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                  <text>Coronavirus</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>SARS-CoV-2 Codon Usage Bias Downregulates Host Expressed Genes With Similar Codon Usage</text>
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                <text>Andres Mariano Alonso, Andres Mariano Alonso, Luis Diambra, Luis Diambra</text>
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                <text>Severe acute respiratory syndrome has spread quickly throughout the world and was declared a pandemic by the World Health Organization (WHO). The pathogenic agent is a new coronavirus (SARS-CoV-2) that infects pulmonary cells with great effectiveness. In this study we focus on the codon composition for the viral protein synthesis and its relationship with the protein synthesis of the host. Our analysis reveals that SARS-CoV-2 preferred codons have poor representation of G or C nucleotides in the third position, a characteristic which could result in an unbalance in the tRNAs pools of the infected cells with serious implications in host protein synthesis. By integrating this observation with proteomic data from infected cells, we observe a reduced translation rate of host proteins associated with highly expressed genes and that they share the codon usage bias of the virus. The functional analysis of these genes suggests that this mechanism of epistasis can contribute to understanding how this virus evades the immune response and the etiology of some deleterious collateral effect as a result of the viral replication. In this manner, our finding contributes to the understanding of the SARS-CoV-2 pathogeny and could be useful for the design of a vaccine based on the live attenuated strategy.</text>
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                <text>2020</text>
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                <text>translational control, SARS-CoV-2, codon usage bias, vaccine design, pathogeny, codon optimality</text>
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                <text>10.3389/fcell.2020.00831</text>
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                <text>Epidemiology and Health</text>
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                <text>Korean Society of Epidemiology</text>
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                <text>Biology (General)</text>
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                  <text>Coronavirus</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>SARS-CoV-2 colonization of maternal and fetal cells of the human placenta promotes alteration of local renin-angiotensin system.</text>
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                <text>Sonam Verma, Chetanchandra S Joshi, Rachel B Silverstein, Mai He, Ebony B Carter, Indira U Mysorekar</text>
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                <text>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection appears to increase the risk of adverse pregnancy outcomes, such as pre-eclampsia in pregnant women. The mechanism(s) by which this occurs remains unclear. We investigated the pathophysiology of SARS-CoV-2 at maternal-fetal interface in pregnant women who tested positive for the virus using RNA in situ hybridization (viral RNA), immunohistochemistry, and hematoxylin and eosin staining. To investigate whether viral infection alters the renin angiotensin system (RAS) in placenta, which controls blood pressure, we treated human trophoblasts with recombinant spike protein or a live modified virus with a vesicular stomatitis viral backbone expressing spike protein (VSV-S). Viral colonization was highest in maternal decidua, fetal trophoblasts, Hofbauer cells, and in placentas delivered prematurely. We localized SARS-CoV-2 to cells expressing angiotensin-converting enzyme 2 (ACE2) and demonstrate that infected placentas had significantly reduced ACE2. In response to both spike protein and VSV-S, cellular ACE2 decreased although angiotensin II receptor type 1 (AT1R) increased with concomitant increase in soluble fms-like tyrosine kinase-1 (sFlt1). Viral infection decreased pro-angiogenic factors, AT2R, and placental growth factor, which competitively binds to sFlt1. Sera from infected pregnant women had elevated levels of sFlt1 and angiotensin II type 1-receptor autoantibodies prior to delivery, both signatory markers of pre-eclampsia. SARS-CoV-2 colonizes ACE2-expressing maternal and fetal cells in the placenta. Infection in pregnant women correlates with alteration of placental RAS. As RAS regulates blood pressure, SARS-CoV-2 infection may thus increase adverse hemodynamic outcomes, such as pre-eclampsia in pregnant women. NIH/NICHD grants R01 HD091218 and 3R01HD091218-04S1 (RADx-UP Supplement).</text>
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                <text>2021</text>
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                <text>Pregnancy, ACE2, AT1R, placenta, Preeclampsia, decidua, PlGF, AT1-AA, extravillous trophoblasts, sFlt1</text>
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                <text>10.1016/j.medj.2021.04.009</text>
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                <text>Med (New York, N.Y.)</text>
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                  <text>Dominio científico: Coronavirus</text>
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        <description>The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/.</description>
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            <name>Title</name>
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                <text>SARS-CoV-2 detection goes mobile.</text>
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            <name>Creator</name>
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              <elementText elementTextId="71966">
                <text>Dorothy Clyde</text>
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            <name>Date</name>
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                <text>2021</text>
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              <elementText elementTextId="71968">
                <text>10.1038/s41576-020-00321-9</text>
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              <elementText elementTextId="71969">
                <text>Nature reviews. Genetics</text>
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        <src>https://socictopen.socict.org/files/original/f33b10273212b4b15d01f723e6423db2.pdf</src>
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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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        <name>Dublin Core</name>
        <description>The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/.</description>
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          <element elementId="50">
            <name>Title</name>
            <description>A name given to the resource</description>
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                <text>SARS-CoV-2 detection in setting of viral swabs scarcity: Are MRSA swabs and viral swabs equivalent?</text>
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            <name>Creator</name>
            <description>An entity primarily responsible for making the resource</description>
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              <elementText elementTextId="60984">
                <text>Daniel G Federman, Shaili Gupta, Gary Stack, Sheldon M Campbell, David R Peaper, Louise M Dembry, Ann Fisher, Asim F Tarabar, Michael Kozal, Christopher B Ruser</text>
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            <name>Description</name>
            <description>An account of the resource</description>
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                <text>BackgroundThe global pandemic of Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV2) has resulted in unprecedented challenges for healthcare systems. One barrier to widespread testing has been a paucity of traditional respiratory viral swab collection kits relative to the demand. Whether other sample collection kits, such as widely available MRSA nasal swabs can be used to detect SARS-CoV-2 is unknown.MethodsWe compared simultaneous nasal MRSA swabs (COPAN ESwabs ® 480C flocked nasal swab in 1mL of liquid Amies medium) and virals wabs (BD H192(07) flexible mini-tip flocked nasopharyngeal swabs in 3mL Universal Transport Medium) for SARS-CoV-2 PCR testing using Simplexa COVID-19 Direct assay on patients over a 4-day period. When the results were discordant, the viral swab sample was run again on the Cepheid Xpert Xpress ® SARS-CoV-2 assay.ResultsOf the 81 included samples, there were 19 positives and 62 negatives in viral media and 18 positives and 63 negative in the MRSA swabs. Amongst all included samples, there was concordance between the COPAN ESwabs ® 480C and the viral swabs in 78 (96.3%).ConclusionWe found a high rate of concordance in test results between COPAN ESwabs ® 480C in Amies solution and BD H192(07) nasopharyngeal swabs in in 3 mL of Universal Viral Transport medium viral media. Clinicians and laboratories should feel better informed and assured using COPAN ESwabs ® 480C to help in the diagnosis of COVID-19.</text>
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                <text>2020</text>
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                <text>10.1371/journal.pone.0237127</text>
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                <text>Epidemiology and Health</text>
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                <text>Korean Society of Epidemiology</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>
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                <text>Science, Medicine</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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                <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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                <text>SARS-CoV-2 detection on self-collected saliva or anterior nasal specimens compared with healthcare personnel-collected nasopharyngeal specimens.</text>
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                <text>Grace E Marx, Brad J Biggerstaff, Courtney C Nawrocki, Sarah E Totten, Emily A Travanty, Alexis W Burakoff, Tracy Scott, Jesse Chavez-Van De Hey, Jesse J Carlson, Karen A Wendel, Jennifer L Harcourt, Azaibi Tamin, Jennifer D Thomas, Sarah E Rowan</text>
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                <text>Nasopharyngeal specimens (NPS) are commonly used for SARS-CoV-2 testing but can be uncomfortable for patients. Self-collected saliva or anterior nasal specimens (ANS) for SARS-CoV-2 detection are less invasive but the sensitivity of these specimen types has not been thoroughly evaluated. During September-November 2020, 730 adults undergoing SARS-CoV-2 testing at community testing events and homeless shelters in Denver provided self-collected saliva and ANS specimens before NPS collection and answered a short survey about symptoms and specimen preference. Specimens were tested for SARS-CoV-2 by rRT-PCR; viral culture was performed on a subset of specimens positive by rRT-PCR. Sensitivity of saliva and ANS for SARS-CoV-2 detection by rRT-PCR was measured against NPS. Subgroup analyses included test outcomes by symptom status and culture results. Sensitivity for SARS-CoV-2 detection by rRT-PCR appeared higher for saliva than for ANS (85% vs. 80%) and among symptomatic participants than among those without symptoms (94% vs. 29% for saliva; 87% vs. 50% for ANS). Among participants with culture-positive SARS-CoV-2 by any specimen type, sensitivity of saliva and ANS by rRT-PCR was 94% and 100%, respectively. Saliva and ANS were equally preferred by participants; most would undergo NPS again despite being least preferred. Saliva was slightly more sensitive than ANS for SARS-CoV-2 detection by rRT-PCR. Both saliva and ANS reliably detected SARS-CoV-2 among participants with symptoms. Self-collected saliva and ANS offer practical advantages, are preferred by patients, and might be most useful for testing people with COVID-19 symptoms.</text>
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                <text>saliva, covid-19, SARS-CoV-2, nasopharyngeal, anterior nasal</text>
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                <text>10.1093/cid/ciab330</text>
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                <text>Clinical infectious diseases : an official publication of the Infectious Diseases Society of America</text>
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                <text>Nathalie De Vos, Nicolas Yin, Magali Wautier, Marius Gilbert, Cyril Debuysschere, Marc Decroly, Fatima-Zohra Bouazza, Vincent Collot, Charlotte Martin, Fanny Ponthieux, Hafid Dahma, Cecile Duterme, Marie-Luce Delforge, Stefano Malinverni, Frédéric Cotton, Magali Bartiaux, Marie Hallin, Marie Hallin</text>
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                <text>Introduction: Since the first wave of COVID-19 in Europe, new diagnostic tools using antigen detection and rapid molecular techniques have been developed. Our objective was to elaborate a diagnostic algorithm combining antigen rapid diagnostic tests, automated antigen dosing and rapid molecular tests and to assess its performance under routine conditions.Methods: An analytical performance evaluation of four antigen rapid tests, one automated antigen dosing and one molecular point-of-care test was performed on samples sent to our laboratory for a SARS-CoV-2 reverse transcription PCR. We then established a diagnostic algorithm by approaching median viral loads in target populations and evaluated the limit of detection of each test using the PCR cycle threshold values. A field performance evaluation including a clinical validation and a user-friendliness assessment was then conducted on the antigen rapid tests in point-of-care settings (general practitioners and emergency rooms) for outpatients who were symptomatic for &amp;lt;7 days. Automated antigen dosing was trialed for the screening of asymptomatic inpatients.Results: Our diagnostic algorithm proposed to test recently symptomatic patients using rapid antigen tests, asymptomatic patients using automated tests, and patients requiring immediate admission using molecular point-of-care tests. Accordingly, the conventional reverse transcription PCR was kept as a second line tool. In this setting, antigen rapid tests yielded an overall sensitivity of 83.3% (not significantly different between the four assays) while the use of automated antigen dosing would have spared 93.5% of asymptomatic inpatient screening PCRs.Conclusion: Using tests not considered the “gold standard” for COVID-19 diagnosis on well-defined target populations allowed for the optimization of their intrinsic performances, widening the scale of our testing arsenal while sparing molecular resources for more seriously ill patients.</text>
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                <text>10.3389/fmed.2021.650581</text>
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                <text>Epidemiology and Health</text>
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                <text>Korean Society of Epidemiology</text>
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                <text>Ioana  Roxana Bordea, Francesco Inchingolo, Maria Contaldo, Alessio Danilo Inchingolo, Angelo Michele Inchingolo, Giuseppina Malcangi, Antonio Scarano, Felice Lorusso, Ciro Gargiulo Isacco, Grazia Marinelli, Maria Teresa D’Oria, Denisa Hazballa, Luigi Santacroce, Gianna Dipalma, Andrea Ballini, Edit Xhajanka, Marco Farronato, Gianluca  Martino Tartaglia</text>
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                <text>The SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), which is believed to have originated in China towards the end of November 2019, has now spread across the globe, causing a pandemic in 192 countries. The World Health Organization has called it the SARS-CoV-2 pandemic. Rapid dissemination of the virus occurs mainly through the saliva (Flügge’s droplets) and aerosol, together with nasal and lachrymal passages. The literature associated with the recent advancement in terms of rapid diagnostics and SARS-CoV-2 vaccines has thoroughly studied the role of ACE2 receptors and Furin, as well as viral agent access into the host cell and its significant persistence at the level of the oral mucosa, which represents the main access to the virus. The purpose of this review was to underline the processes of SARS-CoV-2 infection mechanisms and novel breakthroughs in diagnostics and vaccines. Different technologies, such as the RT-PCR molecular test and the antigenic test, have been developed to identify subjects affected by the SARS-CoV-2 in order to improve the tracking of infection geographical diffusion. Novel rapid and highly sensitive diagnostic tests has been proposed for the detection of SARS-CoV-2 to improve the screening capability of suspected contagions. The strengthening of the vaccination campaign represents the most effective means to combat the SARS-CoV-2 infection and prevent severe manifestations of the virus—different classes of vaccines have been developed for this purpose. Further attention on the novel SARS-CoV-2 variant is necessary in order to verify the protection efficacy and virulence reduction of the infective agent in the recent vaccine campaign.</text>
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                <text>TMPRSS2, ACE2, furin, SARS-CoV-2 (COVID-19 pandemic), oral mucosa (salivary glands), Cytokine Storm Syndrome (CSS)</text>
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                <text>10.3390/microorganisms9040793</text>
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                <text>Epidemiology and Health</text>
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                <text>Korean Society of Epidemiology</text>
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                <text>SARS-CoV-2 endgame: attitudes and predictions of Australian and New Zealand infectious diseases and microbiology specialists.</text>
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                <text>Ravindra Dotel, Matthew V N O'Sullivan, Nicky Gilroy, Shobini Sivagnanam, Joshua S Davis</text>
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                <text>10.1111/imj.14985</text>
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                <text>Internal medicine journal</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Sars-CoV-2 Envelope and Membrane Proteins: Structural Differences Linked to Virus Characteristics?</text>
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                <text>Massimo Ciccozzi, Silvia Angeletti, Martina Bianchi, Stefano Pascarella, Marta Giovanetti, Domenico Benvenuto</text>
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                <text>The Coronavirus Disease 2019 (COVID-19) is a new viral infection caused by the severe acute respiratory coronavirus 2 (SARS-CoV-2). Genomic analyses have revealed that SARS-CoV-2 is related to Pangolin and Bat coronaviruses. In this report, a structural comparison between the Sars-CoV-2 Envelope and Membrane proteins from different human isolates with homologous proteins from closely related viruses is described. The analyses here reported show the high structural similarity of Envelope and Membrane proteins to the counterparts from Pangolin and Bat coronavirus isolates. However, the comparisons have also highlighted structural differences specific of Sars-CoV-2 proteins which may be correlated to the cross-species transmission and/or to the properties of the virus. Structural modelling has been applied to map the variant sites onto the predicted three-dimensional structure of the Envelope and Membrane proteins.</text>
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                <text>DOI: 10.1155/2020/4389089</text>
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                <text>BioMed Research International</text>
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                <text>Hindawi Limited</text>
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                <text>SARS-CoV-2 epidemic in India: epidemiological features and in silico analysis of the effect of interventions [version 1; peer review: 2 approved]</text>
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                <text>Archisman Mazumder, Mehak Arora, Vishwesh Bharadiya, Parul Berry, Mudit Agarwal, Priyamadhaba Behera, Hemant Deepak Shewade, Ayush Lohiya, Mohak Gupta, Aditi Rao, Giridara Gopal Parameswaran</text>
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                <text>Background: After SARS-CoV-2 set foot in India, the Government took a number of steps to limit the spread of the virus in the country. This included restricted testing, isolation, contact tracing and quarantine, and enforcement of a nation-wide lockdown starting 25 March 2020. The objectives of this study were to i) describe the age,gender distribution and mortality among COVID-19 patients identified till 14 April 2020 and predict the range of contact rate; and ii) predict the number of active COVID-19 patients after 40 days of lockdown. Methods: We used a cross-sectional descriptive design for first objective and a susceptible-infected-removed model for in silico predictions. We collected data from government-controlled and crowdsourced websites. Results: Studying age and gender parameters of 1161 Indian COVID-19 patients, the median age was 38 years (IQR, 27-52) with 20-39 year-old males being the most affected group. The number of affected patients were 854 (73.6%) men and 307 (26.4%) women. If the current contact rate continues (0.25-27), India may have 110460 to 220575 infected persons at the end of 40 days lockdown. Conclusion: The disease is majorly affecting a younger age group in India. Interventions have been helpful in preventing the worst-case scenario in India, but will be unable to prevent the spike in number of cases.</text>
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          <element elementId="40">
            <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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              <elementText elementTextId="48402">
                <text>2020</text>
              </elementText>
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          <element elementId="43">
            <name>Identifier</name>
            <description>An unambiguous reference to the resource within a given context</description>
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              <elementText elementTextId="48403">
                <text>10.12688/f1000research.23496.1</text>
              </elementText>
            </elementTextContainer>
          </element>
          <element elementId="48">
            <name>Source</name>
            <description>A related resource from which the described resource is derived</description>
            <elementTextContainer>
              <elementText elementTextId="48404">
                <text>Biotemas</text>
              </elementText>
            </elementTextContainer>
          </element>
          <element elementId="45">
            <name>Publisher</name>
            <description>An entity responsible for making the resource available</description>
            <elementTextContainer>
              <elementText elementTextId="48405">
                <text>Universidade Federal de Santa Catarina</text>
              </elementText>
            </elementTextContainer>
          </element>
          <element elementId="38">
            <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>
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              <elementText elementTextId="48406">
                <text>Science, Medicine</text>
              </elementText>
            </elementTextContainer>
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