title: T10B9 monoclonal antibody: A short-acting nonstimulating monoclonal antibody that spares γδ T-cells and treats and prevents cellular rejection

text: T10B9.1A-31/MEDI-500 is a nonmitogenic immunoglobulin M kappa murine monoclonal antibody (mAb) directed against the alpha-beta (αβ) heterodimer of the T-lymphocyte receptor complex. The hybridoma was first produced by fusing spleen cells from BALB/C mice immunized with human peripheral blood T-lymphocytes with SP2/O-Ag14 mutant myeloma cells. The mAb is produced and purified using multistep ion exchange and molecular sieve chromatography protocols. T10B9 has been used successfully to treat acute cellular rejection in renal transplantation and as an immunosuppression induction agent in heart and simultaneous kidney-pancreas transplantation. Because T10B9 is nonmitogenic and causes minimal cytokine release, both treatment of rejection and induction of immunosuppression were accomplished with significantly fewer and milder untoward effects (cytokine release syndrome) than its comparator OKT3. Since T10B9 is directed against the αβ heterodimer of the CD3 epitope, it spares the gamma delta (γδ) region. These gamma delta (γδ) T cells have a unique role in the immune response controlling many serious human diseases and perhaps facilitating the development of immunologic tolerance. T10B9 has a relatively short duration of action, depleting T cells for only 10 to 14 days, unlike the protracted depletion seen with thymoglobulin and Campath-1H. There is no B-lymphocyte depletion with T10B9 as there is with both of the aforementioned reagents. The lack of prolonged lymphocyte depletion may account for less infection observed with T10B9 treatment.


SARS and the maternal neonatal unit


title: Translational Studies of Alcoholism: Bridging the Gap

text: Human studies are necessary to identify and classify the brain systems predisposing individuals to develop alcohol use disorders and those modified by alcohol, while animal models of alcoholism are essential for a mechanistic understanding of how chronic voluntary alcohol consumption becomes compulsive, how brain systems become damaged, and how damage resolves. Our current knowledge of the neuroscience of alcohol dependence has evolved from the interchange of information gathered from both human alcoholics and animal models of alcoholism. Together, studies in humans and animal models have provided support for the involvement of specific brain structures over the course of alcohol addiction, including the prefrontal cortex, basal ganglia, cerebellum, amygdala, hippocampus, and the hypothalamic–pituitary–adrenal axis.


title: Spatial Distribution of Diarrhoea and Microbial Quality of Domestic Water during an Outbreak of Diarrhoea in the Tshikuwi Community in Venda, South Africa

text: Total microbial quality assessment and geographical information system were used for evaluating the quality of water and the spatial distribution of diarrhoea cases in Tshikuwi, a rural community in South Africa, during an outbreak of diarrhoea. The water-abstraction points included two groundwater storage tanks, namely Tank 1 and Tank 2 and the Khandanama river. Indicator microbial counts for total coliforms, faecal coliforms, enterococci, and heterotrophic bacteria exceeded the limit for no risk as stipulated by the South African water-quality guidelines for domestic use for Tank 1 and the Khandanama river. Vibrio, Salmonella, and Shigella species were prevalent in the Khandanama river. The spatial distribution of diarrhoea cases showed a hot-spot of diarrhoea cases close to Tank 1 and the Khandanama river. Results of chi-square analysis showed that the proportion of infection from each water source was different or that infection depends on the type of water source (α=0.05). The demonstrated spatial clustering of diarrhoea cases might have been influenced by the poor microbial quality of water used from Tank 1 and the Khandanama river. The results further highlight the urgent need of water-treatment facilities and monitoring of water quality in rural communities of South Africa.


title: Two resource distribution strategies for dynamic mitigation of influenza pandemics

text: As recently pointed out by the Institute of Medicine, the existing pandemic containment and mitigation models lack the dynamic decision support capabilities. We present two simulation-based optimization models for developing dynamic predictive resource distribution strategies for cross-regional pandemic outbreaks. In both models, the underlying simulation mimics the disease and population dynamics of the affected regions. The quantity-based optimization model generates a progressive allocation of limited quantities of mitigation resources, including vaccines, antiviral, administration capacities, and social distancing enforcement resources. The budget-based optimization model strives instead allocating a total resource budget. Both models seek to minimize the impact of ongoing outbreaks and the expected impact of potential outbreaks. The models incorporate measures of morbidity, mortality, and social distancing, translated into the societal and economic costs of lost productivity and medical expenses. The models were calibrated using historic pandemic data and implemented on a sample outbreak in Florida, with over four million inhabitants. The quantity-based model was found to be inferior to the budget-based model, which was advantageous in its ability to balance the varying relative cost and effectiveness of individual resources. The models are intended to assist public health policy makers in developing effective distribution policies for mitigation of influenza pandemics.


title: 2009 H1N1 Influenza and Experience in Three Critical Care Units

text: Aim: We describe futures of ICU admission, demographic characteristics, treatment and outcome for critically ill patients with laboratory-confirmed and suspected infection with the H1N1 virus admitted to the three different critical care departments in Turkey. Methods: Retrospective study of critically ill patients with 2009 influenza A(H1N1) at ICU. Demographic data, symptoms, comorbid conditions, and clinical outcomes were collected using a case report form. Results: Critical illness occurred in 61 patients admitted to an ICU with confirmed (n=45) or probable and suspected 2009 influenza A(H1N1). Patients were young (mean, 41.5 years), were female (54%). Fifty-six patients, required mechanical ventilation (14 invasive, 27 noninvasive, 15 both) during the course of ICU. On admission, mean APACHE II score was 18.7±6.3 and median PaO(2)/FIO(2) was 127.9±70.4. 31 patients (50.8%) was die. There were no significant differences in baseline PaO(2)/FIO(2 )and ventilation strategies between survivors and nonsurvivors. Patients who survived were more likely to have NIMV use at the time of admission to the ICU. Conclusion: Critical illness from 2009 influenza A(H1N1) in ICU predominantly affects young patients with little major comorbidity and had a high case-fatality rate. NIMV could be used in 2009 influenza A (H1N1) infection-related hypoxemic respiratory failure.


Authors’ reply


title: Delivery Systems for In Vivo Use of Nucleic Acid Drugs

text: The notorious biotechnological advance of the last few decades has allowed the development of experimental methods for understanding molecular mechanisms of genes and new therapeutic approaches. Gene therapy is maturing into a viable, practical method with the potential to cure a variety of human illnesses. Some nucleic-acid-based drugs are now available for controlling the progression of genetic diseases by inhibiting gene expression or the activity of their gene products. New therapeutic strategies employ a wide range of molecular tools such as bacterial plasmids containing transgenic inserts, RNA interference and aptamers. A nucleic-acid based constitution confers a lower immunogenic potential and as result of the high stringency selection of large molecular variety, these drugs have high affinity and selectivity for their targets. However, nucleic acids have poor biostability thus requiring chemical modifications and delivery systems to maintain their activity and ease their cellular internalization. This review discusses some of the mechanisms of action and the application of therapies based on nucleic acids such as aptamers and RNA interference as well as platforms for cellular uptake and intracellular delivery of therapeutic oligonucleotides and their trade-offs.


title: Targeting Human Immunodeficiency Virus Type 1 Assembly, Maturation and Budding

text: The targets for licensed drugs used for the treatment of human immunodeficiency virus type 1 (HIV-1) are confined to the viral reverse transcriptase (RT), protease (PR), and the gp41 transmembrane protein (TM). While currently approved drugs are effective in controlling HIV-1 infections, new drug targets and agents are needed due to the eventual emergence of drug resistant strains and drug toxicity. Our increased understanding of the virus life-cycle and how the virus interacts with the host cell has unveiled novel mechanisms for blocking HIV-1 replication. This review focuses on inhibitors that target the late stages of virus replication including the synthesis and trafficking of the viral polyproteins, viral assembly, maturation and budding. Novel approaches to blocking the oligomerization of viral enzymes and the interactions between viral proteins and host cell factors, including their feasibility as drug targets, are discussed.


title: Re-establishment of olfactory and taste functions

text: The incidence of olfactory disorders is appoximately 1-2% and they can seriously impact on the quality of life. Quantitative disorders (hyposmia, anosmia) are distinguished from qualitative disorders (parosmia, phantosmia). Olfactory disorders are classified according to the etiology and therapy is planned according to the underlying pathophysiology. In ENT patients olfactory disorders caused by sinonasal diseases are the most common ones, followed by postviral disorders. Therapy consists of topical and systemic steroids, whereas systemic application seems to be of greater value. It is very difficult to predict the improvement of olfactory function using surgery, moreover, the long term - success in surgery is questionable. Isolated taste disorders are rare and in most often caused by underlying diseases or side effects of medications. A meticulous history is necessary and helps to choose effective treatment. In selected cases zinc might be useful.


title: Experiences of nursing students in caring of patients in source isolation

text: BACKGROUND: Infectious disease control is one of the important components of patient care which can assist in reducing morbidity and mortality. Source isolation is one of the strategies that have used in order to prevent from the spread of contagious infectious diseases. Since nursing student should be able to do the caring in source isolation patients after learning the principles, it's necessary to assess the students’ perception of caring for this client group in order to prepare them for the role of caring. METHODS: This is a qualitative phenomenological study; its participants were selected with maximum variation by purposed sampling from first to fourth year nursing and midwifery students of Isfahan School of Nursing and Midwifery. The students used to do the patient caring during the clinical internship. The sampling done until 10 interview data saturation was obtained. In order to collect data, researcher used depth interview method. Data analysis was performed by seven-stage Collaizzi method. RESULTS: The findings of this study included 6 main concept (themes) from participants’ experiences as following: 1. Stressor agents of caring, 2. Response to stress, 3. Care requirments, 4. Care provider performance, 5. Consequence of care, and 6. Improper caring. CONCLUSIONS: Providing educational programs in terms of isolated patients can reduce anxiety in students which this can lead to more control and prevent the spread of infectious diseases. In addition, studying about patients’ needs can be useful for improving practical interventions and clinical care.


title: Mucosal Delivery of ACNPV Baculovirus Driving Expression of the Gal-Lectin LC3 Fragment Confers Protection against Amoebic Liver Abscess in Hamster

text: Mucosal vaccination against amoebiasis using the Gal-lectin of E. histolytica has been proposed as one of the leading strategies for controlling this human disease. However, most mucosal adjuvants used are toxic and the identification of safe delivery systems is necessary. Here, we evaluate the potential of a recombinant Autographa californica baculovirus driving the expression of the LC3 fragment of the Gal-lectin to confer protection against amoebic liver abscess (ALA) in hamsters following oral or nasal immunization. Hamsters immunized by oral route showed complete absence (57.9%) or partial development (21%) of ALA, resulting in some protection in 78.9% of animals when compared with the wild type baculovirus and sham control groups. In contrast, nasal immunization conferred only 21% of protection efficacy. Levels of ALA protection showed lineal correlation with the development of an anti-amoebic cellular immune response evaluated in spleens, but not with the induction of seric IgG anti-amoeba antibodies. These results suggest that baculovirus driving the expression of E. histolytica vaccine candidate antigens is useful for inducing protective cellular and humoral immune responses following oral immunization, and therefore it could be used as a system for mucosal delivery of an anti-amoebic vaccine.


title: Characterization of spontaneously generated prion-like conformers in cultured cells

text: A distinct conformational transition from the α-helix-rich cellular prion protein (PrP(C)) into its β-sheet-rich pathological isoform (PrP(Sc)) is the hallmark of prion diseases, a group of fatal transmissible encephalopathies that includes spontaneous and acquired forms. Recently, a PrP(Sc)-like intermediate form characterized by the formation of insoluble aggregates and protease-resistant PrP species termed insoluble PrP(C) (iPrP(C)) has been identified in uninfected mammalian brains and cultured neuronal cells, providing new insights into the molecular mechanism(s) of these diseases. Here, we explore the molecular characteristics of the spontaneously formed iPrP(C) in cultured neuroblastoma cells expressing wild-type or mutant human PrP linked to two familial prion diseases. We observed that although PrP mutation at either residue 183 from Thr to Ala (PrP(T183A)) or at residue 198 from Phe to Ser (PrP(F198S)) affects glycosylation at both N-linked glycosylation sites, the T183A mutation that results in intracellular retention significantly increased the formation of iPrP(C). Moreover, while autophagy is increased in F198S cells, it was significantly decreased in T183A cells. Our results indicate that iPrP(C) may be formed more readily in an intracellular compartment and that a significant increase in PrP(T183A) aggregation may be attributable to the inhibition of autophagy.


title: Ocular pathogenesis and immune reaction after intravitreal dispase injection in mice

text: PURPOSE: The purpose of the current study was to examine the ocular pathogenesis and immune reaction in mice after intravitreal dispase injection. METHODS: Three microliters of dispase at a concentration of 0.2 U/μl were injected into the vitreal cavities of 4–6-week-old mice. Hematoxylin and eosin staining, immunofluorescence analysis, and electroretinograms of the eyes were then performed to assess ocular changes, and enzyme-linked immunospot assays and intracellular staining of single-cell suspensions of the spleens were used to detect immune changes during an 8 week observation period. RESULTS: Neutrophils were the main inflammatory infiltrating cells appearing at the anterior chamber. No cluster of differentiation (CD)3+ labeled T cells, F4/80+ labeled macrophages, or CD56+ labeled natural killer cells were found in the vitreal cavities or retinas in dispase-injected mice within 5 days after injection. Proliferative vitreoretinopathy (PVR)-like signs first appeared at 2 weeks, gradually increased thereafter, and reached peak values at 8 weeks. There was a statistically significant difference in b-wave amplitudes between the PVR and saline-control eyes. Enzyme-linked immunospot assays and intracellular staining showed that specific CD4+ and CD8+ labeled T cells were not involved in dispase-injected mice. CONCLUSIONS: Our data show that neutrophils in the anterior chamber and PVR-like signs in the retinas were found, and that specific immune reactions were not involved after intravitreal dispase injection in mice.


title: Introducing Alphitobius diaperinus, (Insecta: Tenebrionidae) as a New Intermediate Host of Hadjelia truncata (Nematoda)

text: BACKGROUND: Hadjelia truncata is a nematode that causes lesions in the gizzard lining of pigeons, which may even lead to death. The aim of this study was to introduce Alphitobius diaperinus as a new intermediate host for Hadjelia truncata. METHODS: H. truncata infection was identified in a pigeon flock in Ahvaz City, Khuzestan Province, Iran by performing fecal examination and autopsy. Adult and larval stages of beetles were collected from the litter of pigeon houses, and identified morphologically. The beetle larvae were cultured in a medium, containing feces of the infected pigeons. Nematode larval stages from naturally and experimentally (culturally) infected adult beetles were fed to two groups of pigeons RESULTS: The collected beetles were identified as Alphitobius diaperinus. Average length and width of the adult beetles were 6.31 mm and 2.88 mm respectively. Infection rates of naturally and experimentally infected beetles with larval stages of the nematode were 66.2% and 45.1% respectively. The adult nematodes collected from gizzards of experimentally infected pigeons were identified as H. truncata. Nematode infection rates in pigeons after feeding the infective larvae collected from naturally and experimentally infected beetles were 44.7% and 32.5% respectively. CONCLUSION: A. diaperinus can serve as a natural intermediate host for H. truncata.


title: First Report of Respiratory Syncytial Virus and Human Metapneumovirus Co-Infection in a 2-Year-Old Kawasaki Patient in Iran

text: BACKGROUND: Respiratory virus infections in children are a leading cause of morbidity and mortality worldwide. METHODS: A total of 897 clinical specimens were collected from February 2007 to January 2008 and transported to the National Influenza Center. Two hundred and two samples belonged to children under the age of six from 897 specimens, described above, were selected. Then they were tested for influenza virus types and subtypes by real time PCR assay subsequently, the specimens were tested for RSV and hMPV by hemi-nested multiplex PCR and parainfluenza viruses type 1–4 by hemi-nested multiplex PCR and adenovirus by hemi-nested PCR. RESULTS: The throat swab was taken from the Kawasaki case with the history of chicken’s contact. The specimen was tested for all influenza subtypes especially H5N1 and the results were negative. Meanwhile PCR was done for screening of other respiratory viruses that results came out positive for RSV and hMPV. CONCLUSION: In the present study, we demonstrated the possibility to detect dual infection caused by RSV and hMPV, but because of the extravagant pattern of this case, more investigation is suggested specially on Kawasaki patients.


title: The Role of the Charged Residues of the GP2 Helical Regions in Ebola Entry()

text: The glycoprotein (GP) of Ebola is the sole structural protein that forms the spikes on the viral envelope. The GP contains two subunits, GP1 and GP2, linked by a disulfide bond, which are responsible for receptor binding and membrane fusion, respectively. In this study, the full length of GP gene of Ebola Zaire species, 2028 base pairs in length, was synthesized using 38 overlapping oligonucleotides by multiple rounds of polymerase chain reaction (PCR). The synthesized GP gene was shown to be efficiently expressed in mammalian cells. Furthermore, an efficient HIV-based pseudotyping system was developed using the synthetic GP gene, providing a safe approach to dissecting the entry mechanism of Ebola viruses. Using this pseudotyping system and mutational analysis, the role of the charged residues in the GP2 helical regions was examined. It was found that substitutions of the most charged residues in the regions did not adversely affect GP expression, processing, or viral incorporation, however, most of the mutations greatly impaired the ability of GP to mediate efficient viral infection. These results demonstrate that these charged residues of GP2 play an important role in GP-mediated Ebola entry into its host cells. We propose that these charged residues are involved in forming the intermediate conformation(s) of GP in membrane fusion and Ebola entry.


title: Use of Transgenic Animals in Biotechnology: Prospects and Problems

text: During the past two decades, there have been numerous attempts at using animals in order to produce recombinant human proteins and monoclonal antibodies. However, it is only recently that the first two therapeutic agents isolated from the milk of transgenic animals, C1 inhibitor (Ruconest) and antithrombin (ATryn), appeared on the market. This inspires hope that a considerable number of new recombinant proteins created using such technology could become available for practical use in the near future. In this review, the methods applied to produce transgenic animals are described and the advantages and drawbacks related to their use for producing recombinant human proteins and monoclonal antibodies are discussed.


title: The human Transmembrane Protease Serine 2 is necessary for the production of Group 2 influenza A virus pseudotypes

text: The monomer of influenza haemagglutinin is synthesized as a single polypeptide precursor that during maturation is cleaved by proteases into two active subunits. Other studies have demonstrated that the human Transmembrane Protease Serine 2 (TMPRSS2) can cleave the HA of human seasonal influenza viruses. Consequently, we have investigated the use of human Transmembrane Protease Serine 2 to produce high titre influenza haemmagglutinin (HA) lentiviral pseudotypes from Group 2 influenza viruses. Such pseudotypes represent powerful and safe tools to study viral entry and immune responses. Influenza pseudotype particles are obtained by co-transfecting human embryonic kidney HEK293T/17 cells using plasmids coding for the influenza HA, HIV gag-pol and a lentiviral vector incorporating firefly luciferase. However, in order to produce Group 2 pseudotypes, it was necessary to co-transfect a plasmid expressing the TMPRSS2 endoprotease, to achieve the necessary HA cleavage for infective particle generation. These lentiviral pseudotypes were shown to transduce HEK293T/17 cells with high efficiency. This demonstrates that TMPRSS2 is necessary for the functional activation, in vitro, of both the HA of human seasonal influenza and other Group 2 HA influenza strains. Additionally, we show that the Group 2 influenza pseudotype particles can be used as surrogate antigens in neutralization assays and are efficiently neutralized by corresponding influenza virus reference sera. These data demonstrate that the viral pseudotype system is a powerful method for serological surveillance of a wide range of influenza viruses.


title: Downregulation of Signaling-active IGF-1 by Dipeptidyl Peptidase IV (DPP-IV)

text: Functioning as an extracellular protease, dipeptidyl peptidase IV (DPP-IV) preferentially cleaves the peptide bond after the penultimate proline residue. We report here that DPP-IV cleaves the first two amino acids from insulin-like growth factor 1 (IGF-1), revealed by mass spectrometry. The kinetic parameters of the proteolytic cleavage indicate that this reaction is physiologically relevant. Interestingly, truncated IGF-1 is less potent than the full-length protein in activating the IGF-1R, but binds more readily to IGF-binding protein 3 (IGFBP3). Quantitative RT–PCR showed that the level of DPP-IV mRNA is dramatically lower in lung squamous cell carcinoma tissues than in adjacent nonneoplastic lung tissues. However, this reduction was not observed in lung adenocarcinoma tissues. Our study suggests a possible link between IGF-1 and DPP-IV in cancer development in a specific tumor niche. A DPP-IV-related pathway may be important in mitigating IGF-1 signaling. Consequently, a robust IGF signaling pathway may accelerate early carcinogenesis in environments lacking DPP-IV.


title: Lithium chloride promotes host resistance against Pseudomonas aeruginosa keratitis

text: PURPOSE: To explore the role of lithium chloride (LiCl) in Pseudomonas aeruginosa (PA) keratitis. METHODS: B6 mice were subconjunctivally injected with LiCl in contrast to appropriate control sodium chloride (NaCl), and then routinely infected with PA. Clinical score, slit-lamp photography, hematoxylin and eosin (H&E) staining, and bacterial plate counts were used to determine the role of LiCl in PA keratitis. Messenger ribonucleic acid and protein levels of inflammatory cytokines in PA-challenged mouse corneas and in vitro cultured macrophages and neutrophils were measured with real-time PCR and enzyme-linked immunosorbent assay (ELISA), respectively. Apoptosis of the infiltrating inflammatory cells in the PA-infected murine corneas was assessed using terminal deoxynucleotidyl transferase-mediated uridine 5′-triphosphate-biotin nick end labeling staining and propidium iodide staining associated with flow cytometry. In cultured murine macrophages and neutrophils, cell apoptosis was determined with annexin V/propidium iodide double staining associated with flow cytometry and western blot analysis for cleaved caspase-3 and cleaved poly(ADP-ribose) polymerase. RESULTS: Treatment with LiCl reduced the severity of corneal disease by reducing corneal inflammatory response and bacterial burden. Moreover, LiCl increased anti-inflammatory cytokine interleukin-10 levels, decreased proinflammatory cytokine tumor necrosis factor-α levels, and enhanced apoptosis of infiltrating macrophages and neutrophils in the PA-infected mouse corneas. In vitro studies further confirmed that LiCl elevated anti-inflammatory cytokine expression but reduced proinflammatory cytokine production, as well as promoted cell apoptosis in murine macrophages and neutrophils. CONCLUSIONS: This study demonstrates a protective role of LiCl in PA keratitis. LiCl promotes host resistance against PA infection by suppressing inflammatory responses, enhancing inflammatory cell apoptosis, and promoting bacterial clearance.


title: Pre-clinical toxicity & immunobiological evaluation of DNA rabies vaccine & combination rabies vaccine in rhesus monkeys (Macaca mulatta)

text: BACKGROUND & OBJECTIVES: Pre-clinical toxicology evaluation of biotechnology products is a challenge to the toxicologist. The present investigation is an attempt to evaluate the safety profile of the first indigenously developed recombinant DNA anti-rabies vaccine [DRV (100 μg)] and combination rabies vaccine [CRV (100 μg DRV and 1.25 IU of cell culture-derived inactivated rabies virus vaccine)], which are intended for clinical use by intramuscular route in Rhesus monkeys. METHODS: As per the regulatory requirements, the study was designed for acute (single dose - 14 days), sub-chronic (repeat dose - 28 days) and chronic (intended clinical dose - 120 days) toxicity tests using three dose levels, viz. therapeutic, average (2x therapeutic dose) and highest dose (10 x therapeutic dose) exposure in monkeys. The selection of the model i.e. monkey was based on affinity and rapid higher antibody response during the efficacy studies. An attempt was made to evaluate all parameters which included physical, physiological, clinical, haematological and histopathological profiles of all target organs, as well as Tiers I, II, III immunotoxicity parameters. RESULTS: In acute toxicity there was no mortality in spite of exposing the monkeys to 10XDRV. In sub chronic and chronic toxicity studies there were no abnormalities in physical, physiological, neurological, clinical parameters, after administration of test compound in intended and 10 times of clinical dosage schedule of DRV and CRV under the experimental conditions. Clinical chemistry, haematology, organ weights and histopathology studies were essentially unremarkable except the presence of residual DNA in femtogram level at site of injection in animal which received 10X DRV in chronic toxicity study. No Observational Adverse Effects Level (NOAEL) of DRV is 1000 ug/dose (10 times of therapeutic dose) if administered on 0, 4, 7, 14, 28(th) day. INTERPRETATION & CONCLUSIONS: The information generated by this study not only draws attention to the need for national and international regulatory agencies in formulating guidelines for pre-clinical safety evaluation of biotech products but also facilitates the development of biopharmaceuticals as safe potential therapeutic agents.


title: In Vitro Anti-rotaviral Activity of Achillea kellalensis

text: BACKGROUND: Achillea kellalensis, which is frequently used by Chaharmahal va Bakhtiarians residing in, Southwest of Iran, as a traditional herbal medicine for the treatment of acute diarrhea, has been selected to examine its antiviral activities against bovine rotavirus and cell toxicity activity in MA-104 cells. OBJECTIVES: The aim of this study was to evaluate the in vitro cytotoxic and anti-rotavirus properties of crude extracts of A. kellalensis. MATERIALS AND METHODS: The dried and powdered flowers of Achillea kellalensis were extracted with hot water and ethanol 50% (v/v). The cell viability and toxicity of the extracts were evaluated on MA-104 cells using four methods; trypan blue dye, NR, crystal violet and MTT assay. The in vitro anti-rotavirus properties were determined via four different assays, in order to evaluate the direct inhibition and/or the inhibition of viral replication. RESULTS: Cytotoxicity of two A. kellalensis extracts showed different concentrations. Hydro-alcoholic extract had low CC(50) at 600 µg/mL by the NR assay while the aqueous extract had high CC(50) at 1000µg/mL by the crystal violet method. In the simultaneous treatment assay and post treatment assay, the extracts were able to prevent viral replication and inhibit the viral CPE on MA-104 cells at 10 TCID(50), but the extracts did not exhibit direct antiviral activity on rotavirus adsorption. The effective concentration (EC(50)) of both extracts was observed to be 100 µg/mL. CONCLUSIONS: These results indicate that A. kellalensis extracts exert potent anti-rotaviral activity only after viral adsorption. The two extracts from A. kellalensis showed a good selectivity index. Also these results suggest that extracts prepared from the flowers of A. kellalensis may be potential anti-rotaviral agents in vivo and be useful in veterinary medicine.


title: Biologic functions of the IFN-γ receptors

text: Interferon-gamma (IFN-γ) is a cytokine that plays an important role in inducing and modulating an array of immune responses. Cellular responses to IFN-γ are mediated by its heterodimeric cell-surface receptor (IFN-γR), which activates downstream signal transduction cascades, ultimately leading to the regulation of gene expression. In order to study the role of IFN-γ in a number of immune responses and pathways, researchers have generated mice with altered patterns of IFN-γR gene expression. These studies, together with analyses of naturally occurring mutations of the IFN-γR in man, have been instrumental in elucidating the diverse functions of IFN-γ, and are the subject of this review.


Rapidly Building Global Health Security Capacity — Uganda Demonstration Project, 2013


title: Ebola Hemorrhagic Fever as a Public Health Emergency of International Concern; a Review Article

text: Ebola hemorrhagic fever (EHF) was first reported in 1976 with two concurrent outbreaks of acute viral hemorrhagic fever centered in Yambuku (near the Ebola river), Democratic Republic of Congo, and in Nzara, Sudan. The current outbreak of the Ebola virus was started by reporting the first case in March 2014 in the forest regions of southeastern Guinea. Due to infection rates raising over 13,000% within a 6-month period, Ebola is now considered as a global public health emergency and on August 8(th), 2014 the World Health Organization (WHO) declared the epidemic to be a Public Health Emergency of International Concern. With more than 5000 involved cases and nearly 3000 deaths, this event has turned into the largest and most dangerous Ebola virus outbreak in the world. Based on the above-mentioned, the present article aimed to review the virologic characteristics, transmission, clinical manifestation, diagnosis, treatment, and prevention of Ebola virus disease.


title: A HLA-A2-restricted CTL epitope induces anti-tumor effects against human lung cancer in mouse xenograft model

text: Cancer immunotherapy is attractive for antigen-specific T cell-mediated anti-tumor therapy, especially in induction of cytotoxic T lymphocytes. In this report, we evaluated human CTL epitope-induced anti-tumor effects in human lung cancer xenograft models. The tumor associated antigen L6 (TAL6) is highly expressed in human lung cancer cell lines and tumor specimens as compared to normal lung tissues. TAL6 derived peptides strongly inhibited tumor growth, cancer metastasis and prolonged survival time in HLA-A2 transgenic mice immunized with a formulation of T-helper (Th) peptide, synthetic CpG ODN, and adjuvant Montanide ISA-51 (ISA-51). Adoptive transfer of peptide-induced CTL cells from HLA-A2 transgenic mice into human tumor xenograft SCID mice significantly inhibited tumor growth. Furthermore, combination of CTL-peptide immunotherapy and gemcitabine additively improved the therapeutic effects. This pre-clinical evaluation model provides a useful platform to develop efficient immunotherapeutic drugs to treat lung cancer and demonstrates a promising strategy with benefit of antitumor immune responses worthy of further development in clinical trials.


title: Miniaturization for Point-of-Care Analysis: Platform Technology for Almost Every Biomedical Assay

text: Platform technologies for the changing need of diagnostics are one of the main challenges in medical device technology. From one point-of-view the demand for new and more versatile diagnostic is increasing due to a deeper knowledge of biomarkers and their combination with diseases. From another point-of-view a decentralization of diagnostics will occur since decisions can be made faster resulting in higher success of therapy. Hence, new types of technologies have to be established which enables a multiparameter analysis at the point-of-care. Within this review-like article a system called Fraunhofer ivD-platform is introduced. It consists of a credit-card sized cartridge with integrated reagents, sensors and pumps and a read-out/processing unit. Within the cartridge the assay runs fully automated within 15-20 minutes. Due to the open design of the platform different analyses such as antibody, serological or DNA-assays can be performed. Specific examples of these three different assay types are given to show the broad applicability of the system.


title: An Ecological Framework of the Human Virome Provides Classification of Current Knowledge and Identifies Areas of Forthcoming Discovery

text: Recent advances in sequencing technologies have opened the door for the classification of the human virome. While taxonomic classification can be applied to the viruses identified in such studies, this gives no information as to the type of interaction the virus has with the host. As follow-up studies are performed to address these questions, the description of these virus-host interactions would be greatly enriched by applying a standard set of definitions that typify them. This paper describes a framework with which all members of the human virome can be classified based on principles of ecology. The scaffold not only enables categorization of the human virome, but can also inform research aimed at identifying novel virus-host interactions.


title: Glucose-6-phosphate dehydrogenase deficiency (G6PD) as a risk factor of male neonatal sepsis

text: Introduction.Neonatal sepsis is a disease process, which represents the systemic response of bacteria entering the bloodstream during the first 28 days of life. The prevalence of sepsis is higher in male infants than in females, but the exact cause is unknown. Glucose-6-phosphate dehydrogenase (G6PD) is an enzyme in the pentose phosphate pathway, which leads to the production of NADPH. NADPH is required for the respiratory burst reaction in white blood cells (WBCs) to destroy microorganisms. The purpose of this study was to evaluate the prevalence of G6PD deficiency in neonates with sepsis. Materials and methods.This study was performed on 76 neonates with sepsis and 1214 normal neonates from February 2012 to November 2014 in the west of Iran. The G6PD deficiency status was determined by fluorescent spot test. WBCs number and neutrophils percentages were measured and compared in patients with and without G6PD deficiency. Results.The prevalence of the G6PD deficiency in neonates with sepsis was significantly higher compared to the control group (p=0.03). WBCs number and neutrophils percentages in G6PD deficient patients compared with patients without G6PD deficiency were decreased, but were not statistically significant (p=0.77 and p=0.86 respectively). Conclusions.G6PD deficiency is a risk factor of neonatal sepsis and also a justification for more male involvement in this disease. Therefore, newborn screening for this disorder is recommended.


title: Triterpene Constituents of Euphorbia Erythradenia Bioss. and their Anti-HIV Activity

text: Phytochemical investigation of the aerial parts of Euphorbia erythradenia Bioss. (Euphorbiaceae), one of Iranian endemic Euphorbias, with particular attention to triterpene constituents, using methanol solvent extraction was carried out. Five known triterpenes, including four cycloartanes and oleanolic acid, were isolated for the first time and identified using NMR and Mass techniques. Anti HIV activity of the isolated triterpenes and ingenoid diterpenes was evaluated using single cycle replicable HIV-1 (SCR HIV-1) virions. Molecular features of the most active compound (IC(50) = 0.008 μM, CC(50) = 3.264 μM, TI = 380.64), which showed higher therapeutic index than nevirapine, was assessed using molecular docking. Docking studies demonstrated three hydrogen bonds between HIV-1 virion protease active site and this compound with a distance less than 3 A° which can be responsible for the observed anti HIV-1 activity.


title: Primary demyelination in transgenic mice expressing interferon-γ

text: Ever since the use of interferon-γ to treat patients with multiple sclerosis resulted in enhanced disease, the role of IFN-γ in demyelinatlon has been under question. To address this issue directly, transgenic mice were generated that expressed the cDNA of murlne IFN-γ in the central nervous system by using an oligodendrocyte-specific promoter. Expression of the transgene occurred after 8 weeks of age, at which time the murlne immune and central nervous systems are both fully developed. Directly associated with transgene expression, primary demyelination occurred and was accompanied by clinical abnormalities consistent with CNS disorders. Additionally, multiple hallmarks of immune-mediated CNS disease were observed including upregulation of MHC molecules, gliosis and lymphocytlc infiltration. These results demonstrate a direct role for IFN-γ as an Inducer of CNS demyellnatlon leading to disease and provide new opportunities for dissecting the mechanism of demyelinatlon.


title: Loop Mediated Isothermal Amplification (LAMP) for Embryo Sex Determination in Pregnant Women at Eight Weeks of Pregnancy

text: BACKGROUND: In human, SRY (sex-determining region of the Y chromosome) is the major gene for the testis-determining factor which is found in normal XY males and in the rare XX males, and it is absent in normal XX females and many XY females. There are several methods which can indicate a male genotype by the presence of the amplified product of SRY gene. The aim of this study was to identify the SRY gene for embryo sex determination in human during pregnancy using loop mediated isothermal amplification (LAMP) method. METHODS: A total of 15 blood samples from pregnant women at eight weeks of pregnancy were collected, and Plasma DNA was extracted. LAMP assay was performed using DNA obtained for detection of SRY gene. Furthermore, colorimetric LAMP assay for rapid and easy detection of SRY gene was developed. RESULTS: LAMP results revealed that the positive reaction was highly specific only with samples containing XY chromosomes, while no amplification was found in samples containing XX chromosomes. A total of 15 blood samples from pregnant women were seven male embryos (46.6%) and eight female embryos (53.4%). All used visual components in the colorimetric assay could successfully make a clear distinction between positive and negative ones. CONCLUSION: The LAMP assay developed in this study is a valuable tool capable of monitoring the purity and detection of SRY gene for sex determination.


title: Extracting geographic locations from the literature for virus phylogeography using supervised and distant supervision methods

text: The field of phylogeography allows researchers to model the spread and evolution of viral genetic sequences. Phylogeography plays a major role in infectious disease surveillance, viral epidemiology and vaccine design. When conducting viral phylogeographic studies, researchers require the location of the infected host of the virus, which is often present in public databases such as GenBank. However, the geographic metadata in most GenBank records is not precise enough for many phylogeographic studies; therefore, researchers often need to search the articles linked to the records for more information, which can be a tedious process. Here, we describe two approaches for automatically detecting geographic location mentions in articles pertaining to virus-related GenBank records: a supervised sequence labeling approach with innovative features and a distant-supervision approach with novel noise- reduction methods. Evaluated on a manually annotated gold standard, our supervised sequence labeling and distant supervision approaches attained F-scores of 0.81 and 0.66, respectively.


title: Recomendaciones para la atención del paciente con neumonía adquirida en la comunidad en los Servicios de Urgencias

text: The incidence of community-acquired pneumonia (CAP) ranges from 2-15 cases / 1,000 inhabitants / year, being higher in those older than 65 years and in patients with high comorbidity. Around 75% of all CAP diagnosed are treated in the Emergency Department (ED). The CAP represents the main cause for sepsis and septic shock in ED, and the most frequent cause of death and admission to the Intensive Care Unit (ICU) due to infectious disease. Overall mortality is 10-14% according to age and associated risk factors. Forty to 60% of CAP will require hospital admission, including observation units (with very variable ranges from 22-65% according to centers, seasonal of the year and patients´ characteristics). Between the admissions, 2-10% will be in the ICU. All of previously mentioned reflects the importance of the CAP in the ED, as well as the “impact of the emergency care on the patient with CAP”, as it is the establishment where the initial, but key decisions, are made and could condition the outcome of the illness. It is known the great variability among physicians in the diagnostic and therapeutic management of CAP, which is one of the reasons that explains the great differences in the admission rates, achievement of the microbiological diagnosis, request for complementary studies, the choice of antimicrobial treatment, or the diversity of applied care. In this sense, the implementation of clinical practice guidelines with the use of the severity scores and the new tools available, such as biomarkers, can improve patient care with CAP in ED. Therefore, a multidisciplinary group of emergency professionals and specialists involved in the care process of CAP has designed a guideline with several recommendations for decisions-making during the key moments in patients with CAP attended in the ED.


title: A Novel Questionnaire to Ergonomically Assess Respirators among Health Care Staff: Development and Validation

text: BACKGROUND: Health care workers are at a high risk of exposure to infectious diseases spread by airborne transmission. N95 respirators are the most common respirators used in the health care system and negligence in using them may cause health problems. Hence, more emphasis should be on ergonomic aspects of this mask. This study aimed to develop a tool for ergonomic evaluation of these respirators. MATERIALS AND METHODS: After reviewing previous studies and employees’ problems in the use of the N95 respirators, 50 questionnaires were designed and their validity was assessed. Then, the questionnaire was completed by 290 staff members of Masih Daneshvari Hospital and its internal consistency and reproducibility were investigated using Cronbach’s alpha coefficient and test-retest method, respectively. Confirmatory factor analysis was used to assess its consistency and internal consistency (construct validity). RESULTS: With the confirmation of the face and content validities, internal consistency (0.89) calculated by the Cronbach’s alpha coefficient and reproducibility of the questionnaire (0.997; p<0.001) assessed by using the ICC Index, were approved. Following examining internal consistency and stability, the questionnaire convergent construct validity was also confirmed using confirmatory factor analysis. CONCLUSION: The questionnaire contained 42 items and it is beneficial to use it in the health care system to evaluate the ergonomic problems of the respirators and to have optimal choice in this respect. Also, it can be used in the promotion of the staffs’ behavior in wearing these respirators when necessary.


Coronavirus MHV-JHM: nucleotide sequence of the mRNA that encodes the membrane protein.


New nucleotide sequence data on the EMBL File Server


title: Relation between genomic and capsid structures in RNA viruses.

text: We described a new computer program for calculation of RNA secondary structure. Calculation of 20 viral RNAs with this program showed that genomes of the icosahedral capsid viruses had higher folding probabilities than those of the helical capsid viruses. As this explains virus assembly quite well, the information of capsid structure must be imprinted not only in the capsid protein structures but also in the base sequence of the whole genome. We compared folding probability of the original sequence with that of the random sequence in which base composition was the same as the original. All the actual genomes of RNA viruses were more folded than the corresponding random sequences, even though most transcripts of chromosomal genes tended to be less folded. The data can be related to encapsidation of viral genomes. It was thus suggested that there exists a relation between actual sequences and random sequences with the same base ratios, and that the base ratio itself has some evolutional meaning.


title: Comparative mutational analysis of cis-acting RNA signals for translational frameshifting in HIV-1 and HTLV-2

text: Human immunodeficiency virus type 1 (HIV-1) and human T cell leukemia virus type II (HTLV-2) use a similar mechanism for –1 translational frameshifting to overcome the termination codon in viral RNA at the end of the gag gene. Previous studies have identified two important RNA signals for frameshifting, the slippery sequence and a downstream stem–loop structure. However, there have been somewhat conflicting reports concerning the individual contributions of these sequences. In this study we have performed a comprehensive mutational analysis of the cis-acting RNA sequences involved in HIV-1 gag–pol and HTLV-2 gag–pro frameshifting. Using an in vitro translation system we determined frameshifting efficiencies for shuffled HIV-1/HTLV-2 RNA elements in a background of HIV-1 or HTLV-2 sequences. We show that the ability of the slippery sequence and stem–loop to promote ribosomal frameshifting is influenced by the flanking upstream sequence and the nucleotides in the spacer element. A wide range of frameshift efficiency rates was observed for both viruses when shuffling single sequence elements. The results for HIV-1/HTLV-2 chimeric constructs represent strong evidence supporting the notion that the viral wild-type sequences are not designed for maximal frameshifting activity but are optimized to a level suited to efficient viral replication.


New nucleotide sequence data on the EMBL File Server.


title: Translational frameshifting in the Escherichia coli dnaX gene in vitro.

text: Production of the gamma subunit of Escherichia coli DNA polymerase III holoenzyme is dependent on a very efficient translational frameshif in the dnaX gene. I used an E. coli in vitro translation system to analyze the mechanism of this frameshifting event. In this system, gamma was produced almost to the same extent as the inframe translation product, tau, suggesting that efficient frameshifting was reproduced in vitro. Coupling with transcription was not necessary for frameshifting. Addition of purified tau or gamma had no effect on the frameshifting process suggesting the absence of direct feedback regulation. By use of mutant genes, a strong pausing site was identified at or very close to the frameshift site. This pausing was apparently caused by a potential stem-loop structure which was previously shown to enhance frameshifting. Thus, enhancement of frameshifting by this putative stem-loop seems to be mediated by the translation pausing at the frameshift site. Despite the apparent structural similarity of the dnaX frameshift site to that of the eukaryotic retroviral genes, dnaX mRNA synthesized in vitro failed to direct the production of gamma in eukaryotic translation systems. This suggests that frameshifting in the dnaX gene depends on components specific to the E. coli translation system.


title: Trans-splicing of pre-mRNA is predicted to occur in a wide range of organisms including vertebrates.

text: Several known trans-splicing RNA structures were used to define a canonical trans-splicing structure which was then used to perform a computer search of the EMBL nucleotide database. In addition to most known trans-splicing structures, many putative new trans-splicing sites were detected. These were found in a broad range of organisms including the vertebrates. Control experiments indicate that the search predicts known false positives at a rate of only 20%. Trans-splicing may therefore be a very wide-spread phenomenon.


title: The nucleic acid-binding zinc finger protein of potato virus M is translated by internal initiation as well as by ribosomal frameshifting involving a shifty stop codon and a novel mechanism of P-site slippage.

text: The genes for the capsid protein CP and the nucleic acid-binding 12K protein (pr12) of potato virus M (PVM) constitute the 3' terminal gene cluster of the PVM RNA genome. Both proteins are presumably translated from a single subgenomic RNA. We have identified two translational strategies operating in pr12 gene expression. Internal initiation at the first and the second AUG codon of the pr12 coding sequence results in the synthesis of the 12K protein. In addition the protein is produced as a CP/12K transframe protein by ribosomal frameshifting. For these studies parts of the CP and pr12 coding sequences including the putative frameshift region were introduced into an internal position of the beta-glucuronidase gene. Mutational analyses in conjunction with in vitro translation experiments identified a homopolymeric string of four adenosine nucleotides which together with a 3' flanking UGA stop codon were required for efficient frameshifting. The signal AAAAUGA is the first frameshift signal with a shifty stop codon to be analyzed in the eukaryotic system. Substitution of the four consecutive adenosine nucleotides by UUUU increased the efficiency of frameshifting, while substitution by GGGG or CCCC dramatically reduced the synthesis of the transframe protein. Also, UAA and UAG could replace the opal stop codon without effect on the frameshifting event, but mutation of UGA to the sense codon UGG inhibited transframe protein formation. These findings suggest that the mechanism of ribosomal frameshifting at the PVM signal is different from the one described by the 'simultaneous slippage' model in that only the string of four adenosine nucleotides represents the slippery sequence involved in a -1 P-site slippage.


Rapid identification of overlapping cDNA clones by Southern cross-hybridization.


The nucleotide sequence of the extreme 5' end of the avian coronavirus genome; implications for the discontinuous mRNA synthesis.


Infectious bronchitis virus RNA D encodes three potential translation products.


title: Identification and analysis of the pseudoknot-containing gag-pro ribosomal frameshift signal of simian retrovirus-1.

text: The pro and pol genes of simian retrovirus-1 (SRV-1) are expressed as parts of a fusion protein generated by -1 ribosomal frameshifting. To investigate the requirements for frameshifting at the gag-pro overlap, we have inserted a stretch of 58 nucleotides containing the proposed frameshift signal into a plasmid that allows monitoring of translation in all three reading frames. In vitro translation of mRNAs derived from this plasmid indicated that the 58 nucleotides from the SRV-1 gag-pro overlap were sufficient to induce an efficient -1 shift in a heterologous context. Mutational analysis demonstrated that the slip site is formed at the heptanucleotide G GGA AAC. The frameshift efficiency of the wild type sequence in rabbit reticulocyte lysate was 23%. A second component of the frameshift signal is formed by a pseudoknot seven bases downstream of the slip site. The presence of this pseudoknot was confirmed by mutational analysis, employing complementary and compensatory base changes, and by probing the structure of short RNA transcripts containing the frameshift signal. Adding increasing amounts of an SRV-1 pseudoknot containing RNA transcript to a translation reaction programmed with an SRV-1 frameshift reporter mRNA had no effect on the frameshift efficiency, arguing against the role of a specific pseudoknot-recognising factor in the frameshifting process.


Nucleotide sequence of the human coronavirus HCV 229E mRNA 4 and mRNA 5 unique regions.


title: Amino acid sequence of human respiratory syncytial virus nucleocapsid protein.

text: Amino acid sequence of the human respiratory syncytial (RS) virus nucleocapsid (NC) protein, deduced from the DNA sequence of a recombinant plasmid, is presented. The cDNA plasmid (pRSB11) has 1412 bp of RS viral NC sequence and lacks six nucleotides of the 5' end of mRNA. There is a single long open reading frame encoding 467 amino acids. This 51540 dal protein is rich in basic amino acids and has no homologies with other known viral capsid proteins.


title: Programmed ribosomal frameshifting generates the Escherichia coli DNA polymerase III gamma subunit from within the tau subunit reading frame.

text: The Escherichia coli dnaX gene encodes both the tau and gamma subunits of DNA polymerase III holoenzyme in one reading frame. The 71.1 kDa tau and the shorter gamma share N-terminal sequences. Mutagenesis of a potential ribosomal frameshift signal located at codons 428-430 without changing the amino acid sequence of the tau product, eliminated detectable synthesis of the gamma subunit, suggesting that the reading frame is shifted at that sequence and gamma is terminated by a nonsense codon located in the -1 frame 3 nucleotides downstream of the signal. This seems to be the first known case of a frameshift which is used, along with the termination codon in the -1 frame, to terminate a peptide within a reading frame. [Mutagenesis of a dibasic peptide (lys-lys) at codons 498-499, the site at which a tau'-'LacZ fusion protein was cleaved in vitro (1) had no effect on gamma formation in vivo, suggesting that cleavage observed in vitro is not the mechanism of gamma formation in vivo.


title: Characterization of the frameshift stimulatory signal controlling a programmed –1 ribosomal frameshift in the human immunodeficiency virus type 1

text: Synthesis of the Gag-Pol protein of the human immunodeficiency virus type 1 (HIV-1) requires a programmed –1 ribosomal frameshifting when ribosomes translate the unspliced viral messenger RNA. This frameshift occurs at a slippery sequence followed by an RNA structure motif that stimulates frameshifting. This motif is commonly assumed to be a simple stem–loop for HIV-1. In this study, we show that the frameshift stimulatory signal is more complex than believed and consists of a two-stem helix. The upper stem–loop corresponds to the classic stem–loop, and the lower stem is formed by pairing the spacer region following the slippery sequence and preceding this classic stem–loop with a segment downstream of this stem–loop. A three-purine bulge interrupts the two stems. This structure was suggested by enzymatic probing with nuclease V1 of an RNA fragment corresponding to the gag/pol frameshift region of HIV-1. The involvement of the novel lower stem in frameshifting was supported by site-directed mutagenesis. A fragment encompassing the gag/pol frameshift region of HIV-1 was inserted in the beginning of the coding sequence of a reporter gene coding for the firefly luciferase, such that expression of luciferase requires a –1 frameshift. When the reporter was expressed in COS cells, mutations that disrupt the capacity to form the lower stem reduced frameshifting, whereas compensatory changes that allow re-formation of this stem restored the frameshift efficiency near wild-type level. The two-stem structure that we propose for the frameshift stimulatory signal of HIV-1 differs from the RNA triple helix structure recently proposed.


Contamination of DNA database sequence entries with Escherichia coli insertion sequences.


title: Antizyme expression: a subversion of triplet decoding, which is remarkably conserved by evolution, is a sensor for an autoregulatory circuit

text: The efficiency of programmed ribosomal frameshifting in decoding antizyme mRNA is the sensor for an autoregulatory circuit that controls cellular polyamine levels in organisms ranging from the yeast Schizosaccharomyces pombe to Drosophila to mammals. Comparison of the frameshift sites and flanking stimulatory signals in many organisms now permits a reconstruction of the likely evolutionary path of the remarkably conserved mRNA sequences involved in the frameshifting.


title: Structural requirements for efficient translational frameshifting in the synthesis of the putative viral RNA-dependent RNA polymerase of potato leafroll virus.

text: The putative RNA-dependent RNA polymerase of potato leafroll luteovirus (PLRV) is expressed by -1 ribosomal frameshifting in the region where the open reading frames (ORF) of proteins 2a and 2b overlap. The signal responsible for efficient frameshift is composed of the slippery site UUUAAAU followed by a sequence that has the potential to adopt two alternative folding patterns, either a structure involving a pseudoknot, or a simple stem-loop structure. To investigate the structure requirements for efficient frameshifting, mutants in the stem-loop or in the potential pseudoknot regions of a Polish isolate of PLRV (PLRV-P) have been analyzed. Mutations that are located in the second stem (S2) of the potential pseudoknot structure, but are located in unpaired regions of the alternative stem-loop structure, reduce frameshift efficiency. Deletion of the 3' end sequence of the alternative stem-loop structure does not reduce frameshift efficiency. Our results confirm that -1 frameshift in the overlap region depends on the slippery site and on the downstream positioned sequence, and propose that in PLRV-P a pseudoknot is required for efficient frameshifting. These results are in agreement with those recently published for the closely related beet western yellows luteovirus (BWYV).


title: Analysis of effects of tRNA:message stability on frameshift frequency at the Escherichia coli RF2 programmed frameshift site.

text: The codon that is in-frame prior to +1 frameshifting at the E.coli prfB (RF2 gene) frameshift site is randomized to create thirty-two variants. These alleles vary 1000-fold in frameshift-dependent expression in fusions to lacZ. Frameshifting is more frequent at sites where the in-frame codon ends in uridine, as if third position wobble pairs to message uridine facilitate slippage into the +1 frame. Consistent with other studies of programmed frameshift sites, efficient frameshifting depends on stable message:tRNA base pairs after rephasing. For complexes with mispairs, frameshift frequency depends on the nature, number, and position of mispairs. Central purine:purine mispairs are especially inhibitory. Relative stabilities of +1 rephased complexes are estimated from published data on the stabilities of tRNA:tRNA complexes. Stability correlates with frameshifting over its entire range, which suggests that stability is an important determinant of the probability of translation of the rephased complex.


title: Identification of stop codon readthrough genes in Saccharomyces cerevisiae

text: We specifically sought genes within the yeast genome controlled by a non-conventional translation mechanism involving the stop codon. For this reason, we designed a computer program using the yeast database genomic regions, and seeking two adjacent open reading frames separated only by a unique stop codon (called SORFs). Among the 58 SORFs identified, eight displayed a stop codon bypass level ranging from 3 to 25%. For each of the eight sequences, we demonstrated the presence of a poly(A) mRNA. Using isogenic [PSI(+)] and [psi(–)] yeast strains, we showed that for two of the sequences the mechanism used is a bona fide readthrough. However, the six remaining sequences were not sensitive to the PSI state, indicating either a translation termination process independent of eRF3 or a new stop codon bypass mechanism. Our results demonstrate that the presence of a stop codon in a large ORF may not always correspond to a sequencing error, or a pseudogene, but can be a recoding signal in a functional gene. This emphasizes that genome annotation should take into account the fact that recoding signals could be more frequently used than previously expected.


title: Preferred sites of recombination in poliovirus RNA: an analysis of 40 intertypic cross-over sequences.

text: The genome of poliovirus consists of a single strand of RNA approximately 7.5 kb long. Analysis of the sequences around 40 unique recombination sites reveals several features that differ significantly from those expected of randomly located sites. These features, which include a broad zone of elevated homology on the 3' side of the cross-over, support the theory that RNA recombination occurs by a template-switching mechanism during synthesis of the complementary strand, and that sites are chosen to minimise the adverse free energy change involved in switching to a heterotypic template. There is also a strong sequence bias, almost two-thirds of cross-overs, according to a computer simulation, occurring immediately after synthesis of UU. These features shed new light on the extent of base-pairing in replicative intermediate RNA, and on the mechanism of chain initiation.


title: All subgenomic mRNAs of equine arteritis virus contain a common leader sequence.

text: During the replication of equine arteritis virus (EAV) six subgenomic mRNAs are synthesized. We present evidence that the viral mRNAs form a 3'-coterminal nested set and contain a common leader sequence of 208 nucleotides which is encoded by the 5'-end of the genome. The leader is joined to the bodies of mRNA 5 and 6 at positions defined by the sequence 5' UCAAC 3'. The part of the leader sequence flanking the UCAAC motif is very similar to the 5'-splice site of the Tetrahymena pre-rRNA. A possible internal guide sequence has been identified 43 nucleotides downstream of the leader sequence on the genome. Hybridization analysis shows that all EAV intracellular RNAs contain the leader sequence. These data imply that the viral subgenomic mRNAs are composed of leader and body sequences which are non-contiguous on the genome.


title: Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes.

text: In the course of systematic analysis of protein sequences containing the purine NTP-binding motif, a new superfamily was delineated which included 25 established or putative helicases of Escherichia coli, yeast, insects, mammals, pox- and herpesviruses, a yeast mitochondrial plasmid and three groups of positive strand RNA viruses. These proteins contained 7 distinct highly conserved segments two of which corresponded to the "A" and "B" sites of the NTP-binding motif. Typical of the new superfamily was an abridged consensus for the "A" site, GxGKS/T, instead of the classical G/AxxxxGKS/T. Secondary structure predictions indicated that each of the conserved segments might constitute a separate structural unit centering at a beta-turn. All previously characterized mutations impairing the function of the yeast helicase RAD3 in DNA repair mapped to one of the conserved segments. A degree of similarity was revealed between the consensus pattern of conserved amino acid residues derived for the new superfamily and that of another recently described protein superfamily including a different set of prokaryotic, eukaryotic and viral (putative) helicases.


The Big Picture


Errata


Ecological Change: Life Lessons


Abstracts of Poster Session: Abstracts


Technical Report Abstracts: TR-335 to TR-364


Fellowships, Grants, & Awards


Instructions for Authors


World Pneumonia Day — November 12, 2014


Icplm – Speakers’ Abstracts


Epidemic and pandemic-prone diseases


Pool of MERS experts for deployment established by WHO’s Regional Office for the Eastern Mediterranean


Middle East respiratory syndrome coronavirus (MERS-CoV) – Saudi Arabia


Middle East respiratory syndrome coronavirus (MERS-CoV)


WHO LAUNCHES NEW GLOBAL INFLUENZA STRATEGY


Information Diet in Covid-19 Crisis; a Commentary


title: Potential Treatments for COVID-19; a Narrative Literature Review

text: SARS-CoV-2 is a newly emerging human infectious coronavirus that causes COVID-19, which has been recognized as a pandemic by the World Health Organization (WHO) on March 11(th). There is still no vaccine or definitive treatment for this virus because its pathogenesis and proliferation pathways are still unknown. Therefore, in this article, new potential COVID-19 therapies are briefly reviewed.


Daily Situation Report on Coronavirus disease (COVID-19) in Iran; March 13, 2020


Incidentally Diagnosed COVID-19 Infection in Trauma Patients; a Clinical Experience


title: Risks of Novel Coronavirus Disease (COVID-19) in Pregnancy; a Narrative Review

text: INTRODUCTION: The outbreak of the new Coronavirus in China in December 2019 and subsequently in various countries around the world has raised concerns about the possibility of vertical transmission of the virus from mother to fetus. The present study aimed to review published literature in this regard. METHODS: In this narrative review, were searched for all articles published in various databases including PubMed, Scopus, Embase, Science Direct, and Web of Science using MeSH-compliant keywords including COVID-19, Pregnancy, Vertical transmission, Coronavirus 2019, SARS-CoV-2 and 2019-nCoV from December 2019 to March 18, 2020 and reviewed them. All type of articles published about COVID-19 and vertical transmission in pregnancy were included. RESULTS: A review of 13 final articles published in this area revealed that COVID-19 can cause fetal distress, miscarriage, respiratory distress and preterm delivery in pregnant women but does not infect newborns. There has been no report of vertical transmission in pregnancy, and it has been found that clinical symptoms of COVID-19 in pregnant women are not different from those of non-pregnant women. CONCLUSION: Overall, due to lack of appropriate data about the effect of COVID-19 on pregnancy, it is necessary to monitor suspected pregnant women before and after delivery. For confirmed cases both the mother and the newborn child should be followed up comprehensively.


The COVID-19 Intubation and Ventilation Pathway (CiVP); a Commentary


title: Prevalence of Underlying Diseases in Hospitalized Patients with COVID-19: a Systematic Review and Meta-Analysis

text: INTRODUCTION: In the beginning of 2020, an unexpected outbreak due to a new corona virus made the headlines all over the world. Exponential growth in the number of those affected makes this virus such a threat. The current meta-analysis aimed to estimate the prevalence of underlying disorders in hospitalized COVID-19 patients. METHODS: A comprehensive systematic search was performed on PubMed, Scopus, Web of science, and Google scholar, to find articles published until 15 February 2020. All relevant articles that reported clinical characteristics and epidemiological information of hospitalized COVID-19 patients were included in the analysis. RESULTS: The data of 76993 patients presented in 10 articles were included in this study. According to the meta-analysis, the pooled prevalence of hypertension, cardiovascular disease, smoking history and diabetes in people infected with SARS-CoV-2 were estimated as 16.37% (95%CI: 10.15%-23.65%), 12.11% (95%CI 4.40%-22.75%), 7.63% (95%CI 3.83%-12.43%) and 7.87% (95%CI 6.57%-9.28%), respectively. CONCLUSION: According to the findings of the present study, hypertension, cardiovascular diseases, diabetes mellitus, smoking, chronic obstructive pulmonary disease (COPD), malignancy, and chronic kidney disease were among the most prevalent underlying diseases among hospitalized COVID-19 patients, respectively.


title: Daily Situation Report on Coronavirus disease (COVID-19) in Iran; March 16, 2020

text: After detection of the first confirmed cases of COVID-19 in Iran, the National Committee on COVID-19 Epidemiology in Ministry of Health and Medical Education was established. This Committee is official source of gathering, analyzing, and reporting the COVID-19 data in Iran. The data of all sources in the country including, medical care monitoring center (MCMC), Hospitals’ Information Systems (HIS), Laboratory portal, the data of the center for communicable disease control (MOH), as well as the data from community health centers are integrated and used in this regards. This factsheet contain daily situation report on coronavirus disease (covid-19) in Iran; March 16, 2020.


title: Daily Situation Report on Coronavirus disease (COVID-19) in Iran; March 15, 2020

text: After detection of the first confirmed cases of COVID-19 in Iran, the National Committee on COVID-19 Epidemiology in Ministry of Health and Medical Education was established. This Committee is official source of gathering, analyzing, and reporting the COVID-19 data in Iran. The data of all sources in the country including, medical care monitoring center (MCMC), Hospitals’ Information Systems (HIS), Laboratory portal, the data of the center for communicable disease control (MOH), as well as the data from community health centers are integrated and used in this regards. This factsheet contain daily situation report on coronavirus disease (covid-19) in Iran; March 15, 2020.


title: Metronidazole; a Potential Novel Addition to the COVID-19 Treatment Regimen

text: Coronavirus disease 2019 or COVID-19 has rapidly emerged as a global pandemic. This viral infection involves the upper respiratory tract and could lead to severe pneumonia with respiratory distress or even death. Certain studies have found higher initial plasma levels of most pro-inflammatory cytokines during the course of the infection. In this context, both in vitro and in vivo studies have revealed that metronidazole could decrease the levels of several cytokines, which are known to increase during the COVID-19 infection, including interleukin (IL)8, IL6, IL1B, tumor necrosis factor (TNF)α, IL12, IL1α, and interferon (IFN)γ, as well as the levels of C-reactive protein (CRP) and neutrophil count. Furthermore, the drug could decrease neutrophil-generated reactive oxygen species during inflammation. Metronidazole could counteract majority of the immunopathological manifestations of the COVID-19 infection. Therefore, studies with a large sample size are required to determine the efficacy of metronidazole in the treatment of COVID-19 infection.


title: Daily Situation Report on Coronavirus disease (COVID-19) in Iran; March 25, 2020

text: After detection of the first confirmed cases of COVID-19 in Iran, the National Committee on COVID-19 Epidemiology in Ministry of Health and Medical Education was established. This Committee is official source of gathering, analyzing, and reporting the COVID-19 data in Iran. The data of all sources in the country including, medical care monitoring center (MCMC), Hospitals’ Information Systems (HIS), Laboratory portal, the data of the center for communicable disease control (MOH), as well as the data from community health centers are integrated and used in this regards. This factsheet contain daily situation report on coronavirus disease (covid-19) in Iran; March 25, 2020.


title: Daily Situation Report on Coronavirus disease (COVID-19) in Iran; March 22, 2020

text: To forecast the COVID-19 epidemic trend in Iran, a set of dynamic models were created. In these models, the effect of climate and community behavior change on the reproductive number is modeled. A baseline scenario is also defined as letting the epidemic grow naturally, with no prevention/control interventions. Different levels of intervention are also defined based on the extent of population isolation. Outcomes of each scenario on the number of infected cases are computed. Modeling results shows that if effective isolation occurs in 10% of the population, 307,000 individuals will be infected with COVID-19 in Iran by May 20, 2020. For an isolation rate of 25%, started since March 10, 2020, cumulative number of deaths will be 13,450 individuals by May 20, 2020. If preventive efforts can reach a 32% effective isolation rate, a considerable decrease in the number of new cases would be expected during April and May, and the total number of deaths would decrease to 8,630. If the isolation rate increases to 40%, the total number of infected individuals is expected to be 6,030 individuals. It should be acknowledged that this model predicts the number of deaths of all COVID-19 cases, including those who will not be confirmed as COVID-19, because of non-testing or death prior to COVID-19 identification. This serious health issue requires both long-term and short-term planning and arrangements. Social distancing, and identification and isolation of suspected and confirmed cases are believed to be the most important and effective control measure, and should be strengthened soon. For further details on the methodology and results of these models, please visit: http://corona.behdasht.gov.ir/files/site1/files/Covid_Modeling_V14_26.12.98.pdf


title: Daily Situation Report on Coronavirus disease (COVID-19) in Iran; March 23, 2020

text: After detection of the first confirmed cases of COVID-19 in Iran, the National Committee on COVID-19 Epidemiology in Ministry of Health and Medical Education was established. This Committee is official source of gathering, analyzing, and reporting the COVID-19 data in Iran. The data of all sources in the country including, medical care monitoring center (MCMC), Hospitals’ Information Systems (HIS), Laboratory portal, the data of the center for communicable disease control (MOH), as well as the data from community health centers are integrated and used in this regards. This factsheet contain daily situation report on coronavirus disease (covid-19) in Iran; March 23, 2020.


title: Daily Situation Report on Coronavirus disease (COVID-19) in Iran; March 14, 2020

text: After detection of the first confirmed cases of COVID-19 in Iran, the National Committee on COVID-19 Epidemiology in Ministry of Health and Medical Education was established. This Committee is official source of gathering, analyzing, and reporting the COVID-19 data in Iran. The data of all sources in the country including, medical care monitoring center (MCMC), Hospitals’ Information Systems (HIS), Laboratory portal, the data of the center for communicable disease control (MOH), as well as the data from community health centers are integrated and used in this regards. This factsheet contain daily situation report on coronavirus disease (covid-19) in Iran; March 14, 2020.


title: Daily Situation Report on Coronavirus disease (COVID-19) in Iran; March 17, 2020

text: The main strategy of the Ministry of Health (MOH) for the control of COVID-19 is active case finding using electronic tools, taking advantage of the capacity of the national primary health care (PHC) network, and community engagement. To accomplish this, all people are asked to participate in the screening process using the MOH's self-assessment portal (salamat.gov.ir). Health workers and public volunteers actively contact suspected cases using information recorded in this portal, as well as the electronic health record (SIB portal). They actively evaluate individuals, follow-up them, and provide them with necessary information. Where needed, clients are referred to 16-hour treatment clinics, which are specifically set up for the diagnosis and treatment of the disease, to the hospitals, or will be treated at home. The preliminary results of this national campaign (launched nationwide last week) is provided in this factsheet.


title: Epidemiological and Clinical Aspects of COVID-19; a Narrative Review

text: There are significant misconceptions and many obstacles in the way of illuminating the epidemiological and clinical aspects of COVID-19 as a new emerging epidemic. In addition, usefulness of some evidence published in the context of the recent epidemic for decision making in clinic as well as public health is questionable. However, misinterpreting or ignoring strong evidence in clinical practice and public health probably results in less effective and somehow more harmful decisions for individuals as well as subgroups in general populations of countries in the initial stages of this epidemic. Accordingly, our narrative review appraised epidemiological and clinical aspects of the disease including genetic diversity of coronavirus genus, mode of transmission, incubation period, infectivity, pathogenicity, virulence, immunogenicity, diagnosis, surveillance, clinical case management and also successful measures for preventing its spread in some communities.


title: Covid 19 pandemic and gynaecological laparoscopic surgery: knowns and unknowns

text: The worldwide impact of COVID 19 continues to be felt as hospitals in all countries reduce elective and non-urgent cases to allow staffing and resources to be deployed elsewhere. Urgent gynaecological and cancer procedures are continuing, and it is imperative all theatre staff are protected and risks of SARS-CoV-2 viral transmission reduced when operating on asymptomatic, suspected or confirmed COVID 19 patients. In particular, there are concerns relating to the transmission of COVID 19 during gynaecological laparoscopic surgery, arising from the potential generation of SARS-CoV-2 contaminated aerosols from CO(2) leakage and the creation of smoke from the use of energy devices. The aim of this paper is to review all the up to date evidence, including experiences from China and Italy, to guide the safe management of such patients when undergoing gynaecological procedures.


title: Laboratory Parameters in Detection of COVID-19 Patients with Positive RT-PCR; a Diagnostic Accuracy Study

text: INTRODUCTION: The role of laboratory parameters in screening of COVID-19 cases has not been definitely established. This study aimed to evaluate the accuracy of laboratory parameters in predicting cases with positive RT-PCR for COVID-19. METHODS: This diagnostic accuracy study was conducted on suspected COVID-19 patients, who presented to Behpooyan Clinic Medical center in Tehran (Iran) from 22 February to 14 March, 2020. Patients were divided into two groups based on the results of real time reverse transcriptase‐polymerase chain reaction (RT-PCR) for COVID-19, and the accuracy of different laboratory parameters in predicting cases with positive RT-PCR was evaluated using area under the ROC curve (AUC). RESULTS: Two hundred cases with the mean age of 41.3± 14.6 (range: 19-78) years were studied (0.53% male). The result of RT-PCR for COVID-19 was positive in 70 (35%) cases. Patients with positive RT-PCR had significantly higher neutrophil (NEU) count (p = 0.0001), and C-reactive protein (CRP) (p = 0.04), lactate dehydrogenase (LDH) (p = 0.0001), aspartate aminotransferase (AST) (p = 0.001), alanine aminotransferase (ALT) (p = 0.0001), and Urea (p = 0.001) levels in serum. In addition, patients with positive RT-PCR had lower white blood cell (WBC) count (p = 0.0001) and serum albumin level (p = 0.0001) compared to others. ALT (AUC = 0.879), CRP (AUC = 0.870), NEU (AUC = 0.858), LDH (AUC = 0.835), and Urea (AUC = 0.835) had very good accuracy in predicting cases with positive RT-PCR for COVID-19, respectively. CONCLUSION: Our findings suggest that level of LDH, CRP, ALT and NEU can be used to predict the result of COVID-19 test. They can help in detection of COVID-19 patients.


COVID-19 and Ophthalmology: A New Chapter in an Old Story


title: COVID-19: Preliminary Clinical Guidelines for Ophthalmology Practices

text: The zoonotic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and its resultant human coronavirus disease (COVID-19) recently appeared as a global health threat that can cause severe respiratory infection and terminal respiratory distress. By the first week of April, more than 1.3 million people had been globally infected and more than 70,000 had lost their lives to this contagious virus. Clinical manifestations occur shortly after exposure, or a few days later. There is controversy regarding the transmission of the virus through the tear and conjunctiva; however, there are reports that the ocular surface might be a potential target for COVID-19. The ease of transmission of this virus at close proximity presents a risk to eyecare workers. Several recommendations have been issued by local and national organizations to address the issue of safe ophthalmic practice during the ongoing COVID-19 pandemic. These guidelines have numerous similarities; however, subtle differences exist. The purpose of this paper was to discuss measures, with a specific focus on standard precautions, to prevent further dissemination of COVID-19 at Eye Clinics. We have proposed procedures to triage suspected cases of COVID-19, considering emergency conditions.


Global Health Diplomacy: A Closer Look


title: Predicting the mortality due to Covid-19 by the next month for Italy, Iran and South Korea; a simulation study

text: AIM: To estimate the number of confirmed cases and the rate of death and also to investigate the cause of death in Italy, Iran and South Korea in the next month. BACKGROUND: Growing number of confirmed and deaths cases from the coronavirus worldwide, particularly in Italy, Iran and South Korea, has resulted concerns about the future of these countries and their deterioration. Also the European region is likely to face more casualties due to the delay in the virus reaching most of its regions and, of course, as the trend continues. METHODS: We conducted a simulation in both current and ideal situation for the next month to predict the death rate and examine the reason for the difference in Italy, Iran and South Korea individually. If we assume the cultural and political factors and age pyramids distribution are similar across regions, the differences are mainly due either to the heavier health-care burden owing to the larger population or to the medical facilities diversities. RESULTS: Our results for Italy showed higher death number, but the rate would be more for Iran. South Korea is also expected to have a smaller increase in the number of confirmed cases and deaths compared to Iran and Italy by the next month. CONCLUSION: Given the prevailing conditions around the world and the increasing number of casualties, it is essential that all countries, especially those with fewer days of involvement, shall do their best to avoid major losses and damages.


title: Antiviral therapy in management of COVID-19: a systematic review on current evidence

text: BACKGROUND: The purpose of the current systematic review is to evaluate the efficacy of antiviral therapies in treatment of COVID-19. In addition, clinical trials on the efficacy of antiviral therapies in the management of Severe Acute Respiratory Syndrome coronavirus (SARS-Cov) or Middle East Respiratory Syndrome coronavirus (MERS-CoV) have also been reviewed, in order to identify potential treatment options for COVID-19. METHOD: An extensive search was performed in Medline, Embase, Scopus, Web of Science and CENTRAL databases until the end of March 15, 2020. Two independent researchers performed the screening, and finally the related studies were included. RESULTS: Only one clinical trial on the efficacy of antiviral therapy in management of COVID-19 was found. The results depicted that adding Lopinavir-Ritonavir to the standard treatment regimen of patients with severe COVID-19 has no benefits. Moreover, 21 case-series and case-report studies reported the prescription of antiviral agents in COVID-19, none of which can be used to determine the efficacy of antiviral therapies in confronting COVID-19. In addition, no clinical trials were found to be performed on the efficacy of antiviral agents in the management of SARS-CoV and MERS-CoV. CONCLUSION: The current evidence impede researchers from proposing an appropriate antiviral therapy against COVID-19, making the current situation a serious concern for international organizations such as World Health Organization (WHO). In the time of the current pandemic and future epidemics, organizations such as WHO should pursue more proactive actions and plan well-designed clinical trials so that their results can be used in managing future epidemics.


title: Prone Position in Management of COVID-19 Patients; a Commentary

text: SARS-CoV-2 virus causes a pneumonia that was identified through fever, dyspnea, and acute respiratory symptoms and named COVID-19. This disease exacerbates in a number of patients and causes pulmonary edema, multi-organ failure, and acute respiratory distress syndrome (ARDS). Prevalence of ARDS among COVID-19 patients has been reported to be up to 17%. Among the introduced treatment methods for management of ARDS patients, prone position can be used as an adjuvant therapy for improving ventilation in these patients. Here we reviewed the literature regarding the role of prone position in management of COVID-19 patients.


title: COVID-19 Pneumonia in Asymptomatic Trauma Patients; Report of 8 Cases

text: We are currently involved in the novel coronavirus 2019 (COVID-19) pandemic. A considerable number of COVID-19 infected cases are asymptomatic but they can transmit the disease to others, especially healthcare workers. In this study, we reported 8 incidentally detected cases of COVID-19 pneumonia in chest computed tomography (CT) scan of patients referred to emergency department following multiple trauma without any respiratory symptoms.


Canadian Conference on Medical Education


title: COVID-19 in Singapore and Malaysia: Rising to the Challenges of Orthopaedic Practice in an Evolving Pandemic

text: With the increasing number of COVID-19 cases and related deaths worldwide, we decided to share the development of this condition in Singapore and Malaysia. First few cases were diagnosed in the two countries at the end of January 2020, and the numbers have surged to thousands by end of March 2020. We will focus on strategies adopted by the government and also the Orthopaedic community of the two countries up till the beginning of April 2020. We hope that by sharing of relevant information and knowledge on how we are managing the COVID-19 condition, we can help other communities, and health care workers to more effectively overcome this pandemic.


Protecting yourself and your patients from COVID-19 in eye care


title: Review of safety and minimum pricing of nitazoxanide for potential treatment of COVID-19

text: BACKGROUND: Many treatments are being assessed for repurposing to treat coronavirus disease 2019 (COVID-19). One drug that has shown promising results in vitro is nitazoxanide. Unlike other postulated drugs, nitazoxanide shows a high ratio of maximum plasma concentration (C(max)), after 1 day of 500 mg twice daily (BD), to the concentration required to inhibit 50% replication (EC(50)) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (C(max ): EC(50 )roughly equal to 14:1). As such, it is important to investigate the safety of nitazoxanide for further trials. Furthermore, treatments for COVID-19 should be cheap to promote global access, but prices of many drugs are far higher than the costs of production. We aimed to conduct a review of the safety of nitazoxanide for any prior indication and calculate its minimum costs of production. METHODS: A review of nitazoxanide clinical research was conducted using EMBASE and MEDLINE databases, supplemented by ClinicalTrials.gov. We searched for phase 2 or 3 randomised controlled trials (RCTs) comparing nitazoxanide with placebo or active control for 5–14 days in participants experiencing acute infections of any kind. Data extracted were grade 1–4 and serious adverse events (AEs). Data were also extracted on gastrointestinal (GI) AEs, as well as hepatorenal and cardiovascular effects. Active pharmaceutical ingredient cost data from 2016 to 2019 were extracted from the Panjiva database and adjusted for 5% loss during production, costs of excipients, formulation, a 10% profit margin and tax. Two dosages, at 500 mg BD and a higher dose of 1100 mg three times daily (TDS), were considered. Our estimated costs were compared with publicly available list prices from a selection of countries. RESULTS: Nine RCTs of nitazoxanide were identified for inclusion. These RCTs accounted for 1514 participants and an estimated 95.3 person-years-of-follow-up. No significant differences were found in any of the AE endpoints assessed, across all trials or on subgroup analyses of active- or placebo-controlled trials. Mild GI AEs increased with dose. No hepatorenal or cardiovascular concerns were raised, but few appropriate metrics were reported. There were no teratogenic concerns, but the evidence base was very limited. Based on a weighted-mean cost of US $61/kg, a 14-day course of treatment with nitazoxanide 500 mg BD would cost $1.41. The daily cost would therefore be $0.10. The same 14-day course could cost $3944 in US commercial pharmacies, and $3 per course in Pakistan, India and Bangladesh. At a higher dose of 1100 mg TDS, our estimated cost was $4.08 per 14-day course, equivalent to $0.29 per day. CONCLUSION: Nitazoxanide demonstrates a good safety profile at approved doses. However, further evidence is required regarding hepatorenal and cardiovascular effects, as well as teratogenicity. We estimate that it would be possible to manufacture nitazoxanide as generic for $1.41 for a 14-day treatment course at 500 mg BD, up to $4.08 at 1100 mg TDS. Further trials in COVID-19 patients should be initiated. If efficacy against SARS-CoV-2 is demonstrated in clinical studies, nitazoxanide may represent a safe and affordable treatment in the ongoing pandemic.


Summary of the coronavirus disease 2019 (COVID-19) update from the 2020 Conference on Retroviruses and Opportunistic Infections, 8–11 March 2020, Boston, USA


title: A review of the safety of favipiravir – a potential treatment in the COVID-19 pandemic?

text: BACKGROUND: Repurposing broad-spectrum antivirals is an immediate treatment opportunity for 2019 coronavirus disease (COVID-19). Favipiravir is an antiviral previously indicated for influenza and Ebola, which has shown some promise in early trials for treatment of COVID-19. We aim to review existing favipiravir safety evidence, which is vital to informing the potential future use of favipiravir in COVID-19. METHODS: A search was conducted across EMBASE and MEDLINE databases, supplemented by relevant grey-literature and ClinicalTrials.gov. All studies assessing the use of favipiravir in humans by 27 March 2020 were considered for inclusion. Further analysis of available safety data from phase 2 and 3 studies was undertaken. Data extracted were adverse events (AEs) grade 1–4, serious AEs and discontinuation for AEs. Specific AEs of interest highlighted in early-phase studies, including gastrointestinal AEs and hyperuricaemia, were also examined. RESULTS: Twenty-nine studies were identified as potential sources of evidence of the clinical safety of favipiravir. Six were phase 2 and 3 studies reporting relevant safety data for statistical comparison, representing a total of 4299 participants, an estimated 175 person-years-of-follow-up (PYFU). Comparator drugs were oseltamivir, umifenovir, lopinavir/ritonavir or placebo. Study follow-up was between 5 and 21 days. The proportions of grade 1–4 AEs on favipiravir was 28.2% vs 28.4% (P = n.s.) in the comparison arms. The proportion of discontinuations due to AEs on favipiravir was 1.1% vs 1.2% (P = n.s.) in the comparison arms. For serious AEs the proportion was 0.4% in both arms (P = n.s.). There were significantly fewer gastrointestinal AEs occurring on favipiravir vs comparators [8.7% vs 11.5%; P = 0.003]. Favipiravir showed significantly more uric acid elevations than comparators [5.8% vs 1.3%; P<0.0001]. CONCLUSIONS: Favipiravir demonstrates a favourable safety profile regarding total and serious AEs. However, safety concerns remain: hyperuricaemia, teratogenicity and QTc prolongation have not yet been adequately studied. Favipiravir may be safe and tolerable in short-term use, but more evidence is needed to assess the longer-term effects of treatment. Given the limitations of the evidence and unresolved safety concerns, caution is warranted in the widespread use of favipiravir against pandemic COVID-19.


title: Minimum costs to manufacture new treatments for COVID-19

text: INTRODUCTION: ‘Repurposing’ existing drugs to treat COVID-19 is vital to reducing mortality and controlling the pandemic. Several promising drugs have been identified and are in various stages of clinical trials globally. If efficacy of these drugs is demonstrated, rapid, mass availability at an affordable cost would be essential to ensuring equity and access especially amongst low- and middle-income economies. METHODS: Minimum costs of production were estimated from the costs of active pharmaceutical ingredients using established methodology, which had good predictive accuracy for medicines for hepatitis C and HIV amongst others. Data were extracted from global export shipment records or analysis of the route of chemical synthesis. The estimated costs were compared with list prices from a range of countries where pricing data were available. RESULTS: Minimum estimated costs of production were US $0.93/day for remdesivir, $1.45/day for favipiravir, $0.08/day for hydroxychloroquine, $0.02/day for chloroquine, $0.10/day for azithromycin, $0.28/day for lopinavir/ritonavir, $0.39/day for sofosbuvir/daclatasvir and $1.09/day for pirfenidone. Costs of production ranged between $0.30 and $31 per treatment course (10–28 days). Current prices of these drugs were far higher than the costs of production, particularly in the US. CONCLUSIONS: Should repurposed drugs demonstrate efficacy against COVID-19, they could be manufactured profitably at very low costs, for much less than current list prices. Estimations for the minimum production costs can strengthen price negotiations and help ensure affordable access to vital treatment for COVID-19 at low prices globally.


title: Survey of WU and KI polyomaviruses, coronaviruses, respiratory syncytial virus and parechovirus in children under 5 years of age in Tehran, Iran

text: BACKGROUND AND OBJECTIVES: Severe acute respiratory infections (SARI) remain an important cause for childhood morbidity worldwide. We designed a research with the objective of finding the frequency of respiratory viruses, particularly WU and KI polyomaviruses (WUPyV & KIPyV), human coronaviruses (HCoVs), human respiratory syncytial virus (HRSV) and human parechovirus (HPeV) in hospitalized children who were influenza negative. MATERIALS AND METHODS: Throat swabs were collected from children younger than 5 years who have been hospitalized for SARI and screened for WUPyV, KIPyV, HCoVs, HRSV and HPeV using Real time PCR. RESULTS: A viral pathogen was identified in 23 (11.16%) of 206 hospitalized children with SARI. The rate of virus detection was considerably greater in infants <12 months (78.2%) than in older children (21.8%). The most frequently detected viruses were HCoVs with 7.76% of positive cases followed by KIPyV (2%) and WUPyV (1.5%). No HPeV and HRSV were detected in this study. CONCLUSION: This research shown respiratory viruses as causes of childhood acute respiratory infections, while as most of mentioned viruses usually causes mild respiratory diseases, their frequency might be higher in outpatient children. Meanwhile as HRSV is really sensitive to inactivation due to environmental situations and its genome maybe degraded, then for future studies, we need to use fresh samples for HRSV detection. These findings addressed a need for more studies on viral respiratory tract infections to help public health.


Is reporting many cases of COVID-19 in Iran due to strength or weakness of Iran’s health system?