Dieses Ergebnis aus BASE kann Gästen nicht angezeigt werden. Login für vollen Zugriff.

Investigating the evolutionary dynamics and mutational pattern of SARS-CoV-2 spike gene on selected SARS-CoV-2 variants

Title:	Investigating the evolutionary dynamics and mutational pattern of SARS-CoV-2 spike gene on selected SARS-CoV-2 variants
Authors:	Balech, Bachir; Lo Presti, Alessandra; Telegrafo, Claudia; Maisto, Lucia; Giombini, Emanuela; Di Martino, Angela; Ambrosio, Luigina; Tullo, Apollonia; Stefanelli, Paola; null, null; Liborio Stuppia; Federico Anaclerio (Center for Advanced Studies and Technology (CAST); G. d’Annunzio University of Chieti-Pescara; Chieti Italy); Giovanni Savini; Cesare Cammà; Luigi Possenti (Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale”; Teramo Italy); Domenico Dell’Edera (Medical Genetics Unit; “Madonna delle Grazie” Hospital; Matera Italy); Antonio Picerno; Teresa Lopizzo (Clinical Pathology and Microbiology Unit; AOR San Carlo; Potenza Italy); Maria Teresa Fiorillo; Rosaria Oteri (Unit of Microbiology and Virology; North Health Center ASP 5; Reggio Calabria; Italy); Giuseppe Viglietto (CIS (Interdepartmental Center for Services and Research); Genomics and Molecular Pathology; “Magna Graecia” Univer- sity; Catanzaro Italy); Pasquale Minchella (Department of Microbiology and Virology; Pugliese Ciaccio Hospital; Francesca Greco; Microbiology and Virology Unit; “Annunziata” Hospital of Cosenza; Cosenza Italy); Antonio Limone; Giovanna Fusco (Istituto Zooprofilattico Sperimentale del Mezzogiorno; Portici Naples; Claudia Tiberio; Luigi Atripaldi; Mariagrazia Coppola (UOC Microbiologia e Virologia; P. O. Cotugno A. O. dei Colli; Naples Italy); Davide Cacchi- arelli; Antonio Grimaldi (Telethon Institute of Genetics and Medicine (TIGEM); Pozzuoli Napoli; Stefano Pongolini; Erika Scaltriti (Risk Analysis and Genomic Epidemiology Unit; Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna (IZSLER) “Bruno Ubertini”; Parma Italy); Vittorio Sambri; Giorgio Dirani; Silvia Zannoli (Unit of Micro- biology; The Greater Romagna Area Hub Laboratory; Cesena Italy); Tiziana Lazzarotto; Giada Rossini (Microbiology Unit; IRCCS Azienda Ospedaliero-Universitaria di Bologna; Bologna Italy); Federica Baldan; Sabrina Lombino (Department of Laboratory Medicine; Azienda Sanitaria Universitaria Friuli Centrale Udine; Pierlanfranco D’Agaro; Ludovica Segat (Hygiene and Preventive Medicine Clinical Operative Unit; Trieste University Hospital—ASUGI; Trieste Italy); Fabio Barbone; Raffaella Koncan (Department of Medicine; Surgery and Health Sciences; University of Trieste; Antonio Battisti; Patricia Alba (Department of General Diagnostics; Istituto Zooprofilattico Sperimentale del Lazio e della Toscana (IZSLT); Rome Italy); Maria Teresa Scicluna (Department of Virology, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri); Silvia Angeletti; Elisabetta Riva (Unità di ricerca Laboratorio; Fondazione Policlinico Universitario Campus Bio- Medico; Roma Italy); Fulvia Pimpinelli (UOSD Microbiology and Virology; IRCCS San Gallicano Dermatologi- cal Institute; IFO Rome; Maurizio Fanciulli (SAFU Laboratory; IRCCS Regina Elena National Cancer Institute; Alice Massacci (Biostatistics; Bioinformatics and Clinical Trial Center; Maurizio Sanguinetti (Dipartimento di Scienze di Laboratorio e Infettivologiche; Fondazione Policlinico Universitario A. Gemelli IRCCS; Fabrizio Maggi; Martina Rueca; Cesare Ernesto Maria Gruber (Laboratory of Virology; National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS); Ombretta Turriziani (Department of Molecular Medicine; Sapienza University of Rome; Sapienza University Hospital “Policlinico Umberto I”; Carlo Federico Perno (Microbiology and Diagnostic Immunology; Bambino Gesù Children’s Hospital; IRCCS Rome; Francesca Ceccherini-Silberstein; Maria Concetta Bellocchi (Department of Experimental Medicine; University of Rome Tor Vergata; Bianca Bruzzone; Giancarlo Icardi; Andrea Orsi (Hygiene Unit; San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences Genoa; Rea Valaperta (ASST Bergamo Est, Italy); Maria Oggionni (ASST Bergamo Ovest; Bergamo Italy); Sophie Testa; Fabio Sagradi (ASST Cremona; Cre- mona; Arnaldo Caruso (Department of Molecular and Translational Medicine University of Brescia Medical School; Brescia Italy); Serena Messali (Laboratory of Microbiology and Virology; ASST degli Spedali Civili Brescia; Diana Fanti; Alice Nava (S. C. Clinical Microbiology; ASST Grande Ospedale Metropolitano Niguarda Milan; Sergio Malandrin; Annalisa Cavallero (Microbiology and Virology Unit; Fondazione IRCCS San Gerardo dei Tintori; Monza Italy); Claudio Farina; Marco Arosio (Microbiology and Virology Laboratory; ASST Papa Giovanni XXIII; Ferruccio Ceriotti; Sara Colonia Uceda Renteria; Stefania Paganini (UOS Laboratorio di Virologia; UOC Laboratorio Analisi Fondazi- one IRCCS Ca’ Granda Ospedale Maggiore Policlinico); Anna Maria Di Blasio; Erminio Torresani (IRCCS Istituto Auxolog- ico Italiano; Milan Italy); Maria Beatrice Boniotti; Cristina Bertasio (Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna; Nicola Clementi (Laboratory of Microbiology and Virology; Vita-Salute San Raffaele University; Milan Italy; Laboratory of Microbiology and Virology; IRCCS Ospedale San Raffaele; Michela Sampaolo (Laboratory of Microbiology and Virology; IRCCS San Raffaele Hospital; Federica Novazzi; Nicasio Mancini (Laboratory of Microbiology; ASST Sette Laghi; Varese Italy); Maria Rita Gismondo; Valeria Micheli (Laboratory of Clinical Microbiology; Virology and Bioemergencies; ASST Fatebenefratelli Sacco; Luigi Sacco Hospital; Fausto Baldanti (Microbiology and Virology Department; Fondazione IRCCS Policlinico San Matteo; Pavia Italy; Dpt. of Clinical; Surgical; Diagnostics and Pediatric Sciences; University of Pavia; Pavia Italy); Federica AM Giardina (Dpt. of Clinical; Antonio Piralla; Federica Zavaglio; Francesca Rovida (Microbiology and Virology Department; Elena Pariani; Cristina Galli; Laura Pellegrinelli (Department of Biomedical Sciences for Health; University of Milan; Stefano Menzo (Department of Biomedical Sciences and Public Health; Virology Unit; Polytechnic University of Marche; Ancona Italy); Massimiliano Scutellà; Valentina Felice (UOSVD Microbiologia e Diagnostica Molecolare Avanzata ASREM P. O. Cardarelli Campobasso (CB); Elisabetta Pagani; Irene Bianconi; Angela Maria Di Pierro (Laboratory of Microbiol- ogy and Virology; Provincial Hospital of Bolzano; SABES-ASDAA; Lehrkrankenhaus der Paracelsus Medizinischen Priva- tuniversität – Bolzano, Italy); Lucia Collini; Giovanni Lorenzin (Laboratory of Microbiology and Virology; Country Health Service APSS; S. Chiara Hospital; Trento Italy); Valeria Ghisetti (Laboratory of Microbiology and Molecular Biology; Amedeo di Savoia Hospital; Turin Italy); Sara Gilardi; Alice Bartolini; Daniela Cantarella (Candiolo Cancer Institute FPO- IRCCS; Candiolo Turin; Simone Peletto; Giuseppe Ru; Pier Luigi Acutis; Elena Bozzetta (Istituto Zooprofilattico Sperimentale del Piemonte; Liguria e Valle d’Aosta; Maria Chironna; Daniela Loconsole (Hygiene Unit; Interdis- ciplinary Department of Medicine—DIM; University of Bari “Aldo Moro”; Bari Italy); Antonio Parisi (Genetic and Molecular Epidemiology Laboratory; Experimental Zooprophylactic Institute of Apulia and Basilicata; Foggia Italy); Fabio Arena; Rossella De Nittis; Giuseppina Iannelli (Microbiology and Virology; “Policlinico Riuniti”; University Hospital; Florigio Romano Lista (Scientific Department; Army Medical Center; Ferdinando Coghe (Laboratorio Generale (HUB) Analisi Chimico Cliniche e Microbiologia; PO “Duilio Casula”; Azienda Ospedaliera Universitaria di Cagliari; Cagliari Italy); Sergio Uzzau; Salvatore Rubino; Flavia Angioj; Gabriele Ibba; Caterina Serra (Department of Biomedical Sciences; S. C. Microbiology and Virology; Azienda Ospedaliera Universitaria di Sassari; Sassari Italy); Giovanna Piras; Giuseppe Mameli; Rosanna Asproni (Laboratorio Specialistico; UOC Ematologia e CTMO; P. O. “San Francesco; ” ASL Nuoro; Nuoro Italy); Francesca Di Gaudio (Department of Health Promotion; Mother and Child Care; Internal Medicine and medical Specialties “G. D’Alessandro”; University of Palermo; Palermo Italy); Stefano Vullo; Stefano Reale (Istituto Zooprofilattico Sperimentale della Sicilia; Teresa Pollicino (Division of Advanced Diagnostic Laboratories; University Hospital “G. Martino” Messina; Francesco Vitale; Fabio Tramuto (Clinical Epidemiology Unit and Regional Reference Laboratory; University Hospital “P. Giaccone”; Palermo Italy; Department of Health Promotion; Internal Medicine and Medical Specialties “G. D’Alessandro”; Stefania Stefani (Clinical Virol- ogy Laboratory; “G. Rodolico—S. Marco” Hospital; Catania Italy; Department of Biomedical and Biotechnological Sciences; University of Catania; Catania Italy); Guido Scalia (A. O. U. Policlinico “G. Rodolico- S. Marco”; U. O. C. Laboratory Analysis; Virology Section; and Department of Biomedical and Biotechnological Sciences; Concetta Ilenia Palermo (A. O. U. Policlinico “G. Rodolico- S. Marco”; Giuseppe Mancuso (UOC Microbiology; University Hospital “G. Martino”; Messina Italy); Vincenzo Bramanti; Car- melo Fidone; Giuseppe Barrano (U. O. C. Laboratory Analysis; ASP Ragusa; Ragusa Italy); Mauro Pistello (Department of Translational Research, University of Pisa; Pisa University Hospital; Pisa Italy); Gian Maria Rossolini (Department of Experimental and Clinical Medicine; University of Florence; Florence Italy; Florence Careggi University Hospital; Florence Italy); Francesca Malentacchi (Microbiology and Virology Unit; Careggi University Hospital; Maria Grazia Cusi (Virology Unit; Department of Medical Biotechnologies; University of Siena; Siena Italy); Antonella Mencacci; Barbara Camilloni (Microbiology and Clinical Microbiology; Department of Medi- cine and Surgery; University of Perugia; Santa Maria della Misericordia Hospital; Perugia Italy); Calogero Terregino; Alice Fusaro; Isabella Monne; Edoardo Giussani (Division of Comparative Biomedical Sciences; Istituto Zooprofilattico Sperimen- tale delle Venezie; Legnaro Padova; Davide Gibellini; Emil Tonon; Riccardo Cecchetto (Department of Diagnostic and Public Health; Verona University; Verona Italy); Laura Squarzon; Mosè Favarato (Molecular Diagnostics and Genetics; AULSS 3 Serenissima; Venice Italy); Valeria Biscaro; Elisa Vian; Silvia Ragolia (UOC Microbiology Treviso Hospital; Department of specialist and laboratory medicine; AULSS 2 Marca Trevigiana; Michela Pascarella; Fabio Buffoli; Isabella Cerbaro (U. O. C. Microbiology; U. O. S. Molecular Biology applied to Microbiology and Virology; San Bortolo Hospital; AULSS n. 8 Berica; Vicenza Italy).
Contributors:	Bachir, Balech; Alessandra, Lo Presti; Claudia, Telegrafo; Lucia, Maisto; Emanuela, Giombini; Angela, Di Martino; Luigina, Ambrosio; Apollonia, Tullo; Paola, Stefanelli; Null, Null; Stuppia, Liborio; Anaclerio (Center for Advanced Studies and Technology (CAST), Federico; d’Annunzio University of Chieti-Pescara, G.; Italy), Chieti; Savini, Giovanni; Cammà, Cesare; e del Molise “Giuseppe Caporale”, Luigi Possenti (Istituto Zooprofilattico Sperimentale dell’Abruzzo; Italy), Teramo; Dell’Edera (Medical Genetics Unit, Domenico; delle Grazie” Hospital, “Madonna; Italy), Matera; Picerno, Antonio; Lopizzo (Clinical Pathology and Microbiology Unit, Teresa; San Carlo, Aor; Italy), Potenza; Teresa Fiorillo, Maria; Oteri (Unit of Microbiology and Virology, Rosaria; 5, North Health Center Asp; Calabria, Reggio; Italy); Viglietto (CIS (Interdepartmental Center for Services and Research), Giuseppe; And Molecular Pathology, Genomic; Graecia” Univer- sity, “Magna; Italy), Catanzaro; Minchella (Department of Microbiology and Virology, Pasquale; Ciaccio Hospital, Pugliese; Greco, Francesca; And Virology Unit, Microbiology; Hospital Of Cosenza, “Annunziata”; Italy), Cosenza; Limone, Antonio; Fusco (Istituto Zooprofilattico Sperimentale del Mezzogiorno, Giovanna; Naples, Portici; Tiberio, Claudia; Atripaldi, Luigi; E Virologia, Mariagrazia Coppola (UOC Microbiologia; Dei Colli, P. O. Cotugno A. O.; Italy), Naple; Cacchi- arelli, Davide; Grimaldi (Telethon Institute of Genetics and Medicine (TIGEM), Antonio; Napoli, Pozzuoli; Pongolini, Stefano; Scaltriti (Risk Analysis and Genomic Epidemiology Unit, Erika; e dell’Emilia-Romagna (IZSLER) “Bruno Ubertini”, Istituto Zooprofilattico Sperimentale Della Lombardia; Italy), Parma; Sambri, Vittorio; Dirani, Giorgio; Zannoli (Unit of Micro- biology, Silvia; Greater Romagna Area Hub Laboratory, The; Italy), Cesena; Lazzarotto, Tiziana; Rossini (Microbiology Unit, Giada; Azienda Ospedaliero-Universitaria di Bologna, Ircc; Italy), Bologna; Baldan, Federica; Lombino (Department of Laboratory Medicine, Sabrina; Sanitaria Universitaria Friuli Centrale Udine, Azienda; D’Agaro, Pierlanfranco; Segat (Hygiene and Preventive Medicine Clinical Operative Unit, Ludovica; University Hospital—asugi, Trieste; Italy), Trieste; Barbone, Fabio; Koncan (Department of Medicine, Raffaella; And Health Sciences, Surgery; Of Trieste, University; Battisti, Antonio; Alba (Department of General Diagnostics, Patricia; e della Toscana (IZSLT), Istituto Zooprofilattico Sperimentale Del Lazio; Italy), Rome; Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri), Maria Teresa Scicluna (Department of Virology; Angeletti, Silvia; Riva (Unità di ricerca Laboratorio, Elisabetta; Policlinico Universitario Campus Bio- Medico, Fondazione; Italy), Roma; Pimpinelli (UOSD Microbiology and Virology, Fulvia; San Gallicano Dermatologi- cal Institute, Ircc; Rome, Ifo; Fanciulli (SAFU Laboratory, Maurizio; Regina Elena National Cancer Institute, Ircc; Massacci (Biostatistics, Alice; And Clinical Trial Center, Bioinformatic
Publication Year:	2025
Collection:	IRIS Università degli Studi di Perugia
Description:	The continuous evolution of SARS-CoV-2 has led to the emergence of several variants representing significant challenges for public health. Many studies highlight the relevance of phylogenetic inference or mutational pattern analysis to understand the evolutionary relatedness of viral variants and to estimate the potential effect of new mutations on viral transmission, virulence and antigenicity. Here we describe an evolutionary investigation approach combined with mutational analyses of SARS-CoV-2 Spike gene to annotate and potentially track important amino acid site variation of specific functional domain relevant for viral survival. This approach was applied on XBB, EG and BA* and their sub-lineages (see materials and methods) available from GISAID. In addition, we considered the major variants of concern (Alpha, Delta, Omicron) and Wuhan-Hu-1 strain as references. Maximum likelihood phylogenetic tree was constructed from the complete dataset while selection pressure and mutational analyses were conducted on single variants separately. The obtained phylogenetic tree of Spike amino acid gene sequence showed a clear separation of viral variants as well as their expected appearance order. This result supported the significance of selection pressure analyses outcomes combined with amino acid mutational frequencies where in many cases they showed a linear and parallel trend. This allowed also to hypothesize the potential importance of low-frequency mutations in new potential virus variants. This study constitutes an asset of important insights to be considered in regular monitoring programs. In addition, the analysis framework described here introduces a starting point for further standardization, optimization and application on different data types and in large-scale studies.
Document Type:	article in journal/newspaper
Language:	English
Relation:	info:eu-repo/semantics/altIdentifier/pmid/41118444; info:eu-repo/semantics/altIdentifier/wos/WOS:001598166800025; volume:20; issue:10; journal:PLOS ONE; https://hdl.handle.net/11391/1615347
DOI:	10.1371/journal.pone.0333093
Availability:	https://hdl.handle.net/11391/1615347; https://doi.org/10.1371/journal.pone.0333093
Accession Number:	edsbas.F71396F0
Database:	BASE