title: Selective bottlenecks shape evolutionary pathways taken during mammalian adaptation of a 1918-like avian influenza virus

text: Avian influenza virus reassortants resembling the 1918 human pandemic virus can become transmissible among mammals by acquiring mutations in hemagglutinin (HA) and polymerase. Using the ferret model, we trace the evolutionary pathway by which an avian-like virus evolves the capacity for mammalian replication and airborne transmission. During initial infection, within-host HA diversity increased drastically. Then, airborne transmission fixed 2 polymerase mutations that do not confer a detectable replication advantage. In later transmissions, selection fixed advantageous HA1 variants. Transmission initially involved a “loose” bottleneck, which became strongly selective after additional HA mutations emerged. The stringency and evolutionary forces governing between-host bottlenecks may therefore change throughout host adaptation. Mutations occurred in multiple combinations in transmitted viruses, suggesting that mammalian transmissibility can evolve through multiple genetic pathways despite phenotypic constraints. Our data provide a glimpse into avian influenza virus adaptation in mammals, with broad implications for surveillance on potentially zoonotic viruses.


title: Identification of amino acid residues important for anti-IFN activity of porcine reproductive and respiratory syndrome virus non-structural protein 1

text: Abstract The non-structural protein 1 (nsp1) of porcine reproductive and respiratory syndrome virus is partly responsible for inhibition of type I interferon (IFN) response by the infected host. By performing alanine-scanning mutagenesis, we have identified amino acid residues in nsp1α and nsp1β (the proteolytic products of nsp1) that when substituted with alanine(s) exhibited significant relief of IFN-suppression. A mutant virus (16-5A, in which residues 16–20 of nsp1β were substituted with alanines) encoding mutant nsp1β recovered from infectious cDNA clone was shown to be attenuated for growth in vitro and induced significantly higher amount of type I IFN transcripts in infected macrophages. In infected pigs, the 16-5A virus exhibited reduced growth at early times after infection but quickly regained wild type growth properties as a result of substitutions within the mutated sequences. The results indicate a strong selection pressure towards maintaining the IFN-inhibitory property of the virus for successful propagation in pigs.


title: Mycoplasma pneumoniae Infection Affects the Serum Levels of Vascular Endothelial Growth Factor and Interleukin-5 in Atopic Children

text: PURPOSE: Previous studies have outlined mechanisms by which Mycoplasma pneumonia (M. pneumonia) infection may promote allergic lung inflammation and airway remodeling, and increasing evidence from human studies suggests that atypical bacterial infections contribute to asthma exacerbation, chronic asthma, and disease severity with changes in cytokine expression. The present study evaluated changes in serum levels of vascular endothelial growth factor (VEGF) and interleukin (IL)-5 in atopic children with Mycoplasma pneumoniae pneumonia. METHODS: We recruited a total of 72 children with pneumonia. The patients were divided into 4 groups: atopic children with M. pneumonia pneumonia (group I, n=24), non-atopic children with M. pneumonia pneumonia (group II, n=23), atopic children with viral pneumonia (group III, n=13), and non-atopic children with viral pneumonia (group IV, n=12). Serum levels of IL-5, IL-13, VEGF, and tumor necrosis factor-α were measured at admission and at recovery using enzyme-linked immunosorbent assays. RESULTS: Serum levels of VEGF and IL-5 were elevated in group I compared with the other groups at both admission phase and clinical recovery phase. In group I, serum levels of VEGF and IL-5 were higher at recovery phase than at admission phase (VEGF: 1,102.2±569.4 vs. 874.9±589.9 pg/mL, respectively; IL-5: 150.5±63.9 vs. 120.2±46.7 pg/mL, respectively). CONCLUSIONS: The serum levels of VEGF and IL-5 were more increased in atopic children with M. pneumonia pneumonia than in the other groups. In this group, the serum levels of VEGF and IL-5 were more increased at recovery phase than at admission phase. The results of this study suggest that increases in VEGF and IL-5 may contribute to the development of hypersensitivity during M. pneumonia infection. These cytokines may act through their respective pro-inflammatory pathways to aggravate the allergic status and induce airway hypersensitivity during M. pneumonia pneumonia in atopic children.


title: First infection by all four non-severe acute respiratory syndrome human coronaviruses takes place during childhood

text: BACKGROUND: Non-severe acute respiratory syndrome (non-SARS)-related human coronaviruses (HCoVs), including HCoV-229E, -HKU1, -NL63, and -OC43, have been detected in respiratory tract samples from children and adults. However, the natural prevalence of antibodies against these viruses in serum among population is unknown. METHODS: To measure antibodies to the spike (S) protein of the four common non-SARS HCoVs, recombinant S proteins of the four HCoVs were expressed and characterised in 293 T cell. An S-protein-based indirect immunofluorescence assay (IFA) was then developed to detect anti-S IgG and IgM for the four individual HCoVs and applied to serum samples from a general asymptomatic population (218 children and 576 adults) in Beijing. RESULTS: Of 794 blood samples tested, only 29 (3.65%) were negative for anti-S IgG. The seropositivity of the four anti-S IgG antibodies was >70% within the general population. The majority of seroconversions to four-HCoV positivity first occurred in children. Both S-IgG and S-IgM antibodies were detectable among children and increased with age, reaching a plateau at 6 years of age. However, no anti-S IgM was detected in healthy adults. CONCLUSION: Large proportions of children and adults in Beijing have evidence of anti-S IgG against four the HCoVs, and first infections by all four non-SARS HCoVs takes place during childhood.


title: Infectious diseases in children and adolescents in China: analysis of national surveillance data from 2008 to 2017

text: OBJECTIVES: To outline which infectious diseases in the pre-covid-19 era persist in children and adolescents in China and to describe recent trends and variations by age, sex, season, and province. DESIGN: National surveillance studies, 2008-17. SETTING: 31 provinces in mainland China. PARTICIPANTS: 4 959 790 Chinese students aged 6 to 22 years with a diagnosis of any of 44 notifiable infectious diseases. The diseases were categorised into seven groups: quarantinable; vaccine preventable; gastrointestinal and enteroviral; vectorborne; zoonotic; bacterial; and sexually transmitted and bloodborne. MAIN OUTCOME MEASURES: Diagnosis of, and deaths from, 44 notifiable infectious diseases. RESULTS: From 2008 to 2017, 44 notifiable infectious diseases were diagnosed in 4 959 790 participants (3 045 905 males, 1 913 885 females) and there were 2532 deaths (1663 males, 869 females). The leading causes of death among infectious diseases shifted from rabies and tuberculosis to HIV/AIDS, particularly in males. Mortality from infectious diseases decreased steadily from 0.21 per 100 000 population in 2008 to 0.07 per 100 000 in 2017. Quarantinable conditions with high mortality have effectively disappeared. The incidence of notifiable infectious diseases in children and adolescents decreased from 280 per 100 000 in 2008 to 162 per 100 000 in 2015, but rose again to 242 per 100 000 in 2017, largely related to mumps and seasonal influenza. Excluding mumps and influenza, the incidence of vaccine preventable diseases fell from 96 per 100 000 in 2008 to 7 per 100 000 in 2017. The incidence of gastrointestinal and enterovirus diseases remained constant, but typhoid, paratyphoid, and dysentery continued to decline. Vectorborne diseases all declined, with a particularly noticeable reduction in malaria. Zoonotic infections remained at low incidence, but there were still unpredictable outbreaks, such as pandemic A/H1N1 2009 influenza. Tuberculosis remained the most common bacterial infection, although cases of scarlet fever doubled between 2008 and 2017. Sexually transmitted diseases and bloodborne infections increased significantly, particularly from 2011 to 2017, among which HIV/AIDS increased fivefold, particularly in males. Difference was noticeable between regions, with children and adolescents in western China continuing to carry a disproportionate burden from infectious diseases. CONCLUSIONS: China’s success in infectious disease control in the pre-covid-19 era was notable, with deaths due to infectious diseases in children and adolescents aged 6-22 years becoming rare. Many challenges remain around reducing regional inequalities, scaling-up of vaccination, prevention of further escalation of HIV/AIDS, renewed efforts for persisting diseases, and undertaking early and effective response to highly transmissible seasonal and unpredictable diseases such as that caused by the novel SARS-CoV-2 virus.


title: Sequencing the Biology of Entry: The Retroviral env Gene

text: The surface envelope protein of any virus is major determinant of the host cell that is infected and as a result a major determinant of viral pathogenesis. Retroviruses have a single surface protein named Env. It is a trimer of heterodimers and is responsible for binding to the host cell receptor and mediating fusion between the viral and host membranes. In this review we will discuss the history of the discovery of the avian leukosis virus (ALV) and human immunodeficiency virus type 1 (HIV-1) Env proteins and their receptor specificity, comparing the many differences but having some similarities. Much of the progress in these fields has relied on viral genetics and genetic polymorphisms in the host population. A special feature of HIV-1 is that its persistent infection in its human host, to the point of depleting its favorite target cells, allows the virus to evolve new entry phenotypes to expand its host range into several new cell types. This variety of entry phenotypes has led to confusion in the field leading to the major form of entry phenotype of HIV-1 being overlooked until recently. Thus an important part of this story is the description and naming of the most abundant entry form of the virus: R5 T cell-tropic HIV-1.


title: Update on therapeutic options for Middle East Respiratory Syndrome Coronavirus (MERS-CoV)

text: Introduction: The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an important emerging respiratory pathogen. MERS-CoV resulted in multiple hospital outbreaks within and outside the Arabian Peninsula. The disease has a high case fatality rate, with the need for a therapeutic option. Areas covered: In this review, we provide an overview of the progress in the development of therapeutic strategies for MERS. We searched PubMed, Embase, Cochrane, Scopus, and Google Scholar, using the following terms: ‘MERS’, ‘MERS-CoV’, ‘Middle East respiratory syndrome’ in combination with ‘treatment’ or ‘therapy’. Expert commentary: There are multiple agents tried in vitro and in vivo. None of these agents were used in large clinical studies. Available clinical studies are limited to the use of the combination of interferon and other agents. These clinical studies are based solely on case reports and case series. There are no prospective or randomized trials. There is a need to have prospective and randomized clinical trials for the therapy of MERS-CoV. However, this strategy might be hampered by the sporadic cases outside the large hospital outbreaks.


title: Cell lines from the Egyptian fruit bat are permissive for modified vaccinia Ankara

text: Abstract Bats are reservoir hosts for a spectrum of infectious diseases. Some pathogens (such as Hendra, Nipah and Marburg viruses) appear to use mainly fruit bats as reservoir. We describe designed immortalization of primary fetal cells from the Egyptian fruit bat (Rousettus aegyptiacus) to facilitate isolation and characterization of pathogens associated with these mammals. Three cell lines with different properties were recovered and successful immortalization was confirmed by continuous cultivation for over 18 months. Surprisingly, the cell lines are fully permissive for a highly attenuated poxvirus, modified vaccinia Ankara (MVA). MVA is a safe and well characterized vaccine vector that cannot replicate in most mammalian cells. High permissivity of Rousettus cell lines could justify testing bats for susceptibility to MVA as a replication competent vector with low zoonotic potential to induce herd immunity in bat colonies against viruses causing rabies or haemorrhagic fevers.


title: Aquaporin water channels: unanswered questions and unresolved controversies

text: Abstract The long-standing biophysical question of how water crosses plasma membranes has been answered by the recent discovery of the aquaporins. Identification of this large family of membrane water-transport proteins has generated new questions about the physiological functions, tissue distributions, and regulatory mechanisms of individual aquaporins. The fast pace of developments in this field has also resulted in major discrepancies in published reports which warrant resolution.


Therapeutic Options for Coronavirus Disease 2019 (COVID-19) - Modulation of Type I Interferon Response as a Promising Strategy?


title: Mechanistic Models of Infectious Disease and Their Impact on Public Health

text: From the 1930s through the 1940s, Lowell Reed and Wade Hampton Frost used mathematical models and mechanical epidemic simulators as research tools and to teach epidemic theory to students at the Johns Hopkins Bloomberg School of Public Health (then the School of Hygiene and Public Health). Since that time, modeling has become an integral part of epidemiology and public health. Models have been used for explanatory and inferential purposes, as well as in planning and implementing public health responses. In this article, we review a selection of developments in the history of modeling of infectious disease dynamics over the past 100 years. We also identify trends in model development and use and speculate as to the future use of models in infectious disease dynamics.


title: Plant-Derived Antigens as Mucosal Vaccines

text: During the last two decades, researchers have developed robust systems for recombinant subunit vaccine production in plants. Stably and transiently transformed plants have particular advantages that enable immunization of humans and animals via mucosal delivery. The initial goal to immunize orally by ingestion of plant-derived antigens has proven difficult to attain, although many studies have demonstrated antibody production in both humans and animals, and in a few cases, protection against pathogen challenge. Substantial hurdles for this strategy are low-antigen content in crudely processed plant material and limited antigen stability in the gut. An alternative is intranasal delivery of purified plant-derived antigens expressed with robust viral vectors, especially virus-like particles. The use of pattern recognition receptor agonists as adjuvants for mucosal delivery of plant-derived antigens can substantially enhance serum and mucosal antibody responses. In this chapter, we briefly review the methods for recombinant protein expression in plants, and describe progress with human and animal vaccines that use mucosal delivery routes. We do not attempt to compile a comprehensive list, but focus on studies that progressed to clinical trials or those that showed strong indications of efficacy in animals. Finally, we discuss some regulatory concerns regarding plant-based vaccines.


title: Incidence and Outcomes of Acute Respiratory Distress Syndrome: A Nationwide Registry-Based Study in Taiwan, 1997 to 2011

text: Most epidemiological studies of acute respiratory distress syndrome (ARDS) have been conducted in western countries, and studies in Asia are limited. The aim of our study was to evaluate the incidence, in-hospital mortality, and 1-year mortality of ARDS in Taiwan. We conducted a nationwide inpatient cohort study based on the Taiwan National Health Insurance Research Database between 1997 and 2011. A total of 40,876 ARDS patients (68% male; mean age 66 years) were identified by International Classification of Diseases, 9th edition coding and further analyzed for clinical characteristics, medical costs, and mortality. The overall crude incidence of ARDS was 15.74 per 100,000 person-years, and increased from 2.53 to 19.26 per 100,000 person-years during the study period. The age-adjusted incidence of ARDS was 15.19 per 100,000 person-years. The overall in-hospital mortality was 57.8%. In-hospital mortality decreased from 59.7% in 1997 to 47.5% in 2011 (P < 0.001). The in-hospital mortality rate was lowest (33.5%) in the youngest patients (age 18–29 years) and highest (68.2%) in the oldest patients (>80 years, P < 0.001). The overall 1-year mortality rate was 72.1%, and decreased from 75.8% to 54.7% during the study period. Patients who died during hospitalization were older (69 ± 17 versus 62 ± 19, P < 0.001) and predominantly male (69.8% versus 65.3%, P < 0.001). In addition, patients who died during hospitalization had significantly higher medical costs (6421 versus 5825 US Dollars, P < 0.001) and shorter lengths of stay (13 versus 19 days, P < 0.001) than patients who survived. We provide the first large-scale epidemiological analysis of ARDS incidence and outcomes in Asia. Although the overall incidence was lower than has been reported in a prospective US study, this may reflect underdiagnosis by International Classification of Diseases, 9th edition code and identification of only patients with more severe ARDS in this analysis. Overall, there has been a decreasing trend in in-hospital and 1-year mortality rates in recent years, likely because of the implementation of lung-protective ventilation.


Letter to the Editor “A longitudinal study on the mental health of general population during the COVID-19 epidemic in China”


title: Overview of new vaccines and technologies

text: Abstract Molecular technology has given us a greater insight into the aetiology of disease, the functioning of the immune system and the mode of action of veterinary pathogens. The knowledge gained has been used to develop new vaccines with specific, reactive antigens which elicit protective immune mediated responses (humoral and/or cell mediated) in the host. These vaccines should not burden the immune system by initiating responses against non-essential antigens. However, the efficacy of these vaccines is only as good as the delivery technology or route used to present them to the immune system. Some vaccines, traditionally given by the parenteral route, are now given by the natural route; either orally or intranasally. Two major advantages, often interrelated, are the rapid onset of immunity and stimulation of the local, mucosal immunity. These new technologies are now making an impact on current vaccine development. The balance has to be found between what is technologically feasible and what will provide at least as good a protective immunity as current, conventional vaccines. As new and emerging diseases appear globally, new opportunities arise for molecular and conventional technologies to be applied to both the development and delivery of novel vaccines, as well as the improvement of vaccines in current use.


title: A single centre study of viral community-acquired pneumonia in children: no evidence of SARS-CoV-2 from October 2019 to March 2020

text: Abstract Pneumonia is an important cause of morbidity and mortality in children. We described viral aetiologies, with particular interest in detecting SARS-CoV-2, in hospitalized pneumonia children. Human rhinovirus was the most frequently detected agent. No children tested positive for SARS-CoV-2. Our findings suggest that SARS-CoV-2 infection is rare in children and it was not circulating in Rome before COVID-19 outbreak.


title: Thalamic perforating artery stroke on computed tomography perfusion in a patient with coronavirus disease 2019

text: Emerging evidence suggests that patients with coronavirus disease 2019 (COVID-19) are at risk of thromboembolic complications, including ischemic strokes. We present a case illustrating the value of CT perfusion to identify acute small subcortical infarcts in a patient with COVID-19 admitted to an intensive care unit for bilateral pneumonia and pulmonary embolism presenting with sudden right limb weakness.


A Case of COVID-19 Encephalitis


Additional clinical pharmacists roles during COVID‐19


title: Respiratory disease in calves: Microbiological investigations on trans-tracheally aspirated bronchoalveolar fluid and acute phase protein response

text: Abstract Trans-tracheal aspirations from 56 apparently healthy calves and 34 calves with clinical signs of pneumonia were collected in six different herds during September and November 2002. The 90 samples were cultivated and investigated by PCR tests targeting the species Histophilus somni, Mannheimia haemolytica, Pasteurella multocida, Mycoplasma bovis, Mycoplasma dispar, and Mycoplasma bovirhinis. A PCR test amplifying the lktC-artJ intergenic region was evaluated and shown to be specific for the two species M. haemolytica and Mannheimia glucosida. All 90 aspirations were also analyzed for bovine respiratory syncytial virus (BRSV), parainfluenza-3 virus, and bovine corona virus by antigen ELISA. Surprisingly, 63% of the apparently healthy calves harbored potentially pathogenic bacteria in the lower respiratory tract, 60% of these samples contained either pure cultures or many pathogenic bacteria in mixed culture. Among diseased calves, all samples showed growth of pathogenic bacteria in the lower respiratory tract. All of these were classified as pure culture or many pathogenic bacteria in mixed culture. A higher percentage of the samples were positive for all bacterial species in the group of diseased animals compared to the clinically healthy animals, however this difference was only significant for M. dispar and M. bovirhinis. M. bovis was not detected in any of the samples. BRSV was detected in diseased calves in two herds but not in the clinically healthy animals. Among the diseased calves in these two herds a significant increase in haptoglobin and serum amyloid A levels was observed compared to the healthy calves. The results indicate that haptoglobin might be the best choice for detecting disease under field conditions. For H. somni and M. haemolytica, a higher percentage of the samples were found positive by PCR than by cultivation, whereas the opposite result was found for P. multocida. Detection of P. multocida by PCR or cultivation was found to be significantly associated with the disease status of the calves. For H. somni a similar association with disease status was only observed for cultivation and not for PCR.


title: Upper Airway Stem Cells: Understanding the Nose and Role for Future Cell Therapy

text: The nose together with the paranasal sinuses has an approximate surface area of 100 to 200 cm(2) in adults, which is lined with pseudostratified columnar ciliated epithelium. It serves several important physiological functions such as conditioning and filtration of the inspired air and the provision of end organ for the sense of smell. It is also a physical and immunological barrier as it is the first site of interaction between the host tissue and foreign invaders (viruses, bacteria, and allergens). Our understanding of the complex cellular events occurring in response to inhaled agents during the development of common airway diseases has been significantly enhanced by the current status of in vivo and in vitro nasal experimental models. This will allow the development of novel therapeutic strategies designed to improve the physiological and immune defense functions of the nasal epithelium, as well as novel therapies for other common nasal diseases.


title: Function, Architecture, and Biogenesis of Reovirus Replication Neoorganelles

text: Most viruses that replicate in the cytoplasm of host cells form neoorganelles that serve as sites of viral genome replication and particle assembly. These highly specialized structures concentrate viral proteins and nucleic acids, prevent the activation of cell-intrinsic defenses, and coordinate the release of progeny particles. Reoviruses are common pathogens of mammals that have been linked to celiac disease and show promise for oncolytic applications. These viruses form nonenveloped, double-shelled virions that contain ten segments of double-stranded RNA. Replication organelles in reovirus-infected cells are nucleated by viral nonstructural proteins µNS and σNS. Both proteins partition the endoplasmic reticulum to form the matrix of these structures. The resultant membranous webs likely serve to anchor viral RNA–protein complexes for the replication of the reovirus genome and the assembly of progeny virions. Ongoing studies of reovirus replication organelles will advance our knowledge about the strategies used by viruses to commandeer host biosynthetic pathways and may expose new targets for therapeutic intervention against diverse families of pathogenic viruses.


title: Improved detection of human influenza A and B viruses in respiratory tract specimens by hemi-nested PCR

text: Abstract RT-PCR is the most sensitive assay for diagnosis of influenza, due to enhanced rapidity and sensitivity as compared to classical methods. Hemi-nested RT-PCR was developed, targeting NP gene for influenza A and NS gene for influenza B, based on a previous single round RT-PCR method. The new method was compared with the previous technique for analytical sensitivity and specificity, and was applied to clinical samples from the lower and upper respiratory tract. The analytical sensitivity of hemi-nested RT-PCR was 10 (influenza A) and 4 times (influenza B) higher than the previous method. A high specificity of the new hemi-nested RT-PCR assay was observed by using whole respiratory viruses. When applied to lower respiratory tract specimens, the new method showed an increased rate of positivity as compared to the previous technique (9.3% versus 0.7% for influenza A, and 0.9% versus 0.2% for influenza B). Screening of upper respiratory tract samples collected during the seasonal 2005–2006 outbreak indicated 26.4% and 5.8% positivity for influenza A and B, respectively. The results were confirmed by sequence analysis: apart from influenza B, both influenza A subtypes H3N2 and H1N1, associated with the seasonal outbreak, were detected.


title: Economic impact of viral respiratory disease in children

text: Abstract The single most important respiratory pathogen in infancy and early childhood is respiratory syncytial virus (RSV). Approximately 40% of primary RSV infections in children result in lower respiratory tract disease. Approximately 1% of RSV-infected children require hospitalization. Especially in high-risk children, primary RSV infection results in significant morbidity and, sometimes, death. This high-risk group includes children with bronchopulmonary dysplasia, children with congenital heart disease, premature infants less than 6 months of age, and children with immunodeficiency diseases. It has been estimated that, in the United States, 14,000 infants with chronic lung disease and 16,400 infants with heart disease will be identified by 12 months of age. More than 91,000 children are hospitalized annually with lower respiratory tract disease caused by RSV, and 4500 deaths occur. In 1985 a report from the Institute of Medicine calculated that the annual hospitalization costs attributable to RSV infection were $300 million. Data collected at the New England Medical Center in 1991 show that the average cost of hospitalization of a child with RSV was $808 each day. Because of difficulty in developing a safe and effective RSV vaccine, attention is now focused on passive immunization using an RSV immune globulin. On the basis of a recently completed multiinstitutional trial, RSV immune globulin appears to be a safe and cost-effective option for prevention of severe RSV disease in high-risk children. (J PEDIATR 1994;124:S17-S21)


title: Evaluation of candidate vaccine approaches for MERS-CoV

text: The emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) as a cause of severe respiratory disease highlights the need for effective approaches to CoV vaccine development. Efforts focused solely on the receptor-binding domain (RBD) of the viral Spike (S) glycoprotein may not optimize neutralizing antibody (NAb) responses. Here we show that immunogens based on full-length S DNA and S1 subunit protein elicit robust serum-neutralizing activity against several MERS-CoV strains in mice and non-human primates. Serological analysis and isolation of murine monoclonal antibodies revealed that immunization elicits NAbs to RBD and, non-RBD portions of S1 and S2 subunit. Multiple neutralization mechanisms were demonstrated by solving the atomic structure of a NAb-RBD complex, through sequencing of neutralization escape viruses and by constructing MERS-CoV S variants for serological assays. Immunization of rhesus macaques confers protection against MERS-CoV-induced radiographic pneumonia, as assessed using computerized tomography, supporting this strategy as a promising approach for MERS-CoV vaccine development.


title: Surveillance and taxonomic analysis of the coronavirus dominant in pigeons in China

text: Coronaviruses (CoVs) are found in humans and a wide variety of wild and domestic animals, and of substantial impact on human and animal health. In poultry, the genetic diversity, evolution, distribution and taxonomy of CoVs dominant in birds other than chickens remain enigmatic. In our previous study, we proposed that the CoVs dominant (i.e. mainly circulating) in ducks (DdCoVs) should represent a novel species, which was different from the one represented by the CoVs dominant in chickens (CdCoVs). In this study, we conducted a large‐scale surveillance of CoVs in chickens, ducks, geese, pigeons and other birds (quails, sparrows and partridges) using a conserved RT‐PCR assay. The surveillance demonstrated that CdCoVs, DdCoVs and the CoVs dominant in pigeons (PdCoVs) belong to different lineages, and they are all prevalent in live poultry markets and the backyard flocks in some regions of China. We further sequenced seven Coronaviridae‐wide conserved domains in their replicase polyprotein pp1ab of seven PdCoVs and found that the genetic distances in these domains between PdCoVs and DdCoVs or CdCoVs are large enough to separate PdCoVs into a novel species, which were different from the ones represented by DdCoVs or CdCoVs within the genus Gammacoronavirus, per the species demarcation criterion of International Committee on Taxonomy of Viruses. This report shed novel insight into the genetic diversity, distribution, evolution and taxonomy of avian CoVs.


title: The Potential Influence of Common Viral Infections Diagnosed during Hospitalization among Critically Ill Patients in the United States

text: Viruses are the most common source of infection among immunocompetent individuals, yet they are not considered a clinically meaningful risk factor among the critically ill. This work examines the association of viral infections diagnosed during the hospital stay or not documented as present on admission to the outcomes of ICU patients with no evidence of immunosuppression on admission. This is a population-based retrospective cohort study of University HealthSystem Consortium (UHC) academic centers in the U.S. from the years 2006 to 2009. The UHC is an alliance of over 90% of the non-profit academic medical centers in the U.S. A total of 209,695 critically ill patients were used in this analysis. Eight hospital complications were examined. Patients were grouped into four cohorts: absence of infection, bacterial infection only, viral infection only, and bacterial and viral infection during same hospital admission. Viral infections diagnosed during hospitalization significantly increased the risk of all complications. There was also a seasonal pattern for viral infections. Specific viruses associated with poor outcomes included influenza, RSV, CMV, and HSV. Patients who had both viral and bacterial infections during the same hospitalization had the greatest risk of mortality RR 6.58, 95% CI (5.47, 7.91); multi-organ failure RR 8.25, 95% CI (7.50, 9.07); and septic shock RR 271.2, 95% CI (188.0, 391.3). Viral infections may play a significant yet unrecognized role in the outcomes of ICU patients. They may serve as biological markers or play an active role in the development of certain adverse complications by interacting with coincident bacterial infection.


title: The Role of Sociodemographic and Psychological Variables on Risk Perception of the Flu

text: Influenza is a source of mortality and morbidity, and vigilance of health authorities for flu viruses is high. The World Health Organization (WHO) highlighted that the first lines of defense against infectious diseases are behavioral, and risk perception affects behavioral measures. This study investigated risk perception of influenza and the role of sociodemographic and psychological variables on perceived risk. Participants were 442 adults. The research was conducted using three measures: an adjustment of the “Risk Perception of Infectious Disease Questionnaire,” the “General Self-Efficacy Scale,” and the short form of the “Italian Personality Inventory.” The results showed that age, education, self-efficacy, and personality influenced risk perception. The evidence that sociodemographic and psychological factors contribute to risk perception of a disease shows the need to take into account these variables in the planning of informative campaigns, with the aim to achieve favorable changes in public behavior. These issues might have implications for the ameliorating health communication efforts and successful response to new influenza outbreaks.


title: Human Genomic Loci Important in Common Infectious Diseases: Role of High-Throughput Sequencing and Genome-Wide Association Studies

text: HIV/AIDS, tuberculosis (TB), and malaria are 3 major global public health threats that undermine development in many resource-poor settings. Recently, the notion that positive selection during epidemics or longer periods of exposure to common infectious diseases may have had a major effect in modifying the constitution of the human genome is being interrogated at a large scale in many populations around the world. This positive selection from infectious diseases increases power to detect associations in genome-wide association studies (GWASs). High-throughput sequencing (HTS) has transformed both the management of infectious diseases and continues to enable large-scale functional characterization of host resistance/susceptibility alleles and loci; a paradigm shift from single candidate gene studies. Application of genome sequencing technologies and genomics has enabled us to interrogate the host-pathogen interface for improving human health. Human populations are constantly locked in evolutionary arms races with pathogens; therefore, identification of common infectious disease-associated genomic variants/markers is important in therapeutic, vaccine development, and screening susceptible individuals in a population. This review describes a range of host-pathogen genomic loci that have been associated with disease susceptibility and resistant patterns in the era of HTS. We further highlight potential opportunities for these genetic markers.


title: COVID-19: An Appeal for an Intersectoral Approach to Tackle With the Emergency

text: The knowledge of disease determinants is a pre-requisite for disease prevention. Infectious diseases determinants can be classified in three ways, as: primary or secondary; intrinsic or extrinsic; and associated with host, agent, or environment. In the specific case of COVID-19 several of these determinants are currently unknown leading to difficulties in public health approach to this disease. In this paper, we attempt to address several of the current gaps on COVID-19 using a systematic analysis on recent findings and some preliminary knowledge on animal coronaviruses. A discussion on the impact of COVID-19 determinants in disease prevention and control will be based on the Environmental Change and Infectious Disease (EnVID) systemic framework to address several challenges that may affect the control of the SARS- CoV-2 pandemic spread both in industrialized and in developing Countries.


title: Results of an online questionnaire to survey calf management practices on dairy cattle breeding farms in Austria and to estimate differences in disease incidences depending on farm structure and management practices

text: BACKGROUND: Calf disease may result in great economic losses. To implement prevention strategies it is important to gain information on management and to point out risk factors. The objective of this internet based survey was to describe calf management practices on registered dairy breeding farms in Austria and to estimate differences in calf disease incidences depending on farm structure and management practices. RESULTS: A total of 1287 questionnaires were finally analysed (response rate 12.2 %). Herd characteristics and regional distribution of farms indicated that this survey gives a good overview on calf management practices on registered dairy farms in Austria. The median number of cows per farm was 20 (interquartile range 13–30). Significant differences regarding farm characteristics and calf management between small and large farms (≤20 vs >20 cows) were present. Only 2.8 % of farmers tested first colostrum quality by use of a hydrometer. Storing frozen colostrum was more prevalent on large farms (80.8 vs 64.2 %). On 85.1 % of the farms, whole milk, including waste milk, was fed to the calves. Milk replacer and waste milk were more often used on large farms. In accordance with similar studies from other countries, calf diarrhoea was indicated as the most prevalent disease. Multivariable logistic regression analysis revealed that herd size was associated with calf diarrhoea and calf respiratory tract disease, with higher risk of disease on large farms. Furthermore, feeding waste milk to the calves was associated with increasing calf diarrhoea incidence on farm. In the final model with calf respiratory tract disease as outcome, respondents from organic farms reported less often a respiratory tract disease incidence of over 10 % compared with conventional farms [odds ratio (OR) 0.40, 95 % confidence interval (CI) 0.21–0.75] and farmers that housed calves individually or in groups after birth significantly reported more often to have an incidence of respiratory tract disease >10 % compared with farms where all calves were housed individually (OR 2.28, 95 % CI 1.16–4.48). CONCLUSION: The results obtained in this study provide an overview on calf management on dairy breeding farms in Austria and may help to further point out areas to be improved on farm. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13028-015-0134-y) contains supplementary material, which is available to authorized users.


title: Comprehensive codon usage analysis of porcine deltacoronavirus

text: Abstract Porcine deltacoronavirus (PDCoV) is a newly identified coronavirus of pigs that was first reported in Hong Kong in 2012. Since then, many PDCoV isolates have been identified worldwide. In this study, we analyzed the codon usage pattern of the S gene using complete coding sequences and complete PDCoV genomes to gain a deeper understanding of their genetic relationships and evolutionary history. We found that during evolution three groups evolved with a relatively low codon usage bias (effective number of codons (ENC) of 52). The factors driving bias were complex. However, the primary element influencing the codon bias of PDCoVs was natural selection. Our results revealed that different natural environments may have a significant impact on the genetic characteristics of the strains. In the future, more epidemiological surveys are required to examine the factors that resulted in the emergence and outbreak of this virus.


title: COVID-19 Q&A: Animal care continues

text: Thea Brabb and Sally Thompson-Iritani explain to Lab Animal how their mouse and nonhuman primate colonies continue to be cared for at the University of Washington and Washington National Primate Research Center.


title: Identification of the spinal cord as a major site of persistence during during chronic infection with a murine coronavirus

text: Abstract After intranasal inoculation, mouse hepatitis virus (MHV) gains entry into the central nervous system (CNS) via the olfactory and trigeminal nerves. Under the appropriate conditions, some mice develop clinically apparent demyelinating encephalomyelitis several weeks later, with virus always present in the spinal cord. To determine the pathway by which virus reaches the cord, brains and spinal cords of infected, asymptomatic mice were analyzed by in situ hybridization. Viral RNA was always detected in the anterior part of the upper spinal cord. A similar analysis of mice with the recent onset of hindlimb weakness showed that viral RNA was detected in the same location. The results suggest that MHV is transported to the spinal cord via well-defined neuroanatomic pathways and that viral amplification with resultant clinical disease occurs from this site of persistence in the anterior spinal cord. This process of viral amplification may involve the generation of viral variants as has been described for MHV-infected rats. No major changes in viral RNA or protein could be detected when MHV isolated from mice with hindlimb paralysis was analyzed. The data suggest that the generation of viral variants is not important in the pathogenesis of the late onset neurological disease induced by MHV in mice.


title: Detection of negative-stranded subgenomic RNAs but not of free leader in LDV-infected macrophages

text: Abstract The mechanism of synthesis of the seven subgenomic mRNAs of lactate dehydrogenase-elevating virus (LDV) was explored. One proposed mechanism, leader-primed transcription, predicts the formation of free 5'-leader in infected cells which then primes reinitiation of transcription at specific complementary sites on the antigenomic template. No free LDV 5'-leader of 156 nucleotides was detected in LDV-infected macrophages. Another mechanism, independent replication of the subgenomic mRNAs, predicts the presence of negative complements to all subgenomic mRNAs in infected cells which might be generated from subgenomic mRNAs in virions. Full-length antigenomic RNA was detected in LDV-infected macrophages by Northern hybridization at a level of < 1% of that of genomic RNA, but no negative polarity subgenomic RNAs. Negative complements to all subgenomic mRNAs, however, were detected by reverse transcription of total RNA from infected macrophages using as primer an oligonucleotide complementary to the antileader followed by polymerase chain reaction amplification using this sense primer in combination with various oligonucleotide primers complementary to a segment downstream of the junction between the 5' leader and the body of each subgenomic RNA. It is unclear whether these minute amounts of negative subgenomic RNAs function in the replication of the subgenomic mRNAs. They could also be by-products of the RNA replication process. Finally, no subgenomic mRNAs were detected in LDV virions.


title: Isolation and genetic properties of Bartonella in eastern bent-wing bats (Miniopterus fuliginosus) in Japan

text: Abstract The prevalence and genetic characteristics of Bartonella species in eastern bent-wing bats (Miniopterus fuliginosus) from Japan were investigated. Bartonella bacteria were isolated from 12/50 (24%) of bats examined. Analyses of sequence similarities of the citrate synthase gene (gltA) and RNA polymerase beta-subunit-encoding (rpoB) genes indicated that the isolates from M. fuliginosus were distinct from those present in known Bartonella species as the levels of similarity for both of the genes were lower than the cut-off values for species identification in Bartonella. A phylogenetic analysis of the gltA sequences revealed that the Miniopterus bat-associated strains fell into five genotypes (I to V). Though genotypes I to IV formed a clade with Bartonella from Miniopterus bats from Taiwan, genotype V made a monophyletic clade separate from other bat isolates. In a phylogenetic analysis with the concatenated sequences of the 16S rRNA, gltA, rpoB, cell division protein (ftsZ) gene, and riboflavin synthase gene (ribC) gene, isolates belonging to genotypes I to IV clustered with Bartonella strains from Taiwanese Miniopterus bats, similar to the outcome of the phylogenetic analysis with gltA, whereas genotype V also made a monophyletic clade separate from other bat-associated Bartonella strains. The present study showed that M. fuliginosus in Japan harbor both genus Miniopterus-specific Bartonella suggesting to be specific to the bats in Japan.


title: Can atmospheric pollution be considered a co-factor in extremely high level of SARS-CoV-2 lethality in Northern Italy?

text: Abstract This paper investigates the correlation between the high level of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) lethality and the atmospheric pollution in Northern Italy. Indeed, Lombardy and Emilia Romagna are Italian regions with both the highest level of virus lethality in the world and one of Europe’s most polluted area. Based on this correlation, this paper analyzes the possible link between pollution and the development of acute respiratory distress syndrome and eventually death. We provide evidence that people living in an area with high levels of pollutant are more prone to develop chronic respiratory conditions and suitable to any infective agent. Moreover, a prolonged exposure to air pollution leads to a chronic inflammatory stimulus, even in young and healthy subjects. We conclude that the high level of pollution in Northern Italy should be considered an additional co-factor of the high level of lethality recorded in that area.


Management of Severe Asthma During the COVID-19 Pandemic in Korea


title: Effects of humidity and other factors on the generation and sampling of a coronavirus aerosol

text: Suspensions of transmissible gastroenteritis virus (TGEV), a porcine coronavirus, were nebulized at rates of 0.1–0.2 ml/min into moving air using a Collison nebulizer or a plastic medical nebulizer operating at pressures ranging from 7 to 15 psi. The airborne viruses were collected on heating, ventilating, and air conditioning (HVAC) filters in an experimental apparatus and also sampled upstream of these test filters using AGI-30 and BioSampler impinger samplers. To study the effects of relative humidity (RH) on TGEV collection by the filters and samplers, the virus was nebulized into air at 30, 50, 70, and 90% RH. There were no significant changes in virus titer in the nebulizer suspension before and after nebulization for either nebulizer at any of the pressures utilized. Aerosolization efficiency – the ratio of viable virus sampled with impingers to the quantity of viable virus nebulized – decreased with increasing humidity. BioSamplers detected more airborne virus than AGI-30 samplers at all RH levels. This difference was statistically significant at 30 and 50% RH. Nebulizer type and pressure did not significantly affect the viability of the airborne virus. Virus recovery from test filters relative to the concentration of virus in the nebulizer suspension was less than 10%. The most and the least virus were recovered from filter media at 30% and 90% RH, respectively. The results suggest that TGEV, and perhaps other coronaviruses, remain viable longer in an airborne state and are sampled more effectively at low RH than at high humidity.


title: Strangles, convalescent Streptococcus equi subspecies equi M antibody titers, and presence of complications

text: BACKGROUND: Streptococcus equi subspecies equi infection elicits M protein antibody titers in equids. Interpretation of titers is not generally accepted. HYPOTHESIS: The magnitude of S. equi M protein (SeM) antibody titer after infection (titer ≥1:12 800) will be useful to monitor for the presence of complications or the risk of development of complications. ANIMALS: Forty‐eight horses on 1 farm involved in strangles outbreak. METHODS: Clinical and observational study. S. equi M protein antibody titers were measured on all horses 8 weeks after infection and select horses 12 and 28 weeks after infection. Horses were categorized: no disease, uncomplicated case, persistent guttural pouch (GP) infection, or complicated cases (metastatic abscesses, purpura hemorrhagica, secondary infections, and dysphagia). Category was compared to titer. RESULTS: Twenty‐eight of 48 (58%) developed clinical signs of S. equi infection. Of those, 11 (39%) had uncomplicated strangles, 9 (21%) had persistent GP infection, 5 (18%) were complicated cases, and 3 (11%) had both persistent GP infection and complications. Thirty‐three percent of horses (16 of 48) had SeM antibody titers ≥1:12 800 eight weeks after infection. Of horses with titers ≥1:12 800, 6 of 16 had evidence of complications. Of complicated cases, 6 of 8 had titers ≥1:12 800. In this outbreak, the sensitivity (75%; 95% CI [confidence interval] 45‐105) for a SeM antibody titer ≥1:12 800 detecting complications was higher than the specificity (43%; 95% CI 23‐64). CONCLUSIONS AND CLINICAL IMPORTANCE: This outbreak demonstrates that SeM antibody titers can be increased after infection (≥1:12 800) in the absence of complications of strangles.


title: Development of an optimized protocol for the detection of classical swine fever virus in formalin-fixed, paraffin-embedded tissues by seminested reverse transcription-polymerase chain reaction and comparison with in situ hybridization

text: Abstract An optimized protocol was developed for the detection of classical swine fever virus (CSFV) in formalin-fixed, paraffin-embedded tissues obtained from experimentally and naturally infected pigs by seminested reverse transcription-polymerase chain reaction (RT-PCR). The results for seminested RT-PCR were compared with those determined by in situ hybridization. The results obtained show that the use of deparaffinization with xylene, digestion with proteinase K, extraction with Trizol LS, followed by seminested RT-PCR is a reliable detection method. An increase in sensitivity was observed as amplicon size decreased. The highest sensitivity for RT-PCR on formalin-fixed, paraffin-embedded tissues RNA was obtained with amplicon sizes less than approximately 200 base pairs. An hybridization signal for CSFV was detected in lymph nodes from 12 experimentally and 12 naturally infected pigs. The sensitivity of seminested RT-PCR compared with in situ hybridization was 100% for CSFV. When only formalin-fixed tissues are available, seminested RT-PCR and in situ hybridization would be useful diagnostic methods for the detection of CSFV nucleic acid.


Schattenseiten der Globalisierung


title: Respirators used by healthcare workers due to the COVID-19 outbreak increase end-tidal carbon dioxide and fractional inspired carbon dioxide pressure

text: • As the requirement of personal protective equipment (PPE) has increased rapidly in a short time due to COVID-19, the compliance of the manufactured respirators with the standards seems to have been placed in the second plan. • Frequent use of PPE such as filtering facepiece respirators (FFRs) causes carbon dioxide re-breathing in healthcare workers during COVID-19 outbreak. • Even when resting, both expiratory and inspiratory carbon dioxide levels increase significantly with the use of PPE. • It should be kept in mind that healthcare workers may experience symptoms related to hypercapnia during their use of PPE.


title: Management challenges for chronic dysimmune neuropathies during the COVID‐19 pandemic

text: Since March 2020, the COVID‐19 pandemic has led to the need to re‐think the delivery of services to patients with chronic dysimmune neuropathies. Telephone/video consultations have become widespread but have compounded concerns about objective evaluation. Therapeutic decisions need, more than ever before, to be considered in the best interests of both patients, and society, while not denying function‐preserving/restoring treatment. Immunoglobulin therapy and plasma exchange, for those treated outside of the home, expose patients to the hazards of hospital or outpatient infusion centers. Steroid therapy initiation and continuation pose increased infectious risk. Immunosuppressant therapy similarly becomes highly problematic, with the risks of treatment continuation enhanced by uncertainties regarding duration of the pandemic. The required processes necessitate considerable time and effort especially as resources and staff are re‐deployed to face the pandemic, but are essential for protecting this group of patients and as an integral part of wider public health actions.


title: Prevention and control strategies of general surgeons under COVID-19 pandemic

text: Abstract The novel coronavirus SARS-CoV-2 and the disease caused by it, COVID-19, have spread to virtually all countries worldwide within just a few months. The economic and sanitary impact has been enormous. In March 2020, the World Health Organization declared COVID-19 a pandemic. How to effectively prevent and control SARS-CoV-2 transmission while providing care to surgical patients during the pandemic is a crucial topic. In order to minimize the risk of cross-infection between patients and physicians, many hospitals have taken measures to limit outpatient services, elective hospitalizations, and the number of operations. Based on the prevention and control measures stipulated by major medical institutions in China, this overview provides recommendations for surgeons from three aspects: outpatient treatment, ward management and perioperative protection. Telemedicine should be encouraged as a means of social distancing. Outpatient examination should be selected. Reasonable spatial arrangement and effective environmental disinfection are important for ward management. Patient selection for surgery and timing of operations should be carefully discussed within multi-disciplinary teams. Appropriate personal protective equipment should be worn adapted to the situational risk. On December 31, 2019, China reported to the WHO Country Office a pneumonia of unknown cause detected in Wuhan [2,4]. Subsequently, the disease later named COVID-19 affected a substantial proportion of the population in Wuhan and spread to other areas of China. Relying on a nationwide shutdown and mandatory quarantine, China has effectively curtailed the domestic outbreak. However, due to the high transmissibility of SARS-Cov-2 and the mobility of people, COVID-19 spread to the rest of the world. Many hospitals worldwide were faced with confirmed and suspected SARS-Cov-2 infections, putting a huge strain on the safety of patients and employees. Consequently, surgical patients who seek medical care during the COVID-19 pandemic present significant challenges. This paper summarizes medical care and infection prevention and control in general surgery patients during the COVID-19, pandemic in the light of the current situation in China. It provides reference for surgeons and decision makers in health care in other countries suffering from the COVID-19 pandemic.


title: Long-term bone and lung consequences associated with hospital-acquired severe acute respiratory syndrome: a 15-year follow-up from a prospective cohort study

text: The most severe sequelae after rehabilitation from SARS are femoral head necrosis and pulmonary fibrosis. We performed a 15-year follow-up on the lung and bone conditions of SARS patients. We evaluated the recovery from lung damage and femoral head necrosis in an observational cohort study of SARS patients using pulmonary CT scans, hip joint MRI examinations, pulmonary function tests and hip joint function questionnaires. Eighty medical staff contracted SARS in 2003. Two patients died of SARS, and 78 were enrolled in this study from August 2003 to March 2018. Seventy-one patients completed the 15-year follow-up. The percentage of pulmonary lesions on CT scans diminished from 2003 (9.40 ± 7.83)% to 2004 (3.20 ± 4.78)% (P < 0.001) and remained stable thereafter until 2018 (4.60 ± 6.37)%. Between 2006 and 2018, the proportion of patients with interstitial changes who had improved pulmonary function was lower than that of patients without lesions, as demonstrated by the one-second ratio (FEV(1)/FVC%, t = 2.21, P = 0.04) and mid-flow of maximum expiration (FEF(25%–75%), t = 2.76, P = 0.01). The volume of femoral head necrosis decreased significantly from 2003 (38.83 ± 21.01)% to 2005 (30.38 ± 20.23)% (P = 0.000 2), then declined slowly from 2005 to 2013 (28.99 ± 20.59)% and plateaued until 2018 (25.52 ± 15.51)%. Pulmonary interstitial damage and functional decline caused by SARS mostly recovered, with a greater extent of recovery within 2 years after rehabilitation. Femoral head necrosis induced by large doses of steroid pulse therapy in SARS patients was not progressive and was partially reversible.


title: An Outbreak of Coronavirus OC43 Respiratory Infection in Normandy, France

text: The 2 groups of human coronaviruses (HCoVs) represented by the prototype strains HCoV 229E and HCoV OC43 are mostly known as viruses responsible for common cold syndrome. HCoVs are difficult to detect, and epidemiological data are rare. From October 2000 through April 2001, we tested 1803 respiratory samples for HCoV by reverse-transcriptase polymerase chain reaction. From 8 February through 27 March 2001, HCoV OC43 was detected in samples obtained from 30 (6%) of 501 patients. The other viruses detected were respiratory syncytial virus (6.1%), parainfluenza virus 3 (1%), influenza virus A (7.8%), influenza virus B (7.2%), rhinovirus (6.4%), enterovirus (1%), and adenovirus (2%). Infection with HCoV OC43 was detected in patients of all age groups. The following clinical symptoms were noted: fever (in 59.8% of patients), general symptoms (in 30%), digestive problems (in 56.8%), rhinitis (in 36.6%), pharyngitis (in 30%), laryngitis (in 3.3%), otitis (in 13.3%), bronchitis (in 16.6%), bronchiolitis (in 10%), and pneumonia (in 6.6%). This study shows that an outbreak of HCoV OC43 respiratory infection was responsible for the lower respiratory tract symptoms observed in nearly one-third of patients identified by active surveillance for coronavirus infection.


title: Non-uniform refinement: Adaptive regularization improves single particle cryo-EM reconstruction

text: Single particle cryo-EM is a powerful method for studying proteins and other biological macromolecules. Many of these molecules comprise regions with varying structural properties including disorder, flexibility, and partial occupancy. These traits make computational 3D reconstruction from 2D images challenging. Detergent micelles and lipid nanodiscs, used to keep membrane proteins in solution, are common examples of locally disordered structures that can negatively affect existing iterative refinement algorithms which assume rigidity (or spatial uniformity). We introduce a cross-validation approach to derive non-uniform refinement, an algorithm that automatically regularizes 3D density maps during iterative refinement to account for spatial variability, yielding dramatically improved resolution and 3D map quality. We find that in common iterative refinement methods, regularization using spatially uniform filtering operations can simultaneously over- and under-regularize local regions of a 3D map. In contrast, non-uniform refinement removes noise in disordered regions while retaining signal useful for aligning particle images. Our results include state-of-the-art resolution 3D reconstructions of multiple membrane proteins with molecular weight as low as 90kDa. These results demonstrate that higher resolutions and improved 3D density map quality can be achieved even for small membrane proteins, an important use case for single particle cryo-EM, both in structural biology and drug discovery. Non-uniform refinement is implemented in the cryoSPARC software package and has already been used successfully in several notable structural studies.


title: Lethal Respiratory Disease Associated with Human Rhinovirus C in Wild Chimpanzees, Uganda, 2013

text: We describe a lethal respiratory outbreak among wild chimpanzees in Uganda in 2013 for which molecular and epidemiologic analyses implicate human rhinovirus C as the cause. Postmortem samples from an infant chimpanzee yielded near-complete genome sequences throughout the respiratory tract; other pathogens were absent. Epidemiologic modeling estimated the basic reproductive number (R(0)) for the epidemic as 1.83, consistent with the common cold in humans. Genotyping of 41 chimpanzees and examination of 24 published chimpanzee genomes from subspecies across Africa showed universal homozygosity for the cadherin-related family member 3 CDHR3-Y(529) allele, which increases risk for rhinovirus C infection and asthma in human children. These results indicate that chimpanzees exhibit a species-wide genetic susceptibility to rhinovirus C and that this virus, heretofore considered a uniquely human pathogen, can cross primate species barriers and threatens wild apes. We advocate engineering interventions and prevention strategies for rhinovirus infections for both humans and wild apes.


title: Post-malaria neurological syndrome: a rare neurological complication of malaria

text: BACKGROUND: Post-malaria neurological syndrome (PMNS) is a rare self-limiting neurological complication that can occur after recovery from malaria, usually severe falciparum malaria. It is characterized by a myriad of neuropsychiatric manifestations including mild neurological deficit to severe encephalopathy. PMNS was first described in 1996 and since then there have been 48 cases reported in the English literature. We report another case of PMNS in a 24-year-old healthy male and present a review of the disease entity. METHOD: We searched PMNS-related journal articles and case reports in the English literature, using PubMed and Google search engines. A total of forty-nine cases meeting the diagnostic criteria of PMNS were selected in this review. CONCLUSION: PMNS is a rare complication of severe malaria that might be underreported. It can develop up to 2 months after clearance of parasitemia. Clinical features can be variable. Most cases are self-limited, but more severe cases may benefit from steroid therapy.


title: Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability

text: The rapid spread of SARS-CoV-2 has a significant impact on global health, travel and economy. Therefore, preventative and therapeutic measures are urgently needed. Here, we isolated monoclonal antibodies from three convalescent COVID-19 patients using a SARS-CoV-2 stabilized prefusion spike protein. These antibodies had low levels of somatic hypermutation and showed a strong enrichment in VH1-69, VH3-30-3 and VH1-24 gene usage. A subset of the antibodies were able to potently inhibit authentic SARS-CoV-2 infection as low as 0.007 μg/mL. Competition and electron microscopy studies illustrate that the SARS-CoV-2 spike protein contains multiple distinct antigenic sites, including several receptor-binding domain (RBD) epitopes as well as non-RBD epitopes. In addition to providing guidance for vaccine design, the antibodies described here are promising candidates for COVID-19 treatment and prevention.


title: Antigenic relationships of murine coronaviruses

text: Two serological tests were used to examine the antigenic relationships between murine hepatitis viruses that cause different diseases in mice. Antisera prepared by immunization of mice with the individual viruses were tested for their ability to neutralize both the homologous immunogen and the other viruses. By a plaque reduction neutralization test, each antiserum was found to be specific for the immunizing virus; however, there was substantial cross-reactivity, indicating the viruses were closely related. By kinetic neutralization, two of the viruses tested, MHV-JHM and MHV-2, were found to be antigenically distinct. MHV-3 and MHV-A59 were found to be antigenically very similar but distinct. These data show that kinetic neutralization is a more precise method for determining the antigenic relationships between murine coronaviruses.


title: Specificity switching in virus–receptor complexes

text: Several structures of complexes between viral attachment proteins and their cellular receptors have been determined recently, enhancing our understanding of the molecular recognition processes that guide formation of virus–receptor complexes. Moreover, these structures also highlight strategies by which highly similar viral proteins within a single virus family can adapt to engage different receptors. Consequences of such differences are altered tropism and pathogenicity. An improved understanding of the molecular details of this specificity switching in receptor binding will help to establish links between receptor tropism, spread, and disease. Moreover, it also has relevance for the design and use of viruses as gene delivery vehicles with altered properties as well as for the identification of target viral epitopes of new vaccines.


title: Synovial Fluid Changes in Induced Infectious Arthritis in Calves

text: The objective was to develop an experimental model of septic arthritis in calves and to evaluate the effect of treatment on cytologic and bacteriologic variables of synovial fluid. The right tarsus of 7 healthy Holstein bull calves were inoculated with 10(8) colony‐forming units of viable Escherichia coli of a pap‐positive strain (day 1). On day 2, joint lavage was performed and antibiotic treatment was instituted. Cytologic examinations, bacterial cultures, and pap factor determinations by polymerase chain reaction (PCR) were performed on synovial fluid samples that were collected daily until day 4, then every 4 days until day 24. Results of physical examination, the severity of lameness, and swelling were recorded. Clinical signs of septic arthritis appeared on day 2 and persisted until day 9 for all calves. Bacterial cultures from all calves were positive for E coli on day 2, and remained positive until day 3 for 1 calf and until day 4 for 5 calves. In addition, PCR results were positive for all calves, with 6 positive through day 3 and 1 positive through day 4, after which a positive result was again obtained on day 24. Synovial fluid neutrophil counts and white blood cell counts were significantly increased on days 2–4; however, synovial total protein concentrations were increased (P < .05) throughout the experiment in comparison to day 1. Results of all bacterial cultures were negative on day 8, although clinicopathologic signs of inflammation persisted until day 20. This model successfully induced acute septic arthritis in calves. Rapid recovery occurred within 1 week when an appropriate treatment was instituted early in the course of the disease


title: Engineering Infectious cDNAs of Coronavirus as Bacterial Artificial Chromosomes

text: The large size of the coronavirus (CoV) genome (around 30 kb) and the instability in bacteria of plasmids carrying CoV replicase sequences, represent serious restrictions for the development of CoV infectious clones using reverse genetic systems similar to those used for smaller positive sense RNA viruses. To overcome these problems, several approaches have been established in the last thirteen years. Here we describe the engineering of CoV full-length cDNA clones as bacterial artificial chromosomes (BACs), using the Middle East respiratory syndrome CoV (MERS-CoV) as a model.


title: Ultrasound on the Frontlines of COVID‐19: Report from an International Webinar

text: The COVID‐19 pandemic has spread to 185 countries with over 2.1 million confirmed cases and 145,000 deaths, as per the Johns Hopkins University COVID‐19 dashboard provided at https://coronavirus.jhu.edu/map.html. Imaging modalities such as chest radiography, thoracic and cardiovascular ultrasound, and computed tomography have roles in the diagnosis, prognosis, monitoring, and therapy of COVID‐19. However, the potential benefits of imaging need to be balanced against resource utilization and infectious risk.


title: COVID-19 pandemic and the risk of infection in multiple sclerosis patients on disease modifying therapies: “what the bleep do we know?”

text: The novel coronavirus which emerged in Wuhan province of China has taken world by surprise. Since been diagnosed in December 2019, it has been termed a “Pandemic” and there is a growing concern in physicians across the globe. As new evidence is emerging, there are various preventative strategies which are being deployed. Multiple sclerosis patients who are on disease modifying therapies (DMTs) might be at a higher risk of acquiring or a poorer outcome due to their immune status. This review looks at the available evidence in managing this global crisis.


title: Olfactory and gustatory function impairment in COVID‐19 patients: Italian objective multicenter‐study

text: BACKGROUND: Objective data on chemosensitive disorders during COVID‐19 are lacking in the Literature. METHODS: Multicenter cohort study that involved four Italian hospitals. Three hundred and forty‐five COVID‐19 patients underwent objective chemosensitive evaluation. RESULTS: Chemosensitive disorders self‐reported by 256 patients (74.2%) but the 30.1% of the 89 patients who did not report dysfunctions proved objectively hyposmic. Twenty‐five percentage of patients were seen serious long‐lasting complaints. All asymptomatic patients had a slight lowering of the olfactory threshold. No significant correlations were found between the presence and severity of chemosensitive disorders and the severity of the clinical course. On the contrary, there is a significant correlation between the duration of the olfactory and gustatory symptoms and the development of severe COVID‐19. CONCLUSIONS: Patients under‐report the frequency of chemosensitive disorders. Contrary to recent reports, such objective testing refutes the proposal that the presence of olfactory and gustatory dysfunction may predict a milder course, but instead suggests that those with more severe disease neglect such symptoms in the setting of severe respiratory disease.


title: A Cross-sectional Surveillance Study of the Frequency and Etiology of Acute Respiratory Illness Among Pregnant Women

text: BACKGROUND: Other than influenza, little is known about the consequences of viral acute respiratory illness (ARI) on pregnant women and fetuses. Our objectives were to determine the frequency of ARI due to respiratory viruses and the associated clinical outcomes during pregnancy. METHODS: Pregnant women in their second or third trimester were enrolled if they reported having symptoms of ARI or were healthy within the preceding 2 weeks. Nasopharyngeal secretions were evaluated for respiratory viruses by molecular diagnostic assays. Clinical outcomes were evaluated at enrollment and via a follow-up telephone-based questionnaire 2 weeks later. RESULTS: There were 155 pregnant participants, with 81 ARI cases and 91 healthy controls. Acute lower respiratory tract illness (ALRTI) was identified in 29 cases (36%). Human rhinovirus (HRV), respiratory syncytial virus (RSV), and influenza virus accounted for 75% of virus-positive cases of ALRTI. Cases with ALRTI often reported a longer duration of illness, history of allergies, symptoms of wheezing, shortness of breath, or chest pain, and use of prescription medication. Two cases with ALRTI reported decreased fetal movement; a third case with ALRTI was hospitalized. CONCLUSIONS: In over one third of ARI cases, participants had symptoms consistent with ALRTI. Infection with HRV, RSV, or influenza virus was commonly detected in patients with ALRTI. Viral ALRTI during pregnancy appears to be common and is associated with significant morbidity.


title: System effectiveness of detection, brief intervention and refer to treatment for the people with post-traumatic emotional distress by MERS: a case report of community-based proactive intervention in South Korea

text: BACKGROUND: Korea has experienced diverse kind of disasters these days. Among them the 2015 middle eastern respiratory syndrome (MERS) outbreak imposed great psychological stress on almost all Korean citizens. Following the MERS outbreak, government is reviewing overall infectious disease management system and prioritizing the establishment of mental health service systems for infectious disease. This study makes suggestions for implementing disaster-related mental health service systems by analyzing the example of Gyeonggi Province, which proactively intervened with residents’ psychological problems caused by the large-scale outbreak of an infectious disease. CASE DESCRIPTION: Mental health service system for MERS victims had the following two parts: a mental health service for people who had been placed in quarantine and a service provided to families of patients who had died or recovered patients. The government of Gyeonggi province, public health centers, regional and local Community Mental Health Centers and the National Center for Crisis Mental Health Management participated in this service system. Among 1221 Gyeonggi people placed in quarantine and who experienced psychological and emotional difficulties, 350 required continuing services; 124 of this group received continuing services. That is, 35 % of people who required psychological intervention received contact from service providers and received the required services. CONCLUSIONS: This study reflects a proactive monitoring system for thousands of people placed under quarantine for the first time in Korea. It is significant that the service utilization rate by a proactive manner, that is the professionals administering it actively approached and contacted people with problems rather than passively providing information was much higher than other general mental health situation in Korea. The core value of public mental health services is adequate public accessibility; it is therefore essential for governments to strengthen their professional competence and establish effective systems. These criteria should also be applied to psychological problems caused by disastrous infectious disease outbreaks.


title: Age- and gender-related difference of ACE2 expression in rat lung

text: Abstract Epidemiologic data suggested that there was an obvious predominance of young adult patients with a slight female proneness in severe acute respiratory syndrome (SARS). The angiotensin-converting enzyme 2 (ACE2) was very recently identified as a functional receptor for SARS virus and is therefore a prime target for pathogenesis and pharmacological intervention. Rats of both genders at three distinct ages (young-adult, 3 months; middle-aged, 12 months; old, 24 months) were evaluated to determine the characteristic of ACE2 expression in lung and the effect of aging and gender on its expression. ACE2 was predominantly expressed in alveolar epithelium, bronchiolar epithelium, endothelium and smooth muscle cells of pulmonary vessels with similar content, whereas no obvious signal was detected in the bronchiolar smooth muscle cells. ACE2 expression is dramatically reduced with aging in both genders: young-adult vs. old P <0.001 (by 78% in male and 67% in female, respectively) and middle-aged vs. old P <0.001 (by 71% in male rats and 59% in female rats, respectively). The decrease of ACE2 content was relatively slight between young-adult and middle-aged groups (by 25% in male and 18% in female, respectively). Although there was no gender-related difference of ACE2 in young-adult and middle-aged groups, a significantly higher ACE2 content was detected in old female rats than male. In conclusion, the more elevated ACE2 in young adults as compared to aged groups may contribute to the predominance in SARS attacks in this age group.


Data sharing in the era of COVID-19


title: Laparoscopic surgery for benign adnexal conditions under spinal anaesthesia: Towards a multidisciplinary minimally invasive approach

text: BACKGROUND: Laparoscopic gynaecological surgery is commonly performed under general anaesthesia with endotracheal intubation. In general surgery, locoregional anaesthesia was applied to laparoscopic procedures, increasing minimally invasive surgery advantages. AIMS: To assess and compare postoperative pain after laparoscopic adnexal procedures for benign conditions under spinal anaesthesia (SA) versus general anaesthesia (GA). Furthermore, anaesthesiologic, surgical and clinical data were evaluated in both groups. MATERIALS AND METHODS: This is a prospective cohort study performed in a tertiary level referral centre for minimally invasive gynaecological surgery (Gynaecology and Human Reproduction Physiopathology, University of Bologna). Women scheduled for adnexal laparoscopic surgery for benign conditions between February and May 2019 were assigned to receive either SA or GA with endotracheal intubation. A sample size of 13 women per group was needed to detect a 2-point difference in pain scores. MAIN FINDINGS: 13 women were enrolled in the SA arm, 15 in the GA arm. In the SA cohort, the most common intraoperative adverse event was shoulder pain, reported by 3/12 women. At 1, 8, 12, 24 and 48 h after surgery pain was significantly lower in the SA arm (p < .05). Patients submitted to SA experienced no need for opioid drugs administration, unlike those receiving GA. Patients’ mobilization and return of bowel function were noted significantly earlier in the SA group (p < .05). CONCLUSIONS: SA is a feasible, safe and effective anaesthesiologic technique for laparoscopic gynaecological procedures for benign conditions, allowing a better control of postoperative pain. Women undergoing SA achieve earlier mobilization and bowel canalization. During the Covid-19 pandemics, SA could be useful in reducing the need for invasive procedures on respiratory tract.


Possible Controlling Measures of Panic Buying During COVID-19


title: Estimation of the probable outbreak size of novel coronavirus (COVID-19) in social gathering events and industrial activities

text: Abstract Background The reproduction number (R0) is vital in epidemiology to estimate the number infected people and trace the close contacts. The R0 values varies depending on social activity and type of gathering events that induce infection transmissibility, in addition to its pathophysiology dependence. Objectives In this study, we estimated the probable outbreak size of COVID-19 at clusters mathematically using a simple model that can predict the number of COVID-19 cases, as a function of time. Methods We proposed mathematical model to estimate the R0 of COVID-19 in the outbreak occurring in both of local and international clusters in light of published data. Different types of clusters (religious, wedding, and industrial activity) were selected based on reported events in different countries between February and April 2020. Results The highest R0 values were found in wedding party events (5), followed by religious gathering events (2.5), while the lowest value was found in the industrial cluster (2). This in return, shall enable us to assess the trend coronavirus spread by comparing the model results and observed patterns.. Conclusions This study provides a predictive COVID-19 transmission patterns in different clusters types based on different R0 values. This model offers the decision makers in the contact-tracing task the predicted number of cases, which would help them in epidemiology investigations by knowing when to stop.


title: Structural basis of HIV-1 Vpu-mediated BST2 antagonism via hijacking of the clathrin adaptor protein complex 1

text: BST2/tetherin, an antiviral restriction factor, inhibits the release of enveloped viruses from the cell surface. Human immunodeficiency virus-1 (HIV-1) antagonizes BST2 through viral protein u (Vpu), which downregulates BST2 from the cell surface. We report the crystal structure of a protein complex containing Vpu and BST2 cytoplasmic domains and the core of the clathrin adaptor protein complex 1 (AP1). This, together with our biochemical and functional validations, reveals how Vpu hijacks the AP1-dependent membrane trafficking pathways to mistraffick BST2. Vpu mimics a canonical acidic dileucine-sorting motif to bind AP1 in the cytosol, while simultaneously interacting with BST2 in the membrane. These interactions enable Vpu to build on an intrinsic interaction between BST2 and AP1, presumably causing the observed retention of BST2 in juxtanuclear endosomes and stimulating its degradation in lysosomes. The ability of Vpu to hijack AP-dependent trafficking pathways suggests a potential common theme for Vpu-mediated downregulation of host proteins. DOI: http://dx.doi.org/10.7554/eLife.02362.001


title: Chapter 35 Acute disseminated encephalomyelitis

text: Abstract Acute disseminated encephalomyelitis (ADEM) is an acute multifocal demyelinating disease of the central nervous system that typically follows an infectious illness. Its clinical course in most cases is monophasic; however, relapsing ADEM is rarely seen, which poses a diagnostic challenge for distinguishing this disease from multiple sclerosis (MS). Although typically encountered in children, it also occurs in adults with disease characteristics slightly different from the pediatric cases. Formerly, ADEM occurred particularly often in children with measles. However, the illness most often follows a non-descript viral or even bacterial infectious illness. ADEM occurs throughout the world, and may even be more common in less-developed countries, where MS is rare, than in developed ones, where MS is common. Children seldom get MS as opposed to adults, indicating that ADEM constitutes a distinct entity from MS. The prognosis of ADEM is generally good, but severe neurologic sequelae after ADEM are occasionally seen. In this chapter, the etiology, clinical/laboratory/radiologic characteristics, treatment options, and prognosis of ADEM are discussed.


title: Principles of ethics and critical communication during the COVID-19 pandemic()

text: • During the COVID-19 pandemic, the primary clinical emphasis has shifted to optimizing community health. • Scarce resources should be allocated to maximize benefit without unfairly affecting any group. • Healthcare systems should consider adopting a formal, tier-based response to COVID-19 related demand on resources. • Clinicians should use principles of high-stakes communication to guide care planning during the pandemic.


title: Reopening the Doors to Center-Based ABA Services: Clinical and Safety Protocols During COVID-19

text: In the wake of the coronavirus (COVID-19) pandemic, U.S. organizations that provide applied behavior analysis (ABA) programs to individuals with autism spectrum disorder have implemented a variety of safety precautions to minimize the spread of the virus, often shifting center-based services to the home or telehealth. Considered essential workers, ABA providers are exempt from government directives to close, so they have both the freedom and the great responsibility to make their own decisions about how best to keep their clients safe while continuing to provide medically necessary services. In the coming weeks and months, ABA providers will be faced with the decision about whether to reopen centers. This article does not address that decision, except to acknowledge the urgency to reopen, both to help clients and to remain solvent. Political rhetoric and contradictory public information further complicate this daunting decision. Because ABA providers do not have legal guidance to shift the burden of such decisions to local and state regulators, the burden is theirs alone. The unprecedented nature of the COVID-19 pandemic means that no decision is clearly wrong or right, and every decision has consequences. Although ABA providers do not have their own state guidance, many states have issued guidelines for childcare providers whose operations have continued throughout the pandemic. This article analyzes that guidance, identifies common variables potentially relevant to ABA organizations, highlights clinical considerations and procedural compliance, and provides ABA organizations with the tools to make the best decision for their clients, in their community, and on their timeline. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s40617-020-00462-7) contains supplementary material, which is available to authorized users.


title: A 2a/1b full-length p7 inter-genotypic chimeric genome of hepatitis C virus is infectious in vitro

text: Abstract The p7 protein of hepatitis C virus (HCV) functions as an ion channel in planar lipid bilayers, and its function is vital for the virus life cycle. In this study, we replaced either the entire or partial p7 of genotype 2a (strain JFH1), an HCV strain that replicates and produces virus progeny in vitro, with the corresponding regions of the p7 protein from genotype 1b (Australian isolate, HCV-A). Compared to wild type, the chimeric viruses reached their peak of infectivity with a delay but they produced a comparable titer to the wild type virus and the progeny viruses were able to infect naive permissive cells. Amantadine treatment of wild type and chimeric viruses reduced the virus titers by about 50% and 45%, respectively. Therefore, in this study, for the first time, we demonstrated that genotype 2a (JFH1 strain) genome encoding a full-length genotype 1b p7 gene produces infectious particles in vitro. These chimeric viruses are valuable instruments for comparative studies of the p7 proteins.


title: Metabolite, Protein, and Lipid Extraction (MPLEx): A Method that Simultaneously Inactivates Middle East Respiratory Syndrome Coronavirus and Allows Analysis of Multiple Host Cell Components Following Infection

text: Mass spectrometry (MS)-based, integrated proteomics, metabolomics, and lipidomics (collectively, multi-omics) studies provide a very detailed snapshot of virus-induced changes to the host following infection and can lead to the identification of novel prophylactic and therapeutic targets for preventing or lessening disease severity. Multi-omics studies with Middle East respiratory syndrome coronavirus (MERS-CoV) are challenging as the requirements of biosafety level 3 containment limit the numbers of samples that can be safely managed. To address these issues, the multi-omics sample preparation technique MPLEx (metabolite, protein, and lipid extraction) was developed to partition a single sample into three distinct parts (metabolites, proteins, and lipids) for multi-omics analysis, while simultaneously inactivating MERS-CoV by solubilizing and disrupting the viral envelope and denaturing viral proteins. Here we describe the MPLEx protocol, highlight the step of inactivation, and describe the details of downstream processing, instrumental analysis of the three separate analytes, and their subsequent informatics pipelines.


title: Amid COVID-19 pandemic: Challenges with access to care for COPD patients

text: Chronic Obstructive Pulmonary Disease (COPD) is a chronic inflammation in the lungs that causes obstruction in the airway, poor airflow, and irreversible loss of lung function. In clinical practice, comprehensive care for COPD patients includes the diagnosis using spirometry, clinical examination and comprehensive pharmacological and non-pharmacological management. The diagnosis is based on symptoms, dyspnea and lung function impairment and can be mild to very severe. Symptoms are examined using the COPD assessment test (CAT) score, and dyspnea grade are examined using a modified MRC from GOLD guidelines. When mild, the care includes self-management education, smoking cessation, lifestyle modifications, vaccination, and short-acting bronchodilators. Self-management education involves inhaler device training, breathing technique, early recognition of acute exacerbations and writing action plans. As the disease progresses, other care measures are added. These measures include the addition of long-acting inhaler therapies, pulmonary rehabilitation, oral therapies, oxygen and lung transplantation. During the final stages of COPD, patients receive end-of-life care( Bourbeau et al., 2019) .11 The novel coronavirus disease (COVID-19) is a viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that is spread through respiratory droplets. This infectious disease has led to a pandemic and is affecting the lives of many around the world, including Canadians. During this pandemic, the non-essential health services, including caring for patients with COPD, have been put on hold to reduce the risk of spread. Other implications of this pandemic for COPD patients include the health risk in case of infection. A meta-analysis including studies from January to March 2020 in Wuhan showed that pre-existing COPD worsens the risk of COVID-19 progression and leads to poorer prognostics. The sub-group analysis showed a significantly higher risk of ICU requirements and death in COPD patients who are infected with the SARS-CoV-2 virus. Studies suggest strong efforts to mitigate the risk of infection in this population( Zhao et al., May 2020) .22 This makes caring for this population even more critical during the pandemic.


title: IFIT3 and IFIT2/3 promote IFIT1-mediated translation inhibition by enhancing binding to non-self RNA

text: Interferon-induced proteins with tetratricopeptide repeats (IFITs) are highly expressed during the cell-intrinsic immune response to viral infection. IFIT1 inhibits translation by binding directly to the 5′ end of foreign RNAs, particularly those with non-self cap structures, precluding the recruitment of the cap-binding eukaryotic translation initiation factor 4F and ribosome recruitment. The presence of IFIT1 imposes a requirement on viruses that replicate in the cytoplasm to maintain mechanisms to avoid its restrictive effects. Interaction of different IFIT family members is well described, but little is known of the molecular basis of IFIT association or its impact on function. Here, we reconstituted different complexes of IFIT1, IFIT2 and IFIT3 in vitro, which enabled us to reveal critical aspects of IFIT complex assembly. IFIT1 and IFIT3 interact via a YxxxL motif present in the C-terminus of each protein. IFIT2 and IFIT3 homodimers dissociate to form a more stable heterodimer that also associates with IFIT1. We show for the first time that IFIT3 stabilizes IFIT1 protein expression, promotes IFIT1 binding to a cap0 Zika virus reporter mRNA and enhances IFIT1 translation inhibition. This work reveals molecular aspects of IFIT interaction and provides an important missing link between IFIT assembly and function.


title: Increased talin–vinculin spatial proximities in livers in response to spotted fever group rickettsial and Ebola virus infections

text: Talin and vinculin, both actin-cytoskeleton-related proteins, have been documented to participate in establishing bacterial infections, respectively, as the adapter protein to mediate cytoskeleton-driven dynamics of the plasma membrane. However, little is known regarding the potential role of the talin–vinculin complex during spotted fever group rickettsial and Ebola virus infections, two dreadful infectious diseases in humans. Many functional properties of proteins are determined by their participation in protein–protein complexes, in a temporal and/or spatial manner. To resolve the limitation of application in using mouse primary antibodies on archival, multiple formalin-fixed mouse tissue samples, which were collected from experiments requiring high biocontainment, we developed a practical strategic proximity ligation assay (PLA) capable of employing one primary antibody raised in mouse to probe talin–vinculin spatial proximal complex in mouse tissue. We observed an increase of talin–vinculin spatial proximities in the livers of spotted fever Rickettsia australis or Ebola virus-infected mice when compared with mock mice. Furthermore, using EPAC1-knockout mice, we found that deletion of EPAC1 could suppress the formation of spatial proximal complex of talin–vinculin in rickettsial infections. In addition, we observed increased colocalization between spatial proximity of talin–vinculin and filamentous actin-specific phalloidin staining in single survival mouse from an ordinarily lethal dose of rickettsial or Ebola virus infection. These findings may help to delineate a fresh insight into the mechanisms underlying liver specific pathogenesis during infection with spotted fever rickettsia or Ebola virus in the mouse model.


title: Remarkable enhancement of flavonoid production in a co-cultivation system of Isatis tinctoria L. hairy root cultures and immobilized Aspergillus niger

text: Abstract The dried roots of Isatis tinctoria L. are highly traded in the pharmaceutical industry due to their notable anti-influenza efficacy. For the first time, I. tinctoria hairy root cultures (ITHRCs) were co-cultured with two immobilized live GRAS (Generally Recognized as Safe) fungi, i.e. Aspergillus niger and Aspergillus niger, for the elevated production of pharmacologically active flavonoids. Immobilized A. niger (IAN) was exhibited as the superior elicitor in the plant-fungus co-cultivation system. The highest flavonoid production (3018.31±48.66μg/g DW) were achieved in IAN-treated ITHRCs under the optimal conditions of IAN spore concentration ca.104 spores/mL, temperature 30°C, initial pH value of media 7.0 and time 72h, which remarkably increased 6.83-fold relative to non-treated control (441.91±7.35μg/g DW). Also, this study revealed that IAN elicitation could trigger the sequentially transient accumulation of signal molecules and intensify the oxidative stress in ITHRCs, which both contributed to the up-regulated expression of associated genes involved in flavonoid biosynthetic pathway. Moreover, IAN could be reused at least five cycles with satisfactory performance. Overall, the coupled culture of IAN and ITHRCs is a promising and effective approach for the enhanced production of flavonoids, which allows for the improved applicability of these valuable compounds in pharmaceutical fields.


title: Crisis hits end-of-life care

text: The covid-19 pandemic has encouraged more people to make advance treatment decisions relating to CPR and ventilation, reports Clare Wilson


title: Tree and rate estimation by local evaluation of heterochronous nucleotide data

text: Motivation: Heterochronous gene sequence data is important for characterizing the evolutionary processes of fast-evolving organisms such as RNA viruses. A limited set of algorithms exists for estimating the rate of nucleotide substitution and inferring phylogenetic trees from such data. The authors here present a new method, Tree and Rate Estimation by Local Evaluation (TREBLE) that robustly calculates the rate of nucleotide substitution and phylogeny with several orders of magnitude improvement in computational time. Methods: For the basis of its rate estimation TREBLE novelly utilizes a geometric interpretation of the molecular clock assumption to deduce a local estimate of the rate of nucleotide substitution for triplets of dated sequences. Averaging the triplet estimates via a variance weighting yields a global estimate of the rate. From this value, an iterative refinement procedure relying on statistical properties of the triplets then generates a final estimate of the global rate of nucleotide substitution. The estimated global rate is then utilized to find the tree from the pairwise distance matrix via an UPGMA-like algorithm. Results: Simulation studies show that TREBLE estimates the rate of nucleotide substitution with point estimates comparable with the best of available methods. Confidence intervals are comparable with that of BEAST. TREBLE's phylogenetic reconstruction is significantly improved over the other distance matrix method but not as accurate as the Bayesian algorithm. Compared with three other algorithms, TREBLE reduces computational time by a minimum factor of 3000. Relative to the algorithm with the most accurate estimates for the rate of nucleotide substitution (i.e. BEAST), TREBLE is over 10 000 times more computationally efficient. Availability: Contact: jdobrien@ucla.edu


title: Psychometric Testing of Three COVID-19-Related Scales Among People with Mental Illness

text: Fear of novel coronavirus 2019 (COVID-19) may result in psychological health problems among different populations. Moreover, believing COVID-19 information and preventive COVID-19 infection behaviors are relevant constructs associated with fear of COVID-19. Therefore, the present study validated three instruments assessing fear, beliefs, and preventive behaviors related to COVID-19 among individuals with mental illness. Moreover, relationships between the three constructs were examined. Individuals with mental illness (N = 400; 178 females; mean age = 46.91 years) completed the Fear of COVID-19 Scale (FCV-19S), Believing COVID-19 Information Scale (BCIS), Preventive COVID-19 Infection Behaviors Scale (PCIBS), and Depression Anxiety Stress Scale-21 (DASS-21). The FCV-19S, BCIS, and PCIBS demonstrated a single-factor structure with satisfactory fit indices. Moreover, believing COVID-19 information positively and significantly associated with fear of COVID-19, and fear of COVID-19 negatively and significantly associated with preventive behaviors and positively and significantly associated with psychological distress. The FCV-19S, BCIS, and PCIBS may assist healthcare providers in assessing COVID-19-related information among individuals with mental illness. Consequently, relevant programs may be designed to help individuals with mental illness going through the period of crisis.