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Evidence for an Ancestral Association of Human Coronavirus 229E with Bats

Identifieur interne : 002E37 ( Main/Exploration ); précédent : 002E36; suivant : 002E38

Evidence for an Ancestral Association of Human Coronavirus 229E with Bats

Auteurs : Victor Max Corman [Allemagne] ; Heather J. Baldwin [Allemagne, Australie] ; Adriana Fumie Tateno [Allemagne, Brésil] ; Rodrigo Melim Zerbinati [Allemagne, Brésil] ; Augustina Annan [Ghana] ; Michael Owusu [Ghana] ; Evans Ewald Nkrumah [Ghana] ; Gael Darren Maganga [Gabon] ; Samuel Oppong [Ghana] ; Yaw Adu-Sarkodie [Ghana] ; Peter Vallo [Allemagne, République tchèque] ; Luiz Vicente Ribeiro Ferreira Da Silva Filho [Brésil] ; Eric M. Leroy [Gabon, France] ; Volker Thiel [Suisse] ; Lia Van Der Hoek [Pays-Bas] ; Leo L. M. Poon [République populaire de Chine] ; Marco Tschapka [Allemagne, Panama] ; Christian Drosten [Allemagne] ; Jan Felix Drexler [Allemagne]

Source :

RBID : PMC:4645311

Descripteurs français

English descriptors

Abstract

ABSTRACT

We previously showed that close relatives of human coronavirus 229E (HCoV-229E) exist in African bats. The small sample and limited genomic characterizations have prevented further analyses so far. Here, we tested 2,087 fecal specimens from 11 bat species sampled in Ghana for HCoV-229E-related viruses by reverse transcription-PCR (RT-PCR). Only hipposiderid bats tested positive. To compare the genetic diversity of bat viruses and HCoV-229E, we tested historical isolates and diagnostic specimens sampled globally over 10 years. Bat viruses were 5- and 6-fold more diversified than HCoV-229E in the RNA-dependent RNA polymerase (RdRp) and spike genes. In phylogenetic analyses, HCoV-229E strains were monophyletic and not intermixed with animal viruses. Bat viruses formed three large clades in close and more distant sister relationships. A recently described 229E-related alpaca virus occupied an intermediate phylogenetic position between bat and human viruses. According to taxonomic criteria, human, alpaca, and bat viruses form a single CoV species showing evidence for multiple recombination events. HCoV-229E and the alpaca virus showed a major deletion in the spike S1 region compared to all bat viruses. Analyses of four full genomes from 229E-related bat CoVs revealed an eighth open reading frame (ORF8) located at the genomic 3′ end. ORF8 also existed in the 229E-related alpaca virus. Reanalysis of HCoV-229E sequences showed a conserved transcription regulatory sequence preceding remnants of this ORF, suggesting its loss after acquisition of a 229E-related CoV by humans. These data suggested an evolutionary origin of 229E-related CoVs in hipposiderid bats, hypothetically with camelids as intermediate hosts preceding the establishment of HCoV-229E.

IMPORTANCE The ancestral origins of major human coronaviruses (HCoVs) likely involve bat hosts. Here, we provide conclusive genetic evidence for an evolutionary origin of the common cold virus HCoV-229E in hipposiderid bats by analyzing a large sample of African bats and characterizing several bat viruses on a full-genome level. Our evolutionary analyses show that animal and human viruses are genetically closely related, can exchange genetic material, and form a single viral species. We show that the putative host switches leading to the formation of HCoV-229E were accompanied by major genomic changes, including deletions in the viral spike glycoprotein gene and loss of an open reading frame. We reanalyze a previously described genetically related alpaca virus and discuss the role of camelids as potential intermediate hosts between bat and human viruses. The evolutionary history of HCoV-229E likely shares important characteristics with that of the recently emerged highly pathogenic Middle East respiratory syndrome (MERS) coronavirus.


Url:
DOI: 10.1128/JVI.01755-15
PubMed: 26378164
PubMed Central: 4645311


Affiliations:


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<nlm:aff id="aff1">Institute of Virology, University of Bonn Medical Centre, Bonn, Germany</nlm:aff>
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<wicri:regionArea>Institute of Virology, University of Bonn Medical Centre, Bonn</wicri:regionArea>
<placeName>
<region type="land" nuts="1">Rhénanie-du-Nord-Westphalie</region>
<region type="district" nuts="2">District de Cologne</region>
<settlement type="city">Bonn</settlement>
</placeName>
</affiliation>
<affiliation wicri:level="3">
<nlm:aff id="aff2">German Centre for Infection Research, (DZIF), Partner Site Bonn-Cologne, Bonn, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>German Centre for Infection Research, (DZIF), Partner Site Bonn-Cologne, Bonn</wicri:regionArea>
<placeName>
<region type="land" nuts="1">Rhénanie-du-Nord-Westphalie</region>
<region type="district" nuts="2">District de Cologne</region>
<settlement type="city">Bonn</settlement>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Baldwin, Heather J" sort="Baldwin, Heather J" uniqKey="Baldwin H" first="Heather J." last="Baldwin">Heather J. Baldwin</name>
<affiliation wicri:level="4">
<nlm:aff id="aff3">Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm</wicri:regionArea>
<placeName>
<region type="land" nuts="1">Bade-Wurtemberg</region>
<region type="district" nuts="2">District de Tübingen</region>
<settlement type="city">Ulm</settlement>
<settlement type="city">Ulm</settlement>
</placeName>
<orgName type="university">Université d'Ulm</orgName>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff4">Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Department of Biological Sciences, Macquarie University, Sydney, New South Wales</wicri:regionArea>
<wicri:noRegion>New South Wales</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Tateno, Adriana Fumie" sort="Tateno, Adriana Fumie" uniqKey="Tateno A" first="Adriana Fumie" last="Tateno">Adriana Fumie Tateno</name>
<affiliation wicri:level="3">
<nlm:aff id="aff1">Institute of Virology, University of Bonn Medical Centre, Bonn, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Institute of Virology, University of Bonn Medical Centre, Bonn</wicri:regionArea>
<placeName>
<region type="land" nuts="1">Rhénanie-du-Nord-Westphalie</region>
<region type="district" nuts="2">District de Cologne</region>
<settlement type="city">Bonn</settlement>
</placeName>
</affiliation>
<affiliation wicri:level="4">
<nlm:aff id="aff5">Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, Brazil</nlm:aff>
<country xml:lang="fr">Brésil</country>
<wicri:regionArea>Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo</wicri:regionArea>
<placeName>
<settlement type="city">São Paulo</settlement>
<region type="state">État de São Paulo</region>
<settlement type="city">São Paulo</settlement>
</placeName>
<orgName type="university">Université de São Paulo</orgName>
</affiliation>
</author>
<author>
<name sortKey="Zerbinati, Rodrigo Melim" sort="Zerbinati, Rodrigo Melim" uniqKey="Zerbinati R" first="Rodrigo Melim" last="Zerbinati">Rodrigo Melim Zerbinati</name>
<affiliation wicri:level="3">
<nlm:aff id="aff1">Institute of Virology, University of Bonn Medical Centre, Bonn, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Institute of Virology, University of Bonn Medical Centre, Bonn</wicri:regionArea>
<placeName>
<region type="land" nuts="1">Rhénanie-du-Nord-Westphalie</region>
<region type="district" nuts="2">District de Cologne</region>
<settlement type="city">Bonn</settlement>
</placeName>
</affiliation>
<affiliation wicri:level="4">
<nlm:aff id="aff5">Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, Brazil</nlm:aff>
<country xml:lang="fr">Brésil</country>
<wicri:regionArea>Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo</wicri:regionArea>
<placeName>
<settlement type="city">São Paulo</settlement>
<region type="state">État de São Paulo</region>
<settlement type="city">São Paulo</settlement>
</placeName>
<orgName type="university">Université de São Paulo</orgName>
</affiliation>
</author>
<author>
<name sortKey="Annan, Augustina" sort="Annan, Augustina" uniqKey="Annan A" first="Augustina" last="Annan">Augustina Annan</name>
<affiliation wicri:level="1">
<nlm:aff id="aff6">Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana</nlm:aff>
<country xml:lang="fr">Ghana</country>
<wicri:regionArea>Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi</wicri:regionArea>
<wicri:noRegion>Kumasi</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Owusu, Michael" sort="Owusu, Michael" uniqKey="Owusu M" first="Michael" last="Owusu">Michael Owusu</name>
<affiliation wicri:level="1">
<nlm:aff id="aff6">Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana</nlm:aff>
<country xml:lang="fr">Ghana</country>
<wicri:regionArea>Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi</wicri:regionArea>
<wicri:noRegion>Kumasi</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Nkrumah, Evans Ewald" sort="Nkrumah, Evans Ewald" uniqKey="Nkrumah E" first="Evans Ewald" last="Nkrumah">Evans Ewald Nkrumah</name>
<affiliation wicri:level="1">
<nlm:aff id="aff6">Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana</nlm:aff>
<country xml:lang="fr">Ghana</country>
<wicri:regionArea>Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi</wicri:regionArea>
<wicri:noRegion>Kumasi</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Maganga, Gael Darren" sort="Maganga, Gael Darren" uniqKey="Maganga G" first="Gael Darren" last="Maganga">Gael Darren Maganga</name>
<affiliation wicri:level="1">
<nlm:aff id="aff7">Centre International de Recherches Médicales de Franceville, Franceville, Gabon</nlm:aff>
<country xml:lang="fr">Gabon</country>
<wicri:regionArea>Centre International de Recherches Médicales de Franceville, Franceville</wicri:regionArea>
<wicri:noRegion>Franceville</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Oppong, Samuel" sort="Oppong, Samuel" uniqKey="Oppong S" first="Samuel" last="Oppong">Samuel Oppong</name>
<affiliation wicri:level="1">
<nlm:aff id="aff8">Kwame Nkrumah University of Science and Technology, Kumasi, Ghana</nlm:aff>
<country xml:lang="fr">Ghana</country>
<wicri:regionArea>Kwame Nkrumah University of Science and Technology, Kumasi</wicri:regionArea>
<wicri:noRegion>Kumasi</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Adu Sarkodie, Yaw" sort="Adu Sarkodie, Yaw" uniqKey="Adu Sarkodie Y" first="Yaw" last="Adu-Sarkodie">Yaw Adu-Sarkodie</name>
<affiliation wicri:level="1">
<nlm:aff id="aff8">Kwame Nkrumah University of Science and Technology, Kumasi, Ghana</nlm:aff>
<country xml:lang="fr">Ghana</country>
<wicri:regionArea>Kwame Nkrumah University of Science and Technology, Kumasi</wicri:regionArea>
<wicri:noRegion>Kumasi</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Vallo, Peter" sort="Vallo, Peter" uniqKey="Vallo P" first="Peter" last="Vallo">Peter Vallo</name>
<affiliation wicri:level="4">
<nlm:aff id="aff3">Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm</wicri:regionArea>
<placeName>
<region type="land" nuts="1">Bade-Wurtemberg</region>
<region type="district" nuts="2">District de Tübingen</region>
<settlement type="city">Ulm</settlement>
<settlement type="city">Ulm</settlement>
</placeName>
<orgName type="university">Université d'Ulm</orgName>
</affiliation>
<affiliation wicri:level="3">
<nlm:aff id="aff9">Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic</nlm:aff>
<country xml:lang="fr">République tchèque</country>
<wicri:regionArea>Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno</wicri:regionArea>
<placeName>
<settlement type="city">Brno</settlement>
<region>Moravie</region>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Da Silva Filho, Luiz Vicente Ribeiro Ferreira" sort="Da Silva Filho, Luiz Vicente Ribeiro Ferreira" uniqKey="Da Silva Filho L" first="Luiz Vicente Ribeiro Ferreira" last="Da Silva Filho">Luiz Vicente Ribeiro Ferreira Da Silva Filho</name>
<affiliation wicri:level="4">
<nlm:aff id="aff5">Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, Brazil</nlm:aff>
<country xml:lang="fr">Brésil</country>
<wicri:regionArea>Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo</wicri:regionArea>
<placeName>
<settlement type="city">São Paulo</settlement>
<region type="state">État de São Paulo</region>
<settlement type="city">São Paulo</settlement>
</placeName>
<orgName type="university">Université de São Paulo</orgName>
</affiliation>
<affiliation wicri:level="3">
<nlm:aff id="aff10">Instituto da Criança, Hospital das Clínicas da FMUSP, São Paulo, Brazil</nlm:aff>
<country xml:lang="fr">Brésil</country>
<wicri:regionArea>Instituto da Criança, Hospital das Clínicas da FMUSP, São Paulo</wicri:regionArea>
<placeName>
<settlement type="city">São Paulo</settlement>
<region type="state">État de São Paulo</region>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Leroy, Eric M" sort="Leroy, Eric M" uniqKey="Leroy E" first="Eric M." last="Leroy">Eric M. Leroy</name>
<affiliation wicri:level="1">
<nlm:aff id="aff7">Centre International de Recherches Médicales de Franceville, Franceville, Gabon</nlm:aff>
<country xml:lang="fr">Gabon</country>
<wicri:regionArea>Centre International de Recherches Médicales de Franceville, Franceville</wicri:regionArea>
<wicri:noRegion>Franceville</wicri:noRegion>
</affiliation>
<affiliation wicri:level="3">
<nlm:aff id="aff11">Institut de Recherche pour le Développement, UMR 224 (MIVEGEC), IRD/CNRS/UM1, Montpellier, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Institut de Recherche pour le Développement, UMR 224 (MIVEGEC), IRD/CNRS/UM1, Montpellier</wicri:regionArea>
<placeName>
<region type="region">Occitanie (région administrative)</region>
<region type="old region">Languedoc-Roussillon</region>
<settlement type="city">Montpellier</settlement>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Thiel, Volker" sort="Thiel, Volker" uniqKey="Thiel V" first="Volker" last="Thiel">Volker Thiel</name>
<affiliation wicri:level="4">
<nlm:aff id="aff12">Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty Bern, University of Bern, Bern, Switzerland</nlm:aff>
<country xml:lang="fr">Suisse</country>
<wicri:regionArea>Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty Bern, University of Bern, Bern</wicri:regionArea>
<placeName>
<settlement type="city">Berne</settlement>
<region type="région" nuts="3">Canton de Berne</region>
<settlement type="city">Berne</settlement>
</placeName>
<orgName type="university">Université de Berne</orgName>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff13">Federal Department of Home Affairs, Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland</nlm:aff>
<country xml:lang="fr">Suisse</country>
<wicri:regionArea>Federal Department of Home Affairs, Institute of Virology and Immunology, Bern and Mittelhäusern</wicri:regionArea>
<wicri:noRegion>Bern and Mittelhäusern</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Van Der Hoek, Lia" sort="Van Der Hoek, Lia" uniqKey="Van Der Hoek L" first="Lia" last="Van Der Hoek">Lia Van Der Hoek</name>
<affiliation wicri:level="4">
<nlm:aff id="aff14">Department of Medical Microbiology, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>Department of Medical Microbiology, Academic Medical Center of the University of Amsterdam, Amsterdam</wicri:regionArea>
<placeName>
<settlement type="city">Amsterdam</settlement>
<region nuts="2" type="province">Hollande-Septentrionale</region>
<settlement type="city">Amsterdam</settlement>
</placeName>
<orgName type="university">Université d'Amsterdam</orgName>
</affiliation>
</author>
<author>
<name sortKey="Poon, Leo L M" sort="Poon, Leo L M" uniqKey="Poon L" first="Leo L. M." last="Poon">Leo L. M. Poon</name>
<affiliation wicri:level="1">
<nlm:aff id="aff15">School of Public Health, The University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>School of Public Health, The University of Hong Kong, Hong Kong, Special Administrative Region</wicri:regionArea>
<wicri:noRegion>Special Administrative Region</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Tschapka, Marco" sort="Tschapka, Marco" uniqKey="Tschapka M" first="Marco" last="Tschapka">Marco Tschapka</name>
<affiliation wicri:level="4">
<nlm:aff id="aff3">Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm</wicri:regionArea>
<placeName>
<region type="land" nuts="1">Bade-Wurtemberg</region>
<region type="district" nuts="2">District de Tübingen</region>
<settlement type="city">Ulm</settlement>
<settlement type="city">Ulm</settlement>
</placeName>
<orgName type="university">Université d'Ulm</orgName>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff16">Smithsonian Tropical Research Institute, Balboa, Panama</nlm:aff>
<country xml:lang="fr">Panama</country>
<wicri:regionArea>Smithsonian Tropical Research Institute, Balboa</wicri:regionArea>
<wicri:noRegion>Balboa</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Drosten, Christian" sort="Drosten, Christian" uniqKey="Drosten C" first="Christian" last="Drosten">Christian Drosten</name>
<affiliation wicri:level="3">
<nlm:aff id="aff1">Institute of Virology, University of Bonn Medical Centre, Bonn, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Institute of Virology, University of Bonn Medical Centre, Bonn</wicri:regionArea>
<placeName>
<region type="land" nuts="1">Rhénanie-du-Nord-Westphalie</region>
<region type="district" nuts="2">District de Cologne</region>
<settlement type="city">Bonn</settlement>
</placeName>
</affiliation>
<affiliation wicri:level="3">
<nlm:aff id="aff2">German Centre for Infection Research, (DZIF), Partner Site Bonn-Cologne, Bonn, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>German Centre for Infection Research, (DZIF), Partner Site Bonn-Cologne, Bonn</wicri:regionArea>
<placeName>
<region type="land" nuts="1">Rhénanie-du-Nord-Westphalie</region>
<region type="district" nuts="2">District de Cologne</region>
<settlement type="city">Bonn</settlement>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Drexler, Jan Felix" sort="Drexler, Jan Felix" uniqKey="Drexler J" first="Jan Felix" last="Drexler">Jan Felix Drexler</name>
<affiliation wicri:level="3">
<nlm:aff id="aff1">Institute of Virology, University of Bonn Medical Centre, Bonn, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Institute of Virology, University of Bonn Medical Centre, Bonn</wicri:regionArea>
<placeName>
<region type="land" nuts="1">Rhénanie-du-Nord-Westphalie</region>
<region type="district" nuts="2">District de Cologne</region>
<settlement type="city">Bonn</settlement>
</placeName>
</affiliation>
<affiliation wicri:level="3">
<nlm:aff id="aff2">German Centre for Infection Research, (DZIF), Partner Site Bonn-Cologne, Bonn, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>German Centre for Infection Research, (DZIF), Partner Site Bonn-Cologne, Bonn</wicri:regionArea>
<placeName>
<region type="land" nuts="1">Rhénanie-du-Nord-Westphalie</region>
<region type="district" nuts="2">District de Cologne</region>
<settlement type="city">Bonn</settlement>
</placeName>
</affiliation>
</author>
</analytic>
<series>
<title level="j">Journal of Virology</title>
<idno type="ISSN">0022-538X</idno>
<idno type="eISSN">1098-5514</idno>
<imprint>
<date when="2015">2015</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc>
<textClass>
<keywords scheme="KwdEn" xml:lang="en">
<term>Animals</term>
<term>Base Sequence</term>
<term>Bayes Theorem</term>
<term>Biological Evolution</term>
<term>Camelids, New World (virology)</term>
<term>Chiroptera (virology)</term>
<term>Coronavirus 229E, Human (genetics)</term>
<term>DNA Primers (genetics)</term>
<term>Feces (virology)</term>
<term>Genetic Variation</term>
<term>Ghana</term>
<term>Humans</term>
<term>Models, Genetic</term>
<term>Molecular Sequence Data</term>
<term>Phylogeny</term>
<term>RNA Replicase (genetics)</term>
<term>Reverse Transcriptase Polymerase Chain Reaction</term>
<term>Sequence Analysis, DNA</term>
<term>Spike Glycoprotein, Coronavirus (genetics)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr">
<term>Amorces ADN (génétique)</term>
<term>Analyse de séquence d'ADN</term>
<term>Animaux</term>
<term>Camélidés du Nouveau Monde (virologie)</term>
<term>Chiroptera (virologie)</term>
<term>Coronavirus humain 229E (génétique)</term>
<term>Données de séquences moléculaires</term>
<term>Fèces (virologie)</term>
<term>Ghana</term>
<term>Glycoprotéine de spicule des coronavirus (génétique)</term>
<term>Humains</term>
<term>Modèles génétiques</term>
<term>Phylogénie</term>
<term>RNA replicase (génétique)</term>
<term>RT-PCR</term>
<term>Séquence nucléotidique</term>
<term>Théorème de Bayes</term>
<term>Variation génétique</term>
<term>Évolution biologique</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en">
<term>DNA Primers</term>
<term>RNA Replicase</term>
<term>Spike Glycoprotein, Coronavirus</term>
</keywords>
<keywords scheme="MESH" type="geographic" xml:lang="en">
<term>Ghana</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en">
<term>Coronavirus 229E, Human</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr">
<term>Amorces ADN</term>
<term>Coronavirus humain 229E</term>
<term>Glycoprotéine de spicule des coronavirus</term>
<term>RNA replicase</term>
</keywords>
<keywords scheme="MESH" qualifier="virologie" xml:lang="fr">
<term>Camélidés du Nouveau Monde</term>
<term>Chiroptera</term>
<term>Fèces</term>
</keywords>
<keywords scheme="MESH" qualifier="virology" xml:lang="en">
<term>Camelids, New World</term>
<term>Chiroptera</term>
<term>Feces</term>
</keywords>
<keywords scheme="MESH" xml:lang="en">
<term>Animals</term>
<term>Base Sequence</term>
<term>Bayes Theorem</term>
<term>Biological Evolution</term>
<term>Genetic Variation</term>
<term>Humans</term>
<term>Models, Genetic</term>
<term>Molecular Sequence Data</term>
<term>Phylogeny</term>
<term>Reverse Transcriptase Polymerase Chain Reaction</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr">
<term>Analyse de séquence d'ADN</term>
<term>Animaux</term>
<term>Données de séquences moléculaires</term>
<term>Ghana</term>
<term>Humains</term>
<term>Modèles génétiques</term>
<term>Phylogénie</term>
<term>RT-PCR</term>
<term>Séquence nucléotidique</term>
<term>Théorème de Bayes</term>
<term>Variation génétique</term>
<term>Évolution biologique</term>
</keywords>
<keywords scheme="Wicri" type="geographic" xml:lang="fr">
<term>Ghana</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front>
<div type="abstract" xml:lang="en">
<title>ABSTRACT</title>
<p>We previously showed that close relatives of human coronavirus 229E (HCoV-229E) exist in African bats. The small sample and limited genomic characterizations have prevented further analyses so far. Here, we tested 2,087 fecal specimens from 11 bat species sampled in Ghana for HCoV-229E-related viruses by reverse transcription-PCR (RT-PCR). Only hipposiderid bats tested positive. To compare the genetic diversity of bat viruses and HCoV-229E, we tested historical isolates and diagnostic specimens sampled globally over 10 years. Bat viruses were 5- and 6-fold more diversified than HCoV-229E in the
<italic>RNA-dependent RNA polymerase</italic>
(
<italic>RdRp</italic>
) and
<italic>spike</italic>
genes. In phylogenetic analyses, HCoV-229E strains were monophyletic and not intermixed with animal viruses. Bat viruses formed three large clades in close and more distant sister relationships. A recently described 229E-related alpaca virus occupied an intermediate phylogenetic position between bat and human viruses. According to taxonomic criteria, human, alpaca, and bat viruses form a single CoV species showing evidence for multiple recombination events. HCoV-229E and the alpaca virus showed a major deletion in the spike S1 region compared to all bat viruses. Analyses of four full genomes from 229E-related bat CoVs revealed an eighth open reading frame (ORF8) located at the genomic 3′ end. ORF8 also existed in the 229E-related alpaca virus. Reanalysis of HCoV-229E sequences showed a conserved transcription regulatory sequence preceding remnants of this ORF, suggesting its loss after acquisition of a 229E-related CoV by humans. These data suggested an evolutionary origin of 229E-related CoVs in hipposiderid bats, hypothetically with camelids as intermediate hosts preceding the establishment of HCoV-229E.</p>
<p>
<bold>IMPORTANCE</bold>
The ancestral origins of major human coronaviruses (HCoVs) likely involve bat hosts. Here, we provide conclusive genetic evidence for an evolutionary origin of the common cold virus HCoV-229E in hipposiderid bats by analyzing a large sample of African bats and characterizing several bat viruses on a full-genome level. Our evolutionary analyses show that animal and human viruses are genetically closely related, can exchange genetic material, and form a single viral species. We show that the putative host switches leading to the formation of HCoV-229E were accompanied by major genomic changes, including deletions in the viral spike glycoprotein gene and loss of an open reading frame. We reanalyze a previously described genetically related alpaca virus and discuss the role of camelids as potential intermediate hosts between bat and human viruses. The evolutionary history of HCoV-229E likely shares important characteristics with that of the recently emerged highly pathogenic Middle East respiratory syndrome (MERS) coronavirus.</p>
</div>
</front>
</TEI>
<affiliations>
<list>
<country>
<li>Allemagne</li>
<li>Australie</li>
<li>Brésil</li>
<li>France</li>
<li>Gabon</li>
<li>Ghana</li>
<li>Panama</li>
<li>Pays-Bas</li>
<li>République populaire de Chine</li>
<li>République tchèque</li>
<li>Suisse</li>
</country>
<region>
<li>Bade-Wurtemberg</li>
<li>Canton de Berne</li>
<li>District de Cologne</li>
<li>District de Tübingen</li>
<li>Hollande-Septentrionale</li>
<li>Languedoc-Roussillon</li>
<li>Moravie</li>
<li>Occitanie (région administrative)</li>
<li>Rhénanie-du-Nord-Westphalie</li>
<li>État de São Paulo</li>
</region>
<settlement>
<li>Amsterdam</li>
<li>Berne</li>
<li>Bonn</li>
<li>Brno</li>
<li>Montpellier</li>
<li>São Paulo</li>
<li>Ulm</li>
</settlement>
<orgName>
<li>Université d'Amsterdam</li>
<li>Université d'Ulm</li>
<li>Université de Berne</li>
<li>Université de São Paulo</li>
</orgName>
</list>
<tree>
<country name="Allemagne">
<region name="Rhénanie-du-Nord-Westphalie">
<name sortKey="Corman, Victor Max" sort="Corman, Victor Max" uniqKey="Corman V" first="Victor Max" last="Corman">Victor Max Corman</name>
</region>
<name sortKey="Baldwin, Heather J" sort="Baldwin, Heather J" uniqKey="Baldwin H" first="Heather J." last="Baldwin">Heather J. Baldwin</name>
<name sortKey="Corman, Victor Max" sort="Corman, Victor Max" uniqKey="Corman V" first="Victor Max" last="Corman">Victor Max Corman</name>
<name sortKey="Drexler, Jan Felix" sort="Drexler, Jan Felix" uniqKey="Drexler J" first="Jan Felix" last="Drexler">Jan Felix Drexler</name>
<name sortKey="Drexler, Jan Felix" sort="Drexler, Jan Felix" uniqKey="Drexler J" first="Jan Felix" last="Drexler">Jan Felix Drexler</name>
<name sortKey="Drosten, Christian" sort="Drosten, Christian" uniqKey="Drosten C" first="Christian" last="Drosten">Christian Drosten</name>
<name sortKey="Drosten, Christian" sort="Drosten, Christian" uniqKey="Drosten C" first="Christian" last="Drosten">Christian Drosten</name>
<name sortKey="Tateno, Adriana Fumie" sort="Tateno, Adriana Fumie" uniqKey="Tateno A" first="Adriana Fumie" last="Tateno">Adriana Fumie Tateno</name>
<name sortKey="Tschapka, Marco" sort="Tschapka, Marco" uniqKey="Tschapka M" first="Marco" last="Tschapka">Marco Tschapka</name>
<name sortKey="Vallo, Peter" sort="Vallo, Peter" uniqKey="Vallo P" first="Peter" last="Vallo">Peter Vallo</name>
<name sortKey="Zerbinati, Rodrigo Melim" sort="Zerbinati, Rodrigo Melim" uniqKey="Zerbinati R" first="Rodrigo Melim" last="Zerbinati">Rodrigo Melim Zerbinati</name>
</country>
<country name="Australie">
<noRegion>
<name sortKey="Baldwin, Heather J" sort="Baldwin, Heather J" uniqKey="Baldwin H" first="Heather J." last="Baldwin">Heather J. Baldwin</name>
</noRegion>
</country>
<country name="Brésil">
<region name="État de São Paulo">
<name sortKey="Tateno, Adriana Fumie" sort="Tateno, Adriana Fumie" uniqKey="Tateno A" first="Adriana Fumie" last="Tateno">Adriana Fumie Tateno</name>
</region>
<name sortKey="Da Silva Filho, Luiz Vicente Ribeiro Ferreira" sort="Da Silva Filho, Luiz Vicente Ribeiro Ferreira" uniqKey="Da Silva Filho L" first="Luiz Vicente Ribeiro Ferreira" last="Da Silva Filho">Luiz Vicente Ribeiro Ferreira Da Silva Filho</name>
<name sortKey="Da Silva Filho, Luiz Vicente Ribeiro Ferreira" sort="Da Silva Filho, Luiz Vicente Ribeiro Ferreira" uniqKey="Da Silva Filho L" first="Luiz Vicente Ribeiro Ferreira" last="Da Silva Filho">Luiz Vicente Ribeiro Ferreira Da Silva Filho</name>
<name sortKey="Zerbinati, Rodrigo Melim" sort="Zerbinati, Rodrigo Melim" uniqKey="Zerbinati R" first="Rodrigo Melim" last="Zerbinati">Rodrigo Melim Zerbinati</name>
</country>
<country name="Ghana">
<noRegion>
<name sortKey="Annan, Augustina" sort="Annan, Augustina" uniqKey="Annan A" first="Augustina" last="Annan">Augustina Annan</name>
</noRegion>
<name sortKey="Adu Sarkodie, Yaw" sort="Adu Sarkodie, Yaw" uniqKey="Adu Sarkodie Y" first="Yaw" last="Adu-Sarkodie">Yaw Adu-Sarkodie</name>
<name sortKey="Nkrumah, Evans Ewald" sort="Nkrumah, Evans Ewald" uniqKey="Nkrumah E" first="Evans Ewald" last="Nkrumah">Evans Ewald Nkrumah</name>
<name sortKey="Oppong, Samuel" sort="Oppong, Samuel" uniqKey="Oppong S" first="Samuel" last="Oppong">Samuel Oppong</name>
<name sortKey="Owusu, Michael" sort="Owusu, Michael" uniqKey="Owusu M" first="Michael" last="Owusu">Michael Owusu</name>
</country>
<country name="Gabon">
<noRegion>
<name sortKey="Maganga, Gael Darren" sort="Maganga, Gael Darren" uniqKey="Maganga G" first="Gael Darren" last="Maganga">Gael Darren Maganga</name>
</noRegion>
<name sortKey="Leroy, Eric M" sort="Leroy, Eric M" uniqKey="Leroy E" first="Eric M." last="Leroy">Eric M. Leroy</name>
</country>
<country name="République tchèque">
<region name="Moravie">
<name sortKey="Vallo, Peter" sort="Vallo, Peter" uniqKey="Vallo P" first="Peter" last="Vallo">Peter Vallo</name>
</region>
</country>
<country name="France">
<region name="Occitanie (région administrative)">
<name sortKey="Leroy, Eric M" sort="Leroy, Eric M" uniqKey="Leroy E" first="Eric M." last="Leroy">Eric M. Leroy</name>
</region>
</country>
<country name="Suisse">
<region name="Canton de Berne">
<name sortKey="Thiel, Volker" sort="Thiel, Volker" uniqKey="Thiel V" first="Volker" last="Thiel">Volker Thiel</name>
</region>
<name sortKey="Thiel, Volker" sort="Thiel, Volker" uniqKey="Thiel V" first="Volker" last="Thiel">Volker Thiel</name>
</country>
<country name="Pays-Bas">
<region name="Hollande-Septentrionale">
<name sortKey="Van Der Hoek, Lia" sort="Van Der Hoek, Lia" uniqKey="Van Der Hoek L" first="Lia" last="Van Der Hoek">Lia Van Der Hoek</name>
</region>
</country>
<country name="République populaire de Chine">
<noRegion>
<name sortKey="Poon, Leo L M" sort="Poon, Leo L M" uniqKey="Poon L" first="Leo L. M." last="Poon">Leo L. M. Poon</name>
</noRegion>
</country>
<country name="Panama">
<noRegion>
<name sortKey="Tschapka, Marco" sort="Tschapka, Marco" uniqKey="Tschapka M" first="Marco" last="Tschapka">Marco Tschapka</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>

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