Genome-Wide Approach Identifies Natural Large-Fragment Deletion in ASFV Strains Circulating in Italy During 2023
Claudia Torresi,
Roberta Biccheri,
Cesare Cammà,
Carmina Gallardo,
Maurilia Marcacci,
Simona Zoppi,
Barbara Secondini,
Caterina Riverso,
Alejandro Soler,
Cristina Casciari,
Michela Pela,
Elisabetta Rossi,
Claudia Pellegrini,
Carmen Iscaro,
Francesco Feliziani,
Monica Giammarioli
Affiliations
Claudia Torresi
National Reference Laboratory (NRL) for Swine Fever, Istituto Zooprofilattico Sperimentale dell’ Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy
Roberta Biccheri
National Reference Laboratory (NRL) for Swine Fever, Istituto Zooprofilattico Sperimentale dell’ Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy
Cesare Cammà
National Reference Center for Whole Genome Sequencing of Microbial Pathogens, Database and Bioinformatic Analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy
Carmina Gallardo
European Union Reference Laboratory for African swine fever (EURL), Centro de Investigación en Sanidad Animal (CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Consejo Superior de Investigaciones Científicas (CSIC), Valdeolmos, 28130 Madrid, Spain
Maurilia Marcacci
National Reference Center for Whole Genome Sequencing of Microbial Pathogens, Database and Bioinformatic Analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy
Simona Zoppi
Istituto Zooprofilattico Sperimentale Piemonte, Liguria e Valle d’Aosta “I. Altara”, 10154 Turin, Italy
Barbara Secondini
National Reference Center for Whole Genome Sequencing of Microbial Pathogens, Database and Bioinformatic Analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy
Caterina Riverso
Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, 80055 Napoli, Italy
Alejandro Soler
European Union Reference Laboratory for African swine fever (EURL), Centro de Investigación en Sanidad Animal (CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Consejo Superior de Investigaciones Científicas (CSIC), Valdeolmos, 28130 Madrid, Spain
Cristina Casciari
National Reference Laboratory (NRL) for Swine Fever, Istituto Zooprofilattico Sperimentale dell’ Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy
Michela Pela
National Reference Laboratory (NRL) for Swine Fever, Istituto Zooprofilattico Sperimentale dell’ Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy
Elisabetta Rossi
National Reference Laboratory (NRL) for Swine Fever, Istituto Zooprofilattico Sperimentale dell’ Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy
Claudia Pellegrini
National Reference Laboratory (NRL) for Swine Fever, Istituto Zooprofilattico Sperimentale dell’ Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy
Carmen Iscaro
National Reference Laboratory (NRL) for Swine Fever, Istituto Zooprofilattico Sperimentale dell’ Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy
Francesco Feliziani
National Reference Laboratory (NRL) for Swine Fever, Istituto Zooprofilattico Sperimentale dell’ Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy
Monica Giammarioli
National Reference Laboratory (NRL) for Swine Fever, Istituto Zooprofilattico Sperimentale dell’ Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy
African swine fever (ASF), characterized by high mortality rates in infected animals, remains a significant global veterinary and economic concern, due to the widespread distribution of ASF virus (ASFV) genotype II across five continents. In this study, ASFV strains collected in Italy during 2022–2023 from two geographical clusters, North-West (Alessandria) and Calabria, were fully sequenced. In addition, an in vivo experiment in pigs was performed. Complete genomic sequencing of 30 strains revealed large-fragment deletions and translocations. In Alessandria, five samples showed two different deletions in the 5′ genomic region: a ~4340 bp deletion (positions ~9020–13,356 in Georgia 2007/1) in four samples and a 2162 bp deletion (positions 17,837–19,998) in one sample. Another strain showed a truncation of 1950 bp at the 3′ end. In Calabria, strains showed a 5137 bp deletion (positions 10,755–15,891) and ~2 kb truncations in the 3′ region. Two strains showed a translocation from the region 1–2244 to positions 188,631–190,584. In vivo characterization of the deleted strain 22489.4_2312/RC/2023 revealed identical disease progression to the wild-type strain, with severe ASF symptoms in inoculated pigs. This study is the first to report natural deleted strains of ASFV in Italy, revealing unique genomic deletions distinct from those in previously known strains.
