Molecular characterization of human coronaviruses and their circulation dynamics in Kenya, 2009–2012
Identifieur interne : 001462 ( Ncbi/Merge ); précédent : 001461; suivant : 001463Molecular 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.
Descripteurs français
- KwdFr :
- ARN viral, Coronavirus (), Coronavirus (génétique), Coronavirus (isolement et purification), Gènes pol, Histoire du 21ème siècle, Humains, Infections à coronavirus (histoire), Infections à coronavirus (virologie), Infections à coronavirus (épidémiologie), Kenya (épidémiologie), Phylogénie, Prévalence, Surveillance de la population.
- MESH :
- génétique : Coronavirus.
- histoire : Infections à coronavirus.
- isolement et purification : Coronavirus.
- virologie : Infections à coronavirus.
- épidémiologie : Infections à coronavirus, Kenya.
- ARN viral, Coronavirus, Gènes pol, Histoire du 21ème siècle, Humains, Phylogénie, Prévalence, Surveillance de la population.
English descriptors
- KwdEn :
- Coronavirus (classification), Coronavirus (genetics), Coronavirus (isolation & purification), Coronavirus Infections (epidemiology), Coronavirus Infections (history), Coronavirus Infections (virology), Genes, pol, History, 21st Century, Humans, Kenya (epidemiology), Phylogeny, Population Surveillance, Prevalence, RNA, Viral.
- MESH :
- chemical : RNA, Viral.
- classification : Coronavirus.
- epidemiology : Coronavirus Infections, Kenya.
- genetics : Coronavirus.
- history : Coronavirus Infections.
- isolation & purification : Coronavirus.
- virology : Coronavirus Infections.
- Genes, pol, History, 21st Century, Humans, Phylogeny, Population Surveillance, Prevalence.
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
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PMC:4736488Le document en format XML
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<term>Coronavirus (genetics)</term>
<term>Coronavirus (isolation & purification)</term>
<term>Coronavirus Infections (epidemiology)</term>
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<term>Histoire du 21ème siècle</term>
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<term>Infections à coronavirus (histoire)</term>
<term>Infections à coronavirus (virologie)</term>
<term>Infections à coronavirus (épidémiologie)</term>
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<term>Phylogénie</term>
<term>Prévalence</term>
<term>Surveillance de la population</term>
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</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Coronavirus</term>
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<keywords scheme="MESH" qualifier="histoire" xml:lang="fr"><term>Infections à coronavirus</term>
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<keywords scheme="MESH" qualifier="history" xml:lang="en"><term>Coronavirus Infections</term>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p id="Par1">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 id="Par2">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 id="Par3">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 id="Par4">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>
</div>
</front>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p id="Par1">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 id="Par2">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 id="Par3">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 id="Par4">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>
</div>
</front>
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<affiliation wicri:level="1"><nlm:affiliation>College of Health Sciences (COHES), Jomo Kenyatta University of Agriculture and Technology, (JKUAT), Nairobi, Kenya. lenata7@gmail.com.</nlm:affiliation>
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<affiliation wicri:level="1"><nlm:affiliation>College of Health Sciences (COHES), Jomo Kenyatta University of Agriculture and Technology, (JKUAT), Nairobi, Kenya. julietteongus@jkuat.ac.ke.</nlm:affiliation>
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<affiliation wicri:level="1"><nlm:affiliation>Department of Emerging Infectious Diseases, US Army Medical Research Unit-Kenya, P.O. Box 606 00621, Village Market, Nairobi, Kenya. Rodney.Coldren@usamru-k.org.</nlm:affiliation>
<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>
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<affiliation wicri:level="1"><nlm:affiliation>Department of Emerging Infectious Diseases, US Army Medical Research Unit-Kenya, P.O. Box 606 00621, Village Market, Nairobi, Kenya. Wallace.bulimo@uonbi.ac.ke.</nlm:affiliation>
<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>
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<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:affiliation>Department of Emerging Infectious Diseases, US Army Medical Research Unit-Kenya, P.O. Box 606 00621, Village Market, Nairobi, Kenya. Rodney.Coldren@usamru-k.org.</nlm:affiliation>
<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>
</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:affiliation>Department of Emerging Infectious Diseases, US Army Medical Research Unit-Kenya, P.O. Box 606 00621, Village Market, Nairobi, Kenya. Wallace.bulimo@uonbi.ac.ke.</nlm:affiliation>
<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>
</author>
</analytic>
<series><title level="j">Virology journal</title>
<idno type="eISSN">1743-422X</idno>
<imprint><date when="2016" type="published">2016</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Coronavirus (classification)</term>
<term>Coronavirus (genetics)</term>
<term>Coronavirus (isolation & purification)</term>
<term>Coronavirus Infections (epidemiology)</term>
<term>Coronavirus Infections (history)</term>
<term>Coronavirus Infections (virology)</term>
<term>Genes, pol</term>
<term>History, 21st Century</term>
<term>Humans</term>
<term>Kenya (epidemiology)</term>
<term>Phylogeny</term>
<term>Population Surveillance</term>
<term>Prevalence</term>
<term>RNA, Viral</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ARN viral</term>
<term>Coronavirus ()</term>
<term>Coronavirus (génétique)</term>
<term>Coronavirus (isolement et purification)</term>
<term>Gènes pol</term>
<term>Histoire du 21ème siècle</term>
<term>Humains</term>
<term>Infections à coronavirus (histoire)</term>
<term>Infections à coronavirus (virologie)</term>
<term>Infections à coronavirus (épidémiologie)</term>
<term>Kenya (épidémiologie)</term>
<term>Phylogénie</term>
<term>Prévalence</term>
<term>Surveillance de la population</term>
</keywords>
<keywords scheme="MESH" type="chemical" xml:lang="en"><term>RNA, Viral</term>
</keywords>
<keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Coronavirus</term>
</keywords>
<keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Coronavirus Infections</term>
<term>Kenya</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coronavirus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Coronavirus</term>
</keywords>
<keywords scheme="MESH" qualifier="histoire" xml:lang="fr"><term>Infections à coronavirus</term>
</keywords>
<keywords scheme="MESH" qualifier="history" xml:lang="en"><term>Coronavirus Infections</term>
</keywords>
<keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Coronavirus</term>
</keywords>
<keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Coronavirus</term>
</keywords>
<keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Infections à coronavirus</term>
</keywords>
<keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Coronavirus Infections</term>
</keywords>
<keywords scheme="MESH" qualifier="épidémiologie" xml:lang="fr"><term>Infections à coronavirus</term>
<term>Kenya</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Genes, pol</term>
<term>History, 21st Century</term>
<term>Humans</term>
<term>Phylogeny</term>
<term>Population Surveillance</term>
<term>Prevalence</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>ARN viral</term>
<term>Coronavirus</term>
<term>Gènes pol</term>
<term>Histoire du 21ème siècle</term>
<term>Humains</term>
<term>Phylogénie</term>
<term>Prévalence</term>
<term>Surveillance de la population</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">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.</div>
</front>
</TEI>
</pubmed>
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