Molecular characterization of human coronaviruses and their circulation dynamics in Kenya, 2009–2012
Identifieur interne : 000845 ( Main/Exploration ); précédent : 000844; suivant : 000846Molecular characterization of human coronaviruses and their circulation dynamics in Kenya, 2009–2012
Auteurs : Lenata A. Sipulwa [Kenya] ; Juliette R. Ongus [Kenya] ; Rodney L. Coldren [Kenya, États-Unis] ; Wallace D. Bulimo [Kenya, États-Unis]Source :
- Virology Journal [ 1743-422X ] ; 2016.
Abstract
Human Coronaviruses (HCoV) are a common cause of respiratory illnesses and are responsible for considerable morbidity and hospitalization across all age groups especially in individuals with compromised immunity. There are six known species of HCoV: HCoV-229E, HCoV-NL63, HCoV-HKU1, HCoV-OC43, MERS-CoV and SARS-HCoV. Although studies have shown evidence of global distribution of HCoVs, there is limited information on their presence and distribution in Kenya.
HCoV strains that circulated in Kenya were retrospectively diagnosed and molecularly characterized. A total of 417 nasopharyngeal specimens obtained between January 2009 and December 2012 from around Kenya were analyzed by a real time RT-PCR using HCoV-specific primers. HCoV-positive specimens were subsequently inoculated onto monolayers of LL-CMK2 cells. The isolated viruses were characterized by RT-PCR amplification and sequencing of the partial polymerase (
The prevalence of HCoV infection was as follows: out of the 417 specimens, 35 (8.4 %) were positive for HCoV, comprising 10 (2.4 %) HCoV-NL63, 12 (2.9 %) HCoV-OC43, 9 (2.1 %) HCoV-HKU1, and 4 (1 %) HCoV-229E. The Kenyan HCoV strains displayed high sequence homology to the prototypes and contemporaneous strains. Evolution analysis showed that the Kenyan HCoV-OC43 and HCoV-NL63 isolates were under purifying selection. Phylogenetic evolutionary analyses confirmed the identities of three HCoV-HKU1, five HCoV-NL63, eight HCoV-OC43 and three HCoV-229E.
There were yearly variations in the prevalence and circulation patterns of individual HCoVs in Kenya. This paper reports on the first molecular characterization of human Coronaviruses in Kenya, which play an important role in causing acute respiratory infections among children.
Url:
DOI: 10.1186/s12985-016-0474-x
PubMed: 26833249
PubMed Central: 4736488
Affiliations:
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Ongus</name><affiliation wicri:level="1"><nlm:aff id="Aff1">College of Health Sciences (COHES), Jomo Kenyatta University of Agriculture and Technology, (JKUAT), Nairobi, Kenya</nlm:aff><country xml:lang="fr">Kenya</country><wicri:regionArea>College of Health Sciences (COHES), Jomo Kenyatta University of Agriculture and Technology, (JKUAT), Nairobi</wicri:regionArea><wicri:noRegion>Nairobi</wicri:noRegion></affiliation></author><author><name sortKey="Coldren, Rodney L" sort="Coldren, Rodney L" uniqKey="Coldren R" first="Rodney L." last="Coldren">Rodney L. Coldren</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Department of Emerging Infectious Diseases, US Army Medical Research Unit–Kenya, P.O. Box 606 00621, Village Market, Nairobi, Kenya</nlm:aff><country xml:lang="fr">Kenya</country><wicri:regionArea>Department of Emerging Infectious Diseases, US Army Medical Research Unit–Kenya, P.O. Box 606 00621, Village Market, Nairobi</wicri:regionArea><wicri:noRegion>Nairobi</wicri:noRegion></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff3">Special Foreign Activity of the Walter Reed Army Institute of Research, Silver Spring, MD USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Special Foreign Activity of the Walter Reed Army Institute of Research, Silver Spring</wicri:cityArea></affiliation></author><author><name sortKey="Bulimo, Wallace D" sort="Bulimo, Wallace D" uniqKey="Bulimo W" first="Wallace D." last="Bulimo">Wallace D. Bulimo</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Department of Emerging Infectious Diseases, US Army Medical Research Unit–Kenya, P.O. Box 606 00621, Village Market, Nairobi, Kenya</nlm:aff><country xml:lang="fr">Kenya</country><wicri:regionArea>Department of Emerging Infectious Diseases, US Army Medical Research Unit–Kenya, P.O. Box 606 00621, Village Market, Nairobi</wicri:regionArea><wicri:noRegion>Nairobi</wicri:noRegion></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff3">Special Foreign Activity of the Walter Reed Army Institute of Research, Silver Spring, MD USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Special Foreign Activity of the Walter Reed Army Institute of Research, Silver Spring</wicri:cityArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff4">Department of Biochemistry, School of Medicine, University of Nairobi, Nairobi, Kenya</nlm:aff><country xml:lang="fr">Kenya</country><wicri:regionArea>Department of Biochemistry, School of Medicine, University of Nairobi, Nairobi</wicri:regionArea><wicri:noRegion>Nairobi</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26833249</idno><idno type="pmc">4736488</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4736488</idno><idno type="RBID">PMC:4736488</idno><idno type="doi">10.1186/s12985-016-0474-x</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000165</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000165</idno><idno type="wicri:Area/Pmc/Curation">000165</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000165</idno><idno type="wicri:Area/Pmc/Checkpoint">000255</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000255</idno><idno type="wicri:Area/Ncbi/Merge">000525</idno><idno type="wicri:Area/Ncbi/Curation">000525</idno><idno type="wicri:Area/Ncbi/Checkpoint">000525</idno><idno type="wicri:Area/Main/Merge">000847</idno><idno type="wicri:Area/Main/Curation">000845</idno><idno type="wicri:Area/Main/Exploration">000845</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Molecular characterization of human coronaviruses and their circulation dynamics in Kenya, 2009–2012</title><author><name sortKey="Sipulwa, Lenata A" sort="Sipulwa, Lenata A" uniqKey="Sipulwa L" first="Lenata A." last="Sipulwa">Lenata A. Sipulwa</name><affiliation wicri:level="1"><nlm:aff id="Aff1">College of Health Sciences (COHES), Jomo Kenyatta University of Agriculture and Technology, (JKUAT), Nairobi, Kenya</nlm:aff><country xml:lang="fr">Kenya</country><wicri:regionArea>College of Health Sciences (COHES), Jomo Kenyatta University of Agriculture and Technology, (JKUAT), Nairobi</wicri:regionArea><wicri:noRegion>Nairobi</wicri:noRegion></affiliation></author><author><name sortKey="Ongus, Juliette R" sort="Ongus, Juliette R" uniqKey="Ongus J" first="Juliette R." last="Ongus">Juliette R. Ongus</name><affiliation wicri:level="1"><nlm:aff id="Aff1">College of Health Sciences (COHES), Jomo Kenyatta University of Agriculture and Technology, (JKUAT), Nairobi, Kenya</nlm:aff><country xml:lang="fr">Kenya</country><wicri:regionArea>College of Health Sciences (COHES), Jomo Kenyatta University of Agriculture and Technology, (JKUAT), Nairobi</wicri:regionArea><wicri:noRegion>Nairobi</wicri:noRegion></affiliation></author><author><name sortKey="Coldren, Rodney L" sort="Coldren, Rodney L" uniqKey="Coldren R" first="Rodney L." last="Coldren">Rodney L. Coldren</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Department of Emerging Infectious Diseases, US Army Medical Research Unit–Kenya, P.O. Box 606 00621, Village Market, Nairobi, Kenya</nlm:aff><country xml:lang="fr">Kenya</country><wicri:regionArea>Department of Emerging Infectious Diseases, US Army Medical Research Unit–Kenya, P.O. Box 606 00621, Village Market, Nairobi</wicri:regionArea><wicri:noRegion>Nairobi</wicri:noRegion></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff3">Special Foreign Activity of the Walter Reed Army Institute of Research, Silver Spring, MD USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Special Foreign Activity of the Walter Reed Army Institute of Research, Silver Spring</wicri:cityArea></affiliation></author><author><name sortKey="Bulimo, Wallace D" sort="Bulimo, Wallace D" uniqKey="Bulimo W" first="Wallace D." last="Bulimo">Wallace D. Bulimo</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Department of Emerging Infectious Diseases, US Army Medical Research Unit–Kenya, P.O. Box 606 00621, Village Market, Nairobi, Kenya</nlm:aff><country xml:lang="fr">Kenya</country><wicri:regionArea>Department of Emerging Infectious Diseases, US Army Medical Research Unit–Kenya, P.O. Box 606 00621, Village Market, Nairobi</wicri:regionArea><wicri:noRegion>Nairobi</wicri:noRegion></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff3">Special Foreign Activity of the Walter Reed Army Institute of Research, Silver Spring, MD USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Special Foreign Activity of the Walter Reed Army Institute of Research, Silver Spring</wicri:cityArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff4">Department of Biochemistry, School of Medicine, University of Nairobi, Nairobi, Kenya</nlm:aff><country xml:lang="fr">Kenya</country><wicri:regionArea>Department of Biochemistry, School of Medicine, University of Nairobi, Nairobi</wicri:regionArea><wicri:noRegion>Nairobi</wicri:noRegion></affiliation></author></analytic><series><title level="j">Virology Journal</title><idno type="eISSN">1743-422X</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Human Coronaviruses (HCoV) are a common cause of respiratory illnesses and are responsible for considerable morbidity and hospitalization across all age groups especially in individuals with compromised immunity. There are six known species of HCoV: HCoV-229E, HCoV-NL63, HCoV-HKU1, HCoV-OC43, MERS-CoV and SARS-HCoV. Although studies have shown evidence of global distribution of HCoVs, there is limited information on their presence and distribution in Kenya.</p></sec><sec><title>Methods</title><p>HCoV strains that circulated in Kenya were retrospectively diagnosed and molecularly characterized. A total of 417 nasopharyngeal specimens obtained between January 2009 and December 2012 from around Kenya were analyzed by a real time RT-PCR using HCoV-specific primers. HCoV-positive specimens were subsequently inoculated onto monolayers of LL-CMK2 cells. The isolated viruses were characterized by RT-PCR amplification and sequencing of the partial polymerase (<italic>po</italic>l) gene.</p></sec><sec><title>Results</title><p>The prevalence of HCoV infection was as follows: out of the 417 specimens, 35 (8.4 %) were positive for HCoV, comprising 10 (2.4 %) HCoV-NL63, 12 (2.9 %) HCoV-OC43, 9 (2.1 %) HCoV-HKU1, and 4 (1 %) HCoV-229E. The Kenyan HCoV strains displayed high sequence homology to the prototypes and contemporaneous strains. Evolution analysis showed that the Kenyan HCoV-OC43 and HCoV-NL63 isolates were under purifying selection. Phylogenetic evolutionary analyses confirmed the identities of three HCoV-HKU1, five HCoV-NL63, eight HCoV-OC43 and three HCoV-229E.</p></sec><sec><title>Conclusions</title><p>There were yearly variations in the prevalence and circulation patterns of individual HCoVs in Kenya. 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Mclntosh</name></author><author><name sortKey="Englund, Ja" uniqKey="Englund J">JA Englund</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Elden, Lj" uniqKey="Van Elden L">LJ van Elden</name></author><author><name sortKey="Van Loon, Am" uniqKey="Van Loon A">AM van Loon</name></author><author><name sortKey="Van Alphen, F" uniqKey="Van Alphen F">F van Alphen</name></author><author><name sortKey="Hendriksen, Ka" uniqKey="Hendriksen K">KA Hendriksen</name></author><author><name sortKey="Hoepelman, Ai" uniqKey="Hoepelman A">AI Hoepelman</name></author><author><name sortKey="Van Kraaij, Mg" uniqKey="Van Kraaij M">MG van Kraaij</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Kraaij, Mg" uniqKey="Van Kraaij M">MG van Kraaij</name></author><author><name sortKey="Van Elden, Lj" uniqKey="Van Elden L">LJ van Elden</name></author><author><name sortKey="Van Loon, Am" uniqKey="Van Loon A">AM van Loon</name></author><author><name sortKey="Hendriksen, Ka" uniqKey="Hendriksen K">KA Hendriksen</name></author><author><name sortKey="Laterveer, L" uniqKey="Laterveer L">L Laterveer</name></author><author><name sortKey="Dekker, Aw" uniqKey="Dekker A">AW Dekker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pyrc, K" uniqKey="Pyrc K">K Pyrc</name></author><author><name sortKey="Sims, Ac" uniqKey="Sims A">AC Sims</name></author><author><name sortKey="Dijkman, R" uniqKey="Dijkman R">R Dijkman</name></author><author><name sortKey="Jebbink, M" uniqKey="Jebbink M">M Jebbink</name></author><author><name sortKey="Long, C" uniqKey="Long C">C Long</name></author><author><name sortKey="Deming, D" uniqKey="Deming D">D Deming</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Kenya</li><li>États-Unis</li></country><region><li>Maryland</li></region></list><tree><country name="Kenya"><noRegion><name sortKey="Sipulwa, Lenata A" sort="Sipulwa, Lenata A" uniqKey="Sipulwa L" first="Lenata A." last="Sipulwa">Lenata A. Sipulwa</name></noRegion><name sortKey="Bulimo, Wallace D" sort="Bulimo, Wallace D" uniqKey="Bulimo W" first="Wallace D." last="Bulimo">Wallace D. Bulimo</name><name sortKey="Bulimo, Wallace D" sort="Bulimo, Wallace D" uniqKey="Bulimo W" first="Wallace D." last="Bulimo">Wallace D. Bulimo</name><name sortKey="Coldren, Rodney L" sort="Coldren, Rodney L" uniqKey="Coldren R" first="Rodney L." last="Coldren">Rodney L. Coldren</name><name sortKey="Ongus, Juliette R" sort="Ongus, Juliette R" uniqKey="Ongus J" first="Juliette R." last="Ongus">Juliette R. Ongus</name></country><country name="États-Unis"><region name="Maryland"><name sortKey="Coldren, Rodney L" sort="Coldren, Rodney L" uniqKey="Coldren R" first="Rodney L." last="Coldren">Rodney L. Coldren</name></region><name sortKey="Bulimo, Wallace D" sort="Bulimo, Wallace D" uniqKey="Bulimo W" first="Wallace D." last="Bulimo">Wallace D. Bulimo</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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