Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates.
Identifieur interne : 000B55 ( PubMed/Corpus ); précédent : 000B54; suivant : 000B56Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates.
Auteurs : Yan Li ; Abdelmalik Ibrahim Khalafalla ; Clinton R. Paden ; Mohammed F. Yusof ; Yassir M. Eltahir ; Zulaikha M. Al Hammadi ; Ying Tao ; Krista Queen ; Farida Al Hosani ; Susan I. Gerber ; Aron J. Hall ; Salama Al Muhairi ; Suxiang TongSource :
- PloS one [ 1932-6203 ] ; 2017.
English descriptors
- KwdEn :
- MESH :
- classification : Coronaviridae.
- epidemiology : United Arab Emirates.
- genetics : Coronaviridae.
- isolation & purification : Coronaviridae.
- veterinary : Virus Diseases.
- virology : Camelus, Virus Diseases, Zoonoses.
- Animals, Humans, Metagenomics, Phylogeny, Sequence Analysis, DNA.
Abstract
Camels are known carriers for many viral pathogens, including Middle East respiratory syndrome coronavirus (MERS-CoV). It is likely that there are additional, as yet unidentified viruses in camels with the potential to cause disease in humans. In this study, we performed metagenomic sequencing analysis on nasopharyngeal swab samples from 108 MERS-CoV-positive dromedary camels from a live animal market in Abu Dhabi, United Arab Emirates. We obtained a total of 846.72 million high-quality reads from these nasopharyngeal swab samples, of which 2.88 million (0.34%) were related to viral sequences while 512.63 million (60.5%) and 50.87 million (6%) matched bacterial and eukaryotic sequences, respectively. Among the viral reads, sequences related to mammalian viruses from 13 genera in 10 viral families were identified, including Coronaviridae, Nairoviridae, Paramyxoviridae, Parvoviridae, Polyomaviridae, Papillomaviridae, Astroviridae, Picornaviridae, Poxviridae, and Genomoviridae. Some viral sequences belong to known camel or human viruses and others are from potentially novel camel viruses with only limited sequence similarity to virus sequences in GenBank. A total of five potentially novel virus species or strains were identified. Co-infection of at least two recently identified camel coronaviruses was detected in 92.6% of the camels in the study. This study provides a comprehensive survey of viruses in the virome of upper respiratory samples in camels that have extensive contact with the human population.
DOI: 10.1371/journal.pone.0184718
PubMed: 28902913
Links to Exploration step
pubmed:28902913Le document en format XML
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Paden</name><affiliation><nlm:affiliation>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Yusof, Mohammed F" sort="Yusof, Mohammed F" uniqKey="Yusof M" first="Mohammed F" last="Yusof">Mohammed F. Yusof</name><affiliation><nlm:affiliation>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates.</nlm:affiliation></affiliation></author><author><name sortKey="Eltahir, Yassir M" sort="Eltahir, Yassir M" uniqKey="Eltahir Y" first="Yassir M" last="Eltahir">Yassir M. Eltahir</name><affiliation><nlm:affiliation>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates.</nlm:affiliation></affiliation></author><author><name sortKey="Al Hammadi, Zulaikha M" sort="Al Hammadi, Zulaikha M" uniqKey="Al Hammadi Z" first="Zulaikha M" last="Al Hammadi">Zulaikha M. Al Hammadi</name><affiliation><nlm:affiliation>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates.</nlm:affiliation></affiliation></author><author><name sortKey="Tao, Ying" sort="Tao, Ying" uniqKey="Tao Y" first="Ying" last="Tao">Ying Tao</name><affiliation><nlm:affiliation>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Queen, Krista" sort="Queen, Krista" uniqKey="Queen K" first="Krista" last="Queen">Krista Queen</name><affiliation><nlm:affiliation>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Hosani, Farida Al" sort="Hosani, Farida Al" uniqKey="Hosani F" first="Farida Al" last="Hosani">Farida Al Hosani</name><affiliation><nlm:affiliation>Health Authority Abu Dhabi, Abu Dhabi, United Arab Emirates.</nlm:affiliation></affiliation></author><author><name sortKey="Gerber, Susan I" sort="Gerber, Susan I" uniqKey="Gerber S" first="Susan I" last="Gerber">Susan I. Gerber</name><affiliation><nlm:affiliation>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Hall, Aron J" sort="Hall, Aron J" uniqKey="Hall A" first="Aron J" last="Hall">Aron J. Hall</name><affiliation><nlm:affiliation>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Al Muhairi, Salama" sort="Al Muhairi, Salama" uniqKey="Al Muhairi S" first="Salama" last="Al Muhairi">Salama Al Muhairi</name><affiliation><nlm:affiliation>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates.</nlm:affiliation></affiliation></author><author><name sortKey="Tong, Suxiang" sort="Tong, Suxiang" uniqKey="Tong S" first="Suxiang" last="Tong">Suxiang Tong</name><affiliation><nlm:affiliation>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.</nlm:affiliation></affiliation></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Camelus (virology)</term><term>Coronaviridae (classification)</term><term>Coronaviridae (genetics)</term><term>Coronaviridae (isolation & purification)</term><term>Humans</term><term>Metagenomics</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term><term>United Arab Emirates (epidemiology)</term><term>Virus Diseases (veterinary)</term><term>Virus Diseases (virology)</term><term>Zoonoses (virology)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Coronaviridae</term></keywords><keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>United Arab Emirates</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coronaviridae</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Coronaviridae</term></keywords><keywords scheme="MESH" qualifier="veterinary" xml:lang="en"><term>Virus Diseases</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Camelus</term><term>Virus Diseases</term><term>Zoonoses</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Humans</term><term>Metagenomics</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Camels are known carriers for many viral pathogens, including Middle East respiratory syndrome coronavirus (MERS-CoV). It is likely that there are additional, as yet unidentified viruses in camels with the potential to cause disease in humans. In this study, we performed metagenomic sequencing analysis on nasopharyngeal swab samples from 108 MERS-CoV-positive dromedary camels from a live animal market in Abu Dhabi, United Arab Emirates. We obtained a total of 846.72 million high-quality reads from these nasopharyngeal swab samples, of which 2.88 million (0.34%) were related to viral sequences while 512.63 million (60.5%) and 50.87 million (6%) matched bacterial and eukaryotic sequences, respectively. Among the viral reads, sequences related to mammalian viruses from 13 genera in 10 viral families were identified, including Coronaviridae, Nairoviridae, Paramyxoviridae, Parvoviridae, Polyomaviridae, Papillomaviridae, Astroviridae, Picornaviridae, Poxviridae, and Genomoviridae. Some viral sequences belong to known camel or human viruses and others are from potentially novel camel viruses with only limited sequence similarity to virus sequences in GenBank. A total of five potentially novel virus species or strains were identified. Co-infection of at least two recently identified camel coronaviruses was detected in 92.6% of the camels in the study. This study provides a comprehensive survey of viruses in the virome of upper respiratory samples in camels that have extensive contact with the human population.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28902913</PMID><DateCompleted><Year>2017</Year><Month>10</Month><Day>24</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>12</Volume><Issue>9</Issue><PubDate><Year>2017</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS ONE</ISOAbbreviation></Journal><ArticleTitle>Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates.</ArticleTitle><Pagination><MedlinePgn>e0184718</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0184718</ELocationID><Abstract><AbstractText>Camels are known carriers for many viral pathogens, including Middle East respiratory syndrome coronavirus (MERS-CoV). It is likely that there are additional, as yet unidentified viruses in camels with the potential to cause disease in humans. In this study, we performed metagenomic sequencing analysis on nasopharyngeal swab samples from 108 MERS-CoV-positive dromedary camels from a live animal market in Abu Dhabi, United Arab Emirates. We obtained a total of 846.72 million high-quality reads from these nasopharyngeal swab samples, of which 2.88 million (0.34%) were related to viral sequences while 512.63 million (60.5%) and 50.87 million (6%) matched bacterial and eukaryotic sequences, respectively. Among the viral reads, sequences related to mammalian viruses from 13 genera in 10 viral families were identified, including Coronaviridae, Nairoviridae, Paramyxoviridae, Parvoviridae, Polyomaviridae, Papillomaviridae, Astroviridae, Picornaviridae, Poxviridae, and Genomoviridae. Some viral sequences belong to known camel or human viruses and others are from potentially novel camel viruses with only limited sequence similarity to virus sequences in GenBank. A total of five potentially novel virus species or strains were identified. Co-infection of at least two recently identified camel coronaviruses was detected in 92.6% of the camels in the study. This study provides a comprehensive survey of viruses in the virome of upper respiratory samples in camels that have extensive contact with the human population.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Yan</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Khalafalla</LastName><ForeName>Abdelmalik Ibrahim</ForeName><Initials>AI</Initials><AffiliationInfo><Affiliation>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Paden</LastName><ForeName>Clinton R</ForeName><Initials>CR</Initials><AffiliationInfo><Affiliation>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yusof</LastName><ForeName>Mohammed F</ForeName><Initials>MF</Initials><AffiliationInfo><Affiliation>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Eltahir</LastName><ForeName>Yassir M</ForeName><Initials>YM</Initials><AffiliationInfo><Affiliation>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Al Hammadi</LastName><ForeName>Zulaikha M</ForeName><Initials>ZM</Initials><AffiliationInfo><Affiliation>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tao</LastName><ForeName>Ying</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Queen</LastName><ForeName>Krista</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hosani</LastName><ForeName>Farida Al</ForeName><Initials>FA</Initials><AffiliationInfo><Affiliation>Health Authority Abu Dhabi, Abu Dhabi, United Arab Emirates.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gerber</LastName><ForeName>Susan I</ForeName><Initials>SI</Initials><AffiliationInfo><Affiliation>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hall</LastName><ForeName>Aron J</ForeName><Initials>AJ</Initials><AffiliationInfo><Affiliation>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Al Muhairi</LastName><ForeName>Salama</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tong</LastName><ForeName>Suxiang</ForeName><Initials>S</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-8439-8826</Identifier><AffiliationInfo><Affiliation>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>09</Month><Day>13</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002162" MajorTopicYN="N">Camelus</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003332" MajorTopicYN="N">Coronaviridae</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056186" MajorTopicYN="N">Metagenomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" 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