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

doi:10.1016/j.ijid.2024.107262

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

Int J Infect Dis. 2024 Oct 8:107262. doi: 10.1016/j.ijid.2024.107262. Online ahead of print.

Authors

Eleonora Cella¹, Vagner Fonseca², Francesco Branda³, Stephane Tosta⁴, Keldenn Moreno⁴, Gabriel Schuab⁵, Sobur Ali¹, Svetoslav Nanev Slavov⁶, Fabio Scarpa⁷, Luciane Amorim Santos⁸, Simone Kashima⁹, Eduan Wilkinson¹⁰, Houriiyah Tegally¹⁰, Carla Mavian¹¹, Alessandra Borsetti¹², Francesca Caccuri¹³, Marco Salemi¹⁴, Tulio de Oliveira¹⁰, Taj Azarian¹, Ana Maria Bispo de Filippis⁵, Luiz Carlos Junior Alcantara¹⁵, Giancarlo Ceccarelli¹⁶, Arnaldo Caruso¹³, Vittorio Colizzi¹⁷, Alessandro Marcello¹⁸, José Lourenço¹⁹, Massimo Ciccozzi³, Marta Giovanetti²⁰

Affiliations

¹ Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA.
² Department of Exact and Earth Sciences, University of the State of Bahia, Salvador, Brazil.
³ Unit of Medical Statistics and Molecular Epidemiology, University of Campus Bio-Medico di Roma, Rome, Italy.
⁴ Programa Interunidades de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
⁵ Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil.
⁶ Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil; Butantan Institute, São Paulo, Brazil.
⁷ Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy.
⁸ Bahiana School of Medicine and Public Health, Salvador, Bahia, Brazil.
⁹ Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
¹⁰ Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
¹¹ Emerging Pathogens Institute, Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Global Health Program Smithsonian's National Zoo & Conservation Biology Institute, DC, USA.
¹² National HIV/AIDS Research Center (CNAIDS), Istituto Superiore di Sanità, Rome, Italy.
¹³ Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy.
¹⁴ Emerging Pathogens Institute, Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
¹⁵ Instituto René Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil.
¹⁶ Infectious Diseases Department, Azienda Ospedaliero Universitaria Policlinico Umberto I, 00161 Rome, Italy.
¹⁷ UNESCO Chair of Interdisciplinary Biotechnology and Bioethics, University of Rome Tor Vergata.
¹⁸ Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy.
¹⁹ Universidade Católica Portuguesa, Faculdade de Medicina, Biomedical Research Center, Lisboa, Portugal.
²⁰ Department of Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di Roma, Italy; Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil. Electronic address: [email protected].

PMID: 39389289
DOI: 10.1016/j.ijid.2024.107262

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.

Keywords: D614G variant; Italy; SARS-CoV-2; genomic epidemiology; pandemic.