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                <text>Sampling for global epidemic models and the topology of an international airport network.</text>
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                <text>Georgiy Bobashev, Robert J Morris, D Michael Goedecke</text>
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                <text>Mathematical models that describe the global spread of infectious diseases such as influenza, severe acute respiratory syndrome (SARS), and tuberculosis (TB) often consider a sample of international airports as a network supporting disease spread. However, there is no consensus on how many cities should be selected or on how to select those cities. Using airport flight data that commercial airlines reported to the Official Airline Guide (OAG) in 2000, we have examined the network characteristics of network samples obtained under different selection rules. In addition, we have examined different size samples based on largest flight volume and largest metropolitan populations. We have shown that although the bias in network characteristics increases with the reduction of the sample size, a relatively small number of areas that includes the largest airports, the largest cities, the most-connected cities, and the most central cities is enough to describe the dynamics of the global spread of influenza. The analysis suggests that a relatively small number of cities (around 200 or 300 out of almost 3000) can capture enough network information to adequately describe the global spread of a disease such as influenza. Weak traffic flows between small airports can contribute to noise and mask other means of spread such as the ground transportation.</text>
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                <text>DOI: 10.1371/journal.pone.0003154</text>
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                <text>PLoS ONE</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Viral etiology of influenza-like illnesses in Antananarivo, Madagascar, July 2008 to June 2009.</text>
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                <text>Norosoa Harline Razanajatovo, Vincent Richard, Jonathan Hoffmann, Jean-Marc Reynes, Girard Marcellin Razafitrimo, Rindra Vatosoa Randremanana, Jean-Michel Heraud</text>
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                <text>In Madagascar, despite an influenza surveillance established since 1978, little is known about the etiology and prevalence of viruses other than influenza causing influenza-like illnesses (ILIs).From July 2008 to June 2009, we collected respiratory specimens from patients who presented ILIs symptoms in public and private clinics in Antananarivo (the capital city of Madagascar). ILIs were defined as body temperature ≥38°C and cough and at least two of the following symptoms: sore throat, rhinorrhea, headache and muscular pain, for a maximum duration of 3 days. We screened these specimens using five multiplex real time Reverse Transcription and/or Polymerase Chain Reaction assays for detection of 14 respiratory viruses. We detected respiratory viruses in 235/313 (75.1%) samples. Overall influenza virus A (27.3%) was the most common virus followed by rhinovirus (24.8%), RSV (21.2%), adenovirus (6.1%), coronavirus OC43 (6.1%), influenza virus B (3.9%), parainfluenza virus-3 (2.9%), and parainfluenza virus-1 (2.3%). Co-infections occurred in 29.4% (69/235) of infected patients and rhinovirus was the most detected virus (27.5%). Children under 5 years were more likely to have one or more detectable virus associated with their ILI. In this age group, compared to those ≥5 years, the risk of detecting more than one virus was higher (OR = 1.9), as was the risk of detecting of RSV (OR = 10.1) and adenovirus (OR = 4.7). While rhinovirus and adenovirus infections occurred year round, RSV, influenza virus A and coronavirus OC43 had defined period of circulation.In our study, we found that respiratory viruses play an important role in ILIs in the Malagasy community, particularly in children under 5 years old. These data provide a better understanding of the viral etiology of outpatients with ILI and describe for the first time importance of these viruses in different age group and their period of circulation.</text>
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                <text>DOI: 10.1371/journal.pone.0017579</text>
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                <text>PLoS ONE</text>
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                <text>Unexpected diversity of cellular immune responses against Nef and Vif in HIV-1-infected patients who spontaneously control viral replication.</text>
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                <text>Leandro F Tarosso, Mariana M. Sauer, Sabri Sanabani, Maria Teresa Giret, Helena I. Tomiyama, John Sidney, Shari M. Piaskowski, Ricardo S. Diaz, Ester C. Sabino, Alessandro Sette, Jorge Kalil Filho, David I. Watkins, Esper G Kallas</text>
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                <text>HIV-1-infected individuals who spontaneously control viral replication represent an example of successful containment of the AIDS virus. Understanding the anti-viral immune responses in these individuals may help in vaccine design. However, immune responses against HIV-1 are normally analyzed using HIV-1 consensus B 15-mers that overlap by 11 amino acids. Unfortunately, this method may underestimate the real breadth of the cellular immune responses against the autologous sequence of the infecting virus.Here we compared cellular immune responses against nef and vif-encoded consensus B 15-mer peptides to responses against HLA class I-predicted minimal optimal epitopes from consensus B and autologous sequences in six patients who have controlled HIV-1 replication. Interestingly, our analysis revealed that three of our patients had broader cellular immune responses against HLA class I-predicted minimal optimal epitopes from either autologous viruses or from the HIV-1 consensus B sequence, when compared to responses against the 15-mer HIV-1 type B consensus peptides.This suggests that the cellular immune responses against HIV-1 in controller patients may be broader than we had previously anticipated.</text>
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                <text>2010</text>
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                <text>DOI: 10.1371/journal.pone.0011436</text>
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                <text>PLoS ONE</text>
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                <text>Novel coronavirus and astrovirus in Delaware Bay shorebirds.</text>
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                <text>Kirsi S. Honkavuori, Thomas Briese, Scott Krauss, Maria D Sanchez, Komal Jain, Stephen K. Hutchison, Robert G. Webster, W. Ian Lipkin</text>
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                <text>Wild birds are an important but to some extent under-studied reservoir for emerging pathogens. We used unbiased sequencing methods for virus discovery in shorebird samples from the Delaware Bay, USA; an important feeding ground for thousands of migratory birds.Analysis of shorebird fecal samples indicated the presence of a novel astrovirus and coronavirus. A sanderling sample yielded sequences with distant homology to avian nephritis virus 1, an astrovirus associated with acute nephritis in poultry. A ruddy turnstone sample yielded sequences with homology to deltacoronaviruses.Our findings highlight shorebirds as a virus reservoir and the need to closely monitor wild bird populations for the emergence of novel virus variants.</text>
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                <text>DOI: 10.1371/journal.pone.0093395</text>
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                <text>PLoS ONE</text>
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                <text>Identification of residues of SARS-CoV nsp1 that differentially affect inhibition of gene expression and antiviral signaling.</text>
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                <text>Andrew R Jauregui, Dhruti Savalia, Virginia K Lowry, Cara M Farrell, Marc G Wathelet</text>
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                <text>An epidemic of Severe Acute Respiratory Syndrome (SARS) led to the identification of an associated coronavirus, SARS-CoV. This virus evades the host innate immune response in part through the expression of its non-structural protein (nsp) 1, which inhibits both host gene expression and virus- and interferon (IFN)-dependent signaling. Thus, nsp1 is a promising target for drugs, as inhibition of nsp1 would make SARS-CoV more susceptible to the host antiviral defenses. To gain a better understanding of nsp1 mode of action, we generated and analyzed 38 mutants of the SARS-CoV nsp1, targeting 62 solvent exposed residues out of the 180 amino acid protein. From this work, we identified six classes of mutants that abolished, attenuated or increased nsp1 inhibition of host gene expression and/or antiviral signaling. Each class of mutants clustered on SARS-CoV nsp1 surface and suggested nsp1 interacts with distinct host factors to exert its inhibitory activities. Identification of the nsp1 residues critical for its activities and the pathways involved in these activities should help in the design of drugs targeting nsp1. Significantly, several point mutants increased the inhibitory activity of nsp1, suggesting that coronaviruses could evolve a greater ability to evade the host response through mutations of such residues.</text>
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                <text>DOI: 10.1371/journal.pone.0062416</text>
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                <text>PLoS ONE</text>
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              <name>Title</name>
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                  <text>Coronavirus</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Comparative Epidemiology of Human Infections with Middle East Respiratory Syndrome and Severe Acute Respiratory Syndrome Coronaviruses among Healthcare Personnel.</text>
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            <name>Creator</name>
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              <elementText elementTextId="3174">
                <text>Shelan Liu, Ta-Chien Chan, Yu-Tseng Chu, Joseph Tsung-Shu Wu, Xingyi Geng, Na Zhao, Wei Cheng, Enfu Chen, Chwan-Chuen King</text>
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                <text>The largest nosocomial outbreak of Middle East respiratory syndrome (MERS) occurred in South Korea in 2015. Health Care Personnel (HCP) are at high risk of acquiring MERS-Coronavirus (MERS-CoV) infections, similar to the severe acute respiratory syndrome (SARS)-Coronavirus (SARS-CoV) infections first identified in 2003. This study described the similarities and differences in epidemiological and clinical characteristics of 183 confirmed global MERS cases and 98 SARS cases in Taiwan associated with HCP. The epidemiological findings showed that the mean age of MERS-HCP and total MERS cases were 40 (24~74) and 49 (2~90) years, respectively, much older than those in SARS [SARS-HCP: 35 (21~68) years, p = 0.006; total SARS: 42 (0~94) years, p = 0.0002]. The case fatality rates (CFR) was much lower in MERS-HCP [7.03% (9/128)] or SARS-HCP [12.24% (12/98)] than the MERS-non-HCP [36.96% (34/92), p</text>
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                <text>2016</text>
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              <elementText elementTextId="3177">
                <text>DOI: 10.1371/journal.pone.0149988</text>
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              <elementText elementTextId="3178">
                <text>PLoS ONE</text>
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            <name>Publisher</name>
            <description>An entity responsible for making the resource available</description>
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              <elementText elementTextId="3179">
                <text>Public Library of Science (PLoS)</text>
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            <description>The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant</description>
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                <text>Science, Medicine</text>
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            <description>A language of the resource</description>
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                <text>EN</text>
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              <name>Title</name>
              <description>A name given to the resource</description>
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                  <text>Coronavirus</text>
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              <name>Description</name>
              <description>An account of the resource</description>
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                  <text>Dominio científico: Coronavirus</text>
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      <name>Text</name>
      <description>A resource consisting primarily of words for reading. Examples include books, letters, dissertations, poems, newspapers, articles, archives of mailing lists. Note that facsimiles or images of texts are still of the genre Text.</description>
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          <element elementId="50">
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            <description>A name given to the resource</description>
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              <elementText elementTextId="3182">
                <text>Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs.</text>
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            <name>Creator</name>
            <description>An entity primarily responsible for making the resource</description>
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              <elementText elementTextId="3183">
                <text>James A Gagnon, Eivind Valen, Summer B. Thyme, Peng Huang, Laila Akhmetova, Andrea Pauli, Tessa G Montague, Steven Zimmerman, Constance Richter, Alexander F. Schier</text>
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          <element elementId="41">
            <name>Description</name>
            <description>An account of the resource</description>
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              <elementText elementTextId="3184">
                <text>The CRISPR/Cas9 system has been implemented in a variety of model organisms to mediate site-directed mutagenesis. A wide range of mutation rates has been reported, but at a limited number of genomic target sites. To uncover the rules that govern effective Cas9-mediated mutagenesis in zebrafish, we targeted over a hundred genomic loci for mutagenesis using a streamlined and cloning-free method. We generated mutations in 85% of target genes with mutation rates varying across several orders of magnitude, and identified sequence composition rules that influence mutagenesis. We increased rates of mutagenesis by implementing several novel approaches. The activities of poor or unsuccessful single-guide RNAs (sgRNAs) initiating with a 5' adenine were improved by rescuing 5' end homogeneity of the sgRNA. In some cases, direct injection of Cas9 protein/sgRNA complex further increased mutagenic activity. We also observed that low diversity of mutant alleles led to repeated failure to obtain frame-shift mutations. This limitation was overcome by knock-in of a stop codon cassette that ensured coding frame truncation. Our improved methods and detailed protocols make Cas9-mediated mutagenesis an attractive approach for labs of all sizes.</text>
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            <name>Date</name>
            <description>A point or period of time associated with an event in the lifecycle of the resource</description>
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                <text>2014</text>
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            <name>Identifier</name>
            <description>An unambiguous reference to the resource within a given context</description>
            <elementTextContainer>
              <elementText elementTextId="3186">
                <text>DOI: 10.1371/journal.pone.0098186</text>
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            <name>Source</name>
            <description>A related resource from which the described resource is derived</description>
            <elementTextContainer>
              <elementText elementTextId="3187">
                <text>PLoS ONE</text>
              </elementText>
            </elementTextContainer>
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            <name>Publisher</name>
            <description>An entity responsible for making the resource available</description>
            <elementTextContainer>
              <elementText elementTextId="3188">
                <text>Public Library of Science (PLoS)</text>
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            <name>Coverage</name>
            <description>The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant</description>
            <elementTextContainer>
              <elementText elementTextId="3189">
                <text>Science, Medicine</text>
              </elementText>
            </elementTextContainer>
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            <name>Language</name>
            <description>A language of the resource</description>
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              <elementText elementTextId="3190">
                <text>EN</text>
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              <name>Title</name>
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                  <text>Coronavirus</text>
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              <name>Description</name>
              <description>An account of the resource</description>
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                <elementText elementTextId="2">
                  <text>Dominio científico: Coronavirus</text>
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      <name>Text</name>
      <description>A resource consisting primarily of words for reading. Examples include books, letters, dissertations, poems, newspapers, articles, archives of mailing lists. Note that facsimiles or images of texts are still of the genre Text.</description>
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      <elementSet elementSetId="1">
        <name>Dublin Core</name>
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                <text>The More the Better? A Comparison of the Information Sources Used by the Public during Two Infectious Disease Outbreaks.</text>
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            <description>An entity primarily responsible for making the resource</description>
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              <elementText elementTextId="3192">
                <text>Cynthia G. Jardine, Franziska U Boerner, Amanda D Boyd, S Michelle Driedger</text>
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            <description>An account of the resource</description>
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                <text>Recent infectious disease outbreaks have resulted in renewed recognition of the importance of risk communication planning and execution to public health control strategies. Key to these efforts is public access to information that is understandable, reliable and meets their needs for informed decision-making on protective health behaviours. Learning from the trends in sources used in previous outbreaks will enable improvements in information access in future outbreaks. Two separate random-digit dialled telephone surveys were conducted in Alberta, Canada, to explore information sources used by the public, together with their perceived usefulness and credibility, during the 2003 Severe Acute Respiratory Syndrome (SARS) epidemic (n = 1209) and 2009-2010 H1N1 pandemic (n = 1206). Traditional mass media were the most used information sources in both surveys. Although use of the Internet increased from 25% during SARS to 56% during H1N1, overall use of social media was not as high as anticipated. Friends and relatives were commonly used as an information source, but were not deemed very useful or credible. Conversely, doctors and health professionals were considered credible, but not consulted as frequently. The use of five or more information sources increased by almost 60% between the SARS and H1N1 surveys. There was a shift to older, more educated and more affluent respondents between the surveys, most likely caused by a decrease in the use of landlines amongst younger Canadians. It was concluded that people are increasingly using multiple sources of health risk information, presumably in a complementary manner. Subsequently, although using online media is important, this should be used to augment rather than replace more traditional information channels. Efforts should be made to improve knowledge transfer to health care professionals and doctors and provide them with opportunities to be more accessible as information sources. Finally, the future use of telephone surveys needs to account for the changing demographics of the respondents accessed through such surveys.</text>
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                <text>2015</text>
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              <elementText elementTextId="3195">
                <text>DOI: 10.1371/journal.pone.0140028</text>
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              <elementText elementTextId="3196">
                <text>PLoS ONE</text>
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            <name>Publisher</name>
            <description>An entity responsible for making the resource available</description>
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              <elementText elementTextId="3197">
                <text>Public Library of Science (PLoS)</text>
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            <name>Coverage</name>
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                <text>Science, Medicine</text>
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              <name>Title</name>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Middle East Respiratory Syndrome Coronavirus Intra-Host Populations Are Characterized by Numerous High Frequency Variants.</text>
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                <text>Monica K. Borucki, Victoria Lao, Mona Hwang, Shea Gardner, Danielle Adney, Vincent Munster, Richard Bowen, Jonathan E Allen</text>
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                <text>Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging human pathogen related to SARS virus. In vitro studies indicate this virus may have a broad host range suggesting an increased pandemic potential. Genetic and epidemiological evidence indicate camels serve as a reservoir for MERS virus but the mechanism of cross species transmission is unclear and many questions remain regarding the susceptibility of humans to infection. Deep sequencing data was obtained from the nasal samples of three camels that had been experimentally infected with a human MERS-CoV isolate. A majority of the genome was covered and average coverage was greater than 12,000x depth. Although only 5 mutations were detected in the consensus sequences, 473 intrahost single nucleotide variants were identified. Many of these variants were present at high frequencies and could potentially influence viral phenotype and the sensitivity of detection assays that target these regions for primer or probe binding.</text>
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                <text>DOI: 10.1371/journal.pone.0146251</text>
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                <text>PLoS ONE</text>
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            <name>Coverage</name>
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                <text>Science, Medicine</text>
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        <src>https://www.socictopen.socict.org/files/original/fc477d096bd7c834c202e938133f1bf9.pdf</src>
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              <name>Title</name>
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                  <text>Coronavirus</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Critically ill healthcare workers with the middle east respiratory syndrome (MERS): A multicenter study.</text>
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                <text>Sarah Shalhoub, Fahad Al Hameed, Yasser Mandourah, Hanan H Balkhy, Awad Al-Omari, Ghaleb A. Almekhlafi, Ayman Kharaba, Basem Alraddadi, Abdullah Almotairi, Kasim Al Khatib, Ahmed Abdulmomen, Ismael Qushmaq, Ahmed Mady, Othman Solaiman, Abdulsalam M. Al-Aithan, Rajaa Al-Raddadi, Ahmed Ragab, Abdulrahman AL-Harthy, Eman Al Qasim, Jesna Jose, Ghassan Al-Ghamdi, Laura Merson, Robert Fowler, Frederick G. Hayden, Yaseen M. Arabi</text>
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                <text>BACKGROUND:Middle East Respiratory Syndrome Coronavirus (MERS-CoV) leads to healthcare-associated transmission to patients and healthcare workers with potentially fatal outcomes. AIM:We aimed to describe the clinical course and functional outcomes of critically ill healthcare workers (HCWs) with MERS. METHODS:Data on HCWs was extracted from a multi-center retrospective cohort study on 330 critically ill patients with MERS admitted between (9/2012-9/2015). Baseline demographics, interventions and outcomes were recorded and compared between survivors and non-survivors. Survivors were approached with questionnaires to elucidate their functional outcomes using Karnofsky Performance Status Scale. FINDINGS:Thirty-Two HCWs met the inclusion criteria. Comorbidities were recorded in 34% (11/32) HCW. Death resulted in 8/32 (25%) HCWs including all 5 HCWs with chronic renal impairment at baseline. Non-surviving HCW had lower PaO2/FiO2 ratios 63.5 (57, 116.2) vs 148 (84, 194.3), p = 0.043, and received more ECMO therapy compared to survivors, 9/32 (28%) vs 4/24 (16.7%) respectively (p = 0.02).Thirteen of the surviving (13/24) HCWs responded to the questionnaire. Two HCWs confirmed functional limitations. Median number of days from hospital discharge until the questionnaires were filled was 580 (95% CI 568, 723.5) days. CONCLUSION:Approximately 10% of critically ill patients with MERS were HCWs. Hospital mortality rate was substantial (25%). Patients with chronic renal impairment represented a particularly high-risk group that should receive extra caution during suspected or confirmed MERS cases clinical care assignment and during outbreaks. Long-term repercussions of critical illness due to MERS on HCWs in particular, and patients in general, remain unknown and should be investigated in larger studies.</text>
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                <text>2018</text>
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                <text>DOI: 10.1371/journal.pone.0206831</text>
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                <text>PLoS ONE</text>
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            <name>Publisher</name>
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                <text>Public Library of Science (PLoS)</text>
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            <name>Coverage</name>
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                <text>Science, Medicine</text>
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            <name>Language</name>
            <description>A language of the resource</description>
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                <text>EN</text>
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