title: Total Chemical Synthesis of ISGylated-Ubiquitin Hybrid Chain Assisted by Acetamidomethyl Derivatives with Dual Functions

text: [Image: see text] Interferon-stimulated gene 15 (ISG15) is a member of the ubiquitin-like modifiers (ULM) family, which adopts a β-grasp fold domain(s) similar to ubiquitin (Ub) with only minor sequence homology. ISG15 consists of two Ub-like domains and aids the immune system in neutralizing infections by numerous pathogens and plays an important role in defending cells against many viruses including influenza A. Recently, Ub was found to be a substrate for ISG15, which can be ISGylated on Lys29 and Lys48, while the former is more dominant. The discovery of such hybrid ISG15-Ub chains brought forward various fundamental questions regarding the nature and effect of this conjugation. To further investigate the role of hybrid ISG15-Ub chains, the pure homogeneous material of these chains is needed in workable quantities. By applying advanced chemical strategies for protein synthesis, we report the total chemical synthesis of a 231-residue ISG15-Lys29-Ub hybrid chain. During the synthesis we encountered insoluble peptide fragments, and therefore we developed a new reversible Acm based solubilizing tag to efficiently tackle this hurdle. This new Acm tag was compared with the known Arg based Acm solubilizing tag and was found to be more reliable in terms of incorporation and efficiency as demonstrated in the synthesis of the native ISG15-Ub hybrid chain.


Infectious Diseases of the Nervous System and Their Impact in Developing Countries


title: Interferon-λ: immune functions at barrier surfaces and beyond

text: When type III interferon (IFN-λ; also known as interleukin-28 (IL-28) and IL-29) was discovered in 2003, its antiviral function was expected to be analogous to the type I IFNs (IFN-α and IFN-β), via the induction of IFN-stimulated genes (ISGs). While IFN-λ stimulates expression of antiviral ISGs preferentially in cells of epithelial origin, recent studies have defined additional antiviral mechanisms in other cell types and tissues. Models of viral infection using mice lacking IFN-λ signaling and single nucleotide polymorphism (SNP) associations with human disease have expanded our understanding of the contribution of IFN-λ to the antiviral response at anatomic barriers and the immune response beyond these barriers. In this review, we highlight recent insights into the functions of IFN-λ, including its ability to restrict virus spread into the brain and to clear chronic viral infections in the gastrointestinal tract. We also discuss how IFN-λ modulates innate and adaptive immunity, autoimmunity, and tumor progression and its possible therapeutic applications in human disease.


title: The Middle East Respiratory Syndrome—How Worried Should We Be?

text: Ten years after the severe acute respiratory syndrome epidemic, a second coronavirus, the Middle East respiratory syndrome coronavirus (MERS-CoV), has been identified as the cause of a highly lethal pneumonia in patients in the Middle East and in travelers from this region. Over the past 9 months, since the virus was first isolated, much has been learned about the biology of the virus. It is now clear that MERS-CoV is transmissible from person to person, and its close relationship with several bat coronaviruses suggests that these animals may be the ultimate source of the infection. However, many key issues need to be addressed, including identification of the proximate, presumably zoonotic, source of the infection, the prevalence of the infection in human populations, details regarding clinical and pathological features of the human infection, the establishment of a small rodent model for the infection, and the virological and immune basis for the severe disease observed in most patients. Most importantly, we do not know whether a MERS-CoV epidemic is likely or not. Infection with the virus has so far resulted in only 91 cases and 46 deaths (as of 29 July 2013), but it is nonetheless setting off alarm bells among public health officials, including Margaret Chan, Director-General of the World Health Organization, who called MERS-CoV “a threat to the entire world.” This article reviews some of the progress that has been made and discusses some of the questions that need to be answered.


title: A Simulation of a COVID-19 Epidemic Based on a Deterministic SEIR Model

text: An epidemic disease caused by a new coronavirus has spread in Northern Italy with a strong contagion rate. We implement an SEIR model to compute the infected population and the number of casualties of this epidemic. The example may ideally regard the situation in the Italian Region of Lombardy, where the epidemic started on February 24, but by no means attempts to perform a rigorous case study in view of the lack of suitable data and the uncertainty of the different parameters, namely, the variation of the degree of home isolation and social distancing as a function of time, the initial number of exposed individuals and infected people, the incubation and infectious periods, and the fatality rate. First, we perform an analysis of the results of the model by varying the parameters and initial conditions (in order for the epidemic to start, there should be at least one exposed or one infectious human). Then, we consider the Lombardy case and calibrate the model with the number of dead individuals to date (May 5, 2020) and constrain the parameters on the basis of values reported in the literature. The peak occurs at day 37 (March 31) approximately, with a reproduction ratio R(0) of 3 initially, 1.36 at day 22, and 0.8 after day 35, indicating different degrees of lockdown. The predicted death toll is approximately 15,600 casualties, with 2.7 million infected individuals at the end of the epidemic. The incubation period providing a better fit to the dead individuals is 4.25 days, and the infectious period is 4 days, with a fatality rate of 0.00144/day [values based on the reported (official) number of casualties]. The infection fatality rate (IFR) is 0.57%, and it is 2.37% if twice the reported number of casualties is assumed. However, these rates depend on the initial number of exposed individuals. If approximately nine times more individuals are exposed, there are three times more infected people at the end of the epidemic and IFR = 0.47%. If we relax these constraints and use a wider range of lower and upper bounds for the incubation and infectious periods, we observe that a higher incubation period (13 vs. 4.25 days) gives the same IFR (0.6 vs. 0.57%), but nine times more exposed individuals in the first case. Other choices of the set of parameters also provide a good fit to the data, but some of the results may not be realistic. Therefore, an accurate determination of the fatality rate and characteristics of the epidemic is subject to knowledge of the precise bounds of the parameters. Besides the specific example, the analysis proposed in this work shows how isolation measures, social distancing, and knowledge of the diffusion conditions help us to understand the dynamics of the epidemic. Hence, it is important to quantify the process to verify the effectiveness of the lockdown.


title: Liberation of SARS-CoV main protease from the viral polyprotein: N-terminal autocleavage does not depend on the mature dimerization mode

text: The main protease (M(pro)) plays a vital role in proteolytic processing of the polyproteins in the replicative cycle of SARS coronavirus (SARS-CoV). Dimerization of this enzyme has been shown to be indispensable for transcleavage activity. However, the auto-processing mechanism of M(pro), i.e. its own release from the polyproteins through autocleavage, remains unclear. This study elucidates the relationship between the N-terminal autocleavage activity and the dimerization of “immature” M(pro). Three residues (Arg4, Glu290, and Arg298), which contribute to the active dimer conformation of mature M(pro), are selected for mutational analyses. Surprisingly, all three mutants still perform N-terminal autocleavage, while the dimerization of mature protease and transcleavage activity following auto-processing are completely inhibited by the E290R and R298E mutations and partially so by the R4E mutation. Furthermore, the mature E290R mutant can resume N-terminal autocleavage activity when mixed with the “immature” C145A/E290R double mutant whereas its trans-cleavage activity remains absent. Therefore, the N-terminal auto-processing of M(pro) appears to require only two “immature” monomers approaching one another to form an “intermediate” dimer structure and does not strictly depend on the active dimer conformation existing in mature protease. In conclusion, an auto-release model of M(pro) from the polyproteins is proposed, which will help understand the auto-processing mechanism and the difference between the autocleavage and trans-cleavage proteolytic activities of SARS-CoV M(pro).


title: SARS-CoV-2-specific T cells exhibit unique features characterized by robust helper function, lack of terminal differentiation, and high proliferative potential

text: Convalescing COVID-19 patients mount robust T cell responses against SARS-CoV-2, suggesting an important role for T cells in viral clearance. To date, the phenotypes of SARS-CoV-2-specific T cells remain poorly defined. Using 38-parameter CyTOF, we phenotyped longitudinal specimens of SARS-CoV-2-specific CD4+ and CD8+ T cells from four individuals who recovered from mild COVID-19. SARS-CoV-2-specific CD4+ T cells were exclusively Th1 cells, and predominantly Tcm with phenotypic features of robust helper function. SARS-CoV-2-specific CD8+ T cells were predominantly atypical Temra cells in a state of less terminal differentiation and therefore capable of expansion. Subsets of SARS-CoV-2-specific T cells exhibit features of being long-lived and capable of homeostatic proliferation consistent with their persistence for over two months. Our results suggest that long-lived and robust T cell immunity is generated following natural SARS-CoV-2 infection, and support an important role for SARS-CoV-2-specific T cells in host control of COVID-19.


title: A new recruit for the army of the men of death

text: The army of the men of death, in John Bunyan's memorable phrase, has a new recruit, and fear has a new face: a face wearing a surgical mask.


RNA pseudoknots that interact with components of the translation apparatus


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title: Chapter 2 Standard Precautions


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title: Survival in a zombie apocalypse

text: The Resident Evil 3 remake was in development long before the coronavirus outbreak, but it holds up a mirror to the strange times we live in today, says Jacob Aron


title: Monoclonal antibodies for prophylactic and therapeutic use against viral infections

text: Abstract Neutralizing antibodies play an essential part in antiviral immunity and are instrumental in preventing or modulating viral diseases. Polyclonal antibody preparations are increasingly being replaced by highly potent monoclonal antibodies (mAbs). Cocktails of mAbs and bispecific constructs can be used to simultaneously target multiple viral epitopes and to overcome issues of neutralization escape. Advances in antibody engineering have led to a large array of novel mAb formats, while deeper insight into the biology of several viruses and increasing knowledge of their neutralizing epitopes has extended the list of potential targets. In addition, progress in developing inexpensive production platforms will make antiviral mAbs more widely available and affordable.


Non-SARS CoV2 positive critical patients: sons of a lesser God?


title: Tracheostomy protocols during COVID‐19 pandemic

text: BACKGROUND: The COVID‐19 pandemic has resulted in the implementation of rapidly changing protocols and guidelines related to the indications and perioperative precautions and protocols for tracheostomy. The purpose of this study was to evaluate current guidelines for tracheostomy during the COVID‐19 pandemic to provide a framework for health systems to prepare as the science evolves over the upcoming months and years. METHODS: Literature review was performed. Articles reporting clinical practice guidelines for tracheostomy in the context of COVID‐19 were included. RESULTS: A total of 13 tracheotomy guidelines were identified. Two were available via PubMed, five in society or organization websites, and six identified via health system websites or other sources. Five were from Otolaryngology‐Head and Neck Surgery specialties, six from Anesthesiology and one from Pulmonary/Critical Care. All (100%) studies recommended postponing elective OR cases in COVID‐19 positive patients, while seven recommended reducing team members to only essential staff and three recommended forming a designated tracheostomy team. Recommendations with supporting references are summarized in the article. CONCLUSIONS: Tracheostomy guidelines during the COVID‐19 pandemic vary by physician groups and specialty, hospital systems, and supply‐chain/resource availability. This summary is provided as a point‐in‐time current state of the guidelines for tracheotomy management in April 2020 and is expected to change in coming weeks and months as the COVID‐19 pandemic, virus testing and antibody testing evolves.


title: Mortality and the use of Antithrombotic Therapies among Nursing Home Residents with COVID‐19

text: BACKGROUND/OBJECTIVES: Nursing home (NH) residents are a vulnerable population, susceptible to respiratory disease outbreaks such as coronavirus disease 2019 (COVID‐19). Poor outcome in COVID‐19 is at least partly attributed to hypercoagulability, resulting in a high incidence of thromboembolic complications. It is unknown whether commonly used antithrombotic therapies may protect the vulnerable NH population with COVID‐19 against mortality. This study aimed to investigate whether the use of oral antithrombotic therapy (OAT) was associated with a lower mortality in NH residents with COVID‐19. DESIGN: A retrospective case‐series SETTING: 14 NH facilities from the NH organization Envida, Maastricht, the Netherlands PARTICIPANTS: 101 NH residents with COVID‐19 were enrolled. MEASUREMENTS: The primary outcome was all‐cause mortality. The association between age, sex, comorbidity, OAT, and mortality was assessed using logistic regression analysis. RESULTS: Overall mortality was 47.5% in NH residents from 14 NH facilities. Age, comorbidity and medication use were comparable among NH residents who survived and who died. OAT was associated with a lower mortality in NH residents with COVID‐19 in the univariable analysis (OR 0.89 95%CI 0.41‐1.95). However, additional adjustments for sex, age and comorbidity, attenuated this difference. Mortality in males was higher compared with female residents (OR 3.96 (95%CI 1.62‐9.65)). Male residents who died were younger compared to female residents (82.2 (SD 6.3) vs. 89.1 years (SD 6.8), p<.001). CONCLUSION: NH residents in the 14 facilities we studied were severely affected by the COVID‐19 pandemic, with a mortality of 47.5%. Male NH residents with COVID‐19 had worse outcomes than females. We did not find evidence for any protection against mortality by OAT, necessitating further research into strategies to mitigate poor outcome of COVID‐19 in vulnerable NH populations. This article is protected by copyright. All rights reserved.


title: International cooperation during the COVID-19 pandemic

text: This paper explores the concept of ‘global public goods’ (GPGs) in the context of the ongoing COVID-19 pandemic. It argues that many of the tasks involved in public health, and in particular those involved in the control of an infectious disease like COVID-19, ought to be treated as GPGs that can only be effectively delivered through international cooperation. It sets out what a cooperative response to the COVID-19 pandemic should look like and introduces ideas for further discussion about how it might be financed.


COVID-19 in pediatric patients: what the prehospital teams need to know


title: Molecular Insights into Poly(ADP-ribose) Recognition and Processing

text: Poly(ADP-ribosyl)ation is a post-translational protein modification involved in the regulation of important cellular functions including DNA repair, transcription, mitosis and apoptosis. The amount of poly(ADP-ribosyl)ation (PAR) in cells reflects the balance of synthesis, mediated by the PARP protein family, and degradation, which is catalyzed by a glycohydrolase, PARG. Many of the proteins mediating PAR metabolism possess specialised high affinity PAR-binding modules that allow the efficient sensing or processing of the PAR signal. The identification of four such PAR-binding modules and the characterization of a number of proteins utilising these elements during the last decade has provided important insights into how PAR regulates different cellular activities. The macrodomain represents a unique PAR-binding module which is, in some instances, known to possess enzymatic activity on ADP-ribose derivatives (in addition to PAR-binding). The most recently discovered example for this is the PARG protein, and several available PARG structures have provided an understanding into how the PARG macrodomain evolved into a major enzyme that maintains PAR homeostasis in living cells.


title: Domestication and the behavior-genetic analysis of captive populations

text: Abstract Captive environments are believed to produce behavioral changes in animal populations that may limit our ability to generalize back to natural populations. These behavioral changes are thought to be associated with one or both of the following: (a) changes in frequencies of genes or gene complexes due to the effects of inbreeding or to changes in selection pressure; (b) changes in development of the phenotype due to the effects of changes in environmental variables. Inbreeding leads to increase in homozygosity, that may result in developmental anomalies because of a breakdown in developmental homeostasis. Changes in selection pressure may disrupt coadapted gene complexes that have evolved in the wild. Often, domestication is believed to result in individuals that are “degenerate”; i.e. inferior to individuals in the wild. However, this notion has received no empirical support. In fact, if phenotype changes do occur under domestication, these are usually quantitative, not qualitative, in nature. We suggest that the study of the domestication process may reveal evolutionary principles that would be difficult to discover in other ways, and the zoological parks may be ideal situations for such research.


title: Reverse transcription polymerase chain reaction (RT‐PCR) for diagnosis of respiratory syncytial virus infection in adults: Use of a single‐tube “hanging droplet” nested PCR

text: Rapid diagnosis of Respiratory Syncytial virus (RSV) infection is difficult in elderly persons due to the low quantities of virus shed. Therefore, reverse transcription‐polymerase chain reaction (RT‐PCR) was used to detect viral RNA in respiratory secretions. A single‐tube nested RT‐PCR that used primers from a conserved F gene sequence was developed using a “hanging droplet” to physically separate outer and inner primer pairs during the first round of the PCR reaction. This was accomplished by placing the inner primers in a 5 μL droplet on the underside on the reaction tube cap and mixing after the first round of PCR. As few as 0.05 pfu of virus could be detected and gave positive results with RSV strains that represented the major groups and subgroups of RSV grown in tissue culture. The nested PCR was ∼100‐fold more sensitive than standard single primer PCR reactions and equivalent to standard two‐tube nested PCR. Viral RNA was detected in nasopharyngeal samples from 12 of 15 culture positive illnesses and in 5 of 17 culture‐negative, seropositive illnesses despite specimen volumes less than 1 μL in some samples. The method was also positive in 14 of 25 elderly volunteers inoculated with a live attenuated RSV vaccine candidate, only one of whom was culture positive. Use of a nested RT‐PCR significantly improves the ability to detect RSV in respiratory samples and should improve the ability to rapidly diagnose RSV infection in adults, especially in the elderly. J. Med. Virol. 63:259–263, 2001. © 2001 Wiley‐Liss, Inc.


title: Learning from Ebola: Interprofessional practice in the Nebraska Biocontainment Unit

text: Abstract Caring for patients with Ebola virus disease (EVD) in the Nebraska Biocontainment Unit (NBU) has necessitated and enabled extensive interprofessional relationships and the creation of a collaborative care model. Critical aspects of NBU functionality include a constructive leadership environment, staff inclusion and consideration during protocol development, and a culture of partnership and communication.


Position Paper: EUFEPS Network on Veterinary Medicines Initiative


Preserving the “human touch” in times of COVID-19


title: Tackling the Global Challenge: Humanitarian Catastrophes

text: “Humanitarian catastrophes,” conflicts and calamities generating both widespread human suffering and destructive events, require a wide range of emergency resources. This paper answers a number of questions that humanitarian catastrophes generate: Why and how do the most-developed countries—those with the resources, capabilities, and willingness to help—intervene in specific types of disasters? What ethical and legal guidelines shape our interventions? How well do we achieve our goals? It then suggests a number of changes to improve humanitarian responses, including better NGO-government cooperation, increased research on the best disaster response methods, clarification of the criteria and roles for humanitarian (military) interventions, and development of post-2015 Millennium Development Goals with more accurate progress measures.


title: An update on feline infectious peritonitis: Diagnostics and therapeutics

text: Abstract This review is concerned with what has been learned about feline infectious peritonitis (FIP) diagnostics and therapeutics since the publication of an extensive overview of literature covering the period 1963–2009. Although progress has been made in both areas, obtaining a definitive diagnosis of FIP remains a problem for those veterinarians and/or cat owners who require absolute certainty. This review will cover both indirect and direct diagnostic tests for the disease and will emphasize their limitations, as well as their specificity and sensitivity. There is still no effective treatment for FIP, although there are both claims that such therapies exist and glimmers of hope coming from new therapies that are under research. FIP has also been identified in wild felids and FIP-like disease is now a growing problem among pet ferrets.


title: Dynamics of an SEIR model with infectivity in incubation period and homestead-isolation on the susceptible

text: Abstract In this paper, we presents an SEIR epidemic model with infectivity in incubation period and homestead-isolation on the susceptible. We prove that the infection-free equilibrium point is locally and globally asymptotically stable with condition R 0 < 1 . We also prove that the positive equilibrium point is locally and globally asymptotically stable with condition R 0 > 1 . Numerical simulations are employed to illustrate our results. In the absence of vaccines or antiviral drugs for the virus, our results suggest that the governments should strictly implement the isolation system to make every effort to curb propagation of disease during the epidemic.


title: 2 US federal oversight of biological materials and the IBC

text: Abstract This chapter will give a thorough overview of the laws and guidelines regulating research use of biological materials in the United States and how Institutional Biosafety Committees (IBC) came to be tasked with providing oversight for these activities. The anthrax attacks after 9/11 demonstrated that information gained from life science research can be used to threaten national security and public health. Since these attacks, the public has demanded increased oversight of research. IBC oversight falls under the National Institutes of Health Guidelines. Over the years, other federal agencies have increased the demands on the IBC by promulgating new legislation and regulations. The following agencies play a role in regulating research: National Science Advisory Board for Biosecurity, National Research Council, National Institutes of Health, Food and Drug Administration, Environmental Protection Agency, Department of Human and Health Services, U.S. Department of Agriculture, and Department of Justice.


title: Cholesterol Supplementation During Production Increases the Infectivity of Retroviral and Lentiviral Vectors Pseudotyped with the Vesicular Stomatitis Virus Glycoprotein (VSV-G)

text: Cholesterol, a major component of plasma membrane lipid rafts, is important for assembly and budding of enveloped viruses, including influenza and HIV-1. Cholesterol depletion impairs virus assembly and infectivity. This study examined the effects of exogenous cholesterol addition (delivered as a complex with methyl beta cyclodextrin) on the production of Molony murine leukemia virus retroviral vector and HIV-1-based lentiviral vector pseudotyped with the vesicular stomatitis virus glycoprotein (VSV-G). Cholesterol supplementation before and during vector production enhanced the infectivity of retroviral and lentiviral vectors up to 4-fold and 6-fold, respectively. In contrast, the amount of retroviral vector produced was unchanged, and that of lentiviral vector was increased less than two-fold. Both free cholesterol and cholesterol ester content in 293-gag-pol producer cells increased with cholesterol addition. In contrast, the phospholipids headgroup composition was essentially unchanged by cholesterol supplementation in 293-gag-pol packaging cells. Based on these results, it is proposed that cholesterol supplementation increases the infectivity of VSV-G-pseudotyped retroviral and lentiviral vectors, possibly by altering the composition of the producer cell membrane where the viral vectors are assembled and bud, and/or by changing the lipid composition of the viral vectors.


Human metapneumovirus infection in children hospitalized for wheezing


title: Fine-tuning of type I IFN-signaling in microglia — implications for homeostasis, CNS autoimmunity and interferonopathies

text: Type I interferons (IFN) are pleiotropic cytokines originally described as molecules used for communication between cells to trigger the protective defenses against viral infections. Upon activation, type I IFN can be produced locally in the central nervous system (CNS) from a number of different cell types including microglia, the CNS-resident macrophages. Increased type I IFN production and signaling in microglia are critically important to limit viral infection and disease progression in multiple sclerosis. However, recent findings suggest that even baseline levels of constitutive IFN expression and secretion are important for homeostasis of the CNS. In fact, in the absence of viral particles chronic elevation of IFN I may be tremendously harmful for the CNS, as assumed for patients suffering from Aicardi-Goutières syndrome, Cree encephalitis or other type I interferonopathies. The highly diverse nature of type I IFN for brain homeostasis during health and disease will be discussed in this report.


title: The devolution of the social licence to operate in the Australian mining industry

text: The aim of this paper is to present a brief historical analysis of the Australian mining industry and the development of its social licence to operate. Commencing with the discovery of coal in the 18th century, to gold and copper and base metals in the 19th century, to the world class iron ore, mineral sands and diamond mines of the 20th century to the current day, the paper will attempt to determine how and why an industry, formerly well-respected by the public, is considered to be a pariah in the eyes of many sections of society. The theory of social licence and its use in the Australian minerals industry is briefly described and a working definition of “an honest, transparent engagement resulting in a beneficial outcome to all parties before, during and after mining” is adopted throughout the paper. Case studies illustrating examples where mining operations were, and continue to be sustained for decades, provide clear evidence of having a social licence to operate. On the other hand, examples are provided illustrating where poor environmental management practices, tailings dam failures, disputes with landowners, and/or government intervention have resulted in the loss of the social licence and early, unplanned closure. The paradox is that despite the industry's acknowledged contribution to the Australian economy, particularly in times of global ructions such as the GFC and the current coronavirus pandemic, there is considerable antipathy towards the industry by the public. Furthermore, the Australian mining industry's approach to environmental management and sustainable development is regularly used as a model for emerging mining economies. The industry has pioneered remediation and rehabilitation on challenging sites, including prime agricultural land, forests, riverine and beach environments. Successes are rarely acknowledged however but failures are highlighted, by the media, opponents of the industry, and governments. Clearly, the business as usual approach is not enough. Mining industry leaders need to take strong measures to ensure the industry is sustainable and maintains its social licence including eliminating all fatalities and serious injuries, ensuring the safety and stability of tailings storage facilities, accelerating progressive rehabilitation particularly on open cut coal mines, successfully closing mines, and lifting the environmental performance of all mines, not just a few.


title: Factores relacionados con el contagio por SARS-CoV-2 en profesionales de la salud en España. Proyecto SANICOVI

text: ABSTRACT Objective: To describe the factors related to the situation of SARS-CoV-2 transmission identified by health professionals in Spain and to propose prevention strategies. Method: Cross-sectional descriptive study. The population were healthcare professionals working in institutions caring for COVID-19 patients and also confirmed cases of SARS-CoV-2 infection. A questionnaire with sociodemographic, occupational and epidemiological variables was used. Descriptive and bivariate analysis was performed according to the nature of the variables. Results: Twenty-two hundred and thirty questionnaires were analysed on a potential population of 41,239 (5.47%). The diagnosis was made based on a suspicious case (63.4%) and a probable case (12.3%). A study of contacts was carried out at 50.3%. The perception about the availability of protective measures as "always/frequently" were: FPP1 mask 57.3%, gloves 89.5%, soap 95% and hydroalcoholic solution 91.5%. In PPE, FPP2, FPP3 mask, goggles and disposable gowns at around 50%. The availability of protective measures, by field of work, presented significant differences. The average number of patients attended related to the performance of hand hygiene at moment 4 and the perception of performing it correctly at moments 4 and 5. Conclusions: Preliminary data are presented, with variability in the response rate by Autonomous Region. Healthcare professionals infected by SARS-CoV-2 identified the management of the chain of infection transmission, the use and adequacy of protective equipment, as well as the effectiveness of handwashing as factors related to the transmission of the virus among professionals.


title: When there is a pandemic there is no time to waste: should we have hydroxychloroquine in our armoury against COVID-19 infected patients?

text: The current use of chloroquine and/or hydroxychloroquine, a drug currently used to treat autoimmune rheumatic diseases, in treating severe acute respiratory syndrome caused by coronavirus 2 (SARSCoV-2) or COVID-19-infected patients with pneumonia is a matter of intense consideration. We wish to enter the ongoing debate as to whether this well-known drug must be given to Greek COVID-19-infected patients, especially those with pneumonia. Our arguments are based on the existing data and the capacity of the Greek health system to afford potent anti-viral treatments, which are under immense investigation. We propose several suggestions related to treatment of COVID-19 pneumonia with chloroquine/hydroxychloroquine that we think must be taken into consideration to fit the evolving situation of the pandemic in Greece.


title: Coronavirus NSP6 restricts autophagosome expansion

text: Autophagy is a cellular response to starvation that generates autophagosomes to carry long-lived proteins and cellular organelles to lysosomes for degradation. Activation of autophagy by viruses can provide an innate defense against infection, and for (+) strand RNA viruses autophagosomes can facilitate assembly of replicase proteins. We demonstrated that nonstructural protein (NSP) 6 of the avian coronavirus, infectious bronchitis virus (IBV), generates autophagosomes from the ER. A statistical analysis of MAP1LC3B puncta showed that NSP6 induced greater numbers of autophagosomes per cell compared with starvation, but the autophagosomes induced by NSP6 had smaller diameters compared with starvation controls. Small diameter autophagosomes were also induced by infection of cells with IBV, and by NSP6 proteins of MHV and SARS and NSP5, NSP6, and NSP7 of arterivirus PRRSV. Analysis of WIPI2 puncta induced by NSP6 suggests that NSP6 limits autophagosome diameter at the point of omegasome formation. IBV NSP6 also limited autophagosome and omegasome expansion in response to starvation and Torin1 and could therefore limit the size of autophagosomes induced following inhibition of MTOR signaling, as well as those induced independently by the NSP6 protein itself. MAP1LC3B-puncta induced by NSP6 contained SQSTM1, which suggests they can incorporate autophagy cargos. However, NSP6 inhibited the autophagosome/lysosome expansion normally seen following starvation. Taken together the results show that coronavirus NSP6 proteins limit autophagosome expansion, whether they are induced directly by the NSP6 protein, or indirectly by starvation or chemical inhibition of MTOR signaling. This may favor coronavirus infection by compromising the ability of autophagosomes to deliver viral components to lysosomes for degradation.


The COVID‐19 Pandemic Illuminates Persistent and Emerging Disparities among Rural Black Populations


title: Knowledge, Attitude, and Practices Toward COVID-19 in Primary Healthcare Providers: A Cross-Sectional Study from Three Tertiary Care Hospitals of Peshawar, Pakistan

text: An online cross-sectional study was carried out to evaluate the knowledge, attitude, and practice about coronavirus disease 2019 (COVID-19) among primary health care providers (PHPs) at three tertiary care hospital, Peshawar, Pakistan. Data was collected via email and online social media platforms. Statistical package for social science (SPSS) version 25.0 was used for data analysis. Among the total participants (n = 114), 74 (66.7%) were male and 37 (33.3%) were female. The mean scores for knowledge, attitude and practice were 12.7 ± 0.89, 8.9 ± 4.1 and 7.3 ± 1.2, respectively. Most of the participants knew the term COVID-19 and its mode of transmission (90%), signs and symptoms (84%) and risk factors (72%) associated with it. Most of the participants agreed that COVID-19 can be transmitted through coughing and sneezing (74.3%) and 84.6% were in favor that COVID-19 can be prevented by adopting preventive measures. Around 68.8% of the participants disagreed with the use of antibiotics in the prevention of COVID-19. Ninety percent of the respondents were avoiding close contact with the people having cough and flu-like symptoms. Most PHPs had good knowledge, positive attitude and reasonable practices regarding COVID-19. Moreover, focused training programs for PHPs at the Government level can further improve their understanding of risks and preventive strategies related to COVID-19, which will help them to provide appropriate care to their patients as well as to protect themselves from this infection.


title: Safety and Efficacy of 0.5% Carbomer 980 Gel for Treatment of Symptoms of Common Cold: Results of 2 Randomized Trials

text: BACKGROUND: Two studies of intranasal 0.5% carbomer 980 gel were conducted evaluating nasal tolerability in healthy volunteers and safety and efficacy in adults with common cold symptoms. METHODS: Study 1 randomly assigned healthy adults to 0.5% carbomer 980 gel (n = 20) or placebo (n = 10) administered intranasally four times daily for 7 days. Nasal examinations were conducted at baseline and daily throughout the study. The primary endpoint was local nasal tolerability. Study 2 randomly assigned adults with an investigator-confirmed diagnosis of symptomatic common cold to 0.5% carbomer 980 gel (n = 87) or placebo (n = 81), administered intranasally four times daily for 7 days (except for day 1, where subjects who received their first dose mid-day administered only three doses). The primary efficacy endpoint was the average nasal symptom score over days 1‒4 (ANSS(1–4)). Secondary efficacy endpoints included ANSS over days 1‒7 and average total symptom score (ATSS). Adverse events (AEs) were recorded throughout the study. RESULTS: In study 1, subjects assigned to 0.5% carbomer 980 gel had no mucosal grading higher than grade 1B (superficial nasal mucosal erosion) and low incidences of mucosal bleeding and crusting. In study 2, there were no statistically significant differences between treatments for any efficacy endpoints. Active treatment was well-tolerated; the most commonly reported AEs were headache, myalgia, and cough. CONCLUSION: While 0.5% carbomer 980 gel nasal spray demonstrated good local nasal tolerability in healthy volunteers, the spray did not significantly impact the course of infection or resolution of cold symptoms in subjects with common cold.


title: Ebola virus secreted glycoprotein decreases the anti-viral immunity of macrophages in early inflammatory responses

text: Abstract During Ebola virus (EBOV) infection, secreted glycoprotein (sGP) is found in large quantities in the serum of both patients and infected animal models. It is thought to serve as a decoy for anti-EBOV antibodies. Using an in vitro model incorporating treatment of non-infected human THP-1 macrophages with recombinant EBOV sGP, this study sought to examine the impact of sGP upon key macrophage functions. Macrophage polarization and phagocytic capacity of activated macrophages were found to be unaltered by sGP treatment. However, treatment with sGP inhibited macrophage production of the pro-inflammatory cytokines TNFα and IL-6 while the yield of anti-inflammatory cytokine, IL-10, remained intact. Interestingly, the migratory ability of macrophages was also diminished by sGP, potentially due to a decrease in expression of CD11b, a vital macrophage integrin. Thus, EBOV sGP may operate to diminish functional contributions of non-infected macrophages to increase the potential viral dissemination.


title: T cell mediated suppression of neurotropic coronavirus replication in neural precursor cells

text: Abstract Neural precursor cells (NPCs) are the subject of intense investigation for their potential to treat neurodegenerative disorders, yet the consequences of neuroinvasive virus infection of NPCs remain unclear. This study demonstrates that NPCs support replication following infection by the neurotropic JHM strain of mouse hepatitis virus (JHMV). JHMV infection leads to increased cell death and dampens IFN-γ-induced MHC class II expression. Importantly, cytokines secreted by CD4+ T cells inhibit JHMV replication in NPCs, and CD8+ T cells specifically target viral peptide-pulsed NPCs for lysis. Furthermore, treatment with IFN-γ inhibits JHMV replication in a dose-dependent manner. Together, these findings suggest that T cells play a critical role in controlling replication of a neurotropic virus in NPCs, a finding which has important implications when considering immune modulation for NPC-based therapies for treatment of human neurologic diseases.


title: COVID-19 patients and the radiology department – advice from the European Society of Radiology (ESR) and the European Society of Thoracic Imaging (ESTI)

text: ABSTRACT: This document from the European Society of Radiology (ESR) and the European Society of Thoracic Imaging (ESTI) aims to present the main imaging features, and the role of CT scan in the early diagnosis of COVID-19, describing, in particular, the typical findings which make it possible to identify the disease and distinguish it from bacterial causes of infection, and to define which category of patients may benefit from CT imaging. The precautions that must be taken when performing scans to protect radiologists and technologists from infection will be described. The organisational measures that can be taken within radiology departments in order to cope with the influx of patients, while continuing to manage other emergency and time-sensitive activity (e.g. oncology, other infectious diseases etc.), will be discussed. KEY POINTS: • Bilateral ground glass opacities are typical CT manifestations of COVID-19. • Crazy paving and organising pneumonia pattern are seen at a later stage. • Extensive consolidation is associated with a poor prognosis.


title: Chapter Nine Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral”

text: Abstract Computer-assisted technologies of the genomic structure, biological function, and evolution of viruses remain a largely neglected area of research. The attention of bioinformaticians to this challenging field is currently unsatisfying in respect to its medical and biological importance. The power of new genome sequencing technologies, associated with new tools to handle “big data”, provides unprecedented opportunities to address fundamental questions in virology. Here, we present an overview of the current technologies, challenges, and advantages of Next-Generation Sequencing (NGS) in relation to the field of virology. We present how viral sequences can be detected de novo out of current short-read NGS data. Furthermore, we discuss the challenges and applications of viral quasispecies and how secondary structures, commonly shaped by RNA viruses, can be computationally predicted. The phylogenetic analysis of viruses, as another ubiquitous field in virology, forms an essential element of describing viral epidemics and challenges current algorithms. Recently, the first specialized virus-bioinformatic organizations have been established. We need to bring together virologists and bioinformaticians and provide a platform for the implementation of interdisciplinary collaborative projects at local and international scales. Above all, there is an urgent need for dedicated software tools to tackle various challenges in virology.


Disrupting the Disruption: Using Digital Tools to Support Psychiatry Residency Training in Singapore During the COVID-19 Pandemic


title: SARS-associated Coronavirus Transmission, United States

text: To better assess the risk for transmission of the severe acute respiratory syndrome–associated coronavirus (SARS-CoV), we obtained serial specimens and clinical and exposure data from seven confirmed U.S. SARS patients and their 10 household contacts. SARS-CoV was detected in a day-14 sputum specimen from one case-patient and in five stool specimens from two case-patients. In one case-patient, SARS-CoV persisted in stool for at least 26 days after symptom onset. The highest amounts of virus were in the day-14 sputum sample and a day-14 stool sample. Residual respiratory symptoms were still present in recovered SARS case-patients 2 months after illness onset. Possible transmission of SARS-CoV occurred in one household contact, but this person had also traveled to a SARS-affected area. The data suggest that SARS-CoV is not always transmitted efficiently. Laboratory diagnosis of SARS-CoV infection is difficult; thus, sputum and stool specimens should be included in the diagnostic work-up for SARS-CoV infection.


title: Complete Genome Sequencing of a Novel Strain of Sapelovirus A Circulating in Vietnam

text: Sapelovirus A (SV-A) is currently spreading as an enteric pathogen of pigs worldwide. We isolated SV-A strain XTND/2018 from the small intestine of a dead pig with severe diarrhea in the north of Vietnam and determined the genomic sequence. This is the first report of the genomic sequence of SV-A circulating in Vietnam.


title: Ebola virus disease: The use of fluorescents as markers of contamination for personal protective equipment

text: The recent Ebola virus disease (EVD) outbreak has created interest in personal protective equipment (PPE) content and usage. PPE testing has historically been done by individual component, rather than as a bundle for contact isolation. Fluorescent agents are commonly used in training for infection control techniques. The purpose of our study was to compare 2 PPE bundles and to evaluate the feasibility of fluorescent markers as an assessment tool for PPE effectiveness. Eight healthcare providers volunteered for this preliminary study. Participants were randomized to 1 of 2 PPE bundles that meet current (October 20, 2014) CDC recommendations. One PPE bundle utilized commercial EVD-recommended components. The other PPE bundle used components already available at local hospitals or retail stores. Participants were also randomized to standard or high volume exposures (HVE) to simulate fluid splash. Each participant was assisted in PPE donning and doffing by an experienced trainer. A training mannequin was contaminated with fluorescent agents to simulate bodily fluids. Participants were then given clinical tasks to care for the EVD “patient.” De-gowned participants were examined under “black light” for fluorescence indicative of contamination. One participant in each PPE arm had evidence of contamination. One of the contamination events was suspected during the patient care exercise. The other contamination event was not suspected until black light examination. In spite of a large difference in cost of PPE, the two bundle arms performed similarly. Bundle testing using fluorescent markers could help identify optimal PPE systems.


title: Phages Bearing Affinity Peptides to Bovine Rotavirus Differentiate the Virus from Other Viruses

text: The aim of this study was to identify potential ligands and develop a novel diagnostic test to pathogenic bovine rotavirus (BRV) using phage display technology. The viruses were used as an immobilized target followed by incubation with a 12-mer phage display random peptide library. After five rounds of biopanning, phages had a specific binding activity to BRV were isolated. DNA sequencing indicated that phage displayed peptides HVHPPLRPHSDK, HATNHLPTPHNR or YPTHHAHTTPVR were potential ligands to BRV. Using the specific peptide-expressing phages, we developed a phage-based ELISA to differentiate BRV from other viruses. Compared with quantitative real-time PCR (qPCR), the phage-mediated ELISA was more suitable for the capture of BRV and the detection limitation of this approach was 0.1 µg/ml of samples. The high sensitivity, specificity and low cross-reactivity for the phage-based ELISA were confirmed in receiver operating characteristics (ROC) analysis.


“The Duty to Prevent” during an epidemic situation like 2015 Korean MERS outbreak


title: Single detection of human bocavirus 1 with a high viral load in severe respiratory tract infections in previously healthy children

text: BACKGROUND: Human bocavirus is a newly discovered parvovirus. Multiple studies have confirmed the presence of human bocavirus1 (HBoV1) in respiratory tract samples of children. The viral load, presentation of single detection and its role as a causative agent of severe respiratory tract infections have not been thoroughly elucidated. METHODS: We investigated the presence of HBoV1 by quantitative polymerase chain reaction (PCR) of nasopharyngeal aspirate specimens from 1229 children hospitalized for respiratory tract infections. The samples were analyzed for 15 respiratory viruses by PCR and 7 respiratory viruses by viral culture. RESULTS: At least one virus was detected in 652 (53.1%) of 1229 children, and two or more viruses were detected in 266 (21.6%) children. HBoV1 was detected in 127 children (10.3%), in which 66/127 (52%) of the cases were the only HBoV1 virus detected. Seasonal variation was observed with a high HBoV1 infection rate in summer. A cutoff value of 10(7) copies/mL was used to distinguish high and low HBoV1 viral loads in the nasopharyngeal aspirates. High viral loads of HBoV1 were noted predominantly in the absence of other viral agents (28/39, 71.8%) whereas there was primarily co-detection in cases of low HBoV1 viral loads (50/88, 56.8%). There were no differences in the clinical symptoms and severity between HBoV1 single detection and co-detection. In cases of HBoV1 single detection, the high viral load group was more prevalent among children with dyspnea and wheezing than was the low viral load group (42.9% vs. 23.7%, P = 0.036; 60.7% vs. 31.6%, P = 0.018). In clinical severity, a significant difference was recorded (25.0% vs. 5.3%, P = 0.003) between high viral load and low viral load groups. Of the HBoV1 positive patients associated with severe respiratory tract infections, 10/18 (55.6%) patients belonged to the HBoV1 high viral load group, and 7/10 (70%) patients had cases of HBoV1 single detection. CONCLUSIONS: HBoV1 at a high viral load is not frequently found in co-detection with other respiratory viruses, and a single detection with a high viral load could be an etiological agent of severe respiratory tract infections. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2334-14-424) contains supplementary material, which is available to authorized users.


title: Colostrum Management for Dairy Calves

text: Colostrum management is the single most important management factor in determining calf health and survival. Additional benefits of good colostrum management include improved rate of gain and future productivity. Successful colostrum management requires producers to provide calves with a sufficient volume of clean, high-quality colostrum within the first few hours of life. This article reviews the process of colostrogenesis and colostrum composition, and discusses key components in developing a successful colostrum management program. In addition, the article discusses approaches for monitoring and proposes new goals for passive immunity in dairy herds.


title: Point-of-care chest ultrasonography as a diagnostic resource for COVID-19 outbreak in nursing homes

text: ABSTRACT Objective Bedside chest ultrasound, when integrated with clinical data, is an accurate tool improving the diagnostic process of many respiratory diseases. This study aims to evaluate the feasibility of a chest ultrasound screening program in nursing homes for detecting coronavirus disease-19 (COVID-19)-related pneumonia and improving the appropriateness of hospital referral of residents. Design Pragmatic, descriptive, feasibility study from April 2nd to April 9th, 2020. Setting and participants: A total of 83 older residents (age 85±8) presenting mild to moderate respiratory symptoms and not previously tested for COVID-19, residing in five nursing homes in Northern Italy. Methods Chest ultrasound was performed at the bedside by a team of hospital specialists with certified expertise in thoracic ultrasonography, following a systematic approach exploring four different areas for each hemithorax, from the anterior and posterior side. Presence of ultrasonographic signs of interstitial pneumonia, including comet-tail artifacts (B-lines) with focal or diffuse distribution, subpleural consolidations and pleural line indentation was detected. The specialist team integrated ultrasound data with clinical and anamnestic information, and gave personalized therapeutic advice for each patient, including hospital referral when needed. Results The most frequent reasons for ultrasound evaluation were fever (63% of participants) and mild dyspnea (40%). Fifty-six patients (67%) had abnormal ultrasound findings. The most common patterns were presence of multiple subpleural consolidations (32 patients) and diffuse B-lines (24 patients), with bilateral involvement. A diagnosis of suspect COVID-19 pneumonia was made in 44 patients, and six of them required hospitalization. Twelve patients had ultrasound patterns suggesting other respiratory diseases, and two patients with normal ultrasound findings were diagnosed with COPD exacerbation. Conclusions and implications In nursing home residents, screening of COVID-19 pneumonia with bedside chest ultrasonography is feasible and may represent a valid diagnostic aid for an early detection of COVID-19 outbreaks and adequate patient management.


title: Antimicrobial Use in the Treatment of Calf Diarrhea

text: Calves with diarrhea often have small intestinal overgrowth with Escherichia coli bacteria, regardless of the inciting cause for the diarrhea, and 30% of systemically ill calves with diarrhea have bacteremia, predominantly because of E coli. Antimicrobial treatment of diarrheic calves should therefore be focused against E coli in the small intestine and blood, the 2 sites of infection. Fecal bacterial culture and antimicrobial susceptibility testing is not recommended in calves with diarrhea because fecal bacterial populations do not accurately reflect small intestinal or blood bacterial populations and because the break points for susceptibility test results have not been validated. Antimicrobial efficacy is therefore best evaluated by the clinical response of a number of calves to treatment, with calves randomly assigned to treatment groups. Amoxicillin, chlortetracycline, neomycin, oxytetracycline, streptomycin, sulfachloropyridazine, sulfamethazine, and tetracycline administered PO are currently labeled in the United States for the treatment of calf diarrhea. On the basis of published evidence for the oral administration of these antimicrobial agents, only amoxicillin can be recommended for the treatment of diarrhea. Dosage recommendations are amoxicillin trihydrate (10 mg/kg PO q12h) or amoxicillin trihydrate‐clavulanate potassium (12.5 mg combined drug/kg PO q12h) for at least 3 days; the latter constitutes extra‐label drug use. Parenteral administration of broad‐spectrum β‐lactam antimicrobials–eftiofur (2.2mg/kg IM orSCq12h) and amoxicillin or ampicillin (10 mg/kg IM q12h)–rpotentiatedsulfonamides(25 mg/kg IV or IM q24h) is recommended for treating calves with diarrhea and systemic illness; both constitute extra‐label drug use. In calves with diarrhea and no systemic illness (normal appetite for milk, no fever), it is recommended that the health of the calf be monitored and that oral or parenteral antimicrobials not be administered.


title: Association between multiple respiratory viral infections and pediatric intensive care unit admission among infants with bronchiolitis

text: Abstract Background It is unclear whether multiple respiratory viral infections are associated with more severe bronchiolitis requiring pediatric intensive care unit (PICU) admission. We aimed to identify the association between multiple respiratory viral infections and PICU admission among infants with bronchiolitis. Methods We performed a 1:1 case-control study enrolling previously healthy full-term infants (≤12 months) with bronchiolitis admitted to the PICU as cases and those to the general pediatric ward as controls from 2015 to 2017. Multiplex polymerase chain reaction (PCR) was used for detection of the respiratory viruses. We summarized the characteristics of infants admitted to the PICU and the general pediatric unit. Multivariable logistic regression analysis was used to fit the association between multiple respiratory viral infections (≥2 strains) and PICU admission. Results A total of 135 infants admitted to the PICU were compared with 135 randomly selected control infants admitted to the general pediatric unit. The PICU patients were younger (median: 2.2 months, interquartile range: 1.3–4.2) than the general ward patients (median: 3.2 months, interquartile range: 1.6–6.4). Respiratory syncytial virus (74.1%), rhinovirus (28.9%), and coronavirus (5.9%) were the most common viruses for bronchiolitis requiring PICU admission. Patients with bronchiolitis admitted to the PICU tended to have multiple viral infections compared with patients on the general ward (23.0% vs. 10.4%, P <0.001). In the multivariable logistic regression analysis, bronchiolitis with multiple viral infections was associated with higher odds of PICU admission (adjusted odds ratio: 2.56, 95% confidence interval: 1.17–5.57, P =0.02). Conclusion Infants with multiviral bronchiolitis have higher odds of PICU admission compared with those with a single or nondetectable viral infection.


title: Prevalence of viral respiratory tract infections in children with asthma

text: Background Previous studies support a strong association between viral respiratory tract infections and asthma exacerbations. The effect of newly discovered viruses on asthma control is less well defined. Objective We sought to determine the contribution of respiratory viruses to asthma exacerbations in children with a panel of PCR assays for common and newly discovered respiratory viruses. Methods Respiratory specimens from children aged 2 to 17 years with asthma exacerbations (case patients, n = 65) and with well-controlled asthma (control subjects, n = 77), frequency matched by age and season of enrollment, were tested for rhinoviruses, enteroviruses, respiratory syncytial virus, human metapneumovirus, coronaviruses 229E and OC43, parainfluenza viruses 1 to 3, influenza viruses, adenoviruses, and human bocavirus. Results Infection with respiratory viruses was associated with asthma exacerbations (63.1% in case patients vs 23.4% in control subjects; odds ratio, 5.6; 95% CI, 2.7- 11.6). Rhinovirus was by far the most prevalent virus (60% among case patients vs 18.2% among control subjects) and the only virus significantly associated with exacerbations (odds ratio, 6.8; 95% CI, 3.2-14.5). However, in children without clinically manifested viral respiratory tract illness, the prevalence of rhinovirus infection was similar in case patients (29.2%) versus control subjects (23.4%, P > .05). Other viruses detected included human metapneumovirus (4.6% in patients with acute asthma vs 2.6% in control subjects), enteroviruses (4.6% vs 0%), coronavirus 229E (0% vs 1.3%), and respiratory syncytial virus (1.5% vs 0%). Conclusion Symptomatic rhinovirus infections are an important contributor to asthma exacerbations in children. Clinical implications These results support the need for therapies effective against rhinovirus as a means to decrease asthma exacerbations.


title: Contrasting Patterns in Mammal–Bacteria Coevolution: Bartonella and Leptospira in Bats and Rodents

text: BACKGROUND: Emerging bacterial zoonoses in bats and rodents remain relatively understudied. We conduct the first comparative host–pathogen coevolutionary analyses of bacterial pathogens in these hosts, using Bartonella spp. and Leptospira spp. as a model. METHODOLOGY/PRINCIPAL FINDINGS: We used published genetic data for 51 Bartonella genotypes from 24 bat species, 129 Bartonella from 38 rodents, and 26 Leptospira from 20 bats. We generated maximum likelihood and Bayesian phylogenies for hosts and bacteria, and tested for coevoutionary congruence using programs ParaFit, PACO, and Jane. Bartonella spp. and their bat hosts had a significant coevolutionary fit (ParaFitGlobal = 1.9703, P≤0.001; m(2) global value = 7.3320, P≤0.0001). Bartonella spp. and rodent hosts also indicated strong overall patterns of cospeciation (ParaFitGlobal = 102.4409, P≤0.001; m(2) global value = 86.532, P≤0.0001). In contrast, we were unable to reject independence of speciation events in Leptospira and bats (ParaFitGlobal = 0.0042, P = 0.84; m(2) global value = 4.6310, P = 0.5629). Separate analyses of New World and Old World data subsets yielded results congruent with analysis from entire datasets. We also conducted event-based cophylogeny analyses to reconstruct likely evolutionary histories for each group of pathogens and hosts. Leptospira and bats had the greatest number of host switches per parasite (0.731), while Bartonella and rodents had the fewest (0.264). CONCLUSIONS/SIGNIFICANCE: In both bat and rodent hosts, Bartonella exhibits significant coevolution with minimal host switching, while Leptospira in bats lacks evolutionary congruence with its host and has high number of host switches. Reasons underlying these variable coevolutionary patterns in host range are likely due to differences in disease-specific transmission and host ecology. Understanding the coevolutionary patterns and frequency of host-switching events between bacterial pathogens and their hosts will allow better prediction of spillover between mammal reservoirs, and ultimately to humans.


title: Regulation of coronaviral poly(A) tail length during infection is not coronavirus species- or host cell-specific

text: It has been demonstrated that the length of the poly(A) tail in the bovine coronavirus (BCoV), which belongs to genus betacoronaviruses, is regulated throughout infection in human rectal tumor-18 (HRT-18) cells, and the length of the poly(A) tail is associated with the efficiency of virus translation. Here, we examined whether the regulation of viral poly(A) tail length is cell-type independent and whether it is a common feature of coronaviruses to assess the significance of the regulation. By ligating head-to-tail viral RNA positive strands and sequencing, we found that (1) the regulation pattern of coronaviral poly(A) tail length in BCoV-infected hamster kidney-21 (BHK-21) cells was similar to that in BCoV-infected HRT-18 cells and (2) the poly(A) tail length of wild-type avian infectious bronchitis virus (IBV) virulent strain IBV-TW1, which is in the genus gammacoronaviruses, varied throughout infection in primary chicken embryo kidney (CEK) cells and in the tracheas of 1-day-old chicks. Interestingly, the poly(A) tail length variation was similarly found in the avirulent IBV strain H120 in CEK cells, although the overall poly(A) tail length was shorter for this virus. The results suggest that the regulation of coronaviral poly(A) tail length during infection may be a common feature among coronaviruses and can occur in a noncancerous cell line (BHK-21 cells), primary cell culture (CEK cells), and living system (chickens), further reinforcing the biological significance of this regulation during coronavirus infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11262-014-1103-7) contains supplementary material, which is available to authorized users.


title: Influenza C infections in Western Australia and Victoria from 2008 to 2014

text: BACKGROUND: Influenza C is usually considered a minor cause of respiratory illness in humans with many infections being asymptomatic or clinically mild. Large outbreaks can occur periodically resulting in significant morbidity. OBJECTIVES: This study aimed at analyzing the available influenza C clinical samples from two widely separated states of Australia, collected over a 7‐year period and to compare them with influenza C viruses detected in other parts of the world in recent years. PATIENTS/METHODS: Between 2008 and 2014, 86 respiratory samples that were influenza C positive were collected from subjects with influenza‐like illness living in the states of Victoria and Western Australia. A battery of other respiratory viruses were also tested for in these influenza C‐positive samples. Virus isolation was attempted on all of these clinical samples, and gene sequencing was performed on all influenza C‐positive cultures. RESULTS AND CONCLUSIONS: Detections of influenza C in respiratory samples were sporadic in most years studied, but higher rates of infection occurred in 2012 and 2014. Many of the patients with influenza C had coinfections with other respiratory pathogens. Phylogenetic analysis of the full‐length hemagglutinin–esterase–fusion (HE) gene found that most of the viruses grouped in the C/Sao Paulo/378/82 clade with the remainder grouping in the C/Kanagawa/1/76 clade.


title: Achieve Research Continuity During Social Distancing by Rapidly Implementing Individual and Group Videoconferencing with Participants: Key Considerations, Best Practices, and Protocols

text: The novel coronavirus has upended many traditional research procedures as universities and other research entities have closed to activate social distancing. Some social and behavioral research activities (e.g. data analysis, manuscript preparation) can be continued from other environments with appropriate security protocols in place. For studies involving in-person interactions, continuity may be more difficult. Phone-based interactions provide a low-tech solution that may suffice in some cases. Yet, videoconferencing platforms can nearly replicate in-person interactions, activating both auditory and visual senses and potentially resulting in more substantial engagement. Staff can meet with participants individually or in groups, each seeing and hearing one another in real time. This paper provides guidance for researchers transitioning in-person assessments and interventions to a synchronous videoconferencing platform. Best practices, key considerations, examples from the field, and sample protocols are presented to ease transition for ongoing studies and maximize the potential of videoconferencing—and social distancing. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10461-020-02837-x) contains supplementary material, which is available to authorized users.


title: Is the Mortality Trend of Ischemic Heart Disease by the GBD2013 Study in China Real?

text: To determine the reason for the different mortality trends of ischemic heart disease (IHD) for China between Global Burden of Disease (GBD) 2010 and GBD2013, and to improve garbage code (GC) redistribution. All data were obtained from the disease surveillance points system, and two proportions for assigning chronic pulmonary heart disease (PHD) as GC to IHD were from GBD2010 and GBD2013, which were different for years before 2004. By using the GBD2013 approach, the age-standard mortality rate (ASMR) increased by 100.21% in 1991, 44.81% in 1996, and 42.47% in 2000 in comparison with the GBD2010 approach. The different methods of chronic PHD redistribution impacted the trend of IHD mortality, which elevated it in the earlier 1990s by using the GBD2013 approach. Thus, improving the redistribution of GC as a key step in mortality statistics is important.


Life in Hanoi during the Coronavirus Pandemic


docid: dzniszze

title: Comment on “Response to COVID-19 in Breast Imaging”


title: Multiplex detection and dynamics of IgG antibodies to SARS-CoV2 and the highly pathogenic human Coronaviruses SARS-CoV and MERS-CoV

text: BACKGROUND: Knowledge of the COVID-19 epidemic extent and the level of herd immunity is urgently needed to help manage this pandemic. METHODS: We used a panel of 167 samples (77 pre-epidemic and 90 COVID-19 seroconverters) and SARS-CoV1, SARS-CoV2 and MERS-CoV Spike and/or Nucleopcapsid (NC) proteins to develop a high throughput multiplex screening assay to detect IgG antibodies in human plasma. Assay performances were determined by ROC curves analysis. A subset of the COVID-19+ samples (n = 36) were also tested by a commercial NC-based ELISA test and the results compared with those of the novel assay. RESULTS: On samples collected ≥14 days after symptoms onset, the accuracy of the assay is 100% (95% CI: 100-100) for the Spike antigen and 99.9% (95% CI:99.7-100) for NC. By logistic regression, we estimated that 50% of the patients have seroconverted at 5.7 ± 1.6; 5.7 ± 1.8 and 7.9 ± 1.0 days after symptoms onset against Spike, NC or both antigens, respectively and all have seroconverted two weeks after symptoms onset. IgG titration in a subset of samples showed that early phase samples present lower IgG titers than those from later phase. IgG to SARS-CoV2 NC cross-reacted at 100% with SARS-CoV1 NC. Twenty-nine of the 36 (80.5%) samples tested were positive by the commercial ELISA while 31/36 (86.1%) were positive by the novel assay. CONCLUSIONS: Our assay is highly sensitive and specific for the detection of IgG antibodies to SARS-CoV2 proteins, suitable for high throughput epidemiological surveys. The novel assay is more sensitive than a commercial ELISA.


title: A Scientometric Analysis of Global Health Research

text: With the development and deepening of the process of global integration, global health is gaining increasing attention. An increasing number of studies have examined global health from diverse perspectives to promote the realization of global public health. The purpose of this research is to systematically and comprehensively evaluate the knowledge structure, knowledge domain, and evolution trend in the field of global health research. Based on the 14,692 document data retrieved from Web of Science Core Collection from 1996 to 2019, this article carried out a visual analysis of global health research from the perspective of scientific output characteristics, scientific research cooperation networks, keywords, and highly cited literature. The results show that scholars’ interest in global health research is increasing, especially after the outbreak of SARS. USA, England, Canada, Australia, and China have the most prominent contributions to global health research. Significant authors, high impact journals and core institutions also identified. The study found that “global health governance”, “global health diplomacy”, “medical education”, “global health education” and “antimicrobial resistance” are the research frontiers and hot spots. This study provides an overview and valuable guidance for researchers and related personnel to find the research direction and practice of global health.


title: Pathogen reduction of SARS-CoV-2 virus in plasma and whole blood using riboflavin and UV light

text: BACKGROUND: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has recently been identified as the causative agent for Coronavirus Disease 2019 (COVID-19). The ability of this agent to be transmitted by blood transfusion has not been documented, although viral RNA has been detected in serum. Exposure to treatment with riboflavin and ultraviolet light (R + UV) reduces blood-borne pathogens while maintaining blood product quality. Here, we report on the efficacy of R + UV in reducing SARS-CoV-2 infectivity when tested in human plasma and whole blood products. STUDY DESIGN AND METHODS: SARS-CoV-2 (isolate USA-WA1/2020) was used to inoculate plasma and whole blood units that then underwent treatment with riboflavin and UV light (Mirasol Pathogen Reduction Technology System, Terumo BCT, Lakewood, CO). The infectious titers of SARS-CoV-2 in the samples before and after R + UV treatment were determined by plaque assay on Vero E6 cells. Each plasma pool (n = 9) underwent R + UV treatment performed in triplicate using individual units of plasma and then repeated using individual whole blood donations (n = 3). RESULTS: Riboflavin and UV light reduced the infectious titer of SARS-CoV-2 below the limit of detection for plasma products at 60–100% of the recommended energy dose. At the UV light dose recommended by the manufacturer, the mean log reductions in the viral titers were ≥ 4.79 ± 0.15 Logs in plasma and 3.30 ± 0.26 in whole blood units. CONCLUSION: Riboflavin and UV light effectively reduced the titer of SARS-CoV-2 to the limit of detection in human plasma and by 3.30 ± 0.26 on average in whole blood. Two clades of SARS-CoV-2 have been described and questions remain about whether exposure to one strain confers strong immunity to the other. Pathogen-reduced blood products may be a safer option for critically ill patients with COVID-19, particularly those in high-risk categories.


title: Environmental Health, Planetary Boundaries and Limits to Growth

text: Abstract Published almost 50years ago, the Limits to Growth remains relevant to contemporary environmental health, though, paradoxically, this relevance is scarcely recognized. The seminal ideas it presented provide a useful background, as do the later Planetary Boundaries analyses, with which to consider key issues in contemporary environmental health. To be more than reactive, it is necessary to understand the complexity and interactions of integrated environmental health risks, including the possibility of significant global population decline within the current century. This contribution provides an overview to the Limits to Growth, linking it especially to the “planetary boundaries” of climate change, biodiversity loss and novel entities (including artificial substances and genetically modified organisms). The gradual increase in the amount of primary energy required to generate useable energy is also argued to be an under-recognized contributing factor to the decline in real wages growth for much of the world’s population since then, although this aspect may be improving. These elements have positive and negative health effects, which we discuss.


title: Preliminary investigations on the role of Drp-1 dependent mitochondrial fission in attenuating RLR downstream signaling during nervous necrosis virus infection

text: Abstract Member of the dynamin family of large GTPases, dynamin-related protein 1 (Drp1) dependent mitochondrial fission is an intricate process regulating both cellular and organ dynamics. Present study shows that NNV perturbs mitochondrial dynamics by promoting Drp-1 dependent mitochondrial fission, which attenuates MAVS mediated downstream signaling. NNV infected SISS cells revealed induction in Drp1 expression and subsequent translocation into mitochondria. The level of MAVS expression was up-regulated over a period of 24 hpi and declined with the progression of NNV infection at 48 and 72 hpi confirmed by western blot and mRNA transcript analysis. Drp-1 displayed its association with fragmented mitochondria and the transcript abundance was significant post infection along with Mff. Expression levels of IRF-3 IFN-1 and Mx followed a similar pattern with abundant expression at 48 hpi and diminished expression during the further period. Importantly, silencing of Drp1 caused significant elevation in the RLR downstream molecules and reduction in viral RNA expression. These results suggest that NNV-induced mitochondrial fission serve to attenuate host RLR signaling. This provides an illustration of host–pathogen interaction in which the virus evades innate immunity by enhancing mitochondrial fission and perturbs MAVS, and the downstream molecules.


title: Epidemiological studies of parvovirus infections in calves on endemically infected properties

text: Bovine parvovirus serology and virus excretion were monitored in calves located on three endemically infected North Queensland properties. Maternally derived serum antibody to bovine parvovirus was found to have a half-life of 19 days. On all three properties, calves developed intestinal bovine parvovirus infection with seroconversion soon after weaning. This occurred more promptly where the environment was subject to heavier bovine parvovirus contamination due to management practices. The concurrent presence of moderate levels of residual serum antibody had only minor influence on the onset of the infection. On one beef cattle property, onset of intestinal bovine parvovirus infection was associated with an outbreak of post-weaning diarrhoea. Anthelmintic treatment trials indicated that this syndrome was unrelated to helminth burdens, though coccidi-osis appeared responsible for occasional subsequent cases of dysentery. It was considered that bovine parvovirus may have significantly contributed to the development of the diarrhoea syndrome, in conjunction with substantial weaning stresses.


Genomic sequencing and analysis of the first imported Middle East Respiratory Syndrome Coronavirus (MERS CoV) in China


title: Potential Fecal Transmission of SARS-CoV-2: Current Evidence and Implications for Public Health

text: Abstract Coronavirus disease 2019 (COVID-19) emerged in Hubei Province, China in December 2019 and has since become a global pandemic, with hundreds of thousands of cases and over 165 affected countries. Primary routes of transmission of the causative virus, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), are through respiratory droplets and close person-to-person contact. While information about other potential modes of transmission are relatively sparse, evidence supporting the possibility of a fecally-mediated mode of transmission has been accumulating. Here, current knowledge on the potential for fecal transmission is briefly reviewed and the possible implications are discussed from a public health perspective.


Covid-19 pandemic-some cardiovascular considerations from the trench


Challenges to Neurosurgical Residency Training during COVID-19 Pandemic: An Indian Perspective


title: Genetic Immunization With In Vivo Dendritic Cell-targeting Liposomal DNA Vaccine Carrier Induces Long-lasting Antitumor Immune Response

text: A major limiting factor retarding the clinical success of dendritic cell (DC)-based genetic immunizations (DNA vaccination) is the scarcity of biologically safe and effective carrier systems for targeting the antigen-encoded DNA vaccines to DCs under in vivo settings. Herein, we report on a potent, mannose receptor selective in vivo DC-targeting liposomes of a novel cationic amphiphile with mannose-mimicking shikimoyl head-group. Flow cytometric experiments with cells isolated from draining lymph nodes of mice s.c. immunized with lipoplexes of pGFP plasmid (model DNA vaccine) using anti-CD11c antibody-labeled magnetic beads revealed in vivo DC-targeting properties of the presently described liposomal DNA vaccine carrier. Importantly, s.c. immunizations of mice with electrostatic complex of the in vivo DC-targeting liposome and melanoma antigen-encoded DNA vaccine (p-CMV-MART1) induced long-lasting antimelanoma immune response (100 days post melanoma tumor challenge) with remarkable memory response (more than 6 months after the second tumor challenge). The presently described direct in vivo DC-targeting liposomal DNA vaccine carrier is expected to find future exploitations toward designing effective vaccines for various infectious diseases and cancers.


title: When Public Health Crises Collide: Social Disparities and COVID‐19

text: In To Have or to Be?, psychoanalyst Erich Fromm writes about pursuit after domination of nature, material abundance, and unlimited happiness, which made modern society become more interested in having than in being. Income, in his view, should not be as accentuated as to create different experiences of life for different groups [1]. Of the concepts that Fromm presents, the domination of nature, which facilitates zoonotic spillover events by increasing the overlap between the habitat of various species with that of humans [2‐5], and the gap between the rich and the poor, which recently has become the widest in years [6], become particularly relevant in context of the COVID‐19 pandemic.


title: Pharmacokinetic and Pharmacodynamic Considerations for Drugs Binding to Alpha-1-Acid Glycoprotein

text: According to the free drug hypothesis only the unbound drug is available to act at physiological sites of action, and as such the importance of plasma protein binding primarily resides in its impact on pharmacokinetics and pharmacodynamics. Of the major plasma proteins, alpha-1-acid glycoprotein (AAG) represents an intriguing one primarily due to the high affinity, low capacity properties of this protein. In addition, there are marked species and age differences in protein expression, homology and drug binding affinity. As such, a thorough understanding of drug binding to AAG can help aid and improve the translation of pharmacokinetic/pharmacodynamic (PK/PD) relationships from preclinical species to human as well as adults to neonates. This review provides a comprehensive overview of our current understanding of the biochemistry of AAG; endogenous function, impact of disease, utility as a biomarker, and impact on PK/PD. Experimental considerations are discussed as well as recommendations for understanding the potential impact of AAG on PK through drug discovery and early development.


title: Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds

text: We present an optimised metagenomics method for detection and characterisation of all virus types including single and double stranded DNA/RNA and enveloped and non-enveloped viruses. Initial evaluation included both spiked and non-spiked bird faecal samples as well as non-spiked human faecal samples. From the non-spiked bird samples (Australian Muscovy duck and Pacific black ducks) we detected 21 viruses, and we also present a summary of a few viruses detected in human faecal samples. We then present a detailed analysis of selected virus sequences in the avian samples that were somewhat similar to known viruses, and had good quality (Q20 or higher) and quantity of next-generation sequencing reads, and was of interest from a virological point of view, for example, avian coronavirus and avian paramyxovirus 6. Some of these viruses were closely related to known viruses while others were more distantly related with 70% or less identity to currently known/sequenced viruses. Besides detecting viruses, the technique also allowed the characterisation of host mitochondrial DNA present and thus identifying host species, while ribosomal RNA sequences provided insight into the “ribosomal activity microbiome”; of gut parasites; and of food eaten such as plants or insects, which we correlated to non-avian host associated viruses.


title: Sore throat in primary care project: a clinical score to diagnose viral sore throat

text: OBJECTIVE. Viral agents cause the majority of sore throats. However, there is not currently a score to diagnose viral sore throat. The aims of this study were (i) to find the rate of bacterial and viral causes, (ii) to show the seasonal variations and (iii) to form a new scoring system to diagnose viral sore throat. METHODS. A throat culture for group A beta haemolytic streptococci (GABHS) and a nasopharyngeal swab to detect 16 respiratory viruses were obtained from each patient. Over a period of 52 weeks, a total of 624 throat cultures and polymerase chain reaction analyses were performed. Logistic regression analysis was performed to find the clinical score. RESULTS. Viral infection was found in 277 patients (44.3%), and GABHS infection was found in 116 patients (18.5%). An infectious cause was found in 356 patients (57.1%). Rhinovirus was the most commonly detected infectious agent overall (highest in November, 34.5%), and the highest GABHS rate was in November (32.7%). Analysis of data provided a scoring system, called the Mistik Score, to diagnose viral sore throat. The predictive model for positive viral analysis included the following variables: absence of headache, stuffy nose, sneezing, temperature of ≥37.5°C on physical examination, and the absence of tonsillar exudate and/or swelling. The probability of a positive viral analysis for a score of 5 was 82.1%. CONCLUSION. The Mistik Score may be useful to diagnose viral sore throat. We suggest its use either alone or in combination with the Modified Centor Score.


title: Clinical Characteristics of Children with COVID-19

text: BACKGROUND: In December 2019, the infection caused by 2019 novel coronavirus (COVID-19) led to an outbreak in Wuhan, situated in the Hubei Province of China. Following this, there has been a rapid increase in the number of cases. On 12th March 2020, there were over 100,000 confirmed cases and almost 4,300 deaths worldwide. The clinical profile of children with COVID-19 is unknown due to the few number of cases reported. Currently, available data suggest they may have a milder form of illness. METHODS: A review of the literature published from June 2019 to March 2020 was undertaken to evaluate the clinical presentation, management and outcomes of COVID-19 in in children. Data sources included EMBASE, MEDLINE, Cochrane library, ISI Web of Knowledge and references within identified articles. RESULTS: We identified 303 potential studies, and 295 were excluded for reasons including duplicates, experimental studies and case reports. Eight studies were eligible for inclusion, including a total of 820 paediatric cases of COVID-19. Asymptomatic cases represented 14.3% (n = 117) of the total number of cases identified, and thus the remaining 85.7% (n = 703) experienced symptoms. Fever was the commonest symptom in 53.9% (n = 48) of cases, followed by cough in 39.3% (n = 35) of cases, and rhinorrhoea or pharyngeal congestion in 13.5% (n = 12) of cases. Diarrhoea and sore throats were less common symptoms, 7.9% (n = 7) and 9.0% (n = 8) respectively. Other symptoms, including fatigue, headache and dizziness were rare. CONCLUSION: Children are disproportionately affected by COVID-19 and are more likely to run a milder cause of illness following this infection compared to adults. This outbreak only started 3 months ago, therefore, further population wide studies are needed to validate these findings.


title: Projecting hospital utilization during the COVID-19 outbreaks in the United States

text: In the wake of community coronavirus disease 2019 (COVID-19) transmission in the United States, there is a growing public health concern regarding the adequacy of resources to treat infected cases. Hospital beds, intensive care units (ICUs), and ventilators are vital for the treatment of patients with severe illness. To project the timing of the outbreak peak and the number of ICU beds required at peak, we simulated a COVID-19 outbreak parameterized with the US population demographics. In scenario analyses, we varied the delay from symptom onset to self-isolation, the proportion of symptomatic individuals practicing self-isolation, and the basic reproduction number R(0). Without self-isolation, when R(0) = 2.5, treatment of critically ill individuals at the outbreak peak would require 3.8 times more ICU beds than exist in the United States. Self-isolation by 20% of cases 24 h after symptom onset would delay and flatten the outbreak trajectory, reducing the number of ICU beds needed at the peak by 48.4% (interquartile range 46.4–50.3%), although still exceeding existing capacity. When R(0) = 2, twice as many ICU beds would be required at the peak of outbreak in the absence of self-isolation. In this scenario, the proportional impact of self-isolation within 24 h on reducing the peak number of ICU beds is substantially higher at 73.5% (interquartile range 71.4–75.3%). Our estimates underscore the inadequacy of critical care capacity to handle the burgeoning outbreak. Policies that encourage self-isolation, such as paid sick leave, may delay the epidemic peak, giving a window of time that could facilitate emergency mobilization to expand hospital capacity.


title: Electron microscopy detection and characterization of viral particles in dog stools

text: A number of apparently normal dog stool samples, randomly collected on the sidewalks of Paris were examined by Electron Microscopy. The study revealed the presence of viral particles in 27 cases. Morphological criteria lead to the characterization of rotavirus in 2 specimen, coronavirus in 7 and parvovirus in 5. Rotavirus particles appeared always alone while coronavirus and parvovirus particles were present together in 5 cases. Similar particles have been implicated in animal and human gastroenteritis. The importance of their presence in canine dejections is discussed in view of pollution by dog stools of urban and suburban areas.


title: Imaging of round pneumonia and mimics in children

text: Various diseases in the pediatric age group can present as an intrathoracic rounded opacity on a chest radiograph. The purpose of this pictorial essay is to emphasize the imaging appearance of round pneumonia, an entity that occurs especially in the pediatric population. Additional pathologies with similar chest radiographic appearances are also presented. The diagnosis of round pneumonia should be made in children who have the typical clinical presentation along with chest radiographs demonstrating the characteristic findings.


title: Antibody-mediated synergy and interference in the neutralization of SARS-CoV at an epitope cluster on the spike protein

text: Abstract Incomplete neutralization of virus, especially when it occurs in the presence of excess neutralizing antibody, represents a biological phenomenon that impacts greatly on antibody-mediated immune prophylaxis of viral infection and on successful vaccine design. To understand the mechanism by which a virus escapes from antibody-mediated neutralization, we have investigated the interactions of non-neutralizing and neutralizing antibodies at an epitope cluster on the spike protein of severe acute respiratory syndrome coronavirus (SARS-CoV). The epitope cluster was mapped at the C-terminus of the spike protein; it consists of structurally intertwined epitopes recognized by two neutralizing monoclonal antibodies (mAbs), 341C and 540C, and a non-neutralizing mAb, 240C. While mAb 341C binds to a mostly linear epitope composed of residues 507PAT509 and V349, mAb 240C binds to an epitope that partially overlaps the former by at least two residues (P507 and A508). The epitope corresponding to mAb 540C is a conformational one, involving residues L504 and N505. In neutralization assays, non-neutralizing 240C disrupted virus neutralization by mAb 341C and/or mAb 540C, whereas a combination of mAbs 341C and 540C blocked virus infectivity synergistically. These findings indicate that the epitope cluster on the spike protein may serve as an evolutionarily conserved platform at which a dynamic interplay between neutralizing and non-neutralizing antibodies occurs, thereby determining the outcome of SARS-CoV infection.


title: Molecular epidemiological survey and phylogenetic analysis of bovine respiratory coronavirus in Japan from 2016 to 2018

text: Bovine coronavirus (BCoV) is an etiological agent of bovine respiratory disease (BRD). BRD is a costly illness worldwide; thus, epidemiological surveys of BCoV are important. Here, we conducted a molecular epidemiological survey of BCoV in respiratory-diseased and healthy cattle in Japan from 2016 to 2018. We found that 21.2% (58/273) of the respiratory-diseased cattle were infected with BCoV. The respiratory-diseased cattle had virus amounts 4.7 times higher than those in the asymptomatic cattle. Phylogenetic analyses showed that the BCoV identified in Japan after 2005 formed an individual lineage that was distinct from the strains found in other countries. These results suggest that BCoV is epidemic and has evolved uniquely in Japan.


title: System analysis of synonymous codon usage biases in archaeal virus genomes

text: Abstract Recent studies of geothermally heated aquatic ecosystems have found widely divergent viruses with unusual morphotypes. Archaeal viruses isolated from these hot habitats usually have double-stranded DNA genomes, linear or circular, and can infect members of the Archaea domain. In this study, the synonymous codon usage bias (SCUB) and dinucleotide composition in the available complete archaeal virus genome sequences have been investigated. It was found that there is a significant variation in SCUB among different Archaeal virus species, which is mainly determined by the base composition. The outcome of correspondence analysis (COA) and Spearman׳s rank correlation analysis shows that codon usage of selected archaeal virus genes depends mainly on GC richness of genome, and the gene׳s function, albeit with smaller effects, also contributes to codon usage in this virus. Furthermore, this investigation reveals that aromaticity of each protein is also critical in affecting SCUB of these viral genes although it was less important than that of the mutational bias. Especially, mutational pressure may influence SCUB in SIRV1, SIRV2, ARV1, AFV1, and PhiCh1 viruses, whereas translational selection could play a leading role in HRPV1׳s SCUB. These conclusions not only can offer an insight into the codon usage biases of archaeal virus and subsequently the possible relationship between archaeal viruses and their host, but also may help in understanding the evolution of archaeal viruses and their gene classification, and more helpful to explore the origin of life and the evolution of biology.


title: Effects of the common cold and intranasal fluticasone propionate treatment on mucosal host defense assessed by human saliva

text: Abstract Objective. The purpose of this investigation was to study the effect of a potent topical steroid, fluticasone propionate, on patients with early signs and symptoms of the common cold. To characterize the mucosal inflammatory response, salivary defense factors and flow rate in these patients were analyzed. Study Design. Forty patients with symptoms of the common cold were randomized into 2 groups to receive either high-dose fluticasone propionate (100 μg per nostril) or placebo 4 times daily for 6 days. Paraffin-stimulated whole saliva was collected on day 1 (before the onset of medication), day 7 (posttreatment), and day 21 (follow-up). Results. Salivary flow rate, innate host defense factors, and total protein content were not affected by the common cold. IgA increased between day 7 and day 21 (P ≤ .01; Student 2-tailed t test), and the relative proportions of salivary peroxidase and IgA increased on day 7 (P = .01) and day 21 (P = .05). In patients receiving fluticasone, saliva flow rate was lower on day 21 (P ≤ .05) than on days 1 and 7. The innate salivary defense factors were not affected, but IgA increased both on day 7 (P ≤ .001) and on day 21 (P ≤ .001) in comparison with day 1. Conclusions. Of the oral mucosal defense factors, only IgA is activated during the common cold. Intranasally administrated fluticasone propionate does not have a suppressive effect on salivary antimicrobial capacity. (Oral Surg Oral Med Oral Pathol Oral Radiol Endod 1999;87:695-9)


title: “I'm Kinda Stuck at Home With Unsupportive Parents Right Now”: LGBTQ Youths' Experiences With COVID-19 and the Importance of Online Support

text: PURPOSE: LGBTQ youth are a population who experience unique stressors. This study investigated their experiences with the COVID-19 pandemic via Q Chat Space—a national online chat-based support program. METHODS: Transcript data from 31 synchronous, text-based chats collected during the onset of state-based “social distancing” ordinances in Spring 2020 were analyzed. RESULTS: While encountering COVID-19–related stressors likely to be experienced by youth generally, participants' experiences were concomitantly imbued with LGBTQ-specific intrapersonal, interpersonal, and structural challenges. Difficulties included maintaining mental health, being isolated with unsupportive families, and loss of in-person identity-based socialization and support. CONCLUSIONS: Findings highlight the importance of synchronous, text-based online platforms to enable LGBTQ youth to feel safe to seek support while at home. Given the potential for long-term physical distancing, concerted efforts are required to provide necessary resources and support for LGBTQ youth during the COVID-19 pandemic.


title: Target-independent high-throughput sequencing methods provide evidence that already known human viral pathogens play a main role in respiratory infections with unexplained etiology

text: Despite the advanced PCR-based assays available, a fraction of the pediatric respiratory infections remain unexplained every epidemic season, and there is a perception that novel viruses might be present in these specimens. We systematically collected samples from a prospective cohort of pediatric patients with respiratory infections, that returned negative results by validated molecular RT–PCR assays, and studied them with a target-independent, high-throughput sequencing-based approach. We also included a matched cohort of children with no symptoms of respiratory infection, as a contrast study population. More than fifty percent of the specimens from the group of patients with unexplained respiratory infections were resolved. However, the higher rate of detection was not due to the presence of novel viruses, but to the identification of well-known viral respiratory pathogens. Our results show that already known viral pathogens are responsible for the majority of cases that remain unexplained after the epidemic season. High-throughput sequencing approaches that use pathogen-specific probes are easier to standardize because they ensure reproducible library enrichment and sequencing. In consequence, these techniques might be desirable from a regulatory standpoint for diagnostic laboratories seeking to benefit from the many advantages of these sequencing technologies.