title: Detection and characterisation of coronaviruses in migratory and non-migratory Australian wild birds

text: We evaluated the presence of coronaviruses by PCR in 918 Australian wild bird samples collected during 2016–17. Coronaviruses were detected in 141 samples (15.3%) from species of ducks, shorebirds and herons and from multiple sampling locations. Sequencing of selected positive samples found mainly gammacoronaviruses, but also some deltacoronaviruses. The detection rate of coronaviruses was improved by using multiple PCR assays, as no single assay could detect all coronavirus positive samples. Sequencing of the relatively conserved Orf1 PCR amplicons found that Australian duck gammacoronaviruses were similar to duck gammacoronaviruses around the world. Some sequenced shorebird gammacoronaviruses belonged to Charadriiformes lineages, but others were more closely related to duck gammacoronaviruses. Australian duck and heron deltacoronaviruses belonged to lineages with other duck and heron deltacoronaviruses, but were almost 20% different in nucleotide sequence to other deltacoronavirus sequences available. Deltacoronavirus sequences from shorebirds formed a lineage with a deltacoronavirus from a ruddy turnstone detected in the United States. Given that Australian duck gammacoronaviruses are highly similar to those found in other regions, and Australian ducks rarely come into contact with migratory Palearctic duck species, we hypothesise that migratory shorebirds are the important vector for moving wild bird coronaviruses into and out of Australia.


title: Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales

text: Abstract In this study, we calculated the codon usage bias in severe acute respiratory syndrome Coronavirus (SARSCoV) and performed a comparative analysis of synonymous codon usage patterns in SARSCoV and 10 other evolutionary related viruses in the Nidovirales. Although there is a significant variation in codon usage bias among different SARSCoV genes, codon usage bias in SARSCoV is a little slight, which is mainly determined by the base compositions on the third codon position. By comparing synonymous codon usage patterns in different viruses, we observed that synonymous codon usage pattern in these virus genes was virus specific and phylogenetically conserved, but it was not host specific. Phylogenetic analysis based on codon usage pattern suggested that SARSCoV was diverged far from all three known groups of Coronavirus. Compositional constraints could explain most of the variation of synonymous codon usage among these virus genes, while gene function is also correlated to synonymous codon usages to a certain extent. However, translational selection and gene length have no effect on the variations of synonymous codon usage in these virus genes.


AYUSH for COVID-19 management


Middle East Respiratory Syndrome and Blood Donation: Topic for Further Study and Discussion


title: Dipeptidyl Peptidase 4 Distribution in the Human Respiratory Tract: Implications for the Middle East Respiratory Syndrome

text: Dipeptidyl peptidase 4 (DPP4, CD26), a type II transmembrane ectopeptidase, is the receptor for the Middle Eastern respiratory syndrome coronavirus (MERS-CoV). MERS emerged in 2012 and has a high mortality associated with severe lung disease. A lack of autopsy studies from MERS fatalities has hindered understanding of MERS-CoV pathogenesis. We investigated the spatial and cellular localization of DPP4 to evaluate an association MERS clinical disease. DPP4 was rarely detected in the surface epithelium from nasal cavity to conducting airways with a slightly increased incidence in distal airways. DPP4 was also found in a subset of mononuclear leukocytes and in serous cells of submucosal glands. In the parenchyma, DPP4 was found principally in type I and II cells and alveolar macrophages and was also detected in vascular endothelium (eg, lymphatics) and pleural mesothelia. Patients with chronic lung disease, such as chronic obstructive pulmonary disease and cystic fibrosis, exhibited increased DPP4 immunostaining in alveolar epithelia (type I and II cells) and alveolar macrophages with similar trends in reactive mesothelia. This finding suggests that preexisting pulmonary disease could increase MERS-CoV receptor abundance and predispose individuals to MERS morbidity and mortality, which is consistent with current clinical observations. We speculate that the preferential spatial localization of DPP4 in alveolar regions may explain why MERS is characterized by lower respiratory tract disease.


title: Coronavirus envelope protein: A small membrane protein with multiple functions

text: Coronavirus envelope protein is a small membrane protein and minor component of the virus particles. It plays important roles in virion assembly and morphogenesis, alteration of the membrane permeability of host cells and virus-host cell interaction. Here we review recent progress in characterization of the biochemical properties, membrane topology and functions of the protein.


title: The antiviral activities of ISG15

text: Post-translational protein modification is an important strategy for the regulation of the cell proteome independent of the need for new gene expression. Ubiquitin and ubiquitin-like modifiers mediate the regulation of protein levels, signaling pathways, vesicular trafficking, and many other cellular processes through their covalent conjugation to proteins. Interferon stimulated gene 15 (ISG15) is a type I interferon induced ubiquitin-like modifier. In addition to conjugating to potentially hundreds of target proteins, ISG15 can be found in an unconjugated form both inside of the cell and released from interferon stimulated cells into the extracellular environment. Due to its robust expression after type I interferon stimulation and the broad panel of proteins that it targets, ISG15 has drawn much attention as a potential regulator of the immune response and has been shown to mediate protection in a number of different viral infection models. Here we will review the current state of the field of ISG15, the viruses against which ISG15 mediates protection, and the mechanisms by which ISG15 exerts antiviral activity.


title: Reprogramming cellular events by poly(ADP-ribose)-binding proteins

text: Poly(ADP-ribosyl)ation is a posttranslational modification catalyzed by the poly(ADP-ribose) polymerases (PARPs). These enzymes covalently modify glutamic, aspartic and lysine amino acid side chains of acceptor proteins by the sequential addition of ADP-ribose (ADPr) units. The poly(ADP-ribose) (pADPr) polymers formed alter the physico-chemical characteristics of the substrate with functional consequences on its biological activities. Recently, non-covalent binding to pADPr has emerged as a key mechanism to modulate and coordinate several intracellular pathways including the DNA damage response, protein stability and cell death. In this review, we describe the basis of non-covalent binding to pADPr that has led to the emerging concept of pADPr-responsive signaling pathways. This review emphasizes the structural elements and the modular strategies developed by pADPr-binding proteins to exert a fine-tuned control of a variety of pathways. Poly(ADP-ribosyl)ation reactions are highly regulated processes, both spatially and temporally, for which at least four specialized pADPr-binding modules accommodate different pADPr structures and reprogram protein functions. In this review, we highlight the role of well-characterized and newly discovered pADPr-binding modules in a diverse set of physiological functions.


title: Design, synthesis, and evaluation of 3C protease inhibitors as anti-enterovirus 71 agents

text: Abstract Human enterovirus (EV) belongs to the picornavirus family, which consists of over 200 medically relevant viruses. A peptidomimetic inhibitor AG7088 was developed to inhibit the 3C protease of rhinovirus (a member of the family), a chymotrypsin-like protease required for viral replication, by forming a covalent bond with the active site Cys residue. In this study, we have prepared the recombinant 3C protease from EV71 (TW/2231/98), a particular strain which causes severe outbreaks in Asia, and developed inhibitors against the protease and the viral replication. For inhibitor design, the P3 group of AG7088, which is not interacting with the rhinovirus protease, was replaced with a series of cinnamoyl derivatives directly linked to P2 group through an amide bond to simplify the synthesis. While the replacement caused decreased potency, the activity can be largely improved by substituting the α,β-unsaturated ester with an aldehyde at the P1′ position. The best inhibitor 10b showed EC50 of 18nM without apparent toxicity (CC50 >25μM). Our study provides potent inhibitors of the EV71 3C protease as anti-EV71 agents and facilitates the combinatorial synthesis of derivatives for further improving the inhibitory activity.


title: Multifaceted roles for lipids in viral infection

text: Viruses have evolved complex and dynamic interactions with their host cell. In recent years, we have gained insight into the expanding roles for cellular lipids in the viral life cycle. In particular, viruses target lipid signaling, synthesis, and metabolism to remodel their host cells into an environment that is optimal for their replication. This review highlights examples from different viruses that illustrate the importance of these diverse virus-lipid interactions.


title: Pityriasis rosea as a cutaneous manifestation of COVID‐19 infection

text: Cutaneous manifestation has been reported in 0.2% of patients infected by COVID‐19 in China, and 18 out of 88 patients from Italy. The most commonly reported features are exanthomatous rash, urticaria, chickenpox like vesicles, petechiae, and acute hemorrhagic edema of infancy. Herein, we report one case of pityriasis rosea in a patient infected with COVID‐19.


title: Rapid Implementation of Inpatient Telepalliative Medicine Consultations during COVID-19 Pandemic

text: Abstract As COVID-19 cases increase throughout the country and healthcare systems grapple with the need to decrease provider exposure and minimize personal protective equipment (PPE) use while maintaining high quality patient care, our specialty is called upon to consider new methods of delivering inpatient palliative care. Telepalliative medicine has been used to great effect in outpatient and home-based palliative care, but has had fewer applications in the inpatient setting. As we plan for decreased provider availability due to quarantine and redeployment and seek to reach increasingly isolated hospitalized patients in the face of COVID-19, the need for telepalliative medicine in the inpatient setting is now clear. We describe our rapid and ongoing implementation of telepalliative medicine consultation for our inpatient palliative care teams and discuss lessons learned and recommendations for programs considering similar care models.


title: Management of Acute Coronary Syndrome in Patients with Suspected or Confirmed Coronavirus Disease 2019: Consensus from Taiwan Society of Cardiology

text: Abstract Coronavirus disease 2019 (COVID-19) is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Infection with SARS-CoV may cause coronary plaque instability and lead to acute coronary syndrome (ACS). Management of ACS in patients with COVID-19 needs more consideration of the balance between clinical benefit and transmission risk of virus. This review provides recommendations of management strategies for ACS in patients with suspected or confirmed COVID-19 in Taiwan.


title: A long-distance RNA–RNA interaction plays an important role in programmed −1 ribosomal frameshifting in the translation of p88 replicase protein of Red clover necrotic mosaic virus

text: Abstract Programmed −1 ribosomal frameshifting (−1 PRF) is one viral translation strategy to express overlapping genes in positive-strand RNA viruses. Red clover necrotic mosaic virus (RCNMV) uses this strategy to express its replicase component protein p88. In this study, we used a cell-free translation system to map cis-acting RNA elements required for −1 PRF. Our results show that a small stem-loop structure adjacent to the cap-independent translation element in the 3′ untranslated region (UTR) of RCNMV RNA1 is required for −1 PRF. Site-directed mutagenesis experiments suggested that this stem-loop regulates −1 PRF via base-pairing with complementary sequences in a bulged stem-loop adjacent to the shifty site. The existence of RNA elements responsible for −1 PRF and the cap-independent translation of replicase proteins in the 3′ UTR of RNA1 might be important for switching translation to replication and for regulating the ratio of p88 to p27.


title: Etiology of Coinfections in Children with Influenza during 2015/16 Winter Season in Nepal

text: Acute respiratory infections (ARIs) are one of the major public health problems in developing countries like Nepal. Besides the influenza, several other pathogens are responsible for acute respiratory infection in children. Etiology of infections is poorly characterized at the course of clinical management, and hence empirical antimicrobial agents are used. The objective of this study was to characterize the influenza and other respiratory pathogens by real-time PCR assay. A total of 175 throat swab specimens of influenza-positive cases collected at National Influenza Center, Nepal, during the 2015/16 winter season were selected for detecting other respiratory copathogens. Total nucleic acid was extracted using Pure Link viral RNA/DNA mini kit (Invitrogen), and multiplex RT-PCR assays were performed. Influenza A and B viruses were found in 120 (68.6%) and 55 (31.4%) specimens, respectively, among which coinfections were found in 106 (60.6%) specimens. Among the influenza A-positive cases, 25 (20.8%) were A/H1N1 pdm09 and 95 (79.2%) were A/H3 subtypes. Viruses coinfected frequently with influenza virus in children were rhinovirus (26; 14.8%), respiratory syncytial virus A/B (19; 10.8%), adenovirus (14; 8.0%), coronavirus (CoV)-HKU1 (14; 8.0%), CoV-OC43 (5; 2.9%), CoV-229E (2; 1.1%), metapneumovirus A/B (5; 2.9%), bocavirus (6; 3.4%), enterovirus (5; 2.9%), parainfluenza virus-1 (3; 1.7%), and parainfluenza virus-3 (2; 1.1%). Coinfection of Mycoplasma pneumoniae with influenza virus was found in children (5; 2.8%). Most of the viral infection occurred in young children below 5 years of age. In addition to influenza virus, nine different respiratory pathogens were detected, of which coinfections of rhinovirus and respiratory syncytial virus A/B were predominantly found in children. This study gives us better information on the respiratory pathogen profile and coinfection combinations which are important for diagnosis and treatment of ARIs.


title: Electroencephalographic (EEG) features of encephalopathy in the setting of Covid-19: A Case Series

text: OBJECTIVE: The Covid-19 pandemic is a global challenge presenting clinicians with an evolving diagnostic landscape. We sought to describe EEG findings observed from local experience in a typical case series of patients with severe Covid-19. METHODS: Ten cases of Covid-19 were identified in whom EEG recordings had been made during the course of admissions to Bristol hospitals which had required intensive care. Electro-clinical correlation between the EEG and available medical history, imaging and laboratory investigation results was explored. RESULTS: The predominant EEG features in severe Covid-19 are of generalised symmetrical slowing, consistent with encephalopathy. CONCLUSIONS: The presence of focal disturbances or irritative abnormalities may be a pointer away from a pure encephalopathy and warrant further investigation. SIGNIFICANCE: A growing range of neurological sequelae from Covid-19 are now recognised to be common amongst patients hospitalised by with this condition, being seen to affect approximately one third of such cases. Electroencephalography has a unique place in the diagnostic work-up of impaired consciousness, a frequent feature of severe Covid-19. However, there is currently a paucity of literature describing typical EEG findings in this setting.


title: Protection against COVID-19 injury by Qingfei Paidu decoction via anti-viral, anti-inflammatory activity and metabolic programming

text: Qingfei Paidu decoction (QFPD), a multi-component herbal formula, has been widely used to treat COVID-19 in China. However, its active compounds and mechanisms of action are still unknown. Firstly, we divided QFPD into five functional units (FUs) according to the compatibility theory of traditional Chinese medicine. The corresponding common targets of the five FUs were all significantly enriched in Go Ontology (oxidoreductase activity, lipid metabolic process, homeostatic process, etc.), KEGG pathways (steroid biosynthesis, PPAR signaling pathway, adipocytokine signaling pathway, etc.), TTD diseases (chronic inflammatory diseases, asthma, chronic obstructive pulmonary Disease, etc.), miRNA (MIR183), kinase (CDK7) and TF (LXR). QFPD contained 257 specific targets in addition to HCoV, pneumonia and ACE2 co-expression proteins. Then, network topology analysis of the five components-target-pathway-disease networks yielded 67 active ingredients. In addition, ADMET estimations showed that 20 compounds passed the stringent lead-like criteria and in silico drug-likeness test with high gastrointestinal absorption and the median lethal dose (LD50 > 1600 mg/kg). Moreover, 4 specific ingredients (M3, S1, X2 and O2) and 5 common ingredients (MS1, MX16, SX1, WO1 and XO1) of QFPD presented good molecular docking score for 2019-nCov structure and non-structure proteins. Finally, drug perturbation of COVID-19 network robustness showed that all five FUs may protect COVID-19 independently, and target 8 specifically expressed drug-attacked nodes which were related to the bacterial and viral responses, immune system, signaling transduction, etc. In conclusion, our new FUNP analysis showed that QFPD had a protection effect on COVID-19 by regulating a complex molecular network with safety and efficacy. Part of the mechanism was associated with the regulation of anti-viral, anti-inflammatory activity and metabolic programming.


title: Altered pathogenicity, immunogenicity, tissue tropism and 3′-7 kb region sequence of an avian infectious bronchitis coronavirus strain after serial passage in embryos

text: In this study, we attenuated a Chinese LX4-type nephropathogenic infectious bronchitis virus (IBV) strain, CK/CH/LHLJ/04V, by serial passage in embryonated chicken eggs. Based on sequence analysis of the 3′-7 kb region, the CK/CH/LHLJ/04V virus population contained subpopulations with a mixture of genetic mutants. The titers of the virus increased gradually during serial passage, but the replication capacity decreased in chickens. The virus was partially attenuated at passage 40 (P40) and P70, and was fully attenuated at P110. It lost immunogenicity and kidney tropism at P110 and P70, respectively. Amino acid substitutions were found in the 3′-7 kb region, primarily in the spike (S) protein. Substitutions in the S1 subunit occurred between P3 and P40 and all subpopulations in a virus passage showed the same substitutions. Other substitutions that occurred between P70 and P110, however, were found only in some subpopulations of the virus passages. A 109-bp deletion in the 3′-UTR was observed in most subpopulations of P70 and P110, and might be related to virus replication, transcription and pathogenicity. The changes described in the 3′-7 kb region of the virus are possibly responsible for virus attenuation, immunogenicity decrease and tissue tropism changes; however, we cannot exclude the possibility that other parts of the genome may also be involved in those changes.


title: Characteristics of Microbes Most Likely to Cause Pandemics and Global Catastrophes

text: Predicting which pathogen will confer the highest global catastrophic biological risk (GCBR) of a pandemic is a difficult task. Many approaches are retrospective and premised on prior pandemics; however, such an approach may fail to appreciate novel threats that do not have exact historical precedent. In this paper, based on a study and project we undertook, a new paradigm for pandemic preparedness is presented. This paradigm seeks to root pandemic risk in actual attributes possessed by specific classes of microbial organisms and leads to specific recommendations to augment preparedness activities.


title: An epidemiological study of rates of illness in passengers and crew at a busy Caribbean cruise port

text: BACKGROUND: The Caribbean has one of the largest cruise ship industries in the world, with close to 20 million visitors per year. The potential for communicable disease outbreaks on vessels and the transmission by ship between countries is high. Barbados has one of the busiest ports in the Caribbean. Our aim was to describe and analyse the epidemiology of illnesses experienced by passengers and crew arriving at the Bridgetown Port, Barbados between 2009 and 2013. METHODS: Data on the illnesses recorded were extracted from the passenger and crew arrival registers and passenger and crew illness logs for all ships and maritime vessels arriving at Barbados’ Ports and passing through its territorial waters between January 2009 and December 2013. Data were entered into an Epi Info database and most of the analysis undertaken using Epi Info Version 7. Rates per 100,000 visits were calculated, and confidence intervals on these were derived using the software Openepi. RESULTS: There were 1031 cases of illness from over 3 million passenger visits and 1 million crew visits during this period. The overall event rate for communicable illnesses was 15.7 (95 % CI 14.4–17.1) per 100,000 passengers, and for crew was 24.0 (21.6–26.6) per 100, 000 crew. Gastroenteritis was the predominant illness experienced by passengers and crew followed by influenza. The event rate for gastroenteritis among passengers was 13.7 (12.5–15.0) per 100,000 and 14.4 (12.6, 16.5) for crew. The event rate for non-communicable illnesses was 3.4 per 100,000 passengers with myocardial infarction being the main diagnosis. The event rate for non-communicable illnesses among crew was 2.1 per 100,000, the leading cause being injuries. CONCLUSIONS: The predominant illnesses reported were gastroenteritis and influenza similar to previous published reports from around the world. This study is the first of its type in the Caribbean and the data provide a baseline for future surveillance and for comparison with other countries and regions.


title: Estimation of effects of nationwide lockdown for containing coronavirus infection on worsening of glycosylated haemoglobin and increase in diabetes-related complications: A simulation model using multivariate regression analysis

text: Abstract Introduction and aims: To prevent the spread of coronavirus disease (COVID19) total lockdown is in place in India from March 24, 2020 for 21 days. In this study, we aim to assess the impact of the duration of the lockdown on glycaemic control and diabetes-related complications. Materials and methods A systematic search was conducted using Cochrane library. A simulation model was created using glycemic data from previous disasters (taken as similar in impact to current lockdown) taking baseline HBA1c and diabetes-related complications data from India-specific database. A multivariate regression analysis was conducted to analyse the relationship between the duration of lockdown and glycaemic targets & diabetes-related complications. Results The predictive model was extremely robust (R2 = 0.99) and predicted outcomes for period of lockdown up to 90 days. The predicted increment in HBA1c from baseline at the end of 30 days and 45 days lockdown was projected as 2.26% & 3.68% respectively. Similarly, the annual predicted percentage increase in complication rates at the end of 30-day lockdown was 2.8% for non-proliferative diabetic retinopathy, 2.9% for proliferative diabetic retinopathy, 1.5% for retinal photocoagulation, 9.3% for microalbuminuria, 14.2% for proteinuria, 2.9% for peripheral neuropathy, 10.5% for lower extremity amputation, 0.9% for myocardial infarction, 0.5% for stroke and 0.5% for infections. Conclusion The duration of lockdown is directly proportional to the worsening of glycaemic control and diabetes-related complications. Such increase in diabetes-related complications will put additional load on overburdened healthcare system, and also increase COVID19 infections in patients with such uncontrolled glycemia.


Pediatric emergencies: newsletter 9


title: Heeding the Message? Determinants of Risk Behaviours for West Nile Virus

text: METHODS: A telephone survey was administered to a random sample of adults (n=1650) living in the L6L and L6K Forward Sortation Areas of Oakville, Ontario, Canada. RESULTS: While close to 100% of survey respondents were aware of WNv and approximately 80% recalled receiving information from the public health department regarding the virus, levels of reported personal protective behaviours were relatively low. Through a multivariable modeling process, a range of determinants emerged to explain outcome levels. DISCUSSION: The message about public education in the face of emerging health threats is clear; that is, that public education is key. But we cannot end the public health presence there - public health researchers must evaluate the uptake of the message.


title: Psychological Responses among Humidifier Disinfectant Disaster Victims and Their Families

text: To substantiate psychological symptoms following humidifier disinfectant (HD) disasters, counseling records of 26 victims and 92 family members of victims (45 were bereaved) were analyzed retrospectively. Among the victims, 34.6% had Clinical Global Impression-Severity scores of over 4, which meant they were moderately ill. While anxiety/fear and depression with respiratory symptoms were frequently observed in victims and family members, chronic psychological distress such as alcohol/smoking abuse and insomnia was relatively high in bereaved family members. In conclusion, it is important to provide mental health support for victims and their families, focusing on the characteristic symptoms of each group as well as monetary compensation.


title: Structural and molecular modelling studies reveal a new mechanism of action of chloroquine and hydroxychloroquine against SARS-CoV-2 infection

text: ABSTRACT The recent emergence of the novel pathogenic SARS-coronavirus 2 (SARS-CoV-2) is responsible for a worldwide pandemic. Given the global health emergency, drug repositioning is the most reliable option to design an efficient therapy for infected patients without delay. The first step of the viral replication cycle [i.e. attachment to the surface of respiratory cells, mediated by the spike (S) viral protein] offers several potential therapeutic targets. The S protein uses the angiotension-converting enzyme-2 (ACE-2) receptor for entry, but also sialic acids linked to host cell surface gangliosides. Using a combination of structural and molecular modelling approaches, this study showed that chloroquine (CLQ), one of the drugs currently under investigation for SARS-CoV-2 treatment, binds sialic acids and gangliosides with high affinity. A new type of ganglioside-binding domain at the tip of the N-terminal domain of the SARS-CoV-2 S protein was identified. This domain (111–158), which is fully conserved among clinical isolates worldwide, may improve attachment of the virus to lipid rafts and facilitate contact with the ACE-2 receptor. This study showed that, in the presence of CLQ [or its more active derivative, hydroxychloroquine (CLQ-OH)], the viral S protein is no longer able to bind gangliosides. The identification of this new mechanism of action of CLQ and CLQ-OH supports the use of these repositioned drugs to cure patients infected with SARS-CoV-2. The in-silico approaches used in this study might also be used to assess the efficiency of a broad range of repositioned and/or innovative drug candidates before clinical evaluation.


title: Validation of a self‐administered olfactory and gustatory test for the remotely evaluation of COVID‐19 patients in home quarantine

text: BACKGROUND: Chemosensitive disorders are very frequent in the early stages of COVID‐19 and in paucisymptomatic cases. These patients are typically placed in home quarantine. This study has the aim of validating a new olfactory and gustatory objective evaluation test in these patients. METHODS: Thirty‐three home‐quarantined COVID‐19 patients have undergone a self‐administered chemosensitive test the day before the control swab. On this occasion, the patients underwent operator‐administered already validated tests. The results were finally compared. RESULTS: The differences between the results of the two tests were not significant for both the olfaction (P =.201) and the taste (P =.180). CONCLUSION: The olfactory and gustatory evaluation by self‐administered test can be considered a valid tool, fundamental for obtaining objective qualitative and quantitative data on the extent of chemosensitive disorders in home‐quarantined COVID‐19 patients.


title: Identification and formation mechanism of a novel noncoding RNA produced by avian infectious bronchitis virus

text: Abstract Viral noncoding (nc) RNAs have been shown to play important roles in viral life cycle. Many viruses employ different mechanism to produce ncRNAs. Here, we report that coronavirus infectious bronchitis virus (IBV) produces a novel ncRNA in virus-infected cells. This ncRNA consists of 563 nucleotides excluding a poly(A) tail, is mainly derived from the 3′-untranslated region of IBV genome, and contains a 63-nt-long of terminal leader sequence derived from the 5′ end of the viral genome. Using mutagenesis and reverse genetics, we reveal that this ncRNA is a subgenomic RNA generated by discontinuous transcription mechanism.


title: Conseils à un patient se plaignant d’un rhume

text: Le rhume, qui peut sembler bénin au premier abord, ne doit pas être négligé lors d’une visite à l’officine car il peut être très handicapant pour le patient. Une rhinite d’origine virale est dite aiguë, mais elle peut également être d’origine allergique ou occasionnée par des agents irritants. Les premiers conseils à donner sont d’ordre hygiénique. Des antalgiques peuvent être conseillés pour soulager la fièvre, ainsi que des antihistaminiques ou des décongestionnants par voie orale, et un traitement local pour dégager les voies respiratoires. Des traitements par voie générale permettent de traiter l’ensemble des symptômes. Enfin, certaines spécialités utilisées en aromathérapie et en homéopathie peuvent être proposées. A cold, which can at first appear benign, must not be disregarded during a consultation at the community pharmacy as it can be incapacitating for the patient. Rhinitis of a viral origin is said to be acute, but it can also be the result of an allergy or caused by irritating agents. The first advice to give concerns hygiene. Anodynes can be recommended to relieve fever, as well as antihistamines or decongestants taken orally, and a local treatment to unblock the airways. Treatments taken internally help to treat all the symptoms. Finally, some aromatherapy and homeopathic remedies can be recommended.


title: Glycyrrhizic acid attenuates growth of Leishmania donovani by depleting ergosterol levels

text: Abstract In the present study, glycyrrhizic acid (GA) the main component of Glycyrrhiza glabra was evaluated for its efficacy as antileishmanial agent and its mode of action explored. GA inhibits promastigotes and intracellular amastigotes in a dose dependent manner at an IC50 value of 34 ± 3.0 μM and 20 ± 4.2 μM respectively. GA was non-toxic against THP-1 macrophage host cell line. GA was found to inhibit recombinant Leishmania donovani HMG-CoA reductase (LdHMGR) enzyme at the half-maximum inhibitory concentration of 24 ± 4.3 μM indicating the sensitivity and specificity of GA towards the enzyme. However, GA could cause only 30% reduction in HMGR activity when measured in Leishmania promastigotes treated with 34 μM of GA. Interestingly western blot analysis revealed fivefold reduced HMGR expression in GLA treated promastigotes. To further study the mode of action of GA, we used transgenic parasites overexpressing LdHMGR. Results indicated that ∼2 fold resistance was exhibited by LdHMGR overexpressing promastigotes to GA with an IC50 value of 74 μM compared to the wild type parasite. This explained the specific binding of GA to LdHMGR enzyme. There was ∼2 fold depletion in ergosterol levels in wild type promastigotes compared to the HMGR overexpressors. This data was further validated by exogenous supplementation of GA treated cells with ergosterol and 40% reversal of growth inhibition was observed. The results obtained suggested that GA kills the parasite by affecting sterol biosynthetic pathway, especially by inhibiting the L. donovani HMGR and altering ergosterol levels. The finding from the current study shows that GA is a potential antileishmanial chemotherapeutic agent.


title: Induction of a systemic antiviral state in vivo in the domestic cat with a class A CpG oligonucleotide

text: Abstract The evolution of cats as a solitary species has pressured feline viruses to develop highly efficient transmission strategies, the ability to persist within the host for long periods of time and the aptitude to adapt to natural and vaccine-induced immunological pressures. These characteristics render feline viruses particularly dangerous in catteries, shelters and rescue homes, were cats from different backgrounds live in close proximity. The possibility to induce short-term resistance of newcomer cats to a broad variety of viruses could help prevent the dissemination of viruses both within and outside such facilities. Oligonucleotides (ODN) containing unmethylated cytosine phosphate guanosine (CpG) motifs stimulate innate immune responses in mammals. We have previously shown that ODN 2216, a class A CpG ODN, promotes the expression by feline immune cells of potent antiviral molecules that increase resistance of feline fibroblastic and epithelial cell lines to five common feline viruses. With the aim to test the safety and extent of the biological effects of ODN 2216 in the domestic cat, we performed an initial in vivo experiment in which two cats were injected the molecule once subcutaneously and two additional cats received control treatments. No side effects to administration of ODN 2216 were observed. Moreover, this molecule induced the expression of the myxovirus resistance (Mx) gene, a marker for the instigation of innate antiviral processes, in blood as well as in oral, conjunctival and rectal mucosa cells, indicating systemic biological activity of the molecule with protective potential at viral entry sites. Mx mRNA levels were already elevated in blood 6h post injection of ODN 2216, reached peak levels within 24h and returned to basal values by 96–192h after administration of the molecule. Similar induction patterns were observed in all analyzed mucosal cells. Plasma collected from treated cats at regular intervals until 96–192h could moreover induce Mx mRNA expression in fcwf-4 cells and increase resistance of these cells to feline calicivirus inoculation. Finally, Mx mRNA levels measured in blood correlated with the degree of viral inhibition that was induced by plasma from the same cat and the same experimental time point. Our results altogether underline the promising potential of ODN 2216 in promoting antiviral defense mechanisms and inducing temporary resistance to viral infections in vivo in the domestic cat.


title: Plant Virus Expression Vectors: A Powerhouse for Global Health

text: Plant-made biopharmaceuticals have long been considered a promising technology for providing inexpensive and efficacious medicines for developing countries, as well as for combating pandemic infectious diseases and for use in personalized medicine. Plant virus expression vectors produce high levels of pharmaceutical proteins within a very short time period. Recently, plant viruses have been employed as nanoparticles for novel forms of cancer treatment. This review provides a glimpse into the development of plant virus expression systems both for pharmaceutical production as well as for immunotherapy.


title: Contact Tracing for Imported Case of Middle East Respiratory Syndrome, China, 2015

text: Confirmation of an imported case of infection with Middle East respiratory syndrome coronavirus in China triggered intensive contact tracing and mandatory monitoring. Using a hotline and surveillance video footage was effective for tracing all 110 identified contacts. Contact monitoring detected no secondary transmission of infection in China.


title: Visualization of the African swine fever virus infection in living cells by incorporation into the virus particle of green fluorescent protein-p54 membrane protein chimera

text: Abstract Many stages of African swine fever virus infection have not yet been studied in detail. To track the behavior of African swine fever virus (ASFV) in the infected cells in real time, we produced an infectious recombinant ASFV (B54GFP-2) that expresses and incorporates into the virus particle a chimera of the p54 envelope protein fused to the enhanced green fluorescent protein (EGFP). The incorporation of the fusion protein into the virus particle was confirmed immunologically and it was determined that p54-EGFP was fully functional by confirmation that the recombinant virus made normal-sized plaques and presented similar growth curves to the wild-type virus. The tagged virus was visualized as individual fluorescent particles during the first stages of infection and allowed to visualize the infection progression in living cells through the viral life cycle by confocal microscopy. In this work, diverse potential applications of B54GFP-2 to study different aspects of ASFV infection are shown. By using this recombinant virus it was possible to determine the trajectory and speed of intracellular virus movement. Additionally, we have been able to visualize for first time the ASFV factory formation dynamics and the cytophatic effect of the virus in live infected cells. Finally, we have analyzed virus progression along the infection cycle and infected cell death as time-lapse animations.


title: H1N1 Influenza Viral Infection in a Postpartum Young Woman Causes Respiratory Failure: What the Care Providers Ought to Know?

text: Pregnant and postpartum women are considered a population at increased risk of hospitalization of H1N1 infection. We report the case of a young postpartum woman, who developed evidence of respiratory failure reaching the point of requiring intubation due to an H1N1 influenza virus infection two days after a caesarean delivery. We emphasize the diagnosis, management, and the outcome focusing on the question “what the care providers, including obstetric health care workers, ought to know?” Diagnostic and management strategy for pregnant or postpartum women with novel influenza A (H1N1) viral infection and increased awareness amongst patients and health care professionals may result in improved survival.


title: The diversity of viruses infecting humans

text: Most human viruses have been discovered through the diseases they cause in animals, plants, bacteria or fungi. Recent finds include human bocaviruses, which now seem to have a global distribution, and cause respiratory tract disease in infants, and several new pathogenic human coronaviruses. The SARS coronavirus, genetically distinct from all previously known coronaviruses, caused a disease which was highly transmissible and very severe, eventually leading to 8000 cases worldwide with over 800 deaths. Many viruses which are transmitted to humans by invertebrates, such as insects or ticks, have the ability to infect and replicate in cells of both vertebrate and invertebrate origin. However human virology is a rapidly expanding field and recent technologies such as the polymerase chain reaction (PCR) amplification system have made it possible to look for previously unrecognized viruses which may or may not be involved in pathogenesis. For example viruses in the genus Anellovirus are found in 80% of human blood samples yet do not seem to cause any disease. This paper overviews known human vertebrate viruses, more recent discoveries, and recommends a systematic search for viruses which may already infect the human population but have so far remained undetected.


title: Impact of chronic liver disease on outcomes of hospitalized patients with COVID‐19: A multicentre United States experience

text: Liver injury has been described with COVID‐19, and early reports suggested 2%‐11% of patients had chronic liver disease (CLD). In this multicentre retrospective study, we evaluated hospitalized adults with laboratory‐confirmed COVID‐19 and the impact of CLD on relevant clinical outcomes. Of 363 patients included, 19% had CLD, including 15.2% with NAFLD. Patients with CLD had longer length of stay. After controlling for age, gender, obesity, cardiac diseases, hypertension, hyperlipidaemia, diabetes and pulmonary disorders, CLD and NAFLD were independently associated with ICU admission ([aOR 1.77, 95% CI 1.03‐3.04] and [aOR 2.30, 95% CI 1.27‐4.17]) and mechanical ventilation ([aOR 2.08, 95% CI 1.20‐3.60] and [aOR 2.15, 95% CI 1.18‐3.91]). Presence of cirrhosis was an independent predictor of mortality (aOR 12.5, 95% CI 2.16‐72.5). Overall, nearly one‐fifth of hospitalized COVID‐19 patients had CLD, which was associated with more critical illness. Future studies are needed to identify interventions to improve clinical outcomes.


title: Therapeutical use of probiotic formulations in clinical practice

text: Summary Background & Aims The spreading of gastrointestinal diseases is growing all over the world. Although for some of them an effective therapeutic approach has been found, palliation rather than cure is very frequent due to a partial knowledge of their aethiology and pathogenesis. This review, analyzing the main clinical studies, aims at being a state of the art update of the use of probiotic formulations in daily practice. Methods In this review we include all the most significant clinical trials involving the use of probiotic formulations for the treatment of several pathologies. Results Dysbiosis has been observed in irritable bowel syndrome patients. Probiotics may exert a beneficial effect on Crohn’s disease affected patients who have shown gut microbiota antigens and altered wall permeability. Moreover some probiotic formulations seem to enhance the therapy for Helycobacter Pylori reducing its pathogenic potential. Intestinal ecology imbalance has been also linked to cancer induction, allergy, skin and urogenital diseases. In addition probiotics administration seems to be particularly useful to ease post-operative complications. Conclusion Further future clinical trials, involving large numbers of patients, will be mandatory to achieve definite evidence of the preventive and curative role of probiotics in medical practice.


Roadmap for Restarting Elective Surgery During/After COVID-19 Pandemic


title: Longitudinal study of humoral immunity to bovine coronavirus, virus shedding, and treatment for bovine respiratory disease in pre-weaned beef calves

text: BACKGROUND: Bovine coronavirus (BCV) is associated with respiratory infections in cattle of all ages; however, a temporal study to evaluate the effect of BCV immunity on virus shedding and bovine respiratory disease (BRD) incidence in pre-weaned beef calves has not been reported. Thus, we report here a prospective study in three herds of crossbred beef calves (n = 817) with endemic BCV. Serial blood samples for measurement of serum anti-BCV antibody titers and nasal swabs for detection of BCV and other common viral and bacterial BRD pathogens were collected from all calves or subsets of calves at predetermined times from birth through weaning. The calves were monitored for BRD and those that developed signs of respiratory disease were sampled for diagnostic testing. To discover additional risk factors that could have influenced BRD development, sequence analysis of the BCV strain(s) circulating in each herd, and the prevalence of common opportunistic bacterial pathogens in the upper respiratory tract of sick and apparently healthy cattle were also evaluated. RESULTS: Two hundred forty-eight of the 817 study calves (30.4%) were treated for BRD prior to weaning; 246 of those were from a single herd involved in two outbreaks of BRD leading to mass treatment of all calves in that group. Molecular diagnostic testing found BCV and Histophilus somni in nasal swabs taken at the time of BRD treatment. Between herd analyses revealed anti-BCV serum antibody abundance did not associate with the incidence of BRD or BCV shedding, though these measurements may have been hindered by the long periods between sample collections. Analysis of the BCV spike gene hypervariable region revealed four polymorphisms in 15 isolates from the three herds, making strain variation unlikely to account for differences in treatment rates between herds. Persistent or recurrent shedding episodes of BCV occurred in some animals treated for BRD. CONCLUSION: Co-detection of BCV and H. somni at the time of the disease outbreak suggests that these pathogens contributed to disease pathogenesis. Developing appropriate control measures for respiratory BCV infections may help decrease the incidence of pre-weaning BRD. The role of antibodies in protection must still be further defined. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12917-019-1887-8) contains supplementary material, which is available to authorized users.


title: A study of outsourcing strategy: a case involving the hotel industry in Shanghai, China

text: Abstract Hotels in China are attempting to adopt outsourcing. However, they are not always successful. This study investigated outsourcing strategy as perceived by hotel managers in Shanghai, and identified the relationship between the determinant factors in the adoption of outsourcing and types of hotel ownership and job levels of managers. In-depth interviews and self-administered questionnaires were used to collect the data. The results show that in China the outsourcing market is still immature. The incompleteness of laws is a hindrance to the adoption of outsourcing and the compatibility between the corporate cultures of the hotels and the outsourcing vendors is critical.


title: Thrombopoietin levels increased in patients with severe acute respiratory syndrome

text: Abstract Hematological changes in patients with Severe Acute Respiratory Syndrome (SARS) are common and frequently include thrombocytopenia. Using a ELISA method, we found an increase in thrombopoietin (TPO) levels in the plasma of convalesced SARS patients (290±53 pg/ml) and active SARS patients (251±23 pg/ml) comparing to that from normal control patients (228±17 pg/ml). In addition, the plasma from active SARS patients had an inhibitory effect on CFU-MK formation, which could be neutralized by anti-TGF-β antibodies. In the experiment to determine whether SARS-CoV can directly infect hematopoietic stem cells and megakaryocytic cells, incubation of the cells with SARS-CoV did not show active infection. Our findings of increased TPO levels in the plasma of SARS patients provide a possible explanation for the genesis of thrombocytosis, which frequently develops from thrombocytopenia in SARS patients.


title: Deep venous thrombosis in a non-critically ill patient with novel COVID-19 infection

text: • COVID-19 infection is associated with hypercoagulability and a prothrombotic state. • Little is understood about the prevalence of venous thromboembolism in mild disease. • We present a case of mild COVID-19 complicated by extensive deep venous thrombosis.


title: Household Secondary Attack Rate of COVID-19 and Associated Determinants

text: BACKGROUND: As of April 2, 2020, the global reported number of COVID-19 cases has crossed over 1 million with more than 55,000 deaths. The household transmissibility of SARS-CoV-2, the causative pathogen, remains elusive. METHODS: Based on a comprehensive contact-tracing dataset from Guangzhou, we estimated both the population-level effective reproductive number and individual-level secondary attack rate (SAR) in the household setting. We assessed age effects on transmissibility and the infectivity of COVID-19 cases during their incubation period. RESULTS: A total of 195 unrelated clusters with 212 primary cases, 137 nonprimary (secondary or tertiary) cases and 1938 uninfected close contacts were traced. We estimated the household SAR to be 13.8% (95% CI: 11.1–17.0%) if household contacts are defined as all close relatives and 19.3% (95% CI: 15.5–23.9%) if household contacts only include those at the same residential address as the cases, assuming a mean incubation period of 4 days and a maximum infectious period of 13 days. The odds of infection among children (<20 years old) was only 0.26 (95% CI: 0.13–0.54) times of that among the elderly (≥60 years old). There was no gender difference in the risk of infection. COVID-19 cases were at least as infectious during their incubation period as during their illness. On average, a COVID-19 case infected 0.48 (95% CI: 0.39–0.58) close contacts. Had isolation not been implemented, this number increases to 0.62 (95% CI: 0.51–0.75). The effective reproductive number in Guangzhou dropped from above 1 to below 0.5 in about 1 week. CONCLUSION: SARS-CoV-2 is more transmissible in households than SARS-CoV and MERS-CoV, and the elderly ≥60 years old are the most vulnerable to household transmission. Case finding and isolation alone may be inadequate to contain the pandemic and need to be used in conjunction with heightened restriction of human movement as implemented in Guangzhou.


COVID-19 Pandemic: The Challenges for Pediatric Oncology


title: The epidemiology of Middle East respiratory syndrome coronavirus in the Kingdom of Saudi Arabia, 2012–2015

text: Summary Objectives The aim of this study was to review the epidemiology of cases of Middle East respiratory syndrome coronavirus (MERS-CoV) reported in the Kingdom of Saudi Arabia from 2012 when the first MERS-CoV was confirmed up to July 2015. Methods MERS-CoV data were obtained from the Saudi Ministry of Health for the period 2012 to July 2015. Descriptive statistics were used to summarize the results regarding the risk factors and mortality of MERS-CoV infection. Results In this series, the risk factors and outcomes of 939 cases of MERS-CoV occurring in the last 3 years are described. The majority of the affected patients were aged ≥40 years (n =657; 70%). Of the 657 patients aged ≥40 years, 377 (57.3%) died. Conclusions The case-fatality ratio was found to increase significantly with age. It ranged from 12.5% in those aged ≤19 years to 86.2% in those aged ≥80 years. The results confirmed the association between severe MERS-CoV illness and patients with a pre-existing health morbidity. The duration from symptom onset to admission was not statistically associated with the disease outcome.


title: Are your cash-flow tools recession ready?

text: Abstract In good times like those most businesses have enjoyed for the past decade, business owners have typically watched their income statements with pleasure, as year-to-year performance gains have fattened their dividend payouts and increased the valuation of the companies they own and run. All too often in such times, scant attention is paid to what’s between the top line and the bottom line of the income statement. Worse, most business owners, in my experience, give little more than a cursory nod to the balance sheet. Why does this matter? When a recession lands on their doorstep with a sudden thud, as it apparently just has, many of these same people will find themselves having sailed too close to the wind, with cash running out and a dearth of tools to help them weather the storm and understand what has gone wrong. But it need not be so, for there are four simple tools to help any business owner answer these four important questions: (1) Where is cash going in my business, and where is it coming from? (2) To what extent are my profit margins improving or declining, and why? (3) To what extent am I effectively managing the cash-flow relationships with my customers and my suppliers? (4) What, if anything, can I do to better manage the cash that flows into and out of my business? If your business is threatened by the COVID-19 pandemic, here are some tools to help it survive.


title: Chikungunya fever – A new global threat

text: Abstract The recent onset of epidemics caused by viruses such as Ebola, Marburg, Nipah, Lassa, coronavirus, West-Nile encephalitis, Saint Louis encephalitis, human immunodeficiency virus, dengue, yellow fever and Venezuelan haemorrhagic fever alerts about the risk these agents represent for the global health. Chikungunya virus represents a new threat. Surged from remote African regions, this virus has become endemic in the Indic ocean basin, the Indian subcontinent and the southeast of Asia, causing serious epidemics in Africa, Indic Ocean Islands, Asia and Europe. Due to their epidemiological and biological features and the global presence of their vectors, chikungunya represents a serious menace and could become endemic in the Americas. Although chikungunya infection has a low mortality rate, its high attack ratio may collapse the health system during epidemics affecting a sensitive population. In this paper, we review the clinical and epidemiological features of chikungunya fever as well as the risk of its introduction into the Americas. We remark the importance of the epidemiological control and mosquitoes fighting in order to prevent this disease from being introduced into the Americas.


title: Children with coronavirus disease 2019: A review of demographic, clinical, laboratory, and imaging features in pediatric patients

text: There is a current outbreak of coronavirus disease 2019 (COVID‐19), with a global spread. With the rapid increase in the number of infections, an increase is observed in the number of children with COVID‐19. Most research findings are regarding adult cases, which are not always transferrable to children. Evidence‐based studies are still expected to formulate clinical decisions for pediatric patients. In this review, we included 2597 pediatric patients that reported recently and evaluated the demographic, clinical, laboratory, and imaging features of children with COVID‐19. We found that even lymphopenia was the most common lab finding in adults; it infrequently occurred in children (9.8%). Moreover, elevated creatine kinase MB isoenzyme was much more commonly observed in children (27.0%) than that in adults, suggesting that heart injury would be more likely to occur in pediatric patients. Our analysis may contribute to determine the spectrum of disease in children and to develop strategies to control the disease transmission.


title: Synthesis and Translation of Viral mRNA in Reovirus-Infected Cells: Progress and Remaining Questions

text: At the end of my doctoral studies, in 1988, I published a review article on the major steps of transcription and translation during the mammalian reovirus multiplication cycle, a topic that still fascinates me 30 years later. It is in the nature of scientific research to generate further questioning as new knowledge emerges. Our understanding of these fascinating viruses thus remains incomplete but it seemed appropriate at this moment to look back and reflect on our progress and most important questions that still puzzle us. It is also essential of being careful about concepts that seem so well established, but could still be better validated using new approaches. I hope that the few reflections presented here will stimulate discussions and maybe attract new investigators into the field of reovirus research. Many other aspects of the viral multiplication cycle would merit our attention. However, I will essentially limit my discussion to these central aspects of the viral cycle that are transcription of viral genes and their phenotypic expression through the host cell translational machinery. The objective here is not to review every aspect but to put more emphasis on important progress and challenges in the field.


title: An evaluation of the Zambia influenza sentinel surveillance system, 2011–2017

text: BACKGROUND: Over the past decade, influenza surveillance has been established in several African countries including Zambia. However, information on the on data quality and reliability of established influenza surveillance systems in Africa are limited. Such information would enable countries to assess the performance of their surveillance systems, identify shortfalls for improvement and provide evidence of data reliability for policy making and public health interventions. METHODS: We used the Centers for Disease Control and Prevention guidelines to evaluate the performance of the influenza surveillance system (ISS) in Zambia during 2011–2017 using 9 attributes: (i) data quality and completeness, (ii) timeliness, (iii) representativeness, (iv) flexibility, (v) simplicity, (vi) acceptability, (vii) stability, (viii) utility, and (ix) sustainability. Each attribute was evaluated using pre-defined indicators. For each indicator we obtained the proportion (expressed as percentage) of the outcome of interest over the total. A scale from 1 to 3 was used to provide a score for each attribute as follows: < 60% (as obtained in the calculation above) scored 1 (weak performance); 60–79% scored 2 (moderate performance); ≥80% scored 3 (good performance). An overall score for each attribute and the ISS was obtained by averaging the scores of all evaluated attributes. RESULTS: The overall mean score for the ISS in Zambia was 2.6. Key strengths of the system were the quality of data generated (score: 2.9), its flexibility (score: 3.0) especially to monitor viral pathogens other than influenza viruses, its simplicity (score: 2.8), acceptability (score: 3.0) and stability (score: 2.6) over the review period and its relatively low cost ($310,000 per annum). Identified weaknesses related mainly to geographic representativeness (score: 2.0), timeliness (score: 2.5), especially in shipment of samples from remote sites, and sustainability (score: 1.0) in the absence of external funds. CONCLUSIONS: The system performed moderately well in our evaluation. Key improvements would include improvements in the timeliness of samples shipments and geographical coverage. However, these improvements would result in increased cost and logistical complexity. The ISSS in Zambia is largely reliant on external funds and the acceptability of maintaining the surveillance system through national funds would require evaluation.


title: Approach to Peribronchovascular Disease on CT

text: Diseases that are predominantly peribronchovascular in distribution on computed tomography by definition involve the bronchi, adjacent vasculature, and associated lymphatics involving the central or axial lung interstitium. An understanding of diseases that can present with focal peribronchovascular findings is useful for establishing diagnoses and guiding patient management. This review will cover clinical and imaging features that may assist in differentiating amongst the various causes of primarily peribronchovascular disease.


Communicable disease surveillance and management in a globalised world


title: Severe outcomes associated with respiratory viruses in newborns and infants: a prospective viral surveillance study in Jordan

text: OBJECTIVE: To assess virus-specific hospitalisation rates, risk factors for illness severity and seasonal trends in children hospitalised with acute respiratory infections (ARI). DESIGN: Prospective cohort study. SETTING: A government hospital serving low-income and middle-income population in Amman, Jordan. PARTICIPANTS: Children under 2 years of age hospitalised with fever and/or respiratory symptoms (n=3168) from 16 March 2010 to 31 March 2013. Children with chemotherapy-associated neutropenia and newborns who had never been discharged after birth were excluded from the study. OUTCOME MEASURES: Hospitalisation rates and markers of illness severity: admission to intensive care unit (ICU), mechanical ventilation (MV), oxygen therapy, length of stay (LOS) and death. RESULTS: Of the 3168 subjects, 2581 (82%) had at least one respiratory virus detected, with respiratory syncytial virus (RSV) being the most predominant pathogen isolated. During admission, 1013 (32%) received oxygen therapy, 284 (9%) were admitted to ICU, 111 (4%) were placed on MV and 31 (1%) children died. Oxygen therapy was higher in RSV-only subjects compared with human rhinovirus-only (42%vs29%, p<0.001), adenovirus-only (42%vs21%, p<0.001) and human parainfluenza virus-only (42%vs23%, p<0.001) subjects. The presence of an underlying medical condition was associated with oxygen therapy (adjusted OR (aOR) 1.95, 95% CI 1.49 to 2.56), ICU admission (aOR 2.51, 95% CI 1.71 to 3.68), MV (aOR 1.91, 95% CI 1.11 to 3.28) and longer LOS (aOR1.71, 95% CI 1.37 to 2.13). Similarly, younger age was associated with oxygen therapy (0.23, 95% CI 0.17 to 0.31), ICU admission (aOR 0.47, 95% CI 0.30 to 0.74), MV (0.28, 95% CI 0.15 to 0.53) and longer LOS (aOR 0.47, 95% CI 0.38 to 0.59). Pneumonia was strongly associated with longer LOS (aOR 2.07, 95% CI 1.65 to 2.60), oxygen therapy (aOR 2.94, 95% CI 2.22 to 3.89), ICU admission (aOR 3.12, 95% CI 2.16 to 4.50) and MV (aOR 3.33, 95% CI 1.85 to 6.00). Virus-specific hospitalisation rates ranged from 0.5 to 10.5 per 1000 children. CONCLUSION: Respiratory viruses are associated with severe illness in Jordanian children hospitalised with ARI. Prevention strategies such as extended breast feeding, increased access to palivizumab and RSV vaccine development could help decrease hospitalisation rates and illness severity, particularly in young children with underlying medical conditions.


title: Of men, molecules, and (Ir)reducibility

text: The subject of (ir)reducibility in biochemistry has resurfaced recently in the literature. Along with it comes a renewed emphasis on the organizational complexity of the living state and, more broadly, concern over the unity of the sciences.


title: In vitro inhibition of CSFV replication by retroviral vector-mediated RNA interference

text: Abstract Classical swine fever (CSF) is a highly contagious viral disease of pigs which causes major economic losses worldwide. No specific drug is currently available for the effective treatment of CSFV infection. RNA interference (RNAi) technology depends on effective delivery systems, for which several effective vectors have recently been developed. Three retroviral plasmids containing siRNA genes targeting different regions of N pro and NS4A have been constructed, and 3 replication-incompetent retroviral vectors have been produced in the human embryo kidney cell line GP2-293 by retroviral plasmid transfection. PK-15 cells were then infected with these replication-incompetent retroviral vectors and screened for siRNA stably expressing PK-15 cell clones. Growth of CSFV in such siRNA stably expressing cell clones resulted in a 186-fold reduction in viral genome copies and, at 72h post-infection, only a small % of cells showed infection by indirect immunofluorescence microscopy, and effective inhibition of virus replication persisted for up to 120h. Retroviral vector-mediated RNAi can therefore be used to study the specific function of viral genes associated with CSFV replication and may have potential therapeutic application.


title: Does the traditional Chinese medicine theory of five circuits and six qi improve treatment effectiveness? A systematic review of randomized controlled trials

text: Abstract Objective To evaluate whether the traditional Chinese medicine (TCM) theory of five circuits and six qi (FCSQ) is beneficial in terms of improving clinical effectiveness. Methods Randomized controlled trials (RCTs) evaluating the clinical value of FCSQ theory were reviewed. Multiple databases (China Network Knowledge Infrastructure, Chinese Scientific Journals Database, Wanfang Data, SinoMed, Cochrane Library, PubMed, and Embase) were systematically searched from inception to June 12, 2018. Two authors independently extracted the data and performed a methodological quality assessment of the RCTs. RevMan 5.3 software was used for the data analysis. The effect sizes for the primary outcome measures were expressed as relative risks or mean differences with 95% confidence intervals. Results A total of 13 RCTs were selected, involving 12 types of diseases and 4695 patients. The methodological quality of the RCTs was generally low. Five studies compared the effectiveness of TCM treatments guided by FCSQ theory with conventional TCM therapies, and the remaining eight studies compared the effectiveness of TCM treatments guided by FCSQ theory with biomedical treatments. All of the RCTs reported that the effectiveness of the treatment intervention was better than that of the intervention in the control group. Conclusion Because of many methodological problems in existing clinical studies, it remains impossible to definitively conclude that FCSQ theory can improve clinical effectiveness. It is difficult to unify the clinical application of FCSQ theory. The feasibility and repeatability of FCSQ as an intervention should be given more attention in future clinical research. Future work should also follow international norms for clinical research implementation and reporting to provide high-quality evidence for evaluating the clinical value of FCSQ theory.


title: Coronavirus: Why Men are More Vulnerable to Covid-19 Than Women?

text: Amid of coronavirus disease 2019 (Covid-19) pandemic, much emphasis was initially placed on the elderly or those who have preexisting health conditions such as obesity, hypertension, and diabetes as being at high risk of contracting and/or dying of Covid-19. But it is now becoming clear that being male is also a factor. The epidemiological findings reported across different parts of the world indicated higher morbidity and mortality in males than females. While it is still too early to determine why the gender gap is emerging, this article point to several possible factors such as higher expression of angiotensin-converting enzyme-2 (ACE 2; receptors for coronavirus) in male than female, sex-based immunological differences driven by sex hormone and X chromosome. Furthermore, a large part of this difference in number of deaths is caused by gender behavior (lifestyle), i.e., higher levels of smoking and drinking among men compared to women. Lastly, studies reported that women had more responsible attitude toward the Covid-19 pandemic than men. Irresponsible attitude among men reversibly affect their undertaking of preventive measures such as frequent handwashing, wearing of face mask, and stay at home orders.


title: Right-Sizing Technology in the Era of Consumer-Driven Health Care

text: Technology for modern clinical and public health microbiology laboratories has evolved at an impressive rate over the last two decades. Contemporary diagnostics can rapidly provide powerful data that can impact patient lives and support infectious disease outbreak investigations. At the same time, dramatic changes to health care delivery are putting new pressures on a system that is now focusing on patient-centric, value-driven, convenient care. For laboratories, balancing all these demands in a cost-contained environment remains a challenge. This article explores the current and future directions of diagnostics in our dynamic health care environment.


title: Effects of asymptomatic infection on the dynamical interplay between behavior and disease transmission in multiplex networks

text: Abstract Multiplex network theory is widely introduced to deepen the understanding of the dynamical interplay between self-protective behavior and epidemic spreading. Most of the existing studies assumed that all infected individuals can transmit disease- related information or can be perceived by their neighbors. However, owing to lack of distinct symptoms for patients in the initial stage of infection, the disease information cannot be transmitted in the population, which may lead to the wrong perception of infection risk and inappropriate behavior response. In this work, we divide infected individuals into Exposed-state (without obvious clinical symptoms) individuals and Infected-state (with evident clinical symptoms) individuals, both of whom can spread disease, but only Infected-state individuals can diffuse disease information. Then, in this work we establish UAU-SEIS (Unaware–Aware–Unaware–Susceptible–Exposed–Infected–Susceptible) model in multiplex networks and analyze the effect of asymptomatic infection and the isolation of Infected-state individuals on the density of infection and the epidemic threshold. Furthermore, we extend the UAU-SEIS model by taking the individual heterogeneity into consideration. Combined Markov chain approach and Monte-Carlo Simulations, we find that asymptomatic infection has an effect on the density of infected individuals and the epidemic threshold, and the extent of the effect is influenced by whether Infected-state individuals are isolated or treated. In addition, results show that the individual heterogeneity can lower the density of infected individuals, but cannot enhance the epidemic threshold.


title: Cellular composition and interferon-γ expression of the local inflammatory response in feline infectious peritonitis (FIP)

text: Abstract Feline infectious peritonitis (FIP) is one of the most important viral diseases of cats. International studies estimate that approximately 80% of all purebred cats are infected with the causative agent, feline coronavirus (FCoV). Out of these, 5–12% develop clinical symptoms of FIP. The pathogenesis of the disease is complex with many unresolved issues relating to the role of the immune system. The aim of the present study was to determine the proportions of various inflammatory cell types in FIP lesions by using a panel of cat specific, thoroughly validated, monoclonal antibodies. In addition, the expression of interferon-γ within the inflammatory lesions was examined by RT-PCR. Our results confirm the mixed nature of the inflammatory reaction in FIP, involving B cells and plasma cells as well as CD4+ and CD8+ T cells. However, one cell type stands out as being the key element in both the “wet” and “dry” forms of FIP: the macrophage. Upregulation of IFN-γ expression within the inflammatory lesions suggests a local activation of macrophages, which might result in increased viral replication.


title: Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer

text: The tremendous pandemic potential of coronaviruses was demonstrated twice in the last decades by two global outbreaks of deadly pneumonia. Entry of coronaviruses into cells is mediated by the transmembrane spike glycoprotein S, which forms a trimer carrying receptor-binding and membrane fusion functions(1). S also contains the principal antigenic determinants and is the target of neutralizing antibodies. Here we present the structure of a murine coronavirus S trimer ectodomain determined at 4.0 Å resolution by single particle cryo-electron microscopy. It reveals the metastable pre-fusion architecture of S and highlights key interactions stabilizing it. The structure shares a common core with paramyxovirus F proteins(2,3), implicating mechanistic similarities and an evolutionary connection between these viral fusion proteins. The accessibility of the highly conserved fusion peptide at the periphery of the trimer indicates potential vaccinology strategies to elicit broadly neutralizing antibodies against coronaviruses. Finally, comparison with crystal structures of human coronavirus S domains allows rationalization of the molecular basis for species specificity based on the use of spatially contiguous but distinct domains.


Contributing to health security in Europe since 2005 – ECDC’s 15th anniversary


Border closure for island nations? Analysis of pandemic and bioweapon‐related threats suggests some scenarios warrant drastic action


title: COVID‐19’s impact on private practice and academic dentistry in North America

text: The COVID‐19 pandemic is a major public health crisis for countries around the world. In response to this global outbreak, the World Health Organization declared a public health emergency of international concern. Dental professionals are especially at high risk of contracting the COVID‐19 virus due to the unique nature of dentistry, more specifically, exposure to aerosols and droplets. When it comes to dental emergencies, it was crucial to maintain urgent dental care services operational to help reduce the burden on our healthcare system and hospitals already under pressure. The COVID‐19 pandemic has significantly impacted how dentistry is practiced in North America in both the private practice and academic settings. This article shares the perspectives of dentists practicing in private practice and clinician‐researchers in academic dental institutions. More specifically, we discuss about measures implemented to minimize risks of disease transmission, challenges in emergency dental care, impact on patients, as well as impact on the professional and personal lives of the dental team during the COVID‐19 crisis.


title: An ‘Arms Race’ between the Nonsense-mediated mRNA Decay Pathway and Viral Infections

text: The Nonsense-mediated mRNA Decay (NMD) pathway is an RNA quality control pathway conserved among eukaryotic cells. While historically thought to predominantly recognize transcripts with premature termination codons, it is now known that the NMD pathway plays a variety of roles, from homeostatic events to control of viral pathogens. In this review we highlight the reciprocal interactions between the host NMD pathway and viral pathogens, which have shaped both the host antiviral defense and viral pathogenesis.


title: Canine infectious respiratory disease: New insights into the etiology and epidemiology of associated pathogens

text: Canine infectious respiratory disease (CIRD) is a syndrome where multiple viral and bacterial pathogens are involved sequentially or synergistically to cause illness. There is limited information regarding the prevalence of pathogens related to CIRD in the United States as well as the role of co-infections in the pathogenesis of the syndrome. We aimed to conduct a comprehensive etiologic and epidemiologic study of multiple CIRD agents in a diverse dog population using molecular methods and statistical modeling analyses. In addition, a novel probe-based multiplex real-time PCR was developed to simultaneously detect and differentiate two species of Mycoplasma (M. canis and M. cynos). Canine adenovirus, canine distemper virus, canine parainfluenza virus, coronavirus, influenza A virus (H3N2 and H3N8), Bordetella bronchiseptica, M. canis, M. cynos and Streptococcus equi subsp. zooepidemicus were investigated in specimens from clinically ill and asymptomatic dogs received at the Athens Veterinary Diagnostic Laboratory. Results showed low occurrence of classical CIRD agents such as B. bronchiseptica, canine adenovirus and distemper virus, while highlighting the potential role of emerging bacteria such as M. canis and M. cynos. Statistical modeling analyses of CIRD pathogens emphasized the impact of co-infections on the severity of clinical presentation, and showed that host factors, such as animal age, are the most important predictors of disease severity. This study provides new insights into the current understanding of the prevalence and role of co-infections with selected viruses and bacteria in the etiology of CIRD, while underscoring the importance of molecular diagnosis and vaccination against this disease.


title: The N-Terminal Domain of Spike Protein Is Not the Enteric Tropism Determinant for Transmissible Gastroenteritis Virus in Piglets

text: Transmissible gastroenteritis virus (TGEV) is the etiologic agent of transmissible gastroenteritis in pigs, and the N-terminal domain of TGEV spike protein is generally recognized as both the virulence determinant and enteric tropism determinant. Here, we assembled a full-length infectious cDNA clone of TGEV in a bacterial artificial chromosome. Using a novel approach, the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems efficiently and rapidly rescued another recombinant virus with a 224-amino-acid deletion in the N-terminal domain of the TGEV Spike gene (S_NTD224), which is analogous to the N-terminal domain of porcine respiratory coronavirus. S_NTD224 notably affected the TGEV growth kinetics in PK-15 cells but was not essential for recombinant virus survival. In animal experiments with 13 two-day-old piglets, the TGEV recombinant viruses with/without S_NTD224 deletion induced obvious clinical signs and mortality. Together, our results directly demonstrated that S_NTD224 of TGEV mildly influenced TGEV virulence but was not the enteric tropism determinant and provide new insights for the development of a new attenuated vaccine against TGEV. Importantly, the optimized reverse genetics platform used in this study will simplify the construction of mutant infectious clones and help accelerate progress in coronavirus research.


title: Monoclonal antibody analysis of Porcine Reproductive and Respiratory Syndrome virus epitopes associated with antibody-dependent enhancement and neutralization of virus infection

text: Abstract Enhanced infection and replication of porcine reproductive and respiratory syndrome (PRRS) virus in the presence of specific antibody has been demonstrated in vitro and in vivo, a phenomenon known as antibody-dependent enhancement (ADE). ADE is considered to be a significant obstacle to developing effective vaccines for many viruses for which ADE has been reported, since virus-specific antibodies of maternal origin or those conferred by vaccination can facilitate the entry of the virus into target cells, sometimes resulting in increased severity of the disease. In this study, the role of specific PRRS viral epitopes in ADE and/or virus neutralization (VN) was assessed in vitro using 14 monoclonal antibodies (mAbs) to 4 PRRS viral proteins: nucleocapsid (N), matrix (M), glycoprotein (GP) 5, and GP3. Each mAb recongnized a distinct epitope on one of these proteins. One-way ADE and VN assays were performed in vitro using homologous PRRS virus isolates in the presence or absence of each mAb. ADE activity was determined by detecting a significant increase of progeny virus yield in porcine alveolar macrophage cultures in the presence of individual mAbs. Neutralizing activity was determined by detecting a significant reduction or complete blocking of virus replication in MARC-145 cells in the presence of individual mAbs. mAbs could be categorized into 3 groups: enhancing, neutralizing and neither. Viral epitopes which are capable of inducing neutralizing antibodies appeared to reside on the M, GP3 and GP5 proteins, while epitopes that may induce ADE-mediating antibody were associated with the N and GP5 proteins. Identification of the viral proteins and antigens and epitopes responsible for ADE- and VN-mediating antibodies may provide the basis for developing efficacious second-generation vaccines for the control of PRRS virus; yet, further epitope mapping remains to be done.


title: Acute Encephalopathy Associated with Influenza A Virus Infection

text: Twenty-one patients aged 4–78 years with influenza A virus–associated acute encephalopathy were studied. Influenza A virus could be detected only in a cerebrospinal fluid (CSF) specimen obtained from 1 of 18 patients, despite the use of a highly sensitive polymerase chain reaction assay. Six patients experienced influenzal encephalopathy during the course of respiratory illness. Five of these patients had hypoprothrombinemia and 4 had increased serum creatinine levels, indicating hepatic and/or renal dysfunction. Fourteen patients experienced postinfluenzal encephalopathy ⩽3 weeks after resolution of acute respiratory symptoms. In 6 patients, focal areas of high signal intensity were visible on T2-weighted magnetic resonance images of the brain. Adenovirus DNA was detected in CSF specimens obtained from 4 (36%) of 11 patients with postinfluenzal encephalopathy. Thus, influenzal encephalopathy is frequently associated with metabolic disorders, whereas postinfluenzal encephalopathy appears to have different possible etiologies.


title: An Italian Neurology Outpatient Clinic Facing SARS-CoV-2 Pandemic: Data From 2,167 Patients

text: Objective: Neurological sequelae of SARS-CoV-2 infection have already been reported, but there is insufficient data about the impact of the pandemic on the management of the patients with chronic neurological diseases. We aim to analyze the effect of COVID-19 pandemic and social restriction rules on these fragile patients. Methods: Patients with chronic neurologic diseases routinely followed at the outpatient clinic of Gemelli University Hospital, Rome, were assessed for symptoms suggestive of SARS-CoV-2 infection in the pandemic period, consequences of social restrictions, and neurological disease features, concomitant medical conditions, current medical and disease-specific treatments. Data source: a dedicated telephone survey designed to encompass questions on COVID-19 symptoms and on pandemic effects in chronic neurologic conditions. Results: Overall, 2,167 individuals were analyzed: 63 patients reported contact with COVID-19 positive cases, 41 performed the swab, and 2 symptomatic patients tested positive for COVID-19 (0.09%). One hundred fifty-eight individuals (7%) needed urgent neurological care, deferred due to the pandemic; 641 patients (30%) suspended hospital treatments, physiotherapy or other support interventions; 405 individuals (19%) reported a subjective worsening of neurological symptoms. Conclusions: In our population, the presence of neurological chronic diseases did not increase the prevalence of COVID-19 infection. Nevertheless, the burden of neurological disorders has been worsened by the lockdown.


title: The use of RT-PCR for determination of separate end-points for the strains IB H120 and IB D274 in titration of the combination vaccine Poulvac IB® primer

text: Abstract Poulvac IB® Primer is a lyophilized vaccine containing two attenuated infectious bronchitis strains in one vial, IB H120 and IB D274. For quantification of the viral content of the vaccine, dilution series of the final product are inoculated in embryonated chicken eggs. After the incubation period of seven days standard practice is for the embryos to be taken from each egg and examined visually for IB specific lesions; these readings are used to determine an end-point in viral titrations. The result is a titre value to which both strains contribute. However, it is not clear what the live virus titre is for strain IB H120 and for strain IB D274. In order to determine end-points in the titration for each of the two strains, we collected the allantoic fluids from each egg after the incubation period and tested these for the presence of IB H120 and IB D274 by a strain specific reverse phase PCR. Based on the data obtained by PCR we were able to determine an end-point for each of the two strains. For a given commercial batch of Poulvac IB primer we determined titres of 106.31 EID50 per vial for IB H120 and 106.59 EID50 for IB D274 using PCR for end-point determination. These end-points matched well with the end-point determined for both strains cumulatively after visual examination, i.e. 106.67 EID50 per vial. It is concluded that PCR is a suitable means to determine end-points in titrations of live viruses.


title: Risques de contamination virale des soignants au cours d’une laparoscopie pendant la pandémie de la Covid-19

text: Résumé La pandémie de la Covid-19 a notablement modifié nos pratiques. Le but de cet article était d’analyser les risques de contamination des soignants au cours des interventions laparoscopiques réalisées chez des patients atteints de Covid-19. L’effet délétère de l’aérosolisation du pneumopéritoine avec présence du virus n’est actuellement pas quantifié. Même si les mesures de protection des soignants sont une extrapolation des mesures prises pour d’autres épidémies, elles doivent être de rigueur afin de minimiser le risque de contamination virale. Les mesures de protection sont les équipements de protection individuelle des soignants, l’adaptation de la technique chirurgicale (méthode de création du pneumopéritoine, filtres, anastomoses plutôt intracorporelles, précautions lors de l’exsufflation du pneumopéritoine), et l’organisation de la salle d’opération. Abstract The Covid-19 pandemic has markedly changed our practices. This article analyses the risks of contamination among healthcare professionals (HCPs) during laparoscopic surgery on patients with Covid-19. Harmful effects of aerosols from a pneumoperitoneum with the virus present have not yet been quantified. Measures for the protection of HCPs are an extrapolation of those taken during other epidemics. They must still be mandatory to minimise the risk of viral contamination. Protection measures include personal protection equipment for HCPs, adaptation of surgical technique (method for obtaining pneumoperitoneum, filters, preferred intracorporeal anastomosis, precautions during the exsufflation of the pneumoperitoneum), and organisation of the operating room.


title: Linkages between Chiropteran diversity and ecosystem services for sustainable fragmented forest conservation

text: This data article informs about Chiropteran diversity, new records, ecosystem services and possible pathogen carriers in fragmented forests (sub-divided by utility corridors, man-made structures, untouched and secondary plantations) within districts Setiu (Setiu Research Station), Hulu Terengganu (Saok and Lasir waterfalls) and Besut (Gunung Tebu Forest Reserve) of state Terengganu, Peninsular Malaysia. These bats were captured using harp traps and mist nets that were set 10 m apart across flyways, streams and less cluttered trees in the 50 m × 50 m transect zones (identified at each site). All animals were distinguished by morphology and gender before their release at the site of capture. The data comprise of five bat family groups Hipposideridae, Megadermatidae, Pteropodidae, Rhinolophidae and Vespertilionidae. It is interesting to note that untouched Saok Waterfalls is home to wide variety of bats listed (68.8%), followed by secondary forests of Gunung Tebu Forest Reserve (24.8%), untouched Lasir Waterfalls (4.8%) and lastly, Setiu Research Station as least favored (1.6%). Chiroptera like Cynopterus brachyotis (n = 23, 37.7%), Hipposideros bicolor (n = 6, 9.8%) and Scotophilus kuhli (n = 6, 9.8%) were most dominant in the checklist whereas Hipposideros armiger, Murina suilla and Scotophilus kuhlii are new data records in the fragmented forests of Terengganu. The data were interpret into Shannon, Simpson, Margalef, Menhinik and Evenness indices to individually or collectively distinguish chiropteran variety in Terengganu State whereas weight-forearm length (W/FA) informs about chiropteran Body Condition Index (-0.25 to 0.25). The function of bats were also identified to distinguish service providers (pollination and forests regeneration) and zoonotic pathogen carriers (in particular to Leptospira bacteria, Nipah virus and Sindbis virus).


title: Bilan biologique de 59 cas de pneumopathies aiguës atypiques

text: Summary A prospective survey was undertaken in patients hospitalized from january 1976 to april 1978 with clinical, biological and radiological features of atypical pneumonia. In all patients samples were taken early and 15 days after the on set of the disease to detect specific serum antibodies to influenza A and B viruses, parainfluenza type I, II and III, adenoviruses, respiratory syncitial virus, Micoplasma pneumoniae and Chlamydia psittaci. A fourfold rise in antibodies was observed in 23,7 % of patients (M. pneumoniae 43 %, influenza A virus 28,5 % and C. psittaci 14 %). Taking into account titers equal or higher than 1/64, a specific agent can be recognized in 50 % of 59 cases. Because of those poor results, the delay to obtain them and their cost, the interest of such a laboratory study is questionable.


title: Virus detection in critically ill children with acute respiratory disease: a new profile in view of new technology

text: AIM: To describe the epidemiology of critically ill children admitted to a paediatric intensive care unit (PICU) with acute respiratory disease. The association with intubation was analysed for the three most prevalent viruses and in those with and without viral co‐infection. METHODS: Patients admitted to the PICU (2004–2014) with acute respiratory disease were included. Analyses were performed utilising each respiratory viral infection or multiple viral infections as an exposure. RESULTS: There were 1766 admissions with acute respiratory disease of which 1372 had respiratory virus testing and 748 had one or more viruses detected. The risk of intubation before or during the PICU stay was higher if parainfluenza virus was detected compared to respiratory syncytial virus (RSV) (OR: 2.20; 95% CI: 1.06–4.56). Sixty‐three admissions had two or more viruses detected, and the combination of RSV and Rhinovirus/enterovirus was the most common. No significant difference was observed in the risk of intubation between patients with multiple and single viral infections. CONCLUSION: Higher risk of intubation was found in patients with parainfluenza as compared to RSV. The risk of intubation comparing parainfluenza virus to other viruses and for patients with multiple versus single virus needs to be further studied.


title: Children and SARS-CoV-2 infection: innocent bystanders…until proven otherwise

text: In this commentary, we focus our attention on what is known about SARS-CoV-2 infection in the pediatric population. We report literature and National data. The possible and different explanations for understanding why the infection seems to be more benign and less frequent in children are discussed. The possible role of children in the COVID-19 viral disease pandemic is also commented. Finally, our work suggests to search for future evidence and containment strategies to manage virus spread.


title: Potential for Lung Recruitment and Ventilation-Perfusion Mismatch in Patients With the Acute Respiratory Distress Syndrome From Coronavirus Disease 2019

text: Severe cases of coronavirus disease 2019 develop the acute respiratory distress syndrome, requiring admission to the ICU. This study aimed to describe specific pathophysiological characteristics of acute respiratory distress syndrome from coronavirus disease 2019. DESIGN: Prospective crossover physiologic study. SETTING: ICU of a university-affiliated hospital from northern Italy dedicated to care of patients with confirmed diagnosis of coronavirus disease 2019. PATIENTS: Ten intubated patients with acute respiratory distress syndrome and confirmed diagnosis of coronavirus disease 2019. INTERVENTIONS: We performed a two-step positive end-expiratory pressure trial with change of 10 cm H(2)O in random order. MEASUREMENTS AND MAIN RESULTS: At each positive end-expiratory pressure level, we assessed arterial blood gases, respiratory mechanics, ventilation inhomogeneity, and potential for lung recruitment by electrical impedance tomography. Potential for lung recruitment was assessed by the recently described recruitment to inflation ratio. In a subgroup of seven paralyzed patients, we also measured ventilation-perfusion mismatch at lower positive end-expiratory pressure by electrical impedance tomography. At higher positive end-expiratory pressure, respiratory mechanics did not change significantly: compliance remained relatively high with low driving pressure. Oxygenation and ventilation inhomogeneity improved but arterial co(2) increased despite unchanged respiratory rate and tidal volume. The recruitment to inflation ratio presented median value higher than previously reported in acute respiratory distress syndrome patients but with large variability (median, 0.79 [0.53–1.08]; range, 0.16–1.40). The Fio(2) needed to obtain viable oxygenation at lower positive end-expiratory pressure was significantly correlated with the recruitment to inflation ratio (r = 0.603; p = 0.05). The ventilation-perfusion mismatch was elevated (median, 34% [32–45%] of lung units) and, in six out of seven patients, ventilated nonperfused units represented a much larger proportion than perfused nonventilated ones. CONCLUSIONS: In patients with acute respiratory distress syndrome from coronavirus disease 2019, potential for lung recruitment presents large variability, while elevated dead space fraction may be a specific pathophysiological trait. These findings may guide selection of personalized mechanical ventilation settings.


title: COVID-19 vaccines: neutralizing antibodies and the alum advantage

text: Achieving high levels of neutralizing antibodies to the spike protein of SARS-CoV-2 in a safe manner is likely to be crucial for an effective vaccine. Here, we propose that aluminium-based adjuvants might hold the key to this.


title: Platform technology to generate broadly cross‐reactive antibodies to α‐helical epitopes in hemagglutinin proteins from influenza A viruses

text: We have utilized a de novo designed two‐stranded α‐helical coiled‐coil template to display conserved α‐helical epitopes from the stem region of hemagglutinin (HA) glycoproteins of influenza A. The immunogens have all the surface‐exposed residues of the native α‐helix in the native HA protein of interest displayed on the surface of the two‐stranded α‐helical coiled‐coil template. This template when used as an immunogen elicits polyclonal antibodies which bind to the α‐helix in the native protein. We investigated the highly conserved sequence region 421–476 of HA by inserting 21 or 28 residue sequences from this region into our template. The cross‐reactivity of the resulting rabbit polyclonal antibodies prepared to these immunogens was determined using a series of HA proteins from H1N1, H2N2, H3N2, H5N1, H7N7, and H7N9 virus strains which are representative of Group 1 and Group 2 virus subtypes of influenza A. Antibodies from region 449–476 were Group 1 specific. Antibodies to region 421–448 showed the greatest degree of cross‐reactivity to Group 1 and Group 2 and suggested that this region has a great potential as a “universal” synthetic peptide vaccine for influenza A. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 144–159, 2016.


title: COVID-19 Associated Pulmonary Aspergillosis (CAPA)—From Immunology to Treatment

text: Like severe influenza, coronavirus disease-19 (COVID-19) resulting in acute respiratory distress syndrome (ARDS) has emerged as an important disease that predisposes patients to secondary pulmonary aspergillosis, with 35 cases of COVID-19 associated pulmonary aspergillosis (CAPA) published until June 2020. The release of danger-associated molecular patterns during severe COVID-19 results in both pulmonary epithelial damage and inflammatory disease, which are predisposing risk factors for pulmonary aspergillosis. Moreover, collateral effects of host recognition pathways required for the activation of antiviral immunity may, paradoxically, contribute to a highly permissive inflammatory environment that favors fungal pathogenesis. Diagnosis of CAPA remains challenging, mainly because bronchoalveolar lavage fluid galactomannan testing and culture, which represent the most sensitive diagnostic tests for aspergillosis in the ICU, are hindered by the fact that bronchoscopies are rarely performed in COVID-19 patients due to the risk of disease transmission. Similarly, autopsies are rarely performed, which may result in an underestimation of the prevalence of CAPA. Finally, the treatment of CAPA is complicated by drug–drug interactions associated with broad spectrum azoles, renal tropism and damage caused by SARS-CoV-2, which may challenge the use of liposomal amphotericin B, as well as the emergence of azole-resistance. This clinical reality creates an urgency for new antifungal drugs currently in advanced clinical development with more promising pharmacokinetic and pharmacodynamic profiles.


Disseminated Bocavirus Infection after Stem Cell Transplant


title: An Investigation of the Pathology and Pathogens Associated with Porcine Respiratory Disease Complex in Denmark

text: Summary Respiratory infections are among the most important diseases of growing pigs. In order to elucidate the multifactorial aetiology of porcine respiratory disease complex (PRDC) in Denmark, lungs from 148 finishing pigs with cranioventral bronchopneumonia (case group) and 60 pigs without lung lesions (control group) were collected from abattoirs. The pathogens involved in PRDC and their interactions were identified and linked to the histopathological diagnosis. The lung samples were cultured for bacteria and tested by multiplex polymerase chain reaction for presence of swine influenza virus (type A), porcine reproductive and respiratory syndrome virus (both European and US type), porcine circovirus type 2 (PCV2), porcine respiratory coronavirus, porcine cytomegalovirus, Mycoplasma hyopneumoniae and Mycoplasma hyorhinis. All cases had cranioventral lobular bronchopneumonia consistent with PRDC. There was a broad range of microscopical lesions and the cases were characterized as acute (n =10), subacute (n =24) or chronic (n =114) bronchopneumonia. Five bacterial species, five viruses and two Mycoplasma spp. were detected in different combinations. PCV2, M. hyopneumoniae, M. hyorhinis and Pasteurella multocida were detected most frequently among the PRDC affected swine and the diversity and number of pathogens were higher in these animals compared with controls. No clear-cut associations were detected between pathogens and histological lesions or histopathological diagnoses. PRDC occurs more frequently than enzootic pneumonia among Danish finishing pigs and has complex and varied histopathology.