MersV1, Main, Exploration, bibRecord, 001259

Extensive Positive Selection Drives the Evolution of Nonstructural Proteins in Lineage C Betacoronaviruses.

Identifieur interne : 001259 ( Main/Exploration ); précédent : 001258; suivant : 001260

Extensive Positive Selection Drives the Evolution of Nonstructural Proteins in Lineage C Betacoronaviruses.

Auteurs : Diego Forni [Italie] ; Rachele Cagliani [Italie] ; Alessandra Mozzi [Italie] ; Uberto Pozzoli [Italie] ; Nasser Al-Daghri [Arabie saoudite] ; Mario Clerici [Italie] ; Manuela Sironi [Italie]

Source :

Journal of virology [ 1098-5514 ] ; 2016.

RBID : pubmed:26792741

Descripteurs français

KwdFr :
- Animaux, Coronavirus (), Coronavirus (génétique), Génotype, Humains, Protéines virales non structurales (génétique), Sélection génétique, Évolution moléculaire.
MESH :
- génétique : Coronavirus, Protéines virales non structurales.
- Animaux, Coronavirus, Génotype, Humains, Sélection génétique, Évolution moléculaire.

English descriptors

KwdEn :
- Animals, Coronavirus (classification), Coronavirus (genetics), Evolution, Molecular, Genotype, Humans, Selection, Genetic, Viral Nonstructural Proteins (genetics).
MESH :
- chemical , genetics : Viral Nonstructural Proteins.
- classification : Coronavirus.
- genetics : Coronavirus.
- Animals, Evolution, Molecular, Genotype, Humans, Selection, Genetic.

Abstract

Middle East respiratory syndrome-related coronavirus (MERS-CoV) spreads to humans via zoonotic transmission from camels. MERS-CoV belongs to lineage C of betacoronaviruses (betaCoVs), which also includes viruses isolated from bats and hedgehogs. A large portion of the betaCoV genome consists of two open reading frames (ORF1a and ORF1b) that are translated into polyproteins. These are cleaved by viral proteases to generate 16 nonstructural proteins (nsp1 to nsp16) which compose the viral replication-transcription complex. We investigated the evolution of ORF1a and ORF1b in lineage C betaCoVs. Results indicated widespread positive selection, acting mostly on ORF1a. The proportion of positively selected sites in ORF1a was much higher than that previously reported for the surface-exposed spike protein. Selected sites were unevenly distributed, with nsp3 representing the preferential target. Several pairs of coevolving sites were also detected, possibly indicating epistatic interactions; most of these were located in nsp3. Adaptive evolution at nsp3 is ongoing in MERS-CoV strains, and two selected sites (G720 and R911) were detected in the protease domain. While position 720 is variable in camel-derived viruses, suggesting that the selective event does not represent a specific adaptation to humans, the R911C substitution was observed only in human-derived MERS-CoV isolates, including the viral strain responsible for the recent South Korean outbreak. It will be extremely important to assess whether these changes affect host range or other viral phenotypes. More generally, data herein indicate that CoV nsp3 represents a major selection target and that nsp3 sequencing should be envisaged in monitoring programs and field surveys.

DOI: 10.1128/JVI.02988-15
PubMed: 26792741

Affiliations:

Le document en format XML

<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Extensive Positive Selection Drives the Evolution of Nonstructural Proteins in Lineage C Betacoronaviruses.</title>
<author><name sortKey="Forni, Diego" sort="Forni, Diego" uniqKey="Forni D" first="Diego" last="Forni">Diego Forni</name>
<affiliation wicri:level="1"><nlm:affiliation>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini, Italy diego.forni@bp.lnf.it.</nlm:affiliation>
<country wicri:rule="url">Italie</country>
<wicri:regionArea>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini</wicri:regionArea>
<wicri:noRegion>Bosisio Parini</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Cagliani, Rachele" sort="Cagliani, Rachele" uniqKey="Cagliani R" first="Rachele" last="Cagliani">Rachele Cagliani</name>
<affiliation wicri:level="1"><nlm:affiliation>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini, Italy.</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini</wicri:regionArea>
<wicri:noRegion>Bosisio Parini</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Mozzi, Alessandra" sort="Mozzi, Alessandra" uniqKey="Mozzi A" first="Alessandra" last="Mozzi">Alessandra Mozzi</name>
<affiliation wicri:level="1"><nlm:affiliation>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini, Italy.</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini</wicri:regionArea>
<wicri:noRegion>Bosisio Parini</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Pozzoli, Uberto" sort="Pozzoli, Uberto" uniqKey="Pozzoli U" first="Uberto" last="Pozzoli">Uberto Pozzoli</name>
<affiliation wicri:level="1"><nlm:affiliation>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini, Italy.</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini</wicri:regionArea>
<wicri:noRegion>Bosisio Parini</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Al Daghri, Nasser" sort="Al Daghri, Nasser" uniqKey="Al Daghri N" first="Nasser" last="Al-Daghri">Nasser Al-Daghri</name>
<affiliation wicri:level="1"><nlm:affiliation>Biomarker Research Program, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia Prince Mutaib Chair for Biomarkers of Osteoporosis, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia.</nlm:affiliation>
<country xml:lang="fr">Arabie saoudite</country>
<wicri:regionArea>Biomarker Research Program, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia Prince Mutaib Chair for Biomarkers of Osteoporosis, Biochemistry Department, College of Science, King Saud University, Riyadh</wicri:regionArea>
<wicri:noRegion>Riyadh</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Clerici, Mario" sort="Clerici, Mario" uniqKey="Clerici M" first="Mario" last="Clerici">Mario Clerici</name>
<affiliation wicri:level="3"><nlm:affiliation>Department of Physiopathology and Transplantation, University of Milan, Milan, Italy Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy.</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Department of Physiopathology and Transplantation, University of Milan, Milan, Italy Don C. Gnocchi Foundation ONLUS, IRCCS, Milan</wicri:regionArea>
<placeName><settlement type="city">Milan</settlement>
<region nuts="2">Lombardie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Sironi, Manuela" sort="Sironi, Manuela" uniqKey="Sironi M" first="Manuela" last="Sironi">Manuela Sironi</name>
<affiliation wicri:level="1"><nlm:affiliation>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini, Italy.</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini</wicri:regionArea>
<wicri:noRegion>Bosisio Parini</wicri:noRegion>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2016">2016</date>
<idno type="RBID">pubmed:26792741</idno>
<idno type="pmid">26792741</idno>
<idno type="doi">10.1128/JVI.02988-15</idno>
<idno type="wicri:Area/PubMed/Corpus">001288</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001288</idno>
<idno type="wicri:Area/PubMed/Curation">001288</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001288</idno>
<idno type="wicri:Area/PubMed/Checkpoint">001107</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001107</idno>
<idno type="wicri:Area/Ncbi/Merge">001451</idno>
<idno type="wicri:Area/Ncbi/Curation">001451</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">001451</idno>
<idno type="wicri:Area/Main/Merge">001263</idno>
<idno type="wicri:Area/Main/Curation">001259</idno>
<idno type="wicri:Area/Main/Exploration">001259</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">Extensive Positive Selection Drives the Evolution of Nonstructural Proteins in Lineage C Betacoronaviruses.</title>
<author><name sortKey="Forni, Diego" sort="Forni, Diego" uniqKey="Forni D" first="Diego" last="Forni">Diego Forni</name>
<affiliation wicri:level="1"><nlm:affiliation>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini, Italy diego.forni@bp.lnf.it.</nlm:affiliation>
<country wicri:rule="url">Italie</country>
<wicri:regionArea>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini</wicri:regionArea>
<wicri:noRegion>Bosisio Parini</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Cagliani, Rachele" sort="Cagliani, Rachele" uniqKey="Cagliani R" first="Rachele" last="Cagliani">Rachele Cagliani</name>
<affiliation wicri:level="1"><nlm:affiliation>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini, Italy.</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini</wicri:regionArea>
<wicri:noRegion>Bosisio Parini</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Mozzi, Alessandra" sort="Mozzi, Alessandra" uniqKey="Mozzi A" first="Alessandra" last="Mozzi">Alessandra Mozzi</name>
<affiliation wicri:level="1"><nlm:affiliation>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini, Italy.</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini</wicri:regionArea>
<wicri:noRegion>Bosisio Parini</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Pozzoli, Uberto" sort="Pozzoli, Uberto" uniqKey="Pozzoli U" first="Uberto" last="Pozzoli">Uberto Pozzoli</name>
<affiliation wicri:level="1"><nlm:affiliation>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini, Italy.</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini</wicri:regionArea>
<wicri:noRegion>Bosisio Parini</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Al Daghri, Nasser" sort="Al Daghri, Nasser" uniqKey="Al Daghri N" first="Nasser" last="Al-Daghri">Nasser Al-Daghri</name>
<affiliation wicri:level="1"><nlm:affiliation>Biomarker Research Program, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia Prince Mutaib Chair for Biomarkers of Osteoporosis, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia.</nlm:affiliation>
<country xml:lang="fr">Arabie saoudite</country>
<wicri:regionArea>Biomarker Research Program, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia Prince Mutaib Chair for Biomarkers of Osteoporosis, Biochemistry Department, College of Science, King Saud University, Riyadh</wicri:regionArea>
<wicri:noRegion>Riyadh</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Clerici, Mario" sort="Clerici, Mario" uniqKey="Clerici M" first="Mario" last="Clerici">Mario Clerici</name>
<affiliation wicri:level="3"><nlm:affiliation>Department of Physiopathology and Transplantation, University of Milan, Milan, Italy Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy.</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Department of Physiopathology and Transplantation, University of Milan, Milan, Italy Don C. Gnocchi Foundation ONLUS, IRCCS, Milan</wicri:regionArea>
<placeName><settlement type="city">Milan</settlement>
<region nuts="2">Lombardie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Sironi, Manuela" sort="Sironi, Manuela" uniqKey="Sironi M" first="Manuela" last="Sironi">Manuela Sironi</name>
<affiliation wicri:level="1"><nlm:affiliation>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini, Italy.</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Scientific Institute IRCCS E. Medea, Bioinformatics, Bosisio Parini</wicri:regionArea>
<wicri:noRegion>Bosisio Parini</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">Journal of virology</title>
<idno type="eISSN">1098-5514</idno>
<imprint><date when="2016" type="published">2016</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term>
<term>Coronavirus (classification)</term>
<term>Coronavirus (genetics)</term>
<term>Evolution, Molecular</term>
<term>Genotype</term>
<term>Humans</term>
<term>Selection, Genetic</term>
<term>Viral Nonstructural Proteins (genetics)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term>
<term>Coronavirus ()</term>
<term>Coronavirus (génétique)</term>
<term>Génotype</term>
<term>Humains</term>
<term>Protéines virales non structurales (génétique)</term>
<term>Sélection génétique</term>
<term>Évolution moléculaire</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Viral Nonstructural Proteins</term>
</keywords>
<keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Coronavirus</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>
<term>Protéines virales non structurales</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Animals</term>
<term>Evolution, Molecular</term>
<term>Genotype</term>
<term>Humans</term>
<term>Selection, Genetic</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Animaux</term>
<term>Coronavirus</term>
<term>Génotype</term>
<term>Humains</term>
<term>Sélection génétique</term>
<term>Évolution moléculaire</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Middle East respiratory syndrome-related coronavirus (MERS-CoV) spreads to humans via zoonotic transmission from camels. MERS-CoV belongs to lineage C of betacoronaviruses (betaCoVs), which also includes viruses isolated from bats and hedgehogs. A large portion of the betaCoV genome consists of two open reading frames (ORF1a and ORF1b) that are translated into polyproteins. These are cleaved by viral proteases to generate 16 nonstructural proteins (nsp1 to nsp16) which compose the viral replication-transcription complex. We investigated the evolution of ORF1a and ORF1b in lineage C betaCoVs. Results indicated widespread positive selection, acting mostly on ORF1a. The proportion of positively selected sites in ORF1a was much higher than that previously reported for the surface-exposed spike protein. Selected sites were unevenly distributed, with nsp3 representing the preferential target. Several pairs of coevolving sites were also detected, possibly indicating epistatic interactions; most of these were located in nsp3. Adaptive evolution at nsp3 is ongoing in MERS-CoV strains, and two selected sites (G720 and R911) were detected in the protease domain. While position 720 is variable in camel-derived viruses, suggesting that the selective event does not represent a specific adaptation to humans, the R911C substitution was observed only in human-derived MERS-CoV isolates, including the viral strain responsible for the recent South Korean outbreak. It will be extremely important to assess whether these changes affect host range or other viral phenotypes. More generally, data herein indicate that CoV nsp3 represents a major selection target and that nsp3 sequencing should be envisaged in monitoring programs and field surveys.</div>
</front>
</TEI>
<affiliations><list><country><li>Arabie saoudite</li>
<li>Italie</li>
</country>
<region><li>Lombardie</li>
</region>
<settlement><li>Milan</li>
</settlement>
</list>
<tree><country name="Italie"><noRegion><name sortKey="Forni, Diego" sort="Forni, Diego" uniqKey="Forni D" first="Diego" last="Forni">Diego Forni</name>
</noRegion>
<name sortKey="Cagliani, Rachele" sort="Cagliani, Rachele" uniqKey="Cagliani R" first="Rachele" last="Cagliani">Rachele Cagliani</name>
<name sortKey="Clerici, Mario" sort="Clerici, Mario" uniqKey="Clerici M" first="Mario" last="Clerici">Mario Clerici</name>
<name sortKey="Mozzi, Alessandra" sort="Mozzi, Alessandra" uniqKey="Mozzi A" first="Alessandra" last="Mozzi">Alessandra Mozzi</name>
<name sortKey="Pozzoli, Uberto" sort="Pozzoli, Uberto" uniqKey="Pozzoli U" first="Uberto" last="Pozzoli">Uberto Pozzoli</name>
<name sortKey="Sironi, Manuela" sort="Sironi, Manuela" uniqKey="Sironi M" first="Manuela" last="Sironi">Manuela Sironi</name>
</country>
<country name="Arabie saoudite"><noRegion><name sortKey="Al Daghri, Nasser" sort="Al Daghri, Nasser" uniqKey="Al Daghri N" first="Nasser" last="Al-Daghri">Nasser Al-Daghri</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001259 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 001259 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Sante
   |area=    MersV1
   |flux=    Main
   |étape=   Exploration
   |type=    RBID
   |clé=     pubmed:26792741
   |texte=   Extensive Positive Selection Drives the Evolution of Nonstructural Proteins in Lineage C Betacoronaviruses.
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i   -Sk "pubmed:26792741" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd   \
       | NlmPubMed2Wicri -a MersV1

This area was generated with Dilib version V0.6.33.
Data generation: Mon Apr 20 23:26:43 2020. Site generation: Sat Mar 27 09:06:09 2021

Serveur d'exploration MERS

Extensive Positive Selection Drives the Evolution of Nonstructural Proteins in Lineage C Betacoronaviruses.

Extensive Positive Selection Drives the Evolution of Nonstructural Proteins in Lineage C Betacoronaviruses.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki

	Serveur d'exploration MERS
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.