Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates
Identifieur interne : 000D49 ( Main/Exploration ); précédent : 000D48; suivant : 000D50Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates
Auteurs : Yan Li [États-Unis] ; Abdelmalik Ibrahim Khalafalla [Émirats arabes unis] ; Clinton R. Paden [États-Unis] ; Mohammed F. Yusof [Émirats arabes unis] ; Yassir M. Eltahir [Émirats arabes unis] ; Zulaikha M. Al Hammadi [Émirats arabes unis] ; Ying Tao [États-Unis] ; Krista Queen [États-Unis] ; Farida Al Hosani [Émirats arabes unis] ; Susan I. Gerber [États-Unis] ; Aron J. Hall [États-Unis] ; Salama Al Muhairi [Émirats arabes unis] ; Suxiang Tong [États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2017.
Descripteurs français
- KwdFr :
- Analyse de séquence d'ADN, Animaux, Chameaux (virologie), Coronaviridae (), Coronaviridae (génétique), Coronaviridae (isolement et purification), Humains, Maladies virales (médecine vétérinaire), Maladies virales (virologie), Métagénomique, Phylogénie, Zoonoses (virologie), Émirats arabes unis (épidémiologie).
- MESH :
- génétique : Coronaviridae.
- isolement et purification : Coronaviridae.
- médecine vétérinaire : Maladies virales.
- virologie : Chameaux, Maladies virales, Zoonoses.
- épidémiologie : Émirats arabes unis.
- Analyse de séquence d'ADN, Animaux, Coronaviridae, Humains, Métagénomique, Phylogénie.
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
Url:
DOI: 10.1371/journal.pone.0184718
PubMed: 28902913
PubMed Central: 5597213
Affiliations:
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Le document en format XML
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Paden</name><affiliation wicri:level="2"><nlm:aff id="aff001"><addr-line>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia</wicri:regionArea><placeName><region type="state">Géorgie (États-Unis)</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff003"><addr-line>Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></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 wicri:level="1"><nlm:aff id="aff002"><addr-line>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates</addr-line></nlm:aff><country xml:lang="fr">Émirats arabes unis</country><wicri:regionArea>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi</wicri:regionArea><wicri:noRegion>Abu Dhabi</wicri:noRegion></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 wicri:level="1"><nlm:aff id="aff002"><addr-line>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates</addr-line></nlm:aff><country xml:lang="fr">Émirats arabes unis</country><wicri:regionArea>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi</wicri:regionArea><wicri:noRegion>Abu Dhabi</wicri:noRegion></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 wicri:level="1"><nlm:aff id="aff002"><addr-line>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates</addr-line></nlm:aff><country xml:lang="fr">Émirats arabes unis</country><wicri:regionArea>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi</wicri:regionArea><wicri:noRegion>Abu Dhabi</wicri:noRegion></affiliation></author><author><name sortKey="Tao, Ying" sort="Tao, Ying" uniqKey="Tao Y" first="Ying" last="Tao">Ying Tao</name><affiliation wicri:level="2"><nlm:aff id="aff001"><addr-line>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia</wicri:regionArea><placeName><region type="state">Géorgie (États-Unis)</region></placeName></affiliation></author><author><name sortKey="Queen, Krista" sort="Queen, Krista" uniqKey="Queen K" first="Krista" last="Queen">Krista Queen</name><affiliation wicri:level="2"><nlm:aff id="aff001"><addr-line>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia</wicri:regionArea><placeName><region type="state">Géorgie (États-Unis)</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff003"><addr-line>Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></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 wicri:level="1"><nlm:aff id="aff004"><addr-line>Health Authority Abu Dhabi, Abu Dhabi, United Arab Emirates</addr-line></nlm:aff><country xml:lang="fr">Émirats arabes unis</country><wicri:regionArea>Health Authority Abu Dhabi, Abu Dhabi</wicri:regionArea><wicri:noRegion>Abu Dhabi</wicri:noRegion></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 wicri:level="2"><nlm:aff id="aff001"><addr-line>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia</wicri:regionArea><placeName><region type="state">Géorgie (États-Unis)</region></placeName></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 wicri:level="2"><nlm:aff id="aff001"><addr-line>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia</wicri:regionArea><placeName><region type="state">Géorgie (États-Unis)</region></placeName></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 wicri:level="1"><nlm:aff id="aff002"><addr-line>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates</addr-line></nlm:aff><country xml:lang="fr">Émirats arabes unis</country><wicri:regionArea>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi</wicri:regionArea><wicri:noRegion>Abu Dhabi</wicri:noRegion></affiliation></author><author><name sortKey="Tong, Suxiang" sort="Tong, Suxiang" uniqKey="Tong S" first="Suxiang" last="Tong">Suxiang Tong</name><affiliation wicri:level="2"><nlm:aff id="aff001"><addr-line>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia</wicri:regionArea><placeName><region type="state">Géorgie (États-Unis)</region></placeName></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2017">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="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Chameaux (virologie)</term><term>Coronaviridae ()</term><term>Coronaviridae (génétique)</term><term>Coronaviridae (isolement et purification)</term><term>Humains</term><term>Maladies virales (médecine vétérinaire)</term><term>Maladies virales (virologie)</term><term>Métagénomique</term><term>Phylogénie</term><term>Zoonoses (virologie)</term><term>Émirats arabes unis (épidémiologie)</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="génétique" xml:lang="fr"><term>Coronaviridae</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Coronaviridae</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Coronaviridae</term></keywords><keywords scheme="MESH" qualifier="médecine vétérinaire" xml:lang="fr"><term>Maladies virales</term></keywords><keywords scheme="MESH" qualifier="veterinary" xml:lang="en"><term>Virus Diseases</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Chameaux</term><term>Maladies virales</term><term>Zoonoses</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Camelus</term><term>Virus Diseases</term><term>Zoonoses</term></keywords><keywords scheme="MESH" qualifier="épidémiologie" xml:lang="fr"><term>Émirats arabes unis</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><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Coronaviridae</term><term>Humains</term><term>Métagénomique</term><term>Phylogénie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>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 <italic>Coronaviridae</italic>, <italic>Nairoviridae</italic>, <italic>Paramyxoviridae</italic>, <italic>Parvoviridae</italic>, <italic>Polyomaviridae</italic>, <italic>Papillomaviridae</italic>, <italic>Astroviridae</italic>, <italic>Picornaviridae</italic>, <italic>Poxviridae</italic>, and <italic>Genomoviridae</italic>. 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.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Yam, Baz" uniqKey="Yam B">BAZ Yam</name></author><author><name sortKey="Khomeiri, M" uniqKey="Khomeiri M">M Khomeiri</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="De Groot, Rj" uniqKey="De Groot R">RJ de Groot</name></author><author><name sortKey="Baker, Sc" uniqKey="Baker S">SC Baker</name></author><author><name sortKey="Baric, Rs" uniqKey="Baric R">RS Baric</name></author><author><name sortKey="Brown, Cs" uniqKey="Brown C">CS Brown</name></author><author><name sortKey="Drosten, C" uniqKey="Drosten C">C Drosten</name></author><author><name sortKey="Enjuanes, L" uniqKey="Enjuanes L">L Enjuanes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Perera, Ra" 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last="Gerber">Susan I. Gerber</name><name sortKey="Hall, Aron J" sort="Hall, Aron J" uniqKey="Hall A" first="Aron J." last="Hall">Aron J. Hall</name><name sortKey="Paden, Clinton R" sort="Paden, Clinton R" uniqKey="Paden C" first="Clinton R." last="Paden">Clinton R. Paden</name><name sortKey="Paden, Clinton R" sort="Paden, Clinton R" uniqKey="Paden C" first="Clinton R." last="Paden">Clinton R. Paden</name><name sortKey="Queen, Krista" sort="Queen, Krista" uniqKey="Queen K" first="Krista" last="Queen">Krista Queen</name><name sortKey="Queen, Krista" sort="Queen, Krista" uniqKey="Queen K" first="Krista" last="Queen">Krista Queen</name><name sortKey="Tao, Ying" sort="Tao, Ying" uniqKey="Tao Y" first="Ying" last="Tao">Ying Tao</name><name sortKey="Tong, Suxiang" sort="Tong, Suxiang" uniqKey="Tong S" first="Suxiang" last="Tong">Suxiang Tong</name></country><country name="Émirats arabes unis"><noRegion><name sortKey="Khalafalla, Abdelmalik Ibrahim" sort="Khalafalla, Abdelmalik Ibrahim" uniqKey="Khalafalla A" first="Abdelmalik Ibrahim" last="Khalafalla">Abdelmalik Ibrahim Khalafalla</name></noRegion><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><name sortKey="Al Muhairi, Salama" sort="Al Muhairi, Salama" uniqKey="Al Muhairi S" first="Salama" last="Al Muhairi">Salama Al Muhairi</name><name sortKey="Eltahir, Yassir M" sort="Eltahir, Yassir M" uniqKey="Eltahir Y" first="Yassir M." last="Eltahir">Yassir M. Eltahir</name><name sortKey="Hosani, Farida Al" sort="Hosani, Farida Al" uniqKey="Hosani F" first="Farida Al" last="Hosani">Farida Al Hosani</name><name sortKey="Yusof, Mohammed F" sort="Yusof, Mohammed F" uniqKey="Yusof M" first="Mohammed F." last="Yusof">Mohammed F. Yusof</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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