title: Position Statement: Cardiopulmonary Resuscitation of Patients with Confirmed or Suspected COVID-19 - 2020

text: Care for patients with cardiac arrest in the context of the coronavirus disease 2019 (COVID-19) pandemic has several unique aspects that warrant particular attention This joint position statement by the Brazilian Association of Emergency Medicine (ABRAMEDE), Brazilian Society of Cardiology (SBC), Brazilian Association of Intensive Care Medicine (AMIB), and Brazilian Society of Anesthesiology (SBA), all official societies representing the corresponding medical specialties affiliated with the Brazilian Medical Association (AMB), provides recommendations to guide health care workers in the current context of limited robust evidence, aiming to maximize the protection of staff and patients alike It is essential that full aerosol precautions, which include wearing appropriate personal protective equipment, be followed during resuscitation It is also imperative that potential causes of cardiac arrest of particular interest in this patient population, especially hypoxia, cardiac arrhythmias associated with QT prolongation, and myocarditis, be considered and addressed An advanced invasive airway device should be placed early Use of HEPA filters at the bag-valve interface is mandatory Management of cardiac arrest occurring during mechanical ventilation or during prone positioning demands particular ventilator settings and rescuer positioning for chest compressions which deviate from standard cardiopulmonary resuscitation techniques Apart from these logistical issues, care should otherwise follow national and international protocols and guidelines, namely the 2015 International Liaison Committee on Resuscitation (ILCOR) and 2019 American Heart Association (AHA) guidelines and the 2019 Update to the Brazilian Society of Cardiology Cardiopulmonary Resuscitation and Emergency Cardiovascular Care Guideline


title: Interaction between the nasal microbiota and S. pneumoniae in the context of live-attenuated influenza vaccine

text: Streptococcus pneumoniae is the main bacterial pathogen involved in pneumonia. Pneumococcal acquisition and colonization density is probably affected by viral co-infections, the local microbiome composition and mucosal immunity. Here, we report the interactions between live-attenuated influenza vaccine (LAIV), successive pneumococcal challenge, and the healthy adult nasal microbiota and mucosal immunity using an experimental human challenge model. Nasal microbiota profiles at baseline are associated with consecutive pneumococcal carriage outcome (non-carrier, low-dense and high-dense pneumococcal carriage), independent of LAIV co-administration. Corynebacterium/Dolosigranulum-dominated profiles are associated with low-density colonization. Lowest rates of natural viral co-infection at baseline and post-LAIV influenza replication are detected in the low-density carriers. Also, we detected the fewest microbiota perturbations and mucosal cytokine responses in the low-density carriers compared to non-carriers or high-density carriers. These results indicate that the complete respiratory ecosystem affects pneumococcal behaviour following challenge, with low-density carriage representing the most stable ecological state.


title: Épidémie de COVID-19 et prise en charge des conduites suicidaires: challenge et perspectives

text: Resumen Objectifs: La pandémie de Covid-19 touche à ce jour plus de 3,000,000 de personnes à travers le monde et les mesures de prévention ont conduit au confinement de plus de la moitié de l’humanité. La communauté scientifique et les autorités politiques redoutent une épidémie de suicides secondaires à cette crise. L’objectif de cette revue de la littérature est d’analyser l’impact de la pandémie de Covid-19 sur les dimensions du processus suicidaire, son interaction avec les différents facteurs de risque. Nous proposons également des solutions innovantes pour y remédier. Méthodes: Nous avons réalisé une revue narrative des articles internationaux traitant des grandes pandémies (Covid-19, SRAS) et de leur influence sur la vulnérabilité suicidaire. Résultats: De nombreux facteurs sont susceptibles de majorer l’émergence d’idées de suicide et le passage à l’acte suicidaire au cours de cette crise. La distanciation et le confinement pourraient favoriser un sentiment de déconnexion et la perception d’une douleur sociale chez les individus vulnérables. Certaines populations déjà «à risque suicidaire élevé» pourraient être encore fragilisées par la pandémie actuelle: personnes âgées, personnel médical et individus exposés à une forte précarité économique. Plusieurs solutions innovantes adaptées aux contraintes de la distanciation et du confinement permettront de prévenir le risque suicidaire: outils de santé connectée, protocole VigilanS, Thérapie Comportementale et Cognitive de troisième vague et pratique artistique. Conclusions: Il est possible que cette crise inédite exacerbe certaines dimensions du processus suicidaire. Cependant, à l’heure de l’innovation, plusieurs outils de prévention du suicide ont toute leur place dans les nouveaux modes de soins et devront être expérimentés à grande échelle. Abstract Objective: The Covid-19 pandemic affected today more than 3,000,000 worldwide, and more than half of humanity has been placed in quarantine. The scientific community and the political authorities fear an epidemic of suicide secondary to this crisis. The aim of this review is to analyze the impact of the Covid-19 pandemic on the dimensions of the suicidal process and its interaction with the various risk factors. We also propose innovative strategies to manage suicidal behavior in the context of pandemic. Methods: We carried out a narrative review of international publications dealing with major pandemics (Covid-19, SARS) and their influence on suicidal vulnerability. Results: Many factors are likely to increase the emergence of suicidal ideation and suicide attempts during this crisis. Social distancing and quarantine could increase the feeling of disconnection and the perception of social pain in vulnerable individuals. Some populations at high suicidal risk could be further impacted by the current pandemic: the elderly, medical staff and individuals exposed to economic insecurity. Several innovative tools adapted to the constraints of social distancing and quarantine may prevent suicide risk: e-health, VigilanS, buddhist-derived practices and art engagement. Conclusions: This unprecedented crisis may interact with certain dimensions of the suicidal process. However it is time to innovate. Several suicide prevention tools all have their place in new modes of care and should be tested on a large scale.


title: Recent Hits Acquired by BLAST (ReHAB): A tool to identify new hits in sequence similarity searches

text: BACKGROUND: Sequence similarity searching is a powerful tool to help develop hypotheses in the quest to assign functional, structural and evolutionary information to DNA and protein sequences. As sequence databases continue to grow exponentially, it becomes increasingly important to repeat searches at frequent intervals, and similarity searches retrieve larger and larger sets of results. New and potentially significant results may be buried in a long list of previously obtained sequence hits from past searches. RESULTS: ReHAB (Recent Hits Acquired from BLAST) is a tool for finding new protein hits in repeated PSI-BLAST searches. ReHAB compares results from PSI-BLAST searches performed with two versions of a protein sequence database and highlights hits that are present only in the updated database. Results are presented in an easily comprehended table, or in a BLAST-like report, using colors to highlight the new hits. ReHAB is designed to handle large numbers of query sequences, such as whole genomes or sets of genomes. Advanced computer skills are not needed to use ReHAB; the graphics interface is simple to use and was designed with the bench biologist in mind. CONCLUSIONS: This software greatly simplifies the problem of evaluating the output of large numbers of protein database searches.


Infection with Middle East respiratory syndrome coronavirus.


title: Rapid Detection of IgM Antibodies against the SARS-CoV-2 Virus via Colloidal Gold Nanoparticle-Based Lateral-Flow Assay

text: [Image: see text] Last year, the novel coronavirus disease (COVID-19) emerged in Wuhan, and it has rapidly spread to many other countries and regions. COVID-19 exhibits a strong human-to-human transmission infectivity and could cause acute respiratory diseases. Asymptomatic carriers are able to infect other healthy persons, and this poses a challenge for public health; the World Health Organization (WHO) has already announced COVID-19 as a global pandemic. Nucleic acid testing, considered as the current primary method for diagnosing COVID-19, might lead to false negatives and is difficult to be applied for every suspected patient because of the existence of asymptomatic carriers. Meanwhile, detecting specific antibodies in blood, such as the IgM antibody, against the SARS-CoV-2 virus is another choice for COVID-19 diagnosis, as it is widely accepted that IgM is an important indicator in the acute infection period. In this study, a colloidal gold nanoparticle-based lateral-flow (AuNP-LF) assay was developed to achieve rapid diagnosis and on-site detection of the IgM antibody against the SARS-CoV-2 virus through the indirect immunochromatography method. For preparing AuNP-LF strips, the SARS-CoV-2 nucleoprotein (SARS-CoV-2 NP) was coated on an analytical membrane for sample capture, and antihuman IgM was conjugated with AuNPs to form the detecting reporter. Optimization of AuNP-LF assay was carried out by altering the pH value and the amount of antihuman IgM. The performance of AuNP-LF assay was evaluated by testing serum samples of COVID-19 patients and normal humans. The results were compared with the real-time polymerase chain reaction. The sensitivity and specificity of AuNP-LF assay were determined to be 100 and 93.3%, respectively, and an almost perfect agreement was exhibited by Kappa statistics (κ coefficient = 0.872). AuNP-LF assay showed outstanding selectivity in the detection of IgM against the SARS-CoV-2 virus with no interference from other viruses such as severe fever with thrombocytopenia syndrome virus (SFTSV) and dengue virus (DFV). AuNP-LF assay was able to achieve results within 15 min and needed only 10–20 μL serum for each test. As a whole, in the light of its advantages such as excellent specificity and stability, easy operation, low cost, and being less time-consuming, AuNP-LF assay is a feasible method for the diagnosis of COVID-19 in primary hospitals and laboratories, especially in emergency situations in which numerous samples need to be tested on time.


title: Liver sinusoidal endothelial cells — gatekeepers of hepatic immunity

text: Liver sinusoidal endothelial cells (LSECs) line the low shear, sinusoidal capillary channels of the liver and are the most abundant non-parenchymal hepatic cell population. LSECs do not simply form a barrier within the hepatic sinusoids but have vital physiological and immunological functions, including filtration, endocytosis, antigen presentation and leukocyte recruitment. Reflecting these multifunctional properties, LSECs display unique structural and phenotypic features that differentiate them from the capillary endothelium present within other organs. It is now clear that LSECs have a critical role in maintaining immune homeostasis within the liver and in mediating the immune response during acute and chronic liver injury. In this Review, we outline how LSECs influence the immune microenvironment within the liver and discuss their contribution to immune-mediated liver diseases and the complications of fibrosis and carcinogenesis.


title: Chapter 62 Intestinal Microbiota and Susceptibility to Viral Infections Role of Probiotics

text: Abstract During pathogenesis, viruses come in contact with the microbiota that colonizes the mucosal sites they infect. The intestinal microbiota has emerged as a critical factor in intestinal viral susceptibility. While the interaction of virus-intestinal commensal bacteria can lead to enhanced or decreased viral infection capacity, several scientific studies support the use of probiotics as antiviral therapies. Thus, probiotics and the modulation of the intestinal microbiota are envisaged as therapeutic strategies in the prevention and treatment of viral infection.


title: Do Quarantine Experiences and Attitudes Towards COVID-19 Affect the Distribution of Mental Health in China? A Quantile Regression Analysis

text: While quarantine has become a widely used control strategy during the outbreak of the 2019 novel coronavirus disease (COVID-19), empirical research on whether and to what extent quarantine and attitudes towards COVID-19 affect mental health is scant. Using a cross-sectional online survey, this paper is the first from the Chinese outbreak to investigate how quarantine experiences and attitudes towards COVID-19 are related to mental health, and how these relationships change across the distribution of mental health scores. Using quantile regression analysis, we found that home self-quarantine is associated with a decrease in depression and an increase in happiness, while community-level quarantine is associated with decreased happiness, especially for those in the lower happiness quantile. We also found that favorable attitudes towards COVID-19 regarding the credibility of real-time updates and confidence in the epidemic control are associated with lower levels of depression and higher levels of happiness. These effects are stronger in the upper quantile of depression and the median quantile of happiness.


title: Infections virales émergentes et grossesse

text: Résumé Diverses infections émergentes sont rapportées depuis la mise en place d'une surveillance épidémiologique accrue. Ces infections peuvent compromettre le bon déroulement d'une grossesse, en mettant en jeu le pronostic vital maternel ou le développement de l'enfant lors d'une transmission verticale. À travers une revue récente de la littérature, nous rapportons les conséquences de ces virus émergents les plus cités (H5N1, Coronavirus du SRAS, Chikungunya, virus du Nil occidental) et discutons la prise en charge périnatale. Abstract Various emerging diseases have been reported in recent years as epidemiologic monitoring improves. These infections can compromise the pregnancy, through adverse maternal outcomes, as well as the outcome for the child following transmission. We report a review of the literature concerning the most quoted emergent virus (H5N1, SARS Coronavirus, Chikungunya, West Nile virus), and relate the perinatal management.


Changes in Children’s Healthcare Visits During COVID-19 Pandemic in Hangzhou, China


title: COVID-19 and Other Pandemics: How Might They Be Prevented?

text: Pandemics such as influenza, smallpox, and plague have caused the loss of hundreds of millions of lives and have occurred for many centuries. Fortunately, they have been largely eliminated by the use of vaccinations and drugs. More recently, Severe Acute Respiratory Syndrome (SARS), Middle East Respiratory Syndrome (MERS), and now Coronavirus Disease 2019 (COVID-19) have arisen, and given the current absence of highly effective approved vaccines or drugs, brute-force approaches involving physical barriers are being used to counter virus spread. A major basis for physical protection from respiratory infections is eye, nose, and mouth protection. However, eye protection with goggles is problematic due to “fogging”, while nose/mouth protection is complicated by the breathing difficulties associated with non-valved respirators. Here, we give a brief review of the origins and development of face masks and eye protection to counter respiratory infections on the basis of experiments conducted 100 years ago, work that was presaged by the first use of personal protective equipment, “PPE”, by the plague doctors of the 17(th) Century. The results of the review lead to two conclusions: first, that eye protection using filtered eye masks be used to prevent ocular transmission; second, that new, pre-filtered, valved respirators be used to even more effectively block viral transmission.


title: Non-influenza respiratory viruses in adult patients admitted with influenza-like illness: a 3-year prospective multicenter study

text: PURPOSE: To describe the burden, and characteristics, of influenza-like illness (ILI) associated with non-influenza respiratory viruses (NIRV). METHODS: We performed a prospective, multicenter, observational study of adults admitted with ILI during three influenza seasons (2012–2015). Patients were screened for picornavirus, respiratory syncytial virus (RSV), coronavirus, human metapneumovirus, adenovirus, bocavirus, parainfluenza virus, and influenza, by PCR on nasopharyngeal samples. We excluded patients coinfected with NIRV and influenza. RESULTS: Among 1421 patients enrolled, influenza virus was detected in 535 (38%), and NIRV in 215 (15%), mostly picornavirus (n = 61), RSV (n = 53), coronavirus 229E (n = 48), and human metapneumovirus (n = 40). In-hospital mortality was 5% (NIRV), 4% (influenza), and 5% (no respiratory virus). As compared to influenza, NIRV were associated with age (median, 73 years vs. 68, P = 0.026), chronic respiratory diseases (53% vs. 45%, P = 0.034), cancer (14% vs. 9%, P = 0.029), and immunosuppressive drugs (21% vs. 14%, P = 0.028), and inversely associated with diabetes (18% vs. 25%, P = 0.038). On multivariable analysis, only chronic respiratory diseases (OR 1.5 [1.1–2.0], P = 0.008), and diabetes (OR 0.5 [0.4–0.8], P = 0.01) were associated with NIRV detection. CONCLUSIONS: NIRV are common in adults admitted with ILI during influenza seasons. Outcomes are similar in patients with NIRV, influenza, or no respiratory virus.


title: Extracorporeal Blood Purification Treatment Options for COVID-19: The Role of Immunoadsorption

text: Abstract The activation of theinnate and adaptive immune systems by SARS-CoV-2 causes the release of several inflammatory cytokines, including IL-6. The inflammatory hypercytokinemia causes immunopathological changes in the lungs including vascular leakage, and alveolar edema. As a result of these changes in the lungs, hypoxia and acute respiratory distress syndrome occur in patients with COVID-19. Even though there are clinical trials on the development of therapeutics and vaccines, there are currently no licensed vaccines or therapeutics for COVID-19. Pharmacological approaches have shown poor results in sepsis-like syndromes caused by the hypercytokinemia. Suppressing the cytokine storm is an important way to prevent the organ damage in patients with COVID-19. Extracorporeal blood purification could be proposed as an adjunctive therapy for sepsis, aiming to control the associated dysregulation of the immune system, which is known to protect organ functions. Several extracorporeal blood purification therapies are now available, and most of them target endotoxins and/or the cytokines and aim improving the immune response. For this purpose, plasmapheresis and immunoadsorption may be an important adjunctive treatment option to manage the complications caused by cytokine storm in critically ill patients with COVID-19.


title: 16 Pandemic Influenza

text: Abstract This chapter will describe pandemic threats and the steps necessary to reduce morbidity and mortality. An explanation is provided on genetic mutations leading to the emergence of novel influenza strains. Medical countermeasures include vaccination and antiviral medications. Public messaging is also important to promote flu shots, reinforce basic hygiene measures, and instruct those who may be ill to limit contacts. The World Health Organization (WHO) tracks seasonal influenza for anomalies indicating an emerging pandemic influenza strain. WHO updated the international pandemic alert system after the 2009–2010 H1N1 pandemic. With each declaration, temporary recommendations are provided, and added regulatory actions are taken by WHO member states. In addition, the Centers for Disease Control and Prevention (CDC) updated the U.S. framework for pandemic influenza preparedness and response. Each pandemic interval is accompanied by specific recommendations for state and local public health authorities. Effective influenza control includes both pharmaceutical and nonpharmaceutical recommendations. Other severe viral pandemic respiratory threats, including the “Middle East Respiratory Syndrome Coronavirus” (MERS-CoV), require similar resources and infrastructure to manage.


Editorial: Archives of Virology’s 80th anniversary symposium—6 months later


title: Pay attention to situation of SARS-CoV-2 and TCM advantages in treatment of novel coronavirus infection

text: Since the outbreak of the new coronavirus epidemic, novel coronavirus has infected nearly 100,000 people in more than 110 countries. How to face this new coronavirus epidemic outbreak is an important issue. Basic reproduction number (R0) is an important parameter in epidemiology; The basic reproduction number of an infection can be thought of as the expected number of cases directly generated by one case in a population where all individuals are susceptible to infection. Epidemiology dynamics is a mathematical model based on a susceptibility-infection-recovery epidemic model. Researchers analyzed the epidemiological benefits of different transmission rates for the establishment of effective strategy in prevention and control strategies for epidemic infectious diseases. In this review, the early use of TCM for light and ordinary patients, can rapidly improve symptoms, shorten hospitalization days and reduce severe cases transformed from light and normal. Many TCM formulas and products have wide application in treating infectious and non-infectious diseases. The TCM theoretical system of treating epidemic diseases with TCM and the treatment scheme of integrated Chinese and Western medicine have proved their effectiveness in clinical practice. TCM can cure COVID-19 pneumonia, and also shows that the role of TCM in blocking the progress of COVID-19 pneumonia.


title: Government financial support and firm productivity in Vietnam

text: Using the Färe-Primont index and instrumental variable fixed effect estimation for the data of small and medium-sized enterprises (SMEs), this study considers if receiving government financial support enables SMEs in Vietnam to become more productive. The paper discovers no evidence of linkage between financial support and firm productivity. However, access to financial support improves technological progress and growth in firm scale but has a negative effect on improvement in technical efficiency. The estimation results reveal that the use of productivity as an aggregated index in previous studies may hide the real effect of government support on firm productivity.


title: Sequence and expression analysis of potential nonstructural proteins of 4.9, 4.8, 12.7, and 9.5 kDa encoded between the apike and membrane protein genes of the bovine coronavirus

text: Abstract The nucleotide sequence between the spike and membrane protein genes in the bovine coronavirus (BCV) genome was determined by sequencing cDNA clones of the genome, and open reading frames potentially encoding proteins of 4.9, 4.8, 12.7, and 9.5 kDa, in that order, were identified. The 4.9- and 4.8-kDa proteins appear to be vestiges of an 11-kDa protein for which a single nucleotide deletion event in the central part of the gene gave rise to a stop codon. The consensus CYAAAC sequence precedes the 4.9-, 12.7-, and 9.5-kDa ORFs and predicts that transcription will start from each of these sites. Northern analyses using sequence-specific probes and oligo(dT)-selected RNA demonstrated that the predicted transcripts are made, and that these correspond to mRNAs 4, 5, and 5-1. BCV mRNA 4 appears to be a counterpart to mouse hepatitis virus (MHV) mRNA 4 which, in the MHV JHM strain, encodes the putative 15.2-kDa nonstructural protein. BCV mRNAs 5 and 5-1 appear to be used for the synthesis of the 12.7- and 9.5-kDa proteins, respectively, which demonstrates a pattern of expression strikingly different from that utilized by MHV. MHV makes its homologs of the 12.7- and 9.5-kDa proteins from the single mRNA 5. In vitro translation analyses demonstrated that the BCV 9.5-kDa protein, unlike its MHV counterpart, is poorly made from downstream initiation of translation. Thus, from a comparison between BCV and MHV we find evolutionary evidence for the importance of the CYAAAC sequence in regulating coronavirus transcription.


title: Surgical Management of Patients With COVID-19 Infection. Recommendations of the Spanish Association of Surgeons

text: Abstract Due to the current pandemic of respiratory disease known as coronavirus disease 2019 (COVID-19) caused by the SARS-CoV-2 virus, many patients with confirmed or suspected COVID-19 infection will require elective surgery, surgery that cannot be postponed, or emergency surgical treatment. In these situations, special measures need to be adopted in order to minimize the possibility of transmission between patients, exposure of healthcare personnel and the development of postoperative complications. This document explains the main principles to consider when managing confirmed or suspected COVID-19 patients during evaluation as well as when surgical treatment is required.


title: Impact of Coronavirus disease-19 (COVID-19) lockdown on physical activity and energy expenditure among physiotherapy professionals and students using web based open E-survey sent through WhatsApp, Facebook and Instagram messengers

text: BACKGROUND: Coronavirus disease - 19 (COVID-19) spread throughout the world and become pandemic. To stop and control the rapid infection of COVID-19 lockdown is the best option. Sudden lockdown implies change in entire lifestyle of the population. Social isolation affects individual's lives by greater reduction in their physical activity, which might increase chance of infection by reducing the immunity. To what extent, the physical activity is reduced during this lockdown period among physiotherapy professionals and students who propagate physical activity is not known. Hence, we aimed to evaluate the impact of COVID-19 lockdown on physical activity level and energy utilization among physiotherapy professionals and students. MATERIAL AND METHODS: One hundred and forty three volunteered physiotherapy professionals and students participated in web based open E-survey. The survey was carried out by sending the Google Forms link for International Physical activity questionnaire-short form (IPAQ-SF) through social networking sites using Google forms, to gather amount of PA before and during COVID-19 lockdown period and analysed using Wilcoxon signed rank test. RESULTS: Among identified 261 potential survey participants, 143 responded reaching response rate of 54.8%. Total physical activity before and during COVID–19 lockdown period were 7809.7 (3849.7–11769.8) MET-min/week and 4135.7 (867.2–7404.1) MET-min/week; p < 0.0001. While energy expenditure before and during COVID–19 lockdown period were 8189.8 (4242.1–12137.6) kcal/wk and 4221.7 (1004.6–7438.8) kcal/wk; p < 0.0001. CONCLUSION: A significant reduction in self-report PA levels were observed among physiotherapy professionals and students were observed during COVID–19 lockdown period.


title: Management of critically ill patients with COVID-19 in ICU: statement from front-line intensive care experts in Wuhan, China

text: BACKGROUND: The ongoing coronavirus disease 2019 (COVID-2019) pandemic has swept all over the world, posing a great pressure on critical care resources due to large number of patients needing critical care. Statements from front-line experts in the field of intensive care are urgently needed. METHODS: Sixteen front-line experts in China fighting against the COVID-19 epidemic in Wuhan were organized to develop an expert statement after 5 rounds of expert seminars and discussions to provide trustworthy recommendation on the management of critically ill COVID-19 patients. Each expert was assigned tasks within their field of expertise to provide draft statements and rationale. Parts of the expert statement are based on epidemiological and clinical evidence, without available scientific evidences. RESULTS: A comprehensive document with 46 statements are presented, including protection of medical personnel, etiological treatment, diagnosis and treatment of tissue and organ functional impairment, psychological interventions, immunity therapy, nutritional support, and transportation of critically ill COVID-19 patients. Among them, 5 recommendations were strong (Grade 1), 21 were weak (Grade 2), and 20 were experts’ opinions. A strong agreement from voting participants was obtained for all recommendations. CONCLUSION: There are still no targeted therapies for COVID-19 patients. Dynamic monitoring and supportive treatment for the restoration of tissue vascularization and organ function are particularly important.


Multidisciplinary management of the burn injured patient during a pandemic -– The role of telemedicine


title: Arapan-S: a fast and highly accurate whole-genome assembly software for viruses and small genomes

text: BACKGROUND: Genome assembly is considered to be a challenging problem in computational biology, and has been studied extensively by many researchers. It is extremely difficult to build a general assembler that is able to reconstruct the original sequence instead of many contigs. However, we believe that creating specific assemblers, for solving specific cases, will be much more fruitful than creating general assemblers. FINDINGS: In this paper, we present Arapan-S, a whole-genome assembly program dedicated to handling small genomes. It provides only one contig (along with the reverse complement of this contig) in many cases. Although genomes consist of a number of segments, the implemented algorithm can detect all the segments, as we demonstrate for Influenza Virus A. The Arapan-S program is based on the de Bruijn graph. We have implemented a very sophisticated and fast method to reconstruct the original sequence and neglect erroneous k-mers. The method explores the graph by using neither the shortest nor the longest path, but rather a specific and reliable path based on the coverage level or k-mers’ lengths. Arapan-S uses short reads, and it was tested on raw data downloaded from the NCBI Trace Archive. CONCLUSIONS: Our findings show that the accuracy of the assembly was very high; the result was checked against the European Bioinformatics Institute (EBI) database using the NCBI BLAST Sequence Similarity Search. The identity and the genome coverage was more than 99%. We also compared the efficiency of Arapan-S with other well-known assemblers. In dealing with small genomes, the accuracy of Arapan-S is significantly higher than the accuracy of other assemblers. The assembly process is very fast and requires only a few seconds. Arapan-S is available for free to the public. The binary files for Arapan-S are available through http://sourceforge.net/projects/dnascissor/files/.


Do Humidity and Temperature Impact the Spread of the Novel Coronavirus?


title: Rapid Identification of Potential Inhibitors of SARS‐CoV‐2 Main Protease by Deep Docking of 1.3 Billion Compounds

text: The recently emerged 2019 Novel Coronavirus (SARS‐CoV‐2) and associated COVID‐19 disease cause serious or even fatal respiratory tract infection and yet no approved therapeutics or effective treatment is currently available to effectively combat the outbreak. This urgent situation is pressing the world to respond with the development of novel vaccine or a small molecule therapeutics for SARS‐CoV‐2. Along these efforts, the structure of SARS‐CoV‐2 main protease (Mpro) has been rapidly resolved and made publicly available to facilitate global efforts to develop novel drug candidates. Recently, our group has developed a novel deep learning platform – Deep Docking (DD) which provides fast prediction of docking scores of Glide (or any other docking program) and, hence, enables structure‐based virtual screening of billions of purchasable molecules in a short time. In the current study we applied DD to all 1.3 billion compounds from ZINC15 library to identify top 1,000 potential ligands for SARS‐CoV‐2 Mpro protein. The compounds are made publicly available for further characterization and development by scientific community.


title: Response and Operating Room Preparation for the COVID-19 Outbreak: A Perspective from the National Heart Centre Singapore

text: Abstract The outbreak of COVID-19, a respiratory disease from a novel coronavirus that was first detected in Wuhan City, Hubei Province, China is now a public health emergency and fast approaching a pandemic. Singapore, as a major international transportation hub in Asia, is one of the worst hit countries of COVID-19. With the advent of local transmission of cases, we share our preparation and response planning for the operating room from the National Heart Centre Singapore, the largest cardiothoracic tertiary center in Singapore. Protection of staff and patients, environmental concerns as well as other logistic and equipment issues must be considered.


title: COVID-19 in an Adult with Tricuspid Atresia S/P Fontan Palliation

text: Abstract: December 2019, a pathogenic novel human coronavirus (HCoV), termed SARS-CoV-2, was recognized in Wuhan, China causing significant morbidity and mortality. The illness caused by SARS-CoV-2 is labelled COVID-19 by WHO. We report the first case of COVID-19 in an ACHD patient with Single Ventricle (SV) physiology S/P Fontan palliation.


title: Recognition and analysis of protein-coding genes in severe acute respiratory syndrome associated coronavirus

text: Motivation: The recent outbreak of severe acute respiratory syndrome (SARS) caused by SARS coronavirus (SARS-CoV) has necessitated an in-depth molecular understanding of the virus to identify new drug targets. The availability of complete genome sequence of several strains of SARS virus provides the possibility of identification of protein-coding genes and defining their functions. Computational approach to identify protein-coding genes and their putative functions will help in designing experimental protocols. Results: In this paper, a novel analysis of SARS genome using gene prediction method GeneDecipher developed in our laboratory has been presented. Each of the 18 newly sequenced SARS-CoV genomes has been analyzed using GeneDecipher. In addition to polyprotein 1ab(1), polyprotein 1a and the four genes coding for major structural proteins spike (S), small envelope (E), membrane (M) and nucleocapsid (N), six to eight additional proteins have been predicted depending upon the strain analyzed. Their lengths range between 61 and 274 amino acids. Our method also suggests that polyprotein 1ab, polyprotein 1a, S, M and N are proteins of viral origin and others are of prokaryotic. Putative functions of all predicted protein-coding genes have been suggested using conserved peptides present in their open reading frames. Availability: Detailed results of GeneDecipher analysis of all the 18 strains of SARS-CoV genomes are available at http://www.igib.res.in/sarsanalysis.html


How Volunteers Are Dealing With Coronavirus Issues


title: Clinical characteristics and risk factors of mild‐to‐moderate COVID‐19 patients with false‐negative SARS‐CoV‐2 nucleic acid

text: This study investigates the clinical and imaging characteristics of coronavirus disease 2019 (COVID‐19) patients with false‐negative nucleic acids. Mild‐to‐moderate COVID‐19 patients, including 19 cases of nucleic acid false‐negative patients and 31 cases of nucleic acid positive patients, were enrolled. Their epidemiological, clinical, and laboratory examination data and imaging characteristics were analyzed. Risk factors for false negatives were discussed. Compared with the nucleic acid positive group, the false‐negative group had less epidemiological exposure (52.6% vs 83.9%; P = .025), less chest discomfort (5.3% vs 32.3%; P = .035), and faster recovery (10 [8, 13] vs 15 [11, 18.5] days; P = .005). The number of involved lung lobes was (2 [1, 2.5] vs 3 [2, 4] days; P = .004), and the lung damage severity score was (3 [2.5, 4.5] vs 5 [4, 9] days; P = .007), which was lighter in the nucleic acid false‐negative group. Thus, the absence of epidemiological exposure may be a potential risk factor for false‐negative nucleic acids. The false‐negative cases of COVID‐19 are worth noting because they have a risk of viral transmission without positive test results, lighter clinical manifestations, and less history of epidemiological exposure.


title: Adenovirus behavior in air handling unit fiberglass filters

text: Viral aerosols can lead to respiratory viral infections with high infectivity. About 90% of people’s time is spent in closed environments. A few studies have pointed out that the ventilation systems in air handling units (AHUs) that treat and transmit a new synthetic clean and conditioned environment can also spread and transport viral particles in buildings. The aim of this work is to study the characterization of adenovirus, a DNA non-enveloped respiratory virus, on the F7 fiberglass filter used in AHUs. In this study, an experimental setup simulating an AHU was used. The SYBR(®) QPCR, Electrical Low-Pressure Impactor (ELPI™) and Scanning Mobility Particle Sizer (SMPS™) were used to detect, measure and characterize the aerosolized adenovirus solution. The characterization results showed that the nebulized adenovirus could be aerosolized in different forms associated or not with cell debris and proteins. The quantification and level of infectivity of adenovirus demonstrated that viruses passed through filters and remained infectious up- and downstream of the system during the 25 min of aerosolization. This study showed that AHUs should be considered an indoor source of viral contamination.


title: Detection of the Severe Acute Respiratory Syndrome‐Related Coronavirus and Alphacoronavirus in the Bat Population of Taiwan

text: Bats have been demonstrated to be natural reservoirs of severe acute respiratory syndrome coronavirus (SARS CoV) and Middle East respiratory syndrome (MERS) CoV. Faecal samples from 248 individuals of 20 bat species were tested for partial RNA‐dependent RNA polymerase gene of CoV and 57 faecal samples from eight bat species were tested positive. The highest detection rate of 44% for Scotophilus kuhlii, followed by 30% for Rhinolophus monoceros. Significantly higher detection rates of coronaviral RNA were found in female bats and Scotophilus kuhlii roosting in palm trees. Phylogenetic analysis classified the positive samples into SARS‐related (SARSr) CoV, Scotophilus bat CoV 512 close to those from China and Philippines, and Miniopterus bat CoV 1A‐related lineages. Coronaviral RNA was also detected in bat guano from Scotophilus kuhlii and Myotis formosus flavus on the ground and had potential risk for human exposure. Diverse bat CoV with zoonotic potential could be introduced by migratory bats and maintained in the endemic bat population in Taiwan.


title: Taiwan quality indicator project and hospital productivity growth

text: Abstract The Taiwan Quality Indicator Project (TQIP) is a quality management program that measures and monitors the healthcare quality of hospitals in Taiwan. This paper examines the impact of TQIP participation on hospital productivity growth with the application of the Malmquist productivity change index based on data envelopment analysis (DEA). Analyzing operations data from 31 TQIP regional hospitals over the period 1998–2004, we find that TQIP hospitals improved their productivity in the post-TQIP period. This improvement is attributable to quality change and relative efficiency progress. The simultaneous enhancement in both quality and relative efficiency coincides with the philosophy of total quality management (TQM) spirit, and confirms the efficiency improvement and quality assurance functions of TQIP.


title: Characteristics of human metapneumovirus infection in adults hospitalized for community-acquired influenza-like illness in France, 2012-2018: a retrospective observational study

text: Abstract Objectives To describe the prevalence, clinical features and complications of human metapneumovirus (hMPV) infections in a population of adults hospitalized with influenza-like illness (ILI). Methods This was a retrospective, observational, multicenter cohort study using prospectively collected data from adult patients hospitalized during influenza virus circulation, for at least 24h, for community-acquired ILI (with symptom onset <7 days). Data were collected from five French teaching hospitals over six consecutive winters (2012-2018). Respiratory viruses were identified by multiplex RT-PCR on nasopharyngeal specimens. hMPV+ patients were compared to hMPV– patients, influenza+ and respiratory syncytial virus (RSV)+ patients using multivariate logistic regressions. Primary outcome was the prevalence of hMPV in patients hospitalized for ILI. Results Among the 3148 patients included (1449 (46%) women, 1988 (63%) aged 65 and over; 2508 (80%) with chronic disease), at least one respiratory virus was detected in 1604 (51%, 95%CI [49-53]), including 100 cases of hMPV (100/3148, 3% 95%CI [3-4]), of which 10 (10%) were viral co-infection. In the hMPV+ patients, mean length of stay was 7 days, 62% (56/90) developed a complication, 21% (14/68) were admitted to intensive care unit and 4% (4/90) died during hospitalization. In comparison with influenza+ patients, hMPV+ patients were more frequently > 65 years old (aOR=3.3, 95%CI[1.9-6.3]) and presented more acute heart failure during hospitalization (aOR=1.8, 95%CI[1.0-2.9]). Compared to RSV+ patients, hMPV+ patients had less cancer (aOR=0.4, 95%CI[0.2-0.9]) and were less likely to smoke (aOR=0.5, 95%CI[0.2-0.9]) but had similar outcomes especially high rate of respiratory and cardiovascular complications. Conclusions Adult hMPV infections mainly affect the elderly and patients with chronic conditions and are responsible for frequent cardiac and pulmonary complications similar to those of RSV infections. At-risk populations would benefit from the development of antivirals and vaccines targeting hMPV.


title: A short sequence in the COOH-terminus makes an adenovirus membrane glycoprotein a resident of the endoplasmic reticulum

text: Abstract The E19 protein of adenoviruses is a transmembrane protein that abrogates the intracellular transport of class I antigens by forming complexes with them in the ER. We show here that the E19 protein is retained in the ER even in the absence of class I antigens. To define the region conferring residency in the ER, we examined two mutant forms of the viral protein. A 5 amino acid extension of the 15-membered cytoplasmic tail of the protein reduces its interaction with class I antigens but does not change its intracellular distribution. Shortening the tail to 7 amino acids also diminishes the affinity for class I antigens; however, this mutant E19 protein becomes transported to the cell surface. Thus, we concluded that a small stretch of amino acids exposed on the cytoplasmic side of the ER membrane is responsible for the retention of the E19 protein in the ER.


title: Influence of the coronavirus 2 (SARS-Cov-2) pandemic on acute appendicitis()

text: INTRODUCTION: Acute appendicitis (AA) is the most common abdominal surgical emergency. No specific studies have been found that evaluate the impact of the coronavirus 2 (SARS-Cov-2) pandemic on AA and its surgical management. An analysis was made on the influence of this new pathology on the clinical course of AA. MATERIAL AND METHODS: Retrospective observational study was conducted on patients operated on for AA from January to April 2020. They were classified according to the time of the appendectomy, before the declaration of the state of alarm (Pre-COVID-19), and after its declaration (Post-COVID-19) in Spain, one the most affected countries in the world. An evaluation was made of demographic variables, duration of symptoms, type of appendicitis, surgical time, hospital stay, and postoperative complications. RESULTS: The study included 66 patients (41 Pre-COVID-19; 25 Post-COVID-19) with mean age of 10.7 ± 3 and 9.3 ± 3.1; p = .073, respectively. Fever was found in a higher number of post-COVID-19 patients (52 vs 19.5%; p = .013), as well as a higher CRP (72.7±96.2 vs 31.3±36.2 mg/dL; p = .042). This group presented with a higher proportion of complicated appendicitis when compared to Pre-COVID-19 (32 vs 7.3%; p = .015). The mean hospital stay was longer in the Post-COVID-19 group (5.6±5.9 vs 3.2±4.3 days; p = .041). No differences were found in the time of onset of symptoms or surgical time. CONCLUSIONS: The SARS-Cov-2 pandemic influenced the time of diagnosis of appendicitis, as well as its course, and mean hospital stay. Peritonitis was more frequently seen. As a result of the significant circumstances, delaying diagnosis and treatment of AA during SARS-Cov-2 pandemic, inappropriate management of this common surgical disorder has been noticed.


title: Rapid detection of ERG11 gene mutations in clinical Candida albicans isolates with reduced susceptibility to fluconazole by rolling circle amplification and DNA sequencing

text: BACKGROUND: Amino acid substitutions in the target enzyme Erg11p of azole antifungals contribute to clinically-relevant azole resistance in Candida albicans. A simple molecular method for rapid detection of ERG11 gene mutations would be an advantage as a screening tool to identify potentially-resistant strains and to track their movement. To complement DNA sequencing, we developed a padlock probe and rolling circle amplification (RCA)-based method to detect a series of mutations in the C. albicans ERG11 gene using "reference" azole-resistant isolates with known mutations. The method was then used to estimate the frequency of ERG11 mutations and their type in 25 Australian clinical C. albicans isolates with reduced susceptibility to fluconazole and in 23 fluconazole-susceptible isolates. RCA results were compared DNA sequencing. RESULTS: The RCA assay correctly identified all ERG11 mutations in eight "reference" C. albicans isolates. When applied to 48 test strains, the RCA method showed 100% agreement with DNA sequencing where an ERG11 mutation-specific probe was used. Of 20 different missense mutations detected by sequencing in 24 of 25 (96%) isolates with reduced fluconazole susceptibility, 16 were detected by RCA. Five missense mutations were detected by both methods in 18 of 23 (78%) fluconazole-susceptible strains. DNA sequencing revealed that mutations in non-susceptible isolates were all due to homozygous nucleotide changes. With the exception of the mutations leading to amino acid substitution E266D, those in fluconazole-susceptible strains were heterozygous. Amino acid substitutions common to both sets of isolates were D116E, E266D, K128T, V437I and V488I. Substitutions unique to isolates with reduced fluconazole susceptibility were G464 S (n = 4 isolates), G448E (n = 3), G307S (n = 3), K143R (n = 3) and Y123H, S405F and R467K (each n = 1). DNA sequencing revealed a novel substitution, G450V, in one isolate. CONCLUSION: The sensitive RCA assay described here is a simple, robust and rapid (2 h) method for the detection of ERG11 polymorphisms. It showed excellent concordance with ERG11 sequencing and is a potentially valuable tool to track the emergence and spread of azole-resistant C. albicans and to study the epidemiology of ERG11 mutations. The RCA method is applicable to the study of azole resistance in other fungi.


title: Take Advantage of Lessons Learned During the Pandemic

text: The COVID‐19 pandemic has had wide‐ranging effects on the water industry, but now you and your colleagues are getting your utility back to “normal,” whatever normal now means. As of this writing in mid‐May, events are still moving unexpectedly and unevenly, so some things still can't be predicted. However, the fundamentals still apply. You need to ensure employee health and safety, your customers require attention, and operations need to continue.


title: Reflection on passive immunotherapy in those who need most: some novel strategic arguments for obtaining safer therapeutic plasma or autologous antibodies from recovered COVID ‐19 infected patients

text: COVID‐19 pandemic is an emerging new human disease, where no vaccines, or monoclonal antibodies (mAbs), or drugs are currently available for therapy. Active vaccination requires the induction of an immune response against a given agent to a susceptible individual for the purpose of preventing or treating an infectious disease and this usually takes time to develop. Thus, the use of existing autologous Ab administration, obtainable from recovered COVID 19 patients, after 2 weeks recovery, is the best and the most practical strategy for providing immediate passive immunity to susceptible recipients in need.


title: Low performance of rapid antigen detection test as frontline testing for COVID-19 diagnosis

text: BACKGROUND: Ensuring accurate diagnosis is essential to limit the spread of the SARS-CoV-2 and for the clinical management of COVID-19. Although real-time reverse transcription polymerase chain reaction (RT- qPCR) is the current recommended laboratory method to diagnose SARS-CoV-2 acute infection, several factors such as requirement of special equipment and skilled staff limit the use of these time-consuming molecular techniques. Recently, several easy to perform rapid antigen detection tests were developed and recommended in some countries as the first line of diagnostic. OBJECTIVES: The aim of this study was to evaluate the performances of the Coris COVID-19 Ag Respi-Strip. Study design. We performed a comparison study by testing nasopharyngeal samples with RT-qPCR and antigen rapid test. RESULTS: 148 nasopharyngeal swabs were tested. Amongst the 106 positive RT-qPCR samples, 32 were detected by the rapid antigen test, given an overall sensitivity of 30.2%. All the samples detected positive with the antigen rapid tests were also positive with RT-qPCR. CONCLUSIONS: Highest viral load is associated with better antigen detection rates. Unfortunately, the overall poor sensitivity of the COVID-19 Ag Respi-Strip does not allow using it alone as the frontline testing for COVID-19 diagnosis.


title: Comparison of a new Eulerian model with a modified Lagrangian approach for particle distribution and deposition indoors

text: Abstract Understanding of aerosol dispersion characteristics has many scientific and engineering applications. It is recognized that Eulerian or Lagrangian approach has its own merits and limitations. A new Eulerian model has been developed and it adopts a simplified drift–flux methodology in which external forces can be incorporated straightforwardly. A new near-wall treatment is applied to take into account the anisotropic turbulence for the modified Lagrangian model. In the present work, we present and compare both Eulerian and Lagrangian models to simulate particle dispersion in a small chamber. Results reveal that the standard k–ε Lagrangian model over-predicts particle deposition compared to the present turbulence-corrected Lagrangian approach. Prediction by the Eulerian model agrees well with the modified Lagrangian model.


Hospital‐based dental externship during COVID‐19 pandemic: Think virtual!


CASE SUMMARY: A 2-year-old male domestic shorthair cat presented to the University of Liverpool Small Animal Teaching Hospital with a 2 week history of altered mentation, blindness and focal epileptic seizures. MRI examination revealed generalised cerebral and cerebellar atrophy, diffuse T2-weighted hyperintensity of the white matter and meningeal thickening. Neuronal ceroid lipofuscinosis was confirmed on post-mortem examination. RELEVANCE AND NOVEL INFORMATION: This is the first report of the MRI findings of neuronal ceroid lipofuscinosis in a cat.


title: Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community

text: Several viruses within the Coronaviridae family have been categorized as either emerging or re-emerging human pathogens, with Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) being the most well known. The NIAID-sponsored Virus Pathogen Database and Analysis Resource (ViPR, www.viprbrc.org) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses, including the entire Coronaviridae family. ViPR provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, host factor data, and other data types through an intuitive web-based search interface. Records returned from these queries can then be subjected to web-based analyses including: multiple sequence alignment, phylogenetic inference, sequence variation determination, BLAST comparison, and metadata-driven comparative genomics statistical analysis. Additional tools exist to display multiple sequence alignments, view phylogenetic trees, visualize 3D protein structures, transfer existing reference genome annotations to new genomes, and store or share results from any search or analysis within personal private ‘Workbench’ spaces for future access. All of the data and integrated analysis and visualization tools in ViPR are made available without charge as a service to the Coronaviridae research community to facilitate the research and development of diagnostics, prophylactics, vaccines and therapeutics against these human pathogens.


title: The rumouring of SARS during the 2003 epidemic in China

text: By analysing rumour content as covered by major Chinese newspapers, this article explores the multiple dimensions of SARS‐related rumouring throughout China during the 2003 epidemic. Findings indicate a strong correlation between the scale of SARS infections and level of rumour activities across regions. As for channels of dissemination, the rumour process still found a natural habitat in word of mouth, while internet‐based platforms and cell phone text messaging emerged as viable grapevines. Our particular typology of SARS‐incurred rumours leads us to identify four distinct types of rumours: legendary rumours; aetiological narratives; proto‐memorates; and bogies. The four types of rumours are discussed against the background of superstitious beliefs, folklore practices, popular mentalities, and China’s particular socio‐political information environment.


title: Selection of reference genes for quantitative real-time PCR in bovine preimplantation embryos

text: BACKGROUND: Real-time quantitative PCR is a sensitive and very efficient technique to examine gene transcription patterns in preimplantation embryos, in order to gain information about embryo development and to optimize assisted reproductive technologies. Critical to the succesful application of real-time PCR is careful assay design, reaction optimization and validation to maximize sensitivity and accuracy. In most of the studies published GAPD, ACTB or 18S rRNA have been used as a single reference gene without prior verification of their expression stability. Normalization of the data using unstable controls can result in erroneous conclusions, especially when only one reference gene is used. RESULTS: In this study the transcription levels of 8 commonly used reference genes (ACTB, GAPD, Histone H2A, TBP, HPRT1, SDHA, YWHAZ and 18S rRNA) were determined at different preimplantation stages (2-cell, 8-cell, blastocyst and hatched blastocyst) in order to select the most stable genes to normalize quantitative data within different preimplantation embryo stages. CONCLUSION: Using the geNorm application YWHAZ, GAPD and SDHA were found to be the most stable genes across the examined embryonic stages, while the commonly used ACTB was shown to be highly regulated. We recommend the use of the geometric mean of those 3 reference genes as an accurate normalization factor, which allows small expression differences to be reliably measured.


title: Effect of Chicken Egg Yolk Antibodies (IgY) against Diarrhea in Domesticated Animals: A Systematic Review and Meta-Analysis

text: BACKGROUND: IgY antibodies are serum immunoglobulin in birds, reptiles and amphibians, and are transferred from serum to egg yolk to confer passive immunity to their embryos and offspring. Currently, the oral passive immunization using chicken IgY has been focused as an alternative to antibiotics for the treatment and control of diarrhea in animals and humans. This systematic review was focused to determine the effect of IgY in controlling and preventing diarrhea in domesticated animals including Piglets, Mice, Poultry and Calves. METHODS AND RESULTS: Previous research reports focused on treatment effect of Chicken IgY against diarrhea were retrieved from different electronic data bases (MEDLINE, EMBASE, SPRINGER-LINK, WILEY, AGRICOLA, MEDWELL Journals, Scientific Publish, Chinese articles from Core periodicals in 2012). A total of 61 studies in 4 different animal classes met the inclusion criteria. Data on study characteristics and outcome measures were extracted. The pooled relative risk (RR) of 49 studies of different animals [Piglets – 22; Mice – 14; Poultry – 7 and Calves – 6] in meta-analyses revealed that, IgY significantly reduced the risk of diarrhea in treatment group when compare to the placebo. However, the 95% confidence intervals of the majority of studies in animal class piglets and calves embrace RR of one. The same results were obtained in sub group analyses (treatment regiment – prophylactic or therapeutic; pathogen type – bacterial or viral). Perhaps, this inconsistency in the effect of IgY at the individual study level and overall effect measures could be influenced by the methodological heterogeneity. CONCLUSION: The present systematic review (SR) and meta-analysis demonstrated the beneficial effect of IgY. This supports the opinion that IgY is useful for prophylaxis and treatment. However, more intensive studies using the gold standard animal experiments with the focus to use IgY alone or in combination with other alternative strategies are indispensable.


Covid19 y cronicidad. Una oportunidad de reinventar los servicios de medicina física y rehabilitación


title: Middle East Respiratory Syndrome Coronavirus Infection in Dromedary Camels in Saudi Arabia

text: The Middle East respiratory syndrome (MERS) is proposed to be a zoonotic disease; however, the reservoir and mechanism for transmission of the causative agent, the MERS coronavirus, are unknown. Dromedary camels have been implicated through reports that some victims have been exposed to camels, camels in areas where the disease has emerged have antibodies to the virus, and viral sequences have been recovered from camels in association with outbreaks of the disease among humans. Nonetheless, whether camels mediate transmission to humans is unresolved. Here we provide evidence from a geographic and temporal survey of camels in the Kingdom of Saudi Arabia that MERS coronaviruses have been circulating in camels since at least 1992, are distributed countrywide, and can be phylogenetically classified into clades that correlate with outbreaks of the disease among humans. We found no evidence of infection in domestic sheep or domestic goats.


title: Recombinase polymerase amplification–nucleic acid lateral flow immunoassays for Newcastle disease virus and infectious bronchitis virus detection

text: Newcastle disease virus (NDV) and infectious bronchitis virus (IBV) are two poultry pathogens affecting the respiratory tract of chickens, and cause major economic losses in the industry. Rapid detection of these viruses is crucial to inform implementation of appropriate control measures. The objective of our study is developing a simple, rapid and field applicable recombinase polymerase amplification (RPA)–nucleic acid lateral flow (NALF) immunoassay for detection of NDV and IBV. Isothermal amplification of the matrix protein (M) gene of NDV and the nucleoprotein (N) gene of IBV was implemented via recombinase polymerase amplification at 38 °C for 40 min and 20 min, respectively using modified labeled primers. NALF device used in this study utilizes antibodies for detection of labeled RPA amplicons. The results revealed that RPA-NALF immunoassays can detect both viruses after 40 min at 38 °C and only NDV after 20 min. The limit of detection (LOD) was 10 genomic copies/RPA reaction. The assays results on clinical samples collected from diseased chicken farms demonstrated a good performance in comparison with quantitative real time reverse transcription polymerase chain reaction (qRT-PCR). The assays established in this study can facilitate rapid, on-site molecular diagnosis of suspected cases of ND and IB viral infections as the results can be detected by the naked eye without the need for measuring fluorescence. Furthermore, the NALF device could be adapted to detect other infectious agents.


COVID‐19: How Can Rural Community Pharmacies Respond to the Outbreak?


title: Expected immunizations and health protection for Hajj and Umrah 2018 —An overview

text: Abstract Background The annual Hajj and Umrah are one of the largest recurring religious mass gatherings across the globe drawing pilgrims from more than 185 countries. The living circumstances and activities of the pilgrims may create an environment for the occurrence and spread of communicable diseases. Each year, the Health authority of the Kingdom of Saudi Arabia, in coordination with international health authorities, updates health requirements for pilgrims. The Hajj for 2017 took place from August 24 to September 5, 2017. Here, we review the expected obligations for immunizations for the 2018 Hajj and Umrah. Results The Hajj and Umrah vaccine requirements include mandatory vaccinations against yellow fever, quadrivalent meningococcal polysaccharide (every 3 years) or conjugated (every 5 years) vaccines and poliomyelitis vaccine. Influenza vaccine utilizing the 2016 (Southern Hemisphere vaccine to all pilgrims) was recommended but was not obligatory for pilgrims. Ciprofloxacin is required for individuals >12 years excluding pregnant women as chemoprophylaxis to be given at the port of entry for Pilgrims coming from the meningitis belt. With the ongoing outbreaks of measles in Europe, it is recommended that all pilgrims have an updated immunization against vaccine-preventable diseases (diphtheria, tetanus, pertussis, polio, measles and mumps). Conclusion The mandatory vaccines remain the same with continued vigilance for the development of any new or emerging infectious diseases. Continuing surveillance for Zika virus, cholera and MERS-CoV are ongoing.


Un numéro spécial Covid-19 du Journal de chirurgie viscérale : quels problèmes, quels dangers et quelles solutions sont identifiés?


Guide pratique pour la radiothérapie des hémopathies malignes dans la situation d’épidémie de covid-19 : recommandations de l’International Lymphoma Radiation Oncology Group


Mechanisms of epithelial damage: are there parallels between bullous skin diseases and asthma?


title: Crystal structures of Nipah and Hendra virus fusion core proteins

text: The Nipah and Hendra viruses are highly pathogenic paramyxoviruses that recently emerged from flying foxes to cause serious disease outbreaks in humans and livestock in Australia, Malaysia, Singapore and Bangladesh. Their unique genetic constitution, high virulence and wide host range set them apart from other paramyxoviruses. These characteristics have led to their classification into the new genus Henpavirus within the family Paramyxoviridae and to their designation as Biosafety Level 4 pathogens. The fusion protein, an enveloped glycoprotein essential for viral entry, belongs to the family of class I fusion proteins and is characterized by the presence of two heptad repeat (HR) regions, HR1 and HR2. These two regions associate to form a fusion‐active hairpin conformation that juxtaposes the viral and cellular membranes to facilitate membrane fusion and enable subsequent viral entry. The Hendra and Nipah virus fusion core proteins were crystallized and their structures determined to 2.2 Å resolution. The Nipah and Hendra fusion core structures are six‐helix bundles with three HR2 helices packed against the hydrophobic grooves on the surface of a central coiled coil formed by three parallel HR1 helices in an oblique antiparallel manner. Because of the high level of conservation in core regions, it is proposed that the Nipah and Hendra virus fusion cores can provide a model for membrane fusion in all paramyxoviruses. The relatively deep grooves on the surface of the central coiled coil represent a good target site for drug discovery strategies aimed at inhibiting viral entry by blocking hairpin formation.


title: Development of a porcine epidemic diarrhea virus M protein-based ELISA for virus detection

text: A membrane (M), protein-based ELISA was developed to detect porcine epidemic diarrhea virus (PEDV). The M gene of PEDV was expressed in Escherichia coli. The purified recombinant M protein was used to immunize rabbits to generate a polyclonal antibody. Immunofluorescence analysis indicated that the anti-PEDV-M antibody reacted with PEDV-infected cells. The antibody was utilized to develop an indirect ELISA to detect PEDV. Other viruses, porcine transmissible gastroenteritis coronavirus, avian infectious bronchitis coronavirus, porcine reproductive and respiratory syndrome virus, classic swine fever virus and porcine pseudorabies virus, were unreactive.


DETECCIÓN VIRAL Y RESPUESTA SEROLÓGICA EN PACIENTES CRÍTICOS INTUBADOS CON SARS-CoV-2. IMPLICACIONES PARA RETIRADA DE AISLAMIENTO


Reply to “Indications and timing for tracheostomy in patients with SARS CoV2‐related” by Ferri et al.


title: The Nrf2 Activator (DMF) and Covid-19: Is there a Possible Role?

text: INTRODUCTION: COVID-19 is a new viral illness that can affect the lungs and airways with lethal consequences leading to the death of the patients. The ACE2 receptors were widely disturbed among body tissues such as lung, kidney, small intestine, heart, and others in different percent and considered a target for the nCOVID-19 virus. S-protein of the virus was binding to ACE2 receptors caused downregulation of endogenous anti-viral mediators, upregulation of NF-κB pathway, ROS and pro-apoptotic protein. Nrf2 was a transcription factor that’s play a role in generation of anti-oxidant enzymes. AIM: To describe and establish role of Nrf2 activators for treatment COVID-19 positive patients. METHODS: We used method of analysis of the published papers with described studies about COVID-19 connected with pharmacological issues and aspects which are included in global fighting against COVID-19 infection, and how using DMF (Nrf2 activator) in clinical trial for nCOVID-19 produce positive effects in patients for reduce lung alveolar cells damage. RESULTS: we are found that Nrf2 activators an important medication that’s have a role in reduce viral pathogenesis via inhibit virus entry through induce SPLI gene expression as well as inhibit TRMPSS2, upregulation of ACE2 that’s make a competition with the virus on binding site, induce gene expression of anti-viral mediators such as RIG-1 and INFs, induce anti-oxidant enzymes, also they have a role in inhibit NF-κB pathway, inhibit both apoptosis proteins and gene expression of TLRs. CONCLUSION: We are concluded that use DMF (Nrf2 activator) in clinical trial for nCOVID-19 positive patients to reduce lung alveolar cells damage.


title: Anti-Infectious Plants of the Thai Karen: A Meta-Analysis

text: Pharmacology has developed many drugs to treat infections, but many people, especially in developing countries, cannot afford to purchase them, and still depend on traditional knowledge and local medicinal plants to fight off infections. In addition, numerous microbes have developed resistance to the pharmaceutical drugs developed to fight them, and for many, such as Covid-19, effective drugs remain to be found. Ethnomedicinal knowledge is useful, not only for local people as a source of medicine for primary health care, but also for new pharmacological discoveries. This study aimed to identify the plants that the Karen, the largest hill-tribe ethnic minority in northern and western Thailand, use for treatments of infectious diseases. We present a meta-analysis of data from 16 ethnobotanical studies of 25 Karen villages with the aim of understanding traditional knowledge and treatments and point to potential plants for further pharmacological development. The Karen used 127 plant species from 59 plant families to treat infections and infectious diseases. The Cultural Important Index (CI) showed that the Leguminosae, Euphorbiaceae, Asteraceae, Lauraceae, Apocynaceae, Menispermaceae, and Lamiaceae were the most commonly used families. As for species, Cleidion javanicum, Tinospora crispa, Litsea cubeba, Aesculus assamica, Tadehagi triquetrum, Senna alata, Tithonia diversifolia, Embelia sessiliflora, and Combretum indicum were the most commonly used in treatments of infectious diseases. We suggest that these plant species should be the first to be pharmacologically tested for possible development of medicines, and the remaining species registered should subsequently undergo testing.


title: Clinical exacerbation of SARS‐CoV2 infection after fingolimod withdrawal

text: The role of disease‐modifying therapies in patients with autoimmune disorders during SARS‐CoV2 infection is controversial. Immunocompromised patients could have a more severe COVID‐19 disease, due to the absence of an adequate immune response against the SARS‐CoV‐2. However, therapies that act on immune response could play a protective role by dampening the cytokine release syndrome. Fingolimod is a drug used for immune therapy in patients with Multiple Sclerosis (MS) through the sequestration of activated lymphocytes in the lymph nodes. We report the case of a 57‐year‐old man with relapsing‐remitting MS treated with fingolimod that showed a reactivation of COVID‐19 with signs of hyperinflammation syndrome after fingolimod withdrawal. Our case suggests that discontinuation of fingolimod during COVID‐19 could imply a worsening of SARS‐CoV2 infection. This article is protected by copyright. All rights reserved.


title: Endoplasmic Reticulum Stress Interacts With Inflammation in Human Diseases

text: The endoplasmic reticulum is a critical organelle for normal cell function and homeostasis. Disturbed protein folding process in the ER, termed ER stress, leads to the activation of unfolded protein response (UPR) that encompasses a complex network of intracellular signaling pathways. The UPR can either restore ER homeostasis or activate pro-apoptotic pathways depending on specific insults, intensity and duration of the stress, and cell types. ER stress and the UPR have recently been linked to inflammation in a variety of human pathologies including autoimmune diseases, infection, neurodegenerative disease, and metabolic disorders. In the cell, ER stress and inflammatory signaling share extensive regulators and effectors in a broad spectrum of biological processes. In spite of different etiologies, the two signaling pathways were shown to form a vicious cycle in exacerbating cellular dysfunction and causing apoptosis in many cells and tissues. However, the interaction between ER stress and inflammation in many of these diseases remains elusive. Further understanding of those issues may enable the development of novel therapies that spontaneously target these pathogenic pathways.


title: Evaluating Detection of an Inhalational Anthrax Outbreak

text: Timely detection of an inhalational anthrax outbreak is critical for clinical and public health management. Syndromic surveillance has received considerable investment, but little is known about how it will perform relative to routine clinical case finding for detection of an inhalational anthrax outbreak. We conducted a simulation study to compare clinical case finding with syndromic surveillance for detection of an outbreak of inhalational anthrax. After simulated release of 1 kg of anthrax spores, the proportion of outbreaks detected first by syndromic surveillance was 0.59 at a specificity of 0.9 and 0.28 at a specificity of 0.975. The mean detection benefit of syndromic surveillance was 1.0 day at a specificity of 0.9 and 0.32 days at a specificity of 0.975. When syndromic surveillance was sufficiently sensitive to detect a substantial proportion of outbreaks before clinical case finding, it generated frequent false alarms.


title: Development and Initial Validation of the COVID Stress Scales

text: Abstract Research and clinical observations suggest that during times of pandemic many people exhibit stress- or anxiety-related psychopathology that include fear of becoming infected, fear of coming into contact with possibly contaminated objects or surfaces, fear of foreigners who might be carrying infection (i.e., disease-related xenophobia), fear of the socio-economic consequences of the pandemic, compulsive checking and reassurance-seeking regarding possible pandemic-related threats, and traumatic stress symptoms about the pandemic (e.g., nightmares, intrusive thoughts). We developed the 36-item COVID Stress Scales (CSS) to measure these features, as they pertain to COVID-19. The CSS were developed to better understand and assess COVID-19-related psychopathology. The scales were intentionally designed so they could be readily adapted for future pandemics. The CSS were developed and initially validated in population-representative samples from Canada (N = 3,479) and the United States (N = 3,375). A stable 5-factor solution was identified, corresponding to scales assessing COVID-related stress and anxiety symptoms: (1) Danger and contamination fears, (2) fears about economic consequences, (3) xenophobia, (4) compulsive checking, and (5) traumatic stress symptoms about COVID-19. The scales performed well on various indices of reliability and validity. The scales were intercorrelated, providing evidence of a COVID Stress Syndrome. The scales offer promise as tools for better understanding the psychopathology associated with COVID-19 and for identifying people in need of mental health services.


title: Drug Repurposing for Japanese Encephalitis Virus Infection by Systems Biology Methods

text: Japanese encephalitis is a zoonotic disease caused by the Japanese encephalitis virus (JEV). It is mainly epidemic in Asia with an estimated 69,000 cases occurring per year. However, no approved agents are available for the treatment of JEV infection, and existing vaccines cannot control various types of JEV strains. Drug repurposing is a new concept for finding new indication of existing drugs, and, recently, the concept has been used to discover new antiviral agents. Identifying host proteins involved in the progress of JEV infection and using these proteins as targets are the center of drug repurposing for JEV infection. In this study, based on the gene expression data of JEV infection and the phenome-wide association study (PheWAS) data, we identified 286 genes that participate in the progress of JEV infection using systems biology methods. The enrichment analysis of these genes suggested that the genes identified by our methods were predominantly related to viral infection pathways and immune response-related pathways. We found that bortezomib, which can target these genes, may have an effect on the treatment of JEV infection. Subsequently, we evaluated the antiviral activity of bortezomib using a JEV-infected mouse model. The results showed that bortezomib can lower JEV-induced lethality in mice, alleviate suffering in JEV-infected mice and reduce the damage in brains caused by JEV infection. This work provides an agent with new indication to treat JEV infection.


Six pioneers artistically celebrated by the Andalusian Society of Nuclear Medicine


title: Thinking outside the (acrylic) box: a framework for the local use of custom‐made medical devices

text: Before the COVID‐19 pandemic, clinicians were already adept at creating workarounds for day‐to‐day shortages of equipment, inventively cobbling together substitute gadgets together to fulfil a clinical need. This is colloquially known as ‘jury‐rigging’ or ‘MacGyvering’, the latter taken from the eponymous 1980s television series of a problem‐solving crime fighter who could seemingly manufacture anything from a few paperclips and some chewing gum [1].


title: COVID-19 Follow up Testing

text: • Positive cases of SARS-CoV-2 were seen in the Mayo Clinic FL COVID Virtual Clinic. • 70% of patients met CDC guidelines for release from quarantine & still tested (+); • The average time from onset of symptoms to negative testing was 19 days.


title: Provision of Speech-Language Pathology Services for the Treatment of Speech and Language Disorders in Children during the COVID-19 Pandemic: Problems, Concerns, and Solutions

text: Recently, a novel virus has spread worldwide causing the disease called COVID-19. In addition to putting people’s lives at risk and causing mortality, various problems have occurred due to the negative effects of the COVID-19 pandemic. Quarantine, social distancing, and the obligation to use protective tools have led to sometimes long term closing of various jobs and services, including rehabilitation services. For instance, the disease has interrupted the provision of Speech-Language Pathology (SLP) services to children due to the need for face-to-face communication between Speech and Language Pathologists (SLPs) and children during the evaluation and treatment processes. Therefore, here, we described the quality of providing SLP services during the COVID-19 pandemic and the negative effects of the disease on the provision of SLP services. In addition, we made an attempt to explain concerns and problems raised by the families, the importance of providing SLP services during the critical period of speech and language development, telepractice services, the roles of speech-language-hearing related scientific associations, and the roles of SLPs during the outbreak of COVID-19.


title: Endoplasmic Reticulum Calcium Pumps and Tumor Cell Differentiation

text: Endoplasmic reticulum (ER) calcium homeostasis plays an essential role in cellular calcium signaling, intra-ER protein chaperoning and maturation, as well as in the interaction of the ER with other organelles. Calcium is accumulated in the ER by sarco/endoplasmic reticulum calcium ATPases (SERCA enzymes) that generate by active, ATP-dependent transport, a several thousand-fold calcium ion concentration gradient between the cytosol (low nanomolar) and the ER lumen (high micromolar). SERCA enzymes are coded by three genes that by alternative splicing give rise to several isoforms, which can display isoform-specific calcium transport characteristics. SERCA expression levels and isoenzyme composition vary according to cell type, and this constitutes a mechanism whereby ER calcium homeostasis is adapted to the signaling and metabolic needs of the cell, depending on its phenotype, its state of activation and differentiation. As reviewed here, in several normal epithelial cell types including bronchial, mammary, gastric, colonic and choroid plexus epithelium, as well as in mature cells of hematopoietic origin such as pumps are simultaneously expressed, whereas in corresponding tumors and leukemias SERCA3 expression is selectively down-regulated. SERCA3 expression is restored during the pharmacologically induced differentiation of various cancer and leukemia cell types. SERCA3 is a useful marker for the study of cell differentiation, and the loss of SERCA3 expression constitutes a previously unrecognized example of the remodeling of calcium homeostasis in tumors.


title: Medical Student Mobilization During a Crisis: Lessons From a COVID-19 Medical Student Response Team

text: On March 17, 2020, the Association of American Medical Colleges recommended the suspension of all direct patient contact responsibilities for medical students because of the COVID-19 pandemic. Given this change, medical students nationwide had to grapple with how and where they could fill the evolving needs of their schools’ affiliated clinical sites, physicians, and patients and the community. APPROACH: At Harvard Medical School (HMS), student leaders created a COVID-19 Medical Student Response Team to: (1) develop a student-led organizational structure that would optimize students’ ability to efficiently mobilize interested peers in the COVID-19 response, both clinically and in the community, in a strategic, safe, smart, and resource-conscious way; and (2) serve as a liaison with the administration and hospital leaders to identify evolving needs and rapidly engage students in those efforts. OUTCOMES: Within a week of its inception, the COVID-19 Medical Student Response Team had more than 500 medical student volunteers from HMS and had shared the organizational framework of the response team with multiple medical schools across the country. The HMS student volunteers joined any of the 4 virtual committees to complete this work: Education for the Medical Community, Education for the Broader Community, Activism for Clinical Support, and Community Activism. NEXT STEPS: The COVID-19 Medical Student Response Team helped to quickly mobilize hundreds of students and has been integrated into HMS’s daily workflow. It may serve as a useful model for other schools and hospitals seeking medical student assistance during the COVID-19 pandemic. Next steps include expanding the initiative further, working with the leaders of response teams at other medical schools to coordinate efforts, and identifying new areas of need at local hospitals and within nearby communities that might benefit from medical student involvement as the pandemic evolves.


title: Coalition: Advocacy for prospective clinical trials to test the post-exposure potential of hydroxychloroquine against COVID-19

text: Abstract Our coalition of public health experts, doctors, and scientists worldwide want to draw attention to the need for high-quality evaluation protocols of the potential beneficial effect of hydroxychloroquine (HCQ) as a post-exposure drug for exposed people, meaning people with close contact with positive tested patients, including home and medical caregivers. We have reviewed the mechanisms of antiviral effect of HCQ, the risk-benefit ratio taking into consideration the PK/PD of HCQ and the thresholds of efficacy. We have studied its use as an antimalarial, an antiviral, and an immunomodulating drug and concluded that the use of HCQ at does matching that of the standard treatment of Systemic Lupus erythematous, which has proven safety and efficacy in terms of HCQ blood and tissue concentration adapted to bodyweight (2,3), at 6 mg/kg/day 1 (loading dose) followed by 5 mg/kg/day, with a maximum limit of 600 mg/day in all cases should swiftly be clinically evaluated as a post-exposure drug for exposed people.


title: Breaking Bad: How Viruses Subvert the Cell Cycle

text: Interactions between the host and viruses during the course of their co-evolution have not only shaped cellular function and the immune system, but also the counter measures employed by viruses. Relatively small genomes and high replication rates allow viruses to accumulate mutations and continuously present the host with new challenges. It is therefore, no surprise that they either escape detection or modulate host physiology, often by redirecting normal cellular pathways to their own advantage. Viruses utilize a diverse array of strategies and molecular targets to subvert host cellular processes, while evading detection. These include cell-cycle regulation, major histocompatibility complex-restricted antigen presentation, intracellular protein transport, apoptosis, cytokine-mediated signaling, and humoral immune responses. Moreover, viruses routinely manipulate the host cell cycle to create a favorable environment for replication, largely by deregulating cell cycle checkpoints. This review focuses on our current understanding of the molecular aspects of cell cycle regulation that are often targeted by viruses. Further study of their interactions should provide fundamental insights into cell cycle regulation and improve our ability to exploit these viruses.


Chilblain‐like lesions in pediatrics dermatological outpatients during the COVID‐19 outbreak


Back to the spring of Wuhan: facts and hope of COVID-19 outbreak


title: Factors Associated with Hospitalization and Disease Severity in a Racially and Ethnically Diverse Population of COVID-19 Patients

text: Background: The coronavirus disease (COVID-19) first identified in Wuhan in December 2019 became a pandemic within a few months of its discovery. The impact of COVID-19 is due to both its rapid spread and its severity, but the determinants of severity have not been fully delineated. Objective: Identify factors associated with hospitalization and disease severity in a racially and ethnically diverse cohort of COVID-19 patients. Methods: We analyzed data from COVID-19 patients diagnosed at the University of Cincinnati health system from March 13, 2020 to May 31, 2020. Severe COVID-19 was defined as admission to intensive care unit or death. Logistic regression modeling adjusted for covariates was used to identify the factors associated with hospitalization and severe COVID-19. Results: Among the 689 COVID-19 patients included in our study, 29.2% were non-Hispanic White, 25.5% were non-Hispanic Black, 32.5% were Hispanic, and 12.8% were of other race/ethnicity. About 31.3% of patients were hospitalized and 13.2% had severe disease. In adjusted analyses, the sociodemographic factors associated with hospitalization and/or disease severity included older age, non-Hispanic Black or Hispanic race/ethnicity (compared non-Hispanic White), and smoking. The following comorbidities: diabetes, hypercholesterolemia, asthma, chronic obstructive pulmonary disease (COPD), chronic kidney disease, cardiovascular diseases, osteoarthritis, and vitamin D deficiency, were associated with hospitalization and/or disease severity. Hematological disorders such as anemia, coagulation disorders, and thrombocytopenia were associated with higher odds of both hospitalization and disease severity. Conclusion: This study confirms race and ethnicity as predictors of severe COVID-19 and identifies clinical risk factors not previously reported such a vitamin D deficiency, hypercholesterolemia, osteoarthritis, and anemia.


title: Human Coronavirus Infections in Rural Thailand: A Comprehensive Study Using Real-Time Reverse-Transcription Polymerase Chain Reaction Assays

text: Background. We sought to determine whether infections with human coronaviruses (HCoVs) 229E, OC43, HKU1, and NL63 are associated with pneumonia and to define the epidemiology of HCoV infection in rural Thailand. Methods. We developed a real-time reverse-transcription polymerase chain reaction (RT-PCR) assay panel for the recognized HCoV types and compared HCoV infections in patients hospitalized with pneumonia, outpatients with influenza-like illness, and asymptomatic control patients between September 2003 and August 2005. Results. During study year 1, 43 (5.9%) of 734 patients with pneumonia had HCoV infections; 72.1% of the infections were with OC43. During study year 2, when control patients were available, 21 (1.8%) of 1156 patients with pneumonia, 12 (2.3%) of 513 outpatients, and 6 (2.1%) of 281 control patients had HCoV infections. Compared with infection in control patients, infection with any HCoV type or with all types combined was not associated with pneumonia (adjusted odds ratio for all HCoV types, 0.67 [95% confidence interval, 0.26–1.75]; P= .40 ). HCoV infections were detected throughout both study years; 93.6% of OC43 infections in the first year occurred from January through March. Conclusions. HCoV infections were infrequently detected in rural Thailand by use of sensitive real-time RTPCR assays. We found no association between HCoV infection and illness. However, we noted year-to-year variation in the prevalence of HCoV strains, which likely influenced our results.


title: A comparative epidemiologic analysis of SARS in Hong Kong, Beijing and Taiwan

text: BACKGROUND: The 2002-2003 Severe Acute Respiratory Syndrome (SARS) outbreak infected 8,422 individuals leading to 916 deaths around the world. However, there have been few epidemiological studies of SARS comparing epidemiologic features across regions. The aim of this study is to identify similarities and differences in SARS epidemiology in three populations with similar host and viral genotype. METHODS: We present a comparative epidemiologic analysis of SARS, based on an integrated dataset with 3,336 SARS patients from Hong Kong, Beijing and Taiwan, epidemiological and clinical characteristics such as incubation, onset-to-admission, onset-to-discharge and onset-to-death periods, case fatality ratios (CFRs) and presenting symptoms are described and compared between regions. We further explored the influence of demographic and clinical variables on the apparently large differences in CFRs between the three regions. RESULTS: All three regions showed similar incubation periods and progressive shortening of the onset-to-admission interval through the epidemic. Adjusted for sex, health care worker status and nosocomial setting, older age was associated with a higher fatality, with adjusted odds ratio (AOR): 2.10 (95% confidence interval: 1.45, 3.04) for those aged 51-60; AOR: 4.57 (95% confidence interval: 3.32, 7.30) for those aged above 60 compared to those aged 41-50 years. Presence of pre-existing comorbid conditions was also associated with greater mortality (AOR: 1.74; 95% confidence interval: 1.36, 2.21). CONCLUSION: The large discrepancy in crude fatality ratios across the three regions can only be partly explained by epidemiological and clinical heterogeneities. Our findings underline the importance of a common data collection platform, especially in an emerging epidemic, in order to identify and explain consistencies and differences in the eventual clinical and public health outcomes of infectious disease outbreaks, which is becoming increasingly important in our highly interconnected world.


title: Carbochips: a new energy for old biobuilders

text: Abstract Microarray technology has come of age for use in high-throughput operations and large-scale studies. It allows rapid and simultaneous detection of thousands of parameters within a single experiment. Recent developments in the field of carbohydrate microarray technology facilitate applications for different types of protein–carbohydrate interactions. These developments included capture molecule immobilization, surface engineering and detection strategies to analyze entire glycomes and glycosylation in vertebrate systems, the most common post-translational modification.


title: Does genetic diversity limit disease spread in natural host populations?

text: It is a commonly held view that genetically homogenous host populations are more vulnerable to infection than genetically diverse populations. The underlying idea, known as the ‘monoculture effect,' is well documented in agricultural studies. Low genetic diversity in the wild can result from bottlenecks (that is, founder effects), biparental inbreeding or self-fertilization, any of which might increase the risk of epidemics. Host genetic diversity could buffer populations against epidemics in nature, but it is not clear how much diversity is required to prevent disease spread. Recent theoretical and empirical studies, particularly in Daphnia populations, have helped to establish that genetic diversity can reduce parasite transmission. Here, we review the present theoretical work and empirical evidence, and we suggest a new focus on finding ‘diversity thresholds.'


Capacity and the COVID Surge


title: Systematic review with meta-analysis of the accuracy of diagnostic tests for COVID-19

text: OBJECTIVE: . To collate the evidence on the accuracy parameters of all available diagnostic methods for detecting SARS-CoV-2. METHODS: . A systematic review with meta-analysis was performed. Searches were conducted in Pubmed and Scopus (April 2020). Studies reporting data on sensitivity or specificity of diagnostic tests for COVID-19 using any human biological sample were included. RESULTS: . Sixteen studies were evaluated. Meta-analysis showed that computed tomography has high sensitivity (91.9% [89.8–93.7%]), but low specificity (25.1% [21.0–29.5%]). The combination of IgM and IgG antibodies demonstrated promising results for both parameters (84.5% [82.2%-86.6%]; 91.6% [86.0%-95.4%], respectively). For RT-PCR tests, rectal stools/swab, urine, and plasma were less sensitive while sputum (97.2% [90.3–99.7%]) presented higher sensitivity for detecting the virus. CONCLUSIONS: . RT-PCR remains the gold standard for the diagnosis of COVID-19 in sputum samples. However, the combination of different diagnostic tests is highly recommended to achieve adequate sensitivity and specificity.


title: Early childhood environmental education: A systematic review of the research literature

text: Abstract Environmental education focused on the early-childhood years is experiencing dynamic growth in research and practice due to persistent environmental challenges coupled with burgeoning interest in the documented benefits of nature-rich experiences for infants and children. To better understand the landscape of early childhood environmental education (ECEE) pedagogical practices and expected outcomes, we undertook a systematic review of empirical studies of ECEE programs. Focusing on a 25-year span, we surfaced 66 studies that met our inclusion criteria. We found that participants in such programs spanned the early-childhood age range (birth through age eight) with the majority involving three-to six-year-olds in teacher-led, formal (school-like) programs. The primary outcomes documented in our sample studies included environmental literacy development, cognitive development, and social and emotional development. To a lesser extent, the studies addressed physical development and language and literacy development. On balance, our sample of ECEE studies reported strongly positive findings associated with the aforementioned outcomes. The majority emphasized the effectiveness of play-based, nature-rich pedagogical approaches that incorporated movement and social interaction. We include a visualization that synthesizes cross-sample findings with the intention of assisting ECEE practitioners in developing, implementing, and evaluating programs as well as encouraging researchers to further study elements, processes, and theoretical assumptions inherent in them.


title: Making prevention pay

text: Funding for biodefense is spurring new vaccine and anti-infective programs at several biotech companies.


title: Characterization and membrane gene-based phylogenetic analysis of avian infectious bronchitis virus Chinese strain HH06

text: A Chinese isolate of avian infectious bronchitis virus (IBV) designated HH06 was isolated from the kidney tissues of a chicken flock experiencing an outbreak of nephritis. In vivo pathogenicity of the IBV isolate HH06 was determined by inoculating specific pathogen-free (SPF) chickens. The clinical signs and related gross lesions of HH06 infected chickens were similar with those of the field-infected chickens. SPF embryonated eggs were inoculated with virus suspension for serial passage and their genomic RNA was extracted. RT-PCR technique was utilized to amplify the M gene sequence encoding membrane protein of IBV. Recombinant plasmid named T-vector-M was constructed via inserting the M gene into the TA cloning vector, pMD 18-T. The sequenced M gene and its deduced amino acid (aa) sequences were compared with the published sequences of reference strains. The M gene is of 687 bp in length encoding the M protein of 228 amino acids with a predicted molecular weight of 25.4 kDa. The sequences of the M gene and M protein share 83.9–97.9% and 83.6–96.5% homologous identities, respectively, compared with 29 IBV reference strains derived from different regions or countries, which revealed that there are still significant variations between strains. Furthermore, a phylogenetic tree based on these M DNA sequences was generated, and the tree topology suggests that some Chinese IBV strains may have a common ancestor; however, HH06 is a new local IBV isolate that is responsible for the field outbreak of nephritis.


title: High‐cell‐passage canine coronavirus vaccine providing sterilising immunity

text: Objectives: To evaluate the ability of a high‐cell‐passage canine coronavirus vaccine to immunise dogs against challenge with a field isolate of the virus. Methods: Three dogs that had previously tested seronegative and virus‐negative for canine coronavirus were inoculated twice, at 21‐day intervals, with the vaccine and kept under observation. Two seronegative and virus‐negative dogs served as unvaccinated controls. For safety tests, two additional dogs were inoculated oronasally with 10 times the vaccinal dose and no reactions were observed. Faecal samples were collected daily from the vaccinated dogs after the first and second inoculations. Both vaccinated and control dogs were challenged two weeks after the second vaccination with a field canine coronavirus strain. Blood samples were collected for serological tests before vaccination and at weekly intervals after vaccinations and challenge. Results: Virus was not detected in faecal samples after the first or second vaccinations by virus isolation assays and PCR. Significantly, the vaccinated dogs did not have clinical signs after challenge and no virus shedding was observed. The two unvaccinated control dogs had moderate enteritis, and virus was detected in cell cultures starting from three days postchallenge (dog 1) and two days postchallenge (dog 2), and by PCR for 23 median days. Clinical Significance: This study showed the efficacy of a high‐cell‐passage canine coronavirus vaccine in preventing infection of dogs by virulent virus and, specifically, its ability to induce sterilising immunity.