SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy

Marta Giovanetti; Eleonora Cella; Francesca Benedetti; Brittany Rife Magalis; Vagner Fonseca; Silvia Fabris; Giovanni Campisi; Alessandra Ciccozzi; Silvia Angeletti; Alessandra Borsetti; Vittoradolfo Tambone; Caterina Sagnelli; Stefano Pascarella; Alberto Riva; Giancarlo Ceccarelli; Alessandro Marcello; Taj Azarian; Eduan Wilkinson; Tulio de Oliveira; Luiz Carlos Junior Alcantara; Roberto Cauda; Arnaldo Caruso; Natalie E. Dean; Cameron Browne; Jose Lourenco; Marco Salemi; Davide Zella; Massimo Ciccozzi

doi:10.1038/s42003-021-02025-0

SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy

Marta Giovanetti, Eleonora Cella, Francesca Benedetti, Brittany Rife Magalis, Vagner Fonseca, Silvia Fabris, Giovanni Campisi, Alessandra Ciccozzi, Silvia Angeletti, Alessandra Borsetti, Vittoradolfo Tambone, Caterina Sagnelli, Stefano Pascarella, Alberto Riva, Giancarlo Ceccarelli, Alessandro Marcello, Taj Azarian, Eduan Wilkinson, Tulio de Oliveira, Luiz Carlos Junior AlcantaraRoberto Cauda, Arnaldo Caruso, Natalie E. Dean, Cameron Browne, Jose Lourenco, Marco Salemi^*, Davide Zella^*, Massimo Ciccozzi^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

27 Citations (Scopus)

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 interventions is, ultimately, limited by the size and structure of epidemic reservoirs, which may warrant prioritization during vaccine deployment.

Original language	English
Article number	489
Journal	Communications Biology
Volume	4
Issue number	1
DOIs	https://doi.org/10.1038/s42003-021-02025-0
Publication status	Published - Dec 2021
Externally published	Yes

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Giovanetti, M., Cella, E., Benedetti, F., Rife Magalis, B., Fonseca, V., Fabris, S., Campisi, G., Ciccozzi, A., Angeletti, S., Borsetti, A., Tambone, V., Sagnelli, C., Pascarella, S., Riva, A., Ceccarelli, G., Marcello, A., Azarian, T., Wilkinson, E., de Oliveira, T., ... Ciccozzi, M. (2021). SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy. Communications Biology, 4(1), Article 489. https://doi.org/10.1038/s42003-021-02025-0

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title = "SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in 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 interventions is, ultimately, limited by the size and structure of epidemic reservoirs, which may warrant prioritization during vaccine deployment.",

author = "Marta Giovanetti and Eleonora Cella and Francesca Benedetti and {Rife Magalis}, Brittany and Vagner Fonseca and Silvia Fabris and Giovanni Campisi and Alessandra Ciccozzi and Silvia Angeletti and Alessandra Borsetti and Vittoradolfo Tambone and Caterina Sagnelli and Stefano Pascarella and Alberto Riva and Giancarlo Ceccarelli and Alessandro Marcello and Taj Azarian and Eduan Wilkinson and {de Oliveira}, Tulio and Alcantara, {Luiz Carlos Junior} and Roberto Cauda and Arnaldo Caruso and Dean, {Natalie E.} and Cameron Browne and Jose Lourenco and Marco Salemi and Davide Zella and Massimo Ciccozzi",

note = "Publisher Copyright: {\textcopyright} 2021, The Author(s).",

year = "2021",

month = dec,

doi = "10.1038/s42003-021-02025-0",

language = "English",

volume = "4",

journal = "Communications Biology",

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Giovanetti, M, Cella, E, Benedetti, F, Rife Magalis, B, Fonseca, V, Fabris, S, Campisi, G, Ciccozzi, A, Angeletti, S, Borsetti, A, Tambone, V, Sagnelli, C, Pascarella, S, Riva, A, Ceccarelli, G, Marcello, A, Azarian, T, Wilkinson, E, de Oliveira, T, Alcantara, LCJ, Cauda, R, Caruso, A, Dean, NE, Browne, C, Lourenco, J, Salemi, M, Zella, D & Ciccozzi, M 2021, 'SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy', Communications Biology, vol. 4, no. 1, 489. https://doi.org/10.1038/s42003-021-02025-0

TY - JOUR

T1 - SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy

AU - Giovanetti, Marta

AU - Cella, Eleonora

AU - Benedetti, Francesca

AU - Rife Magalis, Brittany

AU - Fonseca, Vagner

AU - Fabris, Silvia

AU - Campisi, Giovanni

AU - Ciccozzi, Alessandra

AU - Angeletti, Silvia

AU - Borsetti, Alessandra

AU - Tambone, Vittoradolfo

AU - Sagnelli, Caterina

AU - Pascarella, Stefano

AU - Riva, Alberto

AU - Ceccarelli, Giancarlo

AU - Marcello, Alessandro

AU - Azarian, Taj

AU - Wilkinson, Eduan

AU - de Oliveira, Tulio

AU - Alcantara, Luiz Carlos Junior

AU - Cauda, Roberto

AU - Caruso, Arnaldo

AU - Dean, Natalie E.

AU - Browne, Cameron

AU - Lourenco, Jose

AU - Salemi, Marco

AU - Zella, Davide

AU - Ciccozzi, Massimo

PY - 2021/12

Y1 - 2021/12

N2 - 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 interventions is, ultimately, limited by the size and structure of epidemic reservoirs, which may warrant prioritization during vaccine deployment.

AB - 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 interventions is, ultimately, limited by the size and structure of epidemic reservoirs, which may warrant prioritization during vaccine deployment.

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U2 - 10.1038/s42003-021-02025-0

DO - 10.1038/s42003-021-02025-0

M3 - Article

C2 - 33883675

AN - SCOPUS:85104775295

SN - 2399-3642

VL - 4

JO - Communications Biology

JF - Communications Biology

IS - 1

M1 - 489

ER -

SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy

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