Molecular characterization of human coronaviruses and their circulation dynamics in Kenya, 2009–2012
Identifieur interne : 000351 ( Pmc/Curation ); précédent : 000350; suivant : 000352Molecular 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.
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DOI: 10.1186/s12985-016-0474-x
PubMed: 26833249
PubMed Central: 4736488
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">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></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></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></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. 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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></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></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></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></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></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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<front><journal-meta><journal-id journal-id-type="nlm-ta">Virol J</journal-id><journal-id journal-id-type="iso-abbrev">Virol. J</journal-id><journal-title-group><journal-title>Virology Journal</journal-title></journal-title-group><issn pub-type="epub">1743-422X</issn><publisher><publisher-name>BioMed Central</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26833249</article-id><article-id pub-id-type="pmc">4736488</article-id><article-id pub-id-type="publisher-id">474</article-id><article-id pub-id-type="doi">10.1186/s12985-016-0474-x</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research</subject></subj-group></article-categories><title-group><article-title>Molecular characterization of human coronaviruses and their circulation dynamics in Kenya, 2009–2012</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Sipulwa</surname><given-names>Lenata A.</given-names></name><address><email>lenata7@gmail.com</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Ongus</surname><given-names>Juliette R.</given-names></name><address><email>julietteongus@jkuat.ac.ke</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Coldren</surname><given-names>Rodney L.</given-names></name><address><email>Rodney.Coldren@usamru-k.org</email></address><xref ref-type="aff" rid="Aff2"></xref><xref ref-type="aff" rid="Aff3"></xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Bulimo</surname><given-names>Wallace D.</given-names></name><address><phone>+254733616602</phone><email>Wallace.bulimo@uonbi.ac.ke</email></address><xref ref-type="aff" rid="Aff2"></xref><xref ref-type="aff" rid="Aff3"></xref><xref ref-type="aff" rid="Aff4"></xref></contrib><aff id="Aff1"><label></label>College of Health Sciences (COHES), Jomo Kenyatta University of Agriculture and Technology, (JKUAT), Nairobi, Kenya</aff><aff id="Aff2"><label></label>Department of Emerging Infectious Diseases, US Army Medical Research Unit–Kenya, P.O. Box 606 00621, Village Market, Nairobi, Kenya</aff><aff id="Aff3"><label></label>Special Foreign Activity of the Walter Reed Army Institute of Research, Silver Spring, MD USA</aff><aff id="Aff4"><label></label>Department of Biochemistry, School of Medicine, University of Nairobi, Nairobi, Kenya</aff></contrib-group><pub-date pub-type="epub"><day>1</day><month>2</month><year>2016</year></pub-date><pub-date pub-type="pmc-release"><day>1</day><month>2</month><year>2016</year></pub-date><pub-date pub-type="collection"><year>2016</year></pub-date><volume>13</volume><elocation-id>18</elocation-id><history><date date-type="received"><day>21</day><month>10</month><year>2015</year></date><date date-type="accepted"><day>20</day><month>1</month><year>2016</year></date></history><permissions><copyright-statement>© Sipulwa et al. 2016</copyright-statement><license license-type="OpenAccess"><license-p><bold>Open Access</bold>This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>) applies to the data made available in this article, unless otherwise stated.</license-p></license></permissions><abstract id="Abs1"><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. 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.</p></sec></abstract><kwd-group xml:lang="en"><title>Keywords</title><kwd>Molecular characterization</kwd><kwd>Human coronaviruses</kwd><kwd>Prevalence</kwd><kwd>Kenya</kwd><kwd>HCOV-NL63</kwd><kwd>HCoV-OC43</kwd><kwd>HCoV-229E</kwd><kwd>HCoV-HKU1</kwd></kwd-group><funding-group><award-group><funding-source><institution>Funding was provided by the US Armed Forces Health Surveillance Center Division of GEIS Operations</institution></funding-source></award-group></funding-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2016</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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