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Borges V, Duque MP, Martins JV, Vasconcelos P, Ferreira R, Sobral D, Pelerito A, de Carvalho IL, Núncio MS, Borrego MJ, Roemer C, Neher RA, O'Driscoll M, Rocha R, Lopo S, Neves R, Palminha P, Coelho L, Nunes A, Isidro J, Pinto M, Santos JD, Mixão V, Santos D, Duarte S, Vieira L, Martins F, Machado J, Veríssimo VC, Grau B, Peralta-Santos A, Neves J, Caldeira M, Pestana M, Fernandes C, Caria J, Pinto R, Póvoas D, Maltez F, Sá AI, Salvador MB, Teófilo E, Rocha M, Moneti V, Duque LM, E Silva FF, Baptista T, Vasconcelos J, Casanova S, Mansinho K, Alves JV, Alves J, Silva A, Alpalhão M, Brazão C, Sousa D, Filipe P, Pacheco P, Peruzzu F, de Jesus RP, Ferreira L, Mendez J, Jordão S, Duarte F, Gonçalves MJ, Pena E, Silva CN, Guimarães AR, Tavares M, Freitas G, Cordeiro R, Gomes JP. Viral genetic clustering and transmission dynamics of the 2022 mpox outbreak in Portugal. Nat Med 2023; 29:2509-2517. [PMID: 37696933 PMCID: PMC10579057 DOI: 10.1038/s41591-023-02542-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 08/08/2023] [Indexed: 09/13/2023]
Abstract
Pathogen genome sequencing during epidemics enhances our ability to identify and understand suspected clusters and investigate their relationships. Here, we combine genomic and epidemiological data of the 2022 mpox outbreak to better understand early viral spread, diversification and transmission dynamics. By sequencing 52% of the confirmed cases in Portugal, we identified the mpox virus sublineages with the highest impact on case numbers and fitted them into a global context, finding evidence that several international sublineages probably emerged or spread early in Portugal. We estimated a 62% infection reporting rate and that 1.3% of the population of men who have sex with men in Portugal were infected. We infer the critical role played by sexual networks and superspreader gatherings, such as sauna attendance, in the dissemination of mpox virus. Overall, our findings highlight genomic epidemiology as a tool for the real-time monitoring and control of mpox epidemics, and can guide future vaccine policy in a highly susceptible population.
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Affiliation(s)
- Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Mariana Perez Duque
- Epidemiology and Statistics Division, Directorate-General of Health, Lisbon, Portugal
- Pathogen Dynamics Group, Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - João Vieira Martins
- Epidemiology and Statistics Division, Directorate-General of Health, Lisbon, Portugal
| | - Paula Vasconcelos
- Public Health Emergency Centre, Directorate-General of Health, Lisbon, Portugal
| | - Rita Ferreira
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniel Sobral
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Ana Pelerito
- Emergency Response and Biopreparedness Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Isabel Lopes de Carvalho
- Emergency Response and Biopreparedness Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Maria Sofia Núncio
- Emergency Response and Biopreparedness Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Maria José Borrego
- National Reference Laboratory for Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Cornelius Roemer
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Megan O'Driscoll
- Pathogen Dynamics Group, Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Raquel Rocha
- National Reference Laboratory for Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Sílvia Lopo
- National Reference Laboratory for Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Raquel Neves
- National Reference Laboratory for Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Paula Palminha
- National Reference Laboratory for Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Coelho
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Alexandra Nunes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Veterinary and Animal Research Centre (CECAV), Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Joana Isidro
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Dourado Santos
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Verónica Mixão
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniela Santos
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Silvia Duarte
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Fátima Martins
- Technical Board, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Jorge Machado
- Department Coordination, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Vítor Cabral Veríssimo
- Epidemiology and Statistics Division, Directorate-General of Health, Lisbon, Portugal
- Public Health Unit, ACES Cascais, ARSLVT, Cascais, Portugal
| | - Berta Grau
- Epidemiology and Statistics Division, Directorate-General of Health, Lisbon, Portugal
- Public Health Emergency Centre, Directorate-General of Health, Lisbon, Portugal
- ECDC Fellowship Programme, Field Epidemiology path (EPIET), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
- Directorate of Information and Analysis, Directorate-General of Health, Lisbon, Portugal
| | - André Peralta-Santos
- Directorate of Information and Analysis, Directorate-General of Health, Lisbon, Portugal
- Comprehensive Health Research Centre (CHRC), Escola Nacional de Saúde Pública, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - José Neves
- Serviço de Dermatovenereologia, Consulta de DST, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Margarida Caldeira
- Serviço de Dermatovenereologia, Consulta de DST, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Mafalda Pestana
- Serviço de Dermatovenereologia, Consulta de DST, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Cândida Fernandes
- Serviço de Dermatovenereologia, Consulta de DST, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - João Caria
- Serviço de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Raquel Pinto
- Serviço de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Diana Póvoas
- Serviço de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Fernando Maltez
- Serviço de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Ana Isabel Sá
- Unidade de Doenças Sexualmente Transmissíveis da Lapa, Lisbon, Portugal
| | | | - Eugénio Teófilo
- GAT - Grupo de Ativistas em Tratamentos, Av. Paris, Lisbon, Portugal
| | - Miguel Rocha
- GAT - Grupo de Ativistas em Tratamentos, Av. Paris, Lisbon, Portugal
| | - Virginia Moneti
- GAT - Grupo de Ativistas em Tratamentos, Av. Paris, Lisbon, Portugal
| | - Luis Miguel Duque
- GAT - Grupo de Ativistas em Tratamentos, Av. Paris, Lisbon, Portugal
| | | | - Teresa Baptista
- GAT - Grupo de Ativistas em Tratamentos, Intendente, Lisbon, Portugal
| | - Joana Vasconcelos
- Serviço de Doenças Infeciosas e Medicina Tropical, Hospital de Egas Moniz, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Sara Casanova
- Serviço de Doenças Infeciosas e Medicina Tropical, Hospital de Egas Moniz, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Kamal Mansinho
- Serviço de Doenças Infeciosas e Medicina Tropical, Hospital de Egas Moniz, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - João Vaz Alves
- Serviço de Doenças Infeciosas e Medicina Tropical, Hospital de Egas Moniz, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - João Alves
- Serviço de Dermatovenereologia, Hospital Garcia de Orta, Almada, Portugal
| | - António Silva
- Serviço de Dermatovenereologia, Hospital Garcia de Orta, Almada, Portugal
| | - Miguel Alpalhão
- Dermatology Department, Centro Hospitalar Universitário Lisboa Norte EPE, Lisbon, Portugal
- Dermatology Research Unit (PFilipe Lab), Instituto de Medicina Molecular João Lobo Antunes, University of Lisbon, Lisbon, Portugal
- Dermatology University Clinic, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | - Cláudia Brazão
- Dermatology Department, Centro Hospitalar Universitário Lisboa Norte EPE, Lisbon, Portugal
| | - Diogo Sousa
- Dermatology Department, Centro Hospitalar Universitário Lisboa Norte EPE, Lisbon, Portugal
| | - Paulo Filipe
- Dermatology Department, Centro Hospitalar Universitário Lisboa Norte EPE, Lisbon, Portugal
- Dermatology Research Unit (PFilipe Lab), Instituto de Medicina Molecular João Lobo Antunes, University of Lisbon, Lisbon, Portugal
- Dermatology University Clinic, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | - Patrícia Pacheco
- Serviço de Infeciologia, Hospital Professor Doutor Fernando Fonseca, Amadora, Portugal
| | - Francesca Peruzzu
- Serviço de Infeciologia, Hospital Professor Doutor Fernando Fonseca, Amadora, Portugal
| | | | - Luís Ferreira
- Serviço Infeciologia do CHUP, Largo Professor Abel Salazar, Porto, Portugal
| | - Josefina Mendez
- Serviço Infeciologia do CHUP, Largo Professor Abel Salazar, Porto, Portugal
| | - Sofia Jordão
- Serviço de Doenças Infeciosas, Hospital Pedro Hispano - ULS Matosinhos, Matosinhos, Portugal
| | - Frederico Duarte
- Serviço de Doenças Infeciosas, Hospital Pedro Hispano - ULS Matosinhos, Matosinhos, Portugal
| | - Maria João Gonçalves
- Serviço de Doenças Infeciosas, Hospital Pedro Hispano - ULS Matosinhos, Matosinhos, Portugal
| | - Eduarda Pena
- Serviço de Doenças Infeciosas, Hospital Pedro Hispano - ULS Matosinhos, Matosinhos, Portugal
| | - Claúdio Nunes Silva
- Serviço de Doenças Infeciosas, Centro Hospitalar Universitário de São João, Porto, Portugal
| | | | - Margarida Tavares
- Serviço de Doenças Infeciosas, Centro Hospitalar Universitário de São João, Porto, Portugal
| | - Graça Freitas
- National Health Authority, Directorate-General of Health, Lisbon, Portugal
| | - Rita Cordeiro
- Emergency Response and Biopreparedness Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal.
- Veterinary and Animal Research Centre (CECAV), Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal.
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