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Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates.

Identifieur interne : 000B55 ( PubMed/Curation ); précédent : 000B54; suivant : 000B56

Identification 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.

RBID : pubmed:28902913

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 :
- Animals, Camelus (virology), Coronaviridae (classification), Coronaviridae (genetics), Coronaviridae (isolation & purification), Humans, Metagenomics, Phylogeny, Sequence Analysis, DNA, United Arab Emirates (epidemiology), Virus Diseases (veterinary), Virus Diseases (virology), Zoonoses (virology).
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

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<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>
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<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>
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<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>
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<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>
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<ForeName>Mohammed F</ForeName>
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<AffiliationInfo><Affiliation>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates.</Affiliation>
</AffiliationInfo>
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<ForeName>Yassir M</ForeName>
<Initials>YM</Initials>
<AffiliationInfo><Affiliation>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates.</Affiliation>
</AffiliationInfo>
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<ForeName>Zulaikha M</ForeName>
<Initials>ZM</Initials>
<AffiliationInfo><Affiliation>Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates.</Affiliation>
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<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>
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<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>
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</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>
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</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>
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<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>
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<Language>eng</Language>
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<Month>09</Month>
<Day>13</Day>
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</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" MajorTopicYN="N">Phylogeny</DescriptorName>
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<MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D014479" MajorTopicYN="N">United Arab Emirates</DescriptorName>
<QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D014777" MajorTopicYN="N">Virus Diseases</DescriptorName>
<QualifierName UI="Q000662" MajorTopicYN="Y">veterinary</QualifierName>
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Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates.

Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates.

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