Molecular Evolution of MERS Coronavirus: Dromedaries as a Recent Intermediate Host or Long-Time Animal Reservoir?
Identifieur interne : 000D68 ( Pmc/Curation ); précédent : 000D67; suivant : 000D69Molecular Evolution of MERS Coronavirus: Dromedaries as a Recent Intermediate Host or Long-Time Animal Reservoir?
Auteurs : Susanna K. P. Lau [Hong Kong] ; Antonio C. P. Wong ; Terrence C. K. Lau ; Patrick C. Y. Woo [Hong Kong]Source :
- International Journal of Molecular Sciences [ 1422-0067 ] ; 2017.
Abstract
While dromedary camels are the immediate animal source of MERS coronavirus (MERS-CoV) infection, the evolutionary origin of MERS-CoV remains obscure. We analyzed 219 camel and human MERS-CoV genome sequences available in GenBank. Phylogenetic analysis showed that 5 and 214 strains belong to clade A and B, respectively, with clade A further divided into lineage A1 (3 human strains) and lineage A2 (2 camel strains), and clade B divided into B1 to B6 (each containing both human and camel strains). Recombination analysis showed potential recombination events in five strains from dromedaries in Saudi Arabia, with recombination between lineage B5 and B3 in four strains, and between lineage B3 and B4 in one strain. The spike protein showed the highest number of amino acid substitutions, especially between A2 and other lineages, and contained positively selected codons. Notably, codon 1020 was positively selected among B and B5 strains, and can distinguish between clade A (Q1020) and B (R1020/H1020) strains, suggesting that this residue may play a role in the evolution of S protein during divergence of different lineages. The time of the most recent common ancestor of all MERS-CoV was dated to approximately 2010. The implications on the role of camels in the evolution of MERS-CoV are discussed.
Url:
DOI: 10.3390/ijms18102138
PubMed: 29035289
PubMed Central: 5666820
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Lau</name><affiliation wicri:level="1"><nlm:aff id="af1-ijms-18-02138">State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam</wicri:regionArea></affiliation><affiliation><nlm:aff id="af2-ijms-18-02138">Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong;<email>antonwcp@hku.hk</email></nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af3-ijms-18-02138">Research Centre of Infection and Immunology, the University of Hong Kong, Pokfulam, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Research Centre of Infection and Immunology, the University of Hong Kong, Pokfulam</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af4-ijms-18-02138">Carol Yu Centre for Infection, the University of Hong Kong, Pokfulam, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Carol Yu Centre for Infection, the University of Hong Kong, Pokfulam</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af5-ijms-18-02138">Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, the University of Hong Kong, Pokfulam</wicri:regionArea></affiliation></author><author><name sortKey="Wong, Antonio C P" sort="Wong, Antonio C P" uniqKey="Wong A" first="Antonio C. 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P." last="Lau">Susanna K. P. Lau</name><affiliation wicri:level="1"><nlm:aff id="af1-ijms-18-02138">State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam</wicri:regionArea></affiliation><affiliation><nlm:aff id="af2-ijms-18-02138">Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong;<email>antonwcp@hku.hk</email></nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af3-ijms-18-02138">Research Centre of Infection and Immunology, the University of Hong Kong, Pokfulam, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Research Centre of Infection and Immunology, the University of Hong Kong, Pokfulam</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af4-ijms-18-02138">Carol Yu Centre for Infection, the University of Hong Kong, Pokfulam, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Carol Yu Centre for Infection, the University of Hong Kong, Pokfulam</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af5-ijms-18-02138">Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, the University of Hong Kong, Pokfulam</wicri:regionArea></affiliation></author><author><name sortKey="Wong, Antonio C P" sort="Wong, Antonio C P" uniqKey="Wong A" first="Antonio C. P." last="Wong">Antonio C. P. Wong</name><affiliation><nlm:aff id="af2-ijms-18-02138">Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong;<email>antonwcp@hku.hk</email></nlm:aff></affiliation></author><author><name sortKey="Lau, Terrence C K" sort="Lau, Terrence C K" uniqKey="Lau T" first="Terrence C. K." last="Lau">Terrence C. K. Lau</name><affiliation><nlm:aff id="af6-ijms-18-02138">Department of Biomedical Sciences, College of Science and Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong;<email>chiklau@cityu.edu.hk</email></nlm:aff></affiliation></author><author><name sortKey="Woo, Patrick C Y" sort="Woo, Patrick C Y" uniqKey="Woo P" first="Patrick C. Y." last="Woo">Patrick C. Y. Woo</name><affiliation wicri:level="1"><nlm:aff id="af1-ijms-18-02138">State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam</wicri:regionArea></affiliation><affiliation><nlm:aff id="af2-ijms-18-02138">Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong;<email>antonwcp@hku.hk</email></nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af3-ijms-18-02138">Research Centre of Infection and Immunology, the University of Hong Kong, Pokfulam, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Research Centre of Infection and Immunology, the University of Hong Kong, Pokfulam</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af4-ijms-18-02138">Carol Yu Centre for Infection, the University of Hong Kong, Pokfulam, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Carol Yu Centre for Infection, the University of Hong Kong, Pokfulam</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af5-ijms-18-02138">Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, the University of Hong Kong, Pokfulam</wicri:regionArea></affiliation></author></analytic><series><title level="j">International Journal of Molecular Sciences</title><idno type="eISSN">1422-0067</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>While dromedary camels are the immediate animal source of MERS coronavirus (MERS-CoV) infection, the evolutionary origin of MERS-CoV remains obscure. We analyzed 219 camel and human MERS-CoV genome sequences available in GenBank. Phylogenetic analysis showed that 5 and 214 strains belong to clade A and B, respectively, with clade A further divided into lineage A1 (3 human strains) and lineage A2 (2 camel strains), and clade B divided into B1 to B6 (each containing both human and camel strains). Recombination analysis showed potential recombination events in five strains from dromedaries in Saudi Arabia, with recombination between lineage B5 and B3 in four strains, and between lineage B3 and B4 in one strain. The spike protein showed the highest number of amino acid substitutions, especially between A2 and other lineages, and contained positively selected codons. Notably, codon 1020 was positively selected among B and B5 strains, and can distinguish between clade A (Q1020) and B (R1020/H1020) strains, suggesting that this residue may play a role in the evolution of S protein during divergence of different lineages. The time of the most recent common ancestor of all MERS-CoV was dated to approximately 2010. The implications on the role of camels in the evolution of MERS-CoV are discussed.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Chan, J F" uniqKey="Chan J">J.F. Chan</name></author><author><name sortKey="Lau, S K" uniqKey="Lau S">S.K. Lau</name></author><author><name sortKey="To, K K" uniqKey="To K">K.K. To</name></author><author><name sortKey="Cheng, V C" uniqKey="Cheng V">V.C. Cheng</name></author><author><name sortKey="Woo, P C" uniqKey="Woo P">P.C. Woo</name></author><author><name sortKey="Yuen, K Y" uniqKey="Yuen K">K.Y. Yuen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zaki, A M" uniqKey="Zaki A">A.M. Zaki</name></author><author><name sortKey="Van Boheemen, S" uniqKey="Van Boheemen S">S. van Boheemen</name></author><author><name sortKey="Bestebroer, T M" uniqKey="Bestebroer T">T.M. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Int J Mol Sci</journal-id><journal-id journal-id-type="iso-abbrev">Int J Mol Sci</journal-id><journal-id journal-id-type="publisher-id">ijms</journal-id><journal-title-group><journal-title>International Journal of Molecular Sciences</journal-title></journal-title-group><issn pub-type="epub">1422-0067</issn><publisher><publisher-name>MDPI</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">29035289</article-id><article-id pub-id-type="pmc">5666820</article-id><article-id pub-id-type="doi">10.3390/ijms18102138</article-id><article-id pub-id-type="publisher-id">ijms-18-02138</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Molecular Evolution of MERS Coronavirus: Dromedaries as a Recent Intermediate Host or Long-Time Animal Reservoir?</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Lau</surname><given-names>Susanna K. P.</given-names></name><xref ref-type="aff" rid="af1-ijms-18-02138">1</xref><xref ref-type="aff" rid="af2-ijms-18-02138">2</xref><xref ref-type="aff" rid="af3-ijms-18-02138">3</xref><xref ref-type="aff" rid="af4-ijms-18-02138">4</xref><xref ref-type="aff" rid="af5-ijms-18-02138">5</xref><xref rid="c1-ijms-18-02138" ref-type="corresp">*</xref></contrib><contrib contrib-type="author"><name><surname>Wong</surname><given-names>Antonio C. P.</given-names></name><xref ref-type="aff" rid="af2-ijms-18-02138">2</xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="true">https://orcid.org/0000-0002-7505-7306</contrib-id><name><surname>Lau</surname><given-names>Terrence C. K.</given-names></name><xref ref-type="aff" rid="af6-ijms-18-02138">6</xref></contrib><contrib contrib-type="author"><name><surname>Woo</surname><given-names>Patrick C. Y.</given-names></name><xref ref-type="aff" rid="af1-ijms-18-02138">1</xref><xref ref-type="aff" rid="af2-ijms-18-02138">2</xref><xref ref-type="aff" rid="af3-ijms-18-02138">3</xref><xref ref-type="aff" rid="af4-ijms-18-02138">4</xref><xref ref-type="aff" rid="af5-ijms-18-02138">5</xref><xref rid="c1-ijms-18-02138" ref-type="corresp">*</xref></contrib></contrib-group><aff id="af1-ijms-18-02138"><label>1</label>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong</aff><aff id="af2-ijms-18-02138"><label>2</label>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong;<email>antonwcp@hku.hk</email></aff><aff id="af3-ijms-18-02138"><label>3</label>Research Centre of Infection and Immunology, the University of Hong Kong, Pokfulam, Hong Kong</aff><aff id="af4-ijms-18-02138"><label>4</label>Carol Yu Centre for Infection, the University of Hong Kong, Pokfulam, Hong Kong</aff><aff id="af5-ijms-18-02138"><label>5</label>Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong</aff><aff id="af6-ijms-18-02138"><label>6</label>Department of Biomedical Sciences, College of Science and Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong;<email>chiklau@cityu.edu.hk</email></aff><author-notes><corresp id="c1-ijms-18-02138"><label>*</label>Correspondence: <email>skplau@hku.hk</email> (S.K.P.L.); <email>pcywoo@hku.hk</email> (P.C.Y.W.); Tel.: +852-2255-4892 (S.K.P.L. & P.C.Y.W.); Fax: +852-2855-1241 (S.K.P.L. & P.C.Y.W.)</corresp></author-notes><pub-date pub-type="epub"><day>16</day><month>10</month><year>2017</year></pub-date><pub-date pub-type="collection"><month>10</month><year>2017</year></pub-date><volume>18</volume><issue>10</issue><elocation-id>2138</elocation-id><history><date date-type="received"><day>15</day><month>8</month><year>2017</year></date><date date-type="accepted"><day>11</day><month>10</month><year>2017</year></date></history><permissions><copyright-statement>© 2017 by the authors.</copyright-statement><copyright-year>2017</copyright-year><license license-type="open-access"><license-p>Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>).</license-p></license></permissions><abstract><p>While dromedary camels are the immediate animal source of MERS coronavirus (MERS-CoV) infection, the evolutionary origin of MERS-CoV remains obscure. We analyzed 219 camel and human MERS-CoV genome sequences available in GenBank. Phylogenetic analysis showed that 5 and 214 strains belong to clade A and B, respectively, with clade A further divided into lineage A1 (3 human strains) and lineage A2 (2 camel strains), and clade B divided into B1 to B6 (each containing both human and camel strains). Recombination analysis showed potential recombination events in five strains from dromedaries in Saudi Arabia, with recombination between lineage B5 and B3 in four strains, and between lineage B3 and B4 in one strain. The spike protein showed the highest number of amino acid substitutions, especially between A2 and other lineages, and contained positively selected codons. Notably, codon 1020 was positively selected among B and B5 strains, and can distinguish between clade A (Q1020) and B (R1020/H1020) strains, suggesting that this residue may play a role in the evolution of S protein during divergence of different lineages. The time of the most recent common ancestor of all MERS-CoV was dated to approximately 2010. The implications on the role of camels in the evolution of MERS-CoV are discussed.</p></abstract><kwd-group><kwd>MERS coronavirus</kwd><kwd>molecular</kwd><kwd>evolution</kwd><kwd>dromedaries</kwd><kwd>origin</kwd><kwd>recent</kwd><kwd>host</kwd><kwd>reservoir</kwd></kwd-group></article-meta></front><floats-group><fig id="ijms-18-02138-f001" orientation="portrait" position="float"><label>Figure 1</label><caption><p>Geographical distribution of human and dromedary MERS-CoV strains with complete genomes. The numbers represent the number of MERS-CoV strains with complete genomes reported from the corresponding countries.</p></caption><graphic xlink:href="ijms-18-02138-g001"></graphic></fig><fig id="ijms-18-02138-f002" orientation="portrait" position="float"><label>Figure 2</label><caption><p>Maximum-likelihood phylogeny based on the complete genome sequences of 219 MERS-CoV strains. A general time-reversible model of nucleotide substitution with estimated base frequencies, the proportion of invariant sites, and the γ distribution of rates across sites were used in the maximum-likelihood analysis. Bootstrap values in percentage are shown next to the branches. The scale bar indicates the number of nucleotide substitutions per site. Different colored letters and numbers represent different clades and lineages respectively: red letter, clade A; red number, lineages within clade A; blue letter, clade B; blue numbers, lineages within clade B. MERS-CoVs from dromedaries and humans are indicated in triangles and circles, respectively. Different colors represent MERS-CoV strains found in different countries: red, Saudi Arabia; blue, United Arab Emirates; green, Jordan; olive, Egypt; maroon, United Kingdom; purple, Qatar; teal, United States; lime, France; aqua, Oman; fuchisa, Thailand; grey, China; yellow, South Korea.</p></caption><graphic xlink:href="ijms-18-02138-g002"></graphic></fig><fig id="ijms-18-02138-f003" orientation="portrait" position="float"><label>Figure 3</label><caption><p>Maximum-likelihood phylogeny based on <italic>S</italic> gene sequences of 219 MERS-CoV strains. GTR + G + I substitution model was selected for the <italic>S</italic> gene tree. Bootstrap values in percentage are shown next to the branches. The scale bar indicates the number of nucleotide substitutions per site. Different colored letters and numbers represent different clades and lineages respectively: red letter, clade A; red number, lineages within clade A; blue letter, clade B; blue numbers, lineages within clade B. Selected MERS-CoV strains were annotated. MERS-CoVs from dromedaries are indicated in triangles. MERS-CoVs from homo sapiens are indicated in circles. The 15 MERS-CoV strains with potential recombination detected in the present study are colored: red, Saudi Arabia; green, Jordan.</p></caption><graphic xlink:href="ijms-18-02138-g003"></graphic></fig><fig id="ijms-18-02138-f004" orientation="portrait" position="float"><label>Figure 4</label><caption><p>Amino acid substitutions in S proteins from the different clades of MERS-CoV. The S1 and S2 subunits, and structural domains are highlighted. The amino acid substitutions are highlighted and the total number of mutations in each clade are shown in the last column.</p></caption><graphic xlink:href="ijms-18-02138-g004"></graphic></fig><fig id="ijms-18-02138-f005" orientation="portrait" position="float"><label>Figure 5</label><caption><p>Detection of potential recombination events by bootscan analysis. Bootscanning was conducted with Simplot version 3.5.1 (F84 model; window size, 1000 bp; step, 200 bp). (<bold>A</bold>) KT368830 was used as the query sequence and compared with the genome sequences of a lineage B5 MERS-CoV strain (red, KT368875), a lineage B3 MERS-CoV (blue, KT368860), and a lineage B1 MERS-CoV strain (purple, KJ650926); (<bold>B</bold>) KT368887 was used as the query sequence and compared with the genome sequences of a lineage B3 MERS-CoV strain (red, KT368878), a lineage B4 MERS-CoV strain (blue, KT368890), and a lineage B1 MERS-CoV strain (purple, KP209313); (<bold>C</bold>) KT368869 was used as the query sequence and compared with the genome sequences of a lineage B4 MERS-CoV strain (red, KJ156934), a lineage B3 MERS-CoV (blue, KT368829), and a lineage A1 MERS-CoV strain (purple, JX869059); (<bold>D</bold>) KJ156910 was used as the query sequence and compared with the genome sequences of a lineage B2 MERS-CoV strain (red, KM210277), a lineage B4 MERS-CoV (blue, KF961222), and a lineage B5 MERS-CoV strain (purple, KR011263).</p></caption><graphic xlink:href="ijms-18-02138-g005a"></graphic><graphic xlink:href="ijms-18-02138-g005b"></graphic><graphic xlink:href="ijms-18-02138-g005c"></graphic></fig><fig id="ijms-18-02138-f006" orientation="portrait" position="float"><label>Figure 6</label><caption><p>Structural view of amino acid substitutions in S protein of different clades of MERS-CoV. The mutated amino acids in clade A and B are highlighted in yellow and red colour, respectively. The figures were produced using Discovery Studio visualizer (Accelrys).</p></caption><graphic xlink:href="ijms-18-02138-g006"></graphic></fig><fig id="ijms-18-02138-f007" orientation="portrait" position="float"><label>Figure 7</label><caption><p>Estimation of time to the most recent common ancestor for MERS-CoV. The time-scaled phylogeny was summarized from all Markov chain Monte Carlo phylogenies of the concatenated coding region S of 138 phylogenetically distinct MERS-CoV genomes, which were analyzed under the relaxed-clock model with an uncorrelated exponential distribution in BEAST version 1.7.4. The clade B lineage 5 MERS-CoV is highlighted. Different colored letters and numbers represent different clades and lineages respectively: red letter, clade A; red number, lineages within clade A; blue letter, clade B; blue numbers, lineages within clade B.</p></caption><graphic xlink:href="ijms-18-02138-g007"></graphic></fig><table-wrap id="ijms-18-02138-t001" orientation="portrait" position="float"><object-id pub-id-type="pii">ijms-18-02138-t001_Table 1</object-id><label>Table 1</label><caption><p>MERS-CoV strains that showed differential clustering for ORF1ab and <italic>S</italic> gene.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">GenBank Accession No.</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Country of Isolation</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Human/Dromedary</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Lineage Whole Genome</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">ORF1ab</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1"><italic>S</italic></th></tr></thead><tbody><tr><td align="center" valign="middle" rowspan="1" colspan="1">JX869059</td><td align="center" valign="middle" rowspan="1" colspan="1">Saudi Arabia</td><td align="center" valign="middle" rowspan="1" colspan="1">Human</td><td align="center" valign="middle" rowspan="1" colspan="1">A1</td><td align="center" valign="middle" rowspan="1" colspan="1">A1</td><td align="center" valign="middle" rowspan="1" colspan="1">A2</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">KF600630</td><td align="center" valign="middle" rowspan="1" colspan="1">Saudi Arabia</td><td align="center" valign="middle" rowspan="1" colspan="1">Human</td><td align="center" valign="middle" rowspan="1" colspan="1">B1</td><td align="center" valign="middle" rowspan="1" colspan="1">B1</td><td align="center" valign="middle" rowspan="1" colspan="1">B2</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">KT368869</td><td align="center" valign="middle" rowspan="1" colspan="1">Saudi Arabia</td><td align="center" valign="middle" rowspan="1" colspan="1">Dromedary</td><td align="center" valign="middle" rowspan="1" colspan="1">B3</td><td align="center" valign="middle" rowspan="1" colspan="1">B4</td><td align="center" valign="middle" rowspan="1" colspan="1">B3</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">KT368879</td><td align="center" valign="middle" rowspan="1" colspan="1">Saudi Arabia</td><td align="center" valign="middle" rowspan="1" colspan="1">Dromedary</td><td align="center" valign="middle" rowspan="1" colspan="1">B3</td><td align="center" valign="middle" rowspan="1" colspan="1">B4</td><td align="center" valign="middle" rowspan="1" colspan="1">B3</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">KT368831</td><td align="center" valign="middle" rowspan="1" colspan="1">Saudi Arabia</td><td align="center" valign="middle" rowspan="1" colspan="1">Dromedary</td><td align="center" valign="middle" rowspan="1" colspan="1">B5</td><td align="center" valign="middle" rowspan="1" colspan="1">B5</td><td align="center" valign="middle" rowspan="1" colspan="1">B3</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">KT368830</td><td align="center" valign="middle" rowspan="1" colspan="1">Saudi Arabia</td><td align="center" valign="middle" rowspan="1" colspan="1">Dromedary</td><td align="center" valign="middle" rowspan="1" colspan="1">B5</td><td align="center" valign="middle" rowspan="1" colspan="1">B5</td><td align="center" valign="middle" rowspan="1" colspan="1">B3</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">KT368829</td><td align="center" valign="middle" rowspan="1" colspan="1">Saudi Arabia</td><td align="center" valign="middle" rowspan="1" colspan="1">Dromedary</td><td align="center" valign="middle" rowspan="1" colspan="1">B5</td><td align="center" valign="middle" rowspan="1" colspan="1">B5</td><td align="center" valign="middle" rowspan="1" colspan="1">B3</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">KT368832</td><td align="center" valign="middle" rowspan="1" colspan="1">Saudi Arabia</td><td align="center" valign="middle" rowspan="1" colspan="1">Dromedary</td><td align="center" valign="middle" rowspan="1" colspan="1">B5</td><td align="center" valign="middle" rowspan="1" colspan="1">B5</td><td align="center" valign="middle" rowspan="1" colspan="1">B3</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">KT861627</td><td align="center" valign="middle" rowspan="1" colspan="1">Jordan</td><td align="center" valign="middle" rowspan="1" colspan="1">Human</td><td align="center" valign="middle" rowspan="1" colspan="1">B4</td><td align="center" valign="middle" rowspan="1" colspan="1">B2</td><td align="center" valign="middle" rowspan="1" colspan="1">B4</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">KJ156910</td><td align="center" valign="middle" rowspan="1" colspan="1">Saudi Arabia</td><td align="center" valign="middle" rowspan="1" colspan="1">Human</td><td align="center" valign="middle" rowspan="1" colspan="1">B4</td><td align="center" valign="middle" rowspan="1" colspan="1">B2</td><td align="center" valign="middle" rowspan="1" colspan="1">B4</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">KJ156874</td><td align="center" valign="middle" rowspan="1" colspan="1">Saudi Arabia</td><td align="center" valign="middle" rowspan="1" colspan="1">Human</td><td align="center" valign="middle" rowspan="1" colspan="1">B4</td><td align="center" valign="middle" rowspan="1" colspan="1">B2</td><td align="center" valign="middle" rowspan="1" colspan="1">B4</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">KT368888</td><td align="center" valign="middle" rowspan="1" colspan="1">Saudi Arabia</td><td align="center" valign="middle" rowspan="1" colspan="1">Dromedary</td><td align="center" valign="middle" rowspan="1" colspan="1">B3</td><td align="center" valign="middle" rowspan="1" colspan="1">B3</td><td align="center" valign="middle" rowspan="1" colspan="1">B4</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">KT368887</td><td align="center" valign="middle" rowspan="1" colspan="1">Saudi Arabia</td><td align="center" valign="middle" rowspan="1" colspan="1">Dromedary</td><td align="center" valign="middle" rowspan="1" colspan="1">B3</td><td align="center" valign="middle" rowspan="1" colspan="1">B3</td><td align="center" valign="middle" rowspan="1" colspan="1">B4</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">KT368824</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Saudi Arabia</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Dromedary</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">B4</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">B5</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">B4</td></tr></tbody></table></table-wrap><table-wrap id="ijms-18-02138-t002" orientation="portrait" position="float"><object-id pub-id-type="pii">ijms-18-02138-t002_Table 2</object-id><label>Table 2</label><caption><p>Selective pressure analysis on the <italic>S</italic> genes of 219 MERS-CoV strains.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Clade/Lineage</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">dN/dS</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Positively Selected Sites by SLAC Method</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Positively Selected Sites by FEL Method</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Positively Selected Sites by MEME Method</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Best Fit Model</th></tr></thead><tbody><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">A and B</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">0.424737</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Codon 26 *, 312 *, 1224 *</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Codon 1224 *, 1250 *</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">010121</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">A</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">0.392404</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Codon 879 *</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">010121</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">B</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">0.439492</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Codon 312 *, 1224 *</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Codon 1020 *, 1224 *, 1250 *</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">010121</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">A1</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">0.234930</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">F81</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">A2</td><td colspan="5" align="center" valign="middle" style="border-bottom:solid thin" rowspan="1">Insufficient available strains for analysis</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">B1</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">0.382699</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">010011</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">B2</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">0.405071</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">010121</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">B3</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">0.400104</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Codon 1250 *</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">001020</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">B4</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">0.641872</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">000010</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">B5</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">0.343586</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nil</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Codon 1020 *</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">010121</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">B6</td><td colspan="5" align="center" valign="middle" style="border-bottom:solid thin" rowspan="1">Insufficient available strains for analysis</td></tr></tbody></table><table-wrap-foot><fn><p>SLAC: single-likelihood ancestor counting; FEL: fixed effects likelihood; MEME: mixed-effects model of evolution; * <italic>p</italic> < 0.1.</p></fn></table-wrap-foot></table-wrap></floats-group></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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