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Grandi N, Cusano R, Piras G, Fiamma M, Monne MI, Fancello T, Milia J, Orrù S, Scognamiglio S, Serra C, Mameli G, Uzzau S, Orrù G, Palmas AD, Rubino S, Tramontano E. The impact of insularity on SARS-CoV-2 diffusion: Recapitulating three years of COVID-19 pandemic in the island of Sardinia. J Infect Public Health 2024; 17:102496. [PMID: 38991412 DOI: 10.1016/j.jiph.2024.102496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Italy has been the first European Country dealing with SARS-CoV-2, whose diffusion on the territory has not been homogeneous. Among Italian regions, Sardinia represented one of the lowest incidence areas, likely due to its insular nature. Despite this, the impact of insularity on SARS-CoV-2 genetic diversity has not been comprehensively described. METHODS In the present study, we performed the high throughput sequencing of 888 SARS-CoV-2 genomes collected in Sardinia during the first 23 months of pandemics. In addition, 1439 high-coverage SARS-CoV-2 genomes circulating in Sardinia along three years (December 2019 - January 2023) were downloaded from GISAID, for a total of 2327 viral sequences that were characterized in terms of phylogeny and genomic diversity. RESULTS Overall, COVID-19 pandemic in Sardinia showed substantial differences with respect to the national panorama, with additional peaks of infections and uncommon lineages that reflects the national and regional policies of re-opening and the subsequent touristic arrivals. Sardinia has been interested by the circulation of at least 87 SARS-CoV-2 lineages, including some that were poorly represented at national and European level, likely linked to multiple importation events. The relative frequency of Sardinian SARS-CoV-2 lineages has been compared to other Mediterranean Islands, revealing a unique composition. CONCLUSIONS The genomic diversity of SARS-CoV-2 in Sardinia has been shaped by a complex interplay of insular geography, low population density, and touristic arrivals, leading on the one side to the importation of lineages remaining rare at the national level, and resulting on the other side in the delayed entry of otherwise common variants.
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Affiliation(s)
- Nicole Grandi
- Lab. of Molecular Virology, Dept. of Life and Environmental Sciences, University of Cagliari, Italy
| | - Roberto Cusano
- CRS4 - Center for Advanced Studies, Research and Development in Sardinia, Science and Technology Park Polaris, Cagliari, Italy
| | | | | | | | | | - Jessica Milia
- CRS4 - Center for Advanced Studies, Research and Development in Sardinia, Science and Technology Park Polaris, Cagliari, Italy
| | - Sandro Orrù
- Dept. of Surgical Sciences, University of Cagliari, Italy
| | - Sante Scognamiglio
- Lab. of Molecular Virology, Dept. of Life and Environmental Sciences, University of Cagliari, Italy
| | - Caterina Serra
- Dept. of Biomedical Sciences, University of Sassari, Italy; S.C. Microbiologia e Virologia, AOU Sassari, Italy
| | - Giuseppe Mameli
- ASL Nuoro, Ospedale San Francesco, Italy; ASL Sassari Ospedale Civile Alghero, Italy
| | - Sergio Uzzau
- Dept. of Biomedical Sciences, University of Sassari, Italy; S.C. Microbiologia e Virologia, AOU Sassari, Italy
| | - Germano Orrù
- Dept. of Surgical Sciences, University of Cagliari, Italy
| | | | - Salvatore Rubino
- Dept. of Biomedical Sciences, University of Sassari, Italy; S.C. Microbiologia e Virologia, AOU Sassari, Italy
| | - Enzo Tramontano
- Lab. of Molecular Virology, Dept. of Life and Environmental Sciences, University of Cagliari, Italy.
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Lai A, Bergna A, Toppo S, Morganti M, Menzo S, Ghisetti V, Bruzzone B, Codeluppi M, Fiore V, Rullo EV, Antonelli G, Sarmati L, Brindicci G, Callegaro A, Sagnelli C, Francisci D, Vicenti I, Miola A, Tonon G, Cirillo D, Menozzi I, Caucci S, Cerutti F, Orsi A, Schiavo R, Babudieri S, Nunnari G, Mastroianni CM, Andreoni M, Monno L, Guarneri D, Coppola N, Crisanti A, Galli M, Zehender G. Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. Sci Rep 2022; 12:5736. [PMID: 35388091 PMCID: PMC8986836 DOI: 10.1038/s41598-022-09738-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 03/25/2022] [Indexed: 12/29/2022] Open
Abstract
The aims of this study were to characterize new SARS-CoV-2 genomes sampled all over Italy and to reconstruct the origin and the evolutionary dynamics in Italy and Europe between February and June 2020. The cluster analysis showed only small clusters including < 80 Italian isolates, while most of the Italian strains were intermixed in the whole tree. Pure Italian clusters were observed mainly after the lockdown and distancing measures were adopted. Lineage B and B.1 spread between late January and early February 2020, from China to Veneto and Lombardy, respectively. Lineage B.1.1 (20B) most probably evolved within Italy and spread from central to south Italian regions, and to European countries. The lineage B.1.1.1 (20D) developed most probably in other European countries entering Italy only in the second half of March and remained localized in Piedmont until June 2020. In conclusion, within the limitations of phylogeographical reconstruction, the estimated ancestral scenario suggests an important role of China and Italy in the widespread diffusion of the D614G variant in Europe in the early phase of the pandemic and more dispersed exchanges involving several European countries from the second half of March 2020.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy.,Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, University of Milan, Milan, Italy
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padua, Italy.,CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Marina Morganti
- Risk Analyses and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Parma, Italy
| | - Stefano Menzo
- Department of Biomedical Sciences and Public Health, Virology Unit, Polytechnic University of Marche, Ancona, Italy
| | - Valeria Ghisetti
- Laboratory of Microbiology and Virology, Amedeo di Savoia, ASL Città di Torino, Torino, Italy
| | | | - Mauro Codeluppi
- UOC of Infectious Diseases, Department of Oncology and Hematology, Guglielmo da Saliceto Hospital, AUSL Piacenza, Piacenza, Italy
| | - Vito Fiore
- Infectious and Tropical Disease Clinic, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Emmanuele Venanzi Rullo
- Unit of Infectious Diseases, Department of Experimental and Clinical Medicine, University of Messina, Messina, Italy
| | - Guido Antonelli
- Department of Molecular Medicine, University Hospital Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | | | | | - Annapaola Callegaro
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Caterina Sagnelli
- Department of Mental Health and Public Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Daniela Francisci
- Department of Medicine and Surgery, Clinic of Infectious Diseases, "Santa Maria della Misericordia" Hospital, University of Perugia, Perugia, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Arianna Miola
- Intesa San Paolo Innovation Center-AI LAB, Turin, Italy
| | - Giovanni Tonon
- Center for Omics Sciences, IRCCS Ospedale San Raffaele, Milan, Italy.,Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Daniela Cirillo
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Ilaria Menozzi
- Risk Analyses and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Parma, Italy
| | - Sara Caucci
- Department of Biomedical Sciences and Public Health, Virology Unit, Polytechnic University of Marche, Ancona, Italy
| | - Francesco Cerutti
- Laboratory of Microbiology and Virology, Amedeo di Savoia, ASL Città di Torino, Torino, Italy
| | - Andrea Orsi
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
| | - Roberta Schiavo
- UOC of Microbiology, Department of Clinical Pathology, Guglielmo da Saliceto Hospital, AUSL Piacenza, Piacenza, Italy
| | - Sergio Babudieri
- Infectious and Tropical Disease Clinic, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Giuseppe Nunnari
- Unit of Infectious Diseases, Department of Experimental and Clinical Medicine, University of Messina, Messina, Italy
| | - Claudio M Mastroianni
- Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | | | - Laura Monno
- Infectious Diseases Unit, University of Bari, Bari, Italy
| | - Davide Guarneri
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Nicola Coppola
- Department of Mental Health and Public Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Andrea Crisanti
- Microbiology and Virology Diagnostic Unit, Padua University Hospital, Padua, Italy.,Department of Life Science, Imperial College London, South Kensington Campus Imperial College Road, London, SW7 AZ, UK
| | - Massimo Galli
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy. .,Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, University of Milan, Milan, Italy. .,CRC-Coordinated Research Center "EpiSoMI", University of Milan, Milan, Italy.
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Malune P, Piras G, Monne M, Fiamma M, Asproni R, Fancello T, Manai A, Carta F, Pira G, Fancello P, Rosu V, Uras A, Mereu C, Mameli G, Lo Maglio I, Garau MC, Palmas AD. Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. Front Microbiol 2022; 12:827799. [PMID: 35095827 PMCID: PMC8795702 DOI: 10.3389/fmicb.2021.827799] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 12/24/2021] [Indexed: 11/18/2022] Open
Abstract
Background The SARS-CoV-2 pandemic stimulated an outstanding global sequencing effort, which allowed to monitor viral circulation and evolution. Nuoro province (Sardinia, Italy), characterized by a relatively isolated geographical location and a low population density, was severely hit and displayed a high incidence of infection. Methods Amplicon approach Next Generation Sequencing and subsequent variant calling in 92 respiratory samples from SARS-CoV-2 infected patients involved in infection clusters from March 2020 to May 2021. Results Phylogenetic analysis displayed a coherent distribution of sequences in terms of lineage and temporal evolution of pandemic. Circulating lineage/clade characterization highlighted a growing diversity over time, with an increasingly growing number of mutations and variability of spike and nucleocapsid proteins, while viral RdRp appeared to be more conserved. A total of 384 different mutations were detected, of which 196 were missense and 147 synonymous ones. Mapping mutations along the viral genome showed an irregular distribution in key genes. S gene was the most mutated gene with missense and synonymous variants frequencies of 58.8 and 23.5%, respectively. Mutation rates were similar for the S and N genes with one mutation every ∼788 nucleotides and every ∼712 nucleotides, respectively. Nsp12 gene appeared to be more conserved, with one mutation every ∼1,270 nucleotides. The frequency of variant Y144F in the spike protein deviated from global values with higher prevalence of this mutation in the island. Conclusion The analysis of the 92 viral genome highlighted evolution over time and identified which mutations are more widespread than others. The high number of sequences also permits the identification of subclusters that are characterized by subtle differences, not only in terms of lineage, which may be used to reconstruct transmission clusters. The disclosure of viral genetic diversity and timely identification of new variants is a useful tool to guide public health intervention measures.
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Affiliation(s)
- Paolo Malune
- UOC Ematologia, P.O. “San Francesco,” Azienda Tutela Salute, ASSL Nuoro, Nuoro, Italy
- UOC Laboratorio Analisi Clinico-Chimiche e Microbiologia, P.O. “San Francesco,” Azienda Tutela Salute, ASSL Nuoro, Nuoro, Italy
| | - Giovanna Piras
- UOC Ematologia, P.O. “San Francesco,” Azienda Tutela Salute, ASSL Nuoro, Nuoro, Italy
- *Correspondence: Giovanna Piras,
| | - Maria Monne
- UOC Ematologia, P.O. “San Francesco,” Azienda Tutela Salute, ASSL Nuoro, Nuoro, Italy
| | - Maura Fiamma
- UOC Laboratorio Analisi Clinico-Chimiche e Microbiologia, P.O. “San Francesco,” Azienda Tutela Salute, ASSL Nuoro, Nuoro, Italy
| | - Rosanna Asproni
- UOC Laboratorio Analisi Clinico-Chimiche e Microbiologia, P.O. “San Francesco,” Azienda Tutela Salute, ASSL Nuoro, Nuoro, Italy
| | - Tatiana Fancello
- UOC Cardiologia, P.O. “San Francesco,” Azienda Tutela Salute, ASSL Nuoro, Nuoro, Italy
| | - Antonio Manai
- UOC Ematologia, P.O. “San Francesco,” Azienda Tutela Salute, ASSL Nuoro, Nuoro, Italy
- UOC Laboratorio Analisi Clinico-Chimiche e Microbiologia, P.O. “San Francesco,” Azienda Tutela Salute, ASSL Nuoro, Nuoro, Italy
| | - Franco Carta
- UOC Laboratorio Analisi Clinico-Chimiche e Microbiologia, P.O. “San Francesco,” Azienda Tutela Salute, ASSL Nuoro, Nuoro, Italy
| | - Giovanna Pira
- UOC Laboratorio Analisi Clinico-Chimiche e Microbiologia, P.O. “San Francesco,” Azienda Tutela Salute, ASSL Nuoro, Nuoro, Italy
| | - Patrizia Fancello
- UOC Laboratorio Analisi Clinico-Chimiche e Microbiologia, P.O. “San Francesco,” Azienda Tutela Salute, ASSL Nuoro, Nuoro, Italy
| | - Valentina Rosu
- UOC Laboratorio Analisi Clinico-Chimiche e Microbiologia, P.O. “San Francesco,” Azienda Tutela Salute, ASSL Nuoro, Nuoro, Italy
| | - Antonella Uras
- UOC Ematologia, P.O. “San Francesco,” Azienda Tutela Salute, ASSL Nuoro, Nuoro, Italy
| | - Caterina Mereu
- UOC Ematologia, P.O. “San Francesco,” Azienda Tutela Salute, ASSL Nuoro, Nuoro, Italy
| | - Giuseppe Mameli
- UOC Laboratorio Analisi Clinico-Chimiche e Microbiologia, P.O. “San Francesco,” Azienda Tutela Salute, ASSL Nuoro, Nuoro, Italy
| | - Iana Lo Maglio
- UOC Laboratorio Analisi Clinico-Chimiche e Microbiologia, P.O. “San Francesco,” Azienda Tutela Salute, ASSL Nuoro, Nuoro, Italy
| | - Maria Cristina Garau
- UOC Laboratorio Analisi Clinico-Chimiche e Microbiologia, P.O. “San Francesco,” Azienda Tutela Salute, ASSL Nuoro, Nuoro, Italy
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