for establishing a diagnostic methodology for distinguishing diarrhoea caused by PDCoV from that caused by other enteric pathogens, such as PEDV.


title: Identification and characterisation of T-cell epitopes for incorporation into dendritic cell-delivered Listeria vaccines

text: Abstract Dendritic cells loaded with antigenic peptides, because of their safety and robust immune stimulation, would be ideal for induction of immunity to protect against listeriosis. However, there is no currently accepted method to predict which peptides derived from the Listeria proteome might confer protection. While elution of peptides from MHC molecules after Listeria infection yields high-affinity immune-dominant epitopes, these individual epitopes did not reliably confer Listeria protection. Instead we applied bioinformatic predictions of MHC class I and II epitopes to generate antigenic peptides that were then formulated with Advax™, a novel polysaccharide particulate adjuvant able to enhance cross-presentation prior to being screened for their ability to induce protective T-cell responses. A combination of at least four intermediate strength MHC-I binding epitopes and one weak MHC-II binding epitope when expressed in a single peptide sequence and formulated with Advax adjuvant induced a potent T-cell response and high TNF-α and IL-12 production by dendritic cells resulting in robust listeriosis protection in susceptible mice. This T-cell vaccine approach might be useful for the design of vaccines to protect against listeriosis or other intracellular infections.


title: Co-Infection with SARS-COV-2 and Parainfluenza in a young adult patient with pneumonia: Case Report

text: Coronavirus 2 (SARS-CoV-2) is now considered a pandemic causing Coronavirus disease (COVID-19), multiple fatalities and morbidities which have been associated with it worldwide. We report a severe pneumonia causing acute respiratory distress syndrome due to a coinfection with SARS-COV-2 and Parainfluenza 4 virus in a Hispanic 21 year old male in Florida, USA. The case represents the importance of prompt diagnosis and awareness of the potential co-infection with other respiratory viruses and this novel deadly virus.


title: Spontaneous intracranial hemorrhage in a patient with Middle East respiratory syndrome corona virus

text: The Middle East respiratory syndrome corona virus (MERS-CoV) is a novel positive sense singlestranded ribonucleic acid virus of the genus Beta corona virus. This virus was first isolated from a patient who died from severe respiratory illness in June 2012 in Jeddah, Kingdom of Saudi Arabia. We describe an unusual case of a 42 year old healthcare worker who was admitted to our Intensive Care Unit (ICU) King Abdul-Aziz Medical City, with MERS-CoV and severe acute respiratory distress Syndrome and developed a sudden-onset diabetes insipidus and spontaneous massive intracranial hemorrhage with intra-ventricular extension and tonsillar herniation. Computed angiogram of the brain did not reveal any aneurysm or structural defects. She never had uncontrolled hypertension, or coagulopathy, nor she received antiplatelets. We are reporting a rare case of structural neurological damage associated with MERS-CoV infection.


title: The characteristics and clinical value of chest CT images of novel coronavirus pneumonia

text: AIM To investigate the characteristics and clinical value of chest computed tomography (CT) images of novel coronavirus pneumonia (NCP). MATERIALS AND METHODS Clinical data and CT images of 80 cases of NCP were collected. The clinical manifestations and laboratory test results of the patients were analysed. The lesions in each lung segment of the patient's chest CT images were characterised. Lesions were scored according to length and diffusivity. RESULTS The main clinical manifestations were fever, dry cough, fatigue, a little white sputum, or diarrhoea. A total of 1,702 scored lesions were found in the first chest CT images of 80 patients. The lesions were located mainly in the subpleural area of the lungs (92.4%). Most of the lesions were ground-glass opacity, and subsequent fusions could increase in range and spread mainly in the subpleural area. Pulmonary consolidation accounted for 44.1% of all of the lesions. Of the 80 cases, 76 patients (95%) had bilateral lung disease, four (5%) patients had unilateral lung disease, and eight (10%) patients had cord shadow. CONCLUSION The chest CT of NCP patients is characterised by the onset of bilateral ground-glass lesions located in the subpleural area of the lung, and progressive lesions that result in consolidation with no migratory lesions. Pleural effusions and mediastinal lymphadenopathy are rare. As patients can have inflammatory changes in the lungs alongside a negative early nucleic acid test, chest CT, in combination with epidemiological and laboratory tests, is a useful examination to evaluate the disease and curative effect.


title: Coronaviren: von der banalen Erkältung zum schweren Lungenversagen: Chronologie einer Pandemie

text: In December 2019 a new human coronavirus emerged in Wuhan, China, which is known as SARS-CoV‑2. The clinical course of the disease known as coronavirus disease 2019 (COVID-19) ranges from mild respiratory symptoms to severe lung failure. The virus is currently rapidly spreading around the world and pushing health systems to the limits of their capacity due to the exponential increase in the number of cases. The origin of SARS-CoV‑2 lies in the bat coronavirus pool and has now emerged in the human population due to interspecies transmission. Molecular diagnostic methods have been established in a very short time and a number of clinical studies on the effectiveness of different antiviral drugs are ongoing. The development of a vaccine using different approaches is also under investigation. Considering the high number of cases and mortality rates of up to 9% there is an urgent need for action. This article summarizes the current state of knowledge on human coronaviruses with a strong focus on the current data on SARS-CoV‑2. Due to the daily changing level of knowledge, the article reflects the status up to 21 March 2020.


Preparedness of healthcare workers at French Ebola referral centres


title: Next Generation Sequencing of T and B cell receptor repertoires from COVID-19 patients showed signatures associated with severity of disease

text: Summary We profiled adaptive immunity in COVID-19 patients with active infection or after recovery and created a repository of currently >14 million B and T cell receptor (BCR, TCR) sequences from blood of these patients. The B cell response showed converging IGHV3-driven BCR clusters closely associated with SARS-CoV-2 antibodies. Clonality and skewing of TCR repertoires was associated with interferon type I and III responses, early CD4+ and CD8+ T cell activation and counterregulation by the coreceptors BTLA, Tim-3, PD-1, TIGIT and CD73. Tfh, Th17-like and nonconventional (but not classical anti-viral) Th1 cell polarizations were induced. SARS-CoV-2-specific T cell responses were driven by TCR clusters shared between patients with a characteristic trajectory of clonotypes and traceability over the disease course. Our data provide fundamental insight into adaptive immunity to SARS-CoV-2 with the actively updated repository providing a resource for the scientific community urgently needed to inform therapeutic concepts and vaccine development.


title: Application of WHO’s guideline for the selection of sentinel sites for hospital-based influenza surveillance in Indonesia

text: BACKGROUND: A sentinel hospital-based severe acute respiratory infection (SARI) surveillance system was established in Indonesia in 2013. Deciding on the number, geographic location and hospitals to be selected as sentinel sites was a challenge. Based on the recently published WHO guideline for influenza surveillance (2012), this study presents the process for hospital sentinel site selection. METHODS: From the 2,165 hospitals in Indonesia, the first step was to shortlist to hospitals that had previously participated in respiratory disease surveillance systems and had acceptable surveillance performance history. The second step involved categorizing the shortlist according to five regions in Indonesia to maximize geographic representativeness. A checklist was developed based on the WHO recommended attributes for sentinel site selection including stability, feasibility, representativeness and the availability of data to enable disease burden estimation. Eight hospitals, a maximum of two per geographic region, were visited for checklist administration. Checklist findings from the eight hospitals were analyzed and sentinel sites selected in the third step. RESULTS: Six hospitals could be selected based on resources available to ensure system stability over a three-year period. For feasibility, all eight hospitals visited had mechanisms for specimen shipment and the capacity to report surveillance data, but two had limited motivation for system participation. For representativeness, the eight hospitals were geographically dispersed around Indonesia, and all could capture cases in all age and socio-economic groups. All eight hospitals had prerequisite population data to enable disease burden estimation. The two hospitals with low motivation were excluded and the remaining six were selected as sentinel sites. CONCLUSIONS: The multi-step process enabled sentinel site selection based on the WHO recommended attributes that emphasize right-sizing the surveillance system to ensure its stability and maximizing its geographic representativeness. This experience may guide other countries interested in adopting WHO’s influenza surveillance standards for sentinel site selection.


title: Development of a nanoparticle-assisted PCR assay for detection of porcine epidemic diarrhea virus

text: Abstract Porcine epidemic diarrhea virus (PEDV) is an important pig pathogen that can cause vomiting, diarrhea, and dehydration, leading to serious damage to the swine industry worldwide. In this study, a nanoparticle-assisted polymerase chain reaction (nanoPCR) assay targeting the N gene of PEDV was developed and the sensitivity and specificity were investigated. Under the optimized conditions for detection of PEDV RNA, the nanoPCR assay was 100-fold more sensitive than a conventional RT-PCR assay. The lower detection limit of the nanoPCR assay was 2.7×10−6 ng/μL of PEDV RNA and no cross-reaction was observed with other viruses. This is the first report to demonstrate the application of a nanoPCR assay for the detection of PEDV. The sensitive and specific nanoPCR assay developed in this study can be applied widely in clinical diagnosis and field surveillance of PEDV-infection.


title: RT-PCR detection of respiratory pathogens in newborn children admitted to a neonatal medium care unit

text: BACKGROUND: This study aimed to determine the prevalence of respiratory pathogens among newborns admitted to a neonatal medium care unit (NMCU) and to identify clinical predictors. METHODS: A 1-y observational study was performed of neonates admitted to an NMCU in Amsterdam, The Netherlands. Nasopharyngeal samples were collected for the detection of respiratory viruses and bacteria by real-time PCR (RT-PCR). Cycle threshold (Ct) values were provided to estimate viral load. Predictors for the presence of study pathogens were identified. RESULTS: From October 2010 through September 2011, 334 neonates (median age 1.3 d, 53.6% male) were included. Overall, 37 respiratory pathogens were detected in 34 children (10.2%): parainfluenza-1 (n = 9), human rhinovirus (n = 7), parainfluenza-3 (n = 6), respiratory syncytial virus (RSV, n = 6), Streptococcus pneumoniae (n = 3), adenovirus (n = 2), human coronavirus (n = 2), influenza A (n = 1), and bocavirus (n = 1). Neonates with higher viral loads (Ct <35; n = 11) were more often clinically ill than those with lower viral loads (Ct ≥35; n = 23). Two variables significantly contributed to the detection of study pathogens: age (odds ratio (OR) 1.21 for each day older; 95% confidence interval 1.12–1.30) and rhinorrhea (OR 6.71; 95% confidence interval 1.54–29.21). CONCLUSION: Respiratory pathogens seem to play a role in neonates admitted to an NMCU. The influence of respiratory pathogen detection on clinical management remains to be determined.


title: Fast Virome Explorer: A Pipeline for Virus and Phage Identification and Abundance Profiling in Metagenomics Data

text: Identifying viruses and phages in a metagenomics sample has important implication in improving human health, preventing viral outbreaks, and developing personalized medicine. With the rapid increase in data files generated by next generation sequencing, existing tools for identifying and annotating viruses and phages in metagenomics samples suffer from expensive running time. In this paper, we developed a stand-alone pipeline, FastViromeExplorer, for rapid identification and abundance quantification of viruses and phages in big metagenomic data. Both real and simulated data validated FastViromeExplorer as a reliable tool to accurately identify viruses and their abundances in large data, as well as in a time efficient manner.


title: CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis

text: The Coronavirus Infectious Disease Ontology (CIDO) is a community-based ontology that supports coronavirus disease knowledge and data standardization, integration, sharing, and analysis.


title: Molecular characterization of a novel orthomyxovirus from rainbow and steelhead trout (Oncorhynchus mykiss)

text: Abstract A novel virus, rainbow trout orthomyxovirus (RbtOV), was isolated in 1997 and again in 2000 from commercially-reared rainbow trout (Oncorhynchus mykiss) in Idaho, USA. The virus grew optimally in the CHSE-214 cell line at 15°C producing a diffuse cytopathic effect; however, juvenile rainbow trout exposed to cell culture-grown virus showed no mortality or gross pathology. Electron microscopy of preparations from infected cell cultures revealed the presence of typical orthomyxovirus particles. The complete genome of RbtOV is comprised of eight linear segments of single-stranded, negative-sense RNA having highly conserved 5′ and 3′-terminal nucleotide sequences. Another virus isolated in 2014 from steelhead trout (also O. mykiss) in Wisconsin, USA, and designated SttOV was found to have eight genome segments with high amino acid sequence identities (89–99%) to the corresponding genes of RbtOV, suggesting these new viruses are isolates of the same virus species and may be more widespread than currently realized. The new isolates had the same genome segment order and the closest pairwise amino acid sequence identities of 16–42% with Infectious salmon anemia virus (ISAV), the type species and currently only member of the genus Isavirus in the family Orthomyxoviridae. However, pairwise comparisons of the predicted amino acid sequences of the 10 RbtOV and SttOV proteins with orthologs from representatives of the established orthomyxoviral genera and a phylogenetic analysis using the PB1 protein showed that while RbtOV and SttOV clustered most closely with ISAV, they diverged sufficiently to merit consideration as representatives of a novel genus. A set of PCR primers was designed using conserved regions of the PB1 gene to produce amplicons that may be sequenced for identification of similar fish orthomyxoviruses in the future.


Neuroleptic Malignant Syndrome in a COVID-19 Patient


title: How Viral Infections Cause Exacerbation of Airway Diseases

text: Exacerbations of asthma and COPD are major causes of morbidity, mortality, and health-care costs. Over the last decade, studies using new molecular diagnostic techniques have established that respiratory viruses are a major cause of exacerbations of both asthma and COPD. The most prevalent viruses detected during exacerbations are the rhinoviruses. Despite the burden of disease associated with exacerbations, little is known about the mechanisms of virus-induced exacerbations of airway diseases. Exacerbations are associated with increased airway inflammation in patients with both asthma and COPD, but many questions remain unanswered regarding the key inflammatory cells and mediators involved. Identifying the key inflammatory mediators involved in exacerbations holds the promise of developing diagnostic and prognostic markers of exacerbation. In addition, such studies can identify new therapeutic targets for the development of novel drugs for the prevention and treatment of exacerbations.


title: Headaches During COVID‐19: My Clinical Case and Review of the Literature

text: OBJECTIVE: To analyze headaches related to COVID‐19 based on personal case experience. BACKGROUND: COVID‐19 is an infection caused by the new coronavirus SARS‐CoV‐2. The first reported case happened in Wuhan on December 1, 2019. At present, at least 1.8 million people are infected around the world and almost 110,000 people have died. Many studies have analyzed the clinical picture of COVID‐19, but they are focused on respiratory symptoms and headache is generically treated. METHODS: I describe and discuss my headaches during my COVID‐19 and I review the MEDLINE literature about headaches and COVID‐19. RESULTS: More than 41,000 COVID‐19 patients have been included in clinical studies and headache was present in 8%‐12% of them. However, no headache characterization was made in these studies. As a headache expert and based on my own personal clinical case, headaches related to COVID‐19 can be classified in the 2 phases of the disease. Acute headache attributed to systemic viral infection, primary cough headache, tension‐type headache and headache attributed to heterophoria can appear in the first phase (the influenza‐like phase); and headache attributed to hypoxia and a new headache, difficult to fit into the ICHD3, can appear if the second phase (the cytokine storm phase) occurs. CONCLUSIONS: Several headaches can appear during COVID‐19 infection. All of them are headaches specified in the ICHD3, except 1 that occurs from the 7th day after the clinical onset. This headache is probably related to the cytokine storm that some patients suffer and it could be framed under the ICHD3 headache of Headache attributed to other non‐infectious inflammatory intracranial disease. Although the reported prevalence of headaches as a symptom of COVID‐19 infection is low, this experience shows that, very probably, it is underestimated.


title: Asthma and the Coronavirus Disease 2019 Pandemic: A Literature Review

text: Even though respiratory viruses are one of the most common triggers for asthma exacerbations, not all of these viruses affect patients equally. There is no strong evidence supporting that patients with asthma have a higher risk of becoming seriously ill from coronavirus disease 2019 (COVID-19), although recent reports from the USA and the UK suggest that asthma is much more common in children and adults with mild to severe COVID-19 than has previously been reported in Asia and in Europe. As in previous severe acute respiratory syndrome (SARS) outbreaks, patients with asthma, especially children, appear to be less susceptible to the coronavirus with a low rate of asthma exacerbations. A different expression of viral receptors and T2 inflammation can be responsible for different outcomes. Future studies focused on asthma and on other allergic disorders are needed to provide a greater understanding of the impact of underlying asthma and allergic inflammation on COVID-19 susceptibility and disease severity. However, for the moment, it is crucial that asthmatic patients maintain their controller medication, from inhaled corticosteroids to biologics, without making any dose adjustments on their own or stopping the medication. New data are emerging daily, rapidly updating our understanding of this novel coronavirus.


title: Middle East respiratory syndrome coronavirus specific antibodies in naturally exposed Israeli llamas, alpacas and camels

text: Thus far, no human MERS-CoV infections have been reported from Israel. Evidence for the circulation of MERS-CoV in dromedaries has been reported from almost all the countries of the Middle East, except Israel. Therefore, we aimed to analyze MERS-CoV infection in Israeli camelids, sampled between 2012 and 2017. A total of 411 camels, 102 alpacas and 19 llamas' sera were tested for the presence of antibodies to MERS-CoV. Our findings indicate a lower MERS-CoV seropositivity among Israeli dromedaries than in the surrounding countries, and for the first time naturally infected llamas were identified. In addition, nasal swabs of 661 camels, alpacas and lamas, obtained from January 2015 to December 2017, were tested for the presence of MERS-CoV RNA. All nasal swabs were negative, indicating no evidence for MERS-CoV active circulation in these camelids during that time period.


title: When Past Isn’t a Prologue: Adapting Informatics Practice During a Pandemic

text: Data and information technology are key to every aspect of our response to the current COVID-19 pandemic—from how we diagnose patients and deliver care, to the development of predictive models of disease spread, to the management of personnel and equipment. The increasing engagement of informaticians at the forefront of these efforts has been a fundamental shift: from an academic to an operational role. However, the past history of informatics as a scientific domain and an area of applied practice provides little guidance or prologue for the incredible challenges that we are now tasked with performing. Building upon our recent experiences, we present four critical lessons-learned that have helped shape our scalable, data-driven response to COVID-19. We describe each of these lessons within the context of specific solutions and strategies we applied in addressing the challenges that we faced.


title: Novel Virus Influenza A (H1N1sw) in South-Eastern France, April-August 2009

text: BACKGROUND: In April 2009, the first cases of pandemic (H1N1)-2009 influenza [H1N1sw] virus were detected in France. Virological surveillance was undertaken in reference laboratories of the seven French Defence Zones. METHODOLOGY/PRINCIPAL FINDINGS: We report results of virological analyses performed in the Public Hospitals of Marseille during the first months of the outbreak. (i) Nasal swabs were tested using rapid influenza diagnostic test (RIDT) and two RT-PCR assays. Epidemiological characteristics of the 99 first suspected cases were analyzed, including detection of influenza virus and 18 other respiratory viruses. During three months, a total of 1,815 patients were tested (including 236 patients infected H1N1sw virus) and distribution in age groups and results of RIDT were analyzed. (ii) 600 sera received before April 2009 and randomly selected from in-patients were tested by a standard hemagglutination inhibition assay for antibody to the novel H1N1sw virus. (iii) One early (May 2009) and one late (July 2009) viral isolates were characterized by sequencing the complete hemagglutinine and neuraminidase genes. (iiii) Epidemiological characteristics of a cluster of cases that occurred in July 2009 in a summer camp were analyzed. CONCLUSIONS/SIGNIFICANCE: This study presents new virological and epidemiological data regarding infection by the pandemic A/H1N1 virus in Europe. Distribution in age groups was found to be similar to that previously reported for seasonal H1N1. The first seroprevalence data made available for a European population suggest a previous exposure of individuals over 40 years old to influenza viruses antigenically related to the pandemic (H1N1)-2009 virus. Genomic analysis indicates that strains harbouring a new amino-acid pattern in the neuraminidase gene appeared secondarily and tended to supplant the first strains. Finally, in contrast with previous reports, our data support the use of RIDT for the detection of infection in children, especially in the context of the investigation of grouped cases.


title: RNase L Mediated Protection from Virus Induced Demyelination

text: IFN-α/β plays a critical role in limiting viral spread, restricting viral tropism and protecting mice from neurotropic coronavirus infection. However, the IFN-α/β dependent mechanisms underlying innate anti-viral functions within the CNS are poorly understood. The role of RNase L in viral encephalomyelitis was explored based on its functions in inhibiting translation, inducing apoptosis, and propagating the IFN-α/β pathway through RNA degradation intermediates. Infection of RNase L deficient (RL(−/−)) mice with a sub-lethal, demyelinating mouse hepatitis virus variant revealed that the majority of mice succumbed to infection by day 12 p.i. However, RNase L deficiency did not affect overall control of infectious virus, or diminish IFN-α/β expression in the CNS. Furthermore, increased morbidity and mortality could not be attributed to altered proinflammatory signals or composition of cells infiltrating the CNS. The unique phenotype of infected RL(−/−) mice was rather manifested in earlier onset and increased severity of demyelination and axonal damage in brain stem and spinal cord without evidence for enhanced neuronal infection. Increased tissue damage coincided with sustained brain stem infection, foci of microglia infection in grey matter, and increased apoptotic cells. These data demonstrate a novel protective role for RNase L in viral induced CNS encephalomyelitis, which is not reflected in overall viral control or propagation of IFN-α/β mediated signals. Protective function is rather associated with cell type specific and regional restriction of viral replication in grey matter and ameliorated neurodegeneration and demyelination.


title: Relationships Between Initial COVID-19 Risk Perceptions and Protective Health Behaviors: A National Survey

text: INTRODUCTION: Perceptions of health risks inform decisions about protective behaviors, but coronavirus disease 2019 (COVID-19) was an unfamiliar risk as it began to spread across the U.S. In the initial stage of the epidemic, authors examined perceived risks for COVID-19 infection and infection fatality, and whether these risk perceptions are associated with protective behaviors. They also examined whether findings differed between later versus earlier responders. METHODS: Between March 10 and 31, 2020, investigators conducted a cross-sectional online survey with a nationally representative U.S. sample (N=6,684). Half responded before March 13, 2020 (versus later). Participants assessed their risks of COVID-19 infection and infection fatality (0%–100%), and were transformed into quartiles (1–4). They reported their implementation of protective behaviors like handwashing and social distancing (yes/no). Analyses were conducted in April‒May 2020. RESULTS: Median perceived risk was 10.00% for COVID-19 infection and 5.00% for infection fatality, but respondents showed large disagreement. An increase of one quartile in perceived infection risk was associated with being 1.45 (95% CI=1.33, 1.58) more likely to report handwashing, with perceived infection fatality risk showing no significant association. When predicting social distancing behaviors such as avoiding crowds, both quartile-based risk perceptions were significant (OR=1.24, 95% CI=1.17, 1.30 for infection and OR=1.19, 95% CI=1.13, 1.26 for infection fatality). Perceived COVID-19 infection risk, protective behaviors, and their relationship increased among later (versus earlier) responders. CONCLUSIONS: Despite disagreements about the risks, people perceiving greater risks were more likely to implement protective behaviors—especially later (versus earlier) in March 2020. These findings have implications for risk communication.


title: Occurrence and sequence analysis of porcine deltacoronaviruses in southern China

text: BACKGROUND: Following the initial isolation of porcine deltacoronavirus (PDCoV) from pigs with diarrheal disease in the United States in 2014, the virus has been detected on swine farms in some provinces of China. To date, little is known about the molecular epidemiology of PDCoV in southern China where major swine production is operated. RESULTS: To investigate the prevalence of PDCoV in this region and compare its activity to other enteric disease of swine caused by porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis coronavirus (TGEV), and porcine rotavirus group C (Rota C), 390 fecal samples were collected from swine of various ages from 15 swine farms with reported diarrhea. Fecal samples were tested by reverse transcription-PCR (RT-PCR) that targeted PDCoV, PEDV, TGEV, and Rota C, respectively. PDCoV was detected exclusively from nursing piglets with an overall prevalence of approximate 1.28 % (5/390), not in suckling and fattening piglets. Interestingly, all of PDCoV-positive samples were from 2015 rather than 2012–2014. Despite a low detection rate, PDCoV emerged in each province/region of southern China. In addition, compared to TGEV (1.54 %, 5/390) or Rota C (1.28 %, 6/390), there were highly detection rates of PEDV (22.6 %, 88/390) in those samples. Notably, all five PDCoV-positive piglets were co-infected by PEDV. Furthermore, phylogenetic analysis of spike (S) and nucleocapsid (N) gene sequences of PDCoVs revealed that currently circulating PDCoVs in southern China were more closely related to other Chinese strains of PDCoVs than to those reported in United States, South Korea and Thailand. CONCLUSIONS: This study demonstrated that PDCoV was present in southern China despite the low prevalence, and supported an evolutionary theory of geographical clustering of PDCoVs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12985-016-0591-6) contains supplementary material, which is available to authorized users.


title: Respiratory syncytial virus and influenza virus infection in adult primary care patients: association of age with prevalence, diagnostic features and illness course

text: Abstract Objectives To better target new vaccines and treatments being developed for respiratory syncytial virus (RSV) and influenza virus (influenza), we studied the association of age with prevalence, diagnostic features and course of illness of these infections in primary care patients. Methods Secondary analysis of observational data on the aetiology, diagnosis and prognosis in adults presenting to primary care with acute cough in 12 European countries (2007-2010) using regression analyses corrected for clustering of patients within countries. Age groups were 18-59 years, 60-74 years, and 75 years and older (75+). Results Nasopharyngeal swabs for 144 (4.6%), 169 (5.4%) and 104 (3.4%) out of 3104 patients were polymerase chain reaction (PCR) positive for RSV, influenza A and influenza B, respectively. RSV-prevalence in patients 75+ (8.5%) was twice the prevalence in those under 60 years (4.2%). Influenza prevalence was not associated with age. Diagnostic features for these viruses were not associated with age. Symptom duration was associated with age for RSV and influenza B, but not for influenza A. The odds of unresolved symptoms after 28 days was associated with age for RSV only. Illness deterioration was associated with age for RSV, with patients 75+ at increased risk, but not for influenza. Conclusion In adults presenting to primary care with acute cough, the diagnostic features of RSV or influenza infection are not associated with age. For RSV both the prevalence and illness course are significantly worse at higher age, for influenza only the illness course is.


title: SARS‐CoV‐2: What do we know so far?

text: We are living in times where a viral disease has brought normal life in much of the world to a halt. Named after its causative agent, coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus recently renamed as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 manifests as dry cough, frequent fevers and in severe cases pneumonia. Older patients and patients with underlying comorbidities are at a higher risk of death. We are living in times where a viral disease has brought normal life in much of the world to a halt. Named after its causative agent, coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus recently renamed as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 manifests as dry cough, frequent fevers and in severe cases pneumonia.


title: Viral RNA load as determined by cell culture as a management tool for discharge of SARS-CoV-2 patients from infectious disease wards

text: In a preliminary clinical study, we observed that the combination of hydroxychloroquine and azithromycin was effective against SARS-CoV-2 by shortening the duration of viral load in Covid-19 patients. It is of paramount importance to define when a treated patient can be considered as no longer contagious. Correlation between successful isolation of virus in cell culture and Ct value of quantitative RT-PCR targeting E gene suggests that patients with Ct above 33–34 using our RT-PCR system are not contagious and thus can be discharged from hospital care or strict confinement for non-hospitalized patients.


Emerging Infections: What Have We Learned from SARS?


title: Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

text: The receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral attachment to ACE2 receptor, and is a major determinant of host range and a dominant target of neutralizing antibodies. Here we experimentally measure how all amino-acid mutations to the RBD affect expression of folded protein and its affinity for ACE2. Most mutations are deleterious for RBD expression and ACE2 binding, and we identify constrained regions on the RBD’s surface that may be desirable targets for vaccines and antibody-based therapeutics. But a substantial number of mutations are well tolerated or even enhance ACE2 binding, including at ACE2 interface residues that vary across SARS-related coronaviruses. However, we find no evidence that these ACE2-affinity enhancing mutations have been selected in current SARS-CoV-2 pandemic isolates. We present an interactive visualization and open analysis pipeline to facilitate use of our dataset for vaccine design and functional annotation of mutations observed during viral surveillance.


title: Dealing in deadly pathogens: Taking stock of the legal trade in live wildlife and potential risks to human health

text: Abstract Zoonotic diseases cause millions of deaths every year. Diseases such as Ebola, severe acute respiratory syndrome (SARS), and avian influenza cause economic losses at the global level and jeopardize diplomatic relations between countries. As wildlife are the source of at least 70% of all emerging diseases and given the on-going concerns associated with wildlife trade as a disease transmission mechanism, we provide a ‘global snapshot’ of the legal trade in live wild animals and take stock of the potential health risks that it poses to global human health. Our analysis showed that 11,569,796 individual live wild animals, representing 1316 different species were exported from 189 different countries between 2012 and 2016. China was the largest exporter of live mammals (with 98,979 animals representing 58.7% of global trade). Nicaragua was the largest exporter of live amphibians (with 122,592 animals representing 53.8% of global trade). South Africa was the largest exporter of live birds (with 889,607 animals representing 39.2% of global trade). Peru was the largest exporter of live reptiles (with 1,675,490 animals representing 18.8% of global trade). Our analysis showed that mostly the USA and other high-income countries, the largest importers, drive the live animal trade. High-income countries and not the countries where wildlife diseases and pathogens are more likely to occur reported almost all of the disease reports to the World Organisation for Animal Health. Based on our findings, we discuss how maximising trade bans; working on human behaviour change and improving regulatory efforts to improve surveillance will decrease the risk of future pandemics, epidemics and outbreaks.


title: Efficacy of an automated ultraviolet C device in a shared hospital bathroom

text: Toilet flushing can contribute to disease transmission by generating aerosolized bacteria and viruses that can land on nearby surfaces or follow air currents. Aerobic and anaerobic bacterial bioaerosol loads, and bacterial counts on 2 surfaces in a bathroom with a permanently installed, automated ultraviolet C (UVC) irradiation device, were significantly lower than in a comparable bathroom without the UVC device. Permanently installed UVC lights may be a useful supplementary decontamination tool in shared patient bathrooms.


title: Natural Killer Cell Receptor Genes in Camels: Another Mammalian Model

text: Due to production of special homodimeric heavy chain antibodies, somatic hypermutation of their T-cell receptor genes and unusually low diversity of their major histocompatibility complex genes, camels represent an important model for immunogenetic studies. Here, we analyzed genes encoding selected natural killer cell receptors with a special focus on genes encoding receptors for major histocompatibility complex (MHC) class I ligands in the two domestic camel species, Camelus dromedarius and Camelus bactrianus. Based on the dromedary genome assembly CamDro2, we characterized the genetic contents, organization, and variability of two complex genomic regions, the leukocyte receptor complex and the natural killer complex, along with the natural cytotoxicity receptor genes NCR1, NCR2, and NCR3. The genomic organization of the natural killer complex region of camels differs from cattle, the phylogenetically most closely related species. With its minimal set of KLR genes, it resembles this complex in the domestic pig. Similarly, the leukocyte receptor complex of camels is strikingly different from its cattle counterpart. With KIR pseudogenes and few LILR genes, it seems to be simpler than in the pig. The syntenies and protein sequences of the NCR1, NCR2, and NCR3 genes in the dromedary suggest that they could be human orthologues. However, only NCR1 and NCR2 have a structure of functional genes, while NCR3 appears to be a pseudogene. High sequence similarities between the two camel species as well as with the alpaca Vicugna pacos were observed. The polymorphism in all genes analyzed seems to be generally low, similar to the rest of the camel genomes. This first report on natural killer cell receptor genes in camelids adds new data to our understanding of specificities of the camel immune system and its functions, extends our genetic knowledge of the innate immune variation in dromedaries and Bactrian camels, and contributes to studies of natural killer cell receptors evolution in mammals.


DRAMÁTICO IMPACTO DE LA EPIDEMIA DE COVID-19 SOBRE LA ACTIVIDAD DE DONACIÓN Y TRASPLANTE EN ESPAÑA


COVID-19: don’t neglect antimicrobial stewardship principles!


title: An evaluation of a liquid antimicrobial (Sal CURB®) for reducing the risk of porcine epidemic diarrhea virus infection of naïve pigs during consumption of contaminated feed

text: BACKGROUND: Since its initial detection in May 2013, porcine epidemic diarrhea virus (PEDV) has spread rapidly throughout the US swine industry. Recently, contaminated feed was confirmed as a vehicle for PEDV infection of naïve piglets. This research provides in vivo data supporting the ability of a liquid antimicrobial product to reduce this risk. RESULTS: Sal CURB® (Kemin Industries, Des Moines, IA, USA) is a FDA-approved liquid antimicrobial used to control Salmonella contamination in poultry and swine diets. To test its effect against PEDV, Sal CURB®-treated feed was spiked with a stock isolate of PEDV (Ct = 25.22), which PEDV-naïve piglets were allowed to ingest via natural feeding behavior (ad libitum) for a 14-day period. For the purpose of a positive control, a separate group of piglets was allowed to ingest non-treated (Sal CURB®-free) feed also spiked with stock PEDV (Ct = 25.22). A negative control group received PEDV-free feed. Clinical signs of PEDV infection (vomiting and diarrhea) and viral shedding in feces were observed in the positive control group 2–3 days post-consumption of non-treated feed. In contrast, no evidence of infection was observed in pigs fed Sal CURB®-treated feed or in the negative controls throughout the 14-day study period. In addition, the Sal CURB®-treated feed samples had higher (p < 0.0001) mean PEDV Ct values than samples from the positive control group. CONCLUSIONS: These data provide proof of concept that feed treated with Sal CURB® can serve as a means to reduce the risk of PEDV infection through contaminated feed. Furthermore, the results from the positive control group provide additional proof of concept regarding the ability of contaminated feed to serve as a risk factor for PEDV infection of naïve piglets.