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SARS-COV-2 SHIFTING TRANSMISSION DYNAMICS AND HIDDEN RESERVOIRS POTENTIALLY LIMIT EFFICACY OF PUBLIC HEALTH INTERVENTIONS IN ITALY
Dinâmica de transmissão
Reservatórios ocultos
Eficácia
Saúde Pública
Itália
COVID-19
Shifting transmission dynamics
Hidden reservoirs
Potentially limit efficacy
Public health
Italy
COVID-19
Author
Giovanetti, Marta
Cella, Eleonora
Benedetti, Francesca
Magalis, Brittany Rife
Fonseca, Vagner
Fabris, Silvia
Campisi, Giovanni
Ciccozzi, Alessandra
Angeletti, Silvia
Borsetti, Alessandra
Tambone, Vittoradolfo
Sagnelli, Caterina
Pascarella, Stefano
Riva, Alberto
Ceccarelli, Giancarlo
Marcello, Alessandro
Azarian, Taj
Wilkinson, Eduan
Oliveira, Tulio de
Alcantara, Luiz Carlos Junior
Cauda, Roberto
Caruso, Arnaldo
Dean, Natalie E.
Browne, Cameron
Lourenço, Jose
Salemi, Marco
Zella, Davide
Ciccozzi, Massimo
Cella, Eleonora
Benedetti, Francesca
Magalis, Brittany Rife
Fonseca, Vagner
Fabris, Silvia
Campisi, Giovanni
Ciccozzi, Alessandra
Angeletti, Silvia
Borsetti, Alessandra
Tambone, Vittoradolfo
Sagnelli, Caterina
Pascarella, Stefano
Riva, Alberto
Ceccarelli, Giancarlo
Marcello, Alessandro
Azarian, Taj
Wilkinson, Eduan
Oliveira, Tulio de
Alcantara, Luiz Carlos Junior
Cauda, Roberto
Caruso, Arnaldo
Dean, Natalie E.
Browne, Cameron
Lourenço, Jose
Salemi, Marco
Zella, Davide
Ciccozzi, Massimo
Affilliation
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivirus. Rio de Janeiro, RJ, Brasil / Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil / Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy.
University of Central Florida. Burnett School of Biomedical Sciences. Orlando, FL, USA.
Institute of Human Virology and Global Virus Network Center, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA.
Emerging Pathogens Institute & Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA.
Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil / KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa. / Ministério da Saúde. Secretaria de Vigilância em Saúde. Coordenação dos Laboratórios de Saúde Pública. Brasília, DF, Brasil.
Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus. Rome, Italy.
Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia. Brescia, Italy.
Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus. Rome, Italy.
Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome. Rome, Italy.
National HIV/AIDS Researh Center, Istituto Superiore di Sanità. Rome, Italy.
Anthropology, and Applied Ethics, Campus Bio-Medico University. Rome, Italy.
Department of Mental Health and Public Medicine, University of Campania “Luigi Vanvitelli”. Naples, Italy.
Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome “La Sapienza”. Rome, Italy.
ICBR, University of Florida, Gainesville. FL, USA..
Department of Public Health and Infectious Diseases, Policlinico Umberto I Università ‘Sapienza’. Rome, Italy.
Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology (ICGEB). Trieste, Italy.
Burnett School of Biomedical Sciences, University of Central Florida. Orlando, FL, USA.
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivirus. Rio de Janeiro, RJ, Brasil / Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil.
Department Infectious Diseases – Fondazione Policlinico Universitario “A. Gemelli” IRCCS. Rome, Italy.
Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia. Brescia, Italy.
Department of Epidemiology, College of Public Health and Health Professions, University of Florida. Gainesville, FL, USA.
Department of Mathematics, University of Lafayette. Lafayette, LA, USA.
Department of Zoology, University of Oxford. Oxford, UK.
Emerging Pathogens Institute & Department of Pathology, College of Medicine, University of Florida. Gainesville, FL, USA
Institute of Human Virology and Global Virus Network Center, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine. Baltimore, MD, USA.
Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus. Rome, Italy..
University of Central Florida. Burnett School of Biomedical Sciences. Orlando, FL, USA.
Institute of Human Virology and Global Virus Network Center, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA.
Emerging Pathogens Institute & Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA.
Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil / KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa. / Ministério da Saúde. Secretaria de Vigilância em Saúde. Coordenação dos Laboratórios de Saúde Pública. Brasília, DF, Brasil.
Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus. Rome, Italy.
Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia. Brescia, Italy.
Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus. Rome, Italy.
Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome. Rome, Italy.
National HIV/AIDS Researh Center, Istituto Superiore di Sanità. Rome, Italy.
Anthropology, and Applied Ethics, Campus Bio-Medico University. Rome, Italy.
Department of Mental Health and Public Medicine, University of Campania “Luigi Vanvitelli”. Naples, Italy.
Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome “La Sapienza”. Rome, Italy.
ICBR, University of Florida, Gainesville. FL, USA..
Department of Public Health and Infectious Diseases, Policlinico Umberto I Università ‘Sapienza’. Rome, Italy.
Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology (ICGEB). Trieste, Italy.
Burnett School of Biomedical Sciences, University of Central Florida. Orlando, FL, USA.
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivirus. Rio de Janeiro, RJ, Brasil / Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular. Belo Horizonte, MG, Brasil.
Department Infectious Diseases – Fondazione Policlinico Universitario “A. Gemelli” IRCCS. Rome, Italy.
Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia. Brescia, Italy.
Department of Epidemiology, College of Public Health and Health Professions, University of Florida. Gainesville, FL, USA.
Department of Mathematics, University of Lafayette. Lafayette, LA, USA.
Department of Zoology, University of Oxford. Oxford, UK.
Emerging Pathogens Institute & Department of Pathology, College of Medicine, University of Florida. Gainesville, FL, USA
Institute of Human Virology and Global Virus Network Center, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine. Baltimore, MD, USA.
Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus. Rome, Italy..
Abstract
We investigated SARS-CoV-2 transmission dynamics in Italy, one of the countries hit hardest by the pandemic, using phylodynamic analysis of viral genetic and epidemiological data. We observed the co-circulation of multiple SARS-CoV-2 lineages over time, which were linked to multiple importations and characterized by large transmission clusters concomitant with a high number of infections. Subsequent implementation of a three-phase nationwide lockdown strategy greatly reduced infection numbers and hospitalizations. Yet we present evidence of sustained viral spread among sporadic clusters acting as “hidden reservoirs” during summer 2020. Mathematical modelling shows that increased mobility among residents eventually catalyzed the coalescence of such clusters, thus driving up the number of infections and initiating a new epidemic wave. Our results suggest that the efficacy of public health inter ventions is, ultimately, limited by the size and structure of epidemic reservoirs, which may warrant prioritization during vaccine deployment.
Keywords in Portuguese
SARS-CoV-2Dinâmica de transmissão
Reservatórios ocultos
Eficácia
Saúde Pública
Itália
COVID-19
Keywords
SARS-CoV-2Shifting transmission dynamics
Hidden reservoirs
Potentially limit efficacy
Public health
Italy
COVID-19
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