title: Determination and application of immunodominant regions of SARS coronavirus spike and nucleocapsid proteins recognized by sera from different animal species

text: Abstract Knowledge of immunodominant regions in major viral antigens is important for rational design of effective vaccines and diagnostic tests. Although there have been many reports of such work done for SARS–CoV, these were mainly focused on the immune responses of humans and mice. In this study, we aim to search for and compare immunodominant regions of the spike (S) and nucleocapsid (N) proteins which are recognized by sera from different animal species, including mouse, rat, rabbit, civet, pig and horse. Twelve overlapping recombinant protein fragments were produced in Escherichia coli, six each for the S and N proteins, which covered the entire coding region of the two proteins. Using a membrane-strip based Western blot approach, the reactivity of each antigen fragment against a panel of animal sera was determined. Immunodominant regions containing linear epitopes, which reacted with sera from all the species tested, were identified for both proteins. The S3 fragment (aa 402–622) and the N4 fragment (aa 220–336) were the most immunodominant among the six S and N fragments, respectively. Antibodies raised against the S3 fragment were able to block the binding of a panel of S-specific monoclonal antibodies (mAb) to SARS–CoV in ELISA, further demonstrating the immunodominance of this region. Based on these findings, one-step competition ELISAs were established which were able to detect SARS–CoV antibodies from human and at least seven different animal species. Considering that a large number of animal species are known to be susceptible to SARS–CoV, these assays will be a useful tool to trace the origin and transmission of SARS–CoV and to minimise the risk of animal-to-human transmission.


title: Structural characterization and immunomodulatory effect of a polysaccharide HCP-2 from Houttuynia cordata

text: Abstract Immunomodulation of natural polysaccharides has been the hot topic of research in recent years. In order to explore the immunomodulatory effect of Houttuynia cordata Thunb., the water extract was studied and a polysaccharide HCP-2 with molecular weight of 60,000Da was isolated by chromatography using DEAE Sepharose CL-6B and Sephacryl S-400 HR columns. The structure characterization of HCP-2 was performed by Fourier transform infrared spectroscopy (FTIR), acidic hydrolysis, PMP derivation, HPLC analysis and nuclear magnetic resonance spectra (NMR). HCP-2 was elucidated as a pectic polysaccharide with a linear chain of 1,4-linked α-d-galacturonic acid residues in which part of the 6-carboxyl groups were methyl esterified and part of 2-hydroxyl groups were acetylated. The bioactivity assays showed that HCP-2 could increase the secretions of interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α), macrophage inhibitory protein-1α (MIP-1α), macrophage inhibitory protein-1β (MIP-1β), and RANTES (regulated on activation, normal T cell expressed and secreted) in human peripheral blood mononuclear cells (PBMCs), which play critical roles in the innate immune system and shape the adaptive immunity. Our results implied that HCP-2 could be an immune enhancer.


title: Porcine Reproductive and Respiratory Syndrome Virus strains with Higher Virulence Cause Marked Protein Profile Changes in MARC-145 Cells

text: Porcine reproductive and respiratory syndrome is an infectious disease that causes serious economic losses to the swine industry worldwide. To better understand the pathogenesis of the porcine reproductive and respiratory syndrome virus (PRRSV), three PRRSV strains with different molecular markers and virulence were used to infect MARC-145 cells. A total of 1804 proteins were identified, and 233 altered proteins and 72 signaling pathways involved in the proteomic profiling of virus-infected MARC-145 cells increased with the virulence of the PRRSV strain. The three types of viral strains shared a common pathway—the electron transport reaction in mitochondria—in the infected-MARC-145 cells. Moreover, the antisense pathway was the most variable of all significant signaling pathways for the highly virulent SX-1 strain, indicating that this unique pathway may be connected to the high virulence of the SX-1 strain. Our study is the first attempt to provide a proteome profile of MARC-145 cells infected with PRRSV strains with different virulence, and these findings will facilitate a deep understanding of the interactions between this virus and its host.


title: Molecular characterization of pathogenic Escherichia coli isolated from diarrheic and in-contact cattle and buffalo calves

text: Escherichia coli field isolates from calves were characterized and categorized into the most significant diarrheagenic pathotypes using polymerase chain reaction (PCR) assays with different specific primers. The used PCR systems were designed to detect sequences representing the group-specific virulence genes encoding fimbriae f5 (K99), Shiga toxins (stx(1) and stx(2)), heat-stable enterotoxins (st), heat-labile enterotoxins (lt), intimin (eae), hemolysin (hylA), and EAEC heat-stable enterotoxin (astA). In the present work, a total of 150 E. coli field isolates were recovered from 150 fecal swabs collected from 100 diarrheic and 50 apparently healthy in-contact cattle and buffalo calves under 3 months old. Out of these 150 isolated E. coli, 106 isolates from 77 diarrheic and 29 in-contact calves harbored one or more of the investigated virulence genes. The pathotyping of the isolates could classify them into shigatoxigenic E. coli (STEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), and enteroaggregative E. coli (EAEC) with a 30.7, 2.7, 12.7, and 7.3% distribution, respectively. Meanwhile, the detection rates of f5, stx(1), stx(2), st, lt, eae, hylA, and astA genes were 17.3, 27.3, 6.7, 10, 37.3, 17.7, 9.3, and 20.7%, respectively. These virulence genes were found either single or in different combinations, such as stx/eae, stx/st/f5, eae/st/f5, or st/lt/f5. Four attaching-effacing shigatoxigenic E. coli isolates (AE-STEC) harboring stx/eae were retrieved from diarrheic calves. Although none of the stx-or eae-positive isolates was verified as O157:H7, STEC isolates detected in apparently healthy calves have potential pathogenicity to humans highlighting their zoonotic importance as reservoirs. Atypical combinations of ETEC/STEC and ETEC/EPEC were also detected in percentages of 14.7 and 2.7%, respectively. Most of these atypical combinations were found more in buffalo calves than in cattle calves. While STEC and EPEC isolates were detected more in cattle calves than in buffalo calves, ETEC isolates were the same in the two species. The pathogenic E. coli infection in calves was recorded to be higher in the first weeks of life with the largest numbers of virulence factor-positive isolates detected at the age of 4 weeks. Histopathological examination of five intestinal samples collected from four dead buffalo calves revealed typical attaching and effacing (AE) lesion which was correlated with the presence of intimin encoding virulence gene (eae). Other lesions characterized by hemorrhagic enteritis, shortening and fusion of intestinal villi and desquamation of the lining epithelium of intestinal mucosa had also been detected.


title: Subacute sclerosing panencephalitis in pregnancy

text: Summary We present a case of subacute sclerosing panencephalitis that developed in a previously healthy 29-year-old pregnant woman who had returned from a trip to rural India shortly before the onset of symptoms. She was admitted to hospital at 27 weeks' gestation with a history of cognitive decline and difficulty completing simple tasks. She had no clinical signs of infection. The working diagnosis was autoimmune encephalitis, although extensive investigations did not lead to a final classifying diagnosis. The patient became comatose and developed hypertension, and an emergency caesarean section was done at 31 weeks to deliver the child, who seemed healthy. The patient died about 6 weeks after the onset of symptoms. The patient was found to have had subacute sclerosing panencephalitis at autopsy. In this Grand Round, we review the clinical features and treatment of subacute sclerosing panencephalitis, and the epidemiological and public health aspects of the case.


title: Analysis of the S spike (peplomer) glycoprotein of bovine coronavirus synthesized in insect cells

text: Abstract The bovine coronavirus (BCV) spike glycoprotein precursor (S, formerly termed peplomer) and its two subunit polypeptides (S1 and S2) were individually expressed in Spodoptera frugiperda (Sf9) insect cells. Each recombinant baculovirus expressed both glycosylated (S, 170K; S1, 95K; S2, 80K) and unglycosylated (S0, 140K; S10, 75K; and S20, 65K) forms of BCV spike polypeptides in Sf9 cells. The mature 95K S1 polypeptide was secreted whereas the S and S2 polypeptides remained cell-associated. The S precursor was partially cleaved in Sf9 cells, and the resulting S1 was also released into the medium. Neutralizing monoclonal antibodies representing two antigenic domains bound to recombinant S and S1 but not the S2 polypeptides, indicating that two major epitopes for BCV neutralization are located on the S1 subunit.


title: Emerging New Concepts of Degrader Technologies

text: Abstract The traditional drug discovery focuses on identifying direct inhibitors of target proteins. This approach typically relies on a specific measurable biochemical readout and amenable binding sites of which the occupancy directly influences the target protein’s function. These requirements preclude many disease-causing proteins from being “druggable” targets, and these proteins are categorized as “undruggable”. The proteolysis-targeting chimera (PROTAC) technology provides powerful tools to degrade these “undruggable” targets and has become a promising approach for drug discovery. However, the PROTAC technology may have limitations and emerging new degrader technologies may greatly broaden the spectrum of targets that could be selectively degraded by harnessing another major degradation pathway in cells. Here we review a few key emerging technologies that exploit the lysosomal degradation pathway and discuss their potential applications as well as limitations.


title: Subversion of host immune responses by otopathogens during otitis media

text: Otitis media (OM) is one of the most common ear diseases affecting humans. Children are at greater risk and suffer most frequently from OM, which can cause serious deterioration in the quality of life. OM is generally classified into two main types: acute and chronic OM (AOM and COM). AOM is characterized by tympanic membrane swelling or otorrhea and is accompanied by signs or symptoms of ear infection. In COM, there is a tympanic membrane perforation and purulent discharge. The most common pathogens that cause AOM are Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis whereas Pseudomonas aeruginosa and Staphylococcus aureus are commonly associated with COM. Innate and adaptive immune responses provide protection against OM. However, pathogens employ a wide arsenal of weapons to evade potent immune responses and these mechanisms likely contribute to AOM and COM. Immunologic evasion is multifactorial, and involves damage to host mucociliary tract, genetic polymorphisms within otopathogens, the number and variety of different otopathogens in the nasopharynx as well as the interaction between the host's innate and adaptive immune responses. Otopathogens utilize host mucin production, phase variation, biofilm production, glycans, as well as neutrophil and eosinophilic extracellular traps to induce OM. The objective of this review article is to discuss our current understanding about the mechanisms through which otopathogens escape host immunity to induce OM. A better knowledge about the molecular mechanisms leading to subversion of host immune responses will provide novel clues to develop effective treatment modalities for OM.


title: Recurrence of positive SARS‐CoV‐2 in patients recovered from COVID‐19

text: Recurrence of positive SARS CoV‐2 PCR has been described in patients discharged from hospital after 2 consecutive negative PCR. We discuss possible explanations including false negative, reactivation and re‐infection and propose different strategy to solve this issue. Prolonged SARS‐CoV‐2 RNA shedding and recurrence of viral RNA shedding in asymptomatic patients remain unknown. Transmission of SARS‐CoV‐2 by asymptomatic carriers had been documented. Considering the significance of this ongoing global public health emergency, it is necessary to carry out large studies to better understand the issue of potential SARS‐CoV‐2 recurrence in COVID‐19 patients. This article is protected by copyright. All rights reserved.


David Oliver: Silencing NHS staff who speak out is sheer stupidity


title: Description of the first acute bovine diarrhea virus-2 outbreak in Israel

text: Abstract This is the first report of an acute and fatal outbreak of bovine diarrhea virus (BVDV)-2 infection in Israel. The clinical presentation varied with the age of the affected animals with a bovine–respiratory–complex–like syndrome in young stock, and diarrhea and dysentery only in the lactating stock. Enteritis first appeared in one shed of post-parturient cows; it spread for 6weeks, until at least 30% of the lactating stock contracted enteritis or dysentery. At the same time, dairy calves aged 10–90days exhibited severe respiratory disease. Of 79 animals that died, 13/350 (3.7%) were adult lactating cows, and 66/1100 (6%) were young feedlot calves. Phylogenetic analysis of the isolated virus revealed a 95% identity with the corresponding genome parts of various BVDV type 2 sequences. The route of introduction of BVDV-2 into Israel could not be elucidated.


title: Pretreatment with EDU decreases rat lung cellular responses to ozone

text: Abstract The phenylurea compound EDU (N-[2-(2-oxo-1-imidazolindinyl)ethyl]-N′-phenylurea) has been shown to protect plants from the damaging effects of ozone exposure. Models of rat lung injury, based on acute exposure to 2 ppm ozone for 3 hr and on exposure to 0.85 ppm ozone for 2 days, were used to determine whether EDU pretreatment of rats protected lungs from oxidant injury. Rats were pretreated with 100 mg/kg body wt EDU by ip administration for 2 days prior to and on the days of ozone exposure. No adverse toxicological effects of EDU pretreatment were observed. Lung superoxide dismutase (SOD) and catalase (CAT) activities were significantly enhanced from 636 to 882 U/lung and from 599 to 856 U/lung, respectively. One day following acute exposure (2 ppm for 3 hr), an ozone-induced increase of polymorphonuclear leukocytes (PMNs) from 0.01 to 1.18 million cells/lung was decreased to 0.68 million by EDU pretreatment. No alteration occurred in the degree of lung permeability indicated by increased lavage fluid albumin. EDU pretreatment also significantly decreased ozone-induced increases in PMN recovery after 2 days exposure to 0.85 ppm ozone from 5.54 to 2.12 million cells/lung. However, in this second case, EDU pretreatment reduced the observed ozone damage, indicated by a decrease in lavage fluid albumin and by a decrease in the macrophage and lymphocyte infiltration associated with this length of ozone exposure. The observation that EDU-treated cultured pulmonary arterial endothelial cells increased SOD and CAT activities identified a potential lung site of EDU interaction. These data demonstrated that although EDU pretreatment appears not to prevent initial ozone damage, it does reduce the infiltration of PMNs and might therefore prevent amplification of the injury associated with this cell type.


title: Respiratory management in severe acute respiratory syndrome coronavirus 2 infection

text: The severe acute respiratory syndrome coronavirus 2 pandemic is to date affecting more than a million of patients and is challenging healthcare professionals around the world. Coronavirus disease 2019 may present with a wide range of clinical spectrum and severity, including severe interstitial pneumonia with high prevalence of hypoxic respiratory failure requiring intensive care admission. There has been increasing sharing experience regarding the patient’s clinical features over the last weeks which has underlined the need for general guidance on treatment strategies. We summarise the evidence existing in the literature of oxygen and positive pressure treatments in patients at different stages of respiratory failure and over the course of the disease, including environment and ethical issues related to the ongoing coronavirus disease 2019 infection.


title: BARRIER DEVICE PROTOTYPE FOR OPEN TRACHEOTOMY DURING COVID-19 PANDEMIC

text: ABSTRACT OBJECTIVE To present a low-cost prototype for a barrier enclosure device which can be used during open surgeries such as tracheotomy. METHODS We provide detailed description of a novel device called COVID-Box, developed by The Surgical Airway Team for COVID-19 Pandemic, a temporary task force formed by Walter Cantídio University Hospital. Safety guidelines for performing tracheotomies in COVID-19 patients are also stated. RESULTS Our prototype device provides greater hand mobility than previous barrier devices reported, making it more suitable for airway surgical procedures, such as tracheotomy. The curved shaped format and the customizable access ports provides ergonomics, without compromising safety. CONCLUSION The COVID-Box appears to be an efficient, reproduceable, low-cost barrier enclosure device that can be used for open tracheotomies in ICU patients during the COVID-19 pandemic.


title: Universal and reusable virus deactivation system for respiratory protection

text: Aerosolized pathogens are a leading cause of respiratory infection and transmission. Currently used protective measures pose potential risk of primary/secondary infection and transmission. Here, we report the development of a universal, reusable virus deactivation system by functionalization of the main fibrous filtration unit of surgical mask with sodium chloride salt. The salt coating on the fiber surface dissolves upon exposure to virus aerosols and recrystallizes during drying, destroying the pathogens. When tested with tightly sealed sides, salt-coated filters showed remarkably higher filtration efficiency than conventional mask filtration layer, and 100% survival rate was observed in mice infected with virus penetrated through salt-coated filters. Viruses captured on salt-coated filters exhibited rapid infectivity loss compared to gradual decrease on bare filters. Salt-coated filters proved highly effective in deactivating influenza viruses regardless of subtypes and following storage in harsh environmental conditions. Our results can be applied in obtaining a broad-spectrum, airborne pathogen prevention device in preparation for epidemic and pandemic of respiratory diseases.


title: Illnesses among recently immigrated children

text: The number of children immigrating to the United States has increased steadily during the last decade. American families are adopting a significant portion of these children, more than 20,000. Recently immigrated children face many different health risks when compared to children born in the United States. They are subject to many infectious diseases no longer seen commonly in the United States such as malaria, tuberculosis, and HIV. They are more likely to have inadequate immunity to vaccine-preventable illnesses. Recent immigrants have a higher likelihood of having malnutrition and developmental delay. Finally, many will have suffered psychological trauma in either institutions or refugee camps. These children require specialized testing, care, and treatment in the pediatric office.


title: Urbanization and the ecology of wildlife diseases

text: Urbanization is intensifying worldwide, with two-thirds of the human population expected to reside in cities within 30 years. The role of cities in human infectious disease is well established, but less is known about how urban landscapes influence wildlife–pathogen interactions. Here, we draw on recent advances in wildlife epidemiology to consider how environmental changes linked with urbanization can alter the biology of hosts, pathogens and vectors. Although urbanization reduces the abundance of many wildlife parasites, transmission can, in some cases, increase among urban-adapted hosts, with effects on rarer wildlife or those living beyond city limits. Continued rapid urbanization, together with risks posed by multi-host pathogens for humans and vulnerable wildlife populations, emphasize the need for future research on wildlife diseases in urban landscapes.


title: Pediatric intensive care unit admission due to respiratory syncytial virus: Retrospective multicenter study

text: BACKGROUND: We investigated the characteristics and clinical outcomes of respiratory syncytial virus (RSV)‐related pediatric intensive care unit (PICU) hospitalization and assessed the palivizumab (PZ) prophylaxis eligibility according to different guidelines from Korea, EU, and USA. METHODS: In this multicenter study, children <18 years of age hospitalized in six PICU from different hospitals due to severe RSV infection between September 2008 and March 2013 were included. A retrospective chart review was performed. RESULTS: A total of 92 patients were identified. The median length of PICU stay was 6 days (range, 1–154 days) and median PICU care cost was USD2,741 (range, USD556–98 243). Of 62 patients who were <2 years old at the beginning of the RSV season, 33 (53.2%) were high‐risk patients for severe RSV infection. Hemodynamically significant congenital heart disease (22.6%) was the most common risk factor, followed by chronic lung disease (11.3%), neuromuscular disease or congenital abnormality of the airway (NMD/CAA) (11.3%), and prematurity (8.1%). The percentage of patients eligible for PZ prophylaxis ranged from 38.7% to 48.4% based on the guidelines, but only two (2.2%) received PZ ≤30 days prior to PICU admission. The median duration of mechanical ventilation was longer in children with NDM/CAA than in those without risk factors (26 days; range, 24–139 days vs 6 days, range, 2–68 days, P = 0.033). RSV‐attributable mortality was 5.4%. CONCLUSIONS: Children <2 years old with already well‐known high risks represent a significant proportion of RSV‐related PICU admissions. Increasing of the compliance for PZ prophylaxis practice among physicians is needed. Further studies are needed to investigate the burden of RSV infection in patients hospitalized in PICU, including children with NMD/CAA.


title: The secrets of human stem cell-derived transfusable RBC for targeted large-scale production and clinical applications: A fresh look into what we need most and lessons to be learned

text: Blood transfusion, using the safest conventional blood bioproducts, is an irreplaceable part of substitution therapy. It is considered the most essential supportive clinical intervention aimed to restore the health of patients in need. Nevertheless, numerous unresolved problems are still associated with current blood substitution therapy. To alleviate our dependency on blood donors, many investigators have been focusing on the quest for stem cell-derived blood cells in line with major developments in the field of regenerative medicine. The main objective is to provide a safe and highly standardized universal cultured red cell concentrate [CRBC] for all clinical applications, regardless of blood groups. Currently, we are close to overcoming some of the main obstacles in culturing cells. This concise report is a prelude to the immortalized cell lines that are ready for in vivo clinical trials. It is only through the sharing of experimental ideas and knowledge-based strategies that we will be able to achieve such an enormous task and better understand ‘’the one for all concept’’ of CRBCs and their universal usage in all clinical settings.


CARACTERÍSTICAS Y RESULTADOS DE UNA SERIE DE 59 PACIENTES CON NEUMONÍA GRAVE POR COVID-19 INGRESADOS EN UCI


title: Therapy of Respiratory Viral Infections with Intranasal siRNAs

text: Chemically synthesized short interfering RNA (siRNA) has ushered a new era in the application of RNA interference (RNAi) against viral genes. We have paid particular attention to respiratory viruses that wreak heavy morbidity and mortality worldwide. The clinically significant ones include respiratory syncytial virus (RSV), parainfluenza virus (PIV) (two Paramyxoviruses), and influenza virus (an Orthomyxovirus). As the infection by these viruses is clinically restricted to the respiratory tissues, mainly the lungs, the logical route for the application of the siRNA was also the same, i.e., via the nasal route. Following the initial success of single intranasal siRNA against RSV, we now offer two new strategies: (1) second-generation siRNAs, used against the paramyxoviral RNA polymerase large subunit (L), (2) siRNA cocktail with a novel transfection reagent, used against influenza virus. Based on these results, we propose the following consensus for designing intranasal antiviral siRNAs: (a) modified 19–27 nt-long double-stranded siRNAs are functional in the lung, (b) excessive 2′-OMe and 2′-F modifications in either or both strands of these siRNAs reduce efficacy, (c) limited modifications in the sense strand are beneficial, although their precise efficacy may be position-dependent, (d) cocktail of multiple siRNAs can be highly effective against multiple viral strains and subtypes.


title: Detection and differentiation of field and vaccine strains of canine distemper virus using reverse transcription followed by nested real time PCR (RT-nqPCR) and RFLP analysis

text: Abstract Canine distemper virus (CDV) is the cause of a severe and highly contagious disease in dogs. Practical diagnosis of canine distemper based on clinical signs and laboratory tests are required to confirm CDV infection. The present study aimed to develop a molecular assay to detect and differentiate field and vaccine CDV strains. Reverse transcription followed by nested real time polymerase chain reaction (RT-nqPCR) was developed, which exhibited analytical specificity (all the samples from healthy dogs and other canine infectious agents were not incorrectly detected) and sensitivity (all replicates of a vaccine strain were positive up to the 3125-fold dilution – 100.7 TCID50). RT-nqPCR was validated for CDV detection on different clinical samples (blood, urine, rectal and conjunctival swabs) of 103 animals suspected to have distemper. A total of 53 animals were found to be positive based on RT-nqPCR in at least one clinical sample. Blood resulted in more positive samples (50 out of 53, 94.3%), followed by urine (44/53, 83.0%), rectal (38/53, 71%) and conjunctival (27/53, 50.9%) swabs. A commercial immunochromatography (IC) assay had detected CDV in only 30 conjunctival samples of these positive dogs. Nucleoprotein (NC) gene sequencing of 25 samples demonstrated that 23 of them were closer to other Brazilian field strains and the remaining two to vaccine strains. A single nucleotide sequences difference, which creates an Msp I restriction enzyme digestion, was used to differentiate between field and vaccine CDV strains by restriction fragment length polymorphism (RFLP) analysis. The complete assay was more sensitive than was IC for the detection of CDV. Blood was the more frequently positive specimen and the addition of a restriction enzyme step allowed the differentiation of vaccine and Brazilian field strains.


title: Human bocavirus infections among children less than two years old in Iran during fall and winter 2012–2013

text: BACKGROUND AND OBJECTIVES: Human bocavirus (HBoV) is a newly discovered parvovirus. It has been detected primarily in children with acute respiratory tract infections. This study was conducted to clarify the frequency and genotype circulation pattern of HBoV in Iran. MATERIALS AND METHODS: Conventional PCR was performed on throat swabs of patients less than two years of age with respiratory illnesses during fall and winter 2012–2013. RESULTS: HBoV virus DNA was detected in 15 of 140 samples (10.7 %). Sequencing and phylogenetic analysis on 5 samples showed that all were HBoV1. The positive samples were negative for influenza A and B viruses while co-infection with RSV was found in 2 (13.3%). CONCLUSION: This study adds to the body of knowledge about the role of HBoV in acute respiratory illnesses in children in Iran.


title: A novel way to numerically characterize DNA sequences and its application

text: We presented a novel way to numerically characterize DNA sequences based on the graphical representation for the sequences comparison and analysis. Instead of calculating the leading eigenvalues of the matrix for graphical representation, we computed curvature and torsion of curves as the descriptor to numerically characterize DNA sequences. The new method was tested on three data sets: the coding sequences of β‐globin gene, all of their exons, and 24 coronavirus geneomes from NCBI. The similarities/dissimilarities and phylogenetic tree of these species verify the validity of our method. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011


title: Zoonoses

text: Abstract Zoonoses are “those diseases and infections which are naturally transmitted between vertebrate animals and man.” Relevant lists of zoonotic diseases are presented. Factors, including environmental aspects that may influence the manifestation of zoonoses and their significance for public health, are discussed. Foodborne, nonfoodborne, and vector-borne diseases are presented, followed by an article on preventative actions and control measures. Specific reference is made to the ‘One Health’ concept, since, for zoonoses containment, an integrated approach and cooperation between all responsible health professionals, at all levels, is a sine qua non precondition.


QT Interval Control to Prevent Torsades de Pointes during Use of Hydroxychloroquine and/or Azithromycin in Patients with COVID-19


title: Coagulopathy and Antiphospholipid Antibodies in Patients with Covid-19

text: The authors describe a 69-year-old man with Covid-19 diagnosed in January 2020 in Wuhan, China, along with two other critically ill patients with Covid-19 who were also seen in the same intensive care unit. Coagulopathy and antiphospholipid antibodies were seen in all three patients.


title: Membrane Fusion☆

text: Abstract Entry of enveloped viruses is mediated by viral glycoproteins that catalyze fusion of viral and cellular membranes. These viral glycoproteins need to be activated which leads to extensive conformational changes that trigger the insertion or attachment of a fusion peptide in or to cellular target membranes thus bridging two bilayers. Further refolding into a hairpin-like structure pulls viral and cellular membranes into close apposition, a process that leads to lipid bilayer fusion. Although viral fusion proteins belong to three different classes based on their structural organization, they follow similar structural principles to achieve fusion.


title: Porcine deltacoronavirus activates the Raf/MEK/ERK pathway to promote its replication

text: Abstract Porcine deltacoronavirus (PDCoV) is a newly emerged swine coronavirus that causes acute enteritis in neonatal piglets. To date, little is known about the host factors or cellular signaling mechanisms associated with PDCoV replication. Since the Raf/MEK/ERK pathway is involved in modulation of various important cellular functions, numerous DNA and RNA viruses coopt this pathway for efficient propagation. In the present study, we found that PDCoV induces the activation of ERK1/2 and its downstream substrate Elk-1 early in infection irrespective of viral biosynthesis. Chemical inhibition or knockdown of ERK1/2 significantly suppressed viral replication, whereas treatment with an ERK activator increased viral yields. Direct pharmacological inhibition of ERK activation had no effect on the viral entry process but sequentially affected the post-entry steps of the virus life cycle. In addition, pharmacological sequestration of cellular or viral cholesterol downregulated PDCoV-induced ERK signaling, highlighting the significance of the cholesterol contents in ERK activation. However, ERK inhibition had no effect on PDCoV-triggered apoptosis through activation of the cytochrome c-mediated intrinsic mitochondrial pathway, suggesting the irrelevance of ERK activation to the apoptosis pathway during PDCoV infection. Altogether, our findings indicate that the ERK signaling pathway plays a pivotal role in viral biosynthesis to facilitate the optimal replication of PDCoV.


title: Promoter structures and differential responses to viral and non-viral inducers of chicken melanoma differentiation-associated gene 5

text: Abstract Melanoma differentiation-associated gene 5 (MDA5) is a member of the retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) family and plays a pivotal role in the anti-viral innate immune response. As RIG-I is absent in chickens, MDA5 is hypothesized to be important in detecting viral nucleic acids in the cytoplasm. However, the molecular mechanism of the regulation of chicken MDA5 (chMDA5) expression has yet to be fully elucidated. With this in mind, a ∼2.5kb chMDA5 gene promoter region was examined and PCR amplified to assess its role in immune response. A chMDA5 promoter reporter plasmid (piggybac-MDA5-DsRed) was constructed and transfected into DF-1 cells to establish a Piggybac-MDA5-DsRed cell line. The MDA5 promoter activity was extremely low under basal condition, but was dramatically increased when cells were stimulated with polyinosinic: polycytidylic acid (poly I:C), interferon beta (IFN-β) or Infectious Bursal Disease Virus (IBDV). The DsRed mRNA level represented the promoter activity and was remarkably increased, which matched the expression of endogenous MDA5. However, Infectious Bronchitis Virus (IBV) and Newcastle disease virus (NDV) failed to increase the MDA5 promoter activity and the expression of endogenous MDA5. The results indicated that the promoter and the Piggybac-MDA5-DsRed cell line could be utilized to determine whether a ligand regulates MDA5 expression. For the first time, this study provides a tool for testing chMDA5 expression and regulation.


title: Sleep quality and mood symptoms in conscripted frontline nurse in Wuhan, China during COVID-19 outbreak: A cross-sectional study

text: The aim of this study was to investigate the prevalence of sleep problems, depression and anxiety symptoms among conscripted frontline nurses fighting coronavirus disease 2019 (COVID-19) in Wuhan. This study was a cross-sectional study conducted with 100 frontline nurses. Sleep quality, depression, and anxiety symptoms were measured using the Pittsburgh sleep quality index (PSQI), the Generalized Anxiety Disorder 7-Item Scale (GAD-7) and the Patient Health Questionnaire-9 (PHQ-9), respectively. Mean sleep duration was 5.71 hours (SD = 1.09) and mean sleep latency was 33.49 minutes (SD = 28.87). A total of 76%, 81%, 45%, and 19% reported difficulty initiating sleep (DIS), difficulty maintaining sleep (DMS) or early morning awakening (EMA), nightmares and using hypnotics respectively. Among 100 participants in this study, 60 (60%) had poor sleep quality, 46 (46%) suffered depression symptoms and 40 (40%) reported anxiety symptoms. Sleep quality (OR = 3.16, 95% CI: 1.17–8.52) and anxiety symptoms (OR = 8.07, 95% CI: 2.92–22.33) were significantly associated with depression symptoms. Depression symptoms (OR = 7.92, 95% CI: 2.89–21.73) were related to anxiety symptoms. Similarly, depression symptoms (OR = 3.24, 95% CI: 1.19–8.79) were associated with poor sleep quality. Sleep disturbance, depression, and anxiety symptoms are very common among frontline nurses who treating patients with COVID-19 in Wuhan, China. Comprehensive measures that involve psychosocial and personal behaviors should be implemented to improve sleep quality and prevent depression and anxiety symptoms.


title: Functional analysis of Rousettus aegyptiacus “signal transducer and activator of transcription 1” (STAT1)

text: Bats are now known as the source of several diseases in humans, but few studies regarding immune responses and factors associated with bats have so far been reported. In this study, we focused on STAT1, one of the critical components in interferon (IFN)-signaling and antiviral activity, which is often targeted by viral proteins to reduce antiviral activity and increase viral replication. We found that Rousettus aegyptiacus STAT1 (bat STAT1) is phosphorylatable and translocates to the nucleus when stimulated with human IFN-α (hIFN-α). Furthermore, phosphorylation of bat STAT1 and inhibition of nuclear translocation was observed in IFN-stimulated cells infected with the HEP-Flury strain of rabies virus, in the same manner as in other mammals. Additionally, quantitative real-time RT-PCR revealed that bat STAT1 mRNA was highly expressed in the liver, while low in muscle and spleen.


title: Nucleolin stabilizes G-quadruplex structures folded by the LTR promoter and silences HIV-1 viral transcription

text: Folding of the LTR promoter into dynamic G-quadruplex conformations has been shown to suppress its transcriptional activity in HIV-1. Here we sought to identify the proteins that control the folding of this region of proviral genome by inducing/stabilizing G-quadruplex structures. The implementation of electrophorethic mobility shift assay and pull-down experiments coupled with mass spectrometric analysis revealed that the cellular protein nucleolin is able to specifically recognize G-quadruplex structures present in the LTR promoter. Nucleolin recognized with high affinity and specificity the majority, but not all the possible G-quadruplexes folded by this sequence. In addition, it displayed greater binding preference towards DNA than RNA G-quadruplexes, thus indicating two levels of selectivity based on the sequence and nature of the target. The interaction translated into stabilization of the LTR G-quadruplexes and increased promoter silencing activity; in contrast, disruption of nucleolin binding in cells by both siRNAs and a nucleolin binding aptamer greatly increased LTR promoter activity. These data indicate that nucleolin possesses a specific and regulated activity toward the HIV-1 LTR promoter, which is mediated by G-quadruplexes. These observations provide new essential insights into viral transcription and a possible low mutagenic target for antiretroviral therapy.


title: Feed additives decrease survival of delta coronavirus in nursery pig diets

text: BACKGROUND: Feed contaminated with feces from infected pigs is believed to be a potential route of transmission of porcine delta coronavirus (PDCoV). The objective of this study was to determine if the addition of commercial feed additives (e.i., acids, salt and sugar) to swine feed can be an effective strategy to inactive PDCoV. RESULTS: Six commercial feed acids (UltraAcid P, Activate DA, KEMGEST, Acid Booster, Luprosil, and Amasil), salt, and sugar were evaluated. The acids were added at the recommended concentrations to 5 g aliquots of complete feed, which were also inoculated with 1 mL of PDCoV and incubated for 0, 7, 14, 21, 28, and 35 days. In another experiment, double the recommended concentrations of these additives were also added to the feed samples and incubated for 0, 1, 3, 7, and 10 days. All samples were stored at room temperature (~25 °C) followed by removal of aliquots at 0, 7, 14, 21, 28, and 35 days. Any surviving virus was eluted in a buffer solution and then titrated in swine testicular cells. Feed samples without any additive were used as controls. Both Weibull and log-linear kinetic models were used to analyze virus survival curves. The presence of a tail in the virus inactivation curves indicated deviations from the linear behavior and hence, the Weibull model was chosen for characterizing the inactivation responses due to the better fit. At recommended concentrations, delta values (days to decrease virus concentration by 1 log) ranged from 0.62–1.72 days, but there were no differences on virus survival among feed samples with or without additives at the manufacturers recommended concentrations. Doubling the concentration of the additives reduced the delta value to ≤ 0.28 days (P < 0.05) for all the additives except for Amasil (delta values of 0.86 vs. 4.95 days). Feed additives that contained phosphoric acid, citric acid, or fumaric acid were the most effective in reducing virus survival, although none of the additives completely inactivated the virus by 10- days post-inoculation. CONCLUSIONS: Commercial feed additives (acidifiers and salt) may be utilized as a strategy to decrease risk of PDCoV in feed, specially, commercial feed acidifiers at double the recommended concentrations reduced PDCoV survival in complete feed during storage at room temperature. However, none of these additives completely inactivated the virus.


title: Clinical and sero-molecular characterization of Escherichia coli with an emphasis on hybrid strain in healthy and diarrheic neonatal calves in Egypt

text: The present study was carried out to characterize pathogenic E. coli in apparently healthy and diarrheic neonatal calves with special reference to the hybrid E. coli strains and evaluate their clinical and hematobiochemical consequences. One hundred and seventy calves (age 1-30 days) were divided into two groups: apparently healthy (n = 70) and diarrheic (n=100). Animals were subjected to thorough clinical, hematobiochemical and bacteriological examinations. Clinically, diarrheic calves showed various degree of diarrhea with the presence of cardinal signs of dehydration in moderate and severe cases. There was a significant increase (p<0.05) in the hemogram parameters with uremia and hyperkalemia in calves with severe diarrhea. The O-H serotyping of cultural and biochemically positive isolates identified 31 isolates belonging to 12 serotypes including O44:H18, O55:H7, O146:H21, O113:H4, O121:H7, O26:H11, O91:H21, O111:H2, O8, O127: H6, O86 and O128:H2. Molecular characterization of E. coli isolates on three toxin genes: heat-stable enterotoxin (sta), shiga toxin type 1 and 2 (stx1 and stx2) revealed two well-known pathotypes (EPEC O44:H18, O55:H7, O146:H21, O113:H4, O121:H7 and EHEC O26:H11 O91:H21 O111:H2) with high frequency of enterohemorrhagic E. coli (EHEC). Molecular analysis also showed a number of E. coli isolates that carry sta and stx1 or sta and stx2 gene and belonged to O8, and O127:H6, O86 and O128:H2. These isolates were identified as hybrid E. coli strains (ETEC-STEC) and found in both apparently healthy and diarrheic calves. In conclusion, the present study identified high frequency of pathogenic E. coli in both apparently healthy and diarrheic calves. Serological and molecular analysis of E. coli isolates showed that high frequency of EHEC and presence of a new phenotype, STEC–ETEC hybrid, revealing their importance in the etiopathogenesis of diarrhea in calves and reinforcing the role of these animals as a reservoir of potentially pathogenic E. coli for humans.


title: Molecular Selection, Modification and Development of Therapeutic Oligonucleotide Aptamers

text: Monoclonal antibodies are the dominant agents used in inhibition of biological target molecules for disease therapeutics, but there are concerns of immunogenicity, production, cost and stability. Oligonucleotide aptamers have comparable affinity and specificity to targets with monoclonal antibodies whilst they have minimal immunogenicity, high production, low cost and high stability, thus are promising inhibitors to rival antibodies for disease therapy. In this review, we will compare the detailed advantages and disadvantages of antibodies and aptamers in therapeutic applications and summarize recent progress in aptamer selection and modification approaches. We will present therapeutic oligonucleotide aptamers in preclinical studies for skeletal diseases and further discuss oligonucleotide aptamers in different stages of clinical evaluation for various disease therapies including macular degeneration, cancer, inflammation and coagulation to highlight the bright commercial future and potential challenges of therapeutic oligonucleotide aptamers.


title: Diagnosis and Treatment of Infectious Enteritis in Adult Ruminants

text: Infectious enteritis in adult ruminants is often a result of 1 or more viral, bacterial, or parasitic pathogens. Diagnosis of etiologic agents causing enteritis is important when considering herd implications and zoonotic potential of some etiologies. Differential diagnoses for enteritis in adult ruminants is not simple based on clinical signs alone. Diagnostic samples include feces, blood, and antemortem and postmortem tissues. Treatment of infectious enteritis is aimed at correcting dehydration and electrolyte imbalances secondary to diarrhea. In cases of some bacterial and parasitic pathogens, additional targeted treatment and control are recommended. Management of enteritis may be instituted while awaiting laboratory test results.


title: Specific probiotics and virological findings in symptomatic conscripts attending military service in Finland

text: Abstract Background Viral upper respiratory tract infections occur frequently among conscripts. Probiotics have reduced viral infections in children attending day care. Limited data are available on the effects of probiotics on the nasopharyngeal presence of respiratory viruses. Objectives To assess, whether probiotics could decrease nasopharyngeal occurrence of respiratory viruses in Finnish conscripts. Study design In a randomized, double-blind, placebo-controlled 90- and 150-day intervention study, 239 nasopharyngeal swab samples were collected from 192 symptomatic conscripts receiving daily chewable probiotic tablet containing Lactobacillus rhamnosus GG and Bifidobacterium animalis ssp. lactis BB-12 (46.9%) or control tablet (53.1%) on visits to a garrison's health care center due to symptoms of infection. The presence of respiratory viruses was tested by PCR-methods, and viral findings were compared between the intervention groups. Results 184 (76.9%) nasopharyngeal samples were positive for at least one respiratory virus. Picornaviruses were the most common viruses and were detected in 155 (84.2%) of samples. Of these, 143 (92.3%) were rhinovirus-positive and 20 (12.9%) were enterovirus-positive. The control group had 83 (64%) and the probiotic group 72 (66%) picornavirus infections (p =0.79). Monthly distribution of picornaviruses showed that there were less picornavirus findings after 3 months in the probiotic group than in the control group (p =0.0069). However, probiotics did not reduce picornavirus occurrence in other months. Conclusions Overall, probiotics did not reduce viral occurrence in symptomatic conscripts. However, probiotics decreased the presence of picornaviruses after 3 months, which may imply that probiotics play a role against viruses causing common cold. Further investigations are necessary to clarify the mechanisms involved in order to target specific probiotics on specific respiratory viruses.


title: Successful treatment of plasma exchange followed by intravenous immunogloblin in a critically ill patient with 2019 novel coronavirus infection

text: Abstract We report a case of a laboratory-confirmed 2019 novel coronavirus infected (known as COVID-19) patient who developed respiratory failure and shock accompanied by persistent diarrhoea despite conventional therapeutic interventions. The patient avoided mechanical ventilation and acquired an immediate clinical and radiological improvement, after treatment of intensive plasma exchange (PE) followed by intravenous immunogloblin (IVIG). Successful therapeutic strategies in our case suggest timely initiating PE treatment followed by IVIG in critically ill patients with COVID-19 may prevent the disease from worsening and help to reduce the requirements for mechanical ventilation and intensive supportive care. What's more, it may improve poor clinical outcomes of these patients.


title: Fecal specimen diagnosis 2019 novel coronavirus–infected pneumonia

text: The emergence and spread of 2019 novel coronavirus–infected pneumonia (COVID‐19) from Wuhan, China, it has spread globally. We extracted the data on 14 patients with laboratory‐confirmed COVID‐19 from Jinhua Municipal Central hospital through 27 January 2020. We found that compared to pharyngeal swab specimens, nucleic acid detection of COVID‐19 in fecal specimens was equally accurate. And we found that patients with a positive stool test did not experience gastrointestinal symptoms and had nothing to do with the severity of the lung infection. These results may help to understand the clinical diagnosis and the changes in clinical parameters of COVID‐19.


title: The nucleolar protein GLTSCR2 is required for efficient viral replication

text: Glioma tumor suppressor candidate region gene 2 protein (GLTSCR2) is a nucleolar protein. In the investigation of the role of GLTSCR2 that played in the cellular innate immune response to viral infection, we found GLTSCR2 supported viral replication of rhabdovirus, paramyxovirus, and coronavirus in cells. Viral infection induced translocation of GLTSCR2 from nucleus to cytoplasm that enabled GLTSCR2 to attenuate type I interferon IFN-β and support viral replication. Cytoplasmic GLTSCR2 was able to interact with retinoic acid-inducible gene I (RIG-I) and the ubiquitin-specific protease 15 (USP15), and the triple interaction induced USP15 activity to remove K63-linked ubiquitination of RIG-I, leading to attenuation of RIG-I and IFN-β. Blocking cytoplasmic translocation of GLTSCR2, by deletion of its nuclear export sequence (NES), abrogated its ability to attenuate IFN-β and support viral replication. GLTSCR2-mediated attenuation of RIG-I and IFN-β led to alleviation of host cell innate immune response to viral infection. Our findings suggested that GLTSCR2 contributed to efficient viral replication, and GLTSCR2 should be considered as a potential target for therapeutic control of viral infection.


title: Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples

text: RNA viruses cause significant human pathology and are responsible for the majority of emerging zoonoses. Mainstream diagnostic assays are challenged by their intrinsic diversity, leading to false negatives and incomplete characterisation. New sequencing techniques are expanding our ability to agnostically interrogate nucleic acids within diverse sample types, but in the clinical setting are limited by overwhelming host material and ultra-low target frequency. Through selective host RNA depletion and compensatory protocol adjustments for ultra-low RNA inputs, we are able to detect three major blood-borne RNA viruses – HIV, HCV and HEV. We recovered complete genomes and up to 43% of the genome from samples with viral loads of 10(4) and 10(3) IU/ml respectively. Additionally, we demonstrated the utility of this method in detecting and characterising members of diverse RNA virus families within a human plasma background, some present at very low levels. By applying this method to a patient sample series, we have simultaneously determined the full genome of both a novel subtype of HCV genotype 6, and a co-infecting human pegivirus. This method builds upon earlier RNA metagenomic techniques and can play an important role in the surveillance and diagnostics of blood-borne viruses.


COVID‐19 epidemic: Regional organization centered on nursing homes


title: Stimulating collaboration between human and veterinary health care professionals

text: BACKGROUND: Despite the need to control outbreaks of (emerging) zoonotic diseases and the need for added value in comparative/translational medicine, jointly addressed in the One Health approach [One health Initiative (n.d.a). About the One Health Initiative. http://www.onehealthinitiative.com/about.php. Accessed 13 September 2016], collaboration between human and veterinary health care professionals is limited. This study focuses on the social dilemma experienced by health care professionals and ways in which an interdisciplinary approach could be developed. RESULTS: Based on Gaertner and Dovidio’s Common Ingroup Identity Model, a number of questionnaires were designed and tested; with PROGRESS, the relation between collaboration and common goal was assessed, mediated by decategorization, recategorization, mutual differentiation and knowledge sharing. This study confirms the Common Ingroup Identity Model stating that common goals stimulate collaboration. Decategorization and mutual differentiation proved to be significant in this relationship; recategorization and knowledge sharing mediate this relation. CONCLUSIONS: It can be concluded that the Common Ingroup Identity Model theory helps us to understand how health care professionals perceive the One Health initiative and how they can intervene in this process. In the One Health approach, professional associations could adopt a facilitating role.


title: Supply chain disruption management and evolutionarily stable strategies of retailers in the quantity-setting duopoly situation with homogeneous goods

text: Abstract This paper develops an indirect evolutionary game model with two-vertically integrated channels to study evolutionarily stable strategies (ESS) of retailers in the quantity-setting duopoly situation with homogeneous goods and analyzes the effects of the demand and raw material supply disruptions on the retailers’ strategies. Every channel consists of one manufacturer and many (a sufficiently large number of) retailers that sell products in different markets by adopting two pure marketing strategies: profit maximization and revenue maximization. We find that revenue maximization strategy may prevail and profit maximization strategy may become extinct. Two strategies may coexist, i.e., all retailers in one channel will choose profit maximization strategy and all retailers in the other will choose revenue maximization strategy. The ESS of retailers depends on the relative size of the market scale and unit cost. The supply chain disruptions affect the ESS of retailers. We also introduce a recovery model of the supply chain under disruptions and illustrate the effect of disruptions on the ESS and on the average profits of channels in a market using a numerical simulation.


title: Diagnosis and epidemiological studies of human metapneumovirus using real-time PCR

text: Abstract Background Human metapneumovirus (hMPV) is prevalent in children, the elderly and immunocompromised individuals, but available epidemiological data is limited. Objectives (1) To develop and validate a real-time PCR method for hMPV diagnosis. (2) To determine the percentage of hMPV in respiratory specimens from the community and its association with outbreaks in our geographic area. (3) To provide epidemiological data in terms of age distribution, seasonality and co-infections. Study design A real-time PCR assay was designed for detection of hMPV lineages A and B. Prospective testing for hMPV over a 22-month period was then undertaken. Results The real-time PCR was sensitive and specific for detection of both lineages of hMPV. hMPV was detected in 9.5% (n =8239) of the specimens and 25% of the outbreaks (n =100) tested. The hMPV-positive patients ranged in age from 18 days to 99 years with a median age of 24 months. The number of positive samples peaked during the winter months of December, January and February. A high rate of co-infections was noted in the samples tested. Conclusions hMPV is common in the community and is associated with outbreaks. Including hMPV in routine testing improves etiological diagnosis of acute respiratory infections.


title: Are your hands clean? Pollen retention on the human hand after washing

text: Pollen retention on clothes, footwear, hair and body has been used to link people to localities with distinctive vegetation, or soils containing distinctive palynomorphs. Little attention has been given to human skin as a possible medium for carrying a forensically important pollen load and whether this might survive attempts to remove it. We report here the results of experiments testing the retention of pollen of 10 flowering plant species on the human skin through repeated cycles of washing and drying hands, using the WHO protocol to standardize hand-washing and drying. Between 0.36% and 2.74% (mean 0.93%) of the initial pollen load was retained through a single hand-wash. Trace amounts of some species survived multiple hand-wash cycles. It is concluded that forensic analyses can be made of the pollen load of those parts of the skin that may have been in contact with palynologically distinctive vegetation, even in cases where the person involved has washed, or been washed. These observations may also be of relevance in cases where human skin became contaminated with other microscopic particulates.


title: Solving the master equation for Indels

text: BACKGROUND: Despite the long-anticipated possibility of putting sequence alignment on the same footing as statistical phylogenetics, theorists have struggled to develop time-dependent evolutionary models for indels that are as tractable as the analogous models for substitution events. MAIN TEXT: This paper discusses progress in the area of insertion-deletion models, in view of recent work by Ezawa (BMC Bioinformatics 17:304, 2016); (BMC Bioinformatics 17:397, 2016); (BMC Bioinformatics 17:457, 2016) on the calculation of time-dependent gap length distributions in pairwise alignments, and current approaches for extending these approaches from ancestor-descendant pairs to phylogenetic trees. CONCLUSIONS: While approximations that use finite-state machines (Pair HMMs and transducers) currently represent the most practical approach to problems such as sequence alignment and phylogeny, more rigorous approaches that work directly with the matrix exponential of the underlying continuous-time Markov chain also show promise, especially in view of recent advances.


SARS, Mars and chocolate bars


title: Coronavirus Disease-19: Quarantine Framework for Travelers Entering Korea

text: South Korea is operating a flexible quarantine management system which is based on the results of epidemiological investigations of patients arriving from overseas with coronavirus disease-19 (COVID-19), and closely monitoring COVID-19 outbreaks. South Korea has designated countries with a localized, high prevalence of infection as “quarantine inspection required areas” and has reinforced quarantine measures by applying special immigration procedures for people entering South Korea. Furthermore, South Korea also provides information on international travel history of entrants (who are South Korean citizens and foreign nationals) to all medical institutions, through the smart quarantine information system. On March 11(th) 2020, the World Health Organization characterized COVID-19 as a pandemic. Inevitably, the number of patients from overseas with COVID-19 (based on 10,000 people entering South Korea), increased to 10 cases in the second week of March, 37 cases in the third week, and 67.7 cases in the fourth week. However, after enforcing quarantine strengthening measures, and with a decrease in the number of people entering the country, the number of cases decreased to 52.0 in the first week of April.


title: A review on recent developments of indole-containing antiviral agents

text: Indole represents one of the most important privileged scaffolds in drug discovery. Indole derivatives have the unique property of mimicking the structure of peptides and to bind reversibly to enzymes, which provide tremendous opportunities to discover novel drugs with different modes of action. There are seven indole-containing commercial drugs in the Top-200 Best Selling Drugs by US Retail Sales in 2012. There are also an amazing number of approved indole-containing drugs in the market as well as compounds currently going through different clinical phases or registration statuses. This review focused on the recent development of indole derivatives as antiviral agents with the following objectives: 1) To present one of the most comprehensive listings of indole antiviral agents, drugs on market or compounds in clinical trials; 2) To focus on recent developments of indole compounds (including natural products) and their antiviral activities, summarize the structure property, hoping to inspire new and even more creative approaches; 3) To offer perspectives on how indole scaffolds as a privileged structure might be exploited in the future.


title: Cross-talking between autophagy and viral infection in mammalian cells

text: Autophagy is a cellular process in degradation of long-lived proteins and organelles in the cytosol for maintaining cellular homeostasis, which has been linked to a wide range of human health and disease states, including viral infection. The viral infected cells exhibit a complicated cross-talking between autophagy and virus. It has been shown that autophagy interacts with both adaptive and innate immunity. For adaptive immunity, viral antigens can be processed in autophagosomes by acidic proteases before major histocompatibility complex (MHC) class II presentation. For innate immunity, autophagy may assist in the delivery of viral nucleic acids to endosomal TLRs and also functions as a part of the TLR-or-PKR-downstream responses. Autophagy was also reported to suppress the magnitude of host innate antiviral immunity in certain cases. On the other hand, viruses has evolved many strategies to combat or utilize the host autophagy for their own benefit. In this review we discussed recent advances toward clarifying the cross-talking between autophagy and viral infection in mammalian cells.


title: Presence of infectious polyadenylated RNA in the coronavirus avian bronchitis virus

text: Abstract Avian infectious bronchitis virus (IBV) was radiolabeled for its nucleic acid component by growth in deembryonated chicken eggs. Purified virions of IBV have a buoyant density in linear sucrose gradients of 1.17-1.18 g/cm3 and contain approximately 4% RNA by weight. The genomic ribonucleic acid of IBV shows the following characteristic: (1) It consists of one size class of single-stranded RNA having a molecular weight of 5.5-5.7 x 108 and a sedimentation coefficient of about 48 S; (2) no evidence for subunit structure is apparent since the RNA resolves as a single species with the same electrophoretic mobility in polyacrylamide gels before and after heat denaturation; (3) at least 20–30% of the RNA molecules extracted from purified virions contain sequences of polyadenylic acid of approximately 4 S size; (4) RNA obtained from detergent-disrupted virus particles by phenol-chloroform extraction is infectious for cultures of chick embryo fibroblasts, giving rise to progeny virus which is lethal for embryonated eggs. These findings, together with the observation that IBV virions do not exhibit detectable transcriptase activity, support the conclusion that the genome of this coronavirus acts directly as a messenger RNA in eukaryotic cells.


In 1969 man landed on the moon, how can we also eradicate COVID‐19?


title: Differential effects of viroporin inhibitors against feline infectious peritonitis virus serotypes I and II

text: Feline infectious peritonitis virus (FIP virus: FIPV), a feline coronavirus of the family Coronaviridae, causes a fatal disease called FIP in wild and domestic cat species. The genome of coronaviruses encodes a hydrophobic transmembrane protein, the envelope (E) protein. The E protein possesses ion channel activity. Viral proteins with ion channel activity are collectively termed “viroporins”. Hexamethylene amiloride (HMA), a viroporin inhibitor, can inhibit the ion channel activity of the E protein and replication of several coronaviruses. However, it is not clear whether HMA and other viroporin inhibitors affect replication of FIPV. We examined the effect of HMA and other viroporin inhibitors (DIDS [4,4′-disothiocyano-2,2′-stilbenedisulphonic acid] and amantadine) on infection by FIPV serotypes I and II. HMA treatment drastically decreased the titers of FIPV serotype I strains Black and KU-2 in a dose-dependent manner, but it only slightly decreased the titer of FIPV serotype II strain 79-1146. In contrast, DIDS treatment decreased the titer of FIPV serotype II strain 79-1146 in dose-dependent manner, but it only slightly decreased the titers of FIPV serotype I strains Black and KU-2. We investigated whether there is a difference in ion channel activity of the E protein between viral serotypes using E. coli cells expressing the E protein of FIPV serotypes I and II. No difference was observed, suggesting that a viroporin other than the E protein influences the differences in the actions of HMA and DIDS on FIPV serotypes I and II.


title: Tyrosine dephosphorylation of STAT3 in SARS coronavirus-infected Vero E6 cells

text: Severe acute respiratory syndrome (SARS) has become a global public health emergency. p38 mitogen-activated protein kinase (MAPK) and its downstream targets are activated in SARS coronavirus (SARS-CoV)-infected Vero E6 cells and activation of p38 MAPK enhances the cytopathic effects of SARS-CoV infection. In addition, weak activation of Akt cannot prevent SARS-CoV infection-induced apoptosis in Vero E6 cells. In the present study, we demonstrated that signal transducer and activator of transcription (STAT) 3, which is constitutively phosphorylated at tyrosine (Tyr)-705 and slightly phosphorylated at serine (Ser)-727 in Vero E6 cells, was dephosphorylated at Tyr-705 on SARS-CoV infection. In addition to phosphorylation of p38 MAPK in virus-infected cells, other MAPKs, i.e., extracellular signal-regulated kinase (ERK) 1/2 and c-Jun N-terminal kinase (JNK), were phosphorylated. Although inhibitors of ERK1/2 and JNK (PD98059 and SP600125) had no effect on phosphorylation status of STAT3, inhibitors of p38 MAPK (SB203580 and SB202190) partially inhibited dephosphorylation of STAT3 at Tyr-705. Tyr-705-phosphorylated STAT3 was localized mainly in the nucleus in mock infected cells, whereas STAT3 disappeared from the nucleus in virus-infected cells. As STAT3 acts as an activator of transcription in the nucleus, these results suggest that STAT3 lacks its activity on transcription in SARS-CoV-infected Vero E6 cells.


title: Defective viral genomes are key drivers of the virus–host interaction

text: Viruses survive often harsh host environments, yet we know little about the strategies they utilize to adapt and subsist given their limited genomic resources. We are beginning to appreciate the surprising versatility of viral genomes and how replication-competent and -defective virus variants can provide means for adaptation, immune escape and virus perpetuation. This Review summarizes current knowledge of the types of defective viral genomes generated during the replication of RNA viruses and the functions that they carry out. We highlight the universality and diversity of defective viral genomes during infections and discuss their predicted role in maintaining a fit virus population, their impact on human and animal health, and their potential to be harnessed as antiviral tools.


title: Comparative analyses of the nucleocapsid genes of several strains of infectious bronchitis virus and other coronaviruses

text: Abstract The natural sequence variations of the nucleocapsid genes of the Gray, Arkansas99 (Ark99), and Holland52 (Holl52) strains of infectious bronchitis virus (IBV) were determined. These were compared with previously published sequencing data of other IBV strains, as well as other coronaviruses, in order to correlate the serological and evolutionary relationship of coronaviruses. IBV nucleotide sequence alignment shows that overall the sequences are highly conserved, with homologies from 91.1 to 96.5%. However, there are also two regions (730 to 800 and 1138 to 1166) that appear to be even more highly conserved. Overall, the nucleocapsid protein is highly variable both in size and composition between coronavirus major antigenic groups but is conserved within these groups. A phylogenetic tree of the nucleocapsid protein of various coronaviruses indicates that the coronaviruses fall into distinct groups that correspond to the three major antigenic groups; however, a phylogenetic tree of the IBV nucleocapsid shows that this does not hold true for the type specific antigenic groups of IBV.


title: Lymphocyte-to-C-Reactive Protein Ratio: A Novel Predictor of Adverse Outcomes in COVID-19

text: BACKGROUND: Systemic inflammation elicited by a cytokine storm is considered a hallmark of coronavirus disease 2019 (COVID-19). This study aims to assess the validity and clinical utility of the lymphocyte-to-C-reactive protein (CRP) ratio (LCR), typically used for gastric carcinoma prognostication, versus the neutrophil-to-lymphocyte ratio (NLR) for predicting in-hospital outcomes in COVID-19. METHODS: A retrospective cohort study was performed to determine the association of LCR and NLR with the need for invasive mechanical ventilation (IMV), dialysis, upgrade to an intensive care unit (ICU) and mortality. Independent t-test and multivariate logistic regression analysis were performed to calculate mean differences and adjusted odds ratios (aORs) with its 95% confidence interval (CI), respectively. RESULTS: The mean age for NLR patients was 63.6 versus 61.6, and for LCR groups, it was 62.6 versus 63.7 years, respectively. The baseline comorbidities across all groups were comparable except that the higher LCR group had female predominance. The mean NLR was significantly higher for patients who died during hospitalization (19 vs. 7, P ≤ 0.001) and those requiring IMV (12 vs. 7, P = 0.01). Compared to alive patients, a significantly lower mean LCR was observed in patients who did not survive hospitalization (1,011 vs. 632, P = 0.04). For patients with a higher NLR (> 10), the unadjusted odds of mortality (odds ratios (ORs) 11.0, 3.6 - 33.0, P < 0.0001) and need for IMV (OR 3.3, 95% CI 1.4 - 7.7, P = 0.008) were significantly higher compared to patients with lower NLR. By contrast, for patients with lower LCR (< 100), the odds of in-hospital all-cause mortality were significantly higher compared to patients with a higher LCR (OR 0.2, 0.06 - 0.47, P = 0.001). The aORs controlled for baseline comorbidities and medications mirrored the overall results, indicating a genuinely significant correlation between these biomarkers and outcomes. CONCLUSIONS: A high NLR and decreased LCR value predict higher odds of in-hospital mortality. A high LCR at presentation might indicate impending clinical deterioration and the need for IMV.


title: SARS Antibody Test for Serosurveillance

text: A peptide-based enzyme-linked immunosorbent assay (ELISA) can be used for retrospective serosurveillance of severe acute respiratory syndrome (SARS) by helping identify undetected chains of disease transmission. The assay was developed by epitope mapping, using synthetic peptides from the spike, membrane, and nucleocapsid protein sequences of SARS-associated coronavirus. The new peptide ELISA consistently detected seroconversion by week 2 of onset of fever, and seropositivity remained through day 100. Specificity was 100% on normal blood donor samples, on serum samples associated with infection by other pathogens, and on an interference panel. The peptide-based test has advantages of safety, standardization, and automation over previous immunoassays for SARS. The assay was used for a retrospective survey of healthy healthcare workers in Taiwan who treated SARS patients. Asymptomatic seroconversions were detected in two hospitals that had nosocomial disease.


title: Mutational analysis of the SDD sequence motif of a PRRSV RNA-dependent RNA polymerase

text: The subgenomic mRNA transcription and genomic replication of the porcine reproductive and respiratory syndrome virus (PRRSV) are directed by the viral replicase. The replicase is expressed in the form of two polyproteins and is subsequently processed into smaller nonstructural proteins (nsps). nsp9, containing the viral replicase, has characteristic sequence motifs conserved among the RNA-dependent RNA polymerases (RdRp) of positive-strand (PS) RNA viruses. To test whether the conserved SDD motif can tolerate other conserved motifs of RNA viruses and the influence of every residue on RdRp catalytic activity, many amino acids substitutions were introduced into it. Only one nsp9 substitution, of serine by glycine (S3050G), could rescue mutant viruses. The rescued virus was genetically stable. Alteration of either aspartate residue was not tolerated, destroyed the polymerase activity, and abolished virus transcription, but did not eliminate virus replication. We also found that the SDD motif was essentially invariant for the signature sequence of PRRSV RdRp. It could not accommodate other conserved motifs found in other RNA viral polymerases, except the GDD motif, which is conserved in all the other PS RNA viruses. These findings indicated that nidoviruses are evolutionarily related to other PS RNA viruses. Our studies support the idea that the two aspartate residues of the SDD motif are critical and essential for PRRSV transcription and represent a sequence variant of the GDD motif in PS RNA viruses.


title: Epidemiology of viral respiratory infections in a tertiary care centre in the era of molecular diagnosis, Geneva, Switzerland, 2011–2012

text: Few studies have examined the epidemiology of respiratory viral infections in large tertiary centres over more than one season in the era of molecular diagnosis. Respiratory clinical specimens received between 1 January 2011 and 31 December 2012 were analysed. Respiratory virus testing was performed using a large panel of real-time PCR or RT-PCR. Results were analysed according to sample type (upper versus lower respiratory tract) and age group. In all, 2996 (2469 (82.4%) upper; 527 (17.6%) lower) specimens were analysed. Overall positivity rate was 47.4% and 23.7% for upper and lower respiratory samples, respectively. The highest positivity rate was observed in patients under 18 years old (p <0.001); picornaviruses were the most frequent viruses detected over the year. Influenza virus, respiratory syncytial virus, human metapneumovirus and coronaviruses showed a seasonal peak during the winter season, while picornaviruses and adenoviruses were less frequently detected in these periods. Multiple viral infections were identified in 12% of positive cases and were significantly more frequent in children (p <0.001). In conclusion, we observed significant differences in viral infection rates and virus types among age groups, clinical sample types and seasons. Follow-up of viral detection over several seasons allows a better understanding of respiratory viral epidemiology.


title: Longitudinal study on morbidity and mortality in white veal calves in Belgium

text: BACKGROUND: Mortality and morbidity are hardly documented in the white veal industry, despite high levels of antimicrobial drug use and resistance. The objective of the present study was to determine the causes and epidemiology of morbidity and mortality in dairy, beef and crossbred white veal production. A total of 5853 calves, housed in 15 production cohorts, were followed during one production cycle. Causes of mortality were determined by necropsy. Morbidity was daily recorded by the producers. RESULTS: The total mortality risk was 5,3% and was significantly higher in beef veal production compared to dairy or crossbreds. The main causes of mortality were pneumonia (1.3% of the calves at risk), ruminal disorders (0.7%), idiopathic peritonitis (0.5%), enterotoxaemia (0.5%) and enteritis (0.4%). Belgian Blue beef calves were more likely to die from pneumonia, enterotoxaemia and arthritis. Detection of bovine viral diarrhea virus at necropsy was associated with chronic pneumonia and pleuritis. Of the calves, 25.4% was treated individually and the morbidity rate was 1.66 cases per 1000 calf days at risk. The incidence rate of respiratory disease, diarrhea, arthritis and otitis was 0.95, 0.30, 0.11 and 0.07 cases per 1000 calf days at risk respectively. Morbidity peaked in the first three weeks after arrival and gradually declined towards the end of the production cycle. CONCLUSIONS: The present study provided insights into the causes and epidemiology of morbidity and mortality in white veal calves in Belgium, housed in the most frequent housing system in Europe. The necropsy findings, identified risk periods and differences between production systems can guide both veterinarians and producers towards the most profitable and ethical preventive and therapeutic protocols.


title: Posicionamiento de la Sociedad Española de Neumología y Cirugía Torácica en el uso del la telemedicina en los trastornos respiratorios del sueño y ventilación mecánica

text: The rapid introduction of new information and communication technologies into medical practice has prompted Spanish Society of Pulmonology and Thoracic SurgeryR to publish a position paper on sleep-disordered breathing, especially in relation to positive pressure treatment. It should be pointed out that the scientific literature is to some extent controversial due to a paucity of large randomized multicenter studies with long-term follow-up. Moreover, the telematics devices and systems on the market vary widely. As a result, the recommendations are based primarily on a consensus of expert professionals. Another very important aspect addressed extensively in this document is the obvious lack of regulations on legal matters and the operations of commercial companies. The most important recommendations included in this position paper are that telemedicine is primarily advocated in subjects with travel problems or who live far from the hospital, in patients with poor CPAP compliance, and in most cases treated with non-invasive mechanical ventilation. A key element is patient individualization. It is imperative that the relevant technical, legal and ethical requirements (medical device regulations, data protection, and informed consent) are met. Finally, expert professionals from our society must contribute to and become involved in spearheading this technological change.


title: COVID-19 infection presenting as pancreatitis in a pregnant woman: A case report

text: BACKGROUND: The coronavirus 2019 (COVID-19) pandemic has posed unique challenges in healthcare. In obstetrics, there is little information available to guide practice. As new data emerge, the spectrum of initial presenting symptoms has expanded from fever, cough, and dyspnea to gastrointestinal and other symptoms in both pregnant and non-pregnant patients. CASE: A 36-year-old woman, G4P2, at 33 weeks of gestation presented very early in the COVID-19 course with four days of cough and fever, without recent travel or known exposure. She appeared well, with stable vital signs, and was sent home to self-quarantine after a specimen for COVID-19 testing was collected. Two days later, she presented with nausea, vomiting, and abdominal pain, and was diagnosed with acute pancreatitis. CONCLUSION: To date, no cases of human pancreatitis have been identified as related to a COVID-19 infection, although multiple other gastrointestinal symptoms have been described. Given the lack of other etiology, we consider the possibility that patient's acute pancreatitis could be secondary to COVID-19 infection.


title: The 19 kDa Mycobacterium tuberculosis Lipoprotein (LpqH) Induces Macrophage Apoptosis through Extrinsic and Intrinsic Pathways: A Role for the Mitochondrial Apoptosis-Inducing Factor

text: We describe the association of caspase-dependent and caspase-independent mechanisms in macrophage apoptosis induced by LpqH, a 19 kDa Mycobacterium tuberculosis lipoprotein. LpqH triggered TLR2 activation, with upregulation of death receptors and ligands, which was followed by a death receptor signaling cascade with activation of initiator caspase 8 and executioner caspase 3. In this caspase-mediated phase, mitochondrial factors were involved in loss of mitochondrial transmembrane potential (ΔΨm), release of cytochrome c, and caspase 9 activation. Interestingly, a caspase-independent pathway was also identified; by immunoblot, the mitochondrial apoptosis inducing factor (AIF) was demonstrated in nuclei and cytosol of LpqH-treated macrophages. Confocal microscopy revealed translocation of AIF to the nuclei of the majority of apoptotic cells. These findings emphasize the complex and redundant nature of the macrophage death response to mycobacteria.


title: The Q-base of asparaginyl-tRNA is dispensable for efficient −1 ribosomal frameshifting in eukaryotes 1 1 Edited by J. Karn

text: Abstract The frameshift signal of the avian coronavirus infectious bronchitis virus (IBV) contains two cis-acting signals essential for efficient frameshifting, a heptameric slippery sequence (UUUAAAC) and an RNA pseudoknot structure located downstream. The frameshift takes place at the slippery sequence with the two ribosome-bound tRNAs slipping back simultaneously by one nucleotide from the zero phase (U UUA AAC) to the −1 phase (UUU AAA). Asparaginyl-tRNA, which decodes the A-site codon AAC, has the modified base Q at the wobble position of the anticodon (5′ QUU 3′) and it has been speculated that Q may be required for frameshifting. To test this, we measured frameshifting in cos cells that had been passaged in growth medium containing calf serum or horse serum. Growth in horse serum, which contains no free queuine, eliminates Q from the cellular tRNA population upon repeated passage. Over ten cell passages, however, we found no significant difference in frameshift efficiency between the cell types, arguing against a role for Q in frameshifting. We confirmed that the cells cultured in horse serum were devoid of Q by purifying tRNAs and assessing their Q-content by tRNA transglycosylase assays and coupled HPLC-mass spectroscopy. Supplementation of the growth medium of cells grown either on horse serum or calf serum with free queuine had no effect on frameshifting either. These findings were recapitulated in an in vitro system using rabbit reticulocyte lysates that had been largely depleted of endogenous tRNAs and resupplemented with Q-free or Q-containing tRNA populations. Thus Q-base is not required for frameshifting at the IBV signal and some other explanation is required to account for the slipperiness of eukaryotic asparaginyl-tRNA.


title: Suspension and resumption of kidney transplant programs during the COVID‐19 pandemic: perspectives from patients, caregivers and potential living donors‐a qualitative study

text: BACKGROUND: Many countries have suspended kidney transplantation programs during the COVID‐19 pandemic because of concerns for patient safety and the shortage of healthcare resources. This study aimed to describe patient, family member and potential donor perspectives on the suspension and resumption of kidney transplant programs due to COVID‐19. METHODS: We conducted seven online focus groups involving 31 adult kidney transplant candidates (n=22), caregivers (n=4) and potential donors (n=5). Transcripts were analyzed thematically. RESULTS: We identified five themes: cascading disappointments and devastation (with subthemes of shattering hope, succumbing to defeat, regret and guilt); helplessness and vulnerability (fear of declining health, confronted by the threat of and change in dialysis, disconnected from healthcare, susceptibility to infective complications); stress from uncertainty (confusion from conflicting information, unable to forward plan), exacerbating burdens (incurring extra financial costs, intensifying caregiver responsibilities), and sustaining health through the delay (protecting eligibility, relying on social support, adapting to emerging modalities of care). CONCLUSIONS: During the suspension of kidney transplantation programs, patients felt medically vulnerable because of declining health, susceptibility to infection and reduced access to care. There is a need to address health vulnerabilities, disappointment, uncertainty and additional burdens arising from the suspension of kidney transplantation programs.


title: Transmission of gastrointestinal diseases: Hygiene as the final barrier()

text: Am J Infect Control 2001;29:218-21


title: Smoking links to the severity of Covid‐19: An update of a meta‐analysis

text: The paper entitled “The impact of COPD and smoking history on the severity of Covid‐19: A systemic review and meta‐analysis.” published in Journal of Medical Virology on 15 April, 20201. The results revealed the pooled OR of COPD and the development of severe Covid‐19 was 4.38 (Fixed effect model, 95% CI: 2.34‐8.20), while the OR of ongoing smoking was 1.98 (Fixed effect model, 95% CI: 1.29‐3.05). This article is protected by copyright. All rights reserved.


title: Antiviral combinations for severe influenza

text: Observational data suggest that the treatment of influenza infection with neuraminidase inhibitors decreases progression to more severe illness, especially when treatment is started soon after symptom onset. However, even early treatment might fail to prevent complications in some patients, particularly those infected with novel viruses such as the 2009 pandemic influenza A H1N1, avian influenza A H5N1 virus subtype, or the avian influenza A H7N9 virus subtype. Furthermore, treatment with one antiviral drug might promote the development of antiviral resistance, especially in immunocompromised hosts and critically ill patients. An obvious strategy to optimise antiviral therapy is to combine drugs with different modes of action. Because host immune responses to infection might also contribute to illness pathogenesis, improved outcomes might be gained from the combination of antiviral therapy with drugs that modulate the immune response in an infected individual. We review available data from preclinical and clinical studies of combination antiviral therapy and of combined antiviral-immunomodulator therapy for influenza. Early-stage data draw attention to several promising antiviral combinations with therapeutic potential in severe infections, but there remains a need to substantiate clinical benefit. Combination therapies with favourable experimental data need to be tested in carefully designed aclinical trials to assess their efficacy.


Novel human coronavirus associated with respiratory disease


RNA Respiratory Viral Infections in Solid Organ Transplant Recipients


title: Enhancement of accuracy and efficiency for RNA secondary structure prediction by sequence segmentation and MapReduce

text: BACKGROUND: Ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation. Their secondary structures are crucial for the RNA functionality, and the prediction of the secondary structures is widely studied. Our previous research shows that cutting long sequences into shorter chunks, predicting secondary structures of the chunks independently using thermodynamic methods, and reconstructing the entire secondary structure from the predicted chunk structures can yield better accuracy than predicting the secondary structure using the RNA sequence as a whole. The chunking, prediction, and reconstruction processes can use different methods and parameters, some of which produce more accurate predictions than others. In this paper, we study the prediction accuracy and efficiency of three different chunking methods using seven popular secondary structure prediction programs that apply to two datasets of RNA with known secondary structures, which include both pseudoknotted and non-pseudoknotted sequences, as well as a family of viral genome RNAs whose structures have not been predicted before. Our modularized MapReduce framework based on Hadoop allows us to study the problem in a parallel and robust environment. RESULTS: On average, the maximum accuracy retention values are larger than one for our chunking methods and the seven prediction programs over 50 non-pseudoknotted sequences, meaning that the secondary structure predicted using chunking is more similar to the real structure than the secondary structure predicted by using the whole sequence. We observe similar results for the 23 pseudoknotted sequences, except for the NUPACK program using the centered chunking method. The performance analysis for 14 long RNA sequences from the Nodaviridae virus family outlines how the coarse-grained mapping of chunking and predictions in the MapReduce framework exhibits shorter turnaround times for short RNA sequences. However, as the lengths of the RNA sequences increase, the fine-grained mapping can surpass the coarse-grained mapping in performance. CONCLUSIONS: By using our MapReduce framework together with statistical analysis on the accuracy retention results, we observe how the inversion-based chunking methods can outperform predictions using the whole sequence. Our chunk-based approach also enables us to predict secondary structures for very long RNA sequences, which is not feasible with traditional methods alone.


title: Association of visitation policy and health care-acquired respiratory viral infections in hospitalized children

text: Visitor restriction policies are meant to prevent health care-acquired viral infections; however, data on their efficacy in hospitalized children are limited. We report a 37% reduction in health care-acquired respiratory viral infections in a children's hospital following standardization of the visitation policy that limited the number of visitors during a patient's hospitalization.


title: Gastrointestinal Disease in Guinea Pigs and Rabbits

text: This article reviews diagnosis and management of gastrointestinal diseases in guinea pigs and rabbits. The review includes established causes of gastrointestinal disease in these species. The authors highlight syndromes that may be considered emerging or less-recognized causes of gastrointestinal stasis, including gastric dilation and volvulus in guinea pigs and lead toxicity, colonic entrapment, and liver torsion in rabbits. Practitioners should recommend initial diagnostics, including radiographs and blood work on guinea pigs and rabbits presenting with nonspecific signs of gastrointestinal stasis, to better determine possible cause and make the best treatment recommendations.


title: A regioselective etherification of pyridoxine via an ortho-pyridinone methide intermediate

text: Abstract The catalyst-free, regioselective synthesis of 4′-O-substituted pyridoxine derivatives under solventless conditions is described. The methodology relies on the highly regioselective formation of the ortho-pyridinone methide from pyridoxine and subsequent oxa-Michael addition of alcohol nucleophiles. This methodology provides good to excellent yields for primary and secondary alcohols and moderate yields for tertiary alcohols.


Correction: Chinese Social Media Reaction to Information about 42 Notifiable Infectious Diseases


title: Productive replication of nephropathogenic infectious bronchitis virus in peripheral blood monocytic cells, a strategy for viral dissemination and kidney infection in chickens

text: In the present study, the replication kinetics of nephropathogenic (B1648) and respiratory (Massachusetts-M41) IBV strains were compared in vitro in respiratory mucosa explants and blood monocytes (KUL01(+) cells), and in vivo in chickens to understand why some IBV strains have a kidney tropism. B1648 was replicating somewhat better than M41 in the epithelium of the respiratory mucosa explants and used more KUL01(+) cells to penetrate the deeper layers of the respiratory tract. B1648 was productively replicating in KUL01(+) monocytic cells in contrast with M41. In B1648 inoculated animals, 10(2.7–6.8) viral RNA copies/100 mg were detected in tracheal secretions at 2, 4, 6, 8, 10 and 12 days post inoculation (dpi), 10(2.4–4.5) viral RNA copies/mL in plasma at 2, 4, 6, 8, 10 and 12 dpi and 10(1.8–4.4) viral RNA copies/10(6) mononuclear cells in blood at 2, 4, 6 and 8 dpi. In M41 inoculated animals, 10(2.6–7.0) viral RNA copies/100 mg were detected in tracheal secretions at 2, 4, 6, 8 and 10 dpi, but viral RNA was not demonstrated in plasma and mononuclear cells (except in one chicken at 6 dpi). Infectious virus was detected only in plasma and mononuclear cells of the B1648 group. At euthanasia (12 dpi), viral RNA and antigen positive cells were detected in lungs, liver, spleen and kidneys of only the B1648 group and in tracheas of both the B1648 and M41 group. In conclusion, only B1648 can easily disseminate to internal organs via a cell-free and -associated viremia with KUL01(+) cells as important carrier cells.


Transpulmonary Electrotherapy for Reduction of Lung Viral Load of SARS-CoV-2 in Patients with COVID-19


title: The impact of influenza-like illness in young children on their parents: a quality of life survey

text: BACKGROUND: Influenza-like illness can cause excess paediatric morbidity and burden on parents. OBJECTIVES: We determined the quality of life (QoL) impact of children’s influenza-like illness (ILI) on their parents. METHODS: We conducted a prospective cohort study in childcare centres and a general practice in Sydney, Australia. Using PAR-ENT-QoL, we measured QoL of parents of children aged 6 months–3 years before the 2010 influenza season, then again for parents of children with ILI (ILI group) using SF-12v2 Acute Form and PAR-ENT-QoL, and contemporaneously for parents of aged-matched children without ILI (non-ILI group). RESULTS: Of 381 children enrolled from 90 childcare centres, 105 developed ILI. PAR-ENT-QoL scores of the ILI group were significantly lower in the post-ILI follow-up interviews than at baseline (60.99 vs. 79.77, p < 0.001), and those of non-ILI group at follow-up interviews (60.99 vs. 84.05, p < 0.001). SF-12v2 scores of the ILI group were also significantly lower than those of non-ILI group: physical component summary (50.66 vs. 53.16, p = 0.011) and mental component summary (45.67 vs. 53.66, p < 0.001). Two factors were significantly associated with parental QoL: total time spent caring child during ILI and whether the child had severe ILI or not. Correlations between PAR-ENT-QoL and SF-12v2 scores were satisfactory. CONCLUSIONS: Parents had significantly lower QoL while their child had ILI, compared with before ILI and with parents of children without ILI. The public health impact of ILI in children on the QoL in families is far from negligible. QoL measurement can complement economic evaluation of ILI disease burden and provide a more complete picture of impact.


title: Rapid and High-Throughput pan-Orthopoxvirus Detection and Identification using PCR and Mass Spectrometry

text: The genus Orthopoxvirus contains several species of related viruses, including the causative agent of smallpox (Variola virus). In addition to smallpox, several other members of the genus are capable of causing human infection, including monkeypox, cowpox, and other zoonotic rodent-borne poxviruses. Therefore, a single assay that can accurately identify all orthopoxviruses could provide a valuable tool for rapid broad orthopovirus identification. We have developed a pan-Orthopoxvirus assay for identification of all members of the genus based on four PCR reactions targeting Orthopoxvirus DNA and RNA helicase and polymerase genes. The amplicons are detected using electrospray ionization-mass spectrometry (PCR/ESI-MS) on the Ibis T5000 system. We demonstrate that the assay can detect and identify a diverse collection of orthopoxviruses, provide sub-species information and characterize viruses from the blood of rabbitpox infected rabbits. The assay is sensitive at the stochastic limit of PCR and detected virus in blood containing approximately six plaque-forming units per milliliter from a rabbitpox virus-infected rabbit.


title: Neurobehavioral Effects of Restricted and Unpredictable Environmental Enrichment in Rats

text: To study how motivational factors modulate experience-dependent neurobehavioral plasticity, we modify a protocol of environmental enrichment (EE) in rats. We assumed that the benefits derived from EE might vary according to the level of incentive salience attributed to it. To enhance the rewarding properties of EE, access to the EE cage varied randomly from 2 to 48 h for 30 days (REE). The REE group was enriched only 50% of the time and was compared to standard housing and continuous EE (CEE) groups. As behavioral readout, we analyzed the spontaneous activity and the ultrasonic vocalizations (USVs) within the EE cage weekly, and in the open field test at the end of the experiment. In the cage, REE increased the utilization of materials, physical activity, and the rate of appetitive USVs. In the OF, the CEE-induced enhancements in novelty habituation and social signaling were equaled by the REE. At the neural level, we measured the expression of genes related to neural plasticity and epigenetic regulations in different brain regions. In the dorsal striatum and hippocampus, REE upregulated the expression of the brain-derived neurotrophic factor, its tropomyosin kinase B receptor, and the DNA methyltransferase 3A. Altogether, our results suggest that the higher activity within the cage and the augmented incentive motivation provoked by the REE boosted its neurobehavioral effects equaling or surpassing those observed in the CEE condition. As constant exposures to treatments or stimulating environments are virtually impossible for humans, restricted EE protocols would have greater translational value than traditional ones.


The dangers of allowing greater coordination between competitors during the COVID-19 crisis