title: Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine

text: [Image: see text] Tremendous effort has been given to the development of diagnostic tests, preventive vaccines, and therapeutic medicines for coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Much of this development has been based on the reference genome collected on January 5, 2020. Based on the genotyping of 15 140 genome samples collected up to June 1, 2020, we report that SARS-CoV-2 has undergone 8309 single mutations which can be clustered into six subtypes. We introduce mutation ratio and mutation h-index to characterize the protein conservativeness and unveil that SARS-CoV-2 envelope protein, main protease, and endoribonuclease protein are relatively conservative, while SARS-CoV-2 nucleocapsid protein, spike protein, and papain-like protease are relatively nonconservative. In particular, we have identified mutations on 40% of nucleotides in the nucleocapsid gene in the population level, signaling potential impacts on the ongoing development of COVID-19 diagnosis, vaccines, and antibody and small-molecular drugs.


title: Diverging temporalities of care work on urban farms: Negotiating history, responsibility, and productivity in Lithuania

text: While scholars have developed a nuanced understanding of agriculture as a form of care, the temporal organization of farming practices has received little consideration. Focusing on how farmers organize and experience agriculture, we track diverging approaches to care work on urban farms in Vilnius, Lithuania. Our ethnographic fieldwork and interviews show how Lithuanian urban farmers are struggling to reconcile the civic ideals of the global urban farming movement with their historical understandings of care for specific plants and the land. Whereas the older generation views farming as kinship-based individualized work focusing on particular plants and garden ecologies, the younger generation approaches it as a way to unwind, mediate, and build a community. These different perspectives on farming translate into divergent temporalities of care in which productivist goals rooted in socialist self-provisioning practices and embodied in orderly landscapes encounter new trends of agricultural care manifested in the natural aesthetics of the farms. We examine dynamic tensions between the two farming modalities by linking them to different understandings of moral commitments and responsibilities for plants and land. Through the lens of temporality, we also show how these divergent care modes are themselves grounded in gender inequalities reproduced on the farms and enabled by by the welfare state institutions, including maternity leave and retirement policies.


title: Real-time fluorescence loop-mediated isothermal amplification assay for direct detection of egg drop syndrome virus

text: BACKGROUND: Egg drop syndrome (EDS), caused by the adenovirus “egg drop syndrome virus” (EDSV) causes severe economic losses through reduced egg production in breeder and layer flocks. The diagnosis of EDSV has been done by molecular tools since its complete genome sequence was identified. In order to enhance the capabilities of the real-time fluorescence loop-mediated isothermal amplification (RealAmp) assay, we aimed to apply the method for direct detection of the EDSV without viral DNA extraction. In order to detect the presence of the EDSV DNA, three pairs of primers were designed, from the conserved region of fiber gene of the EDSV. RESULTS: For our assay, test and control samples were directly used in the reaction mixture in 10-fold serial dilution. The target DNA was amplified at 65 °C, which yield positive results in a relatively short period of 40–45 min. The method reported in this study is highly sensitive as compared to polymerase chain reaction (PCR) and showed no sign of cross-reactivity or false positive results. The RealAmp accomplished specific identification of EDSV among a variety of poultry disease viruses. CONCLUSIONS: The direct RealAmp can be used to detect the presence of EDSV. As our result showed, the RealAmp method could be suitable for the direct detection of other DNA viruses.


title: Identification of essential components of the S. cerevisiae kinetochore

text: Abstract We have designed and utilized two in vivo assays of kinetochore integrity in S. cerevisiae. One assay detects relaxation of a transcription block formed at centromeres; the other detects an increase in the mitotic stability of a dicentric test chromosome. ctf13-30 and ctf14-42 were identified as putative kinetochore mutants by both assays. CTF14 is identical to NDC10 CBF2 , a recently identified essential gene that encodes a 110 kd kinetochore component. CTF13 is an essential gene that encodes a predicted 478 amino acid protein with no homology to known proteins. ctf13 mutants missegregate chromosomes at permissive temperature and transiently arrest at nonpermissive temperature as large-budded cells with a G2 DNA content and a short spindle. Antibodies recognizing epitope-tagged CTF13 protein decrease the electrophoretic mobility of a CEN DNA-protein complex formed in vitro. Together, the genetic and biochemical data indicate that CTF13 is an essential kinetochore protein.


title: Control of canine distemper

text: Abstract Control of canine distemper can realistically only be achieved by the use of vaccination. The types of vaccine in current use are described, together with some of the problems encountered such as interference by maternal antibodies, and usage in species other than dogs. Modified live viral vaccines, as used for more than thirty years, have proved very effective. Nevertheless there is scope for some improvement in vaccine efficacy and recent developments in genetic recombinant methods are described.


title: The potential of molecular diagnostics and serum procalcitonin levels to change the antibiotic management of community-acquired pneumonia

text: Abstract Two diagnostic bundles were compared in 127 evaluable patients admitted with community-acquired pneumonia (CAP). Diagnostic modalities in all patients included cultures of sputum (if obtainable) and blood, urine for detection of the antigens of Streptococcus pneumoniae and Legionella pneumophila, and nasal swabs for PCR probes for S. pneumoniae and Staphylococcus aureus. At least one procalcitonin level was measured in all patients. For virus detection, patients were randomized to either a 5-virus, lab-generated PCR panel or the broader and faster FilmArray PCR panel. Overall, an etiologic diagnosis was established in 71% of the patients. A respiratory virus was detected in 39%. The potential for improved antibiotic stewardship was evident in 25 patients with only detectable respiratory virus and normal levels of PCT.


title: Unraveling virus relationships by structure-based phylogenetic classification

text: Delineation of the intricacies of protein function from macromolecular structure constitutes a continual obstacle in the study of cell and pathogen biology. Structure-based phylogenetic analysis has emerged as a powerful tool for addressing this challenge, allowing the detection and quantification of conserved architectural properties between proteins, including those with low or no detectable sequence homology. With a focus on viral protein structure, we highlight how a number of investigations have utilized this powerful method to infer common functionality and ancestry.


title: Screen mirroring, screen casting and screen sharing during COVID‐19: what dermatologists should know

text: In times of COVID-19, social distancing is an important parameter to contain the spread of novel coronavirus. More than ever, it is important to understand the utility of technology in maintaining connectivity. The wireless connectivity of the devices used in daily routine life (mobile phones, tablets and computers) has changed the way we connect and interact with each other. The same is true in medical field as well. The technological advancement in these devices has brought clinicians closer in ways that has reduced the need for face-to-face meetings. All this has been made possible through streaming of data.


docid: mnetlxxj

title: Multiplex MassTag-PCR for Respiratory Pathogens in Pediatric Nasopharyngeal Washes Negative by Conventional Diagnostic Testing Shows a High Prevalence of Viruses Belonging to a Newly Recognized Picornavirus Clade

text: BACKGROUND: Respiratory infections are the most common infectious diseases in humans worldwide and are a leading cause of death in children less than 5 years of age. OBJECTIVES: Identify candidate pathogens in pediatric patients with unexplained respiratory disease. STUDY DESIGN: Forty-four nasopharyngeal washes collected during the 2004-05 winter season from pediatric patients with respiratory illnesses that tested negative for 7 common respiratory pathogens by culture and direct immunofluorescence assays were analyzed by MassTag-PCR. To distinguish human enteroviruses (HEV) and rhinoviruses (HRV), samples positive for picornaviruses were further characterized by sequence analysis. RESULTS: Candidate pathogens were detected by MassTag PCR in 27 of the 44 (61%) specimens that previously were rated negative. Sixteen of these 27 specimens (59%) contained picornaviruses; of these 9 (57%) contained RNA of a recently discovered clade of rhinoviruses. Bocaviruses were detected in three patients by RT-PCR. CONCLUSIONS: Our study confirms that multiplex MassTag-PCR enhances the detection of pathogens in clinical specimens, and shows that previously unrecognized rhinoviruses, that potentially form a species HRV-C, may cause a significant amount of pediatric respiratory disease.


title: Determination of affinities of a panel of IgGs and Fabs for whole enveloped (influenza A) virions using surface plasmon resonance

text: Abstract The affinity of a panel of neutralizing monoclonal IgGs and their Fab fragments has been measured for the first time with an enveloped type A influenza virus, by surface plasmon resonance (SPR) and the BIAlite™ instrument. Equilibrium constants could be calculated for four of the five mAbs tested. These were in the nanomolar range. The ranking order was very similar to that obtained with an affinity ELISA, (an equilibrium system) but as others have found, affinities were 2–10-fold lower as measured by SPR (a flow system). No data were obtained with mAb HC58 although it had one of the highest affinities using an ELISA format, and was 28-fold higher than another mAb (HC10) which gave good data by SPR. This may relate to the orientation of its binding on the virion surface. The K dissoc. of the Fabs was only 3–10-fold higher compared to their IgGs. Fab from the lowest affinity IgG (HC10) could not be measured, possibly because it fell below the threshold for detection.


title: EFFECTS OF THE COMMON COLD ON MOOD AND PERFORMANCE

text: Abstract Previous research has shown that both experimentally-induced and naturally occurring upper respiratory tract illnesses (URTIs) influence mood and mental functioning. None of the previous studies of naturally occurring colds has conducted appropriate virological assays to determine the nature of the infecting agent. This is an essential methodological step in studies of malaise associated with URTIs. The aim of this research was to investigate the effects of naturally occurring colds on mood and objective measures of performance. This was done by first conducting a cross-sectional comparison of 37 healthy people and 158 volunteers with colds and then a longitudinal study in which 100 volunteers developed colds and 87 remained healthy. Virological techniques were used to identify infecting agents and comparisons made across the different groups. The results showed that having a cold was associated with reduced alertness and slowed reaction times. These effects were observed both for colds where the infecting virus was identified and those where it was not. Similar effects were obtained for both rhinovirus and coronavirus colds. One may conclude that upper respiratory tract illnesses lead to a reduction in subjective alertness and impaired psychomotor functioning. This was true for both illnesses where the infecting agent was identified and for those clinical illnesses where no virus was detected. It is now important to identify the mechanisms linking infection and illness with the behavioural changes. Similarly, the impact of these effects on real-life activities such as driving needs examining. Finally, methods of treatment need to be developed which not only treat the local symptoms of the illnesses but remove the negative mood and the performance impairments. © 1998 Elsevier Science Ltd. All rights reserved.


title: Evidence for SARS-CoV-2 Infection of Animal Hosts

text: COVID-19 is the first known pandemic caused by a coronavirus, SARS-CoV-2, which is the third virus in the family Coronaviridae to cause fatal infections in humans after SARS-CoV and MERS-CoV Animals are involved in the COVID-19 pandemic This review summarizes the role of animals as reservoirs, natural hosts and experimental models SARS-CoV-2 originated from animal reservoir, most likely bats and/or pangolins Anthroponotic transmission has been reported in cats, dogs, tigers, lions and minks As of now, there is no a strong evidence for natural animal-to-human transmission or sustained animal-to-animal transmission of SARS-CoV-2 Experimental infections conducted by several research groups have shown that monkeys, hamsters, ferrets, cats, tree shrews, transgenic mice and fruit bats were permissive, while dogs, pigs and poultry were resistant There is an urgent need to understand the zoonotic potential of different viruses in animals, particularly in bats, before they transmit to humans Vaccines or antivirals against SARS-CoV-2 should be evaluated not only for humans, but also for the protection of companion animals (particularly cats) and susceptible zoo and farm animals


title: Clinical Perspective on 2019 Novel Coronavirus Pneumonia: A Systematic Review of Published Case Reports

text: The ongoing pandemic of 2019 novel coronavirus (2019-nCoV), which originated from Wuhan, China, has led to 68,279 deaths due to 2019-nCoV pneumonia as of May 5, 2020. We conducted a systematic review and included 16 case reports to summarize the transmission and pathology of 2019-nCoV, and clinical presentation, laboratory and imaging findings, and treatment in 2019-nCoV pneumonia. The disease is mild in most people; in some, it may progress to severe pneumonia with acute respiratory distress syndrome (ARDS). Patients with mild illness usually recover at home, with supportive care and isolation in accordance with guidelines. Patients who have moderate to severe pneumonia are usually monitored in the hospital. Although there is no definitive treatment for 2019-nCoV pneumonia so far, some antiviral drugs have shown promising results. The use of lopinavir/ritonavir and remdesivir was associated with significant clinical improvement in severe pneumonia. Nonetheless, we need more randomized clinical trials (RCTs) and treatment guidelines for developing effective management of the 2019-nCoV and improve patient outcomes by reducing mortality in high-risk patients. We also need more clinical trials and management guidelines for the effective management of 2019-nCoV pneumonia.


title: Intracellular sensing of viral genomes and viral evasion

text: During viral infection, virus-derived cytosolic nucleic acids are recognized by host intracellular specific sensors. The efficacy of this recognition system is crucial for triggering innate host defenses, which then stimulate more specific adaptive immune responses against the virus. Recent studies show that signal transduction pathways activated by sensing proteins are positively or negatively regulated by many modulators to maintain host immune homeostasis. However, viruses have evolved several strategies to counteract/evade host immune reactions. These systems involve viral proteins that interact with host sensor proteins and prevent them from detecting the viral genome or from initiating immune signaling. In this review, we discuss key regulators of cytosolic sensor proteins and viral proteins based on experimental evidence.


title: Toroviruses of Animals And Humans: A Review

text: Publisher Summary Toroviruses are a group of enveloped positive-stranded RNA viruses that cause enteric, respiratory, and perhaps generalized infections in animals and humans. Their name refers to their unique morphological features: an elongated bacilliform core with two rounded ends is surrounded by a membrane that may either tightly adhere to or “shrink-wrap” it, without respecting the capsid's rod shape; in the first instance, straight or curved rhabdovirus-like particles are formed, whereas in the latter a biconcave disk results. Torovirus history is brief: the first representative, Berne virus (BEV), was isolated in Berne, Switzerland, in 1972 from a rectal swab taken from a horse with diarrhea 1 week before it died. BEV is the only equine torovirus isolate that replicates in cell culture; since most molecular data have been obtained with this isolate, BEV has been acknowledged as the torovirus prototype. Recognition of toroviruses as a new group of potentially pathogenic viruses came seven years after the discovery of BEV, when morphologically similar particles were discovered by electron microscopy (EM) in stool specimens from calves with severe diarrhea in a dairy herd in Breda, Iowa. Despite repeated attempts, BRV has not been adapted to the growth in cell or tissue culture, a problem which has hampered its biochemical, bio-physical, and molecular characterization. However, its pathogenesis and pathology have been studied in the experimentally infected gnotobiotic calves, showing that BRV infections may cause gastroenteritis. Recently, Vanopdenbosch et al. reported the isolation of a torovirus-like virus from the respiratory tract of calves with pneumonia, suggesting that both enterotropic and pneumotropic bovine toroviruses exist. Besides the established toroviruses of horses and cattle, torovirus-like particles (TVLPs) have been found by EM in different animal species; torovirus antibodies appear to be widespread in higher vertebrates, indicating that these viruses infect a broad range of animal hosts. The possibility of a torovirus infecting humans was first reported in 1984 and has become more likely in view of the recent data. This chapter is intended to update the information about toroviruses, and to describe the similarities and differences with the related coronaviruses.


title: Acute ophthalmic artery occlusion in a Covid-19 patient on apixaban

text: Abstract We report a case of ophthalmic artery occlusion (OAO) in a young patient with Covid-19 infection that was on therapeutic anticoagulation with apixaban for deep venous thrombosis (DVT). A 48-year-old man with obesity was hospitalized with a severe form of Covid-19 infection, complicated with acute respiratory failure, septic shock, dilated cardiomyopathy and fungemia. Despite treatment with prophylactic enoxaparin (initial D-Dimer 1.14 µg/ml FEU (normal < 0.05 µg/ml FEU), D-Dimer increased to above 20 µg/ml FEU and patient continued to spike high fevers. This prompted further investigations and upper and lower extremities DVTs were confirmed and managed with enoxaparin 1mg/kg twice daily. D-dimer level decreased to 4.98 µg/ml FEU while on therapeutic anticoagulation. Three weeks later pending hospital discharge, the anticoagulation was switched to oral apixaban 10 mg twice daily. Patient developed acute severe right eye visual loss of no light perception and was diagnosed with incomplete OAO. D-Dimer was elevated at 2.13 µg/ml FEU. Stroke etiological work-up found no embolic sources, resolution of the dilated cardiomyopathy and negative antiphospholipid antibodies. Treatment was changed to enoxaparin and no thrombotic events were encountered to date. Ocular vascular complications have not yet been reported in Covid-19. Controversy exists on the best management algorithm for the hypercoagulable state associated to Covid-19. Either direct oral anticoagulants or low-molecular-weight-heparin are considered appropriate at discharge for patients with venous thromboembolism. The optimum regimen for ischemic stroke prevention and the significance of D-Dimer for anticoagulation monitoring in Covid-19 remain unclear..


title: Post-exposure prophylaxis for Middle East respiratory syndrome in healthcare workers

text: Summary An effective post-exposure prophylaxis (PEP) strategy may limit the spread of infection. However, there is no consensus regarding PEP for Middle East respiratory syndrome coronavirus (MERS-CoV) infection. This study assessed the efficacy of ribavirin and lopinavir/ritonavir as PEP for healthcare workers (HCWs) exposed to patients with severe MERS-CoV pre-isolation pneumonia. The safety of the PEP regimen was assessed. HCWs with high-risk exposure to MERS-CoV pre-isolation pneumonia were retrospectively enrolled. HCWs who received PEP therapy were classified into the PEP group. PEP therapy was associated with a 40% decrease in the risk of infection. There were no severe adverse events during PEP therapy.


title: Detection of New Viruses by VIDISCA: Virus Discovery Based on cDNA-Amplified Fragment Length Polymorphism

text: Virus discovery based on cDNA-AFLP (amplified fragment length polymorphism) (VIDISCA) is a novel approach that provides a fast and effective tool for amplification of unknown genomes, e.g., of human pathogenic viruses. The VIDISCA method is based on double restriction enzyme processing of a target sequence and ligation of oligonucleotide adaptors that subsequently serve as priming sites for amplification. As the method is based on the common presence of restriction sites, it results in the generation of reproducible, species-specific amplification patterns. The method allows amplification and identification of viral RNA/DNA, with a lower cutoff value of 10(5) copies/ml for DNA viruses and 10(6) copies/ml for the RNA viruses. Previously, we described the identification of a novel human coronavirus, HCoV-NL63, with the use of the VIDISCA method.


docid: urhviyme

title: Infection in the critically ill—questions we should be asking

text: Best practice in infection control and management in the critically ill continues to generate considerable debate. The wide variation in current practice is witness to this continuing uncertainty. In large part this is due to the lack of a decent evidence base and to an over-reliance on deep-set dogma. Data that go against the grain are often conveniently overlooked and political imperatives frequently supervene. This article highlights some of these discrepancies and argues for a more balanced, scientific approach. In this time of financial restraint, we need to identify true priorities from both health and economic perspectives, and to see what practices can safely and effectively be modified or abandoned.


title: Community-acquired Pseudomonas aeruginosa-pneumonia in a previously healthy man occupationally exposed to metalworking fluids

text: Although the Pseudomonas aeruginosa infection is well known and frequently found in hospitals and nursing care facilities, many cases are also reported outside these boundaries. In general, this pathogen infects debilitated patients either by comorbidities or by any form of immunodeficiency. In cases of respiratory infection, tobacco abuse seems to play an important role as a risk factor. In previously healthy patients, community-acquired pneumonia (CAP) with P. aeruginosa as the etiological agent is extremely rare, and unlike the cases involving immunocompromised or hospitalized patients, the outcome is severe, and is fatal in up to 61.1% of cases. Aerosolized contaminated water or solutions are closely linked to the development of respiratory tract infection. In this setting, metalworking fluids used in factories may be implicated in CAP involving previously healthy people. The authors report the case of a middle-aged man who worked in a metalworking factory and presented a right upper lobar pneumonia with a rapid fatal outcome. P. aeruginosa was cultured from blood and tracheal aspirates. The autopsy findings confirmed a hemorrhagic necrotizing pneumonia with bacteria-invading vasculitis and thrombosis. A culture of the metalworking fluid of the factory was also positive for P. aeruginosa. The pulsed-field gel electrophoresis showed that both strains (blood culture and metalworking fluid) were genetically indistinguishable. The authors highlight the occupational risk for the development of this P. aeruginosa-infection in healthy people.


Obstetric network reorganization during the COVID-19 pandemic: suggestions from an Italian regional model


title: Quantitative real-time PCR for the measurement of feline cytokine mRNA

text: Abstract We have developed real-time PCR systems to quantitate feline cytokine gene expression. The method is based on the cleavage of fluorescent dye-labelled probes by the 5′–3′ exonuclease activity of the Taq DNA polymerase during PCR and measurement of fluorescence intensity by a Sequence Detection System. The feline-specific TaqMan probes were designed to encompass an intron, thus allowing differentiation of complementary DNA versus genomic DNA amplification products. Quantitative analysis of cytokine cDNA concentrations was performed in comparison to feline GAPDH. Messenger RNA (mRNA) from the universally expressed housekeeping gene GAPDH proved to be useful as an amplification control and allowed for correction of variations in the efficiencies of RNA extraction and reverse transcription. GAPDH mRNAs were readily detectable in cDNAs prepared from unstimulated feline peripheral blood mononuclear cells (PBMCs) and from frozen cell pellets, while cytokines (Interleukin (IL)-4, IL-10, IL-12 p35, IL-12 p40, IFNγ, IL-16) were expressed at variable amounts. IFNγ transcription was found to be upregulated in stimulated PBMCs and feline cell lines. The synthesis of cDNA and the performance of the PCR in separate tubes proved to be of superior sensitivity compared to a single-tube based system. The assays described are highly reproducible, require no post-PCR manipulation of the amplicons and permit the analysis of several hundred PCR reactions per day. With this method it is possible to detect and quantify cytokine mRNA expression reliably in small amounts of cells even after storage of samples for at least 5 years.


title: COVID-19: a perspective for lifting lockdown in Zimbabwe

text: The Coronavirus disease 2019 (Covid-19) scourge has challenged the world’s health systems and presented multiple socio-economic and public health challenges to the states it has affected. Zimbabwe has been affected by the pandemic, and in response, the government has set up an array of measures, including a national lockdown, to curb transmission. While it is critical to maintain such vigorous containment measures, socio-economic pressures in Zimbabwe will challenge the sustainability of the lockdown. Given the potential for lift of the lockdown before the Covid-19 pandemic ends, we discuss the Covid-19 pandemic situation in Zimbabwe and viewpoints on important considerations and strategies for lifting the lockdown.


title: In vitro RNA interference targeting the DNA polymerase gene inhibits orf virus replication in primary ovine fetal turbinate cells

text: Orf, which is caused by orf virus (ORFV), is distributed worldwide and is endemic in most sheep- and/or goat-raising countries. RNA interference (RNAi) pathways have emerged as important regulators of virus-host cell interactions. In this study, the specific effect of RNAi on the replication of ORFV was explored. The application of RNA interference (RNAi) inhibited the replication of ORFV in cell culture by targeting the ORF025 gene of ORFV, which encodes the viral polymerase. Three small interfering RNA (siRNA) (named siRNA704, siRNA1017 and siRNA1388) were prepared by in vitro transcription. The siRNAs were evaluated for antiviral activity against the ORFV Jilin isolate by the observation of cytopathic effects (CPE), virus titration, and real-time PCR. After 48 h of infection, siRNA704, siRNA1017 and siRNA1388 reduced virus titers by 59- to 199-fold and reduced the level of viral replication by 73-89 %. These results suggest that these three siRNAs can efficiently inhibit ORFV genome replication and infectious virus production. RNAi targeting of the DNA polymerase gene is therefore potentially useful for studying the replication of ORFV and may have potential therapeutic applications.


title: Design of an epitope-based peptide vaccine against spike protein of human coronavirus: an in silico approach

text: Human coronavirus (HCoV), a member of Coronaviridae family, is the causative agent of upper respiratory tract infections and “atypical pneumonia”. Despite severe epidemic outbreaks on several occasions and lack of antiviral drug, not much progress has been made with regard to an epitope-based vaccine designed for HCoV. In this study, a computational approach was adopted to identify a multiepitope vaccine candidate against this virus that could be suitable to trigger a significant immune response. Sequences of the spike proteins were collected from a protein database and analyzed with an in silico tool, to identify the most immunogenic protein. Both T cell immunity and B cell immunity were checked for the peptides to ensure that they had the capacity to induce both humoral and cell-mediated immunity. The peptide sequence from 88–94 amino acids and the sequence KSSTGFVYF were found as the most potential B cell and T cell epitopes, respectively. Furthermore, conservancy analysis was also done using in silico tools and showed a conservancy of 64.29% for all epitopes. The peptide sequence could interact with as many as 16 human leukocyte antigens (HLAs) and showed high cumulative population coverage, ranging from 75.68% to 90.73%. The epitope was further tested for binding against the HLA molecules, using in silico docking techniques, to verify the binding cleft epitope interaction. The allergenicity of the epitopes was also evaluated. This computational study of design of an epitope-based peptide vaccine against HCoVs allows us to determine novel peptide antigen targets in spike proteins on intuitive grounds, albeit the preliminary results thereof require validation by in vitro and in vivo experiments.


title: Immunofluorescence versus xTAG multiplex PCR for the detection of respiratory picornavirus infections in children

text: Abstract Background Polymerase chain reaction (PCR) is a sensitive tool for detection of respiratory picornaviruses. However, the clinical relevance of picornavirus detection by PCR is unclear. Immunofluorescence (IF), widely used to detect other respiratory viruses, has recently been introduced as a promising detection method for respiratory picornaviruses. Objectives To compare the clinical manifestations of respiratory picornavirus infections detected by IF with those of respiratory picornavirus infections detected by xTAG multiplex PCR in hospitalized children. Study design During a 1-year period, nasopharyngeal aspirates (NPA) from all children hospitalized due to an acute respiratory infection were prospectively analyzed by IF. All respiratory picornavirus positive IF samples and 100 IF negative samples were further tested with xTAG multiplex PCR. After exclusion of children with co-morbidities and viral co-infections, monoinfections with respiratory picornaviruses were detected in 108 NPA of 108 otherwise healthy children by IF and/or PCR. We compared group 1 children (IF and PCR positive, n =84) with group 2 children (IF negative and PCR positive, n =24) with regard to clinical manifestations of the infection. Results Wheezy bronchitis was diagnosed more often in group 1 than in group 2 (71% vs. 46%, p =0.028). In contrast, group 2 patients were diagnosed more frequently with pneumonia (17% vs. 6%, p =0.014) accompanied by higher levels of C-reactive protein (46mg/l vs. 11mg/l, p =0.009). Conclusions Picornavirus detection by IF in children with acute respiratory infection is associated with the clinical presentation of wheezy bronchitis. The finding of a more frequent diagnosis of pneumonia in picornavirus PCR positive but IF negative children warrants further investigation.


title: Towards Precision Medicine: Inclusion of Sex and Gender Aspects in COVID-19 Clinical Studies—Acting Now before It Is Too Late—A Joint Call for Action

text: The COVID-19 global pandemic is accelerating investigations for effective vaccines and repurposable validated therapeutics [...].


title: Heterogeneity of porcine reproductive and respiratory syndrome virus: implications for current vaccine efficacy and future vaccine development

text: Abstract Porcine reproductive and respiratory syndrome virus (PRRSV) continues to be a major problem to the pork industry worldwide. Increasing data indicate that PRRSV strains differ in virulence in infected pigs and are biologically, antigenically, and genetically heterogeneous. It is evident that the current vaccines, based on a single PRRSV strain, are not effective in protecting against infections with the genetically diverse field strains of PRRSV. The recent outbreaks of atypical or acute PRRS in vaccinated pigs have raised a serious concern about the efficacy of the current vaccines and provided the impetus for developing more effective vaccines. Special attention in this review is given to published work on antigenic, pathogenic and genetic variations of PRRSV and its potential implications for vaccine efficacy and development. Although there are ample data documenting the heterogeneous nature of PRRSV strains, information regarding how the heterogeneity is generated and what clinical impact it may have is very scarce. The observed heterogeneity will likely pose a major obstacle for effective prevention and control of PRRS. There remains an urgent need for fundamental research on this virus to understand the basic biology and the mechanism of heterogeneity and pathogenesis of PRRSV.


From the Editor of Sexuality and Disability: The Impact of COVID-19 on Sexuality and Disability—Are We Closer or More Isolated?


title: Japanese tactics for suppressing COVID-19 spread

text: Abstract COVID-19 infection is overwhelming the world and death toll is steadily increasing. The first wave in Japan seemed to converge with lower death rate than that in most developed countries. In this letter, we describe how Japanese government suppressed the first wave of COPD-19 spread.


title: Role of fusion protein cleavage site in the virulence of Newcastle disease virus

text: Abstract Newcastle disease virus (NDV) causes a highly contagious and economically important disease in poultry. Viral determinants of NDV virulence are not completely understood. The amino acid sequence at the protease cleavage site of the fusion (F) protein has been postulated as a major determinant of NDV virulence. In this study, we have examined the role of F protein cleavage site sequence in NDV virulence using reverse genetics technology. The sequence G-R-Q-G-R present at the cleavage site of the F protein of avirulent strain LaSota was mutated to R-R-Q-K-R, which is present in the F cleavage site of neurovirulent strain Beaudette C (BC). The resultant mutated LaSota V.F. virus did not require exogenous protease for infectivity in cell culture, indicating that the F protein was cleaved by intracellular proteases. The virulence of the mutant and parental viruses was evaluated in vivo by intracerebral pathogenicity index (ICPI) and intravenous pathogenicity index (IVPI) tests in chickens. Our results showed that the modification of the F protein cleavage site resulted in a dramatic increase in virulence from an ICPI value of 0.00 for LaSota to a value of 1.12 for LaSota V.F. However, the ICPI value of LaSota V.F. was lower than that of BC, which had a value of 1.58. Interestingly, the IVPI tests showed values of 0.00 for both LaSota and LaSota V.F. viruses, compared to the IVPI value of 1.45 of BC. In vitro characteristics of the viruses were also studied. Our results demonstrate that the efficiency of cleavage of the F protein plays an important role if the NDV is delivered directly into the brains of chicks, but there could be other viral factors that probably affect peripheral replication, viremia, or entry into the central nervous system.


title: Professional Identity Formation in Disorienting Times

text: COVID‐19 is a major crisis, disrupting all facets of human life. For medical professionals and trainees, the pandemic creates additional concerns about one’s role in providing care, the effectiveness and limitations of medical care, and personal vulnerability to infection and asymptomatic disease spread. These challenges can shape medical students’ professional identity formation (PIF), defined as how learners come to ‘think, act, and feel like a physician.’(1) Medical students develop their identities as emerging professionals through training, and a crisis such as a pandemic alters, impedes, or accelerates this process. A crisis catalyzes transformative learning by serving as a disorienting dilemma, and educators can harness this opportunity for growth.


title: Simulating the spread of COVID-19 via a spatially-resolved susceptible–exposed–infected–recovered–deceased (SEIRD) model with heterogeneous diffusion

text: We present an early version of a Susceptible–Exposed–Infected–Recovered–Deceased (SEIRD) mathematical model based on partial differential equations coupled with a heterogeneous diffusion model. The model describes the spatio-temporal spread of the COVID-19 pandemic, and aims to capture dynamics also based on human habits and geographical features. To test the model, we compare the outputs generated by a finite-element solver with measured data over the Italian region of Lombardy, which has been heavily impacted by this crisis between February and April 2020. Our results show a strong qualitative agreement between the simulated forecast of the spatio-temporal COVID-19 spread in Lombardy and epidemiological data collected at the municipality level. Additional simulations exploring alternative scenarios for the relaxation of lockdown restrictions suggest that reopening strategies should account for local population densities and the specific dynamics of the contagion. Thus, we argue that data-driven simulations of our model could ultimately inform health authorities to design effective pandemic-arresting measures and anticipate the geographical allocation of crucial medical resources.


title: Chapter 6 Virus Population Dynamics Examined with Experimental Model Systems

text: Abstract Experimental evolution permits exploring the effect of controlled environmental variables in virus evolution. Several designs in cell culture and in vivo have established basic concepts that can assist in the interpretation of evolutionary events in the field. Important information has come from cytolytic and persistent infections in cell culture that have unveiled the power of virus-cell coevolution in virus and cell diversification. Equally informative are comparisons of the response of viral populations when subjected to different passage régimes. In particular, plaque-to-plaque transfers in cell culture have revealed unusual genotypes and phenotypes that populate minority layers of viral quasispecies. Some of these viruses display properties that contradict features established in virology textbooks. Several hypotheses and principles of population genetics have found experimental confirmation in experimental designs with viruses. The possibilities of using experimental evolution to understand virus behavior are still largely unexploited.


title: Genomic Analysis and Surveillance of the Coronavirus Dominant in Ducks in China

text: The genetic diversity, evolution, distribution, and taxonomy of some coronaviruses dominant in birds other than chickens remain enigmatic. In this study we sequenced the genome of a newly identified coronavirus dominant in ducks (DdCoV), and performed a large-scale surveillance of coronaviruses in chickens and ducks using a conserved RT-PCR assay. The viral genome harbors a tandem repeat which is rare in vertebrate RNA viruses. The repeat is homologous to some proteins of various cellular organisms, but its origin remains unknown. Many substitutions, insertions, deletions, and some frameshifts and recombination events have occurred in the genome of the DdCoV, as compared with the coronavirus dominant in chickens (CdCoV). The distances between DdCoV and CdCoV are large enough to separate them into different species within the genus Gammacoronavirus. Our surveillance demonstrated that DdCoVs and CdCoVs belong to different lineages and occupy different ecological niches, further supporting that they should be classified into different species. Our surveillance also demonstrated that DdCoVs and CdCoVs are prevalent in live poultry markets in some regions of China. In conclusion, this study shed novel insight into the genetic diversity, evolution, distribution, and taxonomy of the coronaviruses circulating in chickens and ducks.


title: Arbidol (Umifenovir): A Broad-Spectrum Antiviral Drug That Inhibits Medically Important Arthropod-Borne Flaviviruses

text: Arthropod-borne flaviviruses are human pathogens of global medical importance, against which no effective small molecule-based antiviral therapy has currently been reported. Arbidol (umifenovir) is a broad-spectrum antiviral compound approved in Russia and China for prophylaxis and treatment of influenza. This compound shows activities against numerous DNA and RNA viruses. The mode of action is based predominantly on impairment of critical steps in virus-cell interactions. Here we demonstrate that arbidol possesses micromolar-level anti-viral effects (EC(50) values ranging from 10.57 ± 0.74 to 19.16 ± 0.29 µM) in Vero cells infected with Zika virus, West Nile virus, and tick-borne encephalitis virus, three medically important representatives of the arthropod-borne flaviviruses. Interestingly, no antiviral effects of arbidol are observed in virus infected porcine stable kidney cells (PS), human neuroblastoma cells (UKF-NB-4), and human hepatoma cells (Huh-7 cells) indicating that the antiviral effect of arbidol is strongly cell-type dependent. Arbidol shows increasing cytotoxicity when tested in various cell lines, in the order: Huh-7 < HBCA < PS < UKF-NB-4 < Vero with CC(50) values ranging from 18.69 ± 0.1 to 89.72 ± 0.19 µM. Antiviral activities and acceptable cytotoxicity profiles suggest that arbidol could be a promising candidate for further investigation as a potential therapeutic agent in selective treatment of flaviviral infections.


COVID‐19: Impact and challenges at breast imaging unit


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title: Potential therapeutic use of ebselen for COVID-19 and other respiratory viral infections

text: Ebselen is an organoselenium compound exhibiting hydroperoxide- and peroxynitrite-reducing activity, acting as a glutathione peroxidase and peroxiredoxin enzyme mimetic. Ebselen reacts with a multitude of protein thiols, forming a selenosulfide bond, which results in pleiotropic effects of antiviral, antibacterial and anti-inflammatory nature. The main protease (M(pro)) of the corona virus SARS-CoV-2 is a potential drug target, and a screen with over 10,000 compounds identified ebselen as a particularly promising inhibitor of M(pro) (Jin, Z. et al. (2020) Nature 582, 289–293). We discuss here the reaction of ebselen with cysteine proteases, the role of ebselen in infections with viruses and with other microorganisms. We also discuss effects of ebselen in lung inflammation. In further research on the inhibition of M(pro) in SARS-CoV-2, ebselen can serve as a promising lead compound, if the inhibitory effect is confirmed in intact cells in vivo. Independently of this action, potential beneficial effects of ebselen in COVID-19 are ascribed to a number of targets critical to pathogenesis, such as attenuation of inflammatory oxidants and cytokines.


title: Pediatric COVID-19-associated rhabdomyolysis: a case report

text: COVID-19 is the illness caused by infection with the novel coronavirus SARS-CoV-2. Although myalgia is common in adults, it has not been noted as a common symptom in children. There have been a few reported cases of COVID-19-associated rhabdomyolysis in adults. This case report describes a 16-year-old boy who presented with fever, myalgias, mild shortness of breath with exertion, and dark-colored urine. COVID-19 PCR was positive. His initial creatinine kinase (CK) level was 427,656 U/L. Serum creatinine was normal for age. He was treated with isotonic intravenous fluids containing sodium bicarbonate to maintain urine output of 100–200 mL/h and urine pH > 7.0. His serum creatinine remained normal throughout the hospital stay and he was discharged on hospital day 12 with a CK of 6526 U/L. To our knowledge, no pediatric cases of COVID-19-associated rhabdomyolysis have been previously reported. Adult cases of rhabdomyolysis have been reported and a few reports have noted patients with elevated CK levels without rhabdomyolysis. Given this pediatric case of COVID-19-associated rhabdomyolysis, pediatric clinicians should be aware of this complication and manage fluids appropriately in order to prevent acute kidney injury.


title: Does form meet function in the coronavirus replicative organelle?

text: If we use the analogy of a virus as a living entity, then the replicative organelle is the part of the body where its metabolic and reproductive activities are concentrated. Recent studies have illuminated the intricately complex replicative organelles of coronaviruses, a group that includes the largest known RNA virus genomes. This review takes a virus-centric look at the coronavirus replication transcription complex organelle in the context of the wider world of positive sense RNA viruses, examining how the mechanisms of protein expression and function act to produce the factories that power the viral replication cycle.


title: Human Bocavirus, a Respiratory and Enteric Virus

text: In Spain, human bocavirus (HBoV) was detected in 48 (9.1%) of 527 children with gastroenteritis at similar frequency as for children with respiratory illness (40/520, 7.7%). Fecal excretion adds new concern about the transmission of HBoV. To our knowledge, this report is the first to document HBoV in human feces.


title: Human Metapneumovirus-associated Atypical Pneumonia and SARS

text: Acute pneumonia developed in a previously healthy man during the outbreak of severe acute respiratory syndrome (SARS) in southern China in March 2003. Antibiotic treatment was ineffective, and he died 8 days after illness onset. Human metapneumovirus was isolated from lung tissue. No other pathogen was found. Other etiologic agents should thus be sought in apparent SARS cases when coronavirus infection cannot be confirmed.


title: Performance of six SARS-CoV-2 immunoassays in comparison with microneutralisation

text: There is an urgent need for reliable high-throughput serological assays for the management of the ongoing COVID-19 pandemic. Preferably, the performance of serological tests for a novel virus should be determined with clinical specimens against a gold standard, i.e. virus neutralisation. We compared the performance of six commercial immunoassays for the detection of SARS-CoV-2 IgG, IgA and IgM antibodies, including four automated assays [Abbott SARS-COV-2 IgG (CE marked), Diasorin Liaison® SARS-CoV-2 S1/S2 IgG (research use only, RUO), and Euroimmun SARS-CoV-2 IgG and IgA (CE marked)], and two rapid lateral flow (immunocromatographic) tests [Acro Biotech 2019-nCoV IgG/IgM (CE marked) and Xiamen Biotime Biotechnology SARS-CoV-2 IgG/IgM (CE marked)] with a microneutralisation test (MNT). Two specimen panels from serum samples sent to Helsinki University Hospital Laboratory (HUSLAB) were compiled: the patient panel (N=70) included sera from PCR confirmed COVID-19 patients, and the negative panel (N=81) included sera sent for screening of autoimmune diseases and respiratory virus antibodies in 2018 and 2019. The MNT was carried out for all COVID-19 samples (70 serum samples, 62 individuals) and for 53 samples from the negative panel. Forty-one out of 62 COVID-19 patients showed neutralising antibodies.The specificity and sensitivity values of the commercial tests against MNT, respectively, were as follows: 95.1%/80.5% (Abbott Architect SARS-CoV-2 IgG), 94.9%/43.8% (Diasorin Liaison SARS-CoV-2 IgG; RUO), 68.3%/87.8% (Euroimmun SARS-CoV-2 IgA), 86.6%/70.7% (Euroimmun SARS-CoV-2 IgG), 74.4%/56.1% (Acro 2019-nCoV IgG), 69.5%/46.3% (Acro 2019-nCoV IgM), 97.5%/71.9% (Xiamen Biotime SARS-CoV-2 IgG), and 88.8%/81.3% (Xiamen Biotime SARS-CoV-2 IgM). This study shows variable performance values. Laboratories should carefully consider their testing process, such as a two-tier approach, in order to optimize the overall performance of SARS- CoV-2 serodiagnostics.


title: Viral infections in workers in hospital and research laboratory settings: a comparative review of infection modes and respective biosafety aspects

text: Summary Objectives To compare modes and sources of infection and clinical and biosafety aspects of accidental viral infections in hospital workers and research laboratory staff reported in scientific articles. Methods PubMed, Google Scholar, ISI Web of Knowledge, Scirus, and Scielo were searched (to December 2008) for reports of accidental viral infections, written in English, Portuguese, Spanish, or German; the authors’ personal file of scientific articles and references from the articles retrieved in the initial search were also used. Systematic review was carried out with inclusion criteria of presence of accidental viral infection's cases information, and exclusion criteria of absence of information about the viral etiology, and at least probable mode of infection. Results One hundred and forty-one scientific articles were obtained, 66 of which were included in the analysis. For arboviruses, 84% of the laboratory infections had aerosol as the source; for alphaviruses alone, aerosol exposure accounted for 94% of accidental infections. Of laboratory arboviral infections, 15.7% were acquired percutaneously, whereas 41.6% of hospital infections were percutaneous. For airborne viruses, 81% of the infections occurred in laboratories, with hantavirus the leading causative agent. Aerosol inhalation was implicated in 96% of lymphocytic choriomeningitis virus infections, 99% of hantavirus infections, and 50% of coxsackievirus infections, but infective droplet inhalation was the leading mode of infection for severe acute respiratory syndrome coronavirus and the mucocutaneous mode of infection was involved in the case of infection with influenza B. For blood-borne viruses, 92% of infections occurred in hospitals and 93% of these had percutaneous mode of infection, while among laboratory infections 77% were due to infective aerosol inhalation. Among blood-borne virus infections there were six cases of particular note: three cases of acute hepatitis following hepatitis C virus infection with a short period of incubation, one laboratory case of human immunodeficiency virus infection through aerosol inhalation, one case of hepatitis following hepatitis G virus infection, and one case of fulminant hepatitis with hepatitis B virus infection following exposure of the worker's conjunctiva to hepatitis B virus e antigen-negative patient saliva. Of the 12 infections with viruses with preferential mucocutaneous transmission, seven occurred percutaneously, aerosol was implicated as a possible source of infection in two cases, and one atypical infection with Macacine herpesvirus 1 with fatal encephalitis as the outcome occurred through a louse bite. One outbreak of norovirus infection among hospital staff had as its probable mode of infection the ingestion of inocula spread in the environment by fomites. Conclusions The currently accepted and practiced risk analysis of accidental viral infections based on the conventional dynamics of infection of the etiological agents is insufficient to cope with accidental viral infections in laboratories and to a lesser extent in hospitals, where unconventional modes of infection are less frequently present but still have relevant clinical and potential epidemiological consequences. Unconventional modes of infection, atypical clinical development, or extremely severe cases are frequently present together with high viral loads and high virulence of the agents manipulated in laboratories. In hospitals by contrast, the only possible association of atypical cases is with the individual resistance of the worker. Current standard precaution practices are insufficient to prevent most of the unconventional infections in hospitals analyzed in this study; it is recommended that special attention be given to flaviviruses in these settings.


title: Severe Legionella pneumonia: Rapid presumptive clinical diagnosis with Winthrop-University Hospital's weighted point score system (modified)

text: Legionnaires' disease is a systemic infection involving the lungs and accompanied by a characteristic pattern of extrapulmonary organ involvement. Legionnaires' disease is one of the non-zoonotic causes of atypical community-acquired pneumonia (CAP). Legionnaires' disease commonly presents as severe CAP requiring hospitalization and intensive care. Each atypical CAP has its own characteristic pattern of extrapulmonary laboratory clinical findings and abnormalities that are the basis of clinical syndromic diagnosis. Studies have been unsuccessful in identifying individual clinical and laboratory parameters that are specific for Legionella. Individually, clinical and laboratory abnormalities lack diagnostic specificity. The diagnostic specificity of clinical and laboratory findings is increased when combined and are the basis of a clinical syndromic diagnosis. The importance of serial nonspecific laboratory abnormalities with Legionnaires' disease is emphasized. The sensitivity and specificity of a clinical syndromic diagnosis are enhanced if they are based on a weighted point score system. A diagnostic weighted point score system is based on the varying diagnostic importance of clinical and laboratory diagnostic findings. The Winthrop-University Hospital's Infectious Disease Division's rapid clinical diagnostic weighted point system is based on a weighted point score of clinical and laboratory findings. The case presented is that of a 55-year-old man with severe CAP who required hospitalization and intensive care admission. The presumptive clinical diagnosis of Legionella CAP was based on the Winthrop-University Hospital Infectious Disease Division's weighted point score system, which permitted early empiric anti-Legionella antimicrobial therapy and prompted specific Legionella testing. Legionnaires' disease is definitively diagnosed by serology or a urinary Legionella antigen test. This case of severe Legionnaires' CAP was confirmed by urinary antigen test reported on hospital day 6. The Winthrop-University Hospital is weighted point score system (modified) permits a rapid clinical presumptive diagnosis of Legionnaires' disease and is an accurate predictor of Legionella CAP.


title: Oncolytic viruses in cancer therapy

text: Abstract Oncolytic virotherapy is a promising form of gene therapy for cancer, employing nature’s own agents to find and destroy malignant cells. The purpose of this review is to provide an introduction to this very topical field of research and to point out some of the current observations, insights and ideas circulating in the literature. We have strived to acknowledge as many different oncolytic viruses as possible to give a broader picture of targeting cancer using viruses. Some of the newest additions to the panel of oncolytic viruses include the avian adenovirus, foamy virus, myxoma virus, yaba-like disease virus, echovirus type 1, bovine herpesvirus 4, Saimiri virus, feline panleukopenia virus, Sendai virus and the non-human coronaviruses. Although promising, virotherapy still faces many obstacles that need to be addressed, including the emergence of virus-resistant tumor cells.


Experts’ request to the Spanish Government: move Spain towards complete lockdown


title: Antimicrobial peptides: agents of border protection for companion animals

text: Over the past 20 years, there have been significant inroads into understanding the roles of antimicrobial peptides in homeostatic functions and their involvement in disease pathogenesis. In addition to direct antimicrobial activity, these peptides participate in many cellular functions, including chemotaxis, wound healing, and even determination of canine coat colour. Various biologic and genetic approaches have helped to elucidate the role of antimicrobial peptide with respect innate immunity and host defense. Associations of antimicrobial peptides with various skin diseases, including psoriasis, rosacea and atopic dermatitis, have been documented in humans. In the longer term, therapeutic modulation of antimicrobial peptide expression may provide effective new treatments for disease. This review highlights current knowledge about antimicrobial peptides of the skin and circulating leukocytes, with particular focus on relevance to physiology and disease in companion animals.


title: Implementation of an Alert and Response System in Haiti during the Early Stage of the Response to the Cholera Epidemic

text: The start of the cholera epidemic in Haiti quickly highlighted the necessity of the implementation of an Alert and Response (A&R) System to complement the existing national surveillance system. The national system had been able to detect and confirm the outbreak etiology but required external support to monitor the spread of cholera and coordinate response, because much of the information produced was insufficiently timely for real-time monitoring and directing of a rapid, targeted response. The A&R System was designed by the Pan American Health Organization/World Health Organization in collaboration with the Haiti Ministry of Health, and it was based on a network of partners, including any institution, structure, or individual that could identify, verify, and respond to alerts. The defined objectives were to (1) save lives through early detection and treatment of cases and (2) control the spread through early intervention at the community level. The operational structure could be broken down into three principle categories: (1) alert (early warning), (2) verification and assessment of the information, and (3) efficient and timely response in coordination with partners to avoid duplication. Information generated by the A&R System was analyzed and interpreted, and the qualitative information was critical in qualifying the epidemic and defining vulnerable areas, particularly because the national surveillance system reported incomplete data for more than one department. The A&R System detected a number of alerts unrelated to cholera and facilitated rapid access to that information. The sensitivity of the system and its ability to react quickly was shown in May of 2011, when an abnormal increase in alerts coming from several communes in the Sud-Est Department in epidemiological weeks (EWs) 17 and 18 were noted and disseminated network-wide and response activities were implemented. The national cholera surveillance system did not register the increase until EWs 21 and 22, and the information did not become available until EWs 23 and 24, when the peak of cases had already been reached. Although many of the partners reporting alerts during the peak of the cholera epidemic have since left Haiti, the A&R System has continued to function as an Early Warning (EWARN) System, and it continues to be developed with recent activities, such as the distribution of cell phones to enhance alert communication.


title: SARS-associated Coronavirus Transmitted from Human to Pig

text: SEVERE ACUTE RESPIRATORY SYNDROME–ASSOCIATED: coronavirus (SARS-CoV) was isolated from a pig during a survey for possible routes of viral transmission after a SARS epidemic. Sequence and epidemiology analyses suggested that the pig was infected by a SARS-CoV of human origin.


title: Detection and molecular characterization of infectious bronchitis virus isolated from recent outbreaks in broiler flocks in Thailand

text: Thirteen field isolates of infectious bronchitis virus (IBV) were isolated from broiler flocks in Thailand between January and June 2008. The 878-bp of the S1 gene covering a hypervariable region was amplified and sequenced. Phylogenetic analysis based on that region revealed that these viruses were separated into two groups (I and II). IBV isolates in group I were not related to other IBV strains published in the GenBank database. Group 1 nucleotide sequence identities were less than 85% and amino acid sequence identities less than 84% in common with IBVs published in the GenBank database. This group likely represents the strains indigenous to Thailand. The isolates in group II showed a close relationship with Chinese IBVs. They had nucleotide sequence identities of 97-98% and amino acid sequence identities 96-98% in common with Chinese IBVs (strain A2, SH and QXIBV). This finding indicated that the recent Thai IBVs evolved separately and at least two groups of viruses are circulating in Thailand.


title: Clinical Features, Virus Identification and Sinusitis as a Complication of Upper Respiratory Tract Illness in Children Ages 4-7 Years

text: OBJECTIVE: To determine the rate of sinusitis complicating upper respiratory tract illnesses (URIs) for children in whom we prospectively identified the clinical, virologic, and epidemiologic characteristics of URIs in a population of 4 to 7 year old children followed for one year. STUDY DESIGN: This was an observational cohort study in two primary care pediatric practices in Madison, WI. Nasal samples were obtained during 4 asymptomatic surveillance visits and during symptomatic URIs. A polymerase chain reaction-based assay for 9 respiratory viruses was performed on nasal samples. A diagnosis of sinusitis was based on published criteria. RESULTS: 236 children ages 48-96 months were enrolled. A total of 327 URIs were characterized. The mean number of URIs per child was 1.3 (range 0-9) per year. Viruses were detected in 81% of URIs; rhinovirus (RV) was most common. Seventy-two percent of URIs were resolved clinically by the tenth day. RV-A and RV-C were detected more frequently at URI visits; RV-B was detected at the same rate for both asymptomatic surveillance visits and URI visits. Sinusitis was diagnosed in 8.8% of symptomatic URIs. Viruses were detected frequently (33%) in samples from asymptomatic children. CONCLUSIONS: Sinusitis occured in 8.8% of symptomatic URIs in our study. The virus most frequently detected with URIs in children was RV; RV-A and RV-C detection but not RV-B detection were associated with illness. Viruses, especially RV, are detected frequently in asymptomatic children. Most URIs have improved or resolved by the tenth day after onset. Children experienced a mean of 1.3 URIs per year which was lower than expected.


An underestimated “false negative COVID cholecystitis” in Northern Italy and the contagion of a surgical ward: it can happen everywhere


title: Precision Surveillance for Viral Respiratory Pathogens: Virome Capture Sequencing for the Detection and Genomic Characterization of Severe Acute Respiratory Infection in Uganda

text: BACKGROUND: Precision public health is a novel set of methods to target disease prevention and mitigation interventions to high-risk subpopulations. We applied a precision public health strategy to syndromic surveillance for severe acute respiratory infection (SARI) in Uganda by combining spatiotemporal analytics with genomic sequencing to detect and characterize viral respiratory pathogens with epidemic potential. METHODS: Using a national surveillance network we identified patients with unexplained, influenza-negative SARI from 2010 to 2015. Spatiotemporal analyses were performed retrospectively to identify clusters of unexplained SARI. Within clusters, respiratory viruses were detected and characterized in naso- and oropharyngeal swab samples using a novel oligonucleotide probe capture (VirCapSeq-VERT) and high-throughput sequencing platform. Linkage to conventional epidemiologic strategies further characterized transmission dynamics of identified pathogens. RESULTS: Among 2901 unexplained SARI cases, 9 clusters were detected, accounting for 301 (10.4%) cases. Clusters were more likely to occur in urban areas and during biannual rainy seasons. Within detected clusters, we identified an unrecognized outbreak of measles-associated SARI; sequence analysis implicated cocirculation of endemic genotype B3 and genotype D4 likely imported from England. We also detected a likely nosocomial SARI cluster associated with a novel picobirnavirus most closely related to swine and dromedary viruses. CONCLUSIONS: Using a precision approach to public health surveillance, we detected and characterized the genomics of vaccine-preventable and zoonotic respiratory viruses associated with clusters of severe respiratory infections in Uganda. Future studies are needed to assess the feasibility, scalability, and impact of applying similar approaches during real-time public health surveillance in low-income settings.


title: KDELR2 Competes with Measles Virus Envelope Proteins for Cellular Chaperones Reducing Their Chaperone-Mediated Cell Surface Transport

text: Recently, we found that the cytidine deaminase APOBEC3G (A3G) inhibits measles (MV) replication. Using a microarray, we identified differential regulation of several host genes upon ectopic expression of A3G. One of the up-regulated genes, the endoplasmic reticulum (ER) protein retention receptor KDELR2, reduced MV replication ~5 fold when it was over-expressed individually in Vero and CEM-SS T cells. Silencing of KDELR2 in A3G-expressing Vero cells abrogated the antiviral activity induced by A3G, confirming its role as an A3G-regulated antiviral host factor. Recognition of the KDEL (Lys-Asp-Glu-Leu) motif by KDEL receptors initiates the retrograde transport of soluble proteins that have escaped the ER and play an important role in ER quality control. Although KDELR2 over-expression reduced MV titers in cell cultures, we observed no interaction between KDELR2 and the MV hemagglutinin (H) protein. Instead, KDELR2 retained chaperones in the ER, which are required for the correct folding and transport of the MV envelope glycoproteins H and fusion protein (F) to the cell surface. Our data indicate that KDELR2 competes with MV envelope proteins for binding to calnexin and GRP78/Bip, and that this interaction limits the availability of the chaperones for MV proteins, causing the reduction of virus spread and titers.


title: Prognostic value of interleukin-6, C-reactive protein, and procalcitonin in patients with COVID-19

text: Abstract Background The inflammatory response plays a critical role in coronavirus disease 2019 (COVID-19), and inflammatory cytokine storm increases the severity of COVID-19. Objective To investigate the ability of interleukin-6 (IL-6), C-reactive protein (CRP), and procalcitonin (PCT) to predict mild and severe cases of COVID-19. Study design This retrospective cohort study included 140 patients diagnosed with COVID-19 from January 18, 2020, to March 12, 2020. The study population was divided into two groups according to disease severity: a mild group (MG) (n = 107) and a severe group (SG) (n = 33). Data on demographic characteristics, baseline clinical characteristics, and the levels of IL-6, CRP, and PCT on admission were collected. Results Among the 140 patients, the levels of IL-6, CRP, and PCT increased in 95 (67.9 %), 91 (65.0 %), and 8 (5.7 %) patients on admission, respectively. The proportion of patients with increased IL-6, CRP, and PCT levels was significantly higher in the SG than in the MG. Cox proportional hazard model showed that IL-6 and CRP could be used as independent factors to predict the severity of COVID-19. Furthermore, patients with IL-6 > 32.1 pg/mL or CRP > 41.8 mg/L were more likely to have severe complications. Conclusion The serum levels of IL-6 and CRP can effectively assess disease severity and predict outcome in patients with COVID-19.


title: Epidemiology of a Novel Recombinant Middle East Respiratory Syndrome Coronavirus in Humans in Saudi Arabia

text: BACKGROUND: Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe respiratory illness in humans. Fundamental questions about circulating viruses and transmission routes remain. METHODS: We assessed routinely collected epidemiologic data for MERS-CoV cases reported in Saudi Arabia during 1 January– 30 June 2015 and conducted a more detailed investigation of cases reported during February 2015. Available respiratory specimens were obtained for sequencing. RESULTS: During the study period, 216 MERS-CoV cases were reported. Full genome (n = 17) or spike gene sequences (n = 82) were obtained from 99 individuals. Most sequences (72 of 99 [73%]) formed a discrete, novel recombinant subclade (NRC-2015), which was detected in 6 regions and became predominant by June 2015. No clinical differences were noted between clades. Among 87 cases reported during February 2015, 13 had no recognized risks for secondary acquisition; 12 of these 13 also denied camel contact. Most viruses (8 of 9) from these 13 individuals belonged to NRC-2015. DISCUSSIONS: Our findings document the spread and eventual predominance of NRC-2015 in humans in Saudi Arabia during the first half of 2015. Our identification of cases without recognized risk factors but with similar virus sequences indicates the need for better understanding of risk factors for MERS-CoV transmission.


title: The COVID-19 pandemic: considerations for the waste and wastewater services sector

text: Abstract This article discusses the potential ramifications of the COVID-19 pandemic on waste and wastewater services, focusing on critical points where alternative operating procedures or additional mitigation measures may be advisable. Key concerns are (i) the long half-life of the virus on materials such as waste containers, bags, and in wastewater, and (ii) possible transmission via contaminated waste surfaces and aerosols from wastewater systems. There are opportunities to further the science of wastewater-based epidemiology by monitoring viral RNA in wastewater to assess disease prevalence and spread in defined populations, which may prove beneficial for informing COVID-19 related public health policy.


title: Anti-SARS-CoV immunity induced by a novel CpG oligodeoxynucleotide

text: Abstract To develop CpG oligodeoxynucleotides (CpG ODNs) based therapy for prevention and treatment of severe acute respiratory syndrome (SARS), we selected a novel CpG ODN (BW001), which displays B-type CpG ODN structure feature at the 5′ and A-type CpG ODN structure feature at the 3′, and tested for its anti-SARS-CoV activity. We found that the supernatants of human PBMCs stimulated by BW001 significantly protected Vero cells from SARS-CoV infection. BW001 could stimulate human PBMCs and pDCs to secrete high level of IFN-α and promote human PBMCs and B cells to proliferate. Furthermore, we demonstrated that BW001 could activate CD19+ B cells and CD56+ NK cells in human PBMCs. In addition, BW001 could enhance NK cytotoxicity and IFN-γ secretion in human PBMCs. Together, BW001 represents a novel type of CpG ODN and may have potential for the development of treatment and prevention for SARS as well as other viral associated diseases.


title: Specific Viruses Detected in Nigerian Children in Association with Acute Respiratory Disease

text: Occurrence of different viruses in acute respiratory tract infections of Nigerian children was examined. Respiratory swabs were collected from 246 children referred to hospital clinics because of acute respiratory symptoms from February through May 2009. Validated real-time RT-PCR techniques revealed nucleic acids of at least one virus group in 189 specimens (77%). Human rhinoviruses and parainfluenza viruses were present each in one third of the children. Adenoviruses, enteroviruses, human metapneumovirus, human bocavirus, and influenza C virus were also relatively common. Possibly due to their seasonal occurrence, influenza A and B virus, and respiratory syncytial virus were detected rarely. We conclude that all major groups of respiratory tract viruses are causing illness in Nigerian children.


title: Intriguing interplay between feline infectious peritonitis virus and its receptors during entry in primary feline monocytes

text: Abstract Two potential receptors have been described for the feline infectious peritonitis virus (FIPV): feline aminopeptidase N (fAPN) and feline dendritic cell-specific intercellular adhesion molecule grabbing non-integrin (fDC-SIGN). In cell lines, fAPN serves as a receptor for serotype II, but not for serotype I FIPV. The role of fAPN in infection of in vivo target cells, monocytes, is not yet confirmed. Both serotype I and II FIPVs use fDC-SIGN for infection of monocyte-derived cells but how is not known. In this study, the role of fAPN and fDC-SIGN was studied at different stages in FIPV infection of monocytes. First, the effects of blocking the potential receptor(s) were studied for the processes of attachment and infection. Secondly, the level of co-localization of FIPV and the receptors was determined. It was found that FIPV I binding and infection were not affected by blocking fAPN while blocking fDC-SIGN reduced FIPV I binding to 36% and practically completely inhibited infection. Accordingly, 66% of bound FIPV I particles co-localized with fDC-SIGN. Blocking fAPN reduced FIPV II binding by 53% and infection by 80%. Further, 60% of bound FIPV II co-localized with fAPN. fDC-SIGN was not involved in FIPV II binding but infection was reduced with 64% when fDC-SIGN was blocked. In conclusion, FIPV I infection of monocytes depends on fDC-SIGN. Most FIPV I particles already interact with fDC-SIGN at the plasma membrane. For FIPV II, both fAPN and fDC-SIGN are involved in infection with only fAPN playing a receptor role at the plasma membrane.


MERS-CoV: transmisión y el papel de nuevas especies hospederas


title: A permanent host shift of rabies virus from Chiroptera to Carnivora associated with recombination

text: Bat virus host shifts can result in the spread of diseases with significant effects. The rabies virus (RABV) is able to infect almost all mammals and is therefore a useful model for the study of host shift mechanisms. Carnivore RABVs originated from two historical host shifts from bat viruses. To reveal the genetic pathways by which bat RABVs changed their host tropism from bats to carnivores, we investigated the second permanent bat-to-carnivore shift resulting in two carnivore variants, known as raccoon RABV (RRV) and south-central skunk RABV (SCSKV). We found that their glycoprotein (G) genes are the result of recombination between an American bat virus and a carnivore virus. This recombination allowed the bat RABV to acquire the head of the G-protein ectodomain of the carnivore virus. This region is involved in receptor recognition and binding, response to changes in the pH microenvironment, trimerization of G proteins, and cell-to-cell transmission during the viral infection. Therefore, this recombination event may have significantly improved the variant’s adaptability to carnivores, altering its host tropism and thus leading to large-scale epidemics in striped skunk and raccoon.


title: Mismatch Extension During Strong Stop Strand Transfer and Minimal Homology Requirements for Replicative Template Switching During Moloney Murine Leukemia Virus Replication

text: Abstract Reverse transcription requires two replicative template switches, called minus and plus strand strong stop transfer, and can include additional, recombinogenic switches. Donor and acceptor template homology facilitates both replicative and recombinogenic transfers, but homology-independent determinants may also contribute. Here, improved murine leukemia virus-based assays were established and the effects of varying extents of mismatches and complementarity between primer and acceptor template regions were assessed. Template switch accuracy was addressed by examining provirus structures, and efficiency was measured using a competitive titer assay. The results demonstrated that limited mismatch extension occurred readily during both minus and plus strand transfer. A strong bias for correct targeting to the U3/R junction and against use of alternate regions of homology was observed during minus strand transfer. Transfer to the U3/R junction was as accurate with five bases of complementarity as it was with an intact R, and as few as 3nt targeted transfer to a limited extent. In contrast, 12 base recombinogenic acceptors were utilized poorly and no accurate switch was observed when recombination acceptors retained only five bases of complementarity. These findings confirm that murine leukemia virus replicative and recombinogenic template switches differ in homology requirements, and support the notion that factors other than primer–template complementarity may contribute to strong stop acceptor template recognition.


title: Evaluation of 793/B-like and Mass-like vaccine strain kinetics in experimental and field conditions by real-time RT-PCR quantification

text: Infectious bronchitis virus (IBV) is a great economic burden both for productive losses and costs of the control strategies. Many different vaccination protocols are applied in the same region and even in consecutive cycles on the same farm in order to find the perfect balance between costs and benefits. In Northern Italy, the usual second vaccination is more and more often moved up to the chick's first d of life. The second strain administration together with the common Mass priming by spray at the hatchery allows saving money and time and reducing animal stress. The present work compared the different vaccine strains (Mass-like or B48, and 1/96) kinetics both in field conditions and in a 21-day-long experimental trial in broilers, monitoring the viral replication by upper respiratory tract swabbing and vaccine specific real time reverse transcription PCR (RT-PCR) quantification. In both field and experimental conditions, titers for all the vaccines showed an increasing trend in the first 2 wk and then a decrease, though still remaining detectable during the whole monitored period. IBV field strain and avian Metapneumovirus (aMPV) presence also was also investigated by RT-PCR and sequencing, and by multiplex real-time RT-PCR, respectively, revealing a consistency in the pathogen introduction timing at around 30 d, in correspondence with the vaccine titer's main decrease. These findings suggest the need for an accurate knowledge of live vaccine kinetics, whose replication can compete with the other pathogen one, providing additional protection to be added to what is conferred by the adaptive immune response.


title: Kinetics and pattern of viral excretion in biological specimens of two MERS-CoV cases

text: Abstract Background Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging coronavirus involved in severe acute respiratory distress syndrome (ARDS) and rapid renal failure. Hospital outbreak and nosocomial transmission were reported, however, several issues remain on the viral excretion course. Objectives Describe the kinetics and pattern of viral excretion in two infected patients. Study design After the initial diagnosis, blood, urine, rectal and respiratory samples were collected regularly, aliquoted and stored at −80°C. Real-time reverse transcriptase polymerase chain reaction assay targeted the UpE and Orf1a regions of the MERS-CoV genome. Results In patient 1, who died of refractory ARDS and renal failure, MERS-CoV RNA was detected in pharyngeal and tracheal swabs, as well blood samples and urine samples until the 30th day. Rectal swabs were negative. Patient 2 also developed multiple-organ failure, but survived, with persisting renal insufficiency (creatinine clearance at 30mL/min) and persistent interstitial syndrome albeit weaned off mechanical ventilation and no longer requiring oxygen. Tracheal aspirations were positive until the 33rd day, while nasopharyngeal swabs were negative. All other biological samples were negative. Discussion Lower respiratory tract excretion of MERS-CoV could be observed for more than one month. The most severely ill patient presented an expression of the virus in blood and urine, consistent with a type-1 interferon mediated immunological response impaired in patient 1, but developed by patient 2. These results suggest that infection control precautions must be adequately evaluated in clinical wards and laboratories exposed to MERS-CoV.


docid: uhmxkvit

title: 2019-Novel Coronavirus-Related Acute Cardiac Injury Cannot Be Ignored

text: PURPOSE OF THE REVIEW: Coronavirus disease 2019 (COVID-19), a new infectious disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has reached a pandemic status. Although SARSCoV-2 causes primarily respiratory problems, concurrent cardiac injury cannot be ignored since it may be an independent predictor for adverse outcomes. To resolve these issues, we aim to summarize the prevalence and its underlying mechanisms of acute cardiac injury in the setting of SARS-CoV-2 infection. RECENT FINDINGS: The main clinical manifestation of SARS-CoV-2 infection is pneumonia, cardiovascular complications have also been identified in the earliest reported cases from Wuhan, the epicenter of the outbreak. Given the SARS-CoV-2 likely uses the angiotensin-converting enzyme-2 (ACE2) receptors as its host receptor, ACE2-related signaling pathways may play a key role in mediating myocardial injury. SUMMARY: SARS-CoV-2 infection related acute cardiac injury cannot be ignored, and its underlying mechanisms remain speculated. We would suggest that health professionals investigate cardiac function as part of the routine care.


title: Inhibitory effect of Phyllanthus urinaria L. extract on the replication of lamivudine-resistant hepatitis B virus in vitro

text: BACKGROUND: Long-term treatment of chronic hepatitis B (CHB) with nucleos(t)ide analogs results in the emergence of drug-resistant hepatitis B virus (HBV) harboring mutations in the polymerase (P) gene. The Phyllanthus extract has anti-HBV activity; however, its antiviral activity against lamivudine (LMV)-resistant mutants has not been examined. METHODS: HBV harboring LMV-resistant mutations (rtM204I, rtM204V, and rtM204S) in the P gene at the YMDD ((203)tyrosine-methionine-aspartate-aspartate(206)) reverse transcriptase (RT) active site were generated and their sensitivity to Phyllanthus urinaria koreanis extract examined. Southern blotting and real-time PCR were used to determine the concentration of plant extract required to inhibit HBV DNA synthesis by 50 and 90 % (EC(50) and EC(90), respectively). An enzyme-linked immunosorbent assay was used to measure the EC(50) of HBV surface antigen (HBsAg) and HBV core antigen (HBcAg) secretion, and the 50 % cytotoxic concentration of the extract was measured in a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Real-time RT-PCR was used to measure mRNA expression levels. RESULTS: The expression of intracellular HBV DNAs in HBV WT- or mutant-transfected HepG2 cells decreased upon treatment with Phyllanthus extract. The secretion of HBsAg and HBcAg also fell in a dose-dependent manner. Phyllanthus extract induced interferon-beta (IFN-β), cyclooxygenase-2 (COX-2), and interleukin-6 (IL-6) mRNA expression in HBV WT-transfected HepG2 cells, possibly via activation of extracellular signal-regulated kinases and c-jun N-terminal kinases and the induction of retinoic acid inducible gene-I, toll-like receptor 3, myeloid differentiation primary response gene 88, and/or tumor necrosis factor receptor-associated factor 6 gene expression. HBV transfection in the absence of extract or exposure of cells to extract alone did not trigger these signaling cascades. CONCLUSIONS: Phyllanthus extract inhibited HBV DNA synthesis and HBsAg and HBcAg secretion by replicating cells harboring HBV wild-type and LMV-resistant mutants, likely by inducing the expression of IFN-β, COX-2, and IL-6. These data indicate that Phyllanthus extract may be useful as an alternative therapeutic agent for the treatment of drug-resistant CHB patients. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12906-015-0792-3) contains supplementary material, which is available to authorized users.


Is Brazil prepared for the new era of infectious disease epidemics?


title: A self-assessment of the Thai Department of Disease Control's communication for international response at early phase to the COVID-19

text: Abstract Objectives This study aimed to assess the Thailand Department of Disease Control's (DDC) early responses to COVID-19 in respects to communication with the international community and to identify the manner of Thailand's response during public health emergencies. Methods Documents and international response communication from 4 to 31 January 2020 were reviewed and dates of responses were collected for descriptive analysis. A questionnaire was submitted to the DDC officers responsible for international coordination. A meeting to identify responses was held to evaluate the self-assessed capacities of the department's international communication. Results Thailand began the COVID-19 screening protocol on 3 January 2020. International correspondence subsequently occurred continually either through the ASEAN or International Health Regulations (IHR) mechanisms. The total score of communication for international response was 88.9%. For IHR reporting duties, the median duration to respond was 2.49hours. Official news was sent within a mean of 9.18hours and the English daily situation reports were always uploaded onto the official website within 24hours. Conclusions This study provided a benchmark for international coordination and communication capacities and also identified areas for improvement during public health emergencies, such as the need to identify English-speaking spokespeople to communicate at the international level.


title: Human neutralizing antibodies to SARS-CoV-2: views and perspectives from Professor Linqi Zhang at Tsinghua University

text: Professor Linqi Zhang’s laboratory has uncovered the structure of SARS-CoV-2 spike receptor-binding domain binding with cell receptor angiotensin converting enzyme 2, and isolated more than 200 receptor-binding domain-specific monoclonal antibodies against SARS-CoV-2. The top SARS-CoV-2 neutralizing antibodies are now under development with partnership in pharmaceutical industry.


title: Observer and descriptor satisfying incremental quadratic constraint for class of chaotic systems and its applications in a quadrotor chaotic system

text: A drone based on four rotors is considered in this research paper. Its chaotic solution is shown bounded in an inscribed sphere whose vertices are tangent to faces of octahedron. Based on concept of constrained optimization; Linear Matrix Inequalities (LMIs) satisfying quadratic constraint increment multiplier matrix σ(m), state observers and descriptors with estimated parameter is calculated. Moreover, an image file is decrypted by designing description for mentioned chaotic system and then encrypted on its receiver end. Furthermore, an electric circuit is designed for chaotic quadrotor using LTspice and is fitted into wireless flying robot to observe its dynamics in bounded rectangular region.


title: Differentiating COVID-19 Response Strategies

text: Summary Globally, the COVID-19 pandemic brings different challenges to the impacted countries. To combat this pandemic, different strategies need to be tailored and implemented in countries with different situations. First, in countries with an ongoing explosion of the outbreak (i.e. the USA, Spain, and Italy), strategies suggested by the World Health Organization (WHO) which have been proven useful in China should be adopted for implementation. Secondly, countries in the regions that are still at the early stages of the outbreak (i.e., the Africa region, where many countries have only found imported cases) should further strengthen travel restrictions to reduce the risk of imported cases as well as the risk of developing local transmission. Furthermore, countries that have achieved great success in COVID control (i.e. China, South Korea, and Singapore) should continue implement the successful strategies and further roll-out strengthened new strategies to prevent new imported cases. In addition, surveillance on the genomic changes of SARS-CoV-2 is in need in all countries as some studies have found multiple mutants of SARS-CoV-2, although the impact of the mutation on the infectivity and lethality of the virus was still unclear.


title: Rapid expansion of temporary, reliable airborne-infection isolation rooms with negative air machines for critical COVID-19 patients

text: Abstract More airborne-infection isolation rooms (AIIRs) are needed in centers that treat severely affected COVID-19 patients. Wards and rooms must be carefully checked to ensure an ample supply of medical air and oxygen. Anterooms adjacent to AIIRS are required to maintain pressure differentials and provide an area for donning/doffing or disinfecting medical equipment.


title: Trypanosome mRNAs share a common 5′ spliced leader sequence

text: Abstract A 5′-terminal leader sequence of 35 nucleotides was found to be present on multiple trypanosome RNAs. Based on its representation in cDNA libraries, we estimate that many, if not all, trypanosome mRNAs contain this leader. This same leader was originally identified on mRNAs encoding the molecules responsible for antigenic variation, variant surface glycoproteins. Studies of selected cDNAs containing this leader sequence revealed that leader-containing transcripts can be stage-specific, stage-regulated, or constitutive. They can be abundant or rare, and transcribed from single or multigene families. No linkage between the genomic leader sequences and the structural gene exons was observed. Possible mechanisms by which the leader sequences are added to trypanosome mRNAs are discussed.


title: Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data

text: The geographic spread of 2019 novel coronavirus (COVID-19) infections from the epicenter of Wuhan, China, has provided an opportunity to study the natural history of the recently emerged virus. Using publicly available event-date data from the ongoing epidemic, the present study investigated the incubation period and other time intervals that govern the epidemiological dynamics of COVID-19 infections. Our results show that the incubation period falls within the range of 2–14 days with 95% confidence and has a mean of around 5 days when approximated using the best-fit lognormal distribution. The mean time from illness onset to hospital admission (for treatment and/or isolation) was estimated at 3–4 days without truncation and at 5–9 days when right truncated. Based on the 95th percentile estimate of the incubation period, we recommend that the length of quarantine should be at least 14 days. The median time delay of 13 days from illness onset to death (17 days with right truncation) should be considered when estimating the COVID-19 case fatality risk.


title: Sequence comparison of the N genes of five strains of the coronavirus mouse hepatitis virus suggests a three domain structure for the nucleocapsid protein

text: Abstract To obtain information about the structure and evolution of the nucleocapsid (N) protein of the coronavirus mouse hepatitis virus (MHV), we determined the entire nucleotide sequences of the N genes of MHV-A59, MHV-3, MHV-S, and MHV-1 from cDNA clones. At the nucleotide level, the N gene sequences of these viral strains, and that of MHV-JHM, were more than 92% conserved overall. Even higher nucleotide sequence identity was found in the 3′ untranslated regions (3′ UTRs) of the five strains, which may reflect the role of the 3′ UTR in negative-strand RNA synthesis. All five N genes were found to encode markedly basic proteins of 454 or 455 residues having at least 94% sequence identity in pairwise comparisons. However, amino acid sequence divergences were found to be clustered in two short segments of N, putative spacer regions that, together, constituted only 11% of the molecule. Thus, the data suggest that the MHV N protein is composed of three highly conserved structural domains connected to each other by regions that have much less constraint on their amino acid sequences. The first two conserved domains contain most of the excess of basic amino acid residues; by contrast, the carboxy-terminal domain is acidic. Finally, we noted that four of the five N genes contain an internal open reading frame that potentially encodes a protein of 207 amino acids having a large proportion of basic and hydrophobic residues.


title: Structural, glycosylation and antigenic variation between 2019 novel coronavirus (2019-nCoV) and SARS coronavirus (SARS-CoV)

text: The emergence of 2019 novel coronavirus (2019-nCoV) is of global concern and might have emerged from RNA recombination among existing coronaviruses. CoV spike (S) protein which is crucial for receptor binding, membrane fusion via conformational changes, internalization of the virus, host tissue tropism and comprises crucial targets for vaccine development, remain largely uncharacterized. Therefore, the present study has been planned to determine the sequence variation, structural and antigenic divergence of S glycoprotein which may be helpful for the management of 2019-nCoV infection. The sequences of spike glycoprotein of 2019-nCoV and SARS coronavirus (SARS-CoV) were used for the comparison. The sequence variations were determined using EMBOSS Needle pairwise sequence alignment tools. The variation in glycosylation sites was predicted by NetNGlyc 1.0 and validated by N-GlyDE server. Antigenicity was predicted by NetCTL 1.2 and validated by IEDB Analysis Resource server. The structural divergence was determined by using SuperPose Version 1.0 based on cryo-EM structure of the SARS coronavirus spike glycoprotein. Our data suggests that 2019-nCoV is newly spilled coronavirus into humans in China is closely related to SARS-CoV, which has only 12.8% of difference with SARS-CoV in S protein and has 83.9% similarity in minimal receptor-binding domain with SARS-CoV. Addition of a novel glycosylation sites were observed in 2019-nCoV. In addition, antigenic analysis proposes that great antigenic differences exist between both the viral strains, but some of the epitopes were found to be similar between both the S proteins. In spite of the variation in S protein amino acid composition, we found no significant difference in their structures. Collectively, for the first time our results exhibit the emergence of human 2019-nCoV is closely related to predecessor SARS-CoV and provide the evidence that 2019-nCoV uses various novel glycosylation sites as SARS-CoV and may have a potential to become pandemic owing its antigenic discrepancy. Further, demonstration of novel Cytotoxic T lymphocyte epitopes may impart opportunities for the development of peptide based vaccine for the prevention of 2019-nCoV.


title: ECONOMIC IMPACTS OF VISA RESTRICTIONS ON TOURISM: A CASE OF TWO EVENTS IN CHINA

text: Abstract Increasing attention has been paid to evaluate the impacts of large scale events on tourism demand. For providing policy suggestions, it should consider the economic impact of both events themselves and other factors. This paper evaluates the economic effects of visa restrictions on tourism as a result of the 1989 Tian’an Men Square Incident and the 2008 Beijing Olympic Games by using an innovative combination of econometric and computable general equilibrium (CGE) models. The results show that both events generated economic losses. The unexpected negative economic impact of the Beijing Olympics seems attributable to visa restrictions. Suggestions for the alleviation of the negative impact of visa regulations are provided.


docid: barmkkwx

title: Immunity to Pathogens Taught by Specialized Human Dendritic Cell Subsets

text: Dendritic cells (DCs) are specialized antigen-presenting cells (APCs) that have a key role in immune responses because they bridge the innate and adaptive arms of the immune system. They mature upon recognition of pathogens and upregulate MHC molecules and costimulatory receptors to activate antigen-specific CD4(+) and CD8(+) T cells. It is now well established that DCs are not a homogeneous population but are composed of different subsets with specialized functions in immune responses to specific pathogens. Upon viral infections, plasmacytoid DCs (pDCs) rapidly produce large amounts of IFN-α, which has potent antiviral functions and activates several other immune cells. However, pDCs are not particularly potent APCs and induce the tolerogenic cytokine IL-10 in CD4(+) T cells. In contrast, myeloid DCs (mDCs) are very potent APCs and possess the unique capacity to prime naive T cells and consequently to initiate a primary adaptive immune response. Different subsets of mDCs with specialized functions have been identified. In mice, CD8α(+) mDCs capture antigenic material from necrotic cells, secrete high levels of IL-12, and prime Th1 and cytotoxic T-cell responses to control intracellular pathogens. Conversely, CD8α(−) mDCs preferentially prime CD4(+) T cells and promote Th2 or Th17 differentiation. BDCA-3(+) mDC2 are the human homologue of CD8α(+) mDCs, since they share the expression of several key molecules, the capacity to cross-present antigens to CD8(+) T-cells and to produce IFN-λ. However, although several features of the DC network are conserved between humans and mice, the expression of several toll-like receptors as well as the production of cytokines that regulate T-cell differentiation are different. Intriguingly, recent data suggest specific roles for human DC subsets in immune responses against individual pathogens. The biology of human DC subsets holds the promise to be exploitable in translational medicine, in particular for the development of vaccines against persistent infections or cancer.