Intubating Ebola Patients: Technical Limitations of Extensive Personal Protective Equipment
subject: Ebola, personal protective equipment, Emergency medicine
description: As hospitals across the nation were preparing for thepossibility of Ebola or Middle Eastern respiratory syndrome(MERS-CoV) cases, healthcare workers underwent intricatetraining in the use of personal protective equipment (PPE).An Ebola or MERS-CoV patient requiring intubation placesa healthcare worker at risk for exposure to bodily secretions.The procedure must be performed only after appropriatePPE is donned.1 Intubating while wearing PPE is yet anotherchallenge identified in caring for these patients. Manualdexterity and free movement decreases when wearing PPE,and may increase length of time to successful intubation.
creator: Warren Wiechmann, Shannon Toohey, Cassandra Majestic, Megan Boysen-Osborn
source: Western Journal of Emergency Medicine
publisher: eScholarship Publishing, University of California
date: 2015
language: EN
identifier: DOI: 10.5811/westjem.2015.10.28779
coverage: Medicine, Medical emergencies. Critical care. Intensive care. First aid

Encephalitis with reversible splenial and deep cerebral white matter lesions associated with Epstein–Barr virus infection in adults
subject: Mild encephalitis with reversible splenial, Epstein-Barr virus, magnetic resonance imaging, Adults, Case Report
description: Yanjun Guo,1 Shuhui Wang,1 Bin Jiang,1 Jianle Li,1 Lei Liu,2 Jiawei Wang,2 Weiqin Zhao,1 Jianping Jia1 1Department of Neurology, Beijing Friendship Hospital, Capital Medical University. Beijing, China; 2Department of Neurology, Beijing Tongren Hospital, Capital Medical University, Beijing, China Background: Approximately 200 cases of mild encephalitis with reversible splenial (MERS) and deep cerebral white matter lesions have been reported since MERS was first defined in 2004. MERS occurs more frequently in children; in adults, only ~60 cases have been reported. Until now, only four cases of MERS in adults have been associated with Epstein–Barr virus (EBV). Case presentation: We report three adult cases of MERS associated with EBV infection in China. For all three patients, cranial magnetic resonance imaging (MRI) indicated solitary reversible splenial and/or perilateral ventricle white matter lesions with reduced diffusion. In the present report, all patients were adults presenting with high fever, headache, apathy, and confusion, as well as significant signs of meningeal inflammation. These symptoms peaked 10–14 days after disease onset, with serious hyponatremia (112–129 mmol/L), an elevated cerebrospinal fluid white blood cell count (80–380/mm3), and significantly increased protein levels (1,010–1,650 mg/dL). Cranial MRI indicated abnormal signal intensity in the splenium of corpus callosum and symmetrically reversible lesions scattered in the thalamus and deep cerebral white matter. The clinical symptoms tended to improve after ~10–14 days of antiviral treatment. However, these patients recovered more slowly than patients with viral meningitis. Conclusion: MERS associated with EBV infection in adults occurs less frequently but with more severe symptoms than in children. EBV infection should be considered for patients with MERS symptoms. MERS has a good prognosis. Keywords: mild encephalitis with reversible splenial lesions, Epstein-Barr virus, apathy, hyponatre…
creator: Guo YJ, Wang SH, Jiang B, Li JL, Liu L, Wang J., Zhao WQ, Jia J
source: Neuropsychiatric Disease and Treatment
publisher: Dove Medical Press
date: 2017
language: EN
coverage: Neurosciences. Biological psychiatry. Neuropsychiatry, Neurology. Diseases of the nervous system

Middle East respiratory syndrome in the Republic of Korea: transparency and communication are key
subject: MERS-CoV, health communications, Outbreak
description: None
creator: Isaac Chun-Hai Fung, Zion Tsz Ho Tse, Benedict Shing Bun Chan, King-Wa Fu
source: Western Pacific Surveillance and Response
publisher: World Health Organization
date: 2015
language: EN, ZH
identifier: DOI: 10.5365/wpsar.2015.6.2.011
coverage: Public aspects of medicine, Medicine

Viral genome sequencing by random priming methods
description: Abstract Background Most emerging health threats are of zoonotic origin. For the overwhelming majority, their causative agents are RNA viruses which include but are not limited to HIV, Influenza, SARS, Ebola, Dengue, and Hantavirus. Of increasing importance therefore is a better understanding of global viral diversity to enable better surveillance and prediction of pandemic threats; this will require rapid and flexible methods for complete viral genome sequencing. Results We have adapted the SISPA methodology 123 to genome sequencing of RNA and DNA viruses. We have demonstrated the utility of the method on various types and sources of viruses, obtaining near complete genome sequence of viruses ranging in size from 3,000–15,000 kb with a median depth of coverage of 14.33. We used this technique to generate full viral genome sequence in the presence of host contaminants, using viral preparations from cell culture supernatant, allantoic fluid and fecal matter. Conclusion The method described is of great utility in generating whole genome assemblies for viruses with little or no available sequence information, viruses from greatly divergent families, previously uncharacterized viruses, or to more fully describe mixed viral infections.
creator: Zhang Xinsheng, Afonso Claudio, Feldblyum Jeremy, Sengamalay Naomi, DePasse Jay, Kuzmickas Ryan, Halpin Rebecca, Djikeng Appolinaire, Anderson Norman G, Ghedin Elodie, Spiro David J
source: BMC Genomics
publisher: BMC
date: 2008
language: EN
identifier: DOI: 10.1186/1471-2164-9-5
coverage: Genetics, Biotechnology

A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: Assembly of the duck (Anas platyrhynchos) transcriptome.
subject: RNA-Seq, assembly, high-throughput sequencing, Illumina, de novo transcriptome
description: For vertebrate organisms where a reference genome is not available, de novo transcriptome assembly enables a cost effective insight into the identification of tissue specific or differentially expressed genes and variation of the coding part of the genome. However, since there are a number of different tools and parameters that can be used to reconstruct transcripts, it is difficult to determine an optimal method. Here we suggest a pipeline based on (1) assessing the performance of three different assembly tools (2) using both single and multiple k-mer approaches (3) examining the influence of the number of reads used in the assembly (4) merging assemblies from different tools. We use an example dataset from the vertebrate Anas platyrhynchos domestica (Pekin duck). We find that taking a subset of data enables a robust assembly to be produced by multiple methods without the need for very high memory capacity. The use of reads mapped back to transcripts (RMBT) and CEGMA (Core Eukaryotic Genes Mapping Approach) provides useful metrics to determine the completeness of assembly obtained. For this dataset the use of multiple k-mers in the assembly generated a more complete assembly as measured by greater number of RMBT and CEGMA score. Merged single k-mer assemblies are generally smaller but consist of longer transcripts, suggesting an assembly consisting of fewer fragmented transcripts. We suggest that the use of a subset of reads during assembly allows the relatively rapid investigation of assembly characteristics and can guide the user to the most appropriate transcriptome for particular downstream use. Transcriptomes generated by the compared assembly methods and the final merged assembly are freely available for download at http://dx.doi.org/10.6084/m9.figshare.1032613.
creator: Joanna eMoreton, Stephen P Dunham, Richard D. Emes
source: Frontiers in Genetics
publisher: Frontiers Media S.A.
date: 2014
language: EN
identifier: DOI: 10.3389/fgene.2014.00190
coverage: Genetics

Association of the shuffling of Streptococcus pyogenes clones and the fluctuation of scarlet fever cases between 2000 and 2006 in central Taiwan
description: Abstract Background The number of scarlet fever occurrences reported between 2000 and 2006 fluctuated considerably in central Taiwan and throughout the nation. Isolates of Streptococcus pyogenes were collected from scarlet fever patients in central Taiwan and were characterized by emm sequencing and a standardized pulsed-field gel electrophoresis (PFGE) method. National weekly report data were collected for investigating epidemiological trends. Results A total of 23 emm types were identified in 1,218 S. pyogenes isolates. The five most prevalent emm types were emm12 (50.4%), emm4 (23.2%), emm1 (16.4%), emm6 (3.8%) and emm22 (3.0%). PFGE analysis with SmaI suggested that, with a few exceptions, strains with a common emm type belonged to the same clone. There were two large emm12 clones, one with DNA resistant to cleavage by SmaI. Each prevalent emm clone had major PFGE strain(s) and many minor strains. Most of the minor strains emerged in the population and disappeared soon after. Even some major strains remained prevalent for only 2–3 years before declining. The large fluctuation of scarlet fever cases between 2000 and 2006 was associated with the shuffling of six prevalent emm clones. In 2003, the dramatic drop in scarlet fever cases in central Taiwan and throughout the whole country was associated with the occurrence of a severe acute respiratory syndrome (SARS) outbreak that occurred between late-February and mid-June in Taiwan. Conclusion The occurrences of scarlet fever in central Taiwan in 2000–2006 were primarily caused by five emm types, which accounted for 96.8% of the isolates collected. Most of the S. pyogenes strains (as defined by PFGE genotypes) emerged and lasted for only a few years. The fluctuation in the number of scarlet fever cases during the seven years can be primarily attributed to the shuffling of six prevalent emm clones and to the SARS outbreak in 2003.
creator: Wang Wan-Ling, Chen Pei-Ling, Wang You-Wun, Chiou Chien-Shun, Wu Ping-Fuai, Wei Hsiao-Lun
source: BMC Microbiology
publisher: BMC
date: 2009
language: EN
identifier: DOI: 10.1186/1471-2180-9-115
coverage: Microbiology

Tuberculosis prevention in healthcare workers in China 10 years after the severe acute respiratory syndrome pandemic
creator: Yunfeng Deng, Yan LI, Fengtian Wang, Dachuan Gao, Liang Li, Larry D. Teeter, Edward A. Graviss, Xin Ma
source: ERJ Open Research
publisher: European Respiratory Society
date: 2015
language: EN
identifier: DOI: 10.1183/23120541.00015-2015
coverage: Medicine

Detection of Bovine Leukemia Virus in Brains of Cattle with a Neurological Syndrome: Pathological and Molecular Studies
description: Bovine leukemia virus (BLV) was investigated in the central nervous system (CNS) of cattle with neurological syndrome. A total of 269 CNS samples were submitted to nested-PCR (BLV env gene gp51), and the viral genotypes were identified. The nested-PCR was positive in 4.8% (13/269) CNS samples, with 2.7% (2/74) presenting at histological examination lesions of nonpurulent meningoencephalitis (NPME), whereas 5.6% (11/195) not presenting NPME (P>0.05). No samples presented lymphosarcoma. The PCR products (437 bp) were sequenced and submitted to phylogenetic analysis by neighbor-joining and maximum composite likelihood methods, and genotypes 1, 5, and 6 were detected, corroborating other South American studies. The genotype 6 barely described in Brazil and Argentina was more frequently detected in this study. The identity matrices showed maximum similarity (100%) among some samples of this study and one from Argentina (FJ808582), recovered from GenBank. There was no association among the genotypes and NPME lesions.
creator: Rubens Henrique Ramos D’Angelino, Edviges Maristela Pituco, Eliana Monteforte Cassaro Villalobos, Ricardo Harakava, Fabio Gregori, Claudia Del Fava
source: BioMed Research International
publisher: Hindawi Limited
date: 2013
language: EN
identifier: DOI: 10.1155/2013/425646
coverage: Medicine

Comparison between SARS CoV and MERS CoV Using Apriori Algorithm, Decision Tree, SVM
description: MERS (Middle East Respiratory Syndrome) is a worldwide disease these days. The number of infected people is 1038(08/03/2015) in Saudi Arabia and 186(08/03/2015) in South Korea. MERS is all over the world including Europe and the fatality rate is 38.8%, East Asia and the Middle East. The MERS is also known as a cousin of SARS (Severe Acute Respiratory Syndrome) because both diseases show similar symptoms such as high fever and difficulty in breathing. This is why we compared MERS with SARS. We used data of the spike glycoprotein from NCBI. As a way of analyzing the protein, apriori algorithm, decision tree, SVM were used, and particularly SVM was iterated by normal, polynomial, and sigmoid. The result came out that the MERS and the SARS are alike but also different in some way.
creator: Jang Seongpil, Lee Seunghwan, Choi Seong-Min, Seo Junwon, Choi Hunseok, Yoon Taeseon
source: MATEC Web of Conferences
publisher: EDP Sciences
date: 2016
language: EN, FR
identifier: DOI: 10.1051/matecconf/20164908001
coverage: Engineering (General). Civil engineering (General)

Pathogenicity and Viral Shedding of MERS-CoV in Immunocompromised Rhesus Macaques
subject: Middle East respiratory syndrome coronavirus, immunosuppression, pathology, shedding, macaque monkey
description: Middle East respiratory syndrome coronavirus (MERS-CoV) has recently emerged in the Middle East. Since 2012, there have been approximately 2,100 confirmed cases, with a 35% case fatality rate. Disease severity has been linked to patient health status, as people with chronic diseases or an immunocompromised status fare worse, although the mechanisms of disease have yet to be elucidated. We used the rhesus macaque model of mild MERS to investigate whether the immune response plays a role in the pathogenicity in relation to MERS-CoV shedding. Immunosuppressed macaques were inoculated with MERS-CoV and sampled daily for 6 days to assess their immune statues and to measure viral shedding and replication. Immunosuppressed macaques supported significantly higher levels of MERS-CoV replication in respiratory tissues and shed more virus, and virus disseminated to tissues outside of the respiratory tract, whereas viral RNA was confined to respiratory tissues in non-immunosuppressed animals. Despite increased viral replication, pathology in the lungs was significantly lower in immunosuppressed animals. The observation that the virus was less pathogenic in these animals suggests that disease has an immunopathogenic component and shows that inflammatory responses elicited by the virus contribute to disease.
creator: Joseph Prescott, Darryl Falzarano, Emmie de Wit, Kath Hardcastle, Friederike Feldmann, Elaine Haddock, Dana Scott, Heinz Feldmann, Vincent Jacobus Munster
source: Frontiers in Immunology
publisher: Frontiers Media S.A.
date: 2018
language: EN
identifier: DOI: 10.3389/fimmu.2018.00205
coverage: Immunologic diseases. Allergy