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Pinotti F, Kohnle L, Lourenço J, Gupta S, Hoque MA, Mahmud R, Biswas P, Pfeiffer D, Fournié G. Modelling the transmission dynamics of H9N2 avian influenza viruses in a live bird market. Nat Commun 2024; 15:3494. [PMID: 38693163 PMCID: PMC11063141 DOI: 10.1038/s41467-024-47703-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/08/2024] [Indexed: 05/03/2024] Open
Abstract
H9N2 avian influenza viruses (AIVs) are a major concern for the poultry sector and human health in countries where this subtype is endemic. By fitting a model simulating H9N2 AIV transmission to data from a field experiment, we characterise the epidemiology of the virus in a live bird market in Bangladesh. Many supplied birds arrive already exposed to H9N2 AIVs, resulting in many broiler chickens entering the market as infected, and many indigenous backyard chickens entering with pre-existing immunity. Most susceptible chickens become infected within one day spent at the market, owing to high levels of viral transmission within market and short latent periods, as brief as 5.3 hours. Although H9N2 AIV transmission can be substantially reduced under moderate levels of cleaning and disinfection, effective risk mitigation also requires a range of additional interventions targeting markets and other nodes along the poultry production and distribution network.
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Affiliation(s)
| | - Lisa Kohnle
- City University of Hong Kong, Hong Kong SAR, Hong Kong
| | - José Lourenço
- CBR (Biomedical Research Centre), Universidade Católica Portuguesa, Oeiras, Portugal
| | - Sunetra Gupta
- Department of Biology, University of Oxford, Oxford, UK
| | - Md Ahasanul Hoque
- Chattogram Veterinary and Animal Sciences University, Chittagong, Bangladesh
| | - Rashed Mahmud
- Chattogram Veterinary and Animal Sciences University, Chittagong, Bangladesh
| | - Paritosh Biswas
- Chattogram Veterinary and Animal Sciences University, Chittagong, Bangladesh
| | - Dirk Pfeiffer
- City University of Hong Kong, Hong Kong SAR, Hong Kong
- Royal Veterinary College, London, UK
| | - Guillaume Fournié
- Royal Veterinary College, London, UK
- INRAE, VetAgro Sup, UMR EPIA, Université de Lyon, Marcy l'Etoile, 69280, France
- INRAE, VetAgro Sup, UMR EPIA, Université Clermont Auvergne, Saint Genès Champanelle, 63122, France
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Pinotti F, Lourenço J, Gupta S, Das Gupta S, Henning J, Blake D, Tomley F, Barnett T, Pfeiffer D, Hoque MA, Fournié G. EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networks. PLoS Comput Biol 2024; 20:e1011375. [PMID: 38381804 PMCID: PMC10911595 DOI: 10.1371/journal.pcbi.1011375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 03/04/2024] [Accepted: 02/06/2024] [Indexed: 02/23/2024] Open
Abstract
The rapid intensification of poultry production raises important concerns about the associated risks of zoonotic infections. Here, we introduce EPINEST (EPIdemic NEtwork Simulation in poultry Transportation systems): an agent-based modelling framework designed to simulate pathogen transmission within realistic poultry production and distribution networks. We provide example applications to broiler production in Bangladesh, but the modular structure of the model allows for easy parameterization to suit specific countries and system configurations. Moreover, the framework enables the replication of a wide range of eco-epidemiological scenarios by incorporating diverse pathogen life-history traits, modes of transmission and interactions between multiple strains and/or pathogens. EPINEST was developed in the context of an interdisciplinary multi-centre study conducted in Bangladesh, India, Vietnam and Sri Lanka, and will facilitate the investigation of the spreading patterns of various health hazards such as avian influenza, Campylobacter, Salmonella and antimicrobial resistance in these countries. Furthermore, this modelling framework holds potential for broader application in veterinary epidemiology and One Health research, extending its relevance beyond poultry to encompass other livestock species and disease systems.
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Affiliation(s)
| | - José Lourenço
- Católica Biomedical Research, Católica Medical School, Universidade Católica Portuguesa, Lisbon, Portugal
| | | | - Suman Das Gupta
- School of Veterinary Science, The University of Queensland, Queensland, Australia
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Joerg Henning
- School of Veterinary Science, The University of Queensland, Queensland, Australia
| | - Damer Blake
- Royal Veterinary College, London, United Kingdom
| | - Fiona Tomley
- Royal Veterinary College, London, United Kingdom
| | - Tony Barnett
- Royal Veterinary College, London, United Kingdom
- The Firoz Lalji Centre for Africa, London School of Economics and Political Science, London, United Kingdom
| | - Dirk Pfeiffer
- Royal Veterinary College, London, United Kingdom
- City University of Hong Kong, Hong Kong SAR, Hong Kong
| | - Md. Ahasanul Hoque
- Chattogram Veterinary and Animal Sciences University, Chittagong, Bangladesh
| | - Guillaume Fournié
- Royal Veterinary College, London, United Kingdom
- INRAE, VetAgro Sup, UMR EPIA, Université de Lyon, Marcy l’Etoile, 69280, France
- INRAE, VetAgro Sup, UMR EPIA, Université Clermont Auvergne, Saint Genès Champanelle, 63122, France
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Pinotti F, Giovanetti M, de Lima MM, de Cerqueira EM, Alcantara LCJ, Gupta S, Recker M, Lourenço J. Shifting patterns of dengue three years after Zika virus emergence in Brazil. Nat Commun 2024; 15:632. [PMID: 38245500 PMCID: PMC10799945 DOI: 10.1038/s41467-024-44799-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/03/2024] [Indexed: 01/22/2024] Open
Abstract
In 2015, the Zika virus (ZIKV) emerged in Brazil, leading to widespread outbreaks in Latin America. Following this, many countries in these regions reported a significant drop in the circulation of dengue virus (DENV), which resurged in 2018-2019. We examine age-specific incidence data to investigate changes in DENV epidemiology before and after the emergence of ZIKV. We observe that incidence of DENV was concentrated in younger individuals during resurgence compared to 2013-2015. This trend was more pronounced in Brazilian states that had experienced larger ZIKV outbreaks. Using a mathematical model, we show that ZIKV-induced cross-protection alone, often invoked to explain DENV decline across Latin America, cannot explain the observed age-shift without also assuming some form of disease enhancement. Our results suggest that a sudden accumulation of population-level immunity to ZIKV could suppress DENV and reduce the mean age of DENV incidence via both protective and disease-enhancing interactions.
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Affiliation(s)
- Francesco Pinotti
- Department of Biology, University of Oxford, Oxford, United Kingdom.
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico di Roma, Rome, Italy
| | | | | | - Luiz C J Alcantara
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Sunetra Gupta
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Mario Recker
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - José Lourenço
- Católica Biomedical Research, Católica Medical School, Universidade Católica Portuguesa, Lisbon, Portugal
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4
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Giovanetti M, Pinotti F, Zanluca C, Fonseca V, Nakase T, Koishi AC, Tscha M, Soares G, Dorl GG, Marques AEM, Sousa R, Adelino TER, Xavier J, de Oliveira C, Patroca S, Guimaraes NR, Fritsch H, Mares-Guia MA, Levy F, Passos PH, da Silva VL, Pereira LA, Mendonça AF, de Macêdo IL, Ribeiro de Sousa DE, Rodrigues de Toledo Costa G, Botelho de Castro M, de Souza Andrade M, de Abreu FVS, Campos FS, Iani FCDM, Pereira MA, Cavalcante KRLJ, de Freitas ARR, Campelo de Albuquerque CF, Macário EM, dos Anjos MPD, Ramos RC, Campos AAS, Pinter A, Chame M, Abdalla L, Riediger IN, Ribeiro SP, Bento AI, de Oliveira T, Freitas C, Oliveira de Moura NF, Fabri A, dos Santos Rodrigues CD, Dos Santos CC, Barreto de Almeida MA, dos Santos E, Cardoso J, Augusto DA, Krempser E, Mucci LF, Gatti RR, Cardoso SF, Fuck JAB, Lopes MGD, Belmonte IL, Mayoral Pedroso da Silva G, Soares MRF, de Castilhos MDMS, de Souza e Silva JC, Bisetto Junior A, Pouzato EG, Tanabe LS, Arita DA, Matsuo R, dos Santos Raymundo J, Silva PCL, Santana Araújo Ferreira Silva A, Samila S, Carvalho G, Stabeli R, Navegantes W, Moreira LA, Ferreira AGA, Pinheiro GG, Nunes BTD, de Almeida Medeiros DB, Cruz ACR, Venâncio da Cunha R, Van Voorhis W, Bispo de Filippis AM, Almiron M, Holmes EC, Ramos DG, Romano A, Lourenço J, Alcantara LCJ, Duarte dos Santos CN. Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil. Sci Adv 2023; 9:eadg9204. [PMID: 37656782 PMCID: PMC10854437 DOI: 10.1126/sciadv.adg9204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 07/26/2023] [Indexed: 09/03/2023]
Abstract
Despite the considerable morbidity and mortality of yellow fever virus (YFV) infections in Brazil, our understanding of disease outbreaks is hampered by limited viral genomic data. Here, through a combination of phylogenetic and epidemiological models, we reconstructed the recent transmission history of YFV within different epidemic seasons in Brazil. A suitability index based on the highly domesticated Aedes aegypti was able to capture the seasonality of reported human infections. Spatial modeling revealed spatial hotspots with both past reporting and low vaccination coverage, which coincided with many of the largest urban centers in the Southeast. Phylodynamic analysis unraveled the circulation of three distinct lineages and provided proof of the directionality of a known spatial corridor that connects the endemic North with the extra-Amazonian basin. This study illustrates that genomics linked with eco-epidemiology can provide new insights into the landscape of YFV transmission, augmenting traditional approaches to infectious disease surveillance and control.
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Affiliation(s)
- Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Department of Science and Technology for Humans and the Environment, Università of Campus Bio-Medico di Roma, Italy
| | | | - Camila Zanluca
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | - Vagner Fonseca
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil
| | - Taishi Nakase
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Andrea C. Koishi
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | - Marcel Tscha
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | - Guilherme Soares
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | - Gisiane Gruber Dorl
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | | | - Renato Sousa
- Laboratório de Patologia Veterinária, Hospital Veterinário UFPR, PR Brazil
| | - Talita Emile Ribeiro Adelino
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Joilson Xavier
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Carla de Oliveira
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | | | - Natalia Rocha Guimaraes
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Hegger Fritsch
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Flavia Levy
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Pedro Henrique Passos
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde (CGARB/SVS-MS), Brasília, Distrito Federal, Brazil
| | | | - Luiz Augusto Pereira
- Laboratório Central de Saúde Pública Dr Giovanni Cysneiros, Goiânia, Goiás, Brazil
| | - Ana Flávia Mendonça
- Laboratório Central de Saúde Pública Dr Giovanni Cysneiros, Goiânia, Goiás, Brazil
| | - Isabel Luana de Macêdo
- Veterinary Pathology Laboratory, Campus Darcy Ribeiro, University of Brasília, Brasília, DF 70636- 200, Brazil
| | | | | | - Marcio Botelho de Castro
- Veterinary Pathology Laboratory, Campus Darcy Ribeiro, University of Brasília, Brasília, DF 70636- 200, Brazil
- Graduate Program in Animal Sciences, College of Agronomy and Veterinary Medicine, University of Brasília, Brasília, DF 70910-900, Brazil
| | - Miguel de Souza Andrade
- Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, DF, Brazil
| | | | - Fabrício Souza Campos
- Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, RS, Brazil
| | - Felipe Campos de Melo Iani
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Maira Alves Pereira
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | | | | | | | | | - Marlei Pickler Debiasi dos Anjos
- Laboratorio central de Saude Publica de Santa Catarina, Superintendência de Vigilância em Saúde – SES – Santa Catarina, South Brazil
| | - Rosane Campanher Ramos
- Laboratório Central de Saúde Pública do Estado do Rio Grande do Sul, Superintendência de Vigilância em Saúde – SES – Santa Catarina, South Brazil
| | | | - Adriano Pinter
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | - Marcia Chame
- Oswaldo Cruz Foundation, Biodiversity, Wildlife Health Institutional Platform (PIBSS/Fiocruz), Rio de Janeiro, Brazil
| | - Livia Abdalla
- Oswaldo Cruz Foundation, Biodiversity, Wildlife Health Institutional Platform (PIBSS/Fiocruz), Rio de Janeiro, Brazil
| | | | - Sérvio Pontes Ribeiro
- Laboratory of Ecology of Diseases & Forests, NUPEB/ICEB, Federal University of Ouro Preto, Minas Gerais, Brazil
| | - Ana I. Bento
- Pandemic Prevention Initiative, The Rockefeller Foundation, Washington DC, USA
| | - Tulio de Oliveira
- School for Data Science and Computational Thinking, Faculty of Science and Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Carla Freitas
- Secretaria de Vigilância em Saúde, SVS, Brazilian Ministry of Health, Brasilia, Federal District, Brazil
| | | | - Allison Fabri
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | | | | | - Edmilson dos Santos
- Secretaria Estadual de Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Porto Alegre, RS, Brazil
| | - Jader Cardoso
- Secretaria Estadual de Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Porto Alegre, RS, Brazil
| | - Douglas Adriano Augusto
- Plataforma Institucional Biodiversidade e Saúde Silvestre - Centro de Informação em Saúde Silvestre (CISS) - Fiocruz/RJ, Avenida Brasil, 4365. Manguinhos - Rio de Janeiro - RJ Cep: 21.040-360
| | - Eduardo Krempser
- Plataforma Institucional Biodiversidade e Saúde Silvestre - Centro de Informação em Saúde Silvestre (CISS) - Fiocruz/RJ, Avenida Brasil, 4365. Manguinhos - Rio de Janeiro - RJ Cep: 21.040-360
| | - Luís Filipe Mucci
- Secretaria da Saúde (São Paulo - Estado), Av Dr. Enéas Carvalho de Aguiar, 188 - Cerqueira César, São Paulo - SP, 05403-000, Brazil
- Coordenadoria de Controle de Doenças (CCD), Av. Dr. Enéas Carvalho de Aguiar, 188 - Cerqueira César, São Paulo - SP, 05403-000, Brazil
- Instituto Pasteur (IP), Av. Paulista, 363 Cerqueira Cesar – São Paulo- SP – CEP:01311-000
| | - Renata Rispoli Gatti
- Secretaria de Estado da Saude de Santa Catarina, R. Esteves Júnior, 160 - Centro, Florianópolis - SC, 88015-130, Brazil
| | - Sabrina Fernandes Cardoso
- Secretaria de Estado da Saude de Santa Catarina, R. Esteves Júnior, 160 - Centro, Florianópolis - SC, 88015-130, Brazil
- Department of Cell Biology, Embryology and Genetics, Federal University of Santa Catarina (UFSC), Florianópolis, Brazil
| | - João Augusto Brancher Fuck
- Diretoria de Vigilância Epidemiológica da Secretaria de Estado da Saúde de Santa Catarina, R. Esteves Júnior, 160 - Centro, Florianópolis - SC, 88015-130, Brazil
| | - Maria Goretti David Lopes
- Secretaria de Estado da Saúde do Paraná, Brazil, R. Piquiri, 170 - Rebouças, Curitiba - PR, 80230-140
| | - Ivana Lucia Belmonte
- Secretaria de Estado da Saúde do Paraná, Brazil, R. Piquiri, 170 - Rebouças, Curitiba - PR, 80230-140
| | | | | | | | | | - Alceu Bisetto Junior
- Secretaria de Estado da Saúde do Paraná, Brazil, R. Piquiri, 170 - Rebouças, Curitiba - PR, 80230-140
| | - Emanuelle Gemin Pouzato
- Secretaria de Estado da Saúde do Paraná, Brazil, R. Piquiri, 170 - Rebouças, Curitiba - PR, 80230-140
| | - Laurina Setsuko Tanabe
- Secretaria de Estado da Saúde do Paraná, Brazil, R. Piquiri, 170 - Rebouças, Curitiba - PR, 80230-140
| | - Daniele Akemi Arita
- Secretaria de Estado da Saúde do Paraná, Brazil, R. Piquiri, 170 - Rebouças, Curitiba - PR, 80230-140
| | - Ricardo Matsuo
- Secretaria de Estado da Saúde do Paraná, Brazil, R. Piquiri, 170 - Rebouças, Curitiba - PR, 80230-140
| | | | | | | | - Sandra Samila
- Secretaria de Estado da Saúde do Paraná, Brazil, R. Piquiri, 170 - Rebouças, Curitiba - PR, 80230-140
| | - Glauco Carvalho
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Rodrigo Stabeli
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil
| | - Wildo Navegantes
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil
| | - Luciano Andrade Moreira
- Mosquitos Vetores: Endossimbiontes e Interação Patógeno-Vetor, Instituto René Rachou–Fiocruz, Belo Horizonte 30190-002, MG, Brazil
| | - Alvaro Gil A. Ferreira
- Mosquitos Vetores: Endossimbiontes e Interação Patógeno-Vetor, Instituto René Rachou–Fiocruz, Belo Horizonte 30190-002, MG, Brazil
| | | | | | | | | | | | - Wes Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, WA, USA
| | | | - Maria Almiron
- Pan American Health Organization/World Health Organization, Washington, DC, USA
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Daniel Garkauskas Ramos
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde (CGARB/SVS-MS), Brasília, Distrito Federal, Brazil
| | - Alessandro Romano
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde (CGARB/SVS-MS), Brasília, Distrito Federal, Brazil
| | - José Lourenço
- BioISI (Biosystems and Integrative Sciences Institute), Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa Portugal
| | - Luiz Carlos Junior Alcantara
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
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Lourenço J, Pinotti F, Nakase T, Giovanetti M, Obolski U. Letter to the editor: Atypical weather is associated with the 2022 early start of West Nile virus transmission in Italy. Euro Surveill 2022; 27:2200662. [PMID: 36017714 PMCID: PMC9413859 DOI: 10.2807/1560-7917.es.2022.27.34.2200662] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 08/23/2022] [Indexed: 05/27/2023] Open
Affiliation(s)
- José Lourenço
- Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | | | - Taishi Nakase
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Marta Giovanetti
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Uri Obolski
- School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Porter School of the Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
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6
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Pereira FM, Salomão de Araujo A, Catarina Martins Reis A, Santos da Hora A, Pinotti F, Paton RS, Vilas Boas Figueiredo C, Lopes Damasceno C, Carlos dos Santos D, Souza de Santana D, Freitas Sales D, Ariana Andrade Brandão E, da Silva Batista E, Campos de Sousa FS, Santana Menezes G, Silveira dos Santos J, Gomes Lima J, Tadeu Brito J, Dandara dos Santos L, Reboredo L, Santana Santos M, Kelly Astete Gomez M, Freitas da Cruz M, Rosa Ampuero M, Guerra Lemos da Silva M, S. da Paixão Melo M, Ferreira da Silva M, de Jesus Gonçalves dos Santos N, de Souza Pessoa N, Silva de Araujo R, de Macedo Godim T, Fraga de Oliveira Tosta S, Brandão Nardy V, Cristina Faria E, Frederico de Carvalho Dominguez Souza B, Laís Almeida dos Santos J, Wikramaratna P, Giovanetti M, Alcântara LCJ, Lourenço J, Leal e Silva de Mello A. Dynamics and Determinants of SARS-CoV-2 RT-PCR Testing on Symptomatic Individuals Attending Healthcare Centers during 2020 in Bahia, Brazil. Viruses 2022; 14:v14071549. [PMID: 35891528 PMCID: PMC9321627 DOI: 10.3390/v14071549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/03/2022] [Accepted: 07/05/2022] [Indexed: 02/05/2023] Open
Abstract
RT-PCR testing data provides opportunities to explore regional and individual determinants of test positivity and surveillance infrastructure. Using Generalized Additive Models, we explored 222,515 tests of a random sample of individuals with COVID-19 compatible symptoms in the Brazilian state of Bahia during 2020. We found that age and male gender were the most significant determinants of test positivity. There was evidence of an unequal impact among socio-demographic strata, with higher positivity among those living in areas with low education levels during the first epidemic wave, followed by those living in areas with higher education levels in the second wave. Our estimated probability of testing positive after symptom onset corroborates previous reports that the probability decreases with time, more than halving by about two weeks and converging to zero by three weeks. Test positivity rates generally followed state-level reported cases, and while a single laboratory performed ~90% of tests covering ~99% of the state's area, test turn-around time generally remained below four days. This testing effort is a testimony to the Bahian surveillance capacity during public health emergencies, as previously witnessed during the recent Zika and Yellow Fever outbreaks.
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Affiliation(s)
- Felicidade Mota Pereira
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Aline Salomão de Araujo
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Ana Catarina Martins Reis
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Anadilton Santos da Hora
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Francesco Pinotti
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK; (F.P.); (R.S.P.)
| | - Robert S. Paton
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK; (F.P.); (R.S.P.)
| | - Camylla Vilas Boas Figueiredo
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Caroline Lopes Damasceno
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Daiana Carlos dos Santos
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Daniele Souza de Santana
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Danielle Freitas Sales
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Evelyn Ariana Andrade Brandão
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Everton da Silva Batista
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Fulvia Soares Campos de Sousa
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Gabriela Santana Menezes
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Jackeline Silveira dos Santos
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Jaqueline Gomes Lima
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Jean Tadeu Brito
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Lenisa Dandara dos Santos
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Luciana Reboredo
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Maiara Santana Santos
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Marcela Kelly Astete Gomez
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Marcia Freitas da Cruz
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Mariana Rosa Ampuero
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Mariele Guerra Lemos da Silva
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Mariza S. da Paixão Melo
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Marta Ferreira da Silva
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Nadja de Jesus Gonçalves dos Santos
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Núbia de Souza Pessoa
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Ramile Silva de Araujo
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Taiane de Macedo Godim
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | | | - Vanessa Brandão Nardy
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Elaine Cristina Faria
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Breno Frederico de Carvalho Dominguez Souza
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | - Jessica Laís Almeida dos Santos
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
| | | | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro 21045-900, Brazil;
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Luiz Carlos Junior Alcântara
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro 21045-900, Brazil;
- Correspondence: (L.C.J.A.); (J.L.)
| | - José Lourenço
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências, 1749-016 Lisboa, Portugal
- Correspondence: (L.C.J.A.); (J.L.)
| | - Arabela Leal e Silva de Mello
- Laboratório Central de Saúde Pública Professor Gonçalo Muniz, Salvador 40295-010, Brazil; (F.M.P.); (A.S.d.A.); (A.C.M.R.); (A.S.d.H.); (C.V.B.F.); (C.L.D.); (D.C.d.S.); (D.S.d.S.); (D.F.S.); (E.A.A.B.); (E.d.S.B.); (F.S.C.d.S.); (G.S.M.); (J.S.d.S.); (J.G.L.); (J.T.B.); (L.D.d.S.); (L.R.); (M.S.S.); (M.K.A.G.); (M.F.d.C.); (M.R.A.); (M.G.L.d.S.); (M.S.d.P.M.); (M.F.d.S.); (N.d.J.G.d.S.); (N.d.S.P.); (R.S.d.A.); (T.d.M.G.); (V.B.N.); (E.C.F.); (B.F.d.C.D.S.); (J.L.A.d.S.); (A.L.e.S.d.M.)
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7
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Moreno López JA, Arregui García B, Bentkowski P, Bioglio L, Pinotti F, Boëlle PY, Barrat A, Colizza V, Poletto C. Anatomy of digital contact tracing: Role of age, transmission setting, adoption, and case detection. Sci Adv 2021; 7:eabd8750. [PMID: 33712416 PMCID: PMC8034853 DOI: 10.1126/sciadv.abd8750] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 02/22/2021] [Indexed: 05/12/2023]
Abstract
The efficacy of digital contact tracing against coronavirus disease 2019 (COVID-19) epidemic is debated: Smartphone penetration is limited in many countries, with low coverage among the elderly, the most vulnerable to COVID-19. We developed an agent-based model to precise the impact of digital contact tracing and household isolation on COVID-19 transmission. The model, calibrated on French population, integrates demographic, contact and epidemiological information to describe exposure and transmission of COVID-19. We explored realistic levels of case detection, app adoption, population immunity, and transmissibility. Assuming a reproductive ratio R = 2.6 and 50% detection of clinical cases, a ~20% app adoption reduces peak incidence by ~35%. With R = 1.7, >30% app adoption lowers the epidemic to manageable levels. Higher coverage among adults, playing a central role in COVID-19 transmission, yields an indirect benefit for the elderly. These results may inform the inclusion of digital contact tracing within a COVID-19 response plan.
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Affiliation(s)
- Jesús A Moreno López
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- Institute for Cross-Disciplinary Physics and Complex Systems (IFISC), CSIC-UIB, Palma de Mallorca, Spain
| | - Beatriz Arregui García
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- Institute for Cross-Disciplinary Physics and Complex Systems (IFISC), CSIC-UIB, Palma de Mallorca, Spain
| | - Piotr Bentkowski
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Livio Bioglio
- Department of Computer Science, University of Turin, Turin, Italy
| | - Francesco Pinotti
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Pierre-Yves Boëlle
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Alain Barrat
- Aix-Marseille Univ, Université de Toulon, CNRS, CPT, Turing Center for Living Systems, Marseille, France
- Tokyo Tech World Research Hub Initiative (WRHI), Tokyo Institute of Technology, Tokyo, Japan
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Chiara Poletto
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France.
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8
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Moreno López JA, Arregui García B, Bentkowski P, Bioglio L, Pinotti F, Boëlle PY, Barrat A, Colizza V, Poletto C. Anatomy of digital contact tracing: Role of age, transmission setting, adoption, and case detection. Sci Adv 2021; 7:sciadv.abd8750. [PMID: 33712416 DOI: 10.1101/2020.07.22.20158352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 02/22/2021] [Indexed: 05/21/2023]
Abstract
The efficacy of digital contact tracing against coronavirus disease 2019 (COVID-19) epidemic is debated: Smartphone penetration is limited in many countries, with low coverage among the elderly, the most vulnerable to COVID-19. We developed an agent-based model to precise the impact of digital contact tracing and household isolation on COVID-19 transmission. The model, calibrated on French population, integrates demographic, contact and epidemiological information to describe exposure and transmission of COVID-19. We explored realistic levels of case detection, app adoption, population immunity, and transmissibility. Assuming a reproductive ratio R = 2.6 and 50% detection of clinical cases, a ~20% app adoption reduces peak incidence by ~35%. With R = 1.7, >30% app adoption lowers the epidemic to manageable levels. Higher coverage among adults, playing a central role in COVID-19 transmission, yields an indirect benefit for the elderly. These results may inform the inclusion of digital contact tracing within a COVID-19 response plan.
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Affiliation(s)
- Jesús A Moreno López
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- Institute for Cross-Disciplinary Physics and Complex Systems (IFISC), CSIC-UIB, Palma de Mallorca, Spain
| | - Beatriz Arregui García
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- Institute for Cross-Disciplinary Physics and Complex Systems (IFISC), CSIC-UIB, Palma de Mallorca, Spain
| | - Piotr Bentkowski
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Livio Bioglio
- Department of Computer Science, University of Turin, Turin, Italy
| | - Francesco Pinotti
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Pierre-Yves Boëlle
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Alain Barrat
- Aix-Marseille Univ, Université de Toulon, CNRS, CPT, Turing Center for Living Systems, Marseille, France
- Tokyo Tech World Research Hub Initiative (WRHI), Tokyo Institute of Technology, Tokyo, Japan
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Chiara Poletto
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France.
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9
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Pinotti F, Obolski U, Wikramaratna P, Giovanetti M, Paton R, Klenerman P, Thompson C, Gupta S, Lourenço J. Real-time seroprevalence and exposure levels of emerging pathogens in infection-naive host populations. Sci Rep 2021; 11:5825. [PMID: 33712648 PMCID: PMC7954847 DOI: 10.1038/s41598-021-84672-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/16/2021] [Indexed: 12/29/2022] Open
Abstract
For endemic pathogens, seroprevalence mimics overall exposure and is minimally influenced by the time that recent infections take to seroconvert. Simulating spatially-explicit and stochastic outbreaks, we set out to explore how, for emerging pathogens, the mix of exponential growth in infection events and a constant rate for seroconversion events could lead to real-time significant differences in the total numbers of exposed versus seropositive. We find that real-time seroprevalence of an emerging pathogen can underestimate exposure depending on measurement time, epidemic doubling time, duration and natural variation in the time to seroconversion among hosts. We formalise mathematically how underestimation increases non-linearly as the host's time to seroconversion is ever longer than the pathogen's doubling time, and how more variable time to seroconversion among hosts results in lower underestimation. In practice, assuming that real-time seroprevalence reflects the true exposure to emerging pathogens risks overestimating measures of public health importance (e.g. infection fatality ratio) as well as the epidemic size of future waves. These results contribute to a better understanding and interpretation of real-time serological data collected during the emergence of pathogens in infection-naive host populations.
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Affiliation(s)
| | - Uri Obolski
- School of Public Health, Tel Aviv University, Tel Aviv, Israel
- Porter School of the Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel
| | | | - Marta Giovanetti
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil
| | - Robert Paton
- Department of Zoology, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, Oxford, UK
| | | | - Sunetra Gupta
- Department of Zoology, University of Oxford, Oxford, UK
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, UK.
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10
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Pinotti F, Wikramaratna PS, Obolski U, Paton RS, Damineli DSC, Alcantara LCJ, Giovanetti M, Gupta S, Lourenço J. Potential impact of individual exposure histories to endemic human coronaviruses on age-dependent severity of COVID-19. BMC Med 2021; 19:19. [PMID: 33430856 PMCID: PMC7801230 DOI: 10.1186/s12916-020-01887-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/11/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Cross-reactivity to SARS-CoV-2 from exposure to endemic human coronaviruses (eHCoV) is gaining increasing attention as a possible driver of both protection against infection and COVID-19 severity. Here we explore the potential role of cross-reactivity induced by eHCoVs on age-specific COVID-19 severity in a mathematical model of eHCoV and SARS-CoV-2 transmission. METHODS We use an individual-based model, calibrated to prior knowledge of eHCoV dynamics, to fully track individual histories of exposure to eHCoVs. We also model the emergent dynamics of SARS-CoV-2 and the risk of hospitalisation upon infection. RESULTS We hypothesise that primary exposure with any eHCoV confers temporary cross-protection against severe SARS-CoV-2 infection, while life-long re-exposure to the same eHCoV diminishes cross-protection, and increases the potential for disease severity. We show numerically that our proposed mechanism can explain age patterns of COVID-19 hospitalisation in EU/EEA countries and the UK. We further show that some of the observed variation in health care capacity and testing efforts is compatible with country-specific differences in hospitalisation rates under this model. CONCLUSIONS This study provides a "proof of possibility" for certain biological and epidemiological mechanisms that could potentially drive COVID-19-related variation across age groups. Our findings call for further research on the role of cross-reactivity to eHCoVs and highlight data interpretation challenges arising from health care capacity and SARS-CoV-2 testing.
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Affiliation(s)
| | | | - Uri Obolski
- School of Public Health, Tel Aviv University, Tel Aviv, Israel
- Porter School of the Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel
| | | | - Daniel S C Damineli
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Luiz C J Alcantara
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil
| | - Marta Giovanetti
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil
| | - Sunetra Gupta
- Department of Zoology, University of Oxford, Oxford, UK
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, UK
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11
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Pinotti F, Di Domenico L, Ortega E, Mancastroppa M, Pullano G, Valdano E, Boëlle PY, Poletto C, Colizza V. Tracing and analysis of 288 early SARS-CoV-2 infections outside China: A modeling study. PLoS Med 2020; 17:e1003193. [PMID: 32678827 PMCID: PMC7367442 DOI: 10.1371/journal.pmed.1003193] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/16/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND In the early months of 2020, a novel coronavirus disease (COVID-19) spread rapidly from China across multiple countries worldwide. As of March 17, 2020, COVID-19 was officially declared a pandemic by the World Health Organization. We collected data on COVID-19 cases outside China during the early phase of the pandemic and used them to predict trends in importations and quantify the proportion of undetected imported cases. METHODS AND FINDINGS Two hundred and eighty-eight cases have been confirmed out of China from January 3 to February 13, 2020. We collected and synthesized all available information on these cases from official sources and media. We analyzed importations that were successfully isolated and those leading to onward transmission. We modeled their number over time, in relation to the origin of travel (Hubei province, other Chinese provinces, other countries) and interventions. We characterized the importation timeline to assess the rapidity of isolation and epidemiologically linked clusters to estimate the rate of detection. We found a rapid exponential growth of importations from Hubei, corresponding to a doubling time of 2.8 days, combined with a slower growth from the other areas. We predicted a rebound of importations from South East Asia in the successive weeks. Time from travel to detection has considerably decreased since first importation, from 14.5 ± 5.5 days on January 5, 2020, to 6 ± 3.5 days on February 1, 2020. However, we estimated 36% of detection of imported cases. This study is restricted to the early phase of the pandemic, when China was the only large epicenter and foreign countries had not discovered extensive local transmission yet. Missing information in case history was accounted for through modeling and imputation. CONCLUSIONS Our findings indicate that travel bans and containment strategies adopted in China were effective in reducing the exportation growth rate. However, the risk of importation was estimated to increase again from other sources in South East Asia. Surveillance and management of traveling cases represented a priority in the early phase of the epidemic. With the majority of imported cases going undetected (6 out of 10), countries experienced several undetected clusters of chains of local transmissions, fueling silent epidemics in the community. These findings become again critical to prevent second waves, now that countries have reduced their epidemic activity and progressively phase out lockdown.
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Affiliation(s)
- Francesco Pinotti
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Laura Di Domenico
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | | | - Marco Mancastroppa
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze, Parma, Italy
- INFN, Gruppo Collegato di Parma, Parco Area delle Scienze, Parma, Italy
| | - Giulia Pullano
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- Sociology and Economics of Networks and Services lab at Orange Experience Design Lab (SENSE/XDLab) Chatillion, Paris, France
| | - Eugenio Valdano
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- Center for Biomedical Modeling, The Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, United States of America
| | - Pierre-Yves Boëlle
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Chiara Poletto
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
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Abstract
As at 27 January 2020, 42 novel coronavirus (2019-nCoV) cases were confirmed outside China. We estimate the risk of case importation to Europe from affected areas in China via air travel. We consider travel restrictions in place, three reported cases in France, one in Germany. Estimated risk in Europe remains high. The United Kingdom, Germany and France are at highest risk. Importation from Beijing and Shanghai would lead to higher and widespread risk for Europe.
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Affiliation(s)
- Giulia Pullano
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Francesco Pinotti
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Eugenio Valdano
- Center for Biomedical Modeling, The Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, United States
| | - Pierre-Yves Boëlle
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Chiara Poletto
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France
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13
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Gilbert M, Pullano G, Pinotti F, Valdano E, Poletto C, Boëlle PY, D'Ortenzio E, Yazdanpanah Y, Eholie SP, Altmann M, Gutierrez B, Kraemer MUG, Colizza V. Preparedness and vulnerability of African countries against importations of COVID-19: a modelling study. Lancet 2020. [PMID: 32087820 DOI: 10.1016/s0140‐6736(20)30411‐6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
BACKGROUND The novel coronavirus disease 2019 (COVID-19) epidemic has spread from China to 25 countries. Local cycles of transmission have already occurred in 12 countries after case importation. In Africa, Egypt has so far confirmed one case. The management and control of COVID-19 importations heavily rely on a country's health capacity. Here we evaluate the preparedness and vulnerability of African countries against their risk of importation of COVID-19. METHODS We used data on the volume of air travel departing from airports in the infected provinces in China and directed to Africa to estimate the risk of importation per country. We determined the country's capacity to detect and respond to cases with two indicators: preparedness, using the WHO International Health Regulations Monitoring and Evaluation Framework; and vulnerability, using the Infectious Disease Vulnerability Index. Countries were clustered according to the Chinese regions contributing most to their risk. FINDINGS Countries with the highest importation risk (ie, Egypt, Algeria, and South Africa) have moderate to high capacity to respond to outbreaks. Countries at moderate risk (ie, Nigeria, Ethiopia, Sudan, Angola, Tanzania, Ghana, and Kenya) have variable capacity and high vulnerability. We identified three clusters of countries that share the same exposure to the risk originating from the provinces of Guangdong, Fujian, and the city of Beijing, respectively. INTERPRETATION Many countries in Africa are stepping up their preparedness to detect and cope with COVID-19 importations. Resources, intensified surveillance, and capacity building should be urgently prioritised in countries with moderate risk that might be ill-prepared to detect imported cases and to limit onward transmission. FUNDING EU Framework Programme for Research and Innovation Horizon 2020, Agence Nationale de la Recherche.
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Affiliation(s)
- Marius Gilbert
- Spatial Epidemiology Laboratory, Université Libre de Bruxelles, Brussels, Belgium; Fonds National de la Recherche Scientifiques, Brussels, Belgium
| | - Giulia Pullano
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France; Sociology and Economics of Networks and Services Laboratory at Orange Experience Design Laboratory Chatillion, Paris, France
| | - Francesco Pinotti
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Eugenio Valdano
- Center for Biomedical Modeling, The Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, LA, USA
| | - Chiara Poletto
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Pierre-Yves Boëlle
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Eric D'Ortenzio
- Infection, Antimicrobials, Modelling, Evolution, INSERM, Université de Paris, Paris, France; Bichat Claude Bernard Hospital, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Yazdan Yazdanpanah
- Infection, Antimicrobials, Modelling, Evolution, INSERM, Université de Paris, Paris, France; Bichat Claude Bernard Hospital, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Serge Paul Eholie
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire de Treichville, Abidjan, Côte d'Ivoire; Département de Dermatologie-Infectiologie, Unité de Formation et de Recherche des Sciences Médicales, Université Félix Houphouet-Boigny, Abidjan, Côte d'Ivoire
| | - Mathias Altmann
- IDLIC-Maladies Infectieuses Dans Les Pays à Ressources Limitées, INSERM U1219, Bordeaux, France; Bordeaux Population Health, University of Bordeaux, Bordeaux, France
| | | | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK; Harvard Medical School, Harvard University, Boston, MA, USA; Computational Epidemiology Group, Boston Children's Hospital, Boston, MA, USA
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France.
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14
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Gilbert M, Pullano G, Pinotti F, Valdano E, Poletto C, Boëlle PY, D'Ortenzio E, Yazdanpanah Y, Eholie SP, Altmann M, Gutierrez B, Kraemer MUG, Colizza V. Preparedness and vulnerability of African countries against importations of COVID-19: a modelling study. Lancet 2020; 395:871-877. [PMID: 32087820 PMCID: PMC7159277 DOI: 10.1016/s0140-6736(20)30411-6] [Citation(s) in RCA: 612] [Impact Index Per Article: 153.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/13/2020] [Accepted: 02/15/2020] [Indexed: 11/19/2022]
Abstract
BACKGROUND The novel coronavirus disease 2019 (COVID-19) epidemic has spread from China to 25 countries. Local cycles of transmission have already occurred in 12 countries after case importation. In Africa, Egypt has so far confirmed one case. The management and control of COVID-19 importations heavily rely on a country's health capacity. Here we evaluate the preparedness and vulnerability of African countries against their risk of importation of COVID-19. METHODS We used data on the volume of air travel departing from airports in the infected provinces in China and directed to Africa to estimate the risk of importation per country. We determined the country's capacity to detect and respond to cases with two indicators: preparedness, using the WHO International Health Regulations Monitoring and Evaluation Framework; and vulnerability, using the Infectious Disease Vulnerability Index. Countries were clustered according to the Chinese regions contributing most to their risk. FINDINGS Countries with the highest importation risk (ie, Egypt, Algeria, and South Africa) have moderate to high capacity to respond to outbreaks. Countries at moderate risk (ie, Nigeria, Ethiopia, Sudan, Angola, Tanzania, Ghana, and Kenya) have variable capacity and high vulnerability. We identified three clusters of countries that share the same exposure to the risk originating from the provinces of Guangdong, Fujian, and the city of Beijing, respectively. INTERPRETATION Many countries in Africa are stepping up their preparedness to detect and cope with COVID-19 importations. Resources, intensified surveillance, and capacity building should be urgently prioritised in countries with moderate risk that might be ill-prepared to detect imported cases and to limit onward transmission. FUNDING EU Framework Programme for Research and Innovation Horizon 2020, Agence Nationale de la Recherche.
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Affiliation(s)
- Marius Gilbert
- Spatial Epidemiology Laboratory, Université Libre de Bruxelles, Brussels, Belgium; Fonds National de la Recherche Scientifiques, Brussels, Belgium
| | - Giulia Pullano
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France; Sociology and Economics of Networks and Services Laboratory at Orange Experience Design Laboratory Chatillion, Paris, France
| | - Francesco Pinotti
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Eugenio Valdano
- Center for Biomedical Modeling, The Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, LA, USA
| | - Chiara Poletto
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Pierre-Yves Boëlle
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Eric D'Ortenzio
- Infection, Antimicrobials, Modelling, Evolution, INSERM, Université de Paris, Paris, France; Bichat Claude Bernard Hospital, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Yazdan Yazdanpanah
- Infection, Antimicrobials, Modelling, Evolution, INSERM, Université de Paris, Paris, France; Bichat Claude Bernard Hospital, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Serge Paul Eholie
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire de Treichville, Abidjan, Côte d'Ivoire; Département de Dermatologie-Infectiologie, Unité de Formation et de Recherche des Sciences Médicales, Université Félix Houphouet-Boigny, Abidjan, Côte d'Ivoire
| | - Mathias Altmann
- IDLIC-Maladies Infectieuses Dans Les Pays à Ressources Limitées, INSERM U1219, Bordeaux, France; Bordeaux Population Health, University of Bordeaux, Bordeaux, France
| | | | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK; Harvard Medical School, Harvard University, Boston, MA, USA; Computational Epidemiology Group, Boston Children's Hospital, Boston, MA, USA
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France.
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15
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Gilbert M, Pullano G, Pinotti F, Valdano E, Poletto C, Boëlle PY, D'Ortenzio E, Yazdanpanah Y, Eholie SP, Altmann M, Gutierrez B, Kraemer MUG, Colizza V. Preparedness and vulnerability of African countries against importations of COVID-19: a modelling study. Lancet 2020. [PMID: 32087820 DOI: 10.1016/s0140-6736-20-30411-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
BACKGROUND The novel coronavirus disease 2019 (COVID-19) epidemic has spread from China to 25 countries. Local cycles of transmission have already occurred in 12 countries after case importation. In Africa, Egypt has so far confirmed one case. The management and control of COVID-19 importations heavily rely on a country's health capacity. Here we evaluate the preparedness and vulnerability of African countries against their risk of importation of COVID-19. METHODS We used data on the volume of air travel departing from airports in the infected provinces in China and directed to Africa to estimate the risk of importation per country. We determined the country's capacity to detect and respond to cases with two indicators: preparedness, using the WHO International Health Regulations Monitoring and Evaluation Framework; and vulnerability, using the Infectious Disease Vulnerability Index. Countries were clustered according to the Chinese regions contributing most to their risk. FINDINGS Countries with the highest importation risk (ie, Egypt, Algeria, and South Africa) have moderate to high capacity to respond to outbreaks. Countries at moderate risk (ie, Nigeria, Ethiopia, Sudan, Angola, Tanzania, Ghana, and Kenya) have variable capacity and high vulnerability. We identified three clusters of countries that share the same exposure to the risk originating from the provinces of Guangdong, Fujian, and the city of Beijing, respectively. INTERPRETATION Many countries in Africa are stepping up their preparedness to detect and cope with COVID-19 importations. Resources, intensified surveillance, and capacity building should be urgently prioritised in countries with moderate risk that might be ill-prepared to detect imported cases and to limit onward transmission. FUNDING EU Framework Programme for Research and Innovation Horizon 2020, Agence Nationale de la Recherche.
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Affiliation(s)
- Marius Gilbert
- Spatial Epidemiology Laboratory, Université Libre de Bruxelles, Brussels, Belgium; Fonds National de la Recherche Scientifiques, Brussels, Belgium
| | - Giulia Pullano
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France; Sociology and Economics of Networks and Services Laboratory at Orange Experience Design Laboratory Chatillion, Paris, France
| | - Francesco Pinotti
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Eugenio Valdano
- Center for Biomedical Modeling, The Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, LA, USA
| | - Chiara Poletto
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Pierre-Yves Boëlle
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Eric D'Ortenzio
- Infection, Antimicrobials, Modelling, Evolution, INSERM, Université de Paris, Paris, France; Bichat Claude Bernard Hospital, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Yazdan Yazdanpanah
- Infection, Antimicrobials, Modelling, Evolution, INSERM, Université de Paris, Paris, France; Bichat Claude Bernard Hospital, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Serge Paul Eholie
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire de Treichville, Abidjan, Côte d'Ivoire; Département de Dermatologie-Infectiologie, Unité de Formation et de Recherche des Sciences Médicales, Université Félix Houphouet-Boigny, Abidjan, Côte d'Ivoire
| | - Mathias Altmann
- IDLIC-Maladies Infectieuses Dans Les Pays à Ressources Limitées, INSERM U1219, Bordeaux, France; Bordeaux Population Health, University of Bordeaux, Bordeaux, France
| | | | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK; Harvard Medical School, Harvard University, Boston, MA, USA; Computational Epidemiology Group, Boston Children's Hospital, Boston, MA, USA
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France.
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Pinotti F, Ghanbarnejad F, Hövel P, Poletto C. Interplay between competitive and cooperative interactions in a three-player pathogen system. R Soc Open Sci 2020; 7:190305. [PMID: 32218925 PMCID: PMC7029927 DOI: 10.1098/rsos.190305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
In ecological systems, heterogeneous interactions between pathogens take place simultaneously. This occurs, for instance, when two pathogens cooperate, while at the same time, multiple strains of these pathogens co-circulate and compete. Notable examples include the cooperation of human immunodeficiency virus with antibiotic-resistant and susceptible strains of tuberculosis or some respiratory infections with Streptococcus pneumoniae strains. Models focusing on competition or cooperation separately fail to describe how these concurrent interactions shape the epidemiology of such diseases. We studied this problem considering two cooperating pathogens, where one pathogen is further structured in two strains. The spreading follows a susceptible-infected-susceptible process and the strains differ in transmissibility and extent of cooperation with the other pathogen. We combined a mean-field stability analysis with stochastic simulations on networks considering both well-mixed and structured populations. We observed the emergence of a complex phase diagram, where the conditions for the less transmissible, but more cooperative strain to dominate are non-trivial, e.g. non-monotonic boundaries and bistability. Coupled with community structure, the presence of the cooperative pathogen enables the coexistence between strains by breaking the spatial symmetry and dynamically creating different ecological niches. These results shed light on ecological mechanisms that may impact the epidemiology of diseases of public health concern.
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Affiliation(s)
- Francesco Pinotti
- INSERM, Sorbonne Université, Institut Pierre Louis d’Épidémiologie et de Santé Publique, IPLESP, Paris 75012, France
| | - Fakhteh Ghanbarnejad
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstraße 36, Berlin 10623, Germany
- The Abdus Salam International Centre for Theoretical Physics (ICTP), Trieste, Italy
- Physics Department, Sharif University of Technology, PO Box 11165-9161, Tehran, Iran
| | - Philipp Hövel
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstraße 36, Berlin 10623, Germany
- School of Mathematical Sciences, University College Cork, Western Road, Cork T12 XF62, Republic of Ireland
| | - Chiara Poletto
- INSERM, Sorbonne Université, Institut Pierre Louis d’Épidémiologie et de Santé Publique, IPLESP, Paris 75012, France
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17
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Pinotti F, Fleury É, Guillemot D, Böelle PY, Poletto C. Host contact dynamics shapes richness and dominance of pathogen strains. PLoS Comput Biol 2019; 15:e1006530. [PMID: 31112541 PMCID: PMC6546247 DOI: 10.1371/journal.pcbi.1006530] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 06/03/2019] [Accepted: 04/29/2019] [Indexed: 02/07/2023] Open
Abstract
The interaction among multiple microbial strains affects the spread of infectious diseases and the efficacy of interventions. Genomic tools have made it increasingly easy to observe pathogenic strains diversity, but the best interpretation of such diversity has remained difficult because of relationships with host and environmental factors. Here, we focus on host-to-host contact behavior and study how it changes populations of pathogens in a minimal model of multi-strain interaction. We simulated a population of identical strains competing by mutual exclusion and spreading on a dynamical network of hosts according to a stochastic susceptible-infectious-susceptible model. We computed ecological indicators of diversity and dominance in strain populations for a collection of networks illustrating various properties found in real-world examples. Heterogeneities in the number of contacts among hosts were found to reduce diversity and increase dominance by making the repartition of strains among infected hosts more uneven, while strong community structure among hosts increased strain diversity. We found that the introduction of strains associated with hosts entering and leaving the system led to the highest pathogenic richness at intermediate turnover levels. These results were finally illustrated using the spread of Staphylococcus aureus in a long-term health-care facility where close proximity interactions and strain carriage were collected simultaneously. We found that network structural and temporal properties could account for a large part of the variability observed in strain diversity. These results show how stochasticity and network structure affect the population ecology of pathogens and warn against interpreting observations as unambiguous evidence of epidemiological differences between strains.
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Affiliation(s)
- Francesco Pinotti
- INSERM, Sorbonne Université, Institut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP), 75012 Paris, France
| | | | - Didier Guillemot
- Inserm, UVSQ, Institut Pasteur, Université Paris-Saclay, Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases (B2PHI), Paris, France
| | - Pierre-Yves Böelle
- INSERM, Sorbonne Université, Institut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP), 75012 Paris, France
| | - Chiara Poletto
- INSERM, Sorbonne Université, Institut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP), 75012 Paris, France
- * E-mail:
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