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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Detection of multiple viral sequences in the respiratory tract samples of suspected Middle East respiratory syndrome coronavirus patients in Jakarta, Indonesia 2015–2016</title><author><name sortKey="Setianingsih, Tri Yuli" sort="Setianingsih, Tri Yuli" uniqKey="Setianingsih T" first="Tri Yuli" last="Setianingsih">Tri Yuli Setianingsih</name><affiliation><nlm:aff id="aff0005">Prof. Dr. Sulianti Saroso Infectious Disease Hospital, Jakarta, Indonesia</nlm:aff></affiliation></author><author><name sortKey="Wiyatno, Ageng" sort="Wiyatno, Ageng" uniqKey="Wiyatno A" first="Ageng" last="Wiyatno">Ageng Wiyatno</name><affiliation><nlm:aff id="aff0010">Eijkman Institute of Molecular Biology, Jakarta, Indonesia</nlm:aff></affiliation></author><author><name sortKey="Hartono, Teguh Sarry" sort="Hartono, Teguh Sarry" uniqKey="Hartono T" first="Teguh Sarry" last="Hartono">Teguh Sarry Hartono</name><affiliation><nlm:aff id="aff0005">Prof. Dr. Sulianti Saroso Infectious Disease Hospital, Jakarta, Indonesia</nlm:aff></affiliation></author><author><name sortKey="Hindawati, Evi" sort="Hindawati, Evi" uniqKey="Hindawati E" first="Evi" last="Hindawati">Evi Hindawati</name><affiliation><nlm:aff id="aff0005">Prof. Dr. Sulianti Saroso Infectious Disease Hospital, Jakarta, Indonesia</nlm:aff></affiliation></author><author><name sortKey="Dewantari, Aghnianditya Kresno" sort="Dewantari, Aghnianditya Kresno" uniqKey="Dewantari A" first="Aghnianditya Kresno" last="Dewantari">Aghnianditya Kresno Dewantari</name><affiliation><nlm:aff id="aff0010">Eijkman Institute of Molecular Biology, Jakarta, Indonesia</nlm:aff></affiliation></author><author><name sortKey="Myint, Khin Saw" sort="Myint, Khin Saw" uniqKey="Myint K" first="Khin Saw" last="Myint">Khin Saw Myint</name><affiliation><nlm:aff id="aff0010">Eijkman Institute of Molecular Biology, Jakarta, Indonesia</nlm:aff></affiliation></author><author><name sortKey="Lisdawati, Vivi" sort="Lisdawati, Vivi" uniqKey="Lisdawati V" first="Vivi" last="Lisdawati">Vivi Lisdawati</name><affiliation><nlm:aff id="aff0005">Prof. Dr. Sulianti Saroso Infectious Disease Hospital, Jakarta, Indonesia</nlm:aff></affiliation></author><author><name sortKey="Safari, Dodi" sort="Safari, Dodi" uniqKey="Safari D" first="Dodi" last="Safari">Dodi Safari</name><affiliation><nlm:aff id="aff0010">Eijkman Institute of Molecular Biology, Jakarta, Indonesia</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">31238156</idno><idno type="pmc">7110706</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7110706</idno><idno type="RBID">PMC:7110706</idno><idno type="doi">10.1016/j.ijid.2019.06.022</idno><date when="2019">2019</date><idno type="wicri:Area/Pmc/Corpus">000D56</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000D56</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Detection of multiple viral sequences in the respiratory tract samples of suspected Middle East respiratory syndrome coronavirus patients in Jakarta, Indonesia 2015–2016</title><author><name sortKey="Setianingsih, Tri Yuli" sort="Setianingsih, Tri Yuli" uniqKey="Setianingsih T" first="Tri Yuli" last="Setianingsih">Tri Yuli Setianingsih</name><affiliation><nlm:aff id="aff0005">Prof. Dr. Sulianti Saroso Infectious Disease Hospital, Jakarta, Indonesia</nlm:aff></affiliation></author><author><name sortKey="Wiyatno, Ageng" sort="Wiyatno, Ageng" uniqKey="Wiyatno A" first="Ageng" last="Wiyatno">Ageng Wiyatno</name><affiliation><nlm:aff id="aff0010">Eijkman Institute of Molecular Biology, Jakarta, Indonesia</nlm:aff></affiliation></author><author><name sortKey="Hartono, Teguh Sarry" sort="Hartono, Teguh Sarry" uniqKey="Hartono T" first="Teguh Sarry" last="Hartono">Teguh Sarry Hartono</name><affiliation><nlm:aff id="aff0005">Prof. Dr. Sulianti Saroso Infectious Disease Hospital, Jakarta, Indonesia</nlm:aff></affiliation></author><author><name sortKey="Hindawati, Evi" sort="Hindawati, Evi" uniqKey="Hindawati E" first="Evi" last="Hindawati">Evi Hindawati</name><affiliation><nlm:aff id="aff0005">Prof. Dr. Sulianti Saroso Infectious Disease Hospital, Jakarta, Indonesia</nlm:aff></affiliation></author><author><name sortKey="Dewantari, Aghnianditya Kresno" sort="Dewantari, Aghnianditya Kresno" uniqKey="Dewantari A" first="Aghnianditya Kresno" last="Dewantari">Aghnianditya Kresno Dewantari</name><affiliation><nlm:aff id="aff0010">Eijkman Institute of Molecular Biology, Jakarta, Indonesia</nlm:aff></affiliation></author><author><name sortKey="Myint, Khin Saw" sort="Myint, Khin Saw" uniqKey="Myint K" first="Khin Saw" last="Myint">Khin Saw Myint</name><affiliation><nlm:aff id="aff0010">Eijkman Institute of Molecular Biology, Jakarta, Indonesia</nlm:aff></affiliation></author><author><name sortKey="Lisdawati, Vivi" sort="Lisdawati, Vivi" uniqKey="Lisdawati V" first="Vivi" last="Lisdawati">Vivi Lisdawati</name><affiliation><nlm:aff id="aff0005">Prof. Dr. Sulianti Saroso Infectious Disease Hospital, Jakarta, Indonesia</nlm:aff></affiliation></author><author><name sortKey="Safari, Dodi" sort="Safari, Dodi" uniqKey="Safari D" first="Dodi" last="Safari">Dodi Safari</name><affiliation><nlm:aff id="aff0010">Eijkman Institute of Molecular Biology, Jakarta, Indonesia</nlm:aff></affiliation></author></analytic><series><title level="j">International Journal of Infectious Diseases</title><idno type="ISSN">1201-9712</idno><idno type="eISSN">1878-3511</idno><imprint><date when="2019">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Highlights</title><p><list list-type="simple" id="lis0005"><list-item id="lsti0005"><label>•</label><p id="par0005">Nine viral etiological agents were identified from 13 MERS-CoV patients with pneumonia in Indonesia from 2015- to 2016.</p></list-item><list-item id="lsti0010"><label>•</label><p id="par0010">Patients with lower respiratory infections and travel history to Middle East should be screened for other respiratory viruses in addition to MERS-CoV.</p></list-item><list-item id="lsti0015"><label>•</label><p id="par0015">This study confirmed that there was no MERS-CoV in the 13 suspected MERS-CoV patients with pneumonia.</p></list-item></list></p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Ahmed, A E" uniqKey="Ahmed A">A.E. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Int J Infect Dis</journal-id><journal-id journal-id-type="iso-abbrev">Int. J. Infect. Dis</journal-id><journal-title-group><journal-title>International Journal of Infectious Diseases</journal-title></journal-title-group><issn pub-type="ppub">1201-9712</issn><issn pub-type="epub">1878-3511</issn><publisher><publisher-name>The Author(s). Published by Elsevier Ltd on behalf of International Society for Infectious Diseases.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">31238156</article-id><article-id pub-id-type="pmc">7110706</article-id><article-id pub-id-type="publisher-id">S1201-9712(19)30267-X</article-id><article-id pub-id-type="doi">10.1016/j.ijid.2019.06.022</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Detection of multiple viral sequences in the respiratory tract samples of suspected Middle East respiratory syndrome coronavirus patients in Jakarta, Indonesia 2015–2016</article-title></title-group><contrib-group><contrib contrib-type="author" id="aut0005"><name><surname>Setianingsih</surname><given-names>Tri Yuli</given-names></name><xref rid="aff0005" ref-type="aff">a</xref></contrib><contrib contrib-type="author" id="aut0010"><name><surname>Wiyatno</surname><given-names>Ageng</given-names></name><xref rid="aff0010" ref-type="aff">b</xref></contrib><contrib contrib-type="author" id="aut0015"><name><surname>Hartono</surname><given-names>Teguh Sarry</given-names></name><xref rid="aff0005" ref-type="aff">a</xref></contrib><contrib contrib-type="author" id="aut0020"><name><surname>Hindawati</surname><given-names>Evi</given-names></name><xref rid="aff0005" ref-type="aff">a</xref></contrib><contrib contrib-type="author" id="aut0025"><name><surname>Rosamarlina</surname></name><xref rid="aff0005" ref-type="aff">a</xref></contrib><contrib contrib-type="author" id="aut0030"><name><surname>Dewantari</surname><given-names>Aghnianditya Kresno</given-names></name><xref rid="aff0010" ref-type="aff">b</xref></contrib><contrib contrib-type="author" id="aut0035"><name><surname>Myint</surname><given-names>Khin Saw</given-names></name><xref rid="aff0010" ref-type="aff">b</xref></contrib><contrib contrib-type="author" id="aut0040"><name><surname>Lisdawati</surname><given-names>Vivi</given-names></name><xref rid="aff0005" ref-type="aff">a</xref></contrib><contrib contrib-type="author" id="aut0045"><name><surname>Safari</surname><given-names>Dodi</given-names></name><email>safari@eijkman.go.id</email><xref rid="aff0010" ref-type="aff">b</xref><xref rid="cor0005" ref-type="corresp">⁎</xref></contrib></contrib-group><aff id="aff0005"><label>a</label>Prof. Dr. Sulianti Saroso Infectious Disease Hospital, Jakarta, Indonesia</aff><aff id="aff0010"><label>b</label>Eijkman Institute of Molecular Biology, Jakarta, Indonesia</aff><author-notes><corresp id="cor0005"><label>⁎</label>Corresponding author. <email>safari@eijkman.go.id</email></corresp></author-notes><pub-date pub-type="pmc-release"><day>22</day><month>6</month><year>2019</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub"><month>9</month><year>2019</year></pub-date><pub-date pub-type="epub"><day>22</day><month>6</month><year>2019</year></pub-date><volume>86</volume><fpage>102</fpage><lpage>107</lpage><history><date date-type="received"><day>17</day><month>4</month><year>2019</year></date><date date-type="rev-recd"><day>17</day><month>6</month><year>2019</year></date><date date-type="accepted"><day>18</day><month>6</month><year>2019</year></date></history><permissions><copyright-statement>© 2019 The Author(s)</copyright-statement><copyright-year>2019</copyright-year><license><license-p>Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.</license-p></license></permissions><abstract abstract-type="author-highlights" id="abs0005"><title>Highlights</title><p><list list-type="simple" id="lis0005"><list-item id="lsti0005"><label>•</label><p id="par0005">Nine viral etiological agents were identified from 13 MERS-CoV patients with pneumonia in Indonesia from 2015- to 2016.</p></list-item><list-item id="lsti0010"><label>•</label><p id="par0010">Patients with lower respiratory infections and travel history to Middle East should be screened for other respiratory viruses in addition to MERS-CoV.</p></list-item><list-item id="lsti0015"><label>•</label><p id="par0015">This study confirmed that there was no MERS-CoV in the 13 suspected MERS-CoV patients with pneumonia.</p></list-item></list></p></abstract><abstract id="abs0010"><sec><title>Objectives</title><p>The identification and analysis of viral etiological agents from suspected Middle East respiratory syndrome coronavirus (MERS-CoV) cases admitted to Prof. Dr. Sulianti Saroso Infectious Disease Hospital (IDH) using molecular assays.</p></sec><sec><title>Methods</title><p>Biological samples were collected from 13 hospitalized patients suspected of MERS-CoV infection in Prof. Dr. Sulianti Saroso IDH from July 2015 to December 2016. The majority of patients presented with pneumonia, with symptoms including fever (≥37.5 °C), labored breathing, and cough, and with a history of travel to the Middle East. Viral RNA was isolated and converted to cDNA, which was used as a template for the detection of 12 viral panels using conventional PCR and sequencing.</p></sec><sec><title>Results</title><p>Viral etiological agents detected in the patients were enterovirus D68, dengue virus type 3, rhinovirus C, human coronavirus 229E, herpes simplex virus type 1, influenza virus H1N1, influenza virus H3N2, human metapneumovirus, and rhinovirus A60.</p></sec><sec><title>Conclusions</title><p>The sequences of nine viral agents under different taxa were detected in suspected MERS-CoV patients, including influenza virus, paramyxovirus, coronavirus, enterovirus, human metapneumovirus, and herpesvirus.</p></sec></abstract><kwd-group id="kwd0005"><title>Keywords</title><kwd>Viral</kwd><kwd>Pneumonia</kwd><kwd>PCR</kwd><kwd>MERS-CoV</kwd><kwd>Indonesia</kwd></kwd-group></article-meta><notes><p id="misc0005"><bold>Corresponding Editor:</bold> Eskild Petersen, Aarhus, Denmark</p></notes></front><body><sec id="sec0005"><title>Introduction</title><p id="par0020">Since 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) has been reported worldwide, with a total of 2206 confirmed cases and 787 deaths in 27 countries (<xref rid="bib0185" ref-type="bibr">WHO, 2019</xref>). The spectrum of MERS-CoV infection ranges from a mild viral respiratory illness to a rapidly fatal pneumonia complicated by acute respiratory distress syndrome and acute renal failure (<xref rid="bib0055" ref-type="bibr">Chong et al., 2015</xref>), with a mortality rate of around 35–50% (<xref rid="bib0140" ref-type="bibr">Noorwali et al., 2015</xref>, <xref rid="bib0195" ref-type="bibr">Yang et al., 2017</xref>, <xref rid="bib0080" ref-type="bibr">Hui et al., 2018</xref>). No specific licensed antiviral treatment is currently available for MERS-CoV infection (<xref rid="bib0170" ref-type="bibr">Rabaan et al., 2017</xref>).</p><p id="par0025">The most common clinical symptoms of MERS-CoV are fever, cough, and dyspnea. The positive detection rate is significantly higher in hospitalized patients with pneumonia compared to those with upper respiratory tract infections. These symptoms usually occur with a mean incubation period of 2–13 days. Comorbidities such as diabetes mellitus, cirrhosis, and others affecting the respiratory, renal, and cardiac systems have been shown to increase the severity of the illness (<xref rid="bib0195" ref-type="bibr">Yang et al., 2017</xref>). However, there is lack of specific clinical symptoms to distinguish MERS-CoV from other respiratory pathogens (<xref rid="bib0045" ref-type="bibr">Butler, 2015</xref>), making it imperative that early detection and laboratory identification of coronavirus infection is performed in suspected patients.</p><p id="par0030">Three neighboring countries in Southeast Asia have reported MERS-CoV infections associated with a history of travel to the Middle East. In April 2014, a man in his mid-50s presented to the emergency ward of a public hospital in Malaysia. He had returned from a pilgrimage to Saudi Arabia 13 days earlier and was confirmed as the first MERS-CoV-infected case in the country (<xref rid="bib0165" ref-type="bibr">Premila Devi et al., 2014</xref>). One year later, in February 2015, a 31-year-old woman in the Philippines was also diagnosed with MERS-CoV; she had a history of being resident in Saudi Arabia as a health worker (<xref rid="bib0175" ref-type="bibr">Racelis et al., 2015</xref>). Four months later, MERS-CoV infection was also detected in an Omani citizen who had visited Thailand (<xref rid="bib0155" ref-type="bibr">Plipat et al., 2017</xref>). MERS-CoV has never been reported in Indonesia, although thousands of pilgrims have visited the Middle East every year. Despite extensive efforts to screen for MERS-CoV in 28 197 returning pilgrims in Indonesia in 2015, the study did not identify any positive cases (<xref rid="bib0015" ref-type="bibr">Amin et al., 2018</xref>).</p><p id="par0035">Prof. Dr. Sulianti Saroso Infectious Disease Hospital (IDH) in Indonesia is one of the referral hospitals for the evaluation of MERS-CoV in suspected patients. Up until 2018, none of the suspected patients returning from the Middle East were positive for MERS-CoV, although they were screened with relevant assays. In addition, none of the specimens were further evaluated to determine other etiologies that could tailor and improve patient management and reduce the inappropriate use of antibiotics.</p><p id="par0040">The aim of this study was to identify emerging viral etiologies in suspected MERS-CoV patients admitted to IDH by screening bio-archived respiratory samples accumulated in 2015–2016.</p></sec><sec id="sec0010"><title>Methods</title><sec id="sec0015"><title>Ethical approval</title><p id="par0045">The testing of archived specimens was approved by Prof. Dr. Sulianti Saroso IDH (ethical clearance number 54/VII.10/IX/2017) and the Eijkman Institute Research Ethics Commission (number 66, January 2017).</p></sec><sec id="sec0020"><title>Patients, clinical data, and specimens</title><p id="par0050">Clinical specimens were collected from a total of 13 hospitalized patients with suspected MERS-CoV infection in Prof. Dr. Sulianti Saroso IDH from July 2015 to December 2016. The majority of patients presented with pneumonia and symptoms including fever (≥37.5 °C), dyspnea, and cough. All patients had a history of travel to the Middle East <14 days prior to biological sampling. All biological specimens collected were sent to the bio-repository of Prof. Dr. Sulianti Saroso IDH for future research. The specimens (when available) including sputum, oropharyngeal swab, nasal swab, nasopharyngeal swab, and serum had tested negative for MERS-CoV by viral-specific PCR performed by the Indonesian Ministry of Health. The primers used in the PCR were designed to amplify the protein E, ORF1b, and ORF1a genes of MERS-CoV, as mentioned in the guidelines for MERS-CoV specimen sampling and laboratory examination of the Indonesian Ministry of Health. The specimens that had tested negative for MERS-CoV were further tested for additional respiratory viruses at the Eijkman Institute for Molecular Biology, Jakarta. Demographic data, risk factors, and clinical data were also analyzed.</p></sec><sec id="sec0025"><title>Nucleic acid extraction and reverse transcription</title><p id="par0055">Total viral RNA was isolated from 140 μl of specimen (serum/respiratory swab) using the QIAamp Viral RNA Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol. Of a total of 60 μl of viral RNA, 4 μl was added to 1 μl random primer for complementary DNA (cDNA) synthesis using the GoScript Reverse Transcription System (Promega, Madison, WI, USA) to develop 20 μl of cDNA. The cDNA was then used as template for the detection of 12 viral families based on conventional PCR.</p></sec><sec id="sec0030"><title>PCR assays for emerging viruses</title><p id="par0060">Panels of a singleplex PCR assay were used for the detection of 12 taxa of viruses in respiratory specimens, including coronavirus, paramyxovirus, influenza virus, enterovirus, arenavirus, astrovirus, bocavirus, Nipah virus, adenovirus, hantavirus, herpesvirus, and respiratory syncytial virus. In addition, testing of serum for two families of arbovirus – flavivirus and alphavirus – was performed because of their endemicity in Indonesia.</p><p id="par0065">All of the primers and positive controls used in the amplification reaction are based on the protocols from PREDICT USAID (<xref rid="bib0025" ref-type="bibr">Anthony et al., 2013</xref>). The singleplex PCR reaction was performed in a thermal cycler ProFlex PCR system. A recombinant plasmid containing all sequences of PCR target or viral genetic materials from vaccines and isolates was used as a positive control in each PCR.</p></sec><sec id="sec0035"><title>Gel visualization</title><p id="par0070">Electrophoresis was done with 1% agarose gel in an electrophoresis chamber at 100 V for 30 min. Five microliters of PCR products were added to each agarose well, and a 100-bp DNA ladder (Invitrogen, Carlsbad, CA, USA) was used as a DNA size marker. Visualization of positive bands was performed using the Gel Imaging BioRad Gel Doc XR System and Quantity One 1-D Analysis Software.</p></sec><sec id="sec0040"><title>Sequencing</title><p id="par0075">Samples with positive viral amplicons were characterized by Sanger sequencing method after purification. Purification of PCR products was performed using the QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol, followed by PCR sequencing and precipitation reaction before loading into an ABI 3130 sequencer. Sequencing results were analyzed using Geneious Software R8 version 8.1 and were compared with sequences in the GenBank database.</p></sec></sec><sec id="sec0045"><title>Results</title><p id="par0080">During admission, 30 clinical specimens (seven oropharyngeal swabs, 11 nasal swabs, and 12 serum samples) were collected from 13 patients with pneumonia and risk factors associated with MERS-CoV infection, including history of travel to the Middle East <14 days before illness. There was no history of contact with animals or sick people during their visit. Demographic and clinical characteristics of the patients are presented in <xref rid="tbl0005" ref-type="table">Table 1</xref>. The numbers of male and female patients were similar (male-to-female ratio, 7:6), and the median age of all patients was 61 years.<table-wrap position="float" id="tbl0005"><label>Table 1</label><caption><p>Demographic characteristics and clinical presentation of suspected MERS-CoV patients in Prof. Dr. Sulianti Saroso Infectious Disease Hospital.</p></caption><alt-text id="at0050">Table 1</alt-text><table frame="hsides" rules="groups"><thead><tr><th align="left">Demographics</th><th colspan="13" align="left">Patient ID<hr></hr></th><th align="left">Prevalence (Average)</th></tr><tr><th align="left"></th><th align="left">MER004 072015</th><th align="left">MER012 042016</th><th align="left">MER001 092016</th><th align="left">MER011 122016</th><th align="left">MER002 092016</th><th align="left">MER009 102015</th><th align="left">MER003 042016</th><th align="left">MER013 112015</th><th align="left">MER006 102015</th><th align="left">MER005 102015</th><th align="left">MER007 102015</th><th align="left">MER008 102015</th><th align="left">MER010 092016</th><th align="left"></th></tr></thead><tbody><tr><td align="left">Age, years</td><td align="left">32</td><td align="left">66</td><td align="left">56</td><td align="left">60</td><td align="left">34</td><td align="left">75</td><td align="left">65</td><td align="left">37</td><td align="left">71</td><td align="left">59</td><td align="left">61</td><td align="left">71</td><td align="left">61</td><td align="left">57.5<break></break>Median: 61 (32–75)</td></tr><tr><td align="left">Sex</td><td align="left">F</td><td align="left">M</td><td align="left">M</td><td align="left">M</td><td align="left">F</td><td align="left">M</td><td align="left">F</td><td align="left">F</td><td align="left">M</td><td align="left">F</td><td align="left">F</td><td align="left">M</td><td align="left">M</td><td align="left">M: 7 (53.8%)</td></tr><tr><td align="left">Travel history to Middle East<xref rid="tblfn0005" ref-type="table-fn">a</xref></td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">1 (100%)</td></tr><tr><td align="left">Purpose of travel</td><td align="left">Umrah</td><td align="left">Umrah</td><td align="left">Umrah</td><td align="left">Umrah</td><td align="left">Hajj</td><td align="left">Hajj</td><td align="left">Umrah</td><td align="left">Hajj</td><td align="left">Hajj</td><td align="left">Hajj</td><td align="left">Hajj</td><td align="left">Hajj</td><td align="left">Hajj</td><td align="left"></td></tr><tr><td align="left">Date of travel</td><td align="left">May 2015</td><td align="left">Apr 2016</td><td align="left">Sept 2016</td><td align="left">Dec 2016</td><td align="left">Sept 2016</td><td align="left">Nov 2015</td><td align="left">Apr 2016</td><td align="left">Nov 2015</td><td align="left">Sept 2015</td><td align="left">Oct 2015</td><td align="left">Oct 2015</td><td align="left">Oct 2015</td><td align="left">Sept 2016</td><td align="left"></td></tr><tr><td align="left">Days of Hospitalization</td><td align="left">6</td><td align="left">NA</td><td align="left">NA</td><td align="left">5</td><td align="left">5</td><td align="left">8</td><td align="left">7</td><td align="left">3</td><td align="left">5</td><td align="left">8</td><td align="left">5</td><td align="left">10</td><td align="left">2</td><td align="left">5.8 days</td></tr><tr><td align="left">Diagnosis</td><td align="left">Pneumonia</td><td align="left">Pneumonia</td><td align="left">Pneumonia</td><td align="left">Pneumonia</td><td align="left">Pneumonia</td><td align="left">Pneumonia</td><td align="left">Pneumonia</td><td align="left">Pneumonia</td><td align="left">Pneumonia</td><td align="left">Pneumonia</td><td align="left">Pneumonia</td><td align="left">Pneumonia</td><td align="left">Pneumonia</td><td align="left"></td></tr><tr><td align="left">Curb-65 severity score</td><td align="left">1</td><td align="left">0</td><td align="left">0</td><td align="left">0</td><td align="left">1</td><td align="left">1</td><td align="left">1</td><td align="left">0</td><td align="left">1</td><td align="left">0</td><td align="left">0</td><td align="left">1</td><td align="left">1</td><td align="left"></td></tr><tr><td align="left">Outcome</td><td align="left">Recovered</td><td align="left">Recovered</td><td align="left">Recovered</td><td align="left">Recovered</td><td align="left">Recovered</td><td align="left">Recovered</td><td align="left">Recovered</td><td align="left">Recovered</td><td align="left">Recovered</td><td align="left">Recovered</td><td align="left">Recovered</td><td align="left">Recovered</td><td align="left">Recovered</td><td align="left"></td></tr><tr><td colspan="15" align="left">Clinical manifestations and laboratory investigations</td></tr><tr><td align="left">Fever (>37.5 °C)</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">13 (100%)</td></tr><tr><td align="left">Cough</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">13 (100%)</td></tr><tr><td align="left">Chest pain</td><td align="left">No</td><td align="left">No</td><td align="left">No</td><td align="left">No</td><td align="left">Yes</td><td align="left">No</td><td align="left">Yes</td><td align="left">No</td><td align="left">No</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">No</td><td align="left">No</td><td align="left">4 (30.8%)</td></tr><tr><td align="left">Difficulty breathing</td><td align="left">Yes</td><td align="left">No</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">12 (92.3%)</td></tr><tr><td align="left">Ronchi</td><td align="left">No</td><td align="left">No</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">No</td><td align="left">No</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">9 (69.2%)</td></tr><tr><td align="left">Wheezing</td><td align="left">No</td><td align="left">No</td><td align="left">No</td><td align="left">No</td><td align="left">No</td><td align="left">No</td><td align="left">No</td><td align="left">No</td><td align="left">No</td><td align="left">No</td><td align="left">Yes</td><td align="left">Yes</td><td align="left">No</td><td align="left">2 (15.4%)</td></tr><tr><td align="left">Respiratory rate (/min)</td><td align="left">24</td><td align="left">25</td><td align="left">24</td><td align="left">28</td><td align="left">29</td><td align="left">28</td><td align="left">28</td><td align="left">24</td><td align="left">24</td><td align="left">22</td><td align="left">22</td><td align="left">27</td><td align="left">30</td><td align="left">25.8</td></tr><tr><td align="left">Chest radiography</td><td align="left">Infiltration</td><td align="left">Infiltration</td><td align="left">Infiltration</td><td align="left">Infiltration</td><td align="left">Infiltration</td><td align="left">Infiltration</td><td align="left">Infiltration</td><td align="left">Infiltration</td><td align="left">Infiltration</td><td align="left">Infiltration</td><td align="left">Infiltration</td><td align="left">Infiltration</td><td align="left">Infiltration</td><td align="left"></td></tr><tr><td align="left">Leukocytes 1<sup>st</sup> (/l)</td><td align="left">4.4</td><td align="left">4.9</td><td align="left">26.5</td><td align="left">25.2</td><td align="left">31.2</td><td align="left">8.5</td><td align="left">20.9</td><td align="left">6.2</td><td align="left">8.1</td><td align="left">NA</td><td align="left">7.7</td><td align="left">32.8</td><td align="left">11.9</td><td align="left">15.6917</td></tr><tr><td align="left">Leukocytes 2<sup>nd</sup> (/l)</td><td align="left">3.0</td><td align="left">NA</td><td align="left">NA</td><td align="left">12.0</td><td align="left">20.7</td><td align="left">9.3</td><td align="left">20.4</td><td align="left">8.3</td><td align="left">NA</td><td align="left">NA</td><td align="left">9.3</td><td align="left">32.9</td><td align="left">NA</td><td align="left">14.4875</td></tr><tr><td align="left">Leukocytes 3<sup>rd</sup> (/μl)</td><td align="left">5.1</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">17.0</td><td align="left">7.3</td><td align="left">12.3</td><td align="left">10.4</td><td align="left">NA</td><td align="left">NA</td><td align="left">19.2</td><td align="left">19.1</td><td align="left">NA</td><td align="left">12.9143</td></tr><tr><td align="left">Lymphocytes 1<sup>st</sup> (%)</td><td align="left">41</td><td align="left">23</td><td align="left">13</td><td align="left">13</td><td align="left">4</td><td align="left">3</td><td align="left">13</td><td align="left">17</td><td align="left">30</td><td align="left">NA</td><td align="left">13</td><td align="left">5</td><td align="left">12</td><td align="left">15.6</td></tr><tr><td align="left">Lymphocytes 2<sup>nd</sup> (%)</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">24</td><td align="left">14</td><td align="left">5</td><td align="left">14</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">19</td><td align="left">4</td><td align="left">NA</td><td align="left">13.3</td></tr><tr><td align="left">Antibiotics<xref rid="tblfn0010" ref-type="table-fn">b</xref></td><td align="left">Cef, Levo</td><td align="left">Cef</td><td align="left">Mero</td><td align="left">Mero</td><td align="left">Mero, Levo</td><td align="left">Mero</td><td align="left">Cefix</td><td align="left">Mero</td><td align="left">Azi</td><td align="left">Cef</td><td align="left">Cef, Levo</td><td align="left">Mero, Levo</td><td align="left">Levo</td><td align="left"></td></tr></tbody></table><table-wrap-foot><fn><p>MERS-CoV, Middle East respiratory syndrome coronavirus; F, female; M, male; NA, not available.</p></fn></table-wrap-foot><table-wrap-foot><fn id="tblfn0005"><label>a</label><p id="npar0005">History of travel to Middle East <14 days before admission to the hospital.</p></fn></table-wrap-foot><table-wrap-foot><fn id="tblfn0010"><label>b</label><p id="npar0010">Cef, ceftriaxone, Levo, levofloxacin, Mero, meropenem, Azi, azithromycin, Cefix, cefixime.</p></fn></table-wrap-foot></table-wrap></p><p id="par0085">All patients were diagnosed with pneumonia, confirmed by chest X-ray and categorized in the low-severity pneumonia risk group based on the British Thoracic Society guidelines (<xref rid="bib0135" ref-type="bibr">NICE, 2019</xref>). The duration of hospital stay varied between 2 and 10 days, with an average duration of 5.8 days. The patients were placed in isolation rooms dedicated for airborne infectious diseases. All patients recovered fully.</p><p id="par0090">A total of 18 respiratory clinical specimens that tested negative for MERS-CoV (by the Indonesian Ministry of Health) were retrospectively tested for 12 respiratory panels. In addition, 12 serum samples were tested for alphavirus and flavivirus to exclude the possibility of endemic viral infection. The coronavirus panel did not detect any MERS-CoV in any of the respiratory specimens, confirming the Indonesian Ministry of Health results. In this study, sequences of nine viral pathogens were detected in seven patients: four with single infections and three with multiple infections (<xref rid="tbl0010" ref-type="table">Table 2</xref>). In patient ID MER004 072015, a co-infection of enterovirus and flavivirus was detected from nasal swab and serum, respectively. Nucleotide comparison of 357 nucleotides of the polyprotein gene using BLAST showed 99% similarity with enterovirus D68; for the flavivirus, 274 bases of the NS5 gene showed 98% similarity with dengue virus type 3. In patient ID MER002 092016, both herpesvirus and coronavirus were detected in the patient’s oropharyngeal swab. Herpes simplex virus type 1 (HSV-1) was identified based on sequence matching of 400 bp through the online database (NCBI). Meanwhile, nucleotide comparison of 387 bases of the RNA-dependent RNA polymerase (RdRp) gene obtained from coronavirus showed 100% similarity with human coronavirus 229E (HCoV-229E). For patient ID MER009 102015, amplification of 400 bp untranslated region (UTR) gene of the enterovirus family and 243 bp M-gene region of influenza virus in a nasal swab revealed a rhinovirus A60 and influenza virus H1N1 (similarity 99% and 100%, respectively) co-infection. Single infections with rhinovirus C, influenza virus H3N2, human metapneumovirus (HMPV), and influenza virus H1N1 were identified in the respiratory swabs of patients with ID MER001 092016, MER007 102015, MER006 102015, and MER010 092016, respectively.<table-wrap position="float" id="tbl0010"><label>Table 2</label><caption><p>Conventional PCR test results for viral agents from suspected MERS-CoV patients.</p></caption><alt-text id="at0055">Table 2</alt-text><table frame="hsides" rules="groups"><thead><tr><th align="left">Patient ID</th><th align="left">Specimen</th><th colspan="13" align="left">Virus panel<hr></hr></th><th align="left">Sequencing results</th></tr><tr><th align="left"></th><th align="left"></th><th align="left">Corona virus</th><th align="left">Influenza virus</th><th align="left">Enterovirus</th><th align="left">Para myxovirus</th><th align="left">Herpes virus</th><th align="left">Henipavirus</th><th align="left">Hanta virus</th><th align="left">Arena virus</th><th align="left">Adenovirus</th><th align="left">Astrovirus</th><th align="left">RSV</th><th align="left">Flavivirus</th><th align="left">Alpha virus</th><th align="left"></th></tr></thead><tbody><tr><td align="left" valign="middle" rowspan="3">MER004 072015</td><td align="left">Oropharyngeal swab</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">NA</td><td align="left">NA</td><td align="left"></td></tr><tr><td align="left">Nasal swab</td><td align="left">−</td><td align="left">−</td><td align="left">+</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">NA</td><td align="left">NA</td><td align="left">Enterovirus D68</td></tr><tr><td align="left">Serum</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">+</td><td align="left">−</td><td align="left">Dengue 3 virus</td></tr><tr><td align="left" valign="middle" rowspan="3">MER012 042016</td><td align="left">Oropharyngeal swab</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">NA</td><td align="left">NA</td><td align="left"></td></tr><tr><td align="left">Nasal swab</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">NA</td><td align="left">NA</td><td align="left"></td></tr><tr><td align="left">Serum</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">−</td><td align="left">−</td><td align="left"></td></tr><tr><td align="left" valign="middle" rowspan="2">MER001 092016</td><td align="left">Nasal swab</td><td align="left">−</td><td align="left">−</td><td align="left">+</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">NA</td><td align="left">NA</td><td align="left">Rhinovirus C</td></tr><tr><td align="left">Serum</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">−</td><td align="left">−</td><td align="left"></td></tr><tr><td align="left" valign="middle" rowspan="3">MER011 122016</td><td align="left">Oropharyngeal swab</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">NA</td><td align="left">NA</td><td align="left"></td></tr><tr><td align="left">Nasal swab</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">NA</td><td align="left">NA</td><td align="left"></td></tr><tr><td align="left">Serum</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">−</td><td align="left">−</td><td align="left"></td></tr><tr><td align="left" valign="middle" rowspan="3">MER002 092016</td><td align="left">Oropharyngeal swab-1</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">+</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">NA</td><td align="left">NA</td><td align="left">Herpes simplex 1 virus</td></tr><tr><td align="left">Oropharyngeal swab-2</td><td align="left">+</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">+</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">NA</td><td align="left">NA</td><td align="left">Coronavirus 229E, herpes simplex 1 virus</td></tr><tr><td align="left">Serum</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">−</td><td align="left">−</td><td align="left"></td></tr><tr><td align="left">MER009 102015</td><td align="left">Nasal swab</td><td align="left">−</td><td align="left">+</td><td align="left">+</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">Influenza virus H1N1, rhinovirus A60</td></tr><tr><td align="left">MER003 042016</td><td align="left">Serum</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left"></td></tr><tr><td align="left">MER013 112015</td><td align="left">Serum</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left"></td></tr><tr><td align="left" valign="middle" rowspan="3">MER006 102015</td><td align="left">Nasal swab-1</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">+</td><td align="left">NA</td><td align="left">NA</td><td align="left">Human metapneumovirus</td></tr><tr><td align="left">Nasal swab-2</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">+</td><td align="left">NA</td><td align="left">NA</td><td align="left">Human metapneumovirus</td></tr><tr><td align="left">Serum</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">−</td><td align="left">−</td><td align="left"></td></tr><tr><td align="left" valign="middle" rowspan="2">MER005 102015</td><td align="left">Nasal swab</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left"></td></tr><tr><td align="left">Serum</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">−</td><td align="left">−</td><td align="left"></td></tr><tr><td align="left" valign="middle" rowspan="2">MER007 102015</td><td align="left">Nasal swab</td><td align="left">−</td><td align="left">+</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">Influenza virus H1N1</td></tr><tr><td align="left">Serum</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">−</td><td align="left">−</td><td align="left"></td></tr><tr><td align="left" valign="middle" rowspan="3">MER008 102015</td><td align="left">Oropharyngeal swab</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">NA</td><td align="left">NA</td><td align="left"></td></tr><tr><td align="left">Nasal swab</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">NA</td><td align="left">NA</td><td align="left"></td></tr><tr><td align="left">Serum</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">−</td><td align="left">−</td><td align="left"></td></tr><tr><td align="left" valign="middle" rowspan="3">MER010 092016</td><td align="left">Oropharyngeal swab</td><td align="left">−</td><td align="left">+</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">NA</td><td align="left">NA</td><td align="left">Influenza virus H3N2</td></tr><tr><td align="left">Nasal swab</td><td align="left">−</td><td align="left">+</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">−</td><td align="left">NA</td><td align="left">NA</td><td align="left">Influenza virus H3N2</td></tr><tr><td align="left">Serum</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">NA</td><td align="left">−</td><td align="left">−</td><td align="left"></td></tr></tbody></table><table-wrap-foot><fn><p>NA, not available.</p></fn></table-wrap-foot></table-wrap></p></sec><sec id="sec0050"><title>Discussion</title><p id="par0095">Although patients with MERS-CoV usually present with an influenza-like illness, asymptomatic infection or cases with mild respiratory symptoms have also been reported (<xref rid="bib0125" ref-type="bibr">Mackay and Arden, 2017</xref>, <xref rid="bib0005" ref-type="bibr">Ahmed, 2017a</xref>). In late infection, most of the MERS-CoV patients have been reported to develop pneumonia. Age, pneumonia, and a history of travel to the Middle East are important markers of MERS-CoV (<xref rid="bib0120" ref-type="bibr">Mackay and Arden, 2015</xref>). Other factors increasing the risk of infection are male sex, contact with a camel or sick patient, diabetes mellitus, severe illness, low white blood cell count, low alanine aminotransferase, and high aspartate aminotransferase (<xref rid="bib0010" ref-type="bibr">Ahmed, 2017b</xref>). The coronavirus family panel used in this study has been validated to detect MERS-CoV (<xref rid="bib0030" ref-type="bibr">Anthony et al., 2017</xref>). However, no MERS-CoV was detected, which could be due to the small sample size. Although the severity of pneumonia of all suspected MERS-CoV patients was categorized as low risk based on the British Thoracic Society guidelines (<xref rid="bib0120" ref-type="bibr">Mackay and Arden, 2015</xref>), they would be categorized as severe pneumonia cases under the Korean guidelines, due to lung infiltrations on chest X-ray and the requirement for oxygen therapy (<xref rid="bib0150" ref-type="bibr">Park et al., 2018</xref>).</p><p id="par0100">A co-infection of enterovirus D68 and dengue virus type 3 was identified in patient ID MER004 072015. She was 32 years old and presented with fever, cough, wheezing, and difficulty breathing. In adults, enterovirus D68 is rarely reported as a cause of severe illness. However, the virus has attracted international attention since it was associated with community-acquired pneumonia in children in China and Italy (<xref rid="bib0070" ref-type="bibr">Esposito et al., 2015</xref>, <xref rid="bib0040" ref-type="bibr">Bosis and Esposito, 2017</xref>, <xref rid="bib0205" ref-type="bibr">Zhang et al., 2015</xref>, <xref rid="bib0075" ref-type="bibr">Esposito et al., 2016</xref>). It is possible that the pneumonia in this case was due to the enterovirus D68 infection; further phylogenetic analysis is needed to compare this strain with other enterovirus D68. In 2014, a large outbreak of enterovirus D68 was confirmed in 49 states in the USA involving at least 1153 cases and 14 deaths. Recent reports have shown a possible association between enterovirus D68 and acute flaccid paralysis (<xref rid="bib0130" ref-type="bibr">Messacar et al., 2016</xref>, <xref rid="bib0065" ref-type="bibr">Dyda et al., 2018</xref>). However, no sign of neurological disorder was observed in this patient.</p><p id="par0105">Patient ID MER002 092016 suffered from pneumonia, sepsis, hypoalbuminemia, and leukocytosis (26.5 × 10<sup>9</sup>/l). This patient was co-infected with HCoV-229E and HSV-1. With the exception of varicella zoster and human herpesvirus 6, human herpesviruses are rarely associated with pneumonitis (<xref rid="bib0060" ref-type="bibr">Duke and Sagar, 2018</xref>, <xref rid="bib0100" ref-type="bibr">Kuwahara-Ota et al., 2018</xref>). However, one case study reported a lower respiratory tract infection caused by HSV-1 in a 72-year-old man with underlying disease (<xref rid="bib0115" ref-type="bibr">Luginbuehl et al., 2017</xref>). HSV-1 is very infectious and highly prevalent in the world, with more than 60% of the population exposed to this virus in 2012 (<xref rid="bib0110" ref-type="bibr">Looker et al., 2015</xref>). It usually causes orolabial ulcers that can lead to neurotrophic complications with lifelong potential for symptomatic or asymptomatic viral shedding episodes (<xref rid="bib0110" ref-type="bibr">Looker et al., 2015</xref>, <xref rid="bib0090" ref-type="bibr">Kaufman et al., 2005</xref>). HCoV-229E is one type of coronavirus commonly infecting humans. An epidemiological study conducted in adults with community-acquired pneumonia confirmed that four human coronaviruses (HCoV-229E, HCoV-NL-63, HCoV-HKU1, and HCoV-OC43) accounted for 0.6–2.5% of pneumonia cases (<xref rid="bib0200" ref-type="bibr">Yin and Wunderink, 2018</xref>). In this case, HCoV-229E was the most likely cause of pneumonia.</p><p id="par0110">In patient MER001 092016, rhinovirus C genetic material was detected from a nasal swab. Rhinoviruses have often been associated with pneumonia in adults. Rhinovirus C was recently discovered; this is not as well characterized as rhinoviruses A and B (<xref rid="bib0050" ref-type="bibr">Choi et al., 2015</xref>). There is controversy regarding the clinical severity of rhinovirus C infection (<xref rid="bib0050" ref-type="bibr">Choi et al., 2015</xref>, <xref rid="bib0035" ref-type="bibr">Arden et al., 2010</xref>). The virus can induce diverse clinical outcomes, with factors including species and type-specific differences as determinants of severity (<xref rid="bib0200" ref-type="bibr">Yin and Wunderink, 2018</xref>, <xref rid="bib0050" ref-type="bibr">Choi et al., 2015</xref>, <xref rid="bib0035" ref-type="bibr">Arden et al., 2010</xref>, <xref rid="bib0020" ref-type="bibr">Annamalay et al., 2016</xref>). Globally, rhinovirus C has been linked to lower respiratory tract infections such as bronchitis, bronchiolitis, and pneumonia, especially when there is co-infection with other viruses, such as bocavirus and influenza virus (<xref rid="bib0105" ref-type="bibr">Langelier et al., 2017</xref>). In Indonesia, data on rhinovirus C are limited, with only one report related to myocarditis (<xref rid="bib0190" ref-type="bibr">Wiyatno et al., 2018</xref>).</p><p id="par0115">Influenza virus H1N1 was detected in patients MER009 102015, MER007 102015, and MER010 092016. In addition, patient MER009 102015 was co-infected with rhinovirus A60. Influenza virus H1N1 is known to cause a serious infection that can lead to the development of pneumonia and death if it progresses to acute respiratory distress syndrome. In the present study, HMPV was detected from a nasal swab of a 71-year-old patient with pneumonia. HMPV is one of the most significant causes of upper and lower respiratory tract infections in children and the elderly, especially the immunocompromised and those with underlying respiratory conditions (<xref rid="bib0145" ref-type="bibr">Oong et al., 2018</xref>, <xref rid="bib0180" ref-type="bibr">Taniguchi et al., 2019</xref>, <xref rid="bib0085" ref-type="bibr">Jallow et al., 2019</xref>). Two genotypes of HMPV have been identified, which can be classified into five lineages, A1, A2a, A2b, B1, and B2. However, their association with disease severity remains unclear (<xref rid="bib0095" ref-type="bibr">Kumar and Srivastava, 2018</xref>). There is only a single report on HMPV from Indonesia, documenting the association of HMPV lineage A1 and A2 with asthma exacerbations and pneumonia, indicating that HMPV should be screened in those with chronic and severe respiratory infections (<xref rid="bib0160" ref-type="bibr">Prasetyo et al., 2015</xref>).</p><p id="par0120">This study, together with that of Amin et al., strengthens the conclusion that Indonesia remained MERS-CoV-free, at least up until 2015–2016. There are some limitations to this study, such as the weakness of statistical power due to the lack of information on the total number of subjects screened and the small number of patients involved in this study. Secondly, although the specimens were mostly obtained during the acute febrile phase, beneficial for molecular screening, serology was not performed for a more comprehensive investigative approach. Thirdly, the detection of viral pathogens in swabs did not imply causality, as additional viral and bacterial panels need to be evaluated.</p><p id="par0125">In conclusion, the sequences of nine viral pathogens were detected in samples from seven suspected MERS-CoV patients hospitalized in Prof. Dr. Sulianti Saroso IDH, Indonesia. Etiological agents detected in the patient samples were enterovirus D68, dengue virus type 3, rhinovirus C, HCoV-229E, HSV-1, influenza virus H1N1, influenza virus H3N2, HMPV, and rhinovirus A60. This study also confirmed that there was no MERS-CoV genetic material detected from these 13 patients. Along with results reported by Amin et al., we confirmed that Indonesia remained MERS-CoV-free in 2015–2016. In conclusion, the early detection and identification of the etiological agent is crucial for the containment of MERS-CoV in those with a history of travel to the Middle East, and if results are negative, testing should be performed for additional pathogens to improve patient management.</p></sec><sec id="sec0055"><title>Conflict of interest</title><p id="par0130">No conflict of interest to declare.</p></sec><sec id="sec0060"><title>Author contributions</title><p id="par0135">TYS, TSH, KSM, VL, and DS were responsible for the initial design of the study. EH and R collected samples from eligible patients and collected clinical data. TYS, AW, and EH, conducted the experiment and data analysis. TSH, R, and AKD performed the data analysis. TYS, AW, and DS wrote the first draft of the paper. All of the authors contributed to the interpretation of the data and reviewed the manuscript for important intellectual content. 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