The Bayesian reconstruction and the evolutionary history of Salivirus type 1 and type 2: the worldwide spreading.
Identifieur interne : 000786 ( Main/Exploration ); précédent : 000785; suivant : 000787The Bayesian reconstruction and the evolutionary history of Salivirus type 1 and type 2: the worldwide spreading.
Auteurs : Silvia Angeletti [Italie] ; Domenico Benvenuto [Italie] ; Marta Fogolari [Italie] ; Cecilia De Flora [Italie] ; Giancarlo Ceccarelli [Italie] ; Ivana Maida [Italie] ; Riccardo Bazzardi [Italie] ; Silvia Spoto [Italie] ; Stefano Pascarella [Italie] ; Boban Mugosa [Monténégro] ; Massimo Ciccozzi [Italie]Source :
- Journal of infection in developing countries [ 1972-2680 ] ; 2021.
Abstract
INTRODUCTION
Salivirus (SalV) represents an emerging problem in public health especially during the recent years. In this study, the Bayesian evolutionary history and the spread of the virus through the different countries have been reported.
METHODOLOGY
a database of 81 sequences of SalV structural VP1 fragment were downloaded from GenBank, aligned and manually edited by Bioedit Software. ModelTest v. 3.7 software was used to estimate the simplest evolutionary model fitting the sequence dataset. A Maximum-Likelihood tree has been generated using MEGA-X to test the "clockliness" signal using TempEst 1.5.1. The Bayesian phylogenetic tree was built by BEAST. Homology modelling was performed by SWISS-Model and protein variability evaluated by ConSurf server.
RESULTS
the phylogenetic tree showed a clade of SalV A2 and three main clades of SalV A1, revealing several infections in humans in South Korea, India, Tunisia, China, Nigeria, Ethiopia and USA. The Bayesian maximum clade credibility tree and the time of the most common recent ancestor dated back the root of the tree to the year 1788 with the probable origin in USA. Selective pressure analysis revealed two positive selection sites, His at 100th and Leu at 116th positions that at the homology modelling resulted important to guarantee protein stability and variability. This could contribute to the development of new mutations modifying the clinical features of this evolving virus.
CONCLUSIONS
Bayesian phylogenetic and phylodynamic represented a useful tool to follow the transmission dynamic of SalV and to prevent new epidemics worldwide.
DOI: 10.3855/jidc.12141
PubMed: 33690212
Affiliations:
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Rossi Fanelli", Sapienza University, Rome, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Biochemical Science "A. Rossi Fanelli", Sapienza University, Rome</wicri:regionArea><placeName><settlement type="city">Rome</settlement><region nuts="2">Latium</region></placeName></affiliation></author><author><name sortKey="Mugosa, Boban" sort="Mugosa, Boban" uniqKey="Mugosa B" first="Boban" last="Mugosa">Boban Mugosa</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Public Health, Podgorica, Montenegro.</nlm:affiliation><country xml:lang="fr">Monténégro</country><wicri:regionArea>Institute of Public Health, Podgorica</wicri:regionArea><wicri:noRegion>Podgorica</wicri:noRegion></affiliation></author><author><name sortKey="Ciccozzi, Massimo" sort="Ciccozzi, Massimo" uniqKey="Ciccozzi M" first="Massimo" last="Ciccozzi">Massimo Ciccozzi</name><affiliation wicri:level="1"><nlm:affiliation>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Unit of Medical Statistics and 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type="wicri:Area/Main/Exploration">000786</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">The Bayesian reconstruction and the evolutionary history of Salivirus type 1 and type 2: the worldwide spreading.</title><author><name sortKey="Angeletti, Silvia" sort="Angeletti, Silvia" uniqKey="Angeletti S" first="Silvia" last="Angeletti">Silvia Angeletti</name><affiliation wicri:level="1"><nlm:affiliation>Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Italy. s.angeletti@unicampus.it.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome</wicri:regionArea><wicri:noRegion>University Campus Bio-Medico of Rome</wicri:noRegion></affiliation></author><author><name sortKey="Benvenuto, Domenico" sort="Benvenuto, Domenico" uniqKey="Benvenuto D" first="Domenico" last="Benvenuto">Domenico Benvenuto</name><affiliation wicri:level="1"><nlm:affiliation>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome</wicri:regionArea><wicri:noRegion>University Campus Bio-Medico of Rome</wicri:noRegion></affiliation></author><author><name sortKey="Fogolari, Marta" sort="Fogolari, Marta" uniqKey="Fogolari M" first="Marta" last="Fogolari">Marta Fogolari</name><affiliation wicri:level="1"><nlm:affiliation>Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome</wicri:regionArea><wicri:noRegion>University Campus Bio-Medico of Rome</wicri:noRegion></affiliation></author><author><name sortKey="De Flora, Cecilia" sort="De Flora, Cecilia" uniqKey="De Flora C" first="Cecilia" last="De Flora">Cecilia De Flora</name><affiliation wicri:level="1"><nlm:affiliation>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome</wicri:regionArea><wicri:noRegion>University Campus Bio-Medico of Rome</wicri:noRegion></affiliation></author><author><name sortKey="Ceccarelli, Giancarlo" sort="Ceccarelli, Giancarlo" uniqKey="Ceccarelli G" first="Giancarlo" last="Ceccarelli">Giancarlo Ceccarelli</name><affiliation wicri:level="3"><nlm:affiliation>Department of Public Health and Infectious Diseases, University of Rome, "Sapienza", Policlinico "Umberto I", Rome, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Public Health and Infectious Diseases, University of Rome, "Sapienza", Policlinico "Umberto I", Rome</wicri:regionArea><placeName><settlement type="city">Rome</settlement><region nuts="2">Latium</region></placeName></affiliation></author><author><name sortKey="Maida, Ivana" sort="Maida, Ivana" uniqKey="Maida I" first="Ivana" last="Maida">Ivana Maida</name><affiliation wicri:level="1"><nlm:affiliation>Department of Medical, Surgical and Experimental Sciences Infectious Diseases, University of Sassari, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Medical, Surgical and Experimental Sciences Infectious Diseases, University of Sassari</wicri:regionArea><wicri:noRegion>University of Sassari</wicri:noRegion></affiliation></author><author><name sortKey="Bazzardi, Riccardo" sort="Bazzardi, Riccardo" uniqKey="Bazzardi R" first="Riccardo" last="Bazzardi">Riccardo Bazzardi</name><affiliation wicri:level="1"><nlm:affiliation>Controllo Microbiologico e Ispezione degli Alimenti, Istituto Zooprofilattico Sperimentale della Sardegna "G. Pegreffi", Sassari, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Controllo Microbiologico e Ispezione degli Alimenti, Istituto Zooprofilattico Sperimentale della Sardegna "G. Pegreffi", Sassari</wicri:regionArea><wicri:noRegion>Sassari</wicri:noRegion></affiliation></author><author><name sortKey="Spoto, Silvia" sort="Spoto, Silvia" uniqKey="Spoto S" first="Silvia" last="Spoto">Silvia Spoto</name><affiliation wicri:level="3"><nlm:affiliation>7Diagnostic and Therapeutic Medicine Department, University Campus Bio-Medico of Rome, Rome, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>7Diagnostic and Therapeutic Medicine Department, University Campus Bio-Medico of Rome, Rome</wicri:regionArea><placeName><settlement type="city">Rome</settlement><region nuts="2">Latium</region></placeName></affiliation></author><author><name sortKey="Pascarella, Stefano" sort="Pascarella, Stefano" uniqKey="Pascarella S" first="Stefano" last="Pascarella">Stefano Pascarella</name><affiliation wicri:level="3"><nlm:affiliation>Department of Biochemical Science "A. Rossi Fanelli", Sapienza University, Rome, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Biochemical Science "A. Rossi Fanelli", Sapienza University, Rome</wicri:regionArea><placeName><settlement type="city">Rome</settlement><region nuts="2">Latium</region></placeName></affiliation></author><author><name sortKey="Mugosa, Boban" sort="Mugosa, Boban" uniqKey="Mugosa B" first="Boban" last="Mugosa">Boban Mugosa</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Public Health, Podgorica, Montenegro.</nlm:affiliation><country xml:lang="fr">Monténégro</country><wicri:regionArea>Institute of Public Health, Podgorica</wicri:regionArea><wicri:noRegion>Podgorica</wicri:noRegion></affiliation></author><author><name sortKey="Ciccozzi, Massimo" sort="Ciccozzi, Massimo" uniqKey="Ciccozzi M" first="Massimo" last="Ciccozzi">Massimo Ciccozzi</name><affiliation wicri:level="1"><nlm:affiliation>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome</wicri:regionArea><wicri:noRegion>University Campus Bio-Medico of Rome</wicri:noRegion></affiliation></author></analytic><series><title level="j">Journal of infection in developing countries</title><idno type="eISSN">1972-2680</idno><imprint><date when="2021" type="published">2021</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>INTRODUCTION</b></p><p>Salivirus (SalV) represents an emerging problem in public health especially during the recent years. In this study, the Bayesian evolutionary history and the spread of the virus through the different countries have been reported.</p></div><div type="abstract" xml:lang="en"><p><b>METHODOLOGY</b></p><p>a database of 81 sequences of SalV structural VP1 fragment were downloaded from GenBank, aligned and manually edited by Bioedit Software. ModelTest v. 3.7 software was used to estimate the simplest evolutionary model fitting the sequence dataset. A Maximum-Likelihood tree has been generated using MEGA-X to test the "clockliness" signal using TempEst 1.5.1. The Bayesian phylogenetic tree was built by BEAST. Homology modelling was performed by SWISS-Model and protein variability evaluated by ConSurf server.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>the phylogenetic tree showed a clade of SalV A2 and three main clades of SalV A1, revealing several infections in humans in South Korea, India, Tunisia, China, Nigeria, Ethiopia and USA. The Bayesian maximum clade credibility tree and the time of the most common recent ancestor dated back the root of the tree to the year 1788 with the probable origin in USA. Selective pressure analysis revealed two positive selection sites, His at 100th and Leu at 116th positions that at the homology modelling resulted important to guarantee protein stability and variability. This could contribute to the development of new mutations modifying the clinical features of this evolving virus.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>Bayesian phylogenetic and phylodynamic represented a useful tool to follow the transmission dynamic of SalV and to prevent new epidemics worldwide.</p></div></front></TEI><affiliations><list><country><li>Italie</li><li>Monténégro</li></country><region><li>Latium</li></region><settlement><li>Rome</li></settlement></list><tree><country name="Italie"><noRegion><name sortKey="Angeletti, Silvia" sort="Angeletti, Silvia" uniqKey="Angeletti S" first="Silvia" last="Angeletti">Silvia Angeletti</name></noRegion><name sortKey="Bazzardi, Riccardo" sort="Bazzardi, Riccardo" uniqKey="Bazzardi R" first="Riccardo" last="Bazzardi">Riccardo Bazzardi</name><name sortKey="Benvenuto, Domenico" sort="Benvenuto, Domenico" uniqKey="Benvenuto D" first="Domenico" last="Benvenuto">Domenico Benvenuto</name><name sortKey="Ceccarelli, Giancarlo" sort="Ceccarelli, Giancarlo" uniqKey="Ceccarelli G" first="Giancarlo" last="Ceccarelli">Giancarlo Ceccarelli</name><name sortKey="Ciccozzi, Massimo" sort="Ciccozzi, Massimo" uniqKey="Ciccozzi M" first="Massimo" last="Ciccozzi">Massimo Ciccozzi</name><name sortKey="De Flora, Cecilia" sort="De Flora, Cecilia" uniqKey="De Flora C" first="Cecilia" last="De Flora">Cecilia De Flora</name><name sortKey="Fogolari, Marta" sort="Fogolari, Marta" uniqKey="Fogolari M" first="Marta" last="Fogolari">Marta Fogolari</name><name sortKey="Maida, Ivana" sort="Maida, Ivana" uniqKey="Maida I" first="Ivana" last="Maida">Ivana Maida</name><name sortKey="Pascarella, Stefano" sort="Pascarella, Stefano" uniqKey="Pascarella S" first="Stefano" last="Pascarella">Stefano Pascarella</name><name sortKey="Spoto, Silvia" sort="Spoto, Silvia" uniqKey="Spoto S" first="Silvia" last="Spoto">Silvia Spoto</name></country><country name="Monténégro"><noRegion><name sortKey="Mugosa, Boban" sort="Mugosa, Boban" uniqKey="Mugosa B" first="Boban" last="Mugosa">Boban Mugosa</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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