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Scarpa F, Sernicola L, Farcomeni S, Ciccozzi A, Sanna D, Casu M, Vitale M, Cicenia A, Giovanetti M, Romano C, Branda F, Ciccozzi M, Borsetti A. Phylodynamic and Evolution of the Hemagglutinin (HA) and Neuraminidase (NA) Genes of Influenza A(H1N1) pdm09 Viruses Circulating in the 2009 and 2023 Seasons in Italy. Pathogens 2024; 13:334. [PMID: 38668289 PMCID: PMC11054071 DOI: 10.3390/pathogens13040334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/29/2024] Open
Abstract
The influenza A(H1N1) pdm09 virus, which emerged in 2009, has been circulating seasonally since then. In this study, we conducted a comprehensive genome-based investigation to gain a detailed understanding of the genetic and evolutionary characteristics of the hemagglutinin (HA) and neuraminidase (NA) surface proteins of A/H1N1pdm09 strains circulating in Italy over a fourteen-year period from 2009 to 2023 in relation to global strains. Phylogenetic analysis revealed rapid transmission and diversification of viral variants during the early pandemic that clustered in clade 6B.1. In contrast, limited genetic diversity was observed during the 2023 season, probably due to the genetic drift, which provides the virus with a constant adaptability to the host; furthermore, all isolates were split into two main groups representing two clades, i.e., 6B.1A.5a.2a and its descendant 6B.1A.5a.2a.1. The HA gene showed a faster rate of evolution compared to the NA gene. Using FUBAR, we identified positively selected sites 41 and 177 for HA and 248, 286, and 455 for NA in 2009, as well as sites 22, 123, and 513 for HA and 339 for NA in 2023, all of which may be important sites related to the host immune response. Changes in glycosylation acquisition/loss at prominent sites, i.e., 177 in HA and 248 in NA, should be considered as a predictive tool for early warning signs of emerging pandemics, and for vaccine and drug development.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (A.C.); (D.S.)
| | - Leonardo Sernicola
- National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, 00162 Rome, Italy; (L.S.); (S.F.)
| | - Stefania Farcomeni
- National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, 00162 Rome, Italy; (L.S.); (S.F.)
| | - Alessandra Ciccozzi
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (A.C.); (D.S.)
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (A.C.); (D.S.)
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy;
| | - Marco Vitale
- Laboratorio di Biologia Molecolare—Fondazione Università Niccolò Cusano, 00166 Rome, Italy; (M.V.); (A.C.)
| | - Alessia Cicenia
- Laboratorio di Biologia Molecolare—Fondazione Università Niccolò Cusano, 00166 Rome, Italy; (M.V.); (A.C.)
| | - Marta Giovanetti
- Department of Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di Roma, 00128 Rome, Italy;
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, MG, Brazil
- Climate Amplified Diseases and Epidemics (CLIMADE), Brasilia 70070-130, DF, Brazil
| | - Chiara Romano
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy; (C.R.); (F.B.); (M.C.)
| | - Francesco Branda
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy; (C.R.); (F.B.); (M.C.)
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy; (C.R.); (F.B.); (M.C.)
| | - Alessandra Borsetti
- National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, 00162 Rome, Italy; (L.S.); (S.F.)
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Scarpa F, Grattarola C, Arillo A, Mattioda V, Testori C, Terracciano G, Senese M, Giorda F, Zoppi S, Sanna D, Casu M, Peletto S. Draft genome of three isolates of Listeria monocytogenes isolated from Stenella coeruleoalba in Italy. Microbiol Resour Announc 2024; 13:e0122123. [PMID: 38415642 PMCID: PMC11008158 DOI: 10.1128/mra.01221-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/11/2024] [Indexed: 02/29/2024] Open
Abstract
Listeria monocytogenes is the etiological agent of the listeriosis. Here, we described three draft genome sequences of L. monocytogenes isolated in Italy from stranded individuals of the striped dolphin Stenella coeruleoalba. All the genomes have been molecular typed through the multilocus sequence typing to identify the phylogenetic lineage, clonal complex, sublineage, and serogroup.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Carla Grattarola
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Turin, Italy
| | - Alessandra Arillo
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Turin, Italy
| | - Virginia Mattioda
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Turin, Italy
| | - Camilla Testori
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Turin, Italy
| | - Giuliana Terracciano
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri, Pisa, Italy
| | - Matteo Senese
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri, Pisa, Italy
| | - Federica Giorda
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Turin, Italy
| | - Simona Zoppi
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Turin, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Simone Peletto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Turin, Italy
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Coradduzza E, Scarpa F, Rocchigiani AM, Cacciotto C, Lostia G, Fiori MS, Rodriguez Valera Y, De Pascali AM, Brandolini M, Azzena I, Locci C, Casu M, Bechere R, Pintus D, Ligios C, Scagliarini A, Sanna D, Puggioni G. The Global Evolutionary History of Orf Virus in Sheep and Goats Revealed by Whole Genomes Data. Viruses 2024; 16:158. [PMID: 38275968 PMCID: PMC10820850 DOI: 10.3390/v16010158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
Orf virus (ORFV) belongs to the genus Parapoxvirus (Poxviridae family). It is the causative agent of contagious ecthyma (CE) that is an economically detrimental disease affecting small ruminants globally. Contagious ecthyma outbreaks are usually reported in intensive breeding of sheep and goats but they have also been reported in wildlife species. Notably, ORFV can infect humans, leading to a zoonotic disease. This study aims to elucidate the global evolutionary history of ORFV genomes in sheep and goats, including the first genomes from Central America in the analyses. In comparison to the last study on ORFV whole genomes, the database now includes 11 more sheep and goat genomes, representing an increase of 42%. The analysis of such a broader database made it possible to obtain a fine molecular dating of the coalescent time for ORFV S and G genomes, further highlighting the genetic structuring between sheep and goat genomes and corroborating their emergence in the latter half of 20th century.
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Affiliation(s)
- Elisabetta Coradduzza
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (E.C.); (A.M.R.); (G.L.); (M.S.F.); (R.B.); (D.P.); (C.L.); (G.P.)
| | - Fabio Scarpa
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy; (F.S.); (I.A.); (C.L.)
| | - Angela Maria Rocchigiani
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (E.C.); (A.M.R.); (G.L.); (M.S.F.); (R.B.); (D.P.); (C.L.); (G.P.)
| | - Carla Cacciotto
- Dipartimento di Medicina Veterinaria, Università di Sassari, 07100 Sassari, Italy; (C.C.); (M.C.)
- Mediterranean Center for Disease Control, 07100 Sassari, Italy
| | - Giada Lostia
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (E.C.); (A.M.R.); (G.L.); (M.S.F.); (R.B.); (D.P.); (C.L.); (G.P.)
| | - Mariangela Stefania Fiori
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (E.C.); (A.M.R.); (G.L.); (M.S.F.); (R.B.); (D.P.); (C.L.); (G.P.)
| | | | - Alessandra Mistral De Pascali
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, 40138 Bologna, Italy; (A.M.D.P.); (M.B.); (A.S.)
| | - Martina Brandolini
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, 40138 Bologna, Italy; (A.M.D.P.); (M.B.); (A.S.)
| | - Ilenia Azzena
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy; (F.S.); (I.A.); (C.L.)
| | - Chiara Locci
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy; (F.S.); (I.A.); (C.L.)
- Dipartimento di Medicina Veterinaria, Università di Sassari, 07100 Sassari, Italy; (C.C.); (M.C.)
| | - Marco Casu
- Dipartimento di Medicina Veterinaria, Università di Sassari, 07100 Sassari, Italy; (C.C.); (M.C.)
| | - Roberto Bechere
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (E.C.); (A.M.R.); (G.L.); (M.S.F.); (R.B.); (D.P.); (C.L.); (G.P.)
| | - Davide Pintus
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (E.C.); (A.M.R.); (G.L.); (M.S.F.); (R.B.); (D.P.); (C.L.); (G.P.)
| | - Ciriaco Ligios
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (E.C.); (A.M.R.); (G.L.); (M.S.F.); (R.B.); (D.P.); (C.L.); (G.P.)
| | - Alessandra Scagliarini
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, 40138 Bologna, Italy; (A.M.D.P.); (M.B.); (A.S.)
| | - Daria Sanna
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy; (F.S.); (I.A.); (C.L.)
| | - Giantonella Puggioni
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (E.C.); (A.M.R.); (G.L.); (M.S.F.); (R.B.); (D.P.); (C.L.); (G.P.)
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Ciccozzi A, Fiori PL, Casu M, Sanna D, Ciccozzi M, Scarpa F. The mutation point of view of the SARS-CoV-2 HV.1 lineage. J Med Virol 2024; 96:e29359. [PMID: 38164631 DOI: 10.1002/jmv.29359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/01/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Affiliation(s)
- Alessandra Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, Rome, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Azienza Ospedaliera Universitaria (AOU) Sassari, Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, Rome, Italy
| | - Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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Sanna D, Azzena I, Locci C, Ankon P, Kružić P, Manfrin C, Pallavicini A, Ciriaco S, Segarich M, Batistini E, Scarpa F, Casu M. Reconstructing the Evolutionary History of Pinna nobilis: New Genetic Signals from the Past of a Species on the Brink of Extinction. Animals (Basel) 2023; 14:114. [PMID: 38200845 PMCID: PMC10778441 DOI: 10.3390/ani14010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Pinna nobilis, commonly known as the noble pen shell, is a marine bivalve endemic to the Mediterranean Sea. Unfortunately, due to a multifactorial disease that began affecting its populations in 2016, the species is currently facing the threat of extinction. To gain insights into the evolutionary history of P. nobilis before the mass mortality event (MME), and to obtain a comprehensive understanding of how evolutionary processes led to the adaptation of the species into the Mediterranean Sea, phylogenetic and phylogeographic analyses were carried out. The dataset analysed includes 469 sequences of COI gene fragment both from GenBank and the present study (100). The analysis performed evidenced that P. nobilis diverged about 2.5 mya, after the entrance of its ancestor into the Mediterranean Sea following the Zanclean flood (5.33 mya). Moreover, our results suggest that the starting point of colonisation was the central part of the western Mediterranean basin, with the eastern basin being populated subsequently. From a conservational viewpoint, these results provide important hints for present and future restocking plans, helping to reconstruct the pre-existing genetic variability in sites where the species became extinct.
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Affiliation(s)
- Daria Sanna
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy; (I.A.); (C.L.); (F.S.)
| | - Ilenia Azzena
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy; (I.A.); (C.L.); (F.S.)
| | - Chiara Locci
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy; (I.A.); (C.L.); (F.S.)
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy;
| | - Pavel Ankon
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (P.A.); (P.K.)
| | - Petar Kružić
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (P.A.); (P.K.)
| | - Chiara Manfrin
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste, Italy; (C.M.); (A.P.)
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste, Italy; (C.M.); (A.P.)
| | - Saul Ciriaco
- WWF AMP Miramare, Via Beirut 2/4, 34151 Trieste, Italy;
- Shoreline Soc. Coop., AREA Science Park, Padriciano 99, 34149 Trieste, Italy; (M.S.); (E.B.)
| | - Marco Segarich
- Shoreline Soc. Coop., AREA Science Park, Padriciano 99, 34149 Trieste, Italy; (M.S.); (E.B.)
| | - Edoardo Batistini
- Shoreline Soc. Coop., AREA Science Park, Padriciano 99, 34149 Trieste, Italy; (M.S.); (E.B.)
| | - Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy; (I.A.); (C.L.); (F.S.)
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy;
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Scarpa F, Pascarella S, Ciccozzi A, Giovanetti M, Azzena I, Locci C, Casu M, Fiori PL, Quaranta M, Cella E, Sanna D, Ciccozzi M. Genetic and structural analyses reveal the low potential of the SARS-CoV-2 EG.5 variant. J Med Virol 2023; 95:e29075. [PMID: 37665162 DOI: 10.1002/jmv.29075] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/05/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 EG.5 lineage is the latest variant under monitoring, and it is generating significant concern due to its recent upward trend in prevalence. Our aim was to gain insights into this emerging lineage and offer insights into its actual level of threat. Both genetic and structural data indicate that this novel variant presently lacks substantial evidence of having a high capacity for widespread transmission. Their viral population sizes expanded following a very mild curve and peaked several months after the earliest detected sample. Currently, neither the viral population size of EG.5 nor that of its first descendant is increasing. The genetic variability appear to be flattened, as evidenced by its relatively modest evolutionary rate (9.05 × 10-4 subs/site/year). As has been observed with numerous prior variants, attributes that might theoretically provide advantages seem to stem from genetic drift, enabling the virus to continually adjust to its host, albeit without a clear association with enhanced dangerousness. These findings further underscore the necessity for ongoing genome-based monitoring, ensuring preparedness and a well-documented understanding of the unfolding situation.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza Università di Roma, Rome, Italy
| | - Alessandra Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, Rome, Italy
| | - Marta Giovanetti
- Department of Science and Technology for Humans and the Environment, Università Campus Bio-Medico di Roma, Rome, Italy
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo, Horizonte, Minas Gerais, Brazil
| | - Ilenia Azzena
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Chiara Locci
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Azienza Ospedaliera Universitaria (AOU) Sassari, Sassari, Italy
| | - Miriana Quaranta
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza Università di Roma, Rome, Italy
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, Rome, Italy
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Scarpa F, Azzena I, Ciccozzi A, Giovanetti M, Locci C, Casu M, Fiori PL, Borsetti A, Cella E, Quaranta M, Pascarella S, Sanna D, Ciccozzi M. Integrative Genome-Based Survey of the SARS-CoV-2 Omicron XBB.1.16 Variant. Int J Mol Sci 2023; 24:13573. [PMID: 37686383 PMCID: PMC10487968 DOI: 10.3390/ijms241713573] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
The XBB.1.16 SARS-CoV-2 variant, also known as Arcturus, is a recent descendant lineage of the recombinant XBB (nicknamed Gryphon). Compared to its direct progenitor, XBB.1, XBB.1.16 carries additional spike mutations in key antigenic sites, potentially conferring an ability to evade the immune response compared to other circulating lineages. In this context, we conducted a comprehensive genome-based survey to gain a detailed understanding of the evolution and potential dangers of the XBB.1.16 variant, which became dominant in late June. Genetic data indicates that the XBB.1.16 variant exhibits an evolutionary background with limited diversification, unlike dangerous lineages known for rapid changes. The evolutionary rate of XBB.1.16, which amounts to 3.95 × 10-4 subs/site/year, is slightly slower than that of its direct progenitors, XBB and XBB.1.5, which have been circulating for several months. A Bayesian Skyline Plot reconstruction suggests that the peak of genetic variability was reached in early May 2023, and currently, it is in a plateau phase with a viral population size similar to the levels observed in early March. Structural analyses indicate that, overall, the XBB.1.16 variant does not possess structural characteristics markedly different from those of the parent lineages, and the theoretical affinity for ACE2 does not seem to change among the compared variants. In conclusion, the genetic and structural analyses of SARS-CoV-2 XBB.1.16 do not provide evidence of its exceptional danger or high expansion capability. Detected differences with previous lineages are probably due to genetic drift, which allows the virus constant adaptability to the host, but they are not necessarily connected to a greater danger. Nevertheless, continuous genome-based monitoring is essential for a better understanding of its descendants and other lineages.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Ilenia Azzena
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Alessandra Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Marta Giovanetti
- Instituto Rene Rachou Fundação Oswaldo Cruz, Belo Horizonte 30190-009, MG, Brazil
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Chiara Locci
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Azienza Ospedaliera Universitaria (AOU) Sassari, 07100 Sassari, Italy
| | - Alessandra Borsetti
- National HIV/AIDS Research Center (CNAIDS), National Institute of Health, 00161 Rome, Italy
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
| | - Miriana Quaranta
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
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Carella F, Palić D, Šarić T, Župan I, Gorgoglione B, Prado P, Andree KB, Giantsis IA, Michaelidis B, Lattos A, Theodorou JA, Luis Barja Perez J, Rodriguez S, Scarpa F, Casu M, Antuofermo E, Sanna D, Otranto D, Panarese R, Iaria C, Marino F, Vico GD. Multipathogen infections and multifactorial pathogenesis involved in noble pen shell ( Pinna nobilis) mass mortality events: Background and current pathologic approaches. Vet Pathol 2023; 60:560-577. [PMID: 37458195 DOI: 10.1177/03009858231186737] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Disease outbreaks in several ecologically or commercially important invertebrate marine species have been reported in recent years all over the world. Mass mortality events (MMEs) have affected the noble pen shell (Pinna nobilis), causing its near extinction. Our knowledge of the dynamics of diseases affecting this species is still unclear. Early studies investigating the causative etiological agent focused on a novel protozoan parasite, Haplosporidium pinnae, although further investigations suggested that concurrent polymicrobial infections could have been pivotal in some MMEs, even in the absence of H. pinnae. Indeed, moribund specimens collected during MMEs in Italy, Greece, and Spain demonstrated the presence of a bacteria from within the Mycobacterium simiae complex and, in some cases, species similar to Vibrio mediterranei. The diagnostic processes used for investigation of MMEs are still not standardized and require the expertise of veterinary and para-veterinary pathologists, who could simultaneously evaluate a variety of factors, from clinical signs to environmental conditions. Here, we review the available literature on mortality events in P. nobilis and discuss approaches to define MMEs in P. nobilis. The proposed consensus approach should form the basis for establishing a foundation for future studies aimed at preserving populations in the wild.
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Affiliation(s)
| | - Dušan Palić
- Ludwig-Maximilians-University Munich, Munich, Germany
| | | | | | | | | | | | | | | | | | | | | | - Sergio Rodriguez
- University of Santiago de Compostela, Santiago de Compostela, Spain
| | | | | | | | | | - Domenico Otranto
- University of Bari, Bari, Italy
- Bu-Ali Sina University, Hamedan, Iran
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9
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Scarpa F, Bazzani L, Giovanetti M, Ciccozzi A, Benedetti F, Zella D, Sanna D, Casu M, Borsetti A, Cella E, Pascarella S, Maruotti A, Ciccozzi M. Update on the Phylodynamic and Genetic Variability of Marburg Virus. Viruses 2023; 15:1721. [PMID: 37632063 PMCID: PMC10458864 DOI: 10.3390/v15081721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
The COVID-19 pandemic has not only strained healthcare systems in Africa but has also intensified the impact of emerging and re-emerging diseases. Specifically in Equatorial Guinea, mirroring the situation in other African countries, unique zoonotic outbreaks have occurred during this challenging period. One notable resurgence is Marburg virus disease (MVD), which has further burdened the already fragile healthcare system. The re-emergence of the Marburg virus amid the COVID-19 pandemic is believed to stem from a probable zoonotic spill-over, although the precise transmission routes remain uncertain. Given the gravity of the situation, addressing the existing challenges is paramount. Though the genome sequences from the current outbreak were not available for this study, we analyzed all the available whole genome sequences of this re-emerging pathogen to advocate for a shift towards active surveillance. This is essential to ensure the successful containment of any potential Marburg virus outbreak in Equatorial Guinea and the wider African context. This study, which presents an update on the phylodynamics and the genetic variability of MARV, further confirmed the existence of at least two distinct patterns of viral spread. One pattern demonstrates a slower but continuous and recurring virus circulation, while the other exhibits a faster yet limited and episodic spread. These results highlight the critical need to strengthen genomic surveillance in the region to effectively curb the pathogen's dissemination. Moreover, the study emphasizes the importance of prompt alert management, comprehensive case investigation and analysis, contact tracing, and active case searching. These steps are vital to support the healthcare system's response to this emerging health crisis. By implementing these strategies, we can better arm ourselves against the challenges posed by the resurgence of the Marburg virus and other infectious diseases.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy;
| | - Liliana Bazzani
- Department of Science and Technology for Humans and the Environment, Università Campus Bio-Medico di Roma, 00128 Rome, Italy; (L.B.); (M.G.)
| | - Marta Giovanetti
- Department of Science and Technology for Humans and the Environment, Università Campus Bio-Medico di Roma, 00128 Rome, Italy; (L.B.); (M.G.)
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, MG, Brazil
| | - Alessandra Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy; (A.C.); (M.C.)
| | - Francesca Benedetti
- Institute of Human Virlogy and Global Virusn Network Center, Deparment of Biochemistry and Molecular Biology, University for Maryland School of Medicine, Baltimore, MD 21201, USA; (F.B.); (D.Z.)
| | - Davide Zella
- Institute of Human Virlogy and Global Virusn Network Center, Deparment of Biochemistry and Molecular Biology, University for Maryland School of Medicine, Baltimore, MD 21201, USA; (F.B.); (D.Z.)
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy;
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy;
| | - Alessandra Borsetti
- National HIV/AIDS Research Center (CNAIDS), National Institute of Health, 00161 Rome, Italy;
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA;
| | - Stefano Pascarella
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy;
| | | | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy; (A.C.); (M.C.)
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10
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Coupé S, Giantsis IA, Vázquez Luis M, Scarpa F, Foulquié M, Prévot J, Casu M, Lattos A, Michaelidis B, Sanna D, García‐March JR, Tena‐Medialdea J, Vicente N, Bunet R. The characterization of toll-like receptor repertoire in Pinna nobilis after mass mortality events suggests adaptive introgression. Ecol Evol 2023; 13:e10383. [PMID: 37546570 PMCID: PMC10401143 DOI: 10.1002/ece3.10383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 08/08/2023] Open
Abstract
The fan mussel Pinna nobilis is currently on the brink of extinction due to a multifactorial disease mainly caused to the highly pathogenic parasite Haplosporidium pinnae, meaning that the selection pressure outweighs the adaptive potential of the species. Hopefully, rare individuals have been observed somehow resistant to the parasite, stretching the need to identify the traits underlying this better fitness. Among the candidate to explore at first intention are fast-evolving immune genes, of which toll-like receptor (TLR). In this study, we examined the genetic diversity at 14 TLR loci across P. nobilis, Pinna rudis and P. nobilis × P. rudis hybrid genomes, collected at four physically distant regions, that were found to be either resistant or sensitive to the parasite H. pinnae. We report a high genetic diversity, mainly observed at cell surface TLRs compared with that of endosomal TLRs. However, the endosomal TLR-7 exhibited unexpected level of diversity and haplotype phylogeny. The lack of population structure, associated with a high genetic diversity and elevated dN/dS ratio, was interpreted as balancing selection, though both directional and purifying selection were detected. Interestingly, roughly 40% of the P. nobilis identified as resistant to H. pinnae were introgressed with P. rudis TLR. Specifically, they all carried a TLR-7 of P. rudis origin, whereas sensitive P. nobilis were not introgressed, at least at TLR loci. Small contributions of TLR-6 and TLR-4 single-nucleotide polymorphisms to the clustering of resistant and susceptible individuals could be detected, but their specific role in resistance remains highly speculative. This study provides new information on the diversity of TLR genes within the P. nobilis species after MME and additional insights into adaptation to H. pinnae that should contribute to the conservation of this Mediterranean endemic species.
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Affiliation(s)
- Stéphane Coupé
- Université de Toulon, Aix Marseille Univ, CNRS, IRD, MIOMarseilleFrance
| | | | - Maite Vázquez Luis
- Instituto Español de Oceanografía (IEO, CSIC), Centro Oceanográfico de BalearesPalma de MallorcaSpain
| | - Fabio Scarpa
- Department of Biomedical SciencesFabio Scarpa, Daria Sanna: University of SassariSassariItaly
| | - Mathieu Foulquié
- Université de Toulon, Aix Marseille Univ, CNRS, IRD, MIOMarseilleFrance
- Institut océanographique Paul RicardIle des Embiez, VarFrance
| | | | - Marco Casu
- Department of Veterinary MedicineUniversity of SassariSassariItaly
| | - Athanasios Lattos
- Faculty of Agricultural SciencesUniversity of Western MacedoniaKozaniGreece
| | - Basile Michaelidis
- Faculty of Agricultural SciencesUniversity of Western MacedoniaKozaniGreece
| | - Daria Sanna
- Department of Biomedical SciencesFabio Scarpa, Daria Sanna: University of SassariSassariItaly
| | - José Rafa García‐March
- IMEDMAR‐UCV, Institute of Environment and Marine Science ResearchUniversidad Católica de Valencia SVMCalpe, AlicanteSpain
| | - José Tena‐Medialdea
- IMEDMAR‐UCV, Institute of Environment and Marine Science ResearchUniversidad Católica de Valencia SVMCalpe, AlicanteSpain
| | - Nardo Vicente
- Institut Méditerranéen de Biodiversité et Ecologie marine et continentale (IMBE), Aix‐Marseille Université, CNRS, IRD, Avignon UniversitéAvignonFrance
| | - Robert Bunet
- Institut océanographique Paul RicardIle des Embiez, VarFrance
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11
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Giovanetti M, Branda F, Cella E, Scarpa F, Bazzani L, Ciccozzi A, Slavov SN, Benvenuto D, Sanna D, Casu M, Santos LA, Lai A, Zehender G, Caccuri F, Ianni A, Caruso A, Maroutti A, Pascarella S, Borsetti A, Ciccozzi M. Epidemic history and evolution of an emerging threat of international concern, the severe acute respiratory syndrome coronavirus 2. J Med Virol 2023; 95:e29012. [PMID: 37548148 DOI: 10.1002/jmv.29012] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/12/2023] [Accepted: 07/20/2023] [Indexed: 08/08/2023]
Abstract
This comprehensive review focuses on the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its impact as the cause of the COVID-19 pandemic. Its objective is to provide a cohesive overview of the epidemic history and evolutionary aspects of the virus, with a particular emphasis on its emergence, global spread, and implications for public health. The review delves into the timelines and key milestones of SARS-CoV-2's epidemiological progression, shedding light on the challenges encountered during early containment efforts and subsequent waves of transmission. Understanding the evolutionary dynamics of the virus is crucial in monitoring its potential for adaptation and future outbreaks. Genetic characterization of SARS-CoV-2 is discussed, with a focus on the emergence of new variants and their implications for transmissibility, severity, and immune evasion. The review highlights the important role of genomic surveillance in tracking viral mutations linked to establishing public health interventions. By analyzing the origins, global spread, and genetic evolution of SARS-CoV-2, valuable insights can be gained for the development of effective control measures, improvement of pandemic preparedness, and addressing future emerging infectious diseases of international concern.
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Affiliation(s)
- Marta Giovanetti
- Instituto Rene Rachou Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, Italy, Rome, Italy
| | - Francesco Branda
- Department of Computer Science, Modeling, Electronics and Systems Engineering (DIMES), University of Calabria, Rende, Italy
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA
| | - Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Liliana Bazzani
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, Italy, Rome, Italy
| | - Alessandra Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Svetoslav Nanev Slavov
- Butantan Institute, São Paulo, Brazil
- Blood Center of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Domenico Benvenuto
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Luciane Amorim Santos
- Escola Bahiana de Medicina e Saúde Pública, Salvador, Bahia, Brazil
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Praça Ramos de Queirós, s/n, Largo do Terreiro de Jesus, Salvador, Bahia, Brazil
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences, L. Sacco Hospital, University of Milan, Milan, Italy
| | - Giangluglielmo Zehender
- Department of Biomedical and Clinical Sciences, L. Sacco Hospital, University of Milan, Milan, Italy
| | - Francesca Caccuri
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Andrea Ianni
- M.G. Vannini Hospital IFSC Rome, Research Unit in Hygiene UCBM Rome, Rome, Italy
| | - Arnaldo Caruso
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | | | - Stefano Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | | | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
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12
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Scarpa F, Locci C, Azzena I, Casu M, Fiori PL, Ciccozzi A, Giovanetti M, Quaranta M, Ceccarelli G, Pascarella S, Ciccozzi M, Sanna D. SARS-CoV-2 Recombinants: Genomic Comparison between XBF and Its Parental Lineages. Microorganisms 2023; 11:1824. [PMID: 37512996 PMCID: PMC10383834 DOI: 10.3390/microorganisms11071824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/05/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Recombination events are very common and represent one of the primary drivers of RNA virus evolution. The XBF SARS-CoV-2 lineage is one of the most recently generated recombinants during the COVID-19 pandemic. It is a recombinant of BA.5.2.3 and BA.2.75.3, both descendants of lineages that caused many concerns (BA.5 and BA.2.75, respectively). Here, we performed a genomic survey focused on comparing the recombinant XBF with its parental lineages to provide a comprehensive assessment of the evolutionary potential, epidemiological trajectory, and potential risks. Genetic analyses indicated that although XBF initially showed the typical expansion depicted by a steep curve, causing several concerns, currently there is no indication of significant expansion potential or a contagion rate surpassing that of other currently active or previously prevalent lineages. BSP indicated that the peak has been reached around 19 October 2022 and then the genetic variability suffered slight oscillations until early 5 March 2023 when the population size reduced for the last time starting its last plateau that is still lasting. Structural analyses confirmed its reduced potential, also indicating that properties of NTDs and RBDs of XBF and its parental lineages present no significant difference. Of course, cautionary measures must still be taken and genome-based monitoring remains the best tool for detecting any important changes in viral genome composition.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Chiara Locci
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Ilenia Azzena
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Azienza Ospedaliera Universitaria (AOU) Sassari, 07100 Sassari, Italy
| | - Alessandra Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Marta Giovanetti
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico of Rome, 00128 Rome, Italy
- Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, Minas Gerais, Brazil
| | - Miriana Quaranta
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Rome, Italy
| | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto I, Sapienza University of Rome, 00161 Rome, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Campus Bio-Medico, Fondazione Policlinico Universitario, 00128 Rome, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
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Scarpa F, Sanna D, Giovanetti M, Pascarella S, Casu M, Ciccozzi M. Avian influenza A H5N1: are we really sure it is a spillover? Pathog Glob Health 2023; 117:323-325. [PMID: 37042611 PMCID: PMC10177696 DOI: 10.1080/20477724.2023.2201980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023] Open
Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo, Cruz, Belo Horizonte, Minas Gerais, Brazil
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico, Rome, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza Università di Roma, Rome, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
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Bazzani L, Imperia E, Scarpa F, Sanna D, Casu M, Borsetti A, Pascarella S, Petrosillo N, Cella E, Giovanetti M, Ciccozzi M. SARS-CoV CH.1.1 Variant: Genomic and Structural Insight. Infect Dis Rep 2023; 15:292-298. [PMID: 37367188 DOI: 10.3390/idr15030029] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023] Open
Abstract
In early February 2023, the Omicron subvariant XBB.1.5, also known as "Kraken", accounted for more than 44% of new COVID-19 cases worldwide, whereas a relatively new Omicron subvariant named CH.1.1, deemed "Orthrus", accounted for less than 6% of new COVID-19 cases during the subsequent weeks. This emerging variant carries a mutation, L452R, previously observed in the highly pathogenic Delta and the highly transmissible BA.4 and BA.5 variants, necessitating a shift to active surveillance to assure adequate preparedness for likely future epidemic peaks. We provide a preliminary understanding of the global distribution of this emerging SARS-CoV-2 variant by combining genomic data with structural molecular modeling. In addition, we shield light on the number of specific point mutations in this lineage that may have functional significance, thereby increasing the risk of disease severity, vaccine resistance, and increased transmission. This variant shared about 73% of the mutations with Omicron-like strains. Our homology modeling analysis revealed that CH.1.1 may have a weakened interaction with ACE2 and that its electrostatic potential surface appears to be more positive than that of the reference ancestral virus. Finally, our phylogenetic analysis revealed that this likely-emerging variant was already cryptically circulating in European countries prior to its first detection, highlighting the importance of having access to whole genome sequences for detecting and controlling emerging viral strains.
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Affiliation(s)
- Liliana Bazzani
- Sciences and Technologies for Sustainable Development and One Health, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Elena Imperia
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Unit of Gastroenterology, Department of Medicine, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Alessandra Borsetti
- National HIV/AIDS Research Center (CNAIDS), National Institute of Health, 00161 Rome, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, 00185 Rome, Italy
| | - Nicola Petrosillo
- Infection Prevention and Control-Infectious Disease Service, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
| | - Marta Giovanetti
- Sciences and Technologies for Sustainable Development and One Health, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Instituto Rene Rachou Fundação Oswaldo Cruz, Belo Horizonte 30190-002, MG, Brazil
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
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15
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Scarpa F, Giovanetti M, Azzena I, Locci C, Casu M, Fiori PL, Ciccozzi A, Imperia E, Bazzani L, Borsetti A, Maruotti A, Pascarella S, Sanna D, Ciccozzi M. Genome-based survey of the SARS-CoV-2 BF.7 variant from Asia. J Med Virol 2023; 95:e28714. [PMID: 37000592 DOI: 10.1002/jmv.28714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/16/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023]
Abstract
The SARS-CoV-2 BF.7 variant represents one of the most recent subvariant under monitoring. At the beginning of the 2023 if caused several concerns especially in Asia because of a resurge in COVID-19 cases. Here we perform a genome-based integrative approach on SARS-CoV-2 BF.7 in order to shed light on this emerging lineage and produce some consideration on its real dangerousness. Both genetic and structural data suggest that this new variant currently does not show evidence of an high expansion capability. It is very common in Asia, but it appears less virulent than other Omicron variants as proved by its relatively low evolutionary rate (5.62 x 10-4 subs/sites/years). The last plateau has been reached around December 14, 2022 and then the genetic variability, and thus the viral population size, no longer increased. As already seen for several previous variants, the features that may be theoretically related to advantages are due to genetic drift that allows to the virus a constant adaptability to the host, but is not strictly connected to a fitness advantage. These results have further pointed that the genome-based monitoring must continue uninterruptedly in order to be prepared and well documented on the real situation. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico
| | - Ilenia Azzena
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Chiara Locci
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Azienza Ospedaliera Universitaria (AOU) Sassari, Sassari, Italy
| | - Alessandra Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Elena Imperia
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
- Unit of Gastroenterology, Department of Medicine, University Campus Bio-Medico of Rome, Rome, Italy
| | - Liliana Bazzani
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico
| | - Alessandra Borsetti
- National HIV/AIDS Research Center (CNAIDS); Istituto Superiore di Sanità (ISS), Rome, Italy
| | | | - Stefano Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza Università di Roma, Rome, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
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16
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Scarpa F, Azzena I, Locci C, Casu M, Fiori PL, Ciccozzi A, Angeletti S, Imperia E, Giovanetti M, Maruotti A, Borsetti A, Cauda R, Cassone A, Via A, Pascarella S, Sanna D, Ciccozzi M. Molecular In-Depth on the Epidemiological Expansion of SARS-CoV-2 XBB.1.5. Microorganisms 2023; 11:microorganisms11040912. [PMID: 37110335 PMCID: PMC10142263 DOI: 10.3390/microorganisms11040912] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Since the beginning of the pandemic, the generation of new variants periodically recurs. The XBB.1.5 SARS-CoV-2 variant is one of the most recent. This research was aimed at verifying the potential hazard of this new subvariant. To achieve this objective, we performed a genome-based integrative approach, integrating results from genetic variability/phylodynamics with structural and immunoinformatic analyses to obtain as comprehensive a viewpoint as possible. The Bayesian Skyline Plot (BSP) shows that the viral population size reached the plateau phase on 24 November 2022, and the number of lineages peaked at the same time. The evolutionary rate is relatively low, amounting to 6.9 × 10−4 subs/sites/years. The NTD domain is identical for XBB.1 and XBB.1.5 whereas their RBDs only differ for the mutations at position 486, where the Phe (in the original Wuhan) is replaced by a Ser in XBB and XBB.1, and by a Pro in XBB.1.5. The variant XBB.1.5 seems to spread more slowly than sub-variants that have caused concerns in 2022. The multidisciplinary molecular in-depth analyses on XBB.1.5 performed here does not provide evidence for a particularly high risk of viral expansion. Results indicate that XBB.1.5 does not possess features to become a new, global, public health threat. As of now, in its current molecular make-up, XBB.1.5 does not represent the most dangerous variant.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Correspondence: (F.S.); (M.C.)
| | - Ilenia Azzena
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Chiara Locci
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Azienza Ospedaliera Universitaria (AOU) Sassari, 07100 Sassari, Italy
| | - Alessandra Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, Department of Medicine and Surgery, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Research Unit of Laboratory, University Hospital Campus Bio-Medico, 00128 Rome, Italy
| | - Elena Imperia
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Unit of Gastroenterology, Department of Medicine, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, Minas Gerais, Brazil
- Science and Technology for Sustainable Development and One Health, University of Campus Bio-Medico of Rome, 00128 Rome, Italy
| | | | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Roberto Cauda
- UOC Malattie Infettive, Infectious Disease Department, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | | | - Allegra Via
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Correspondence: (F.S.); (M.C.)
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Scarpa F, Imperia E, Azzena I, Giovanetti M, Benvenuto D, Locci C, Casu M, Fiori PL, Maruotti A, Ceccarelli G, Borsetti A, Caruso A, Cauda R, Cassone A, Via A, Pascarella S, Sanna D, Ciccozzi M. Genetic and structural genome-based survey reveals the low potential for epidemiological expansion of the SARS-CoV-2 XBB.1.5 sublineage. J Infect 2023; 86:596-598. [PMID: 36863537 PMCID: PMC9974203 DOI: 10.1016/j.jinf.2023.02.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/04/2023]
Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
| | - Elena Imperia
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy; Unit of Gastroenterology, Department of Medicine, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Ilenia Azzena
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy; Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil; Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
| | - Domenico Benvenuto
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Chiara Locci
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy; Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy; Azienza Ospedaliera Universitaria (AOU) Sassari, Sassari, Italy
| | | | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Arnaldo Caruso
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, 25123 Brescia, Italy
| | - Roberto Cauda
- UOC Malattie Infettive, Infectious Disease Department, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | | | - Allegra Via
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Rome, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Rome, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy.
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18
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Scarpa F, Sanna D, Azzena I, Casu M, Cossu P, Fiori PL, Benvenuto D, Imperia E, Giovanetti M, Ceccarelli G, Cauda R, Cassone A, Pascarella S, Ciccozzi M. Genome-based comparison between the recombinant SARS-CoV-2 XBB and its parental lineages. J Med Virol 2023; 95:e28625. [PMID: 36852665 DOI: 10.1002/jmv.28625] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/01/2023] [Accepted: 02/19/2023] [Indexed: 03/01/2023]
Abstract
Recombination is the main contributor to RNA virus evolution, and SARS-CoV-2 during the pandemic produced several recombinants. The most recent SARS-CoV-2 recombinant is the lineage labeled XBB, also known as Gryphon, which arose from BJ.1 and BM.1.1.1. Here we performed a genome-based survey aimed to compare the new recombinant with its parental lineages that never became dominant. Genetic analyses indicated that the recombinant XBB and its first descendant XBB.1 show an evolutionary condition typical of an evolutionary blind background with no further epidemiologically relevant descendant. Genetic variability and expansion capabilities are slightly higher than parental lineages. Bayesian Skyline Plot indicates that XBB reached its plateau around October 6, 2022 and after an initial rapid growth the viral population size did not further expand, and around November 10, 2022 its levels of genetic variability decreased. Simultaneously with the reduction of the XBB population size, an increase of the genetic variability of its first sub-lineage XBB.1 occurred, that in turn reached the plateau around November 9, 2022 showing a kind of vicariance with its direct progenitors. Structure analysis indicates that the affinity for ACE2 surface in XBB/XBB.1 RBDs is weaker than for BA.2 RBD. In conclusion, at present XBB and XBB.1 do not show evidence about a particular danger or high expansion capability. Genome-based monitoring must continue uninterrupted in order to individuate if further mutations can make XBB more dangerous or generate new subvariants with different expansion capability. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Ilenia Azzena
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Piero Cossu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.,Azienza Ospedaliera Universitaria (AOU) Sassari, Sassari, Italy
| | - Domenico Benvenuto
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Elena Imperia
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy.,Unit of Gastroenterology, Department of Medicine, University Campus Bio-Medico of Rome, 00128, Rome, Italy
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil.,Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
| | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | - Roberto Cauda
- UOC Malattie Infettive, Infectious Disease Department, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168, Rome, Italy
| | | | - Stefano Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza Università di Roma, 00185, Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
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19
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Scarpa F, Sanna D, Benvenuto D, Borsetti A, Azzena I, Casu M, Fiori PL, Giovanetti M, Maruotti A, Ceccarelli G, Caruso A, Caccuri F, Cauda R, Cassone A, Pascarella S, Ciccozzi M. Genetic and Structural Data on the SARS-CoV-2 Omicron BQ.1 Variant Reveal Its Low Potential for Epidemiological Expansion. Int J Mol Sci 2022; 23:15264. [PMID: 36499592 PMCID: PMC9739521 DOI: 10.3390/ijms232315264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
The BQ.1 SARS-CoV-2 variant, also known as Cerberus, is one of the most recent Omicron descendant lineages. Compared to its direct progenitor BA.5, BQ.1 has some additional spike mutations in some key antigenic sites, which confer further immune escape ability over other circulating lineages. In such a context, here, we perform a genome-based survey aimed at obtaining a complete-as-possible nuance of this rapidly evolving Omicron subvariant. Genetic data suggest that BQ.1 represents an evolutionary blind background, lacking the rapid diversification that is typical of a dangerous lineage. Indeed, the evolutionary rate of BQ.1 is very similar to that of BA.5 (7.6 × 10-4 and 7 × 10-4 subs/site/year, respectively), which has been circulating for several months. The Bayesian Skyline Plot reconstruction indicates a low level of genetic variability, suggesting that the peak was reached around 3 September 2022. Concerning the affinity for ACE2, structure analyses (also performed by comparing the properties of BQ.1 and BA.5 RBD) indicate that the impact of the BQ.1 mutations may be modest. Likewise, immunoinformatic analyses showed moderate differences between the BQ.1 and BA5 potential B-cell epitopes. In conclusion, genetic and structural analyses on SARS-CoV-2 BQ.1 suggest no evidence of a particularly dangerous or high expansion capability. Genome-based monitoring must continue uninterrupted for a better understanding of its descendants and all other lineages.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Domenico Benvenuto
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Ilenia Azzena
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Marta Giovanetti
- Flavivirus Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, 00128 Rome, Italy
| | | | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto I, Sapienza University of Rome, 00161 Rome, Italy
| | - Arnaldo Caruso
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, 25123 Brescia, Italy
| | - Francesca Caccuri
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, 25123 Brescia, Italy
| | - Roberto Cauda
- UOC Malattie Infettive, Infectious Disease Department, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | | | - Stefano Pascarella
- Department of Biochemical Sciences “A Rossi Fanelli”, Sapienza Università di Roma, 00161 Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
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20
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Scarpa F, Sanna D, Azzena I, Cossu P, Locci C, Angeletti S, Maruotti A, Ceccarelli G, Casu M, Fiori PL, Petrosillo N, Ciccozzi M. Genetic Variability of the Monkeypox Virus Clade IIb B.1. J Clin Med 2022; 11:6388. [PMID: 36362616 PMCID: PMC9695420 DOI: 10.3390/jcm11216388] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 08/27/2023] Open
Abstract
Monkeypox is caused by a sylvatic, double-stranded DNA zoonotic virus. Since 1 January 2022, monkeypox cases have been reported to WHO from 106 Member States across six WHO regions, and as of 2 October 2022, a total of 68,900 confirmed cases, including 25 deaths, occurred. Here, by using a whole genome approach, we perform a genetic and phylodynamic survey of the monkeypox virus Clade IIb B.1, which is the lineage causing the current multi-country outbreak. Results suggest that outbreaks seem to be isolated and localized in several epidemic clusters with geographic consistency. Currently, monkeypox appears to be a virus with a flattened genetic variability in terms of evolutionary path, with a very slow rate of growth in the population size. This scenario confirms that the monkeypox virus lacks the evolutionary advantage, given by the high level of mutation rate, which is very strong in RNA viruses. Of course, constant genome-based monitoring must be performed over time in order to detect the change in its genetic composition, if any.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Ilenia Azzena
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Piero Cossu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Chiara Locci
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Silvia Angeletti
- Department of Medicine and Surgery, Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Research Unit of Laboratory, University Hospital Campus Bio-Medico, 00128 Rome, Italy
| | | | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto I, Sapienza University of Rome, 00161 Rome, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Nicola Petrosillo
- Infection Prevention and Control, University Hospital Campus Bio-Medico, 00128 Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00100 Rome, Italy
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21
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Cossu P, Mura L, Dedola GL, Lai T, Sanna D, Scarpa F, Azzena I, Fois N, Casu M. Detection of Genetic Patterns in Endangered Marine Species Is Affected by Small Sample Sizes. Animals (Basel) 2022; 12:ani12202763. [PMID: 36290149 PMCID: PMC9597844 DOI: 10.3390/ani12202763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
Knowledge of Genetic diversity and its spatial distribution is crucial to improve conservation plans for endangered species. Genetic tools help ensure species' long-term persistence by unraveling connectivity patterns and evolutionary trajectories of populations. Here, microsatellite genotypes of individuals from populations of Patella ferruginea are used to assess the effect of sample size on metrics of within-and between-population genetic diversity by combining empirical and simulated data. Within-population metrics are slightly to moderately affected by small sample size, albeit the magnitude of the bias is proportional to the effective population size and gene flow. The power of detecting genetic differentiation among populations increases with sample size, albeit the gain of increasing the number of sampled individuals tends to be negligible between 30 and 50. Our results line up with those of previous studies and highlight that small sample sizes are not always a hindrance to investigating genetic patterns in endangered marine species. Caution is needed in interpreting genetic patterns based on small sample sizes when the observed genetic differentiation is weak. This study also highlights the importance of carrying out genetic monitoring in seemingly well-preserved but potentially isolated populations.
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Affiliation(s)
- Piero Cossu
- Department of Sciences for Nature and Environmental Resources, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
- Correspondence: ; Tel.: +39-079-2280924
| | - Laura Mura
- Dipartimento per la Ricerca nelle Produzioni Animali, Agris Sardegna, 07040 Olmedo, Italy
| | - Gian Luca Dedola
- Department of Sciences for Nature and Environmental Resources, University of Sassari, 07100 Sassari, Italy
| | - Tiziana Lai
- Department of Sciences for Nature and Environmental Resources, University of Sassari, 07100 Sassari, Italy
| | - Daria Sanna
- Department of Sciences for Nature and Environmental Resources, University of Sassari, 07100 Sassari, Italy
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Fabio Scarpa
- Department of Sciences for Nature and Environmental Resources, University of Sassari, 07100 Sassari, Italy
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Ilenia Azzena
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Nicola Fois
- Dipartimento per la Ricerca nelle Produzioni Animali, Agris Sardegna, 07040 Olmedo, Italy
| | - Marco Casu
- Department of Sciences for Nature and Environmental Resources, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
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22
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Scarpa F, Sanna D, Azzena I, Giovanetti M, Benvenuto D, Angeletti S, Ceccarelli G, Pascarella S, Casu M, Fiori PL, Ciccozzi M. On the SARS-CoV-2 BA.2.75 variant: A genetic and structural point of view. J Med Virol 2022; 95:e28119. [PMID: 36059082 PMCID: PMC9538365 DOI: 10.1002/jmv.28119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 08/27/2022] [Accepted: 08/31/2022] [Indexed: 01/11/2023]
Affiliation(s)
- Fabio Scarpa
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | - Daria Sanna
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | - Ilenia Azzena
- Department of Biomedical SciencesUniversity of SassariSassariItaly,Department of Veterinary MedicineUniversity of SassariSassariItaly
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo CruzFundação Oswaldo CruzRio de JaneiroBrazil,Department of Science and Technology for Humans and the EnvironmentUniversity of Campus Bio‐Medico di RomaRomeItaly
| | - Domenico Benvenuto
- Unit of Medical Statistics and Molecular EpidemiologyUniversity Campus Bio‐Medico of RomeRomeItaly
| | - Silvia Angeletti
- Department of Medicine, Unit of Clinical Laboratory ScienceUniversity Campus Bio‐Medico of RomeRomeItaly
| | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto ISapienza University of RomeRomeItaly
| | - Stefano Pascarella
- Department of Biochemical Sciences “A Rossi Fanelli”Sapienza Università di RomaRomeItaly
| | - Marco Casu
- Department of Veterinary MedicineUniversity of SassariSassariItaly
| | - Pier Luigi Fiori
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular EpidemiologyUniversity Campus Bio‐Medico of RomeRomeItaly
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23
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Coradduzza E, Sanna D, Scarpa F, Azzena I, Fiori MS, Scivoli R, Rocchigiani AM, Bechere R, Dettori MA, Pintus D, Evangelista E, Casu M, Ligios C, Puggioni G. A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ORF Virus through the Whole Genome Sequencing of the First Italian Strains. Viruses 2022; 14:v14071473. [PMID: 35891452 PMCID: PMC9318404 DOI: 10.3390/v14071473] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 02/01/2023] Open
Abstract
Orf virus (ORFV) is distributed worldwide and is the causative agent of contagious ecthyma that mainly occurs in sheep and goats. This disease was reported for the first time at the end of 18th century in Europe but very little is currently known about the temporal and geographic origins of this virus. In the present study, the use of new Italian whole genomes allowed for better inference on the evolutionary history of ORFV. In accordance with previous studies, two genome types (S and G) were described for infection of sheep and goats, respectively. These two well-differentiated groups of genomes originated for evolutive convergence in the late 1800s in two different areas of the world (Europe for S type and Asia for G type), but it was only in the early 1900s that the effective size of ORFV increased among hosts and the virus spread across the whole European continent. The Italian strains which were sequenced in the present study were isolated on the Mediterranean island of Sardinian and showed to be exclusive to this geographic area. One of them is likely representative of the early European forms of ORFV which infected sheep and became extinct about one century ago. Such an ancient Sardinian strain may have reached the island simple by chance, where it quickly adapted to the new habitat.
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Affiliation(s)
- Elisabetta Coradduzza
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (E.C.); (M.S.F.); (R.S.); (A.M.R.); (R.B.); (M.A.D.); (D.P.); (C.L.); (G.P.)
| | - Daria Sanna
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy; (F.S.); (I.A.)
- Correspondence:
| | - Fabio Scarpa
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy; (F.S.); (I.A.)
| | - Ilenia Azzena
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy; (F.S.); (I.A.)
- Dipartimento di Medicina Veterinaria, Università di Sassari, 07100 Sassari, Italy;
| | - Mariangela S. Fiori
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (E.C.); (M.S.F.); (R.S.); (A.M.R.); (R.B.); (M.A.D.); (D.P.); (C.L.); (G.P.)
| | - Rosario Scivoli
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (E.C.); (M.S.F.); (R.S.); (A.M.R.); (R.B.); (M.A.D.); (D.P.); (C.L.); (G.P.)
| | - Angela M. Rocchigiani
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (E.C.); (M.S.F.); (R.S.); (A.M.R.); (R.B.); (M.A.D.); (D.P.); (C.L.); (G.P.)
| | - Roberto Bechere
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (E.C.); (M.S.F.); (R.S.); (A.M.R.); (R.B.); (M.A.D.); (D.P.); (C.L.); (G.P.)
| | - Maria A. Dettori
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (E.C.); (M.S.F.); (R.S.); (A.M.R.); (R.B.); (M.A.D.); (D.P.); (C.L.); (G.P.)
| | - Davide Pintus
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (E.C.); (M.S.F.); (R.S.); (A.M.R.); (R.B.); (M.A.D.); (D.P.); (C.L.); (G.P.)
| | - Eloisa Evangelista
- Ames Polydiagnostic Group Center SRL, Casalnuovo di Napoli, 80013 Naples, Italy;
| | - Marco Casu
- Dipartimento di Medicina Veterinaria, Università di Sassari, 07100 Sassari, Italy;
| | - Ciriaco Ligios
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (E.C.); (M.S.F.); (R.S.); (A.M.R.); (R.B.); (M.A.D.); (D.P.); (C.L.); (G.P.)
| | - Giantonella Puggioni
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (E.C.); (M.S.F.); (R.S.); (A.M.R.); (R.B.); (M.A.D.); (D.P.); (C.L.); (G.P.)
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Ceccherelli G, Addis P, Atzori F, Cadoni N, Casu M, Coppa S, De Luca M, de Lucia GA, Farina S, Fois N, Frau F, Gazale V, Grech D, Guala I, Mariani M, Marras MSG, Navone A, Pansini A, Panzalis P, Pinna F, Ruiu A, Scarpa F, Piazzi L. Sea urchin harvest inside marine protected areas: an opportunity to investigate the effects of exploitation where trophic upgrading is achieved. PeerJ 2022; 10:e12971. [PMID: 35282273 PMCID: PMC8908888 DOI: 10.7717/peerj.12971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/30/2022] [Indexed: 01/11/2023] Open
Abstract
Background Marine protected areas (MPAs) usually have both positive effects of protection for the fisheries' target species and indirect negative effects for sea urchins. Moreover, often in MPAs sea urchin human harvest is restricted, but allowed. This study is aimed at estimating the effect of human harvest of the sea urchin Paracentrotus lividus within MPAs, where fish exploitation is restricted and its density is already controlled by a higher natural predation risk. The prediction we formulated was that the lowest densities of commercial sea urchins would be found where human harvest is allowed and where the harvest is restricted, compared to where the harvest is forbidden. Methods At this aim, a collaborative database gained across five MPAs in Sardinia (Western Mediterranean, Italy) and areas outside was gathered collecting sea urchin abundance and size data in a total of 106 sites at different degrees of sea urchin exploitation: no, restricted and unrestricted harvest sites (NH, RH and UH, respectively). Furthermore, as estimates made in past monitoring efforts (since 2005) were available for 75 of the sampled sites, for each of the different levels of exploitation, the rate of variation in the total sea urchin density was also estimated. Results Results have highlighted that the lowest sea urchin total and commercial density was found in RH sites, likely for the cumulative effects of human harvest and natural predation. The overall rate of change in sea urchin density over time indicates that only NH conditions promoted the increase of sea urchin abundance and that current local management of the MPAs has driven towards an important regression of populations, by allowing the harvest. Overall, results suggest that complex mechanisms, including synergistic effects between natural biotic interactions and human pressures, may occur on sea urchin populations and the assessment of MPA effects on P. lividus populations would be crucial to guide management decisions on regulating harvest permits. Overall, the need to ban sea urchin harvest in the MPAs to avoid extreme reductions is encouraged, as inside the MPAs sea urchin populations are likely under natural predation pressures for the trophic upgrading.
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Affiliation(s)
- Giulia Ceccherelli
- Dipartimento di Chimica e Farmacia, Universitá di Sassari, Via Piandanna, Sassari, Italy
| | - Piero Addis
- Dipartimento di Scienze della Vita e dell’Ambiente, Universitá di Cagliari, Via Fiorelli, Cagliari, Italy
| | - Fabrizio Atzori
- Capo Carbonara –Villasimius Marine Protected Area, Via Roma, Villasimius (CA), Italy
| | - Nicoletta Cadoni
- Capo Carbonara –Villasimius Marine Protected Area, Via Roma, Villasimius (CA), Italy
| | - Marco Casu
- Dipartimento di Medicina Veterinaria –Sez. Fisiologia della Nutrizione e Zoologia, Universitá di Sassari, Sassari, Italy
| | - Stefania Coppa
- Istituto per lo studio degli Impatti Antropici e Sostenibilità in ambiente marino (IAS) –Consiglio Nazionale delle Ricerche (CNR), Loc. Sa Mardini, Torre Grande (OR), Italy
| | - Mario De Luca
- Dipartimento di Chimica e Farmacia, Universitá di Sassari, Via Piandanna, Sassari, Italy
| | - Giuseppe Andrea de Lucia
- Istituto per lo studio degli Impatti Antropici e Sostenibilità in ambiente marino (IAS) –Consiglio Nazionale delle Ricerche (CNR), Loc. Sa Mardini, Torre Grande (OR), Italy
| | - Simone Farina
- IMC –International Marine Centre, Loc. Sa Mardini, Torre Grande, OR, Italy,SZN –Stazione Zoologica Anton Dohrn, Villa Comunale Napoli, Italy
| | - Nicola Fois
- Agris –Agricultural Research Agency of Sardinia –Bonassai SS, Sassari, Italy
| | - Francesca Frau
- Capo Carbonara –Villasimius Marine Protected Area, Via Roma, Villasimius (CA), Italy
| | - Vittorio Gazale
- Isola dell’Asinara Marine Protected Area, via Ponte Romano, Porto Torres (SS), Italy
| | - Daniele Grech
- IMC –International Marine Centre, Loc. Sa Mardini, Torre Grande, OR, Italy
| | - Ivan Guala
- IMC –International Marine Centre, Loc. Sa Mardini, Torre Grande, OR, Italy
| | - Mariano Mariani
- Capo Caccia –Isola Piana Marine Protected Area, Loc. Tramariglio SP, Alghero, SS, Italy
| | - Massimo SG Marras
- Penisola del Sinis –Isola di Mal di Ventre Marine Protected Area, Corso Italia, Cabras, OR, Italy
| | - Augusto Navone
- Tavolara Punta Coda Cavallo Marine Protected Area, Via S. Giovanni, Olbia (SS), Italy
| | - Arianna Pansini
- Dipartimento di Chimica e Farmacia, Universitá di Sassari, Via Piandanna, Sassari, Italy
| | - Pieraugusto Panzalis
- Tavolara Punta Coda Cavallo Marine Protected Area, Via S. Giovanni, Olbia (SS), Italy
| | - Federico Pinna
- Dipartimento di Chimica e Farmacia, Universitá di Sassari, Via Piandanna, Sassari, Italy
| | - Alberto Ruiu
- Capo Caccia –Isola Piana Marine Protected Area, Loc. Tramariglio SP, Alghero, SS, Italy
| | - Fabio Scarpa
- Dipartimento di Medicina Veterinaria –Sez. Fisiologia della Nutrizione e Zoologia, Universitá di Sassari, Sassari, Italy
| | - Luigi Piazzi
- Dipartimento di Chimica e Farmacia, Universitá di Sassari, Via Piandanna, Sassari, Italy
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Tran Thi G, Azzena I, Scarpa F, Cossu P, Danh Le C, Ton Nu PA, Chau Ngo TM, Sanna D, Casu M. Molecular Identification and Appraisal of the Genetic Variation of Taenia saginata in Central Regions of Vietnam. Life (Basel) 2022; 12:70. [PMID: 35054461 PMCID: PMC8781798 DOI: 10.3390/life12010070] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/29/2021] [Accepted: 01/01/2022] [Indexed: 06/14/2023] Open
Abstract
Taenia saginata is a globally distributed tapeworm responsible for human taeniasis due to the ingestion of raw or undercooked beef. T. saginata is present in several Asian countries, including China, Thailand, Lao PDR, Cambodia, and Vietnam, but little is known about its genetic variation. Studying the tapeworm's phylogeographic patterns is crucial to better understanding their association with the geographic distribution of taeniasis/cysticercosis in human populations. In the present study, 38 specimens of this putative species were collected in central regions of Vietnam and analysed using the mitochondrial gene Cytochrome c Oxidase subunit I (COI) as a molecular marker to assess the correct species identification and investigate the level of genetic variation at different geographic scales. Phylogenetic and phylogeographic analyses were carried out on a dataset that included COI sequences from Vietnamese specimens and from all conspecifics available in GenBank to date. The results showed that the collected Vietnamese specimens belonged to the species T. saginata. In Southeast Asia, signs of a possible founder effect were discovered, with the most common haplotypes frequent and present in many countries, except Lao PDR, which shares its most common haplotype only with individuals from Thailand. Remarkably, a unique taxonomic entity was found worldwide, even though the available COI sequences of T. saginata belonging to non-Asiatic countries are, at present, limited. Therefore, future studies including more COI sequences from a higher number of countries and the use of a combined molecular approach with multiple genetic markers would be useful to provide deeper insight into the global genetic variation of this species.
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Affiliation(s)
- Giang Tran Thi
- Department of Parasitology, Hue University of Medicine and Pharmacy, Hue University, 06 Ngo Quyen Street, Hue City 4200, Vietnam; (G.T.T.); (P.A.T.N.); (T.M.C.N.)
| | - Ilenia Azzena
- Dipartimento di Medicina Veterinaria, Università di Sassari, Via Vienna 2, 07100 Sassari, Italy; (I.A.); (F.S.); (P.C.); (M.C.)
- Dipartimento di Scienze Biomediche, Università di Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy
| | - Fabio Scarpa
- Dipartimento di Medicina Veterinaria, Università di Sassari, Via Vienna 2, 07100 Sassari, Italy; (I.A.); (F.S.); (P.C.); (M.C.)
| | - Piero Cossu
- Dipartimento di Medicina Veterinaria, Università di Sassari, Via Vienna 2, 07100 Sassari, Italy; (I.A.); (F.S.); (P.C.); (M.C.)
| | - Cong Danh Le
- Traditional Medicine Hospital of Thua Thien Hue Province, Hue City 4200, Vietnam;
| | - Phuong Anh Ton Nu
- Department of Parasitology, Hue University of Medicine and Pharmacy, Hue University, 06 Ngo Quyen Street, Hue City 4200, Vietnam; (G.T.T.); (P.A.T.N.); (T.M.C.N.)
| | - Thi Minh Chau Ngo
- Department of Parasitology, Hue University of Medicine and Pharmacy, Hue University, 06 Ngo Quyen Street, Hue City 4200, Vietnam; (G.T.T.); (P.A.T.N.); (T.M.C.N.)
| | - Daria Sanna
- Dipartimento di Scienze Biomediche, Università di Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy
| | - Marco Casu
- Dipartimento di Medicina Veterinaria, Università di Sassari, Via Vienna 2, 07100 Sassari, Italy; (I.A.); (F.S.); (P.C.); (M.C.)
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26
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Fiori MS, Sanna D, Scarpa F, Floris M, Di Nardo A, Ferretti L, Loi F, Cappai S, Sechi AM, Angioi PP, Zinellu S, Sirica R, Evangelista E, Casu M, Franzoni G, Oggiano A, Dei Giudici S. A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ASFV Epidemics in Sardinia (Italy) through Extensive Genomic Sequencing. Viruses 2021; 13:1994. [PMID: 34696424 PMCID: PMC8539718 DOI: 10.3390/v13101994] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/25/2021] [Accepted: 10/01/2021] [Indexed: 12/31/2022] Open
Abstract
African swine fever virus (ASFV) is the etiological agent of the devastating disease African swine fever (ASF), for which there is currently no licensed vaccine or treatment available. ASF is defined as one of the most serious animal diseases identified to date, due to its global spread in regions of Africa, Europe and Asia, causing massive economic losses. On the Italian island of Sardinia, the disease has been endemic since 1978, although the last control measures put in place achieved a significant reduction in ASF, and the virus has been absent from circulation since April 2019. Like many large DNA viruses, ASFV mutates at a relatively slow rate. However, the limited availability of whole-genome sequences from spatial-localized outbreaks makes it difficult to explore the small-scale genetic structure of these ASFV outbreaks. It is also unclear if the genetic variability within outbreaks can be captured in a handful of sequences, or if larger sequencing efforts can improve phylogenetic reconstruction and evolutionary or epidemiological inference. The aim of this study was to investigate the phylogenetic patterns of ASFV outbreaks between 1978 and 2018 in Sardinia, in order to characterize the epidemiological dynamics of the viral strains circulating in this Mediterranean island. To reach this goal, 58 new whole genomes of ASFV isolates were obtained, which represents the largest ASFV whole-genome sequencing effort to date. We provided a complete description of the genomic diversity of ASFV in terms of nucleotide mutations and small and large indels among the isolates collected during the outbreaks. The new sequences capture more than twice the genomic and phylogenetic diversity of all the previously published Sardinian sequences. The extra genomic diversity increases the resolution of the phylogenetic reconstruction, enabling us to dissect, for the first time, the genetic substructure of the outbreak. We found multiple ASFV subclusters within the phylogeny of the Sardinian epidemic, some of which coexisted in space and time.
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Affiliation(s)
- Mariangela Stefania Fiori
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (M.S.F.); (A.M.S.); (P.P.A.); (S.Z.); (G.F.); (A.O.); (S.D.G.)
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (D.S.); (M.F.)
| | - Fabio Scarpa
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (F.S.); (M.C.)
| | - Matteo Floris
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (D.S.); (M.F.)
| | | | - Luca Ferretti
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX1 4BH, UK;
| | - Federica Loi
- Osservatorio Epidemiologico Veterinario Regionale, Istituto Zooprofilattico Sperimentale della Sardegna, 09125 Cagliari, Italy;
| | - Stefano Cappai
- Osservatorio Epidemiologico Veterinario Regionale, Istituto Zooprofilattico Sperimentale della Sardegna, 09125 Cagliari, Italy;
| | - Anna Maria Sechi
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (M.S.F.); (A.M.S.); (P.P.A.); (S.Z.); (G.F.); (A.O.); (S.D.G.)
| | - Pier Paolo Angioi
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (M.S.F.); (A.M.S.); (P.P.A.); (S.Z.); (G.F.); (A.O.); (S.D.G.)
| | - Susanna Zinellu
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (M.S.F.); (A.M.S.); (P.P.A.); (S.Z.); (G.F.); (A.O.); (S.D.G.)
| | - Roberto Sirica
- Ames Polydiagnostic Group Center SRL, 80013 Napoli, Italy; (R.S.); (E.E.)
| | - Eloisa Evangelista
- Ames Polydiagnostic Group Center SRL, 80013 Napoli, Italy; (R.S.); (E.E.)
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (F.S.); (M.C.)
| | - Giulia Franzoni
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (M.S.F.); (A.M.S.); (P.P.A.); (S.Z.); (G.F.); (A.O.); (S.D.G.)
| | - Annalisa Oggiano
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (M.S.F.); (A.M.S.); (P.P.A.); (S.Z.); (G.F.); (A.O.); (S.D.G.)
| | - Silvia Dei Giudici
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (M.S.F.); (A.M.S.); (P.P.A.); (S.Z.); (G.F.); (A.O.); (S.D.G.)
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27
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Scarpa F, Sanna D, Azzena I, Cossu P, Giovanetti M, Benvenuto D, Coradduzza E, Alexiev I, Casu M, Fiori PL, Ciccozzi M. Update on the Phylodynamics of SADS-CoV. Life (Basel) 2021; 11:life11080820. [PMID: 34440564 PMCID: PMC8402179 DOI: 10.3390/life11080820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/28/2021] [Accepted: 08/10/2021] [Indexed: 11/30/2022] Open
Abstract
Coronaviruses are known to be harmful and heterogeneous viruses, able to infect a large number of hosts. Among them, SADS-CoV (Swine Acute Diarrhea Syndrome Coronavirus), also known as PEAV (Porcine Enteric Alphacoronavirus), or SeA-CoV (Swine Enteric Alphacoronavirus), is the most recent Alphacoronavirus discovered, and caused several outbreaks reported in Chinese swine herds between late 2016 and 2019. We performed an upgraded phylodinamic reconstruction of SADS-CoV based on all whole genomes available on 21 June 2021. Results showed a very close relationship between SADS-CoV and HKU2-like CoV, which may represent the evolutionary intermediate step towards the present SADS-CoV. The direct progenitor of SADS-CoV is so far unknown and, although it is well known that horseshoe bats are reservoirs for Rhinolophus bat coronavirus HKU2-like (HKU2-like CoVs), the transmission path from bats to pigs is still unclear. The discrepancies in the phylogenetic position of rodent CoV, when different molecular markers were considered, corroborate the recombination hypothesis, suggesting that wild rats, which are frequent in farms, may have played a key role. The failure of the attempt at molecular dating, due to the lack of a clock signal, also corroborates the occurrence of a recombination event hypothesis. Zoonotic infections originating in wildlife can easily become a significant threat for human health. In such a context, due to the high recombination and cross-species capabilities of Coronavirus, SADS-CoV represents a possible high-risk pathogen for humans which needs a constant molecular monitoring.
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Affiliation(s)
- Fabio Scarpa
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (I.A.); (P.C.); (M.C.)
- Correspondence:
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (D.S.); (P.L.F.)
| | - Ilenia Azzena
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (I.A.); (P.C.); (M.C.)
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (D.S.); (P.L.F.)
| | - Piero Cossu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (I.A.); (P.C.); (M.C.)
| | - Marta Giovanetti
- Flavivirus Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil;
| | - Domenico Benvenuto
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy; (D.B.); (M.C.)
| | | | - Ivailo Alexiev
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria;
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (I.A.); (P.C.); (M.C.)
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (D.S.); (P.L.F.)
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy; (D.B.); (M.C.)
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Cossu P, Mura L, Scarpa F, Lai T, Sanna D, Azzena I, Fois N, Casu M. Genetic patterns in Mugil cephalus and implications for fisheries and aquaculture management. Sci Rep 2021; 11:2887. [PMID: 33536511 PMCID: PMC7859195 DOI: 10.1038/s41598-021-82515-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 01/18/2021] [Indexed: 01/30/2023] Open
Abstract
Exploitation of fisheries and aquaculture practices are exposing marine fish populations to increasing genetic risks. Therefore, the integration of genetic information into fisheries and aquaculture management is becoming crucial to ensure species' long-term persistence. The raising commercial value of grey mullet (Mugil cephalus) and its roe represents a growing challenge to the sustainable management of this economically important fishery resource. Here, microsatellites were used to investigate patterns of genetic variation in a Mediterranean area that harbor flourishing fisheries and practice semi-intensive farming of grey mullet. Genetic diversity within populations is smaller than values reported in previous studies as a result of the lower polymorphism displayed by the new microsatellite loci. Lack of genetic structuring points to the existence of a unique genetic stock, which is consistent with the species' high dispersal capabilities. Nonetheless, differences in local population effective size as well as the excess of related individuals do not completely fit the picture of a large panmictic population. Baseline genetic information here gathered will allow to set up the genetic monitoring of regional fish stocks, which is needed to assess the impact of both harvesting and aquaculture on the genetic integrity of Mugil cephalus wild populations.
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Affiliation(s)
- Piero Cossu
- grid.11450.310000 0001 2097 9138Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy ,grid.11450.310000 0001 2097 9138Department of Veterinary Medicine, University of Sassari, Sassari, SS Italy
| | - Laura Mura
- Dipartimento per la Ricerca Nelle Produzioni Animali, Agris Sardegna, Olmedo, SS Italy
| | - Fabio Scarpa
- grid.11450.310000 0001 2097 9138Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy ,grid.11450.310000 0001 2097 9138Department of Veterinary Medicine, University of Sassari, Sassari, SS Italy
| | - Tiziana Lai
- grid.11450.310000 0001 2097 9138Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy
| | - Daria Sanna
- grid.11450.310000 0001 2097 9138Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy ,grid.11450.310000 0001 2097 9138Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Ilenia Azzena
- grid.11450.310000 0001 2097 9138Department of Veterinary Medicine, University of Sassari, Sassari, SS Italy ,grid.11450.310000 0001 2097 9138Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Nicola Fois
- Dipartimento per la Ricerca Nelle Produzioni Animali, Agris Sardegna, Olmedo, SS Italy
| | - Marco Casu
- grid.11450.310000 0001 2097 9138Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy ,grid.11450.310000 0001 2097 9138Department of Veterinary Medicine, University of Sassari, Sassari, SS Italy
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Tamponi C, Scarpa F, Carta S, Knoll S, Sanna D, Gai C, Pipia AP, Dessì G, Casu M, Varcasia A, Scala A. Seroprevalence and risk factors associated with Leishmania infantum in dogs in Sardinia (Italy), an endemic island for leishmaniasis. Parasitol Res 2021; 120:289-300. [PMID: 33205238 PMCID: PMC7846507 DOI: 10.1007/s00436-020-06973-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/08/2020] [Indexed: 11/27/2022]
Abstract
Leishmaniasis is a widespread, vector-borne parasitosis causing clinical manifestations in animals and in humans. In dogs, Canine Leishmaniasis has been reported in as much as 50 countries and the Mediterranean basin is known to be one of the most affected zones. Within these areas, the Island of Sardinia (Italy) has long been considered endemic for leishmaniasis and the presence of two arthropod vectors has recently been reported there. Nevertheless, to date, no epidemiological surveys regarding CanL have been carried out on the island. Hence, for the first time, the seroprevalence and the risk factors were investigated. Blood samples, as well as clinical and general information from 1.147 dogs, were collected and analyzed. Dogs consisted of two distinct populations, namely "owned dogs" and "kennel dogs." Anti-Leishmania IgG antibodies were detected using IFAT and samples were scored as positive at a cut-off dilution of 1:80. Data was analyzed using a Chi-squared test and bivariate and multivariate analyses were performed. Overall, 15.4% of dogs were found to be infected with CanL while only 44.1% of these animals exhibited clinical signs. Owned dogs (27.2%) were found to be infected more often than kennel dogs (10.6%); male dogs were found to be more frequently infected than female dogs and the number of infected animals increases with age. The present survey confirmed the endemic nature of leishmaniasis in Sardinia with a similar seroprevalence as mainland Italy. The results obtained serve as validation for the hypothesis that, in endemic areas, clinical CanL representations constitute only a fraction of the leishmaniasis cases.
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Affiliation(s)
- Claudia Tamponi
- Parassitologia, Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna, 2, 07100 Sassari, Italy
| | - Fabio Scarpa
- Parassitologia, Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna, 2, 07100 Sassari, Italy
| | - Silvia Carta
- Parassitologia, Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna, 2, 07100 Sassari, Italy
| | - Stephane Knoll
- Parassitologia, Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna, 2, 07100 Sassari, Italy
| | - Daria Sanna
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - Carolina Gai
- Parassitologia, Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna, 2, 07100 Sassari, Italy
| | - Anna Paola Pipia
- Parassitologia, Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna, 2, 07100 Sassari, Italy
| | - Giorgia Dessì
- Parassitologia, Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna, 2, 07100 Sassari, Italy
| | - Marco Casu
- Parassitologia, Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna, 2, 07100 Sassari, Italy
| | - Antonio Varcasia
- Parassitologia, Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna, 2, 07100 Sassari, Italy
| | - Antonio Scala
- Parassitologia, Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna, 2, 07100 Sassari, Italy
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Scarpa F, Sanna D, Azzena I, Mugetti D, Cerruti F, Hosseini S, Cossu P, Pinna S, Grech D, Cabana D, Pasquini V, Esposito G, Cadoni N, Atzori F, Antuofermo E, Addis P, Sechi LA, Prearo M, Peletto S, Mossa MA, Saba T, Gazale V, Casu M. Multiple Non-Species-Specific Pathogens Possibly Triggered the Mass Mortality in Pinna nobilis. Life (Basel) 2020; 10:life10100238. [PMID: 33066230 PMCID: PMC7650684 DOI: 10.3390/life10100238] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/03/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022] Open
Abstract
The fan mussel, Pinna nobilis, represents the largest bivalve endemic to the Mediterranean Sea. Since 2016, dramatic mass mortality of this species has been observed in several areas. The first surveys suggested that Haplosporidium pinnae (currently considered species-specific) was the main etiological agent, but recent studies have indicated that a multifactorial disease may be responsible for this phenomenon. In this study, we performed molecular diagnostic analyses on P. nobilis, P. rudis, and bivalve heterologous host species from the island of Sardinia to shed further light on the pathogens involved in the mass mortality. The results support the occurrence of a multifactorial disease and that Mycobacterium spp. and H. pinnae are not necessarily associated with the illness. Indeed, our analyses revealed that H. pinnae is not species-specific for P. nobilis, as it was present in other bivalves at least three years before the mass mortality began, and species of Mycobacterium were also found in healthy individuals of P. nobilis and P. rudis. We also detected the species Rhodococcus erythropolis, representing the first report in fan mussels of a bacterium other than Mycobacterium spp. and Vibrio spp. These results depict a complicated scenario, further demonstrating how the P. nobilis mass mortality event is far from being fully understood.
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Affiliation(s)
- Fabio Scarpa
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna 2, 07100 Sassari, Italy; (F.S.); (I.A.); (P.C.); (G.E.); (E.A.); (M.C.)
| | - Daria Sanna
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy; (S.H.); (L.A.S.)
- Correspondence:
| | - Ilenia Azzena
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna 2, 07100 Sassari, Italy; (F.S.); (I.A.); (P.C.); (G.E.); (E.A.); (M.C.)
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy; (S.H.); (L.A.S.)
| | - Davide Mugetti
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (D.M.); (F.C.); (M.P.); (S.P.)
| | - Francesco Cerruti
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (D.M.); (F.C.); (M.P.); (S.P.)
| | - Sepideh Hosseini
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy; (S.H.); (L.A.S.)
| | - Piero Cossu
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna 2, 07100 Sassari, Italy; (F.S.); (I.A.); (P.C.); (G.E.); (E.A.); (M.C.)
| | - Stefania Pinna
- IMC-International Marine Centre, Loc. Sa Mardini, Torregrande, 09170 Oristano, Italy; (S.P.); (D.G.); (D.C.)
| | - Daniele Grech
- IMC-International Marine Centre, Loc. Sa Mardini, Torregrande, 09170 Oristano, Italy; (S.P.); (D.G.); (D.C.)
| | - David Cabana
- IMC-International Marine Centre, Loc. Sa Mardini, Torregrande, 09170 Oristano, Italy; (S.P.); (D.G.); (D.C.)
| | - Viviana Pasquini
- Dipartimento di Scienze della Vita e dell’Ambiente, Università di Cagliari, Via Fiorelli 1, 09126 Cagliari, Italy; (V.P.); (P.A.)
| | - Giuseppe Esposito
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna 2, 07100 Sassari, Italy; (F.S.); (I.A.); (P.C.); (G.E.); (E.A.); (M.C.)
| | - Nicoletta Cadoni
- Area Marina Protetta Capo Carbonara, Comune di Villasimius, Via Roma 60, 09049 Villasimius, Italy; (N.C.); (F.A.)
| | - Fabrizio Atzori
- Area Marina Protetta Capo Carbonara, Comune di Villasimius, Via Roma 60, 09049 Villasimius, Italy; (N.C.); (F.A.)
| | - Elisabetta Antuofermo
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna 2, 07100 Sassari, Italy; (F.S.); (I.A.); (P.C.); (G.E.); (E.A.); (M.C.)
| | - Piero Addis
- Dipartimento di Scienze della Vita e dell’Ambiente, Università di Cagliari, Via Fiorelli 1, 09126 Cagliari, Italy; (V.P.); (P.A.)
| | - Leonardo Antonio Sechi
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy; (S.H.); (L.A.S.)
| | - Marino Prearo
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (D.M.); (F.C.); (M.P.); (S.P.)
| | - Simone Peletto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (D.M.); (F.C.); (M.P.); (S.P.)
| | - Marianna A. Mossa
- Regiona autonoma della Sardegna, Via Roma 80, 09123 Cagliari, Italy; (M.A.M.); (T.S.)
| | - Tiziana Saba
- Regiona autonoma della Sardegna, Via Roma 80, 09123 Cagliari, Italy; (M.A.M.); (T.S.)
| | - Vittorio Gazale
- Area Marina Protetta “Isola dell’Asinara”, 07046 Porto Torres, Italy;
| | - Marco Casu
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna 2, 07100 Sassari, Italy; (F.S.); (I.A.); (P.C.); (G.E.); (E.A.); (M.C.)
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31
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Martínez A, Eckert EM, Artois T, Careddu G, Casu M, Curini-Galletti M, Gazale V, Gobert S, Ivanenko VN, Jondelius U, Marzano M, Pesole G, Zanello A, Todaro MA, Fontaneto D. Human access impacts biodiversity of microscopic animals in sandy beaches. Commun Biol 2020; 3:175. [PMID: 32313088 PMCID: PMC7170908 DOI: 10.1038/s42003-020-0912-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/23/2020] [Indexed: 01/25/2023] Open
Abstract
Whereas most work to understand impacts of humans on biodiversity on coastal areas has focused on large, conspicuous organisms, we highlight effects of tourist access on the diversity of microscopic marine animals (meiofauna). We used a DNA metabarcoding approach with an iterative and phylogeny-based approach for the taxonomic assignment of meiofauna and relate diversity patterns to the numbers of tourists accessing sandy beaches on an otherwise un-impacted island National Park. Tourist frequentation, independently of differences in sediment granulometry, beach length, and other potential confounding factors, affected meiofaunal diversity in the shallow “swash” zone right at the mean water mark; the impacts declined with water depth (up to 2 m). The indicated negative effect on meiofauna may have a consequence on all the biota including the higher trophic levels. Thus, we claim that it is important to consider restricting access to beaches in touristic areas, in order to preserve biodiversity. Martínez et al. use DNA metabarcoding and a phylogeny-based approach to demonstrate the effects of tourist access on meiofauna diversity of beaches in Asinara National Park. Their results show that tourist frequentation decreases meiofaunal diversity at the shallow “swash” zone, and can be used to inform tourist access and management of beaches.
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Affiliation(s)
- Alejandro Martínez
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council of Italy (CNR), Verbania, Italy
| | - Ester M Eckert
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council of Italy (CNR), Verbania, Italy
| | - Tom Artois
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Giovanni Careddu
- Parco Nazionale dell'Asinara, Area Marina Protetta, Porto Torres, Italy
| | - Marco Casu
- Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy
| | | | - Vittorio Gazale
- Parco Nazionale dell'Asinara, Area Marina Protetta, Porto Torres, Italy
| | - Stefan Gobert
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Viatcheslav N Ivanenko
- Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Ulf Jondelius
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Marinella Marzano
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council of Italy (CNR), Bari, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council of Italy (CNR), Bari, Italy.,Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari "A. Moro", Bari, Italy
| | - Aldo Zanello
- Parco Nazionale dell'Asinara, Area Marina Protetta, Porto Torres, Italy
| | - M Antonio Todaro
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Modena, Italy
| | - Diego Fontaneto
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council of Italy (CNR), Verbania, Italy.
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Langeneck J, Scarpa F, Maltagliati F, Sanna D, Barbieri M, Cossu P, Mikac B, Curini Galletti M, Castelli A, Casu M. A complex species complex: The controversial role of ecology and biogeography in the evolutionary history of
Syllis gracilis
Grube, 1840 (Annelida, Syllidae). J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12336] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - Fabio Scarpa
- Dipartimento di Medicina Veterinaria Università degli Studi di Sassari Sassari Italy
| | | | - Daria Sanna
- Dipartimento di Scienze Biomediche Università degli Studi di Sassari Sassari Italy
| | | | - Piero Cossu
- Dipartimento di Medicina Veterinaria Università degli Studi di Sassari Sassari Italy
| | - Barbara Mikac
- Centro Interdipartimentale di Ricerca per le Scienze Ambientali (CIRSA) Università di Bologna Ravenna Italy
| | - Marco Curini Galletti
- Dipartimento di Medicina Veterinaria Università degli Studi di Sassari Sassari Italy
| | | | - Marco Casu
- Dipartimento di Medicina Veterinaria Università degli Studi di Sassari Sassari Italy
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33
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Rabaoui L, Yacoubi L, Sanna D, Casu M, Scarpa F, Lin YJ, Shen KN, Clardy TR, Arculeo M, Qurban MA. DNA barcoding of marine fishes from Saudi Arabian waters of the Gulf. J Fish Biol 2019; 95:1286-1297. [PMID: 31469430 DOI: 10.1111/jfb.14130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 08/29/2019] [Indexed: 06/10/2023]
Abstract
We used the cytochrome oxidase subunit I (coI) gene DNA to barcode 117 endemic Gulf and cosmopolitan Indo-West Pacific fish species belonging to 54 families and 13 orders. Novel DNA barcodes were provided for 18 fish species (Trachinocephalus sp., Nematalosa sp., Herklotsichthys lossei, Upeneus doriae, Trachurus indicus, Apogonichthyoides taeniatus, Verulux cypselurus, Favonigobius sp., Suezichthus gracilis, Sillago sp., Brachirus orientalis, Pegusa sp., Lepidotrigla bispinosa, Lepidotrigla sp., Grammoplites suppositus, Hippichthys sp., Paramonacanthus sp. and Triacanthus sp.). The species delimitation analysis, conducted with Poisson tree processes- Bayesian PTP (PTP-bPTP) and nucleotide-divergence-threshold (NDT) models), found 137 and 119 entities respectively. Overall, NDT method, neighbour-joining species tree and the prior taxonomic assessment provided similar results. Among the 54 families considered, only 10 (Ariommatidae, Ephippidae, Leiognathidae, Nemipteridae, Plotosidae, Pomacanthidae, Pomacentridae, Priacanthidae and Rachycentridae) showed the occurrence of molecular diagnostic pure characters. The DNA barcoding database developed during this study will help ichthyologists to identify and resolve the taxonomic ambiguities they may encounter with the fishes occurring in The Gulf and throughout the region.
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Affiliation(s)
- Lotfi Rabaoui
- Center for Environment & Water, Research Institute, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
- Geosciences Department, College of Petroleum Engineering & Geosciences, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
| | | | - Daria Sanna
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - Marco Casu
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Sassari, Italy
| | - Fabio Scarpa
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Sassari, Italy
| | - Yu-Jia Lin
- Center for Environment & Water, Research Institute, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
| | - Kang-Ning Shen
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Todd R Clardy
- Center for Environment & Water, Research Institute, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
| | - Marco Arculeo
- Dipartimento STEBICEF, Università degli Studi di Palermo, Palermo, Italy
| | - Mohammad A Qurban
- Center for Environment & Water, Research Institute, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
- Geosciences Department, College of Petroleum Engineering & Geosciences, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
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34
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Cossu P, Scarpa F, Sanna D, Lai T, Dedola GL, Curini-Galletti M, Mura L, Fois N, Casu M. Influence of genetic drift on patterns of genetic variation: The footprint of aquaculture practices in Sparus aurata (Teleostei: Sparidae). Mol Ecol 2019; 28:3012-3024. [PMID: 31125994 DOI: 10.1111/mec.15134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 11/30/2022]
Abstract
Aquaculture finfish production based on floating cage technology has raised increasing concerns regarding the genetic integrity of natural populations. Accidental mass escapes can induce the loss of genetic diversity in wild populations by increasing genetic drift and inbreeding. Farm escapes probably represent an important issue in the gilthead sea bream (Sparus aurata), which accounted for 76.4% of total escapees recorded in Europe during a 3-year survey. Here, we investigated patterns of genetic variation in farmed and wild populations of gilthead sea bream from the Western Mediterranean, a region of long gilthead sea bream farming. We focused on the role that genetic drift may play in shaping these patterns. Results based on microsatellite markers matched those observed in previous studies. Farmed populations showed lower levels of genetic diversity than wild populations and were genetically divergent from their wild counterparts. Overall, farmed populations showed the smallest effective population size and increased levels of relatedness compared to wild populations. The small broodstock size coupled with breeding practices that may favour the variance in individual reproductive success probably boosted genetic drift. This factor appeared to be a major driver of the genetic patterns observed in the gilthead sea bream populations analysed in the present study. These results further stress the importance of recommendations aimed at maintaining broodstock sizes as large as possible and equal sex-ratios among breeders, as well as avoiding unequal contributions among parents.
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Affiliation(s)
- Piero Cossu
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Fabio Scarpa
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Daria Sanna
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Tiziana Lai
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Gian Luca Dedola
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy
| | - Marco Curini-Galletti
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Laura Mura
- AGRIS Sardegna, Servizio Ricerca Prodotti Ittici, Olmedo, Italy
| | - Nicola Fois
- AGRIS Sardegna, Servizio Ricerca Prodotti Ittici, Olmedo, Italy
| | - Marco Casu
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
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Varcasia A, Sanna D, Casu M, Lahmar S, Dessì G, Pipia AP, Tamponi C, Gaglio G, Hrčková G, Otranto D, Scala A. Species delimitation based on mtDNA genes suggests the occurrence of new species of Mesocestoides in the Mediterranean region. Parasit Vectors 2018; 11:619. [PMID: 30514366 PMCID: PMC6278086 DOI: 10.1186/s13071-018-3185-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 11/06/2018] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND This study is the first contribution to the molecular taxonomy of Mesocestoides spp. from domestic and wild carnivores in the Mediterranean area. A total of 13 adult worms and 13 larval stages of Mesocestoides spp. were collected from domestic and wild carnivore hosts in Italy and Tunisia. Samples collected in the Slovak Republic were used as comparative samples from outside the Mediterranean. The genes cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1) of the mitochondrial genome were used as molecular markers to investigate the presence of cryptic Mesocestoides species in the area analysed. RESULTS Results were consistent in showing three well-supported clusters of Mesocestoides spp. in southern Italy and Tunisia, which were strongly divergent from Mesocestoides litteratus, M. corti and M. lineatus. High levels of genetic variation and no evidence of geographical structuring was found between the clusters. CONCLUSIONS Considering the low dispersal capability of the intermediate hosts of Mesocestoides spp., the lack of geographical structuring among the Mediterranean regions could be due to a high potential for dispersion of the definitive hosts. This study provides a foundation for future formal descriptions of new species of the genus Mesocestoides in the Mediterranean area.
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Affiliation(s)
- Antonio Varcasia
- Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy.
| | - Daria Sanna
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Marco Casu
- Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy
| | - Samia Lahmar
- National School of Veterinary Medicine, Laboratory of Parasitology, Sidi Thabet, Tunisia
| | - Giorgia Dessì
- Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy
| | - Anna Paola Pipia
- Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy
| | - Claudia Tamponi
- Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy
| | - Gabriella Gaglio
- Dipartimento di Scienze Veterinarie, Università di Messina, Messina, Italy
| | - Gabriela Hrčková
- Institute of Parasitology, Slovak Academy of Sciences, Košice, Slovak Republic
| | - Domenico Otranto
- Dipartimento di Medicina Veterinaria, Università di Bari, Bari, Italy
| | - Antonio Scala
- Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy
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36
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Taiti S, Argano R, Marcia P, Scarpa F, Sanna D, Casu M. The genus Alpioniscus Racovitza, 1908 in Sardinia: taxonomy and natural history (Isopoda, Oniscidea, Trichoniscidae). Zookeys 2018:229-263. [PMID: 30564038 PMCID: PMC6288260 DOI: 10.3897/zookeys.801.24102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/02/2018] [Indexed: 11/26/2022] Open
Abstract
The genus Alpioniscus Racovitza, 1908 (Trichoniscidae) from Sardinia is revised. Three new cave-dwelling species are described: A.onnisi Taiti & Argano, sp. n., A.stochi Taiti & Argano, sp. n., and A.sideralis Taiti & Argano, sp. n.. The genus Utopioniscus Schmalfuss, 2005 is considered to be a junior synonym of Alpioniscus, after morphological and molecular analyses. Alpioniscusfragilis (Budde-Lund, 1909) and A.kuehni from Grotta del Bue Marino are illustrated. With the new species, the genus Alpioniscus in Sardinia comprises six species: two troglobionts (A.fragilis and A.onnisi), one endogean and troglobiont (A.thanit Taiti & Argano, 2009), and three stygobionts (A.kuehni, A.stochi, and A.sideralis). All the species occur in karstic areas in the central-eastern and south-eastern part of the island. A key to all the Sardinian species of Alpioniscus is provided.
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Affiliation(s)
- Stefano Taiti
- Istituto di Ricerca sugli Ecosistemi Terrestri, Consiglio Nazionale delle Ricerche, Via Madonna del Piano 10, 50019 Sesto Fiorentino (Florence), Italy.,Museo di Storia Naturale dell'Università di Firenze, Sezione di Zoologia "La Specola", Via Romana 17, 50125 Florence, Italy
| | - Roberto Argano
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Università degli Studi "La Sapienza", Viale dell'Università 32, 00185 Rome, Italy
| | - Paolo Marcia
- Dipartimento di Medicina Veterinaria, Via Vienna 2, Università degli Studi di Sassari, 07100 Sassari, Italy
| | - Fabio Scarpa
- Dipartimento di Medicina Veterinaria, Via Vienna 2, Università degli Studi di Sassari, 07100 Sassari, Italy
| | - Daria Sanna
- Dipartimento di Scienze Biomediche, Viale San Pietro 43/C, Università degli Studi di Sassari, 07100 Sassari, Italy
| | - Marco Casu
- Dipartimento di Medicina Veterinaria, Via Vienna 2, Università degli Studi di Sassari, 07100 Sassari, Italy
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Affiliation(s)
- A. Campostano
- Divisone di Medicina, Ospedale S. Martino, Genova - Italy
| | - F. Altomonte
- Divisone di Medicina, Ospedale S. Martino, Genova - Italy
| | - D. Bessarione
- Divisone di Medicina, Ospedale S. Martino, Genova - Italy
| | - M. Casu
- Divisone di Medicina, Ospedale S. Martino, Genova - Italy
| | - A. Triolo
- Divisone di Medicina, Ospedale S. Martino, Genova - Italy
| | - G. Lamedica
- Divisone di Medicina, Ospedale S. Martino, Genova - Italy
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Sanna D, Lai T, Cossu P, Scarpa F, Dedola GL, Cristo B, Francalacci P, Curini-Galletti M, Mura L, Fois N, Maltagliati F, Casu M. Cytochrome c oxidase subunit I variability in Ruditapes decussatus (Veneridae) from the western Mediterranean. The European Zoological Journal 2017. [DOI: 10.1080/24750263.2017.1395914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- D. Sanna
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - T. Lai
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - P. Cossu
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - F. Scarpa
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - G. L. Dedola
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - B. Cristo
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - P. Francalacci
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - M. Curini-Galletti
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - L. Mura
- Dipartimento per la Ricerca nelle Produzioni Animali, Agris Sardegna, Agenzia per la Ricerca in Agricoltura , Olmedo (SS), Italy
| | - N. Fois
- Dipartimento per la Ricerca nelle Produzioni Animali, Agris Sardegna, Agenzia per la Ricerca in Agricoltura , Olmedo (SS), Italy
| | - F. Maltagliati
- Dipartimento di Biologia, Università di Pisa , Pisa (PI), Italy
| | - M. Casu
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
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Scarpa F, Cossu P, Delogu V, Lai T, Sanna D, Leasi F, Norenburg JL, Curini-Galletti M, Casu M. Molecular support for morphology-based family-rank taxa: The contrasting cases of two families of Proseriata (Platyhelminthes). ZOOL SCR 2017. [DOI: 10.1111/zsc.12251] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Fabio Scarpa
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia; Archeozoologia e Genetica; Università di Sassari; Sassari Italy
| | - Piero Cossu
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia; Archeozoologia e Genetica; Università di Sassari; Sassari Italy
| | - Valentina Delogu
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia; Archeozoologia e Genetica; Università di Sassari; Sassari Italy
| | - Tiziana Lai
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia; Archeozoologia e Genetica; Università di Sassari; Sassari Italy
| | - Daria Sanna
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia; Archeozoologia e Genetica; Università di Sassari; Sassari Italy
| | - Francesca Leasi
- Department of Invertebrate Zoology; National Museum of Natural History; Smithsonian Institution; Washington DC USA
| | - Jon L. Norenburg
- Department of Invertebrate Zoology; National Museum of Natural History; Smithsonian Institution; Washington DC USA
| | - Marco Curini-Galletti
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia; Archeozoologia e Genetica; Università di Sassari; Sassari Italy
| | - Marco Casu
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia; Archeozoologia e Genetica; Università di Sassari; Sassari Italy
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Scarpa F, Sanna D, Lai T, Cossu P, Curini-Galletti M, Casu M. New set of nuclear primers for the ribosomal regions in Proseriata (Platyhelminthes). CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0583-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Scarpa F, Cossu P, Lai T, Sanna D, Curini-Galletti M, Casu M. Meiofaunal cryptic species challenge species delimitation: the case of the Monocelis lineata (Platyhelminthes: Proseriata) species complex. CTOZ 2016. [DOI: 10.1163/18759866-08502001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Given the pending biodiversity crisis, species delimitation is a critically important task in conservation biology, but its efficacy based on single lines of evidence has been questioned as it may not accurately reflect species limits and relationships. Hence, the use of multiple lines of evidence has been portrayed as a means to overcome identification issues arising from gene/species tree discordance, morphological convergence or recent adaptive radiations. Here, the integrative taxonomic approach has been used to address the study of the Monocelis lineataspecies complex. The taxonomic resolution of the complex is challenging, as the species lacks sclerotised copulatory structures, which as a rule of thumb aid identification in Proseriata. Eighteen populations, which encompass most of the geographic range of the complex, were studied using morphology, karyology, crossbreeding experiments and molecular analysis. These different markers provided evidence of four (karyology) to eight (morphology) discrete entities, whereas crossings showed various degrees of intersterility among the tested populations. Molecular species delimitation revealed a different number of candidate species, spanning from five (ABGD and K/θ) to 11 (GMYC). Such incongruences reflect the multifaceted evolutionary history of M. lineata s.l.and hamper the full taxonomic resolution of the complex. However, two candidate species were consistently validated by all of the markers and are described as new species: Monocelis algicolanov. sp. and M. exquisitanov. sp. The latter species appear to have a restricted distribution, and the possibility that meiofaunal taxa may be of conservation concern is discussed.
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Affiliation(s)
- Fabio Scarpa
- 1 Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica Università di Sassari Via F. Muroni 25 07100 Sassari Italy
| | - Piero Cossu
- 1 Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica Università di Sassari Via F. Muroni 25 07100 Sassari Italy
| | - Tiziana Lai
- 1 Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica Università di Sassari Via F. Muroni 25 07100 Sassari Italy
| | - Daria Sanna
- 1 Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica Università di Sassari Via F. Muroni 25 07100 Sassari Italy
| | - Marco Curini-Galletti
- 1 Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica Università di Sassari Via F. Muroni 25 07100 Sassari Italy
| | - Marco Casu
- 1 Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica Università di Sassari Via F. Muroni 25 07100 Sassari Italy
- 2 E-mail:
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Sanna D, Scarpa F, Lai T, Cossu P, Falautano M, Castriota L, Andaloro F, Follesa MC, Francalacci P, Curini-Galletti M, Casu M. Fistularia commersonii(Teleostea: Fistulariidae): walking through the Lessepsian paradox of mitochondrial DNA. ACTA ACUST UNITED AC 2015. [DOI: 10.1080/11250003.2015.1046958] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Casu M, Scarpa F, Delogu V, Cossu P, Lai T, Sanna D, Curini-Galletti M. Biodiversity patterns in interstitial marine microturbellaria: a case study within the genus Parotoplana
(Platyhelminthes: Rhabditophora) with the description of four new species. J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marco Casu
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica; Centro di Eccellenza dell'Università di Sassari; Università di Sassari; Sassari Italy
| | - Fabio Scarpa
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica; Centro di Eccellenza dell'Università di Sassari; Università di Sassari; Sassari Italy
| | - Valentina Delogu
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica; Centro di Eccellenza dell'Università di Sassari; Università di Sassari; Sassari Italy
| | - Piero Cossu
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica; Centro di Eccellenza dell'Università di Sassari; Università di Sassari; Sassari Italy
| | - Tiziana Lai
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica; Centro di Eccellenza dell'Università di Sassari; Università di Sassari; Sassari Italy
| | - Daria Sanna
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica; Centro di Eccellenza dell'Università di Sassari; Università di Sassari; Sassari Italy
| | - Marco Curini-Galletti
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica; Centro di Eccellenza dell'Università di Sassari; Università di Sassari; Sassari Italy
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Abstract
This Minireview covers the methodological approaches of (23)Na NMR spectroscopy to the study of the structure and dynamics of the DNA molecule, in particular the application of the (23)Na NMR quadrupolar relaxation to investigate the perturbations on the polyion surface due to exogenous agents. A brief description of the (23)Na NMR quadrupolar relaxation and of the models used to describe the distribution of counterions around DNA, and the results of the application of the (23)Na NMR relaxation to the study of the cation-DNA interaction are also shown. Following sections present results of the investigation on ligand-DNA interaction and on ordered DNA systems.
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Affiliation(s)
- F Cesare Marincola
- Dipartimento di Scienze Chimiche, Università degli Studi di Cagliari, Monserrato, Cagliari, Italy
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Sanna D, Cossu P, Dedola GL, Scarpa F, Maltagliati F, Castelli A, Franzoi P, Lai T, Cristo B, Curini-Galletti M, Francalacci P, Casu M. Mitochondrial DNA reveals genetic structuring of Pinna nobilis across the Mediterranean Sea. PLoS One 2013; 8:e67372. [PMID: 23840684 PMCID: PMC3696058 DOI: 10.1371/journal.pone.0067372] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Accepted: 05/18/2013] [Indexed: 11/18/2022] Open
Abstract
Pinna nobilis is the largest endemic Mediterranean marine bivalve. During past centuries, various human activities have promoted the regression of its populations. As a consequence of stringent standards of protection, demographic expansions are currently reported in many sites. The aim of this study was to provide the first large broad-scale insight into the genetic variability of P. nobilis in the area that encompasses the western Mediterranean, Ionian Sea, and Adriatic Sea marine ecoregions. To accomplish this objective twenty-five populations from this area were surveyed using two mitochondrial DNA markers (COI and 16S). Our dataset was then merged with those obtained in other studies for the Aegean and Tunisian populations (eastern Mediterranean), and statistical analyses (Bayesian model-based clustering, median-joining network, AMOVA, mismatch distribution, Tajima's and Fu's neutrality tests and Bayesian skyline plots) were performed. The results revealed genetic divergence among three distinguishable areas: (1) western Mediterranean and Ionian Sea; (2) Adriatic Sea; and (3) Aegean Sea and Tunisian coastal areas. From a conservational point of view, populations from the three genetically divergent groups found may be considered as different management units.
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Affiliation(s)
- Daria Sanna
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | - Piero Cossu
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | - Gian Luca Dedola
- Dipartimento di Medicina Veterinaria - Sezione di Anatomia, Università di Sassari, Sassari, Italy
| | - Fabio Scarpa
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | | | | | - Piero Franzoi
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Università Cà Foscari, Venezia, Italy
| | - Tiziana Lai
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | - Benedetto Cristo
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | - Marco Curini-Galletti
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | - Paolo Francalacci
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | - Marco Casu
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
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Sanna D, Biagi F, Alaya HB, Maltagliati F, Addis A, Romero A, De Juan J, Quignard JP, Castelli A, Franzoi P, Torricelli P, Casu M, Carcupino M, Francalacci P. Mitochondrial DNA variability of the pipefish Syngnathus abaster. J Fish Biol 2013; 82:856-876. [PMID: 23464548 DOI: 10.1111/jfb.12027] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 11/15/2012] [Indexed: 06/01/2023]
Abstract
This study provides data on the genetic structuring of the pipefish Syngnathus abaster in the western Mediterranean and Adriatic Seas. A total of 109 specimens were collected in brackish-water biotopes. The control region and three other regions of the mitochondrial genome were analysed. The most relevant result was the high genetic structuring found by Bayesian inference (BI), maximum likelihood (ML) and network analyses, which were consistent in showing three well-separated clusters of S. abaster populations. Furthermore, BI and ML did not support the monophyly of the taxon S. abaster. These results suggest the occurrence of a species complex in the study area, whose differentiation may have occurred since the Pleistocene. The results also show a very high genetic variability at the inter-population level, with no shared haplotypes among sites. Evolutionary forces due to the fragmented nature of the brackish-water habitats may account for the high genetic divergence found among the groups and populations. Finally, although dispersal by rafting over long distances may occasionally occur, this study suggests linear stepping-stone model of colonization to be most likely. The complexity of the results obtained suggests that further studies are needed to elucidate the phylogeny of S. abaster.
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Affiliation(s)
- D Sanna
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Via Francesco Muroni 25, 07100, Sassari, Italy
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Mura L, Cossu P, Cannas A, Scarpa F, Sanna D, Dedola G, Floris R, Lai T, Cristo B, Curini-Galletti M, Fois N, Casu M. Genetic variability in the Sardinian population of the manila clam, Ruditapes philippinarum. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2011.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Sanna D, Dedola GL, Lai T, Curini-Galletti M, Casu M. PCR-RFLP: A practical method for the identification of specimens ofPatella ulyssiponensis s.l.(Gastropoda: Patellidae). ACTA ACUST UNITED AC 2012. [DOI: 10.1080/11250003.2011.620988] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Gianiorio FE, Casu M, Patrone V, Egan CG, Murialdo G. Effect of pioglitazone on cardiac sympathovagal modulation in patients with type 2 diabetes. Acta Diabetol 2011; 48:283-290. [PMID: 21312045 DOI: 10.1007/s00592-011-0258-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 01/14/2011] [Indexed: 01/18/2023]
Abstract
This study aims to examine the effect of pioglitazone on potential progression of autonomic damage in addition to changes in control of cardiovascular function in patients with type 2 diabetes (T2DM). Thirty patients with T2DM and 32 healthy subjects participated in the study. Sympathovagal activity, assessed by power spectral analysis (PSA) of R-R intervals variability, and blood pressure (BP) were studied during clinostatism and orthostatism in controls and patients. We have assessed blood pressure control by 24-hour monitoring of ambulatory blood pressure. Patients were treated with pioglitazone (30 mg/day) for 6 months, and then re-evaluated by PSA for heart rate variability (HRV). Reduced levels of HbA1c (P < 0.0001) and urinary albumin (P = 0.008) were observed in pioglitazone-treated patients compared to untreated baseline levels. Arterial BP remained unchanged following pioglitazone treatment. T2DM patients had reduced HRV (low-frequency power; LF; P < 0.0001 and LF/HF; LF/HF; P < 0.0001) at baseline (clinostatism) compared to controls. Baseline clinostatic differences between groups persisted after pioglitazone treatment and no effect of treatment on basal HRV variables was observed. In controls, HF decreased and LF and LF/HF ratio increased in the orthostatic position. A similar effect for HF was observed in patients, but LF and LF/HF did not increase. The normal difference between HF-power in clinostatism versus orthostatism observed for controls (P < 0.0001) was restored in patients following pioglitazone treatment (P = 0.028). A significant decrease from lying to standing position in orthostatic LF-power (P < 0.0001) and LF/HF (P < 0.0001) was also observed between patients and controls. Although no differences in autonomic control of HRV were observed between controls and patients with T2DM, significant differences were observed in sympathovagal balance following either clinostatic or orthostatic challenge. These findings provide initial evidence of a potential additional benefit afforded by pioglitazone for the improvement of cardiac sympathovagal balance in T2DM.
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Affiliation(s)
- F E Gianiorio
- Department of Internal Medicine, University of Genoa, Viale Benedetto XV,6, 16132, Genoa, Italy.
| | - M Casu
- Department of Endocrinological and Medical Sciences, University of Genoa, Genoa, Italy
| | - V Patrone
- Department of Endocrinological and Medical Sciences, University of Genoa, Genoa, Italy
| | - C G Egan
- Primula Multimedia S.R.L., Pisa, Italy
| | - G Murialdo
- Department of Endocrinological and Medical Sciences, University of Genoa, Genoa, Italy
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