title: WU polyomavirus detected in respiratory tract specimens from young children in Japan

text: Polyomaviruses (PyV) WU and KI are reportedly associated with respiratory tract disease (RTD) worldwide but their incidence is unclear in Japan. In a 2 year prospective study, WU/KIPyV were detected in 48 (13.9%) and in five (1.4%) of 345 children hospitalized with lower RTD, respectively. The seasonal distribution was observed in spring and early summer. Other respiratory viruses were co‐detected in 51% of PyV‐positive patients, but eight (2.3%) of the WUPyV‐positive patients were negative for other known pathogens.


title: Caspase cleavage of viral proteins, another way for viruses to make the best of apoptosis

text: Viral infection constitutes an unwanted intrusion that needs to be eradicated by host cells. On one hand, one of the first protective barriers set up to prevent viral replication, spread or persistence involves the induction of apoptotic cell death that aims to limit the availability of the cellular components for viral amplification. On the other hand, while they completely depend on the host molecular machinery, viruses also need to evade the cellular responses that are meant to destroy them. The existence of numerous antiapoptotic products within the viral kingdom proves that apoptosis constitutes a major threat that should better be bypassed. Among the different strategies developed to deal with apoptosis, one is based on what viruses do best: backfiring the cell on itself. Several unrelated viruses have been described to take advantage of apoptosis induction by expressing proteins targeted by caspases, the key effectors of apoptotic cell death. Caspase cleavage of these proteins results in various consequences, from logical apoptosis inhibition to more surprising enhancement or attenuation of viral replication. The present review aims at discussing the characterization and relevance of this post-translational modification that adds a new complexity in the already intricate host–apoptosis–virus triangle.


title: Molecular Characterization and Phylogenetic Analysis of Porcine Epidemic Diarrhea Viruses Associated with Outbreaks of Severe Diarrhea in Piglets in Jiangxi, China 2013

text: Porcine epidemic diarrhea (PED), caused by porcine epidemic diarrhea virus (PEDV), is a highly contagious, acute enteric viral disease of swine characterized by vomiting, watery diarrhea, dehydration and death. To identify and characterize the field PEDVs associated with the outbreaks of severe diarrhea in piglets in Jiangxi, 2013, the complete genome sequences of two representative strains of PEDV, designated CH/JX-1/2013 and CH/JX-2/2013, were determined and analyzed. The genome sequences of both emergent Jiangxi PEDV strains, CH/JX-1/2013 and CH/JX-2/2013, were 28,038 nucleotides in length excluding 3’ poly (A) tail. Compared to the PEDV CV777 strain, CH/JX-1/2013 and CH/JX-2/2013 had some unique genetic characteristics in the proximal region of the 5´-UTRs. Phylogenetic analysis of the complete genomes and the structural proteins revealed that CH/JX-1/2013 and CH/JX-2/2013 had a close relationship with post-2010 Chinese PEDV strains and US strains identified in 2013. The nucleotide identity between the two Jiangxi strains (CH/JX-1/2013 and CH/JX-2/2013) and 30 strains of PEDV identified ante-2010 and post-2010 ranged from 96.3–97.0% and 97.3–99.7%, respectively. Multiple nucleotide and deduced amino acid mutations were observed in the ORF1a/b, S, ORF3, E, M and N genes among the current field PEDV strains when compared to the CV777 strain. Some of the mutations altered the amino acid charge and hydrophilicity, and notably, there was an amino acid substitution in the middle of one neutralizing epitope (L1371I) of the S gene of both CH/JX-1/2013 and CH/JX-2/2013. Taken together, the accumulated genetic variations of the current field PEDV strains might have led to antigenic changes of the viruses, which might confer the less effectiveness or failure of the CV777-based vaccines currently being widely used in Jiangxi, China.


title: Three Novel COVID-19 Pneumonia Cases Successfully Treated With Lopinavir/Ritonavir

text: Following the first case of Coronavirus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-Cov-2), in Wuhan, China, in December 2019, it has spread worldwide. An outbreak in Japan occurred on a cruise ship, and this was followed by community-acquired COVID-19. Herein, we report three cases of COVID-19 that presented pneumonia following admission to Kitasato University Hospital. Patients were admitted based on the positive result of real-time reverse transcriptase–polymerase chain reaction (RT-PCR) tests for COVID-19 nucleic acid. All patients were diagnosed as suffering from non-severe COVID-19 pneumonia and were successfully treated with Lopinavir/Ritonavir (LPV/r). LPV/r could be an option for treating non-severe COVID-19 pneumonia in general and even in elderly patients.


title: État actuel de la prise en charge des infections rhinosinusiennes aiguës de l'enfant en France

text: Résumé Un groupe de médecins généralistes et multidisciplinaire de spécialistes contribue à définir les différentes formes de sinusites ou rhinosinusites aiguës de l'enfant à partir des principaux symptômes et signes cliniques. Le rôle des pathologies associées telles que l'allergie, les troubles immunitaires est envisagé. L'incidence, la présentation clinique et la prise en charge des complications sont présentées. Les indications des examens radiologiques et biologiques sont analysées. La prise en charge médicale en particulier, la place et le type des antibiotiques sont discutés. Des propositions de prise en charge selon des situations cliniques rencontrées en pratique sont présentées. Abstract A multidisciplinary panel of specialists and general practitioners provided definitions for the different forms of acute pediatric rhinosinusitis, with a description of the main symptoms and signs. They emphasized the role of concomitant systemic diseases, such as allergy and immunological disorders. Incidence, description, and management of complications are presented. They also provided the indications for radiological examination and microbiological investigations. The adequate medical management, particularly the place and the type of antibiotics, is analyzed and discussed, and guidelines for practical situations are suggested.


Apnea neonatal como manifestación inicial de infección por sars-cov2


title: Recommended prophylactic and management strategies for severe acute respiratory syndrome coronavirus 2 infection in transplant recipients

text: Abstract Since December 2019, increasing attention has been paid to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in Wuhan, China. SARS-CoV-2 primarily invades the respiratory tract and lungs, leading to pneumonia and other systemic disorders. The effect of SARS-CoV-2 in transplant recipients has raised significant concerns, especially because there is a large population of transplant recipients in China. Based on the current epidemic situation, this study reviewed publications on this virus and coronavirus disease 2019 (COVID-19), analyzed common features of respiratory viral pneumonias, and presented the currently reported clinical characteristics of COVID-19 in transplant recipients to improve strategies regarding the diagnosis and treatment of COVID-19 in this special population.


title: What caused lymphopenia in SARS and how reliable is the lymphokine status in glucocorticoid-treated patients?

text: Severe Acute Respiratory Syndrome (SARS) outbreak in 2002–03 caused morbidity in over 8000 individuals and mortality in 744 in 29 countries. Lymphopenia along with neutrophilia was a feature of SARS, as it is in respiratory syncytial virus (RSV) and Ebola infections, to name a few. Direct infestation of lymphocytes, neutrophils and macrophages by SARS coronavirus (CoV) has been debated as a cause of lymphopenia, but there is no convincing data. Lymphopenia can be caused by glucocorticoids, and thus any debilitating condition has the potential to induce lymphopenia via stress mechanism involving the hypothalamic–pituitary–adrenal axis. Cortisol levels are elevated in patients with RSV and Ebola, and cortisol was higher in SARS patients with lymphopenia before any steroid therapy. Glucocorticoids also down-regulate the production of proinflammatory lymphokines. Because of the insidious presentation, SARS was treated with antibacterial, antiviral and supra-physiological doses of glucocorticoids. Treatment with glucocorticoids complicated the issue regarding lymphopenia, and certainly calls into question the status of lymphokines and their prognostic implications in SARS.


title: Rapid De-Escalation and Triaging Patients in Community-Based Palliative Care

text: Abstract Context The COVID-19 pandemic created a rapid and unprecedented shift in our medical system. Medical providers, teams, and organizations have needed to shift their visits away from face-to-face visits and toward telehealth (both by phone and through video). Palliative care teams who practice in the community setting are faced with a difficult task: How do we actively triage the most urgent visits while keeping our vulnerable patients safe from the pandemic? Measures The following are recommendations created by the Palo Alto Medical Foundation Palliative Care and Support Services team to help triage and coordinate for timely, safe, and effective palliative care in the community and outpatient setting during the ongoing COVID-19 pandemic. Patients are initially triaged based on location followed by acuity. Interdisciplinary care is implemented using strict infection control guidelines in the setting of limited personal protective equipment (PPE) resources. We implement thorough screening for COVID-19 symptoms at multiple levels before a patient is seen by a designated provider. Conclusions/Lessons Learned We recommend active triaging, communication, frequent screening for COVID-19 symptoms for palliative care patients been evaluated in the community setting. An understanding of infection risk, mutual consent between designated providers, patients, and their families are crucial to maintaining safety while delivering community-based palliative care during the COVID-19 pandemic.


title: Study on the resistance of severe acute respiratory syndrome-associated coronavirus

text: Abstract In this study, the persistence of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) was observed in feces, urine and water. In addition, the inactivation of SARS-CoV in wastewater with sodium hypochlorite and chlorine dioxide was also studied. In vitro experiments demonstrated that the virus could only persist for 2 days in hospital wastewater, domestic sewage and dechlorinated tap water, while 3 days in feces, 14 days in PBS and 17 days in urine at 20°C. However, at 4°C, the SARS-CoV could persist for 14 days in wastewater and at least 17 days in feces or urine. SARS-CoV is more susceptible to disinfectants than Escherichia coli and f2 phage. Free chlorine was found to inactivate SARS-CoV better than chlorine dioxide. Free residue chlorine over 0.5mg/L for chlorine or 2.19mg/L for chlorine dioxide in wastewater ensures complete inactivation of SARS-CoV while it does not inactivate completely E. coli and f2 phage.


title: A public antibody lineage that potently inhibits malaria infection by dual binding to the circumsporozoite protein

text: Immunization with attenuated Plasmodium falciparum sporozoites (PfSPZ) has been shown to be protective, but the features of the antibody response induced by this treatment remain unclear. To investigate this response at high resolution, we isolated IgM and IgG monoclonal antibodies from Tanzanian volunteers who were immunized by repeated injection of irradiated PfSPZ and who were found to be protected from controlled human malaria infection (CHMI) with infectious homologous PfSPZ. All IgG monoclonals isolated bound to P. falciparum circumsporozoite protein (PfCSP) and recognized distinct epitopes in the N-terminus, NANP repeat region, and C-terminus. Strikingly, the most effective antibodies, as assessed in a humanized mouse model, bound not only to the repeat region, but also to a minimal peptide at the PfCSP N-terminal junction that is not in the RTS,S vaccine. These dual-specific antibodies were isolated from different donors and used VH3-30 or VH3-33 alleles carrying tryptophan or arginine at position 52. Using structural and mutational data, we describe the elements required for germline recognition and affinity maturation. Our study provides potent neutralizing antibodies and relevant information for lineage-targeted vaccine design and immunization strategies.


title: Genome analysis of a G9P[23] group A rotavirus isolated from a dog with diarrhea in China

text: Abstract Genotype G9 is an emerging genotype among species A rotavirus (RVA) circulating in humans and pigs worldwide. In this study, an RVA strain designated RVA/Dog-tc/CHN/SCCD-A/2017/G9P[23] was isolated in cell culture from a pet dog stool sample with acute diarrhea, and its whole genome was sequenced. The genotype constellation of SCCD-A was G9-P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1. All genome segments except the VP1 gene were closely related to the genes from porcine RVA strains or porcine-like human RVA strains. On the other hand, the VP1 gene clustered in a distinct lineage only with that of a G5P[6] porcine-like human RVA, preventing the identification of the exact host species origin, but very unlikely to be originated from human RVA. In addition, phylogenetic analysis showed that the G9 VP7 gene of SCCD-A clustered into a novel sublineage within the lineage III of G9. This first isolation of a G9P[23] RVA from a pet dog may justify the exploration of the role dogs play in the interaction of RVA circulating in pigs and humans.


title: Subgenomic RNAs with nucleotide sequences derived from RNAs 1 and 2 of cucumber mosaic virus can act as messenger RNAsin Vitro

text: Abstract Encapsidated RNAs of cucumber mosaic virus (CMV) were analyzed by hybridization to specific probes after gel electrophoresis. [32P]-complementary DNA (cDNA) probes were prepared by transcription of genomic RNA 1 and RNA 2 nucleotide sequences that had been cloned in a bacteriophage M13 vector. Probes that correspond to unique sequences near the 3′ ends of RNA 1 and RNA 2 revealed over 20 smaller RNAs. The subgenomic RNAs derived from each genomic RNA were analyzed more definitively by hybrid selection from total encapsidated RNA, using minus DNA clones derived from sequences in either RNA 1 or RNA 2, and a cDNA probe for the 3′ sequence conserved among all the genomic RNAs. Different patterns of over 20 minor RNA species, which were 3′-coterminal with RNAs 1 and 2, were detected, and they were reproducible irrespective of the host, cucumber orNicotiana clevelandii, from which the virus was isolated. The same RNA patterns were found in RNA extracted from the particulate fraction of CMV-infected cucumber orN. clevelandii. In order to determine whether the subgenomic RNAs could function as messenger RNAs, hybrid-selected RNAs were tested byin vitro translation, using the rabbit reticulocyte lysate. The subgenomic RNAs from RNA 1 produced over 10 major polypeptides from Mr 27,000 to Mr 90,000 all of which could be translated from a few RNA species over about 2,300 nucleotides long. The 3′-coterminal subgenomic RNAs derived from RNA 2 gave less than 10 products from Mr , 17,000 toMr 85,000. The smallest product (Mr 17,000) was produced by an RNA about 880 nucleotides long, whereas longer RNAs from 1400 to 2500 nucleotides were efficient mRNAs for polypeptides from Mr 30,000 up to the largest translation products consistent with the size of the RNA.


RASH MACULOPAPULOSO COMO MANIFESTACIÓN INICIAL DE INFECCIÓN POR SARS-CORONAVIRUS-2


title: Rapid Identification of Emerging Pathogens: Coronavirus

text: We describe a new approach for infectious disease surveillance that facilitates rapid identification of known and emerging pathogens. The process uses broad-range polymerase chain reaction (PCR) to amplify nucleic acid targets from large groupings of organisms, electrospray ionization mass spectrometry for accurate mass measurements of PCR products, and base composition signature analysis to identify organisms in a sample. We demonstrate this principle by using 14 isolates of 9 diverse Coronavirus spp., including the severe acute respiratory syndrome–associated coronavirus (SARS-CoV). We show that this method could identify and distinguish between SARS and other known CoV, including the human CoV 229E and OC43, individually and in a mixture of all 3 human viruses. The sensitivity of detection, measured by using titered SARS-CoV spiked into human serum, was ≈1 PFU/mL. This approach, applicable to the surveillance of bacterial, viral, fungal, or protozoal pathogens, is capable of automated analysis of >900 PCR reactions per day.


title: Interpretable detection of novel human viruses from genome sequencing data

text: Viruses evolve extremely quickly, so reliable methods for viral host prediction are necessary to safeguard biosecurity and biosafety alike. Novel human-infecting viruses are difficult to detect with standard bioinformatics workflows. Here, we predict whether a virus can infect humans directly from next-generation sequencing reads. We show that deep neural architectures significantly outperform both shallow machine learning and standard, homology-based algorithms, cutting the error rates in half and generalizing to taxonomic units distant from those presented during training. We propose a new approach for convolutional filter visualization to disentangle the information content of each nucleotide from its contribution to the final classification decision. Nucleotide-resolution maps of the learned associations between pathogen genomes and the infectious phenotype can be used to detect virulence-related genes in novel agents, as we show here for the SARS-CoV-2 coronavirus, unknown before it caused a COVID-19 pandemic in 2020.


title: Association energetics of membrane spanning α-helices

text: Since Popot and Engelman proposed the ‘two-stage’ thermodynamic framework for dissecting the energetics of helical membrane protein folding, scientists have endeavored to measure the free energies of helix–helix associations to better understand how interactions between helices stabilize and specify native membrane protein folds. Chief among the biophysical tools used to probe these energies are sedimentation equilibrium analytical ultracentrifugation, fluorescence resonance energy transfer, and thiol disulfide interchange experiments. Direct and indirect comparisons of thermodynamic results suggest that differences in helix–helix stabilities between micelles and bilayers may not be as large as previously anticipated. Genetic approaches continue to become more quantitative, and the propensities for helices to interact in bacterial membranes generally correlate well with in vitro measurements.


title: Nipah shell disorder, modes of infection, and virulence

text: Abstract The Nipah Virus (NiV) was first isolated during a 1998–9 outbreak in Malaysia. The outbreak initially infected farm pigs and then moved to humans from pigs with a case-fatality rate (CFR) of about 40%. After 2001, regular outbreaks occurred with higher CFRs (~71%, 2001–5, ~93%, 2008–12). The spread arose from drinking virus-laden palm date sap and human-to-human transmission. Intrinsic disorder analysis revealed strong correlation between the percentage of disorder in the N protein and CFR (Regression: r2 = 0.93, p < 0.01, ANOVA: p < 0.01). Distinct disorder and, therefore, genetic differences can be found in all three group of strains. The fact that the transmission modes of the Malaysia strain are different from those of the Bangladesh strains suggests that the correlations may also be linked to the modes of viral transmission. Analysis of the NiV and related viruses suggests links between modes of transmission and disorder of not just the N protein but, also, of M shell protein. The links among shell disorder, transmission modes, and virulence suggest mechanisms by which viruses are attenuated as they passed through different cell hosts from different animal species. These have implications for development of vaccines and epidemiological molecular analytical tools to contain outbreaks.


title: Development of a New Resequencing Pathogen Microarray Based Assay for Detection of Broad-Spectrum Respiratory Tract Viruses in Patients with Community-Acquired Pneumonia

text: A Resequencing Pathogen Microarray (RPM) is a single, highly multiplexed assay for detecting and differentiating similarly related pathogens by using closely overlapping probe sets to determine a target organism’s nucleotide sequence. In this study, a new RPM (RPM-IVDC1) that consisted of 224-bp detector tiles corresponding to 9 influenza A subtypes, 11 rhinoviruses, 28 enteroviruses and 38 other respiratory viruses was developed and optimized to provide individual and simultaneous detection sensitivities ranging from 15 to 750 genomic copies for 16 common respiratory pathogens. A total of 110 consecutive patients with community-acquired pneumonia (CAP) admitted to 5 district general hospitals in Beijing during a 1-year period were assessed using the new assay. Among the children (under age 5) and adult patients (above age 18), respiratory syncytial virus (RSV) and rhinovirus (RV) were the most common etiological agents, respectively, which is consistent with reference assays. Atypical pathogens that may cause CAP-like illness, including rubella virus, measles virus, influenza type C virus, human herpesvirus (HHV) were also detected. The results show the capability of RPM-IVDC1 for the accurate detection and identification of multiple virus types, which may be of significant use in epidemic surveillance and outbreak investigations of atypical pathogens.


title: Diagnosis and Management of Pneumonia in the Emergency Department

text: Pneumonia is a condition that is often treated by emergency physicians. This article reviews the diagnosis and management of pneumonia in the emergency department and highlights dilemmas in diagnostic testing, use of blood and sputum cultures, hospital admission decisions, infection control, quality measures for pneumonia care, and empiric antimicrobial therapy.


title: A Web Resource for Designing Subunit Vaccine Against Major Pathogenic Species of Bacteria

text: Evolution has led to the expansion of survival strategies in pathogens including bacteria and emergence of drug resistant strains proved to be a major global threat. Vaccination is a promising strategy to protect human population. Reverse vaccinology is a more robust vaccine development approach especially with the availability of large-scale sequencing data and rapidly dropping cost of the techniques for acquiring such data from various organisms. The present study implements an immunoinformatic approach for screening the possible antigenic proteins among various pathogenic bacteria to systemically arrive at epitope-based vaccine candidates against 14 pathogenic bacteria. Thousand four hundred and fifty nine virulence factors and Five hundred and forty six products of essential genes were appraised as target proteins to predict potential epitopes with potential to stimulate different arms of the immune system. To address the self-tolerance, self-epitopes were identified by mapping on 1000 human proteome and were removed. Our analysis revealed that 21proteins from 5 bacterial species were found as virulent as well as essential to their survival, proved to be most suitable vaccine target against these species. In addition to the prediction of MHC-II binders, B cell and T cell epitopes as well as adjuvants individually from proteins of all 14 bacterial species, a stringent criteria lead us to identify 252 unique epitopes, which are predicted to be T-cell epitopes, B-cell epitopes, MHC II binders and Vaccine Adjuvants. In order to provide service to scientific community, we developed a web server VacTarBac for designing of vaccines against above species of bacteria. This platform integrates a number of tools that includes visualization tools to present antigenicity/epitopes density on an antigenic sequence. These tools will help users to identify most promiscuous vaccine candidates in a pathogenic antigen. This server VacTarBac is available from URL (http://webs.iiitd.edu.in/raghava/vactarbac/).


title: The global effects of Covid-19-induced uncertainty()

text: We estimate a VAR with world-level variables to simulate the effects of the Covid-19 outbreak-related uncertainty shock. We find a peak (cumulative over one year) negative response of world output of 1.6% (14%).


Infectious diarrhoea in foals


title: THE COMMON COLD

text: The common cold has intrigued physicians and the general public for centuries. It has been defined as an acute epidemic respiratory disease characterized by mild coryzal symptoms of rhinorrhea, nasal obstruction, and sneezing. The nasal discharge is usually copious and thin during the first 2 days of illness, then it generally becomes more viscous and purulent. 22 The disease is self-limited. Symptoms may persist for 2 days to more than 14 days; however, the cold may abort after only 1 day. Fever, cough, sore throat, or lacrimation may or may not be present. The common cold is of itself harmless, but bacterial invasion frequently follows the initial infection. It is these secondary invaders that may produce disorders of serious consequence. The common cold is the most frequent acute illness in the United States and throughout the industrialized world. About half the population gets at least one cold every year. 5 Colds account for 40% of all time lost from jobs among employed people (23 million days of work per year) and about 30% of absenteeism from schools (26 million school days per year). Estimates vary, but the average preschool child has somewhere between 4 and 10 colds per year, and the average adult has about two to four colds per year. The actual cost of caring for patients with colds in US physicians' offices is estimated to be $1.5 billion annually. 64 Seasonal patterns of infection can be identified for some of the various types of viruses that are responsible for outbreaks of the common cold. For example, available epidemiologic data suggest early fall and late spring are the most common times to find more outbreaks of rhinovirus. Respiratory syncytial virus (RSV) tends to follow winter and spring incidence, with a peak number of cases found mainly in January. Parainfluenza types 1 and 2 seem to peak during the autumn, whereas parainfluenza type 3 has an increased incidence during the late spring. Adenoviruses and coronaviruses tend to produce epidemics during the winter and spring (Fig. 1) This article presents data concerning the cause, pathogenesis, and treatment of the common cold, as well as discussion of the available diagnostic tests and their use in formulating differential diagnoses.


title: A Novel Pathogenic Mammalian Orthoreovirus from Diarrheic Pigs and Swine Blood Meal in the United States

text: Since May 2013, outbreaks of porcine epidemic diarrhea have devastated the U.S. swine industry, causing immense economic losses. Two different swine enteric coronaviruses (porcine epidemic diarrhea virus and Delta coronavirus) have been isolated from the affected swine population. The disease has been reported from at least 32 states of the United States and other countries, including Mexico, Peru, Dominican Republic, Canada, Columbia, Ecuador, and Ukraine, with repeated outbreaks in previously infected herds. Here we report the isolation and characterization of a novel mammalian orthoreovirus 3 (MRV3) from diarrheic feces of piglets from these outbreaks in three states and ring-dried swine blood meal from multiple sources. MRV3 could not be isolated from healthy or pigs that had recovered from epidemic diarrhea from four states. Several MRV3 isolates were obtained from chloroform-extracted pig feces or blood meal in cell cultures or developing chicken embryos. Biological characterization of two representative isolates revealed trypsin resistance and thermostability at 90°C. NextGen sequencing of ultrapurified viruses indicated a strong homology of the S1 segment to mammalian and bat MRV3. Neonatal piglets experimentally infected with these viruses or a chloroform extract of swine blood meal developed severe diarrhea and acute gastroenteritis with 100% mortality within 3 days postinfection. Therefore, the novel porcine MRV3 may contribute to enteric disease along with other swine enteric viruses. The role of MRV3 in the current outbreaks of porcine epidemic diarrhea in the United States remains to be determined, but the pathogenic nature of the virus warrants further investigations on its epidemiology and prevalence.


Abstract for the 8th International congress, Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases


title: A novel real-time RT-PCR assay for influenza C tested in Peruvian children

text: Abstract Background Influenza C virus (ICV) is associated with acute respiratory illness. Yet ICV remains under recognized, with most previous studies using only culture to identify cases. Objectives To develop a sensitive and specific real-time RT-PCR assay for ICV that allows for rapid and accurate detection in a clinical or research setting. Study design Multiple ICV sequences obtained from GenBank were analyzed, including 141 hemagglutinin-esterase (HE), 106 matrix (M), and 97 nucleoprotein (NP) sequences. Primers and probes were designed based on conserved regions. Multiple primer-probe sets were tested against multiple ICV strains. Results The ICV M and NP genes offered the most conserved sequence regions. Primers and probes based on newer sequence data offered enhanced detection of ICV, especially for low titer specimens. An NP-targeted assay yielded the best performance and was capable of detecting 10–100 RNA copies per reaction. The NP assay detected multiple clinical isolates of ICV collected in a field epidemiology study conducted in Peru. Conclusions We report a new real-time RT-PCR assay for ICV with high sensitivity and specificity.


title: ACE2: The Key Molecule for Understanding the Pathophysiology of Severe and Critical Conditions of COVID-19: Demon or Angel?

text: Recently, the SARS-CoV-2 induced disease COVID-19 has spread all over the world. Nearly 20% of the patients have severe or critical conditions. SARS-CoV-2 exploits ACE2 for host cell entry. ACE2 plays an essential role in the renin–angiotensin–aldosterone system (RAAS), which regulates blood pressure and fluid balance. ACE2 also protects organs from inflammatory injuries and regulates intestinal functions. ACE2 can be shed by two proteases, ADAM17 and TMPRSS2. TMPRSS2-cleaved ACE2 allows SARS-CoV-2 cell entry, whereas ADAM17-cleaved ACE2 offers protection to organs. SARS-CoV-2 infection-caused ACE2 dysfunction worsens COVID-19 and could initiate multi-organ failure. Here, we will explain the role of ACE2 in the pathogenesis of severe and critical conditions of COVID-19 and discuss auspicious strategies for controlling the disease.


title: Opening the discussion on a closed intubation box

text: Abstract Background Airway management for patients with COVID-19 poses a significant infection risk to clinicians. As such, some providers have adopted the "COVID intubation box", a cuboid barrier which which separates the clinician from the airway. While this device has limitations, there is promising evidence on its effectiveness. Aim To summarize the history, evidence, and limitations of the popular intubation box design. Furthermore, we share our modified design and experiences from airway simulations. Methods Using our prototyping and validation facilities, our team designed and iteratively improved our device to arrive at a final design. The expert panel, consisting of anesthesiologists, infection control staff, and emergency clinicians, trialed the device using airway simulation mannequins and provided feedback. Results Our final device features a dome shape, increased height, wider arm port diameter, additional side port for assistants, and drapes to reduce viral escape. Feedback from simulations was overall positive, especially noting that the height and arm port diameter facilitated arm motion within the box. The infection control team preferred the unique dome shape for safe disinfection. Conclusion Our intubation box overcomes several challenges and criticisms of the popular intubation box. This device is an important harm reduction tool for clinicians during this COVID-19 pandemic.


title: Type I and Type III Interferons Display Different Dependency on Mitogen-Activated Protein Kinases to Mount an Antiviral State in the Human Gut

text: Intestinal epithelial cells (IECs) are constantly exposed to commensal flora and pathogen challenges. How IECs regulate their innate immune response to maintain gut homeostasis remains unclear. Interferons (IFNs) are cytokines produced during infections. While type I IFN receptors are ubiquitously expressed, type III IFN receptors are expressed only on epithelial cells. This epithelium specificity strongly suggests exclusive functions at epithelial surfaces, but the relative roles of type I and III IFNs in the establishment of an antiviral innate immune response in human IECs are not clearly defined. Here, we used mini-gut organoids to define the functions of types I and III IFNs to protect the human gut against viral infection. We show that primary non-transformed human IECs, upon viral challenge, upregulate the expression of both type I and type III IFNs at the transcriptional level but only secrete type III IFN in the supernatant. However, human IECs respond to both type I and type III IFNs by producing IFN-stimulated genes that in turn induce an antiviral state. Using genetic ablation of either type I or type III IFN receptors, we show that either IFN can independently restrict virus infection in human IECs. Importantly, we report, for the first time, differences in the mechanisms by which each IFN establishes the antiviral state. Contrary to type I IFN, the antiviral activity induced by type III IFN is strongly dependent on the mitogen-activated protein kinases signaling pathway, suggesting a pathway used by type III IFNs that non-redundantly contributes to the antiviral state. In conclusion, we demonstrate that human intestinal epithelial cells specifically regulate their innate immune response favoring type III IFN-mediated signaling, which allows for efficient protection against pathogens without producing excessive inflammation. Our results strongly suggest that type III IFN constitutes the frontline of antiviral response in the human gut. We propose that mucosal surfaces, particularly the gastrointestinal tract, have evolved to favor type III IFN-mediated response to pathogen infections as it allows for spatial segregation of signaling and moderate production of inflammatory signals which we propose are key to maintain gut homeostasis.


title: COVID-19 infection and rheumatoid arthritis: Faraway, so close!

text: Abstract The outbreak of the new coronavirus infections COVID-19 in December 2019 in China has quickly become a global health emergency. Given the lack of specific anti-viral therapies, the current management of severe acute respiratory syndrome coronaviruses (SARS-CoV-2) is mainly supportive, even though several compounds are now under investigation for the treatment of this life-threatening disease. COVID-19 pandemic is certainly conditioning the treatment strategy of a complex disorder as rheumatoid arthritis (RA), whose infectious risk is increased compared to the general population because of an overall impairment of immune system typical of autoimmune diseases combined with the iatrogenic effect generated by corticosteroids and immunosuppressive drugs. However, the increasing knowledge about the pathophysiology of SARS-CoV-2 infection is leading to consider some anti-rheumatic drugs as potential treatment options for the management of COVID-19. In this review we will critically analyse the evidences on either positive or negative effect of drugs commonly used to treat RA in this particular scenario, in order to optimize the current approach to RA patients.


title: Genomic organization and adaptive evolution of IGHC genes in marine mammals

text: Abstract Immunoglobulins are important elements of the adaptive immune system that bind to an immense variety of microbial antigens to neutralize infectivity and specify effector functions. In the present study, the immunoglobulin heavy chain constant region (IGHC) genes from marine mammals were identified and compared with those of their terrestrial relatives to explore their genomic organization and evolutionary characteristics. The genomic organization of marine mammal IGHC genes was shown to be conservative with other eutherian mammals. Stronger signals of positive selection on IGHC were revealed in terrestrial mammals than that in marine mammals with the branch-site model, displaying different selective pressure, which might suggest their divergent adaptations to contrasted environments.


title: What does the future hold for clinical microbiology?

text: In the past decade, clinical microbiology laboratories have undergone important changes with the introduction of molecular biology techniques and laboratory automation. In the future, there will be a need for more rapid diagnoses, increased standardization of testing and greater adaptability to cope with new threats from infectious microorganisms, such as agents of bioterrorism and emerging pathogens. The combination of the new tools that are now being developed in research laboratories, the general reorganization of clinical laboratories and improved communication between physicians and clinical microbiologists should lead to profound changes in the way that clinical microbiologists work.


title: Equine Rhinitis A Virus Infection in Thoroughbred Racehorses—A Putative Role in Poor Performance?

text: The aim of this study was to identify respiratory viruses circulating amongst elite racehorses in a training yard by serological testing of serial samples and to determine their impact on health status and ability to race. A six-month longitudinal study was conducted in 30 Thoroughbred racehorses (21 two-year-olds, five three-year-olds and four four-year-olds) during the Flat racing season. Sera were tested for the presence of antibodies against equine herpesvirus 1 and 4 (EHV-1 and EHV-4) and equine rhinitis viruses A and B (ERAV and ERBV) by complement fixation (CF) and equine arteritis virus (EAV) by ELISA. Antibodies against equine influenza (EI) were measured by haemagglutination inhibition (HI). Only ERAV was circulating in the yard throughout the six-month study period. Seroconversion to ERAV frequently correlated with clinical respiratory disease and was significantly associated with subsequent failure to race (p = 0.0009). Over 55% of the two-year-olds in the study seroconverted to ERAV in May and June. In contrast, only one seroconversion to ERAV was observed in the older horses. They remained free of any signs of respiratory disease and raced successfully throughout the study period. The importance of ERAV as a contributory factor in the interruption of training programmes for young horses may be underestimated.


title: Contrast‐Enhanced Ultrasound in Patients With COVID‐19: Pneumonia, Acute Respiratory Distress Syndrome, or Something Else?

text: Coronavirus disease 2019 (COVID‐19) represents a very heterogeneous disease. Some aspects of COVID‐19 pneumonia question the real nature of ground glass opacities and its consolidative lesions. It has been hypothesized that COVID‐19 lung involvement could represent not only a viral effect but also an immune response induced by the infection, causing epithelial/endothelial lesions and coagulation disorders. We report 3 cases of COVID‐19 pneumonia in which contrast‐enhanced ultrasound was suggestive of consolidations with perfusion defects, at least in part caused by ischemic or necrotic changes and not only by inflammatory or atelectasis events.


title: Chapter 25 Therapeutic use of monoclonal antibodies: general aspects and challenges for drug delivery

text: Abstract Monoclonal antibodies are routinely used in several fields but the great challenge has been their use as therapeutic agents for the treatment of diseases, such as breast cancer, leukemia, asthma, macular degeneration, arthritis, Crohn’s disease, and transplants, among others. Monoclonal antibodies are protein molecules made in the laboratory from hybridoma cells by recombinant DNA technology. Important advances have been made over the past decade to improve some critical points, such as safety and efficacy of the first generation of therapeutic antibodies. This type of molecules presents a significant challenge from the pharmaceutical point of view due to their characteristics, such as molecular size, stability, and solubility. In this chapter we have attempted to identify the major issues associated with therapeutic approaches, formulating drawbacks and delivering antibody drugs, particularly focused on the challenges and opportunities that these present for the future.


title: Analysis of severe acute respiratory syndrome coronavirus structural proteins in virus‐like particle assembly

text: SARS‐CoV has four major structural proteins: the N, S, M, and E proteins. To investigate the mechanism of SARS‐CoV assembly, we cloned the genes encoding these four proteins into the eukaryotic expression vector pCAGGS and transfected them into 293T cells. When all four expression vectors were co‐transfected VLP formed, as confirmed using electron microscopy. Using a rabbit polyclonal antibody specific to the N protein, N‐protein‐containing particles similar in size to the VLP were also observed by immunoelectron microscopy, indicating that the VLP contained the N protein. Co‐immunoprecipitation analyses demonstrated an interaction between the N and M proteins, suggesting that N protein binds directly to M protein to be incorporated into VLP.


title: Persistent Airway Obstruction After Virus Infection Is Not Associated With Airway Inflammation

text: Abstract Background:This study examined the contribution of airway inflammation to the delayed lung function recovery that occurs in some people following virus-induced asthma exacerbations. Methods:Subjects (n = 40) were recruited at hospital admission for acute asthma exacerbation. Respiratory virus infection was diagnosed by viral nucleic acid detection and/or cell culture, using induced sputum, nasal, or throat swabs. Data collected included lung function, answers to common cold and asthma control questionnaires, and induced sputum cellular profiles. Subjects were reexamined 4 to 6 weeks postexacerbation and were compared with stable asthmatic subjects (n = 26) who had been recruited from ambulatory care clinics. Results:Persistent airway obstruction, defined as lung function improvement at follow-up (ie, change in FEV1percent predicted [Δ%FEV1]) of <15%, was observed in 10 subjects (25%). Airway recovery (Δ%FEV1, ≥ 15%) was observed in the remaining subjects (30 subjects; 75%). During the acute episode, the airway-recovery group had increased total cell count (p = 0.019), increased number of neutrophils (p = 0.005), and increased percentage of neutrophils (p = 0.0043) compared to the group of stable subjects with asthma. Postexacerbation, the airway-recovery group had reduced numbers of neutrophils and an increased percentage of eosinophils. In contrast, during exacerbation, subjects with persistent airway obstruction showed no differences in inflammatory cell counts compared to stable subjects with asthma, nor did cell counts change postexacerbation. Symptoms improved in both groups postexacerbation. However, in the persistent-airway-obstruction group, asthma remained uncontrolled. Conclusion:Persistent airway obstruction and uncontrolled asthma are observed in some people after viral asthma exacerbations. These abnormalities are not associated with inflammatory cell influx into the airway lining fluid during the exacerbation and may reflect the involvement of noncellular elements. Further work should explore other mechanisms leading to incomplete airway recovery.


title: The classification of viruses infecting the respiratory tract

text: Abstract Following the boom in respiratory virology in the 1960s, species of rhinoviruses, coronaviruses, enteroviruses, adenoviruses, parainfluenza viruses and respiratory syncytial virus were added to influenza and measles viruses as causes of respiratory tract infection. In restricted patient groups, such as the immunocompromised, members of the family of herpesviruses including herpes simplex, cytomegalovirus, varicella-zoster virus, Epstein-Barr virus and human herpes virus 6 have also been associated with respiratory disease. This list of pathogens was extended last year with the discovery of a novel virus, the human metapneumovirus. More than 200 antigenically distinct viruses have been documented as causes of sporadic or epidemic respiratory infections in infants, children and adults. However, this varied and diverse group can be divided among six distinct families. Understanding some of the basic biology of these families gives an insight into possible strategies for diagnosis, control and therapy.


title: Influenza-like illness outbreaks in nursing homes in Corsica, France, 2014–2015: epidemiological and molecular characterization

text: BACKGROUND: To study the molecular epidemiology of the influenza outbreaks in nursing homes (NHs) to determine whether multiple influenza strains were involved. METHODS: From September to December 2014, NHs in Corsica were invited to participate in an ongoing daily epidemiological and microbiological surveillance for influenza-like illness (ILI) among residents and health care workers (HCWs). RESULTS: The study involved 12 NHs. Respiratory illness meeting the ILI case definition was observed among 44 residents from whom 22 specimens were collected. Of the 22 residents with a nasopharyngeal sample, 13 (59 %) were positive for at least one of the 11 pathogens analysed. Among these 13 patients, 11 (92 %) presented a confirmed influenza (A/H3N2) and two had another respiratory virus: one human metapneumovirus and one human coronavirus. Of patients with a confirmed influenza A(H3N2), 10 (91 %) were vaccinated against influenza during the 2014–2015 season. Two influenza outbreaks were reported in two NHs, caused by influenza A(H3N2) strains belonging to cluster 3C.3 and 3C.2a. Although antivirals were available, prophylaxis was not used. CONCLUSIONS: Phylogenetic analysis seems to suggest no multiple introduction into the two NHs reporting the two influenza A(H3N2) outbreaks. A number of factors could have contributed to transmitting influenza in NHs including, the absence of administration of antiviral treatment for prophylaxis of all residents/staff regardless of immunization status because of the poor vaccine match during each outbreak, the intensive contacts with incompletely protected residents and HCWs, and the low adherence of NHs to notification of ILI outbreaks to the health authorities. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40064-016-2957-z) contains supplementary material, which is available to authorized users.


title: Medical Tourism

text: Searches of the literature or Internet using the term “medical tourism” produce two sets of articles: travel for the purpose of delivering health care or travel for the purpose of seeking health care. The first usage primarily appears in the medical literature and is beyond the scope of this article, which focuses on travel to seek health care. Still, there are some aspects these two topics have in common: both are affected by ease and speed of international travel and communication associated with globalization, and both raise questions about continuity of care as well as issues related to cultural, language, and legal differences; both also raise questions about ethics. This article describes some of the motivating factors, contributing elements, and challenges in elucidating trends, as well as implications for clinicians who provide pretravel advice and those who care for ill returning travelers.


title: Prevention of Infectious Diseases in Athletes

text: The sports medicine physician may face challenging issues regarding infectious diseases when dealing with teams or highly competitive athletes who have difficulties taking time off to recover. One must treat the individual sick athlete and take the necessary precautions to contain the spread of communicable disease to the surrounding team, staff, relatives, and other contacts. This article reviews preventive strategies for infectious disease in athletes, including immunization recommendations and prophylaxis guidelines, improvements in personal hygiene and prevention of spread of infectious organisms by direct contact, insect-borne disease precautions, and prevention of sexually transmitted diseases. A special emphasis on immunizations focuses on pertussis, influenza, and meningococcal prophylaxis.


title: Toll-like receptors and signalling in spermatogenesis and testicular responses to inflammation—a perspective

text: Abstract It is self-evident that infection and inflammation in the reproductive tract can inhibit male fertility, but the observation that fertility may also be compromised by systemic inflammation and disease is more difficult to explain. Recent studies implicating microbial pattern-recognition receptors, such as the Toll-like receptors (TLRs), as well as inflammatory cytokines and their signalling pathways, in testicular function have cast new light on this mysterious link between infection/inflammation and testicular dysfunction. It is increasingly evident that signalling pathways normally involved in controlling inflammation play fundamental roles in regulating Sertoli cell activity and responses to reproductive hormones, in addition to promoting immune responses within the testis. Many of the negative effects of inflammation on spermatogenesis may be attributed to elevated production of inflammation-related gene products within the circulation and the testis, which subsequently exert disruptive effects on spermatogenic cell development and survival, as well as the ability of the Sertoli cells to provide support for spermatogenesis. These interactions have important implications for testicular dysfunction and disease, and may eventually provide new opportunities for therapeutic interventions.


title: Genetic diversity of bat orthohepadnaviruses in China and a proposed new nomenclature

text: Abstract The orthohepadnaviruses, which include the major human pathogen hepatitis B virus, exist in a wide range of hosts. Since 2013, a large group of orthohepadnaviruses has been identified in bats worldwide and classified as 4 species within the genus Orthohepadnavirus. To further investigate orthohepadnaviruses in the Chinese bat population, 554 archived bat samples from 20 colonies covering 3 southern provinces were screened with results showing that 9 (1.6%) were positive. A systematic phylogenetic analysis has indicated the need for a new nomenclature for bat hepatitis B virus-like viruses: BtHBV, with the addition of 3 new species, one being divided into 6 genotypes. Viruses identified here shared 9.0–19.2% full genome divergence and classified into 3 different genotypes. This study illustrates the genetic diversity of orthohepadnaviruses in the Chinese bat population, and emphasizes need for further investigation of their public health significance.


Correction to Lancet Gastroenterol Hepatol 2020; 5: 430–31


title: An improved reverse genetics system for generation of bovine viral diarrhea virus as a BAC cDNA

text: Abstract Full length cDNA clones of bovine viral diarrhea virus (BVDV) with a low-copy number plasmid backbone have not proven to be stable when propagated in bacteria. To improve stability, pBAS, a bacterial artificial chromosome (BAC) plasmid was used to construct a full length cDNA clone of BVDV strain SD1, which has a genomic size of 12.3kb. The resulting clone pBSD1 was propagated stably for at least 10 passages in three different Escherichia coli strains at two different incubation temperatures as determined by sequencing the progeny plasmids. In vitro transcripts derived from pBSD1 were homologous in size and had an infectious efficiency as high as ∼5.0×105 FFU/μg RNA in MDBK cells. The recovered virus, BSD1, harbored the five artificially introduced silent point mutations as genetic markers and was similar to wild type SD1 in viral growth kinetics, RNA replication, and protein expression. This BAC clone provides a stable reverse genetics system for manipulation and study of BVDV genes.


title: Comparative Impact of Individual Quarantine vs. Active Monitoring of Contacts for the Mitigation of COVID-19: a modelling study

text: BACKGROUND: Voluntary individual quarantine and voluntary active monitoring of contacts are core disease control strategies for emerging infectious diseases, such as COVID-19. Given the impact of quarantine on resources and individual liberty, it is vital to assess under what conditions individual quarantine can more effectively control COVID-19 than active monitoring. As an epidemic grows, it is also important to consider when these interventions are no longer feasible, and broader mitigation measures must be implemented. METHODS: To estimate the comparative efficacy of these case-based interventions to control COVID-19, we fit a stochastic branching model to reported parameters for the dynamics of the disease. Specifically, we fit to the incubation period distribution and each of two sets of the serial interval distribution: a shorter one with a mean serial interval of 4.8 days and a longer one with a mean of 7.5 days. To assess variable resource settings, we consider two feasibility settings: a high feasibility setting with 90% of contacts traced, a half-day average delay in tracing and symptom recognition, and 90% effective isolation; and low feasibility setting with 50% of contacts traced, a two-day average delay, and 50% effective isolation. FINDINGS: Our results suggest that individual quarantine in high feasibility settings where at least three-quarters of infected contacts are individually quarantined contains an outbreak of COVID-19 with a short serial interval (4.8 days) 84% of the time. However, in settings where this performance is unrealistically high and the outbreak continues to grow, so too will the burden of the number of contacts traced for active monitoring or quarantine. When resources are prioritized for scalable interventions such as social distancing, we show active monitoring or individual quarantine of high-risk contacts can contribute synergistically to mitigation efforts. INTERPRETATION: Our model highlights the urgent need for more data on the serial interval and the extent of presymptomatic transmission in order to make data-driven policy decisions regarding the cost-benefit comparisons of individual quarantine vs. active monitoring of contacts. To the extent these interventions can be implemented they can help mitigate the spread of COVID-19.


title: Enhancement of immunostimulatory properties of exosomal vaccines by incorporation of fusion-competent G protein of vesicular stomatitis virus

text: Exosomes have been proposed as candidates for therapeutic immunization. The present study demonstrates that incorporation of the G protein of vesicular stomatitis virus (VSV-G) into exosome-like vesicles (ELVs) enhances their uptake and induces the maturation of dendritic cells. Targeting of VSV-G and ovalbumin as a model antigen to the same ELVs increased the cross-presentation of ovalbumin via an endosomal acidification mechanism. Immunization of mice with VSV-G and ovalbumin containing ELVs led to an increased IgG2a antibody response, expansion of antigen-specific CD8 T cells, strong in vivo CTL responses, and protection from challenge with ovalbumin expressing tumor cells. Thus, incorporation of VSV-G and targeting of antigens to ELVs are attractive strategies to improve exosomal vaccines.


title: Association between Mannose-Binding Lectin Gene Polymorphisms and Susceptibility to Severe Acute Respiratory Syndrome Coronavirus Infection

text: BackgroundGenetic determinants of susceptibility to severe acute respiratory syndrome coronavirus (SARS-CoV) infection remain unknown. We assessed whether mannose-binding lectin (MBL) gene polymorphisms were associated with susceptibility to SARS-CoV infection or disease severity in an ethnically homogeneous population born in northern China MethodsThe frequencies of 1 mutation in codon 54 and 3 promoter polymorphisms at nt −550, −221, and 4 were ascertained in 352 patients with SARS and 392 control subjects, by means of polymerase chain reaction direct sequencing ResultsOf 352 patients with SARS and 392 control subjects, 120 (34.4%) and 91 (23.2%) were carriers of the codon 54 variant, respectively (odds ratio [OR], 1.73 [95% confidence interval {CI}, 1.25–2.39]; P=.00086). A total of 123 (36.0%) of 352 patients with SARS and 100 (25.5%) of 392 control subjects had haplotype pairs associated with medium or low expression of MBL (OR, 1.67 [95% CI, 1.21–2.29]; P=.00187). The population-attributable fraction of patients with SARS that was associated with having the codon 54 variant was 20.1% (95% CI, 7.9%–32.3%) Conclusions MBL gene polymorphisms were significantly associated with susceptibility to SARS-CoV infection; this might be explained by the reduced expression of functional MBL secondary to having the codon 54 variant


title: Infectious Bronchitis Virus as a Vector for the Expression of Heterologous Genes

text: The avian coronavirus infectious bronchitis virus (IBV) is the causative agent of the respiratory disease infectious bronchitis of domestic fowl, and is controlled by routine vaccination. To explore the potential use of IBV as a vaccine vector a reverse genetics system was utilised to generate infectious recombinant IBVs (rIBVs) expressing the reporter genes enhanced green fluorescent protein (eGFP) or humanised Renilla luciferase (hRluc). Infectious rIBVs were obtained following the replacement of Gene 5 or the intergenic region (IR) with eGFP or hRluc, or the replacement of ORFs 3a and 3b with hRluc. The replacement of Gene 5 with an IBV codon-optimised version of the hRluc gene also resulted in successful rescue of infectious rIBV. Reporter gene expression was confirmed by fluorescence microscopy, or luciferase activity assays, for all successfully rescued rIBVs following infection of primary chick kidney (CK) cells. The genetic stability of rIBVs was analysed by serial passage on CK cells. Recombinant IBV stability varied depending on the genome region being replaced, with the reporter genes maintained up to at least passage 8 (P8) following replacement of Gene 5, P7 for replacement of the IR and P5 for replacement of ORFs 3a and 3b. Codon-optimisation of the hRluc gene, when replacing Gene 5, resulted in an increase in genome stability, with hRluc expression stable up to P10 compared to P8 for standard hRluc. Repeated passaging of rIBVs expressing hRluc at an MOI of 0.01 demonstrated an increase in stability, with hRluc expression stable up to at least P12 following the replacement of Gene 5. This study has demonstrated that heterologous genes can be incorporated into, and expressed from a range of IBV genome locations and that replacement of accessory Gene 5 offers a promising target for realising the potential of IBV as a vaccine vector for other avian pathogens.


title: Enhancement and Neutralization of Feline Infectious Peritonitis Virus Infection in Feline Macrophages by Neutralizing Monoclonal Antibodies Recognizing Different Epitopes

text: The interaction between the enhancing and neutralizing activities of three monoclonal antibodies (MAbs) (5‐6‐2, 6‐4‐2 and 7‐4‐1) to the spike protein of feline infectious peritonitis virus (FIPV) strain 79‐1146 was determined using feline macrophages. At a high MAb concentration, all of the three MAbs completely inhibited the FIPV infection at 37 C. However, two of them (6‐4‐2 and 7‐4‐1) enhanced FIPV infection when either the MAb concentration or reaction temperature was lowered. These MAbs also exerted an immediate infectivity‐enhancing activity for up to 10 min of reaction and by 20 min, neutralizing activities were observed. Only MAb 5‐6‐2 consistently showed neutralizing activity regardless of the reaction conditions. Competition with sera from cats experimentally infected with FIPV strain 79‐1146 or feline enteric coronavirus strain 79‐1683 showed that the two epitopes recognized by MAb 5‐6‐2 and MAb 6‐4‐2, respectively, are also recognized by the natural host.


title: Antimicrobial use Guidelines for Treatment of Respiratory Tract Disease in Dogs and Cats: Antimicrobial Guidelines Working Group of the International Society for Companion Animal Infectious Diseases

text: Respiratory tract disease can be associated with primary or secondary bacterial infections in dogs and cats and is a common reason for use and potential misuse, improper use, and overuse of antimicrobials. There is a lack of comprehensive treatment guidelines such as those that are available for human medicine. Accordingly, the International Society for Companion Animal Infectious Diseases convened a Working Group of clinical microbiologists, pharmacologists, and internists to share experiences, examine scientific data, review clinical trials, and develop these guidelines to assist veterinarians in making antimicrobial treatment choices for use in the management of bacterial respiratory diseases in dogs and cats.


title: A global bibliometric analysis of Plesiomonas-related research (1990 – 2017)

text: Plesiomonas shigelloides is an emerging pathogen with damaging effects on human health such as gastroenteritis and extraintestinal infections. Here, we carried out a bibliometric survey that aimed to examine publication trends in Plesiomonas-related research by time and place, international collaborative works, identify gaps and suggest directions for future research. The search term “Plesiomonas shigelloides” was used to retrieve articles published between 1990 and 2017 from the Web of Science database. Only primary research articles were included in the analysis. A total of 155 articles were published within the survey period, with an average of 5.54±2.66 articles per year and an annual growth rate of −0.8%. Research output peaked in 2000 and 2006 (each accounting for 7.7% of the total). The United States ranked first in terms of numbers of articles (n = 29, 18.1%) and total citations (n = 451). Cameroon, Canada, Cuba, Switzerland and Turkey co-shared the 10(th) position each with 2 articles (1.3%). Research collaboration was low (collaboration index = 3. 32). In addition to Plesiomonas shigelloides (n = 82, 52.9%), the top Authors Keywords and research focus included lipopolysaccharide and nuclear magnetic resonance (n = 13, 8.4%). Diarrhea (n = 43, 27.7%), Aeromonas species (n = 41, 26.5%) and infections (n = 31, 20.0%) were also highly represented in Keywords-Plus. Authors’ collaborations and coupling networks formed two mega-clusters which nodes were shared solely by authors from high-income countries. The common conceptual framework in retrieved articles determined by K-means clustering revealed three clusters with sizes of 7, 16, and 29, representing research responses focused on extraintestinal and gastroenteritis, P. shigelloides lipopolysaccharide structure, and co-infections, respectively. Our bibliometric analysis revealed a global diminishing research in Plesiomonas; greater research outcomes from high-income countries compared to others and low collaboration with developing countries.


title: Middle East Respiratory Syndrome Coronavirus in Dromedaries in Ethiopia Is Antigenically Different From the Middle East Isolate EMC

text: Middle East respiratory syndrome (MERS) is an emerging respiratory disease caused by the MERS coronavirus (MERS-CoV). MERS has been endemic to Saudi Arabia since 2012. The reservoir of MERS-CoV is the dromedary camel, suggesting that MERS is primarily a zoonotic disease. MERS-CoV is common in dromedaries throughout the Middle East, North Africa, and East Africa as evidenced by neutralizing antibodies against MERS-CoV; however, human cases have remained limited to the Middle East. To better understand the cause of this difference, the virological properties of African camel MERS-CoV were analyzed based on the spike (S) protein in Ethiopia. Nasal swabs were collected from 258 young dromedaries (≤ 2 years old) in the Afar region of Ethiopia, of which 39 were positive for MERS-CoV, as confirmed by genetic tests. All positive tests were exclusive to the Amibara woreda region. Using next-generation sequencing, two full-length genomes of Amibara isolates were successfully decoded; both isolates belonged to the C2 clade based on phylogenetic analysis of full-length and S protein sequences. Recombinant EMC isolates of MERS-CoV, in which the S protein is replaced with those of Amibara isolates, were then generated to test the roles of these proteins in viral properties. Amibara S recombinants replicated more slowly in cultured cells than in EMC S recombinants. In neutralizing assays, Amibara S recombinants were neutralized by lower concentrations of sera from both Ethiopian dromedaries and EMC isolate (wild-type)-immunized mouse sera, relative to the EMC S recombinants, indicating that viruses coated in the Amibara S protein were easier to neutralize than the EMC S protein. Neutralization experiments performed using S1/S2 chimeric recombinants of the EMC and Amibara S proteins showed that the neutralization profile was dependent on the S1 region of the S protein. These results suggest that the slower viral replication and the ease of neutralization seen in the Ethiopian MERS-CoV are due to strain-specific differences in the S protein and may account for the absence of human MERS-CoV cases in Ethiopia.


title: CHAPTER 4 Keeping Track of Viruses

text: Publisher Summary This chapter introduces basic concepts of virology and exemplifies the usage of current technology for identifying and tracking viral pathogens. Virus structure, lifestyle, replication strategies, classication, the varied modes of transmission, infection, and disease manifestations are focussed upon in the chapter. Viruses are extremely simple “life” forms without metabolic capacity, organelles, translational machinery, or autonomous replicative potential; the essential elements of a virus are consequently minimal. A virus enters the host through any opportunistic opening of the body—; such as minute breaks in the skin barrier or mucosal linings of the eye, nose, etc. Antibodies produced during an infection often have the ability to bind the virus and reduce infectivity. An immediate question to solve during a virus outbreak is the mechanism by which the virus spreads. Viruses frequently infect animal or insect vectors that serve to pass the virus to humans. By identifying the virus through sequence analysis, a hypothetical reservoir can be predicted by the placement of the sequence on the phylogenetic tree‥ The varied modes of transmission, infection, and disease manifestations as they relate to the different diagnostic methods for virus identification are highlighted. Examples of naturally emerging viruses; such as Sin Nombre, Nipah, West Nile conclude the chapter. New technologies that allow the creation of manmade or “engineered” viruses, new frontiers in viral diagnostics, and a few thoughts on the future of virology are also presented. The global eradication of smallpox ranks as one of humankind's greatest accomplishments yet many viral challenges remain. HIV, hepatitis B and C, influenza, dengue, rotavirus, and many other viral diseases continue to affect tens of millions.


Traditional Chinese medicine contributes to the treatment of COVID-19 patients


title: Treatment–donation-stockpile dynamics in ebola convalescent blood transfusion therapy

text: Abstract The interim guidance issued by the World Health Organization during the West Africa 2014 Ebola outbreak provides guidelines on the use of convalescent blood from Ebola survivors for transfusion therapy. Here we develop a novel mathematical model, based on the interim guidance, to examine the nonlinear transmission–treatment–donation–stockpile dynamics during an Ebola outbreak and with a large scale use of the transfusion therapy in the population. We estimate the reduction of case fatality ratio by introducing convalescent blood transfusion as a therapy, and inform optimal treatment–donation–stockpile strategies to balance the treatment need for case fatality ratio reduction and the strategic need of maintaining a minimal blood bank stockpile for other control priorities.


title: Estimating the transmission potential of supercritical processes based on the final size distribution of minor outbreaks

text: Use of the final size distribution of minor outbreaks for the estimation of the reproduction numbers of supercritical epidemic processes has yet to be considered. We used a branching process model to derive the final size distribution of minor outbreaks, assuming a reproduction number above unity, and applying the method to final size data for pneumonic plague. Pneumonic plague is a rare disease with only one documented major epidemic in a spatially limited setting. Because the final size distribution of a minor outbreak needs to be normalized by the probability of extinction, we assume that the dispersion parameter (k) of the negative-binomial offspring distribution is known, and examine the sensitivity of the reproduction number to variation in dispersion. Assuming a geometric offspring distribution with k = 1, the reproduction number was estimated at 1.16 (95% confidence interval: 0.97–1.38). When less dispersed with k = 2, the maximum likelihood estimate of the reproduction number was 1.14. These estimates agreed with those published from transmission network analysis, indicating that the human-to-human transmission potential of the pneumonic plague is not very high. Given only minor outbreaks, transmission potential is not sufficiently assessed by directly counting the number of offspring. Since the absence of a major epidemic does not guarantee a subcritical process, the proposed method allows us to conservatively regard epidemic data from minor outbreaks as supercritical, and yield estimates of threshold values above unity.


title: Evaluation of a multiplex ligation-dependent probe amplification assay for the detection of respiratory pathogens in oncological patients

text: Abstract Background Respiratory tract infections are widespread and may cause significant morbidity and mortality in immunosuppressed populations such as oncological patients. Objectives The RealAccurate Respiratory RT PCR Kit covering 14 respiratory viruses was compared to the RespiFinder Smart22, a broad-spectrum multiplex ligation-dependent probe amplification (MLPA) test, targeting 22 viral and bacterial respiratory pathogens. Study design After verification of its analytical performance, the clinical performance of the RespiFinder Smart22 was evaluated by re-analysis of 96 respiratory samples from oncological patients. Additionally, the time to result (TTR) of both methods was compared. Results The analytical performance of the RespiFinder Smart22 fulfilled all previously specified criteria. Concordant results in both assays were achieved in 74.0% of all clinical specimens and in 91.2% when only positive results were taken into account. The RespiFinder Smart22 yielded additional results in a total of 22 (22.9% of 96) samples due to higher test sensitivity and a broader, highly multiplexed spectrum of pathogens. The TTR of a typical routine test consisting of three samples were 206 and 356min for the RealAccurate Respiratory RT PCR Kit and the RespiFinder Smart22, respectively. However, hands-on time was reduced by 59.0% applying the MLPA method. Conclusions In our hands, the RespiFinder Smart22 showed excellent analytical performance while hands-on time was halved in comparison to the RT PCR method. Regarding the clinical evaluation, the MLPA method provided additional results in 22.9% (22/96) of specimens due to its comprehensive format, higher test sensitivity and the capability to detect 22 pathogens compared to 14 with the RealAccurate Respiratory RT PCR Kit.


title: Nursing care of patients with severe acute respiratory syndrome in the intensive care unit: case reports in Hong Kong

text: Abstract Severe acute respiratory syndrome (SARS) was diagnosed in more than 8437 patients in 25 countries between February and July 2003. During this period the World Health Organisation issued a global alert about SARS and together with the Centre for Disease Control have coordinated their efforts to investigate its pathogenesis and treatment. The outbreak in Hong Kong has been dramatic due to its geographical proximity with Guangdong province, China where the first case of SARS was reported. SARS has been described as a rapidly progressive, sometimes fatal pneumonia with a case fatality rate of 7.6% requiring intensive care. The four case reports illustrate a number of important points concerning the recognition, treatment, management and prevention of SARS, and highlights the importance of considering vigilant assessment and monitoring of patients with SARS. The purpose of this paper is to share our experiences in caring for critically ill patients with SARS in the intensive care unit to nurses globally in order to reduce SARS’ morbidity and mortality as well as to protect nurses and other healthcare workers from this disease that is so far threatening the community at large.


title: Nanomaterial-based sensors for the detection of biological threat agents

text: The danger posed by biological threat agents and the limitations of modern detection methods to rapidly identify them underpins the need for continued development of novel sensors. The application of nanomaterials to this problem in recent years has proven especially advantageous. By capitalizing on large surface/volume ratios, dispersability, beneficial physical and chemical properties, and unique nanoscale interactions, nanomaterial-based biosensors are being developed with sensitivity and accuracy that are starting to surpass traditional biothreat detection methods, yet do so with reduced sample volume, preparation time, and assay cost. In this review, we start with an overview of bioagents and then highlight the breadth of nanoscale sensors that have recently emerged for their detection.


title: The intergenic recombinant HLA-B*46:01 has a distinctive peptidome which includes KIR2DL3 ligands

text: HLA-B*46:01 was formed by an intergenic mini-conversion, between HLA-B*15:01 and HLA-C*01:02, in South-East Asia during the last 50,000 years and has since become the most common HLA-B allele in the region. A functional effect of the mini-conversion was introduction of the C1 epitope into HLA-B*46:01, making it an exceptional HLA-B allotype that is recognized by the C1-specific natural killer cell receptor KIR2DL3. High-resolution mass spectrometry showed that HLA-B*46:01 has a low diversity peptidome that is distinct from those of its parents. A minority (21%) of HLA-B*46:01 peptides, with common C-terminal characteristics, form ligands for KIR2DL3. The HLA-B*46:01 peptidome is predicted to be enriched for peptide antigens derived from Mycobacterium leprae. Overall, the results indicate that the distinctive peptidome and functions of HLA-B*46:01 provide carriers with resistance to leprosy, which drove its rapid rise in frequency in South-East Asia.


title: Viral Etiology of Acute Exacerbations of COPD in Hong Kong

text: Introduction Viral respiratory infections may precipitate acute exacerbations of COPD (AECOPD). However, little is known about viral etiology related to AECOPD in Asia. We aimed to study the viral etiology of AECOPD in Hong Kong. Methods Patients admitted to an acute hospital in Hong Kong with AECOPD were recruited prospectively from May 1, 2004, to April 30, 2005. Nasopharyngeal aspirate was collected and assessed by polymerase chain reaction (PCR) and viral culture. Spirometry was performed in the stable phase at 2 to 3 months after hospital discharge. Results There were 262 episodes of AECOPD among 196 patients (mean age, 75.7 ± 7.7 years [± SD]; 160 men). Mean FEV1 was 39.6 ± 18.9% of predicted normal, and FEV1/FVC ratio was 58.0 ± 15.2%. Fifty-eight episodes (22.1%) yielded positive viral PCR results. The viruses identified were influenza A (7.3%), coronavirus OC43 (4.6%), rhinovirus (3.1%), influenza B (2.7%), and respiratory syncytial virus (2.3%). The diagnostic yield of viral identification by PCR was 2.7 times higher than that based on conventional viral culture. The rates of identifying a positive viral etiology by PCR were similar among the subjects with FEV1 ≥ 50%, ≥ 30 to 50%, and < 30% of predicted normal. Viral infection appeared to have no effect on subsequent readmissions or mortality rate over a study period of 1 year Conclusion Influenza A and two less-attended viruses, coronavirus OC43 and rhinovirus, were the common etiologic agents in patients hospitalized with AECOPD in Hong Kong. These should be considered in developing diagnostic and intervening strategies pertaining to AECOPD.


title: Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing

text: BACKGROUND: The major role of enzymatic toxins that target nucleic acids in biological conflicts at all levels has become increasingly apparent thanks in large part to the advances of comparative genomics. Typically, toxins evolve rapidly hampering the identification of these proteins by sequence analysis. Here we analyze an unexpectedly widespread superfamily of toxin domains most of which possess RNase activity. RESULTS: The HEPN superfamily is comprised of all α-helical domains that were first identified as being associated with DNA polymerase β-type nucleotidyltransferases in prokaryotes and animal Sacsin proteins. Using sensitive sequence and structure comparison methods, we vastly extend the HEPN superfamily by identifying numerous novel families and by detecting diverged HEPN domains in several known protein families. The new HEPN families include the RNase LS and LsoA catalytic domains, KEN domains (e.g. RNaseL and Ire1) and the RNase domains of RloC and PrrC. The majority of HEPN domains contain conserved motifs that constitute a metal-independent endoRNase active site. Some HEPN domains lacking this motif probably function as non-catalytic RNA-binding domains, such as in the case of the mannitol repressor MtlR. Our analysis shows that HEPN domains function as toxins that are shared by numerous systems implicated in intra-genomic, inter-genomic and intra-organismal conflicts across the three domains of cellular life. In prokaryotes HEPN domains are essential components of numerous toxin-antitoxin (TA) and abortive infection (Abi) systems and in addition are tightly associated with many restriction-modification (R-M) and CRISPR-Cas systems, and occasionally with other defense systems such as Pgl and Ter. We present evidence of multiple modes of action of HEPN domains in these systems, which include direct attack on viral RNAs (e.g. LsoA and RNase LS) in conjunction with other RNase domains (e.g. a novel RNase H fold domain, NamA), suicidal or dormancy-inducing attack on self RNAs (RM systems and possibly CRISPR-Cas systems), and suicidal attack coupled with direct interaction with phage components (Abi systems). These findings are compatible with the hypothesis on coupling of pathogen-targeting (immunity) and self-directed (programmed cell death and dormancy induction) responses in the evolution of robust antiviral strategies. We propose that altruistic cell suicide mediated by HEPN domains and other functionally similar RNases was essential for the evolution of kin and group selection and cell cooperation. HEPN domains were repeatedly acquired by eukaryotes and incorporated into several core functions such as endonucleolytic processing of the 5.8S-25S/28S rRNA precursor (Las1), a novel ER membrane-associated RNA degradation system (C6orf70), sensing of unprocessed transcripts at the nuclear periphery (Swt1). Multiple lines of evidence suggest that, similar to prokaryotes, HEPN proteins were recruited to antiviral, antitransposon, apoptotic systems or RNA-level response to unfolded proteins (Sacsin and KEN domains) in several groups of eukaryotes. CONCLUSIONS: Extensive sequence and structure comparisons reveal unexpectedly broad presence of the HEPN domain in an enormous variety of defense and stress response systems across the tree of life. In addition, HEPN domains have been recruited to perform essential functions, in particular in eukaryotic rRNA processing. These findings are expected to stimulate experiments that could shed light on diverse cellular processes across the three domains of life. REVIEWERS: This article was reviewed by Martijn Huynen, Igor Zhulin and Nick Grishin


title: Impact du SARS-CoV2 sur la structuration de la prise en charge du cancer : exemple de la tenue des RCP de cancérologie en Occitanie

text: Résumé Ce travail étudie l’impact de l’épidémie de SARS-CoV2 et des recommandations qui ont été diffusées depuis le 16 mars sur l’activité des RCP. L’activité des RCP d’Occitanie a été mesurée à partir des fiches RCP extraites du Dossier Communicant de Cancérologie qui regroupe toutes les RCP. L’activité précédant le confinement a été comparée à celles des périodes de confinement (jusqu’au 24 avril) et des périodes équivalentes en 2019. Les critères de jugement étaient le nombre de réunions tenues, le nombre moyen de dossiers examinés par réunion, dont les premières présentations, et le nombre moyen de médecins présents. Les 191 RCP ont organisé 3 943 réunions et étudié 72 070 dossiers (dont 30 127 premières soumissions). On a observé une baisse de 8 % du nombre de réunions après le confinement. Le nombre de dossiers examinés a diminué de 23 % dans le mois suivant et jusqu’à 33 % dans la troisième quinzaine. Le nombre de médecins participant aux réunions a diminué initialement de 25 %. L’impact a été plus important dans la partie méditerranéenne de la région. Cette première étude à l’échelle d’une région montre que si l’impact de l’épidémie sur le nombre de RCP qui se sont réunies a été modeste, et que les RCP ont suivi les recommandations d’optimisation du quorum, la diminution du nombre de premières présentations laisse présager un retard au diagnostic et à la prise en charge des patients. Elle devra être complétée par des travaux qualitatifs et quantitatifs afin d’estimer l’impact réel de l’épidémie sur la prise en charge globale oncologique. Summary This work examines the impact of the SARS-CoV2 epidemic and the organizational recommendations that have been issued since March 16 on tumor boards (TB) activity. The tumor board activity was measured from tumor board sheets extracted from the oncologic electronic file between January 7, 2019 and April 24, 2020. The pre-containment activity was compared to the activity of the containment periods but also to the equivalent periods in 2019. The number of meetings held, the average number of files reviewed per meeting including first presentations and the average number of physicians’ attendance were the evaluation criteria. The study covered 191 TB that held 3,943 multidisciplinary team meetings (MTM) and reviewed 72070 files (including 30127 first submissions). There was a moderate decrease of 8 % in the number of meetings after March 16, 2020. The number of files examined decreased by 23 % in the following month and even more by 33 % in the third period. The physicians’ number who attended MTM also decreased by 25 %. The negative impact was higher in the Mediterranean part of the region. This first study of tumor board activity, covering a large region but little affected by the pandemic, shows that its impact on the participation to the MTM has been moderate. In addition, tumor boards have followed the recommendations for optimizing quorum. However, the decrease in average MTM activity, particularly for first submissions, suggests a potential delay in patient management. Complementary qualitative and quantitative works are warranted to estimate the real impact on carcinologic outcomes.


title: Triaging algorithm for Head & Neck oncology follow-up patients in COVID-19 climate

text: Abstract The current climate is one of uncertainty and immeasurable tragedy for people afflicted by the pandemic of SARS-CoV-2 virus infection. As professionals, we have a duty of care towards all patients especially the vulnerable and those suffering with life-threatening illnesses such as oral cancer. We present a safe & objective triaging method for afflicted with this disease in the prevailing morbid situation.


Diagnosis of Aorto‐Iliac Thrombosis in a Quarter Horse Foal Using Doppler Ultrasound and Nuclear Scintigraphy


title: COVID-19 and rhinology, from the consultation room to the operating theatre

text: ABSTRACT The purpose of this article is to give rhinologists advice on how to adapt their standard practice during the COVID-19 pandemic. The main goal of these recommendations is to protect healthcare workers against COVID-19 while continuing to provide emergency care so as to prevent loss of chance for patients. We reviewed our recommendations concerning consultations, medical prescriptions and surgical activity in rhinology.


title: Chapter 691 Arterivirus Serine Endopeptidase

text: The third edition of the Handbook of Proteolytic Enzymes aims to be a comprehensive reference work for the enzymes that cleave proteins and peptides, and contains over 800 chapters. Each chapter is organized into sections describing the name and history, activity and specificity, structural chemistry, preparation, biological aspects, and distinguishing features for a specific peptidase. The subject of Chapter 691 is Arterivirus Serine Endopeptidase. Keywords Arterivirus, nidovirus, RNA virus, replicase polyproteins, non-structural protein 4, autoproteolytic proteinase, polyprotein processing, RNA virus, multiple-cleavage proteinase.


title: Coronavirus Protein Processing and RNA Synthesis Is Inhibited by the Cysteine Proteinase Inhibitor E64d

text: Abstract Mouse hepatitis virus strain A59 (MHV-A59) encodes within the 22-kb gene 1 a large polypretain containing three proteinase domains with proven or predicted cysteine catalytic residues. E64d, a specific, irreversible inhibitor of cysteine (thiol) proteinases, inhibits the processing of the gene 1 polyprotein. Specifically, E64d blocks the carboxy-terminal cleavage of p65, E64d also inhibits replication of MHV-A59 in murine DBT cells in a dose-dependent manner, resulting in reduced virus titers and viral syncytia formation. This inhibition of replication is associated with a rapid shutoff of new viral RNA synthesis, in a manner similar to that seen in the presence of cycloheximide. The E64d-associated inhibition of RNA synthesis likely results from E64d-specific inhibition of processing of the gene 1 polyprotein, resulting in inactive proteinase or replicase proteins. These results indicate that processing of the MHV-A59 gene 1-encoded polyprotein is required throughout infection to sustain RNA synthesis and virus replication.


title: Multiplex PCR reveals that viruses are more frequent than bacteria in children with cystic fibrosis

text: Abstract Background Cystic fibrosis is a degenerative disease characterized by progressive epithelial secretory gland dysfunction associated with repeated respiratory infections. Bacterial infections are very frequent in children with cystic fibrosis, but because rapid Methods for screening for the wide variety of potentially involved viruses were unavailable until recently, the frequency of viral presence is unknown. Multiplex PCR enables screening for many viruses involved in respiratory infections. Objectives This study aimed to evaluate the frequency of viruses and bacteria in respiratory specimens from children with cystic fibrosis and to clarify the incidence and characteristics (seasonality and age of patients) of different viruses detected in children with cystic fibrosis. Study design In this 2-year prospective study, we obtained paired nasopharyngeal-swab and sputum specimens from children with cystic fibrosis during clinical respiratory examinations separated by at least 14days. We analyzed viruses in nasopharyngeal-swab specimens with multiplex PCR and bacteria in sputum with standard methods. Results We analyzed 368 paired specimens from 33 children. We detected viruses in 154 (41.8%) and bacteria in 132 (35.9%). Bacteria were commoner in spring and summer; viruses were commoner in autumn and winter. In every season, Staphylococcus aureus was the commonest bacteria and rhinovirus was the commonest virus. Nearly all infections with Haemophilus influenzae occurred in autumn and winter. Viruses were more prevalent in children <5 years old, and bacteria were more prevalent in children ≥12 years old. Conclusions Multiplex PCR screening for respiratory viruses is feasible in children with cystic fibrosis; the clinical implications of screening warrant further study.


title: British Columbia's biotechnology industry: blending research, business and lifestyle

text: An overview of British Columbia's biotechnology industry.


title: Oligonucleotide probes in infectious bronchitis virus diagnosis and strain identification

text: Abstract Genomic RNA fingerprints of infectious bronchitis virus (IBV) strains M41 and Conn46 were prepared to identify T1 RNase-resistant oligonucleotides ‘unique’ to each of the two IBV strains. Such oligonucleotides were subsequently eluted from the gels and their nucleotide sequences determined. When oligonucleotide probes of those sequences were synthesized and used in a dot-blot hybridization assay, the probes lacked IBV strain-specificity and reacted with the RNAs of homologous as well as heterologous IBV strains. Based on these results, the methods used in this study need to be applied to a large number of oligonucleotide probes, to find one or a few that might be suitable as IBV strain- or serotype-specific oligonucleotide probes.


title: Virus-induced ER stress and the unfolded protein response

text: The accumulation of unfolded or misfolded proteins in the lumen of the endoplasmic reticulum (ER) results in ER stress that triggers cytoprotective signaling pathways, termed the unfolded protein response (UPR), to restore and maintain homeostasis in the ER or to induce apoptosis if ER stress remains unmitigated. The UPR signaling network encompasses three core elements, i.e., PKR-like ER kinase (PERK), activating transcription factor 6 (ATF6), and inositol-requiring protein-1 (IRE1). Activation of these three branch pathways of the UPR leads to the translation arrest and degradation of misfolded proteins, the expression of ER molecular chaperones, and the expansion of the ER membrane to decrease the load of proteins and increase the protein-folding capacity in the ER. Recently, the essential roles of the UPR have been implicated in a number of mammalian diseases, particularly viral diseases. In virus-infected cells, the cellular translation machinery is hijacked by the infecting virus to produce large amounts of viral proteins, which inevitably perturbs ER homeostasis and causes ER stress. This review summarizes current knowledge about the UPR signaling pathways, highlights two identified UPR pathways in plants, and discuss progress in elucidating the UPR in virus-infected cells and its functional roles in viral infection.


Induction of lactogenic immunity to transmissible gastroenteritis virus of swine using an attenuated coronavirus mutant able to survive in the physicochemical environment of the digestive tract


title: Avian coronavirus Spike Glycoprotein Ectodomain Shows a Low Codon Adaptation to Gallus gallus with Virus-Exclusive Codons in Strategic Amino Acids Positions

text: This is a study on the Avian coronavirus IBV and chicken host-relationship from the codon usage point of view based on fifty-nine non-redundant IBV S1 sequences (nt 1–507) from strains detected worldwide and chicken tissue-specific protein genes sequences from IBV-replicating sites. The effective number of codons (ENC) values ranged from 36 to 47.8, indicating a high-to-moderate codon usage bias. The highest IBV codon adaptation index (CAI) value was 0.7, indicating a distant virus versus host synonymous codons usage. The ENC × GC3 % curve indicates that both mutational pressure and natural selection are the driving forces on codon usage pattern in S1. The low CAI values agree with a low S protein expression and considering that S protein is a determinant for attachment and neutralization, this could be a further mechanism besides mRNA transcription attenuation for a low expression of this protein leading to an immune camouflage.


HIV/AIDS trends in China


title: Epidemiology and disease control in everyday beef practice

text: It is important for food animal veterinarians to understand the interaction among animals, pathogens, and the environment, in order to implement herd-specific biosecurity plans. Animal factors such as the number of immunologically protected individuals influence the number of individuals that a potential pathogen is able to infect, as well as the speed of spread through a population. Pathogens differ in their virulence and contagiousness. In addition, pathogens have various methods of transmission that impact how they interact with a host population. A cattle population's environment includes its housing type, animal density, air quality, and exposure to mud or dust and other health antagonists such as parasites and stress; these environmental factors influence the innate immunity of a herd by their impact on immunosuppression. In addition, a herd's environment also dictates the “animal flow” or contact and mixing patterns of potentially infectious and susceptible animals. Biosecurity is the attempt to keep infectious agents away from a herd, state, or country, and to control the spread of infectious agents within a herd. Infectious agents (bacteria, viruses, or parasites) alone are seldom able to cause disease in cattle without contributing factors from other infectious agents and/or the cattle's environment. Therefore to develop biosecurity plans for infectious disease in cattle, veterinarians must consider the pathogen, as well as environmental and animal factors.


title: A real-time TaqMan® RT-PCR assay with an internal amplification control for rapid detection of transmissible gastroenteritis virus in swine fecal samples

text: Abstract A TaqMan probe-based real-time RT-PCR assay was developed for simultaneous detection of RNA of transmissible gastroenteritis virus (TGEV) in pig fecal samples and RNA of enhanced green fluorescent protein (EGFP) added exogenously as an internal amplification control. The TGEV primers and probe were designed to be specific to a portion of the S gene sequence conserved in all TGEV isolates, but absent in the closely related porcine respiratory coronaviruses. The optimized TaqMan assay detected a minimum of 2.8 copies of in vitro transcribed RNA of the target S gene and RNA extracted from 1 TCID50/ml of TGEV. Using 113 clinical samples received at our diagnostic laboratory over a 4-year period, the performance of the assay was tested and compared with that of a previously described nested RT-PCR assay. All the fecal samples which tested positive for TGEV by the nested RT-PCR assay also tested positive by the TaqMan assay. However, approximately 9% of the samples that tested negative by the nested RT-PCR assay tested positive by the TaqMan assay. These results indicate that the developed TaqMan assay is a highly sensitive diagnostic test for rapid detection of TGEV in pig fecal samples.


title: Business of business is more than business: Managing during the Covid crisis

text: Abstract The economic impact of the lock down and social distancing policy of the governments has been devastating on business. Should business look out for its own interest or deploy its resources and capabilities to fight the coronavirus even at the expense of short-term losses? This paper suggests that business and society are two peas in a pod and are mutually interdependent. One cannot survive without the other. The purpose of business is more than business. It is to nurture all of its stakeholders (employees, customers, suppliers, and community) and not just the investors. This is still common in many small-town manufacturing companies whose families, and their families, live in the community. The paper suggests several implications for B to B companies including developing a stakeholder scorecard, becoming a better customer to suppliers, and redefine the purpose of business.


title: Domestic waste recycling, collective action and economic incentive: The case in Hong Kong

text: Abstract Efficacy of waste recycling is one of the key determinants of environmental sustainability of a city. Like other pro-environmental activities, waste recycling cannot be successfully accomplished by just one or two people, but only by a concerted effort of the community. The collective-action dilemma creates a common underlying difficulty in formulating workable solutions to many environmental problems. With a view to the non-excludability of the outcome, rationality drives people to free-ride efforts of others in waste recycling. To solve this free-rider problem, some scholars suggest the use of economic incentive. This article attempts to study the impacts of reward schemes on waste recycling behaviour of residents in 122 private housing estates in Hong Kong. The study is differentiable from the others as the latter mainly focus on domestic waste recycling in low-rise low-density housing while this one looks into the same in a high-rise high-density residential setting. According to the results of analyses on a set of aggregate data, reward schemes are found to have a significant positive relationship with the per-household weight of recyclables collected, keeping other things constant. The research findings suggest that economic incentives do work in promoting waste recycling in Hong Kong. Practical and policy implications follow.