title: Molecular detection and characterization of unclassified bovine enteric caliciviruses in South Korea

text: Abstract The unclassified bovine enteric calicivirus (BEC) is a new bovine enteric calicivirus that is different from bovine norovirus, and causes diarrhea and pathologies in the small intestine of calves. This virus includes Nebraska (NB)- and Newbury agent 1 (NA1)-like strains. The prevalence of this BEC and its genetic characterization has only been reported in the UK and the USA. This study examined the prevalence and genetic diversity of these BECs in diarrheic calves in South Korea. Among a total of 645 diarrheic fecal specimens obtained from 629 cattle herds, these unclassified BECs were detected in 59 (9.1%) diarrheic fecal samples from 57 herds (9.3%) by either RT-PCR or nested PCR. Sequence and phylogenetic analyses of the partial RdRp gene showed that all the Korean BECs clustered together and were closely related to the NB-like viruses (80.9–88.1% nucleotide and 84.5–98.4% amino acid) but not to the NA1-like viruses (75.8–78.4% nucleotide and 79.7–82.8% amino acid). Although these viruses could not be classified into NA1- and NB-like viruses from the sequence and phylogenetic data of the entire capsid gene, all the Korean BECs clustered together on a branch separate from the other known BECs. These results show that these BEC infections are endemic in diarrheic calves in South Korea. The infecting strains are genetically closer to the NB-like viruses but have a distinct evolutionary pathway.


title: Coronavirus nonstructural protein 1: common and distinct functions in the regulation of host and viral gene expression

text: The recent emergence of two highly pathogenic human coronaviruses (CoVs), severe acute respiratory syndrome CoV and Middle East respiratory syndrome CoV, has ignited a strong interest in the identification of viral factors that determine the virulence and pathogenesis of CoVs. The nonstructural protein 1 (nsp1) of CoVs has attracted considerable attention in this regard as a potential virulence factor and a target for CoV vaccine development because of accumulating evidence that point to its role in the downregulation of host innate immune responses to CoV infection. Studies have revealed both functional conservation and mechanistic divergence among the nsp1 of different mammalian CoVs in perturbing host gene expression and antiviral responses. This review summarizes the current knowledge about the biological functions of CoV nsp1 that provides an insight into the novel strategies utilized by this viral protein to modulate host and viral gene expression during CoV infection.


Clinical placements for medical students in the time of COVID‐19


title: Phylogenetic analysis of partial S1 and N gene sequences of infectious bronchitis virus isolates from Italy revealed genetic diversity and recombination

text: A total of ten infectious bronchitis virus (IBV) isolates collected from commercial chickens in Italy in 1999 were characterized by RT-PCR and sequencing of the S1 and N genes. Phylogenetic analysis based on partial S1 gene sequences showed that five field viruses clustered together with 793/B-type strains, having 91.3–98.5% nucleotide identity within the group, and one isolate had very close sequence relationship (94.6% identity) with 624/I strain. These two IBV types have been identified in Italy previously. The other three variant isolates formed novel genotype detected recently in many countries of Western Europe. For one of these variant viruses, Italy-02, which afterwards became the prototype strain, the entire S1 gene was sequenced to confirm its originality. In contrast, phylogenetic analysis of more conserved partial N gene sequences, comprising 1–300 nucleotides, revealed different clustering. Thus, three variant IBVs of novel Italy-02 genotype, which had 96.7–99.2% S1 gene nucleotide identity with each other, belonged to three separate subgroups based on N gene sequences. 624/I-type isolate Italy-06 together with Italy-03, which was undetectable using S1 gene primers, shared 97.7% and 99.3% identity, respectively, in N gene region with vaccine strain H120. Only one of the 793/B-type isolates, Italy-10, clustered with the 793/B strain sharing 99.3% partial N gene identity, whereas the other four isolates were genetically distant from them (only 87.7–89.7% identity) and formed separate homogenous subgroup. The results demonstrated that both mutations and recombination events could contribute to the genetic diversity of the Italian isolates.


title: Interferons as Therapeutic Agents for Infectious Diseases

text: This article explains the rationale for development of interferons as therapeutic agents, and describes commercial products available today. It also provides a summary of studies that have been performed with interferons for use as exogenous biological response modifiers in viral infections. Overall, the best data exist for treatment of viral hepatitis B and C, for which interferons are a cornerstone of therapy. Although infections with human papillomavirus and common cold viruses sometimes respond favorably to interferons, their outcomes are far from ideal. Finally, the role of interferons as vaccine adjuvants is still being explored but could be promising.


title: Group A streptococcal pharyngitis

text: Abstract Acute pharyngitis is a common illness in both children and adults, caused by a wide variety of microbial agents. In children, approximately 20% of pharyngitis is caused by group A beta-hemolytic streptococci (GABHS); in adults, 5% of pharyngitis is due to GABHS. The signs and symptoms of infection are variable, ranging from mild sore throat with minimal physical findings to high fever and severe pain. The differential diagnosis of GABHS pharyngitis is extensive. Most cases of acute pharyngitis in both children and adults are caused by viruses. The gold standard diagnostic test for GABHS remains the throat culture. It is important to select appropriate candidates for culture to maintain the sensitivity of the test. Penicillin is still recommended as first-line treatment for documented GABHS infections. Prompt treatment is important to prevent serious sequelae of infection.


title: A hospital-based COVID-19 abortion case in the early phase of the pandemic()

text: In this case report we discuss changes in hospital-based abortion care due to the COVID-19 pandemic. We highlight our experience with exposure to an asymptomatic COVID-19 positive patient. We hope early lessons from the United States epicenter will guide clinicians providing abortion care during this and future pandemics.


title: A modular framework for multiscale multicellular spatial modeling of viral infection, immune response and drug therapy timing and efficacy in epithelial tissues: A multiscale model of viral infection in epithelial tissues

text: Development of predictive quantitative models of all aspects of COVID-19 is essential for rapidly understanding the causes of differing disease outcomes and vulnerabilities, suggesting drug and therapeutic targets, and designing optimized personalized interventions. Easy to implement, predictive multiscale modeling frameworks to integrate the wide variety of clinical and research datasets into actionable insights, which could inform therapeutic regime strategies are lacking. We present a multiscale, multicellular, spatiotemporal model of the infection of epithelial tissue by a generic virus, a simplified cellular immune response and viral and immune-induced tissue damage. Our initial model is built of modular components to allow it to be easily extended and adapted in a collaborative fashion to describe specific viral infections, tissue types and immune responses. The model allows us to define three parameter regimes: where viral infection coincides with a massive cytopathic effect, where the immune System rapidly controls the virus and where the immune System controls the virus but extensive tissue damage occurs. We use the model in a proof-of-concept application to evaluate a number of drug therapy concepts. Inhibition of viral internalization and faster immune-cell recruitment lead to containment of infection. Fast viral internalization and slower immune response lead to uncontrolled spread of infection. Simulation of a drug, whose mode of action is to reduce production of viral RNAs, shows that a relatively limited reduction of viral replication at the beginning of infection greatly decreases the total area of tissue damage and maximal viral load, while even a treatment that greatly reduces the rate of genomic replication rapidly loses efficacy as the infection progresses. A number of simulation conditions lead to stochastically variable outcomes, with some replicas clearing or controlling the virus, while others see virus-induced damage sweep the simulated lung patch. The model is open-source and modular, allowing rapid development and extension of its components by groups working in parallel.


title: Multicenter Evaluation of the QIAstat-Dx Respiratory Panel for Detection of Viruses and Bacteria in Nasopharyngeal Swab Specimens

text: The QIAstat-Dx Respiratory Panel (QIAstat-Dx RP) is a multiplex in vitro diagnostic test for the qualitative detection of 20 pathogens directly from nasopharyngeal swab (NPS) specimens. The assay is performed using a simple sample-to-answer platform with results available in approximately 69 min. The pathogens identified are adenovirus, coronavirus 229E, coronavirus HKU1, coronavirus NL63, coronavirus OC43, human metapneumovirus A and B, influenza A, influenza A H1, influenza A H3, influenza A H1N1/2009, influenza B, parainfluenza virus 1, parainfluenza virus 2, parainfluenza virus 3, parainfluenza virus 4, rhinovirus/enterovirus, respiratory syncytial virus A and B, Bordetella pertussis, Chlamydophila pneumoniae, and Mycoplasma pneumoniae. This multicenter evaluation provides data obtained from 1,994 prospectively collected and 310 retrospectively collected (archived) NPS specimens with performance compared to that of the BioFire FilmArray Respiratory Panel, version 1.7. The overall percent agreement between QIAstat-Dx RP and the comparator testing was 99.5%. In the prospective cohort, the QIAstat-Dx RP demonstrated a positive percent agreement of 94.0% or greater for the detection of all but four analytes: coronaviruses 229E, NL63, and OC43 and rhinovirus/enterovirus. The test also demonstrated a negative percent agreement of ≥97.9% for all analytes. The QIAstat-Dx RP is a robust and accurate assay for rapid, comprehensive testing for respiratory pathogens.


title: Human rhinoviruses: coming in from the cold

text: Rhinovirus infections cause at least 70% of virus-related wheezing exacerbations and cold and flu-like illnesses. Infections are also associated with otitis media, sinusitis and pneumonia. The annual impact of human rhinovirus (HRV) infections costs billions of healthcare dollars. To date, 100 serotyped HRV or 'classical' strains have been divided between two genetically distinct species based on subgenomic sequences, but many more, apparently novel strains remain un-characterized, circulating in unknown patterns and causing undefined illnesses. Until recently, the genomes of less than half the classical strains had been sequenced. In April 2009, the remaining classical HRV genome sequences were reported. These data will inform therapeutic development and phylogenetic analysis for this subset of HRV strains but should be viewed as one step in a long road leading to comprehensive HRV characterization.


title: Hijacking the Supplies: Metabolism as a Novel Facet of Virus-Host Interaction

text: Viral replication is a process that involves an extremely high turnover of cellular molecules. Since viruses depend on the host cell to obtain the macromolecules needed for their proper replication, they have evolved numerous strategies to shape cellular metabolism and the biosynthesis machinery of the host according to their specific needs. Technologies for the rigorous analysis of metabolic alterations in cells have recently become widely available and have greatly expanded our knowledge of these crucial host–pathogen interactions. We have learned that most viruses enhance specific anabolic pathways and are highly dependent on these alterations. Since uninfected cells are far more plastic in their metabolism, targeting of the virus-induced metabolic alterations is a promising strategy for specific antiviral therapy and has gained great interest recently. In this review, we summarize the current advances in our understanding of metabolic adaptations during viral infections, with a particular focus on the utilization of this information for therapeutic application.


title: Biophysical Analyses for Probing Glycan-Protein Interactions

text: Glycan-protein interactions occur at many physiological events, and the analyses are of considerable importance for understanding glycan-dependent mechanisms. Biophysical approaches including 3D structural analysis are essential for revealing glycan-protein interactions at the atomic level. The inherent diversity of glycans suits them to function as identification tags, e.g., distinguish self from the nonself components of pathogens. However, the complexity of glycans and poor affinities for interaction partners limit the usefulness of conventional analyses. To cope with such troublesome glycans, a logical sequence of biophysical analyses need to be developed. In this chapter, we introduce a workflow of glycan-protein interaction analysis consisting of six steps: preparation of lectin and glycan, screening of glycan ligand, determination of binding epitope, quantitative interaction analysis, 3D structural analysis, and molecular dynamics simulation. Our increasing knowledge and understanding of lectin-glycan interactions will hopefully lead to the design of glyco-based medicines and vaccines.


Infección respiratoria aguda causada por el metapneumovirus humano: análisis de 39 casos


title: Links and interactions between mycoplasmas and viruses: past confusions and present realities

text: Links between mycoplasmas and viruses are ancient, multiple and complex, from past confusions during the first decades of the virus era to present realities illustrated by the possible implication of mycoplasms as co-factors in natural infections of AIDS. Mycoplasma viruses (phages) may also be responsible for modifying the pathogenic power of mycoplasmas, at least for plants and insects. In addition, several mycoplasmas are able to act as undesirable cell culture contaminants that induce erroneous results in both applied and general virology. These problems are examined within a historical context.


title: Selenium – associated gene signatures within the SARS-CoV-2 – host genomic interaction interface

text: A recent study by Sies and Parnham expanded on the therapeutic potential of Epselen, an organoselenium compound, as an inhibitor of SARS-CoV-2’s main protease. In this study, using an unbiased, data driven bioinformatic screening of two independently extracted SARS-CoV-2 – induced host gene signatures confirms Selenium as a potential drug candidate. This pathway based approach adds transcriptomic evidence complimenting the protein-centered rationale expanded on by the authors. Given that aside from host – protein interactions, antisense transcript mRNA-mRNA interactions have been demonstrated to occur at selenocysteine related insertions in RNA viruses, transcriptomic-level evidence offer unique insight into viral lifecycles. Furthermore, the pathways identified from these two selenium associated signatures provide further insight into the perturbations of selenium metabolism introduced by SARS-CoV-2 during its lifecycle.


title: Genotypic diversity, circulation patterns, and co-detections among rhinoviruses in Queensland, 2001

text: Rhinoviruses (RVs) occur more frequently than other viruses and more often in people displaying symptoms than in those without. RVs exacerbate chronic airway disease and confound the clinical diagnosis of influenza-like illness. We sought to estimate the spectrum of RV diversity, RV species seasonality and to breakdown RV involvement in respiratory virus co-detections by comprehensive molecular testing of a convenience collection of airway sample extracts from patients with suspected respiratory infections, collected during 2001. RVs were the most common virus detected. We were able to genotype ∼90% of RV detections, identifying 70 distinct RVs, spanning all three species. RV-Bs were under-represented. We found RV species co-circulated at times, although one species usually dominated. Each species displayed a bimodal distribution. Notably, RVs and influenza A viruses (IFAV) seldom co-occurred, supporting their roles as primary pathogens of the airway among acutely ill infants. Whether RV circulation has a moderating or controlling effect on the IFAV season or is controlled by it cannot be determined from these data. Despite the frequent perception that RVs commonly co-occur with another virus, our findings indicated this was not the case. Nearly 80% of RV detections occurred alone. Understanding more about population-level interference between viruses may allow us to harness aspects of it to generate a non-specific antiviral intervention that mimics a putative protective effect. For routine respiratory virus screening to best serve the patient, RV testing should be a principal component of any acute respiratory illness testing algorithm throughout the year.


title: Status and strategies for the management of head and neck cancer during COVID‐19 pandemic: Indian scenario

text: In India, oral cancer is the most common head and neck cancer (HNC) in men, mainly caused by the consumption of smoked and smokeless tobacco. During the current pandemic, delaying surgery for even 1 or 2 months may lead to more extensive surgery or inoperability, where only supportive care can be provided. Being semi‐emergent in nature, treatment for these patients is currently on hold or delayed in most centers across the country. This study was conducted to assess the impact of COVID‐19 pandemic and inability of the health system to treat HNC in a timely fashion and how surgeons are coping to this emergent situation. This article highlights the situation in India, a country burdened with one of the highest incidence rates of HNC.


title: A cluster of adenovirus type B55 infection in a neurosurgical inpatient department of a general hospital in Guangdong, China

text: BACKGROUND: Human adenovirus type 55 is a re‐emerging human respiratory pathogen that is associated with several respiratory infections outbreaks in military and school populations. In this study, we describe the first HAdV55‐associated hospital outbreak documented in Guangdong, China. METHODS: Active surveillance was conducted in the involved neurosurgical inpatient department. All staff and patients in the involved neurosurgical department were surveyed for any symptoms of fever (≥38°C) and enlarged tonsils during the outbreak period. Throat swabs and demographic information were collected for all cases. For each specimen, assays for common respiratory viruses were performed using one‐step reverse transcription‐polymerase chain reaction. HAdV‐positive samples were inoculated onto Hep‐2 cells for isolation. Hexon genes, fiber genes, penton genes, and whole genomes were sequenced. A phylogenetic tree was constructed. RESULTS AND CONCLUSIONS: Forty‐three cases, including 24 laboratory‐confirmed cases and 19 possible cases, were identified. Nurses had the highest attack rate of infection, with a rate of 36.4%. The attack rate for doctors and inpatients was 20.0% and 16.7%, respectively. HAdV55 was the sole pathogen identified during this outbreak. The hexon, fiber, and penton genes from seven isolated HAdV55 stains were sequenced. All these genes showed 100% homology and fell into the HAdV55 [P14H11F14] cluster, indicating that HAdV55 was the single viral strain for the outbreak. While not conclusive, the epidemic investigation revealed that the outbreak was introduced by nurses from sources outside the hospital. It was likely that a transmission from staff to inpatients had occurred.


title: MERS: Progress on the global response, remaining challenges and the way forward

text: Abstract This article summarizes progress in research on Middle East Respiratory Syndrome (MERS) since a FAO-OIE-WHO Global Technical Meeting held at WHO Headquarters in Geneva on 25–27 September 2017. The meeting reviewed the latest scientific findings and identified and prioritized the global activities necessary to prevent, manage and control the disease. Critical needs for research and technical guidance identified during the meeting have been used to update the WHO R&D MERS-CoV Roadmap for diagnostics, therapeutics and vaccines and a broader public health research agenda. Since the 2017 meeting, progress has been made on several key actions in animal populations, at the animal/human interface and in human populations. This report also summarizes the latest scientific studies on MERS since 2017, including data from more than 50 research studies examining the presence of MERS-CoV infection in dromedary camels.


A word of caution and call for cross‐society collaboration to develop surgical guidance about COVID‐19


title: Potent antiviral agent WIN 54954: high specific activity labelling with tritium

text: Abstract Valuable antiviral compound WIN 54954 (2) was tritiated at high specific activity and the product was characterized.


title: Oncology services in corona times: a flash interview among German cancer patients and their physicians

text: OBJECTIVE: Public discussion and health-care systems worldwide have been focusing on the COVID-19 pandemic. Does it have an impact on cancer care today? MATERIALS AND METHODS: The PRIO (“Prevention and Integrative Oncology”) Working Group (German Cancer Society) has initiated an online survey for physicians, medical staff and patients on April 16, 2020. Between April 16 and April 19, 47 doctors and 146 patients filled in the questionnaires. The survey is ongoing. We present the first data. RESULTS: A majority of German patients (76%) and physicians (71%) report moderate or high restriction in their daily life. A minority (patients 25%, physicians 13%) was not worried that necessary treatments or diagnostics were restricted. Organizing cancer care needs more time and efforts for 56% of all reporting doctors. 98% of all oncologists think that restriction of family visits has a negative impact on the mental health of cancer patients. Half of all participants (patients 43%, physicians 47%) expect negative consequences on the physical status of our patients. Patients feel the existing emotional stress in 34% of their physicians. 52% of physicians fear mental and/or physical longtime consequences for themselves. CONCLUSION: There is a high level of mental and physical stress triggered by the present COVID-19 management. After only a few weeks, human resources are limited. They will be the most important key for further health-care services for patients with cancer and other chronic diseases.


title: An indirect enzyme-linked immunosorbent assay for the identification of antibodies to Senecavirus A in swine

text: BACKGROUND: Senecavirus A (SVA), a member of the family Picornaviridae, genus Senecavirus, is a recently identified single-stranded RNA virus closely related to members of the Cardiovirus genus. SVA was originally identified as a cell culture contaminant and was not associated with disease until 2007 when it was first observed in pigs with Idiopathic Vesicular Disease (IVD). Vesicular disease is sporadically observed in swine, is not debilitating, but is significant due to its resemblance to foreign animal diseases, such as foot-and-mouth disease (FMD), whose presence would be economically devastating to the United States. IVD disrupts swine production until foreign animal diseases can be ruled out. Identification and characterization of SVA as a cause of IVD will help to quickly rule out infection by foreign animal diseases. METHODS: We have developed and characterized an indirect ELISA assay to specifically identify serum antibodies to SVA. Viral protein 1, 2 and 3 (VP1, VP2, VP3) were expressed, isolated, and purified from E. coli and used to coat plates for an indirect ELISA. Sera from pigs with and without IVD symptoms as well as a time course following animals from an infected farm, were analyzed to determine the antibody responses to VP1, VP2, and VP3. RESULTS: Antibody responses to VP2 were higher than VP1 and VP3 and showed high affinity binding on an avidity ELISA. ROC analysis of the SVA VP2 ELISA showed a sensitivity of 94.2% and a specificity of 89.7%. Compared to IFA, the quantitative ELISA showed an 89% agreement in negative samples and positive samples from 4–60 days after appearance of clinical signs. Immune sera positive for FMDV, encephalomyocarditis virus, and porcine epidemic diarrhea virus antibodies did not cross-react. CONCLUSIONS: A simple ELISA based on detection of antibodies to SVA VP2 will help to differentially diagnose IVD due to SVA and rule out the presence of economically devastating foreign animal diseases.


title: Pregnancy outcome after exposure to injectable ribavirin during embryogenesis

text: Abstract We describe normal pregnancy outcome in a case of first trimester exposure to injectable ribavirin in a 36-year-old pregnant woman who received three intramuscular injections of ribavirin for suspected SARS. She delivered at 40 weeks of gestation a healthy baby girl. In pediatric follow up at 8 month of age, physical examination and neurodevelopmental milestones were normal.


title: Lifestyle Risk Factors for Cardiovascular Disease in Relation to COVID-19 Hospitalization: A Community-Based Cohort Study of 387,109 Adults in UK

text: AIMS: It is important to identify characteristics of people who may be most at risk of COVID-19 to inform policy and intervention. Little is known about the impact of unhealthy lifestyles including smoking, physical inactivity, obesity, and excessive alcohol intake. We conducted the first large-scale general population study on lifestyle risk factors for COVID-19. METHODS: Prospective cohort study with national registry linkage to hospitalisation for COVID-19. Participants were 387,109 men and women (56.4 ±8.8 yr; 55.1% women) residing in England from UK Biobank study. Physical activity, smoking, and alcohol intake, were assessed by questionnaire at baseline (2006–2010). Body mass index, from measured height and weight, was used as an indicator of overall obesity. Outcome was cases of COVID-19 serious enough to warrant a hospital admission from 16-March-2020 to 26-April-2020. RESULTS: There were 760 COVID-19 cases. After adjustment for age, sex and mutually for each lifestyle factor, physical inactivity (Relative risk, 1.32, 95% confidence interval, 1.10, 1.58), smoking (1.42;1.12, 1.79) and obesity (2.05 ;1.68, 2.49) but not heavy alcohol consumption (1.12; 0.93, 1.35) were all related to COVID-19. We also found a dose-dependent increase in risk of COVID-19 with less favourable lifestyle scores, such that participants in the most adverse category had 4-fold higher risk (4.41; 2.52 – 7.71) compared to people with the most optimal lifestyle. This gradient was little affected after adjustment for a wide range of covariates. Based on UK risk factor prevalence estimates, unhealthy behaviours in combination accounted for up to 51% of the population attributable fraction of severe COVID-19. CONCLUSIONS AND RELEVANCE: Our findings suggest that an unhealthy lifestyle synonymous with an elevated risk of non-communicable disease is also a risk factor for COVID-19 hospital admission, accounting for up to half of severe cases. Adopting simple lifestyle changes could lower the risk of severe infection.


title: Thrombosis and Thromboembolism Related to COVID-19 Increase the level of awareness, lower the threshold of suspicion, and keep following the guidelines

text: [Figure: see text]


title: Pathogenicity of Cryptosporidium parvum—evaluation of an animal infection model

text: Abstract With the intention of developing a standardised method for assessment of pathogenicity of Cryptosporidium parvum, the CPB-0 isolate was studied by propagation in 1-day-old calves followed by inoculation into specific pathogen free (SPF) piglets. The experiment was repeated. Diarrhoea and shedding of oocysts were seen in all animals infected with the CPB-0 isolate. Clinical signs included depression, inappetence, vomiting (exclusively in the piglets), and death. Histological examination at 17 and 19 days post-infection revealed parasitic stages and microscopic changes primarily restricted to colon and rectum. The unintended presence of rotavirus in some of the experimental animals revealed an additive or synergistic effect between rotavirus and C. parvum as indicated by prolonged diarrhoea, increased oocyst shedding, decreased weight gain and elevated levels of serum haptoglobin and serum amyloid A (SAA) in piglets infected simultaneously with both pathogens. The difference in daily weight gain between infected and control animals was significant only for piglets co-infected with rotavirus. The acute phase response of haptoglobin and SAA was characterised by a large individual variation. In piglets, co-infected with rotavirus, the levels of serum haptoglobin were 3.5 and 4.6 times higher in the infected versus the controls 6 and 9dpi, respectively (mean values: 2411 μg/ml±S.D. 2023 and 1840 μg/ml±S.D. 1697). In the controls infected with rotavirus, peak haptoglobin concentration was seen 3dpi (mean: 1022 μg/ml±S.D. 425). Elevated levels of SAA were seen in 1 of 6 piglets infected with C. parvum, and in 5 of 6 piglets co-infected with rotavirus. Tumour necrosis factor alpha (TNFα) was undetectable in all serum samples from piglets. The obvious advantages of the SPF pig model are the naturally acquired intestinal microflora, the development of distinct clinical signs similar to cryptosporidiosis in humans and calves, the size of the animals, and the accessibility of individuals born within a short time span. This makes the model ideal for dose–response studies, evaluation of therapeutic agents as well as for assessment of differences in the clinical response to isolates of diverse genetic background. In conclusion, it was shown that the CPB-0 isolate was pathogenic to calves and piglets at a dose of 2.5×105 oocysts, and that the clinical signs could be replicated during separate experiments. Moreover, diarrhoea, oocyst shedding, body weight changes, histological alterations, and the acute phase response of haptoglobin and SAA were identified as useful parameters for discrimination of isolate-specific differences of pathogenicity.


Lessons from Temporary Telemedicine Initiated owing to Outbreak of COVID-19


title: Host phosphatidic acid phosphatase lipin1 is rate limiting for functional hepatitis C virus replicase complex formation

text: Hepatitis C virus (HCV) infection constitutes a significant health burden worldwide, because it is a major etiologic agent of chronic liver disease, cirrhosis and hepatocellular carcinoma. HCV replication cycle is closely tied to lipid metabolism and infection by this virus causes profound changes in host lipid homeostasis. We focused our attention on a phosphatidate phosphate (PAP) enzyme family (the lipin family), which mediate the conversion of phosphatidate to diacylglycerol in the cytoplasm, playing a key role in triglyceride biosynthesis and in phospholipid homeostasis. Lipins may also translocate to the nucleus to act as transcriptional regulators of genes involved in lipid metabolism. The best-characterized member of this family is lipin1, which cooperates with lipin2 to maintain glycerophospholipid homeostasis in the liver. Lipin1-deficient cell lines were generated by RNAi to study the role of this protein in different steps of HCV replication cycle. Using surrogate models that recapitulate different aspects of HCV infection, we concluded that lipin1 is rate limiting for the generation of functional replicase complexes, in a step downstream primary translation that leads to early HCV RNA replication. Infection studies in lipin1-deficient cells overexpressing wild type or phosphatase-defective lipin1 proteins suggest that lipin1 phosphatase activity is required to support HCV infection. Finally, ultrastructural and biochemical analyses in replication-independent models suggest that lipin1 may facilitate the generation of the membranous compartment that contains functional HCV replicase complexes.


title: Identification and evolutionary dynamics of two novel human coronavirus OC43 genotypes associated with acute respiratory infections: phylogenetic, spatiotemporal and transmission network analyses

text: Human coronavirus OC43 (HCoV-OC43) is commonly associated with respiratory tract infections in humans, with five genetically distinct genotypes (A to E) described so far. In this study, we obtained the full-length genomes of HCoV-OC43 strains from two previously unrecognized lineages identified among patients presenting with severe upper respiratory tract symptoms in a cross-sectional molecular surveillance study in Kuala Lumpur, Malaysia, between 2012 and 2013. Phylogenetic, recombination and comparative genomic analyses revealed two distinct clusters diverging from a genotype D-like common ancestor through recombination with a putative genotype A-like lineage in the non-structural protein (nsp) 10 gene. Signature amino acid substitutions and a glycine residue insertion at the N-terminal domain of the S1 subunit of the spike gene, among others, exhibited further distinction in a recombination pattern, to which these clusters were classified as genotypes F and G. The phylogeographic mapping of the global spike gene indicated that the genetically similar HCoV-OC43 genotypes F and G strains were potentially circulating in China, Japan, Thailand and Europe as early as the late 2000s. The transmission network construction based on the TN93 pairwise genetic distance revealed the emergence and persistence of multiple sub-epidemic clusters of the highly prevalent genotype D and its descendant genotypes F and G, which contributed to the spread of HCoV-OC43 in the region. Finally, a more consistent nomenclature system for non-recombinant and recombinant HCoV-OC43 lineages is proposed, taking into account genetic recombination as an important feature in HCoV evolution and classification.


title: IFNL4 ss469415590 Variant Is Associated with Treatment Response in Japanese HCV Genotype 1 Infected Individuals Treated with IFN-Including Regimens

text: Aim. Eradication of hepatitis C virus (HCV) is still challenging even if interferon- (IFN-) free regimens with direct-acting antiviral agents (DAAs) for HCV-infected individuals are available in clinical practice. IFNL4 is a newly described protein, associated with human antiviral defenses. We investigated whether IFNL4 ss469415590 variant has an effect on the prediction of treatment response in HCV-infected patients treated with IFN-including regimens. Patients and Methods. In all, 185 patients infected with HCV genotype 1 treated with peg-IFN plus ribavirin, with or without telaprevir, were genotyped for IFNL4 ss469415590. We retrospectively investigated whether the role of IFNL4 ss469415590 variant and other factors could predict sustained virological response (SVR) in Japanese patients infected with HCV genotype 1. Results. There were 65.7%, 31.5%, and 2.8% patients in the IFNL4 ss469415590 TT/TT, TT/-G, and -G/-G groups, respectively. SVR rates were 82.1% or 49.3% in patients treated with peg-IFN plus ribavirin with or without telaprevir, respectively. IFNL4 ss469415590 variant and HCV viral loads or IFNL4 ss469415590 variant and early virological response were better predictors of SVR in patients treated with peg-IFN plus ribavirin with or without telaprevir, respectively. Conclusion. In the era of DAAs, measurement of IFNL4 ss469415590 variant could help the prediction of SVR in Japanese HCV genotype 1 infected individuals treated with IFN-including regimens.


La recherche clinique à partir d’entrepôts de données. L’expérience de l’Assistance Publique – Hôpitaux de Paris (AP-HP) à l’épreuve de la pandémie Covid-19


title: Potential of large “first generation” human‐to‐human transmission of 2019‐nCoV

text: To investigate the genetic diversity, time origin, and evolutionary history of the 2019‐nCoV outbreak in China and Thailand, a total of 12 genome sequences of the virus with known sampling date (24 December 2019 and 13 January 2020) and geographic location (primarily Wuhan city, Hubei Province, China, but also Bangkok, Thailand) were analyzed. Phylogenetic and likelihood‐mapping analyses of these genome sequences were performed. On the basis of our results, the star‐like signal and topology of 2019‐nCoV may be indicative of potentially large “first generation” human‐to‐human virus transmission. We estimated that 2019‐nCoV likely originated in Wuhan on 9 November 2019 (95% credible interval: 25 September 2019 and 19 December 2019), and that Wuhan is the major hub for the spread of the 2019‐nCoV outbreak in China and elsewhere. Our results could be useful for designing effective prevention strategies for 2019‐nCoV in China and beyond.


MRI evaluation of the olfactory clefts in patients with SARS-CoV-2 infection revealed an unexpected mechanism for olfactory function loss.


title: Immunology of COVID‐19: mechanisms, clinical outcome, diagnostics and perspectives – a report of the European Academy of Allergy and Clinical Immunology (EAACI)

text: With the worldwide spread of the novel Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) resulting in declaration of a pandemic by the World Health Organization (WHO) on March 11, 2020, the SARS‐CoV‐2‐induced Coronavirus disease‐19 (COVID‐19) has become one of the main challenges of our times. The high infection rate and the severe disease course led to major safety and social restriction measures worldwide. There is an urgent need of unbiased expert knowledge guiding the development of efficient treatment and prevention strategies. This report summarizes current immunological data on mechanisms associated with the SARS‐CoV‐2 infection and COVID‐19 development and progression to the most severe forms. We characterize the differences between adequate innate and adaptive immune response in mild disease and the deep immune dysfunction in the severe multi‐organ disease. The similarities of the human immune response to SARS‐CoV‐2 and the SARS‐CoV and MERS‐CoV are underlined. We also summarize known and potential SARS‐CoV‐2 receptors on epithelial barriers, immune cells, endothelium and clinically involved organs such as lung, gut, kidney, cardiovascular and neuronal system. Finally, we discuss the known and potential mechanisms underlying the involvement of comorbidities, gender and age in development of COVID‐19. Consequently, we highlight the knowledge gaps and urgent research requirements to provide a quick roadmap for ongoing and needed COVID‐19 studies.


title: Reprint of ‘Diseases in marine invertebrates associated with mariculture and commercial fisheries’

text: Abstract Diseases in marine invertebrates are increasing in both frequency and intensity around the globe. Diseases in individuals which offer some commercial value are often well documented and subsequently well studied in comparison to those wild groups offering little commercial gain. This is particularly the case with those associated with mariculture or the commercial fisheries. Specifically, these include many Holothuroidea, and numerous crustacea and mollusca species. Pathogens/parasites consisting of both prokaryotes and eukaryotes from all groups have been associated with diseases from such organisms, including bacteria, viruses, fungi and protozoa. Viral pathogens in particular, appear to be an increasingly important group and research into this group will likely highlight a larger number of diseases and pathogens being described in the near future. Interestingly, although there are countless examples of the spread of disease usually associated with transportation of specific infected hosts for development of aquaculture practices, this process appears to be continuing with no real sign of effective management and mitigation strategies being implicated. Notably, even in well developed countries such as the UK and the US, even though live animal trade may be well managed, the transport of frozen food appears to be less well so and as evidence suggests, even these to have the potential to transmit pathogens when used as a food source for example.


title: SARS-CoV-2: An Update on Potential Antivirals in Light of SARS-CoV Antiviral Drug Discoveries.

text: Coronaviruses (CoVs) are a group of RNA viruses that are associated with different diseases in animals, birds, and humans. Human CoVs (HCoVs) have long been known to be the causative agents of mild respiratory illnesses. However, two HCoVs associated with severe respiratory diseases are Severe Acute Respiratory Syndrome-CoV (SARS-CoV) and Middle East Respiratory Syndrome-CoV (MERS-CoV). Both viruses resulted in hundreds of deaths after spreading to several countries. Most recently, SARS-CoV-2 has emerged as the third HCoV causing severe respiratory distress syndrome and viral pneumonia (known as COVID-19) in patients from Wuhan, China, in December 2019. Soon after its discovery, SARS-CoV-2 spread to all countries, resulting in millions of cases and thousands of deaths. Since the emergence of SARS-CoV, many research groups have dedicated their resources to discovering effective antivirals that can treat such life-threatening infections. The rapid spread and high fatality rate of SARS-CoV-2 necessitate the quick discovery of effective antivirals to control this outbreak. Since SARS-CoV-2 shares 79% sequence identity with SARS-CoV, several anti-SARS-CoV drugs have shown promise in limiting SARS-CoV-2 replication in vitro and in vivo. In this review, we discuss antivirals described for SARS-CoV and provide an update on therapeutic strategies and antivirals against SARS-CoV-2. The control of the current outbreak will strongly depend on the discovery of effective and safe anti-SARS-CoV-2 drugs.


title: Sequence of the S gene from a virulent British field isolate of transmissible gastroenteritis virus

text: Abstract Subgenomic mRNA from a virulent field isolate of porcine transmissible gastroenteritis virus (TGEV), strain FS772/70, was used to produce cDNA. The cDNA from three overlapping clones was sequenced by the chain termination method and two open reading frames (ORFs) were identified. The largest ORF, 4350bp, encoded a polypeptide of 1449 amino acids of relative molecular mass (Mr) 159811, which contained 33 potential N-linked glycosylation sites, a cysteine-rich region, and a potential transmembrane region. The C-terminal half of this ORF showed homology to the S proteins of four other coronaviruses. The other ORF consisted of the 3'-end of a gene with homology to the carboxyl terminus of the F2 subunit of infectious bronchitis virus (IBV) RNA polymerase.


title: Clinical and epidemiological characteristics of pediatric SARS-CoV-2 infections in China: A multicenter case series

text: BACKGROUND: As of April 18, 2020, over 2,000,000 patients had been diagnosed with coronavirus disease-2019 (COVID-19) globally, and more than 140,000 deaths had been reported. The clinical and epidemiological characteristics of adult patients have been documented recently. However, information on pediatric patients is limited. We describe the clinical and epidemiological characteristics of pediatric patients to provide valuable insight into the early diagnosis and assessment of COVID-19 in children. METHODS AND FINDINGS: This retrospective, observational study involves a case series performed at 4 hospitals in West China. Thirty-four pediatric patients with COVID-19 were included from January 27 to February 23, 2020. The final follow-up visit was completed by March 16, 2020. Clinical and epidemiological characteristics were analyzed on the basis of demographic data, medical history, laboratory tests, radiological findings, and treatment information. Data analysis was performed for 34 pediatrics patients with COVID-19 aged from 1 to 144 months (median 33.00, interquartile range 10.00–94.25), among whom 14 males (41%) were included. All the patients in the current study presented mild (18%) or moderate (82%) forms of COVID-19. A total of 48% of patients were noted to be without a history of exposure to an identified source. Mixed infections of other respiratory pathogens were reported in 16 patients (47%). Comorbidities were reported in 6 patients (18%). The most common initial symptoms were fever (76%) and cough (62%). Expectoration (21%), vomiting (12%), and diarrhea (12%) were also reported in a considerable portion of cases. A substantial increase was detected in serum amyloid A for 17 patients (among 20 patients with available data; 85%) and in high-sensitivity C-reactive protein for 17 patients (among 29 patients with available data; 59%), whereas a decrease in prealbumin was noticed in 25 patients (among 32 patients with available data; 78%). In addition, significant increases in the levels of lactate dehydrogenase and α-hydroxybutyrate dehydrogenase were detected in 28 patients (among 34 patients with available data; 82%) and 25 patients (among 34 patients with available data; 74%), respectively. Patchy lesions in lobules were detected by chest computed tomographic scans in 28 patients (82%). Ground-glass opacities, which were a typical feature in adults, were rare in pediatric patients (3%). Rapid radiologic progression and a late-onset pattern of lesions in the lobules were also noticed. Lesions in lobules still existed in 24 (among 32 patients with lesions; 75%) patients that were discharged, although the main symptoms disappeared a few days after treatment. All patients were discharged, and the median duration of hospitalization was 10.00 (8.00–14.25) days. The current study was limited by the small sample size and a lack of dynamic detection of inflammatory markers. CONCLUSIONS: Our data systemically presented the clinical and epidemiological features, as well as the outcomes, of pediatric patients with COVID-19. Stratified analysis was performed between mild and moderate cases. The findings offer new insight into early identification and intervention in pediatric patients with COVID-19.


title: Emerging pharmacological therapies for ARDS: COVID-19 and beyond

text: ARDS, first described in 1967, is the commonest form of acute severe hypoxemic respiratory failure. Despite considerable advances in our knowledge regarding the pathophysiology of ARDS, insights into the biologic mechanisms of lung injury and repair, and advances in supportive care, particularly ventilatory management, there remains no effective pharmacological therapy for this syndrome. Hospital mortality at 40% remains unacceptably high underlining the need to continue to develop and test therapies for this devastating clinical condition. The purpose of the review is to critically appraise the current status of promising emerging pharmacological therapies for patients with ARDS and potential impact of these and other emerging therapies for COVID-19-induced ARDS. We focus on drugs that: (1) modulate the immune response, both via pleiotropic mechanisms and via specific pathway blockade effects, (2) modify epithelial and channel function, (3) target endothelial and vascular dysfunction, (4) have anticoagulant effects, and (5) enhance ARDS resolution. We also critically assess drugs that demonstrate potential in emerging reports from clinical studies in patients with COVID-19-induced ARDS. Several therapies show promise in earlier and later phase clinical testing, while a growing pipeline of therapies is in preclinical testing. The history of unsuccessful clinical trials of promising therapies underlines the challenges to successful translation. Given this, attention has been focused on the potential to identify biologically homogenous subtypes within ARDS, to enable us to target more specific therapies ‘precision medicines.’ It is hoped that the substantial number of studies globally investigating potential therapies for COVID-19 will lead to the rapid identification of effective therapies to reduce the mortality and morbidity of this devastating form of ARDS.


title: Consensus français sur la pratique de la chirurgie oncologique ORL pendant la pandémie de COVID-19

text: RESUME Dans le contexte de la pandémie de COVID-19, des conseils spécifiques semblent nécessaires concernant la prise en charge des patients atteints de cancers ORL. La règle est de limiter au maximum le flux de patients afin de réduire les risques de contamination par le virus SARS-Cov-2 aussi bien des patients que du personnel soignant, particulièrement exposé en ORL. L’objectif est de limiter le risque de perte de chance pour le patient et d’anticiper le flux de patients atteints de cancers à traiter à la fin de l’épidémie, en tenant compte du degré d’urgence, de la lourdeur de la chirurgie, du risque de contamination de l’équipe soignante (trachéotomie) et de la situation locale (saturation ou non de l’hôpital et des services de réanimation).


title: Novel analytic tools for the study of porcine reproductive and respiratory syndrome virus (PRRSv) in endemic settings: lessons learned in the U.S.

text: Since its emergence in the late 1980’s, the porcine reproductive and respiratory syndrome virus (PRRSv) has posed a significant challenge to the pig industry worldwide. Since then, a number of epidemiological tools have been created to support control and eventual elimination of the disease at the farm and regional levels. Still, many aspects of the disease dynamics are yet-to-be elucidated, such as what are the economically optimal control strategies at the farm and regional level, what is the role that the voluntary regional control programs may play, how to optimize the use of molecular tools for surveillance and monitoring in infected settings, what is the full impact of the disease in a farm, or what is the relative contribution of alternative transmission routes on the occurrence of PRRSv outbreaks. Here, we summarize a number of projects demonstrating the use of novel analytical tools in the assessment of PRRSv epidemiology in the United States. Results presented demonstrate how quantitative analysis of routinely collected data may help in understanding regional epidemiology of PRRSv and to quantify its full impact, and how the integration of phylodynamic methods as a standard tool for molecular surveillance of PRRSv might help to inform control and prevention strategies in high-risk epidemiological situations. Ultimately, these tools will help to support PRRSv control at farm and regional levels in endemically infected settings.


title: A new method to cluster DNA sequences using Fourier power spectrum

text: Abstract A novel clustering method is proposed to classify genes and genomes. For a given DNA sequence, a binary indicator sequence of each nucleotide is constructed, and Discrete Fourier Transform is applied on these four sequences to attain respective power spectra. Mathematical moments are built from these spectra, and multidimensional vectors of real numbers are constructed from these moments. Cluster analysis is then performed in order to determine the evolutionary relationship between DNA sequences. The novelty of this method is that sequences with different lengths can be compared easily via the use of power spectra and moments. Experimental results on various datasets show that the proposed method provides an efficient tool to classify genes and genomes. It not only gives comparable results but also is remarkably faster than other multiple sequence alignment and alignment-free methods.


title: Impacto de la investigación infectológica en la salud y el bienestar del ser humano

text: Resumen La prolongación de la vida, así como el avance en su calidad, acaecido de manera formidable durante las últimas décadas se debe en gran parte al control de las enfermedades infecciosas. Este control se ha logrado en buena parte gracias al progreso de la investigación biomédica, a estas alturas más que centenaria, fruto del esfuerzo de miles de investigadores que han aportado sus “granos de arena”, generando una sumatoria de nuevo conocimiento. En determinadas ocasiones el conocimiento generado permite una especie de “salto cuántico” o “breakthroughs” con un impacto rápido y evidente en la disminución de la mortalidad y/o morbilidad. Esta es una revisión no sistemática basada en la reflexión personal, con los sesgos que esta conlleva, sobre los hitos en la investigación infectológica reciente que han impactado en la salud humana y lo que podría esperarse en el futuro cercano. Al final se incluye literatura recomendada que profundiza varios de los tópicos presentados. Summary The increase in lifespan together with an improved quality of life during the past decades has been formidable and due in a large part to the control of infectious disease. This control has been made possible through the efforts of thousands of infectious disease related researchers whom have contributed their “grain of salt”; the sum of which has created significant new knowledge and progress in the field. In certain instances this knowledge allows significant breakthroughs with rapid and obvious impact on the reduction of mortality and/or morbidity. This is a non-systematic review based on personal reflection, with the biases that this entails, on relatively recent infectious disease research milestones that have had a significant impact in human health and what can be envisioned for the near future. Recommended literature that further explores some of the topics discussed is included.


title: Randomized, double-blind, placebo-controlled clinical trial to assess the safety and effectiveness of a novel dual-action oral topical formulation against upper respiratory infections

text: BACKGROUND: Current prevention options for upper respiratory infections (URIs) are not optimal. We conducted a randomized, double-blinded, placebo-controlled pilot clinical trial to evaluate the safety and efficacy of ARMS-I™ (currently marketed as Halo™) in the prevention of URIs. METHODS: ARMS-I is patented novel formulation for the prevention and treatment of influenza, comprising a broad-spectrum antimicrobial agent (cetylpyridinium chloride, CPC) and components (glycerin and xanthan gum) that form a barrier on the host mucosa, thus preventing viral contact and invasion. Healthy adults (18–45 years of age) were randomized into ARMS-I or placebo group (50 subjects each). The drug was sprayed intra-orally (3× daily) for 75 days. The primary objectives were to establish whether ARMS-I decreased the frequency, severity or duration of URIs. Secondary objectives were to evaluate safety, tolerability, rate of virus detection, acceptability and adherence; effect on URI-associated absenteeism and medical visits; and effect of prior influenza vaccination on study outcomes. RESULTS: Of the 94 individuals who completed the study (placebo: n = 44, ARMS-I: n = 50), six presented with confirmed URI (placebo: 4, ARMS-I: 2), representing a 55% relative reduction, albeit this was statistically not significant). Influenza, coronavirus or rhinovirus were detected in three participants; all in the placebo group. Moreover, frequency of post-treatment exit visits was reduced by 55% in ARMS-I compared to the placebo group (N = 4 and 2, respectively). Fever was reported only in the placebo group. ARMS-I significantly reduced the frequency and severity of cough and sore throat, and duration of cough (P ≤ .019 for all comparisons). ARMS-I was safe, well tolerated, had high acceptability and high adherence to medication use. Medical visits occurred only in the placebo group while absenteeism did not differ between the two arms. Prior influenza vaccination had no effect on study outcome. CONCLUSIONS: This randomized proof-of-concept clinical trial demonstrated that ARMS-I tended to provide protection against URIs in the enrolled study participants, while reducing severity and duration of cough and sore throat. A clinical trial with a larger number of study participants is warranted. TRIAL REGISTRATION: ClinicalTrials.gov NCT02644135 (retrospectively registered). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-016-2177-8) contains supplementary material, which is available to authorized users.


title: Comparative stigma of HIV/AIDS, SARS, and Tuberculosis in Hong Kong

text: Abstract This study compares public stigma towards three types of infectious diseases— human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS), severe acute respiratory syndrome (SARS), and tuberculosis (TB)—tests an attribution model of stigma, and explores the relationships between stigma and public attitudes towards government policies in Hong Kong. Using a population-based telephone survey, 3011 Hong Kong Chinese adults were randomly assigned to one of the three disease conditions and were interviewed about their attitudes and beliefs towards the assigned disease. Findings showed that public stigma was the highest towards HIV/AIDS, followed by TB and SARS. Using multi-sample model structural equation modeling, we found that the attributions of controllability, personal responsibility, and blame were applicable in explaining stigma across three disease types. Knowledge about the disease had no significant effect on stigma. Participants with less stigmatizing views had significantly more favorable attitudes towards government policies related to the diseases. The study is an important attempt in understanding the attributional mechanisms of stigma towards infectious diseases. Implications for stigma reduction and promotion of public awareness and disease prevention are discussed.


title: Enhanced receptor binding of SARS-CoV-2 through networks of hydrogen-bonding and hydrophobic interactions

text: Molecular dynamics and free energy simulations have been carried out to elucidate the structural origin of differential protein–protein interactions between the common receptor protein angiotensin converting enzyme 2 (ACE2) and the receptor binding domains of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [A. E. Gorbalenya et al., Nat. Microbiol. 5, 536–544 (2020)] that causes coronavirus disease 2019 (COVID-19) [P. Zhou et al., Nature 579, 270–273 (2020)] and the SARS coronavirus in the 2002–2003 (SARS-CoV) [T. Kuiken et al., Lancet 362, 263–270 (2003)] outbreak. Analysis of the dynamic trajectories reveals that the binding interface consists of a primarily hydrophobic region and a delicate hydrogen-bonding network in the 2019 novel coronavirus. A key mutation from a hydrophobic residue in the SARS-CoV sequence to Lys417 in SARS-CoV-2 creates a salt bridge across the central hydrophobic contact region, which along with polar residue mutations results in greater electrostatic complementarity than that of the SARS-CoV complex. Furthermore, both electrostatic effects and enhanced hydrophobic packing due to removal of four out of five proline residues in a short 12-residue loop lead to conformation shift toward a more tilted binding groove in the complex in comparison with the SARS-CoV complex. On the other hand, hydrophobic contacts in the complex of the SARS-CoV–neutralizing antibody 80R are disrupted in the SARS-CoV-2 homology complex model, which is attributed to failure of recognition of SARS-CoV-2 by 80R.


title: Genetic variability of human angiotensin‐converting enzyme 2 (hACE2) among various ethnic populations

text: BACKGROUND: There appears to be large regional variation for susceptibility, severity, and mortality for COVID‐19 infections. Numerous potential factors could explain the wide variability in the number of infections and death among the countries. We examined genetic differences in the human angiotensin‐converting enzyme 2 (hACE2) gene, as its receptor serves as a cellular entry for SARS‐CoV‐2. At present, there is a paucity of data regarding the differences for ACE2 polymorphisms and expression levels between ethnicities. METHODS: We compared the allele frequency of mutations between European and East Asians. Molecular dynamic simulation were performed to investigate the influences of significant mutant on protein structure. The binding free energies were calculated between S protein and hACE2. We also examined hACE2 gene expression in eight global populations from HapMap3. RESULTS: Four missense mutations showed significant minor allele frequency difference between Asians and Caucasians. Molecular dynamic demonstrated that two of these variants (K26R and I468V) may affect binding characteristics between S protein of the virus and hACE2 receptor. We also noted marginal differences in gene expression for some populations in HapMap3 as compared to the Chinese population. CONCLUSION: Our studies reveal subtle changes in the genetics of hACE2 between human populations, but the magnitude of the difference was small and the significance is not clear in the absence of further in vitro and functional studies.


Late STEMI and NSTEMI patients’ emergency calling in CoVID-19 outbreak


title: Simultaneous typing and HA/NA subtyping of influenza A and B viruses including the pandemic influenza A/H1N1 2009 by multiplex real-time RT-PCR

text: Abstract Pandemic influenza A/H1N1 2009 and seasonal influenza viruses are currently co-circulating worldwide. A rapid, sensitive, and specific assay for distinguishing pandemic influenza A/H1N1 2009 from seasonal influenza viruses and for subtyping seasonal influenza A viruses could aid in the surveillance and control of these viral infections. Here, such a multiplex real-time RT-PCR (rRT-PCR) assay for typing influenza A and B viruses and the pandemic influenza A/H1N1 2009 is developed. This assay can also subtype seasonal influenza A viruses simultaneously. The analytical sensitivity is 10–104 copies/reaction. The coefficients of variation of inter-assay and intra-assay are 0.04–0.45% and 0.08–0.97%, respectively. The new multiplex rRT-PCR assay is more sensitive in subtyping seasonal influenza viruses than the conventional PCR techniques. Results obtained with this assay for the detection of pandemic influenza A/H1N1 2009 are highly consistent (96.88%) with those achieved using the US CDC's rRT-PCR protocol. A sample identified as “pandemic influenza A/H1N1 2009 positive” by the US CDC's rRT-PCR was reclassified correctly as subtype H3N2 using this assay. Taken together, this new multiplex rRT-PCR protocol could be an important tool for improving diagnosis and management of the pandemic influenza A/H1N1 2009 and seasonal influenza viruses.


title: Coronavirus mRNA synthesis: Identification of novel transcription initiation signals which are differentially regulated by different leader sequences

text: Abstract The mRNA synthesis of mouse hepatitis virus (MHV) has been proposed to be the result of interaction between the leader RNA and the intergenic sites. Previously, we have identified a transcription initiation site (for mRNA 2-1), which is more efficiently transcribed by viruses containing two copies of UCUAA sequence in the leader RNA than by those with three copies. In this study, we have identified several sites which are regulated in the opposite way, namely, they are efficiently transcribed by the leader RNA with three UCUAA copies but not by those with two copies. These sites were characterized by primer extension and amplification by polymerase chain reaction. One of these sites is in the gene 3 region of a recombinant virus between A59 and JHM strains of MHV. Another is in the gene 2 region of MHV-1 strain. Both of these sites have a sequence similar to but different from the consensus transcription initiation signal (UCUAAUCUAUC and UUUAAUCUU, as opposed to UCUAAAC). These two novel intergenic sequences are not present in the genome of the JHM strain, consistent with the absence of these mRNAs in the JHM-infected cells. The discovery of this type of transcription initiation site provides additional evidence for the importance of the leader RNA in the transcription initiation of MHV mRNAs.


title: Immunogenicity of SARS inactivated vaccine in BALB/c mice

text: Abstract Severe acute respiratory syndrome (SARS) is a serious infectious threat to public health. To create a novel trial vaccine and evaluate its potency, we attempted to generate a SARS inactivated vaccine using SARS coronavirus (SARS-CoV) strain F69 treated with formaldehyde and mixed with Al(OH)3. Three doses of the vaccine were used to challenge three groups of BALB/c mice. We found that the mice exhibited specific IgM on day 4 and IgG on day 8. The peak titers of IgG were at day 47 in low-dose group (1:19,200) and high-dose group (1:38,400) whereas in middle-dose group (1:19,200), the peak was at day 40. On day 63, the IgG levels reached a plateau. Neutralization assay demonstrated that the antisera could protect Vero-E6 cells from SARS-CoV's infection. Analysis of the antibody specificity revealed that the mouse antisera contained a mixture of antibodies specifically against the structure proteins of SARS-CoV. Furthermore, the mouse antisera conferred higher amount of antibodies against protein N, polypeptide S4 and S2 than those of proteins M and 3CL. These findings suggest that the inactivated SARS-CoV could preserve its antigenicity and the inactivated vaccine can stimulate mice to produce high levels of antibodies with neutralization activity. Results also suggest that polypeptides originating from protein N or S might be a potential target for the generation of a recombinant SARS vaccine.


title: Growth of a murine coronavirus in a microcarrier cell culture system

text: Abstract The growth of the murine coronavirus MHV-A59 on murine DBT cells adapted to dextran-made Cytodex 1 microcarriers was studied in comparison with cells grown on plastic dishes. With a microcarrier concentration of 5 g/l in spinner flasks, a density of 3 × 106 cells/ml was reached in 7 days. Under these conditions, cells supported virus growth to the same extent as when they were grown on the plastic substratum. This was shown by a similar development of virus-induced syncytia, the release of an equivalent number of infectious progeny virions per cell, similar recoveries observed after concentration and purification and an identical appearance of the purified virus under the electron microscope. On the other hand, the technical convenience of microcarriers and the ease of scale-up emphasize their potential for the growth of coronaviruses.


title: In vivo and in vitro models of demyelinating diseases XV. Differentiation influences the regulation of coronavirus infection in primary explants of mouse CNS

text: Abstract Mouse oligodendrocytes and astrocytes, in primary cerebral explant cultures, were infected with JHMV and MHV3 coronaviruses. Contrary to previous findings with neural cells from the rat (S. Beushausen and S. Dales, 1985, Virology 141, 89–101), these agents show no discrimination in the tropism and have the ability to replicate in either type of murine glial cell. Effects of the differentiation inducer dbcAMP on levels of the myelin-specific enzyme 2′:3′-cyclic nucleotide-3′-phosphohydrolase (CNPase) activity and virus replication were determined. In the mouse system there was a gradual, continuous elevation of CNPase beyond 30 days whereas in comparable rat cell cultures maximum CNPase enhancement is elicited within 21 days (F. A. McMorris,1983, J. Neurochem. 41, 506–515). After dbcAMP treatment replication of both coronaviruses was profoundly suppressed in murine oligodendrocytes, consistent with our findings on JHMV replication in treated rat oligodendrocytes. By contrast the replication of JHMV and MHV3 in dbcAMP-treated murine astrocytes was influenced only marginally. These findings provide further support for the hypothesis that susceptibility of rodents to CNS infection by coronaviruses is determined, in part, by the age-related maturation process of oligodendrocytes.


COVID-19 in Pregnancy: Consider Thromboembolic Disorders and Thromboprophylaxis


title: Herd level estimation of probability of disease freedom applied on the Norwegian control program for bovine respiratory syncytial virus and bovine coronavirus

text: Abstract A national control program against bovine respiratory syncytial virus (BRSV) and bovine coronavirus (BCV) was launched in Norway in 2016. A key strategy in the program is to test for presence of antibodies and protect test-negative herds from infection. Because these viruses are endemic, the rate of re-introduction can be high, and a disease-free status will become more uncertain as time from testing elapses. The aim of this study was to estimate the probability of freedom (PostPFree) from BRSV and BCV antibodies over time by use of bulk tank milk (BTM) antibody-testing, geographic information and animal movement data, and to validate the herd-level estimates against subsequent BTM testing. BTM samples were collected from 1148 study herds in West Norway in 2013 and 2016, and these were analyzed for BRSV and BCV antibodies. PostPFree was calculated for herds that were negative in 2013/2014, and updated periodically with new probabilities every three months. Input variables were test sensitivity, the probability of introduction through animal purchase and local transmission. Probability of introduction through animal purchase was calculated by using real animal movement data and herd prevalence in the region of the source herd. The PostPFree from the final three months in 2015 was compared to BTM test results from March 2016 using a Wilcoxon Rank Sum Test. The probability of freedom was generally high for test-negative herds immediately after testing, reflecting the high sensitivity of the tests. It did however, decrease with time since testing, and was greatly affected by purchase of livestock. When comparing the median PostPFree for the final three months to the test results in 2016, it was significantly lower (p < 0.01) for test positive herds. Furthermore, there was a large difference in the proportion of test positive herds between the first and fourth quartile of PostPFree. The results show that PostPFree provides a better estimate of herd-level BTM status for both BRSV and BCV than what can be achieved by relying solely on the previous test-result.


title: Acute human bocavirus infection in MDS patient, Cologne, Germany

text: • A clinical case of persisting and reactivated HBoV infection is described. • HBoV can be detected in iliac crest in MDS patients. • The current episode appears to be a reactivation of the HBoV-1 strain that was detected 5 years ago in a colorectal biopsy of the patient.


title: Use of Reporter Genes in the Generation of Vaccinia Virus-Derived Vectors

text: Vaccinia virus (VACV) is one of the most extensively-studied viruses of the Poxviridae family. It is easy to genetically modify, so it has become a key tool for many applications. In this context, reporter genes facilitate the study of the role of foreign genes introduced into the genome of VACV. In this review, we describe the type of reporter genes that have been used to generate reporter-expressing VACV and the applications of the recombinant viruses obtained. Reporter-expressing VACV are currently employed in basic and immunology research, in the development of vaccines and cancer treatment.


title: Respiratory viruses among children with non-severe community-acquired pneumonia: A prospective cohort study

text: Abstract Background Community-acquired pneumonia (CAP) causes a major burden to the health care system among children under-5 years worldwide. Information on respiratory viruses in non-severe CAP cases is scarce. Objectives To estimate the frequency of respiratory viruses among non-severe CAP cases. Study design Prospective study conducted in Salvador, Brazil. Out of 820 children aged 2–59 months with non-severe CAP diagnosed by pediatricians (respiratory complaints and radiographic pulmonary infiltrate/consolidation), recruited in a clinical trial (ClinicalTrials.gov Identifier NCT01200706), nasopharyngeal aspirate samples were obtained from 774 (94.4%) patients and tested for 16 respiratory viruses by PCRs. Results Viruses were detected in 708 (91.5%; 95%CI: 89.3–93.3) cases, out of which 491 (69.4%; 95%CI: 65.9–72.7) harbored multiple viruses. Rhinovirus (46.1%; 95%CI: 42.6–49.6), adenovirus (38.4%; 95%CI: 35.0–41.8), and enterovirus (26.5%; 95%CI: 23.5–29.7) were the most commonly found viruses. The most frequent combination comprised rhinovirus plus adenovirus. No difference was found in the frequency of RSVA (16.1% vs. 14.6%; P = 0.6), RSVB (10.9% vs. 13.2%; P = 0.4) influenza (Flu) A (6.3% vs. 5.1%; P = 0.5), FluB (4.5% vs. 1.8%; P = 0.09), parainfluenza virus (PIV) 1 (5.1% vs. 2.8%; P = 0.2), or PIV4 (7.7% vs. 4.1%; P = 0.08), when children with multiple or sole virus detection were compared. Conversely, rhinovirus, adenovirus, enterovirus, bocavirus, PIV2, PIV3, metapneumovirus, coronavirus OC43, NL63, 229E were significantly more frequent among cases with multiple virus detection. Conclusions Respiratory viruses were detected in over 90% of the cases, out of which 70% had multiple viruses. Several viruses are more commonly found in multiple virus detection whereas other viruses are similarly found in sole and in multiple virus detection.


title: Dynamics of SARS-coronavirus HR2 domain in the prefusion and transition states

text: Abstract The envelope glycoproteins S1 and S2 of severe acute respiratory syndrome coronavirus (SARS-CoV) mediate viral entry by conformational change from a prefusion state to a postfusion state that enables fusion of the viral and target membranes. In this work we present the characterization of the dynamic properties of the SARS-CoV S2-HR2 domain (residues 1141–1193 of S) in the prefusion and newly discovered transition states by NMR 15N relaxation studies. The dynamic properties of the different states, which are stabilized under different experimental conditions, extend the current model of viral membrane fusion and give insight into the design of structure-based antagonists of SARS-CoV in particular, as well as other enveloped viruses such as HIV.


title: 8 INFECTIOUS DISEASES

text: Publisher Summary The emergence of new pathogens, or the concern about bioterrorism, has brought an added urgency to the development of more efficient and rapid methods to detect pathogens and predict their potential virulence. Till date, DNA testing in microbiology has been directed predominantly to the detection of organisms that are difficult to culture in vitro, or for various reasons the growth is unlikely. DNA analysis can be used successfully in infections in which there is a mix of pathogens. Apart from the straightforward diagnostic applications, DNA microbiological testing has been used to detect antimicrobial resistance or toxigenic forms of E. coli. More recently, the availability of DNA technology to quantitate HCV and HIV has been useful in planning and monitoring treatment. The pathogenesis of many infections, particularly viral ones, can also be realized from experimental strategies based on light and electron microscopy, cell culture and immunoassay. The advantages that are provided by DNA techniques include the ability to detect latent (non-replicating) viruses and to localize their genomes to nuclear or cytoplasmic regions within cells. Nucleic acid probe techniques (NAT) can also be manipulated to enable a broad spectrum of serotypes to be detectable. This is particularly valuable in those emerging infections where the underlying serotypes are unknown.


Nursing Home Characteristics Associated with COVID-19 Deaths in Connecticut, New Jersey, and New York


title: Pancreatitis in Cats

text: Abstract Pancreatitis was considered a rare disease in the cat until a couple of decades ago when several retrospective studies of severe acute pancreatitis were published. It was apparent that few of the diagnostic tests of value in the dog were helpful in cats. With increasing clinical suspicion, availability of abdominal ultrasonography, and introduction of pancreas-specific blood tests of increasing utility, it is now accepted that acute pancreatitis is probably almost as common in cats as it is in dogs, although the etiology(s) remain more obscure. Pancreatitis in cats often co-exists with inflammatory bowel disease, less commonly with cholangitis, and sometimes with both. Additionally, pancreatitis may trigger hepatic lipidosis, while other diseases, such as diabetes mellitus, may be complicated by pancreatitis. Therapy is similar to that used in dogs, with added emphasis on early nutritional support to prevent hepatic lipidosis. Less is known about chronic pancreatitis than the acute form, but chronic pancreatitis is more common in cats than it is in dogs and may respond positively to treatment with corticosteroids.


title: An evolving arsenal: viral RNA detection by RIG-I-like receptors

text: RIG-I-like receptors (RLRs) utilize a specialized, multi-domain architecture to detect and respond to invasion by a diverse set of viruses. Structural similarities among these receptors provide a general mechanism for double strand RNA recognition and signal transduction. However, each RLR has developed unique strategies for sensing the specific molecular determinants on subgroups of viral RNAs. As a means to circumvent the antiviral response, viruses escape RLR detection by degrading, or sequestering or modifying their RNA. Patterns of variation in RLR sequence reveal a continuous evolution of the protein domains that contribute to RNA recognition and signaling.


title: Intravenous immunoglobulin fails to improve ARDS in patients undergoing ECMO therapy

text: BACKGROUND: Acute respiratory distress syndrome (ARDS) is associated with high mortality rates. ARDS patients suffer from severe hypoxemia, and extracorporeal membrane oxygenation (ECMO) therapy may be necessary to ensure oxygenation. ARDS has various etiologies, including trauma, ischemia-reperfusion injury or infections of various origins, and the associated immunological responses may vary. To support the immunological response in this patient collective, we used intravenous IgM immunoglobulin therapy to enhance the likelihood of pulmonary recovery. METHODS: ARDS patients admitted to the intensive care unit (ICU) who were placed on ECMO and treated with (IVIG group; n = 29) or without (control group; n = 28) intravenous IgM-enriched immunoglobulins for 3 days in the initial stages of ARDS were analyzed retrospectively. RESULTS: The baseline characteristics did not differ between the groups, although the IVIG group showed a significantly reduced oxygenation index compared to the control group. We found no differences in the length of ICU stay or ventilation parameters. We did not find a significant difference between the groups for the extent of inflammation or for overall survival. CONCLUSION: We conclude that administration of IgM-enriched immunoglobulins as an additional therapy did not have a beneficial effect in patients with severe ARDS requiring ECMO support. TRIAL REGISTRATION: Clinical Trials: NCT02961166; retrospectively registered.


Covid 19-Journal de Bord - 25 mars 2020 - La création d’une réanimation éphémère–Entretien avec Thomas Lescot


title: Detection of mumps virus RNA in cerebrospinal fluid of patients with neuromyelitis optica

text: Neuromyelitis optica (NMO) is an acute inflammatory disease that preferentially involves the optic nerves and spinal cord. Although many infectious agents, including mumps virus, are postulated to have a role in the pathogenesis of multiple sclerosis (MS), the relationship between NMO and infectious agents remains uncertain. To investigate the relationship between NMO and viruses that have special affinity for the central nervous system, we performed a nested polymerase chain reaction (PCR) to detect mumps virus or enterovirus RNA in cerebrospinal fluid samples from 13 patients with MS, 8 with NMO and 20 with other neurological diseases (ONDs). Nested PCR was positive for mumps virus in 2 (25%) of NMO patients, but in none of those with MS and ONDs. Moreover, nested PCR results became negative in the remission phase in the two PCR-positive NMO patients. Mumps virus may have some role in the pathogenesis of NMO.


title: Modelling COVID-19

text: As the COVID-19 pandemic continues, mathematical epidemiologists share their views on what models reveal about how the disease has spread, the current state of play and what work still needs to be done.


title: Translational recoding: canonical translation mechanisms reinterpreted

text: During canonical translation, the ribosome moves along an mRNA from the start to the stop codon in exact steps of one codon at a time. The collinearity of the mRNA and the protein sequence is essential for the quality of the cellular proteome. Spontaneous errors in decoding or translocation are rare and result in a deficient protein. However, dedicated recoding signals in the mRNA can reprogram the ribosome to read the message in alternative ways. This review summarizes the recent advances in understanding the mechanisms of three types of recoding events: stop-codon readthrough, –1 ribosome frameshifting and translational bypassing. Recoding events provide insights into alternative modes of ribosome dynamics that are potentially applicable to other non-canonical modes of prokaryotic and eukaryotic translation.


Rules of Engagement: The Principles of Underserved Global Health Volunteerism


title: Should We Adapt the Prescription Criteria for Specific Treatments for Migraine Due to the COVID‐19 Pandemic?

text: We have read with great interest the article by Ali et al regarding the delay in Onabotulinumtoxin (OBT) during the COVID-19 pandemic in three patients published in Headache (1). During the pandemic, Headache units have had to adapt by replacing face-to-face care with phone calls or visits using electronic means. Unfortunately, in many cases this has led to deterioration in patient treatment (2). As discussed in the article by Ali et al, many patients understand the situation, but as spread of COVID-19 and the associated lockdown extend over time, their viewpoint is prone to shift (1).


title: Structural and Functional Analysis of the Surface Protein of Human Coronavirus OC43

text: Abstract The two surface glycoproteins S and HE of human coronavirus OC43 (HCV-OC43) were isolated from the viral membrane and purified. Only the S protein was able to agglutinate chicken erythrocytes, indicating that this viral protein is the major hemagglutinin of HCV-OC43. The receptor determinant recognized by this virus on the surface of erythrocytes is N-acetyl-9-O-acetylneuraminic acid (Neu5,9Ac2) which is also used by bovine coronavirus for attachment to cells. By analyzing erythrocytes containing different amounts of Neu5,9Ac2 in either of two linkage types, it was found that there are subtle differences in the affinity of both viruses for 9-O-acetylated sialic acid. Bovine coronavirus was more efficient in recognizing low amounts of Neu5,9Ac2 β2,3 linked to galactose, whereas HCV-OC43 was superior with respect to the β2,6 linkage. The gene coding for the S protein of HCV-OC43 was cloned and sequenced. A large open reading frame predicts a polypeptide of 150 kDa in the unglycosylated form. A protein of about 190 kDa is expected if the 20 potential glycosylation sites are used for attachment of N-linked oligosaccharide side chains. These predictions were confirmed by in vitro transcription and translation of the gene in the presence or absence of canine pancreatic microsomal membranes. A high degree of sequence homology was found between the S proteins of HCV-OC43 and bovine coronavirus. Structural and functional analyses of more strains should help to identify the location of the sialic acid-binding site.


title: Characterization of G-Quadruplex Motifs in espB, espK, and cyp51 Genes of Mycobacterium tuberculosis as Potential Drug Targets

text: G-quadruplex structure forming motifs are among the most studied evolutionarily conserved drug targets that are present throughout the genome of different organisms and susceptible to influencing various biological processes. Here we report highly conserved potential G-quadruplex motifs (PGQs) in three essential genes (espK, espB, and cyp51) among 160 strains of the Mycobacterium tuberculosis genome. Products of these genes are involved in pathways that are responsible for virulence determination of bacteria inside the host cell and its survival by maintaining membrane fluidity. The espK and espB genes are essential players that prevent the formation of mature phagolysosome and antigen presentation by host macrophages. The cyp51 is another PGQ-possessing gene involved in sterol biosynthesis pathway and membrane formation. In the present study, we revealed the formation of stable intramolecular parallel G-quadruplex structures by Mycobacterium PGQs using a combination of techniques (NMR, circular dichroism [CD], and gel electrophoresis). Next, isothermal titration calorimetry (ITC) and CD melting analysis demonstrated that a well-known G-quadruplex ligand, TMPyP4, binds to and stabilizes these PGQ motifs. Finally, polymerase inhibition and qRT-PCR assays highlight the biological relevance of PGQ-possessing genes in this pathogen and demonstrate that G-quadruplexes are potential drug targets for the development of effective anti-tuberculosis therapeutics.


title: Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin

text: Since the SARS outbreak 18 years ago, a large number of severe acute respiratory syndrome related coronaviruses (SARSr-CoV) have been discovered in their natural reservoir host, bats1-4. Previous studies indicated that some of those bat SARSr-CoVs have the potential to infect humans5-7. Here we report the identification and characterization of a novel coronavirus (nCoV-2019) which caused an epidemic of acute respiratory syndrome in humans, in Wuhan, China. The epidemic, started from December 12th, 2019, has caused 198 laboratory confirmed infections with three fatal cases by January 20th, 2020. Full-length genome sequences were obtained from five patients at the early stage of the outbreak. They are almost identical to each other and share 79.5% sequence identify to SARS-CoV. Furthermore, it was found that nCoV-2019 is 96% identical at the whole genome level to a bat coronavirus. The pairwise protein sequence analysis of seven conserved non-structural proteins show that this virus belongs to the species of SARSr-CoV. The nCoV-2019 virus was then isolated from the bronchoalveolar lavage fluid of a critically ill patient, which can be neutralized by sera from several patients. Importantly, we have confirmed that this novel CoV uses the same cell entry receptor, ACE2, as SARS-CoV.


Haemophilus parainfluenzae endocarditis with multiple cerebral emboli in a pregnant woman with coronavirus


title: Diagnostic performance of multiplex PCR on pulmonary samples versus nasopharyngeal aspirates in community-acquired severe lower respiratory tract infections

text: Abstract Background PCR-based techniques for the diagnosis of community- acquired severe lower respiratory tract infections are becoming the standard of care. However, their relative ability to identify either atypical bacteria or viruses that cause LRTI from clinical samples from various sources is yet to be determined. Objectives and study design The aim of our study was to compare the diagnostic yield of nasopharyngeal aspirates with that of pulmonary samples for the etiological diagnosis of severe acute lower respiratory tract infections by multiplex PCR. Patients were adults with community-acquired pneumonia or acute exacerbation of chronic obstructive pulmonary disease. Results We obtained concordant results for 81 (79%) of the 103 pairs of samples. In 14 of the 22 discordant results, more pathogens were evidenced in the lower respiratory tract samples. Conclusions Pulmonary samples had a similar diagnostic sensitivity for virus detection by multiplex PCR as nasopharyngeal aspirates. In contrast, in our study, the diagnostic efficacy of pulmonary samples for Legionella pneumophila over simple aspirates was clearly superior.


Letter to editor in response to article “COVID-19: From bench to bedside” (Singh et al.)


title: Quantitative and sensitive detection of SARS coronavirus nucleocapsid protein using quantum dots‐conjugated RNA aptamer on chip

text: BACKGROUND: Globally, severe acute respiratory syndrome coronavirus (SARS‐CoV) is a newly emerging virus that causes SARS with high mortality rate in infected people. The nucleocapsid (N) protein of the severe acute respiratory syndrome (SARS)‐associated coronavirus (SARS‐CoV) is an important antigen for the early diagnosis of SARS and the detection of diseases. Here, a new quantum dots (QDs)‐conjugated RNA aptamer with high sensitivity and rapidity is proposed for the detection of SARS‐CoV N protein using an on chip system. RESULTS: A QDs‐conjugated RNA aptamer can specifically hybridize on the immobilized SARS‐CoV N protein on the surface of a glass chip. Detection is based on the optical signal variation of a QDs‐supported RNA aptamer interacting on an immobilized protein chip. Using an optical QDs‐based RNA aptamer chip, SARS N protein was detected at concentrations as low as 0.1 pg mL(−1). CONCLUSIONS: It was demonstrated that the QDs‐conjugated RNA aptamer could interact on a designed chip specifically and sensitively. This device could form a QDs‐conjugated biosensor prototype chip for SARS‐CoV N protein diagnosis. The proposed visual SARS‐CoV N protein detection technique may avoid the limitations of other reported methods because of its high sensitivity, good specificity, ease of use, and the ability to perform one‐spot monitoring. Copyright © 2011 Society of Chemical Industry


title: rVSVΔG-ZEBOV-GP (also designated V920) recombinant vesicular stomatitis virus pseudotyped with Ebola Zaire Glycoprotein: Standardized template with key considerations for a risk/benefit assessment

text: The Brighton Collaboration Viral Vector Vaccines Safety Working Group (V3SWG) was formed to evaluate the safety and characteristics of live, recombinant viral vector vaccines. A recent publication by the V3SWG described live, attenuated, recombinant vesicular stomatitis virus (rVSV) as a chimeric virus vaccine for HIV-1 (Clarke et al., 2016). The rVSV vector system is being explored as a platform for development of multiple vaccines. This paper reviews the molecular and biological features of the rVSV vector system, followed by a template with details on the safety and characteristics of a rVSV vaccine against Zaire ebolavirus (ZEBOV). The rVSV-ZEBOV vaccine is a live, replication competent vector in which the VSV glycoprotein (G) gene is replaced with the glycoprotein (GP) gene of ZEBOV. Multiple copies of GP are expressed and assembled into the viral envelope responsible for inducing protective immunity. The vaccine (designated V920) was originally constructed by the National Microbiology Laboratory, Public Health Agency of Canada, further developed by NewLink Genetics Corp. and Merck & Co., and is now in final stages of registration by Merck. The vaccine is attenuated by deletion of the principal virulence factor of VSV (the G protein), which also removes the primary target for anti-vector immunity. The V920 vaccine caused no toxicities after intramuscular (IM) or intracranial injection of nonhuman primates and no reproductive or developmental toxicity in a rat model. In multiple studies, cynomolgus macaques immunized IM with a wide range of virus doses rapidly developed ZEBOV-specific antibodies measured in IgG ELISA and neutralization assays and were fully protected against lethal challenge with ZEBOV virus. Over 20,000 people have received the vaccine in clinical trials; the vaccine has proven to be safe and well tolerated. During the first few days after vaccination, many vaccinees experience a mild acute-phase reaction with fever, headache, myalgia, and arthralgia of short duration; this period is associated with a low-level viremia, activation of anti-viral genes, and increased levels of chemokines and cytokines. Oligoarthritis and rash appearing in the second week occur at a low incidence, and are typically mild-moderate in severity and self-limited. V920 vaccine was used in a Phase III efficacy trial during the West African Ebola epidemic in 2015, showing 100% protection against Ebola Virus Disease, and it has subsequently been deployed for emergency control of Ebola outbreaks in central Africa. The template provided here provides a comprehensive picture of the first rVSV vector to reach the final stage of development and to provide a solution to control of an alarming human disease.


title: Suicidal Ideation During the COVID-19 Pandemic: The Role of Insomnia

text: There is growing concern over the potential for increased suicide risk in vulnerable populations as the COVID-19 pandemic unfolds. To contextualize this risk during the first weeks of the nation-wide lockdown efforts, we had 1,013 U.S. adults complete questionnaires assessing worries over COVID-19, insomnia severity, and suicidal ideation. Anxiety about COVID-19 correlated positively with insomnia severity and suicidal ideation. Analysis revealed that the statistical association between pandemic fears and suicidal thinking was fully accounted for by insomnia severity, suggesting that interventions aimed at improving sleep may be useful in reducing suicide risk during the current pandemic.


title: Séances par téléphone dans le contexte du Covid-19: le cadre et ses limites

text: Abstract To deal with the Covid 19 pandemic, health protection measures require changes to our clinical practices. Faced up with the unprecedented nature of this situation, the liberal psychotherapist is led to rethink some aspects of the framework of his practice in order to preserve the thread of the transferential relationship. The authors develop a clinical reflection on the clinical setting in a pandemic period by exploring in particular the dynamics of telephone sessions. For telephone interviews, the question of the sound envelope is central, in particular regarding the psychic function of silence. We choose to illustrate our point with short vignettes than by relying on long-term clinical cases, more likely to represent the variety of new clinical situations encountered and the questions that accompany them. This article introduces his point by recounting the plague epidemic in ancient Greece to show the impact of the environment on humans and its collective fantasy implications. Being faced up with death, contamination, the invisible enemy brings out a palpable concern. It is indeed quite remarkable that these same reactions and concerns in front of death caused by the pandemic match whith what is related by Thucydides who survived the plague which affected Athens during the Peloponnesian War. In another context, Winnicott highlights the place and importance of the therapeutic environment. It is both a question of adjusting the framework according to the context while maintaining certain intangible aspects representing the permanence of the link and its framework. A framework cannot exist without being kept, which is equivalent to thinking of the framework above all as an internal framework, questioning the clinician about what he values and what he makes sense in his practice. In the current context, these questions arise from the perspective of a certain flexibility, depending on the human context (child, adolescent, consultations, etc.) or external context (crisis linked to a virus, etc.) showing that it is more than never question of exercising on a case-by-case basis, taking into account changes in the environment. The initial observation during this period of confinement concerns the fact that some patients contact a therapist for the first time by telephone and wish to initiate psychotherapy (during this period) when they explain that such an initiative was not possible. despite the difficulties already encountered in the past. But there is also the opposite case: patients who have no intention of continuing the work already started during this time. Thus, faced up with the injunction of confinement, they show themselves in the psychic impossibility of following the treatment by other means such as, for example, telephone sessions. In this perspective, the silence on the phone takes on a different tone; silence reveals itself to be a source of greater anxiety than in presence: the presence of bodies, of its movements perceptible as imperceptible, of a gesture that carries or accompanies the senses, breathing, the visual context of the office and of its "decor", represent as many essential elements in the usual capacity of the frame; in the absence of these basic sensory elements, silence can be experienced as a void, or even a gap in the bond, opening Pandora’s box of paranoid fantasies acting unconsciously.If silence is representative of the whole framework, it promotes in this context the partialization of the clinician’s body reduced to one ear and not to a whole body. Here, it is the change of framework that mobilizes the difference, established by Mr. Klein, between the partial and total object; this circumstance neo-framework could therefore call for regressive movements, undoing the silence of its symbolic function when the bodies are present.