Prevalence and genetic diversity analysis of human coronaviruses among cross-border children
Identifieur interne : 000C29 ( Main/Exploration ); précédent : 000C28; suivant : 000C30Prevalence and genetic diversity analysis of human coronaviruses among cross-border children
Auteurs : Peilin Liu [République populaire de Chine] ; Lei Shi [République populaire de Chine] ; Wei Zhang [République populaire de Chine] ; Jianan He [République populaire de Chine] ; Chunxiao Liu [République populaire de Chine] ; Chunzhong Zhao [République populaire de Chine] ; Siu Kai Kong ; Jacky Fong Chuen Loo ; Dayong Gu [République populaire de Chine] ; Longfei Hu [République populaire de Chine]Source :
- Virology Journal [ 1743-422X ] ; 2017.
Descripteurs français
- KwdFr :
- Chine (épidémiologie), Coronavirus (), Coronavirus (génétique), Dépistage génétique, Enfant, Enfant d'âge préscolaire, Femelle, Hong Kong (épidémiologie), Humains, Infections de l'appareil respiratoire (virologie), Infections à coronavirus (virologie), Infections à coronavirus (épidémiologie), Mutation, Mâle, Nourrisson, Nouveau-né, Phylogénie, Prévalence, Saisons, Séquence nucléotidique, Variation génétique, Épidémiologie moléculaire, Épidémiosurveillance.
- MESH :
- génétique : Coronavirus.
- virologie : Infections de l'appareil respiratoire, Infections à coronavirus.
- épidémiologie : Chine, Hong Kong, Infections à coronavirus.
- Coronavirus, Dépistage génétique, Enfant, Enfant d'âge préscolaire, Femelle, Humains, Mutation, Mâle, Nourrisson, Nouveau-né, Phylogénie, Prévalence, Saisons, Séquence nucléotidique, Variation génétique, Épidémiologie moléculaire, Épidémiosurveillance.
English descriptors
- KwdEn :
- Base Sequence, Child, Child, Preschool, China (epidemiology), Coronavirus (classification), Coronavirus (genetics), Coronavirus Infections (epidemiology), Coronavirus Infections (virology), Epidemiological Monitoring, Female, Genetic Testing, Genetic Variation, Hong Kong (epidemiology), Humans, Infant, Infant, Newborn, Male, Molecular Epidemiology, Mutation, Phylogeny, Prevalence, Respiratory Tract Infections (virology), Seasons.
- MESH :
- classification : Coronavirus.
- epidemiology : China, Coronavirus Infections, Hong Kong.
- genetics : Coronavirus.
- virology : Coronavirus Infections, Respiratory Tract Infections.
- Base Sequence, Child, Child, Preschool, Epidemiological Monitoring, Female, Genetic Testing, Genetic Variation, Humans, Infant, Infant, Newborn, Male, Molecular Epidemiology, Mutation, Phylogeny, Prevalence, Seasons.
Abstract
More than a decade after the outbreak of human coronaviruses (HCoVs) SARS in Guangdong province and Hong Kong SAR of China in 2002, there is still no reoccurrence, but the evolution and recombination of the coronaviruses in this region are still unknown. Therefore, surveillance on the prevalence and the virus variation of HCoVs circulation in this region is conducted.
A total of 3298 nasopharyngeal swabs samples were collected from cross-border children (<6 years, crossing border between Southern China and Hong Kong SAR) showing symptoms of respiratory tract infection, such as fever (body temperature > 37.5 °C), from 2014 May to 2015 Dec. Viral nucleic acids were analyzed and sequenced to study the prevalence and genetic diversity of the four human coronaviruses. The statistical significance of the data was evaluated with Fisher chi-square test.
78 (2.37%; 95%CI 1.8-2.8%) out of 3298 nasopharyngeal swabs specimens were found to be positive for OC43 (36;1.09%), HKU1 (34; 1.03%), NL63 (6; 0.18%) and 229E (2;0.01%). None of SARS or MERS was detected. The HCoVs predominant circulating season was in transition of winter to spring, especially January and February and NL63 detected only in summer and fall. Complex population with an abundant genetic diversity of coronaviruses was circulating and they shared homology with the published strains (99-100%). Besides, phylogenetic evolutionary analysis indicated that OC43 coronaviruses were clustered into three clades (B,D,E), HKU1 clustered into two clades(A,B) and NL63 clustered into two clades(A,B). Moreover, several novel mutations including nucleotides substitution and the insertion of spike of the glycoprotein on the viral surface were discovered.
The detection rate and epidemic trend of coronaviruses were stable and no obvious fluctuations were found. The detected coronaviruses shared a conserved gene sequences in S and RdRp. However, mutants of the epidemic strains were detected, suggesting continuous monitoring of the human coronaviruses is in need among cross-border children, who are more likely to get infected and transmit the viruses across the border easily, in addition to the general public.
Url:
DOI: 10.1186/s12985-017-0896-0
PubMed: 29166910
PubMed Central: 5700739
Affiliations:
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Le document en format XML
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Shenzhen, 518010 People’s Republic of China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Shenzhen</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="GRID">grid.488141.0</institution-id>
<institution>Central Laboratory of Health quarantine, Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Entry-exit Inspection and Quarantine Bureau,</institution>
</institution-wrap>
Shenzhen, 518033 People’s Republic of China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Shenzhen</wicri:regionArea>
</affiliation>
</author>
</analytic>
<series><title level="j">Virology Journal</title>
<idno type="eISSN">1743-422X</idno>
<imprint><date when="2017">2017</date>
</imprint>
</series>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term>
<term>Child</term>
<term>Child, Preschool</term>
<term>China (epidemiology)</term>
<term>Coronavirus (classification)</term>
<term>Coronavirus (genetics)</term>
<term>Coronavirus Infections (epidemiology)</term>
<term>Coronavirus Infections (virology)</term>
<term>Epidemiological Monitoring</term>
<term>Female</term>
<term>Genetic Testing</term>
<term>Genetic Variation</term>
<term>Hong Kong (epidemiology)</term>
<term>Humans</term>
<term>Infant</term>
<term>Infant, Newborn</term>
<term>Male</term>
<term>Molecular Epidemiology</term>
<term>Mutation</term>
<term>Phylogeny</term>
<term>Prevalence</term>
<term>Respiratory Tract Infections (virology)</term>
<term>Seasons</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Chine (épidémiologie)</term>
<term>Coronavirus ()</term>
<term>Coronavirus (génétique)</term>
<term>Dépistage génétique</term>
<term>Enfant</term>
<term>Enfant d'âge préscolaire</term>
<term>Femelle</term>
<term>Hong Kong (épidémiologie)</term>
<term>Humains</term>
<term>Infections de l'appareil respiratoire (virologie)</term>
<term>Infections à coronavirus (virologie)</term>
<term>Infections à coronavirus (épidémiologie)</term>
<term>Mutation</term>
<term>Mâle</term>
<term>Nourrisson</term>
<term>Nouveau-né</term>
<term>Phylogénie</term>
<term>Prévalence</term>
<term>Saisons</term>
<term>Séquence nucléotidique</term>
<term>Variation génétique</term>
<term>Épidémiologie moléculaire</term>
<term>Épidémiosurveillance</term>
</keywords>
<keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Coronavirus</term>
</keywords>
<keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>China</term>
<term>Coronavirus Infections</term>
<term>Hong Kong</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="virologie" xml:lang="fr"><term>Infections de l'appareil respiratoire</term>
<term>Infections à coronavirus</term>
</keywords>
<keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Coronavirus Infections</term>
<term>Respiratory Tract Infections</term>
</keywords>
<keywords scheme="MESH" qualifier="épidémiologie" xml:lang="fr"><term>Chine</term>
<term>Hong Kong</term>
<term>Infections à coronavirus</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term>
<term>Child</term>
<term>Child, Preschool</term>
<term>Epidemiological Monitoring</term>
<term>Female</term>
<term>Genetic Testing</term>
<term>Genetic Variation</term>
<term>Humans</term>
<term>Infant</term>
<term>Infant, Newborn</term>
<term>Male</term>
<term>Molecular Epidemiology</term>
<term>Mutation</term>
<term>Phylogeny</term>
<term>Prevalence</term>
<term>Seasons</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Coronavirus</term>
<term>Dépistage génétique</term>
<term>Enfant</term>
<term>Enfant d'âge préscolaire</term>
<term>Femelle</term>
<term>Humains</term>
<term>Mutation</term>
<term>Mâle</term>
<term>Nourrisson</term>
<term>Nouveau-né</term>
<term>Phylogénie</term>
<term>Prévalence</term>
<term>Saisons</term>
<term>Séquence nucléotidique</term>
<term>Variation génétique</term>
<term>Épidémiologie moléculaire</term>
<term>Épidémiosurveillance</term>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p id="Par1">More than a decade after the outbreak of human coronaviruses (HCoVs) SARS in Guangdong province and Hong Kong SAR of China in 2002, there is still no reoccurrence, but the evolution and recombination of the coronaviruses in this region are still unknown. Therefore, surveillance on the prevalence and the virus variation of HCoVs circulation in this region is conducted.</p>
</sec>
<sec><title>Methods</title>
<p id="Par2">A total of 3298 nasopharyngeal swabs samples were collected from cross-border children (<6 years, crossing border between Southern China and Hong Kong SAR) showing symptoms of respiratory tract infection, such as fever (body temperature > 37.5 °C), from 2014 May to 2015 Dec. Viral nucleic acids were analyzed and sequenced to study the prevalence and genetic diversity of the four human coronaviruses. The statistical significance of the data was evaluated with Fisher chi-square test.</p>
</sec>
<sec><title>Results</title>
<p id="Par3">78 (2.37%; 95%CI 1.8-2.8%) out of 3298 nasopharyngeal swabs specimens were found to be positive for OC43 (36;1.09%), HKU1 (34; 1.03%), NL63 (6; 0.18%) and 229E (2;0.01%). None of SARS or MERS was detected. The HCoVs predominant circulating season was in transition of winter to spring, especially January and February and NL63 detected only in summer and fall. Complex population with an abundant genetic diversity of coronaviruses was circulating and they shared homology with the published strains (99-100%). Besides, phylogenetic evolutionary analysis indicated that OC43 coronaviruses were clustered into three clades (B,D,E), HKU1 clustered into two clades(A,B) and NL63 clustered into two clades(A,B). Moreover, several novel mutations including nucleotides substitution and the insertion of spike of the glycoprotein on the viral surface were discovered.</p>
</sec>
<sec><title>Conclusions</title>
<p id="Par4">The detection rate and epidemic trend of coronaviruses were stable and no obvious fluctuations were found. The detected coronaviruses shared a conserved gene sequences in S and RdRp. However, mutants of the epidemic strains were detected, suggesting continuous monitoring of the human coronaviruses is in need among cross-border children, who are more likely to get infected and transmit the viruses across the border easily, in addition to the general public.</p>
</sec>
</div>
</front>
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<affiliations><list><country><li>République populaire de Chine</li>
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<tree><noCountry><name sortKey="Kong, Siu Kai" sort="Kong, Siu Kai" uniqKey="Kong S" first="Siu Kai" last="Kong">Siu Kai Kong</name>
<name sortKey="Loo, Jacky Fong Chuen" sort="Loo, Jacky Fong Chuen" uniqKey="Loo J" first="Jacky Fong Chuen" last="Loo">Jacky Fong Chuen Loo</name>
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<country name="République populaire de Chine"><noRegion><name sortKey="Liu, Peilin" sort="Liu, Peilin" uniqKey="Liu P" first="Peilin" last="Liu">Peilin Liu</name>
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