International Journal of Infectious Diseases (Dec 2024)
Integrated analyses of the transmission history of SARS-CoV-2 and its association with molecular evolution of the virus underlining the pandemic outbreaks in Italy, 2019-2023
- Eleonora Cella,
- Vagner Fonseca,
- Francesco Branda,
- Stephane Tosta,
- Keldenn Moreno,
- Gabriel Schuab,
- Sobur Ali,
- Svetoslav Nanev Slavov,
- Fabio Scarpa,
- Luciane Amorim Santos,
- Simone Kashima,
- Eduan Wilkinson,
- Houriiyah Tegally,
- Carla Mavian,
- Alessandra Borsetti,
- Francesca Caccuri,
- Marco Salemi,
- Tulio de Oliveira,
- Taj Azarian,
- Ana Maria Bispo de Filippis,
- Luiz Carlos Junior Alcantara,
- Giancarlo Ceccarelli,
- Arnaldo Caruso,
- Vittorio Colizzi,
- Alessandro Marcello,
- José Lourenço,
- Massimo Ciccozzi,
- Marta Giovanetti
Affiliations
- Eleonora Cella
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
- Vagner Fonseca
- Department of Exact and Earth Sciences, University of the State of Bahia, Salvador, Brazil
- Francesco Branda
- Unit of Medical Statistics and Molecular Epidemiology, University of Campus Bio-Medico di Roma, Rome, Italy
- Stephane Tosta
- Programa Interunidades de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Keldenn Moreno
- Programa Interunidades de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Gabriel Schuab
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
- Sobur Ali
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
- Svetoslav Nanev Slavov
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil; Butantan Institute, São Paulo, Brazil
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Luciane Amorim Santos
- Bahiana School of Medicine and Public Health, Salvador, Bahia, Brazil
- Simone Kashima
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Carla Mavian
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Global Health Program Smithsonian's National Zoo & Conservation Biology Institute, DC, USA
- Alessandra Borsetti
- National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, Rome, Italy
- Francesca Caccuri
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
- Marco Salemi
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Taj Azarian
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
- Ana Maria Bispo de Filippis
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
- Luiz Carlos Junior Alcantara
- Fundação Oswaldo Cruz, Instituto René Rachou, Belo Horizonte, Minas Gerais, Brazil
- Giancarlo Ceccarelli
- Infectious Diseases Department, Azienda Ospedaliero Universitaria Policlinico Umberto I, Rome, Italy
- Arnaldo Caruso
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
- Vittorio Colizzi
- UNESCO Chair of Interdisciplinary Biotechnology and Bioethics, University of Rome Tor Vergata, Rome, Italy
- Alessandro Marcello
- Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- José Lourenço
- Faculdade de Medicina, Biomedical Research Center, Universidade Católica Portuguesa, Lisboa, Portugal
- Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University of Campus Bio-Medico di Roma, Rome, Italy
- Marta Giovanetti
- Department of Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di Roma, Rome, Italy; Oswaldo Cruz Foundation, Oswaldo Cruz Institute, Rio de Janeiro, Brazil; Corresponding author.
- Journal volume & issue
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Vol. 149
p. 107262
Abstract
Background: Italy was significantly affected by the COVID-19 pandemic, experiencing multiple waves of infection following the sequential emergence of new variants. Understanding the transmission patterns and evolution of SARS-CoV-2 is vital for future preparedness. Methods: We conducted an analysis of viral genome sequences, integrating epidemiological and phylodynamic approaches, to characterize how SARS-CoV-2 variants have spread within the country. Results: Our findings indicate bidirectional international transmission, with Italy transitioning between importing and exporting the virus. Italy experienced four distinct epidemic waves, each associated with a significant reduction in fatalities from 2021 to 2023. These waves were primarily driven by the emergence of VOCs such as Alpha, Delta, and Omicron, which were reflected in observed transmission dynamics and effectiveness of public health measures. Conclusions: The changing patterns of viral spread and variant prevalence throughout Italy's pandemic response underscore the continued importance of flexible public health strategies and genomic surveillance, both of which are crucial for tracking the evolution of variants and adapting control measures effectively to ensure preparedness for future outbreaks.
