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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Complete Genome Sequence of Middle East Respiratory Syndrome Coronavirus Isolated from a Dromedary Camel in Egypt</title>
<author><name sortKey="Kandeil, Ahmed" sort="Kandeil, Ahmed" uniqKey="Kandeil A" first="Ahmed" last="Kandeil">Ahmed Kandeil</name>
<affiliation><nlm:aff id="aff1"><addr-line>Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Shehata, Mahmoud M" sort="Shehata, Mahmoud M" uniqKey="Shehata M" first="Mahmoud M." last="Shehata">Mahmoud M. Shehata</name>
<affiliation><nlm:aff id="aff1"><addr-line>Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="El Shesheny, Rabeh" sort="El Shesheny, Rabeh" uniqKey="El Shesheny R" first="Rabeh" last="El Shesheny">Rabeh El Shesheny</name>
<affiliation><nlm:aff id="aff1"><addr-line>Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Gomaa, Mokhtar R" sort="Gomaa, Mokhtar R" uniqKey="Gomaa M" first="Mokhtar R." last="Gomaa">Mokhtar R. Gomaa</name>
<affiliation><nlm:aff id="aff1"><addr-line>Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Ali, Mohamed A" sort="Ali, Mohamed A" uniqKey="Ali M" first="Mohamed A." last="Ali">Mohamed A. Ali</name>
<affiliation><nlm:aff id="aff1"><addr-line>Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Kayali, Ghazi" sort="Kayali, Ghazi" uniqKey="Kayali G" first="Ghazi" last="Kayali">Ghazi Kayali</name>
<affiliation><nlm:aff id="aff2"><addr-line>Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA</addr-line>
</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff3"><addr-line>Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas Health Sciences Center, Houston, Texas, USA</addr-line>
</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff4"><addr-line>Human Link, Hazmieh, Lebanon</addr-line>
</nlm:aff>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">27125484</idno>
<idno type="pmc">4850855</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4850855</idno>
<idno type="RBID">PMC:4850855</idno>
<idno type="doi">10.1128/genomeA.00309-16</idno>
<date when="2016">2016</date>
<idno type="wicri:Area/Pmc/Corpus">000065</idno>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Complete Genome Sequence of Middle East Respiratory Syndrome Coronavirus Isolated from a Dromedary Camel in Egypt</title>
<author><name sortKey="Kandeil, Ahmed" sort="Kandeil, Ahmed" uniqKey="Kandeil A" first="Ahmed" last="Kandeil">Ahmed Kandeil</name>
<affiliation><nlm:aff id="aff1"><addr-line>Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Shehata, Mahmoud M" sort="Shehata, Mahmoud M" uniqKey="Shehata M" first="Mahmoud M." last="Shehata">Mahmoud M. Shehata</name>
<affiliation><nlm:aff id="aff1"><addr-line>Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="El Shesheny, Rabeh" sort="El Shesheny, Rabeh" uniqKey="El Shesheny R" first="Rabeh" last="El Shesheny">Rabeh El Shesheny</name>
<affiliation><nlm:aff id="aff1"><addr-line>Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Gomaa, Mokhtar R" sort="Gomaa, Mokhtar R" uniqKey="Gomaa M" first="Mokhtar R." last="Gomaa">Mokhtar R. Gomaa</name>
<affiliation><nlm:aff id="aff1"><addr-line>Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Ali, Mohamed A" sort="Ali, Mohamed A" uniqKey="Ali M" first="Mohamed A." last="Ali">Mohamed A. Ali</name>
<affiliation><nlm:aff id="aff1"><addr-line>Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Kayali, Ghazi" sort="Kayali, Ghazi" uniqKey="Kayali G" first="Ghazi" last="Kayali">Ghazi Kayali</name>
<affiliation><nlm:aff id="aff2"><addr-line>Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA</addr-line>
</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff3"><addr-line>Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas Health Sciences Center, Houston, Texas, USA</addr-line>
</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff4"><addr-line>Human Link, Hazmieh, Lebanon</addr-line>
</nlm:aff>
</affiliation>
</author>
</analytic>
<series><title level="j">Genome Announcements</title>
<idno type="eISSN">2169-8287</idno>
<imprint><date when="2016">2016</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
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<front><div type="abstract" xml:lang="en"><p>We generated the near-full genome sequence of Middle East respiratory syndrome coronavirus (MERS-CoV) from a collected nasal sample of dromedary camel in Egypt. The newly characterized Egyptian strain has high similarity to the previously characterized Egyptian virus and both of viruses fell into a cluster distinct from other MERS-CoVs.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Zaki, Am" uniqKey="Zaki A">AM Zaki</name>
</author>
<author><name sortKey="Van Boheemen, S" uniqKey="Van Boheemen S">S van Boheemen</name>
</author>
<author><name sortKey="Bestebroer, Tm" uniqKey="Bestebroer T">TM Bestebroer</name>
</author>
<author><name sortKey="Osterhaus, Ad" uniqKey="Osterhaus A">AD Osterhaus</name>
</author>
<author><name sortKey="Fouchier, Ra" uniqKey="Fouchier R">RA Fouchier</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Shehata, Mm" uniqKey="Shehata M">MM Shehata</name>
</author>
<author><name sortKey="Gomaa, Mr" uniqKey="Gomaa M">MR Gomaa</name>
</author>
<author><name sortKey="Ali, Ma" uniqKey="Ali M">MA Ali</name>
</author>
<author><name sortKey="Kayali, G" uniqKey="Kayali G">G Kayali</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chu, Dk" uniqKey="Chu D">DK Chu</name>
</author>
<author><name sortKey="Poon, Ll" uniqKey="Poon L">LL Poon</name>
</author>
<author><name sortKey="Gomaa, Mm" uniqKey="Gomaa M">MM Gomaa</name>
</author>
<author><name sortKey="Shehata, Mm" uniqKey="Shehata M">MM Shehata</name>
</author>
<author><name sortKey="Perera, Ra" uniqKey="Perera R">RA Perera</name>
</author>
<author><name sortKey="Abu Zeid, D" uniqKey="Abu Zeid D">D Abu Zeid</name>
</author>
<author><name sortKey="El Rifay, As" uniqKey="El Rifay A">AS El Rifay</name>
</author>
<author><name sortKey="Siu, Ly" uniqKey="Siu L">LY Siu</name>
</author>
<author><name sortKey="Guan, Y" uniqKey="Guan Y">Y Guan</name>
</author>
<author><name sortKey="Webby, Rj" uniqKey="Webby R">RJ Webby</name>
</author>
<author><name sortKey="Ali, Ma" uniqKey="Ali M">MA Ali</name>
</author>
<author><name sortKey="Peiris, M" uniqKey="Peiris M">M Peiris</name>
</author>
<author><name sortKey="Kayali, G" uniqKey="Kayali G">G Kayali</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Graham, R" uniqKey="Graham R">R Graham</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Tamura, K" uniqKey="Tamura K">K Tamura</name>
</author>
<author><name sortKey="Peterson, D" uniqKey="Peterson D">D Peterson</name>
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<biblStruct><analytic><author><name sortKey="Hall, Ta" uniqKey="Hall T">TA Hall</name>
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</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<pmc article-type="brief-report"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Announc</journal-id>
<journal-id journal-id-type="iso-abbrev">Genome Announc</journal-id>
<journal-id journal-id-type="hwp">ga</journal-id>
<journal-id journal-id-type="pmc">ga</journal-id>
<journal-id journal-id-type="publisher-id">GA</journal-id>
<journal-title-group><journal-title>Genome Announcements</journal-title>
</journal-title-group>
<issn pub-type="epub">2169-8287</issn>
<publisher><publisher-name>American Society for Microbiology</publisher-name>
<publisher-loc>1752 N St., N.W., Washington, DC</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">27125484</article-id>
<article-id pub-id-type="pmc">4850855</article-id>
<article-id pub-id-type="publisher-id">genomeA00309-16</article-id>
<article-id pub-id-type="doi">10.1128/genomeA.00309-16</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Viruses</subject>
</subj-group>
</article-categories>
<title-group><article-title>Complete Genome Sequence of Middle East Respiratory Syndrome Coronavirus Isolated from a Dromedary Camel in Egypt</article-title>
<alt-title alt-title-type="running-head">Genome Announcement</alt-title>
<alt-title alt-title-type="short-authors">Kandeil et al.</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author" corresp="yes"><name><surname>Kandeil</surname>
<given-names>Ahmed</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Shehata</surname>
<given-names>Mahmoud M.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>El Shesheny</surname>
<given-names>Rabeh</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Gomaa</surname>
<given-names>Mokhtar R.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ali</surname>
<given-names>Mohamed A.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kayali</surname>
<given-names>Ghazi</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>b</sup>
</xref>
<xref ref-type="aff" rid="aff3"><sup>c</sup>
</xref>
<xref ref-type="aff" rid="aff4"><sup>d</sup>
</xref>
</contrib>
<aff id="aff1"><label>a</label>
<addr-line>Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt</addr-line>
</aff>
<aff id="aff2"><label>b</label>
<addr-line>Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA</addr-line>
</aff>
<aff id="aff3"><label>c</label>
<addr-line>Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas Health Sciences Center, Houston, Texas, USA</addr-line>
</aff>
<aff id="aff4"><label>d</label>
<addr-line>Human Link, Hazmieh, Lebanon</addr-line>
</aff>
</contrib-group>
<author-notes><corresp id="cor1">Address correspondence to Ahmed Kandeil, <email>kandeil_a@hotmail.com</email>
.</corresp>
<fn fn-type="equal"><p>A.K. and M.M.S. contributed equally to this work.</p>
</fn>
</author-notes>
<pub-date pub-type="epub"><day>28</day>
<month>4</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="collection"><season>Mar-Apr</season>
<year>2016</year>
</pub-date>
<volume>4</volume>
<issue>2</issue>
<elocation-id>e00309-16</elocation-id>
<history><date date-type="received"><day>3</day>
<month>3</month>
<year>2016</year>
</date>
<date date-type="accepted"><day>8</day>
<month>3</month>
<year>2016</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2016 Kandeil et al.</copyright-statement>
<copyright-year>2016</copyright-year>
<copyright-holder>Kandeil et al.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International license</ext-link>
.</license-p>
</license>
</permissions>
<self-uri content-type="pdf" xlink:href="jga002163812001.pdf"></self-uri>
<abstract><p>We generated the near-full genome sequence of Middle East respiratory syndrome coronavirus (MERS-CoV) from a collected nasal sample of dromedary camel in Egypt. The newly characterized Egyptian strain has high similarity to the previously characterized Egyptian virus and both of viruses fell into a cluster distinct from other MERS-CoVs.</p>
</abstract>
<funding-group><award-group id="award1"><funding-source id="gs1">the Egyptian Science and Technology Development Fund (contract no. 5175)
<named-content content-type="funder-id">http://dx.doi.org/10.13039/100007787</named-content>
</funding-source>
<principal-award-recipient>Mohamed Ahmed Ali</principal-award-recipient>
</award-group>
<award-group id="award2"><funding-source id="gs2">the National Institute of Allergy and Infectious Diseases (contract no. HHSN272201400006C)
</funding-source>
<principal-award-recipient>Ghazi Kayali</principal-award-recipient>
</award-group>
</funding-group>
<counts><fig-count count="0"></fig-count>
<table-count count="0"></table-count>
<equation-count count="0"></equation-count>
<ref-count count="6"></ref-count>
<page-count count="2"></page-count>
<word-count count="1013"></word-count>
</counts>
<custom-meta-group><custom-meta><meta-name>cover-date</meta-name>
<meta-value>March/April 2016</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
<body><sec id="h0.0"><title>GENOME ANNOUNCEMENT</title>
<p>The Middle East respiratory syndrome coronavirus (MERS-CoV) is a new member of the <italic>Betacoronavirus</italic>
genus. It was first detected in 2012 in samples of an infected human and was later found to be related to camels (<xref rid="B1" ref-type="bibr">1</xref>
, <xref rid="B2" ref-type="bibr">2</xref>
). MERS-CoV is a positive-sense, single-stranded RNA virus, encoding 11 proteins: two replicase polyproteins (open reading frames [ORFs] 1ab and 1a), four structural proteins (surface spike glycoprotein [S], envelope [E], nucleoprotein [N], and membrane protein [M]), and five nonstructural proteins (ORFs 3, 4a, 4b, 5, and 8b) (<xref rid="B2" ref-type="bibr">2</xref>
).</p>
<p>The first complete genome of MERS-CoV from an infected dromedary camel (<italic>Camelus dromedarius</italic>
) in Egypt was named NRCE-HKU205 and deposited in GenBank under accession number KJ477102 (<xref rid="B3" ref-type="bibr">3</xref>
). Here, we report the near full genome sequence of another MERS-CoV detected through systematic surveillance in Egypt. It was detected in the nasal swab from a healthy adult dromedary camel collected on 17 December 2014 from an abattoir in Cairo, Egypt.</p>
<p>Viral RNA was extracted using a QIAmp viral RNA minikit (Qiagen, Germany). Reverse transcription was performed using the Superscript III system (Invitrogen, Carlsbad, CA) with random hexamers. The cDNA was subjected to 11 PCRs to generate overlapping amplicons covering the full-length MERS-CoV genome as previously described (<xref rid="B4" ref-type="bibr">4</xref>
). The PCR products were purified from agarose gels using a QIAquick gel extraction kit (Qiagen). Purified amplicons were Sanger sequenced according to the primer/amplicon combinations (123 sequencing reactions) as shown previously (<xref rid="B4" ref-type="bibr">4</xref>
) at the Macrogen sequencing facility (Macrogen, South Korea). Finally, 29,949 nucleotides (nt) were assembled using SeqMan (DNASTAR, Madison, WI) with a G+C content of 41.2%.</p>
<p>The NRC163 strain shows the typical MERS-CoV genome order with 5′ untranslated region (UTR) (nt 1 to 199), ORF1ab and ORF1a (nt 200 to 21,508), S (nt 21,377 to 25,438), ORF3 (nt 25,453 to 25,764), ORF4a (nt 25,773 to 26,102), ORF4b (nt 26,014 to 26,754), ORF5 (nt 26,761 to 27,435), E (nt 27,511 to 27,759), M (nt 27,774 to 28,433), N (nt 28,487 to 29,728), ORF8b (nt 28,683 to 29,021), and 3′ UTR (nt 29,729 to 29,949). The closest strains to the NRC163 were NRCE-HKU205 and human betacoronavirus 2c Jordan-N3/2012 (accession no. KC776174.1) with 99.5% similarity.</p>
<p>To further investigate the genetic relationship between Egyptian MERS-CoVs and other strains whose genomes are available in GenBank, we performed whole-genome phylogenetic analysis using MEGA 5 (<xref rid="B5" ref-type="bibr">5</xref>
). Egyptian strains fell into a cluster distinct from other MERS-CoVs detected elsewhere.</p>
<p>Sequence analysis was performed using BioEdit (<xref rid="B6" ref-type="bibr">6</xref>
). Egyptian MERS-CoVs had 14 characteristic amino acids (aa) in the ORF1ab protein (Y581, F664, F1024, F1583, T1911, L1970, I2000, V2333, C2481, L2639, T2676, S3361, I3721, M5537). No specific aa variations were identified in the S, ORF3, ORF4a, ORF4b, E, M, and N proteins. An aa deletion that was previously identified at site 1,293 of the S protein of NRCE-HKU205 (<xref rid="B3" ref-type="bibr">3</xref>
) was not identified in NRC163. The biological impact of such differences among MERS-CoV strains needs to be fully examined.</p>
<sec id="s1"><title>Nucleotide sequence accession number.</title>
<p>The complete genome sequence of the MERS-CoV/Egypt/NRC163/2014 was deposited in GenBank under the accession number <ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/nuccore/KU740200">KU740200</ext-link>
.</p>
</sec>
</sec>
</body>
<back><fn-group><fn fn-type="other"><p><bold>Citation</bold>
Kandeil A, Shehata MM, El Shesheny R, Gomaa MR, Ali MA, Kayali G. 2016. Complete genome sequence of Middle East respiratory syndrome coronavirus isolated from a dromedary camel in Egypt. Genome Announc 4(2):e00309-16. doi:10.1128/genomeA.00309-16.</p>
</fn>
</fn-group>
<ack><title>ACKNOWLEDGMENTS</title>
<p>We express gratitude to the field personnel who conduct the MERS CoV surveillance in Egypt and the laboratory personnel who conduct the laboratory screening at the National Research Centre in Egypt.</p>
</ack>
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