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1
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Burgueño A, Giovanetti M, Fonseca V, Morel N, Lima M, Castro E, Guimarães NR, Iani FCM, Bormida V, Cortinas MN, Ramas V, Coppola L, Bento AI, Franco L, Rico JM, Lourenço J, Junior Alcantara LC, Chiparelli H. Genomic and eco-epidemiological investigations in Uruguay reveal local Chikungunya virus transmission dynamics during its expansion across the Americas in 2023. Emerg Microbes Infect 2024; 13:2332672. [PMID: 38517841 PMCID: PMC11020592 DOI: 10.1080/22221751.2024.2332672] [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: 11/27/2023] [Accepted: 03/15/2024] [Indexed: 03/24/2024]
Abstract
Uruguay experienced its first Chikungunya virus outbreak in 2023, resulting in a significant burden to its healthcare system. We conducted analysis based on real-time genomic surveillance (30 novel whole genomes) to offer timely insights into recent local transmission dynamics and eco-epidemiological factors behind its emergence and spread in the country.
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Affiliation(s)
- Analía Burgueño
- Laboratorio de Virus Emergentes/reemergentes. Unidad de Virología, Departamento de Laboratorios de Salud Pública Montevideo, Uruguay
| | - Marta Giovanetti
- Department of Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, Rome, Italy
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Climate Amplified Diseases And Epidemics (CLIMADE), Brazil
| | - Vagner Fonseca
- Department of Exact and Earth Sciences, University of the State of Bahia, Salvador, Brazil
- Coordenação de Vigilância, Preparação e Resposta à Emergências e Desastres (PHE), Organização Pan-Americana da Saúde / Organização Mundial da Saúde (OPAS/OMS), Brasilia, Brazil
| | - Noelia Morel
- Laboratorio de Virus Emergentes/reemergentes. Unidad de Virología, Departamento de Laboratorios de Salud Pública Montevideo, Uruguay
| | - Mauricio Lima
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Emerson Castro
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Natália R. Guimarães
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Felipe C. M. Iani
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Victoria Bormida
- Laboratorio de Genómica Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Maria Noel Cortinas
- Laboratorio de Genómica Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Viviana Ramas
- Laboratorio de Virus Respiratorios, Unidad de Virología. Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Leticia Coppola
- Laboratorio de Virus Respiratorios, Unidad de Virología. Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Ana I. Bento
- Pandemic Prevention Initiative, The Rockefeller Foundation, Washington, DC, USA
| | - Leticia Franco
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization / World Health Organization (PAHO/WHO), WashingtonDC, USA
| | - Jairo Mendez Rico
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization / World Health Organization (PAHO/WHO), WashingtonDC, USA
| | - José Lourenço
- Faculty of Medicine, Católica Biomedical Research Center, Universidade Católica Portuguesa, Lisbon, Portugal
- Climate Amplified Diseases and Epidemics (CLIMADE), Portugal
| | - Luiz Carlos Junior Alcantara
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Climate Amplified Diseases And Epidemics (CLIMADE), Brazil
| | - Hector Chiparelli
- Departamento de Laboratorios de Salud Pública, Unidad de Virología, Montevideo, Uruguay
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2
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Vazquez C, Fonseca V, de la Fuente AG, Gonzalez S, Fleitas F, Lima M, Guimarães NR, Iani FCM, Rojas A, Alfonso T, Cantero C, Barrios J, Villalba S, Ortega MJ, Torales J, Gamarra ML, Aquino C, Franco L, Rico JM, Alcantara LCJ, Giovanetti M. Exploring the Genomic Dynamics of the Monkeypox Epidemic in Paraguay. Viruses 2024; 16:83. [PMID: 38257783 PMCID: PMC10821367 DOI: 10.3390/v16010083] [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: 11/07/2023] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 01/24/2024] Open
Abstract
In recent months, Paraguay has been grappled with a notable monkeypox outbreak, straining its healthcare infrastructure. The sudden spike in cases underlines the imperative need for a comprehensive understanding of the virus's dynamics, enabling the formulation of robust containment measures. To address this challenge, our team joined forces with the Central Public Health Laboratory of Asunción and the Pan-American Health Organization. Through this collaboration, we employed portable whole-genome sequencing combined with phylodynamic analysis to examine the MPXV strains circulating in Paraguay. Our genomic monitoring approach has produced the first 30 whole-genome sequences from Paraguay, all of which were identified under lineage IIb. Interestingly, our data suggest that the origin of the monkeypox virus in Paraguay at the beginning of 2022 can be traced back to Brazil. This introduction subsequently catalyzed further community spread that was further exacerbated by several independent introduction events as time progressed. These findings not only shed light on the transmission patterns of the virus but also highlight the pivotal role such insights play in sculpting effective response strategies and driving impactful public health measures. Furthermore, our findings strongly advocate intensified surveillance at international borders, ensuring swift detection and proactive countermeasures against potential outbreaks in the future.
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Affiliation(s)
- Cynthia Vazquez
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay; (C.V.); (A.G.d.l.F.); (S.G.); (F.F.); (A.R.); (T.A.); (C.C.); (J.B.); (S.V.); (M.J.O.); (J.T.); (M.L.G.); (C.A.)
| | - Vagner Fonseca
- Coordenação de Vigilância, Preparação e Resposta à Emergências e Desastres (PHE), Organização Pan-Americana da Saúde/Organização Mundial da Saúde (OPAS/OMS), Brasilia 70312-970, Brazil
- Department of Exact and Earth Sciences, University of the State of Bahia, Salvador 41150-000, Brazil
| | - Andrea Gomez de la Fuente
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay; (C.V.); (A.G.d.l.F.); (S.G.); (F.F.); (A.R.); (T.A.); (C.C.); (J.B.); (S.V.); (M.J.O.); (J.T.); (M.L.G.); (C.A.)
| | - Sandra Gonzalez
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay; (C.V.); (A.G.d.l.F.); (S.G.); (F.F.); (A.R.); (T.A.); (C.C.); (J.B.); (S.V.); (M.J.O.); (J.T.); (M.L.G.); (C.A.)
| | - Fatima Fleitas
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay; (C.V.); (A.G.d.l.F.); (S.G.); (F.F.); (A.R.); (T.A.); (C.C.); (J.B.); (S.V.); (M.J.O.); (J.T.); (M.L.G.); (C.A.)
| | - Mauricio Lima
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil; (M.L.); (N.R.G.); (F.C.M.I.)
| | - Natália R. Guimarães
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil; (M.L.); (N.R.G.); (F.C.M.I.)
| | - Felipe C. M. Iani
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil; (M.L.); (N.R.G.); (F.C.M.I.)
| | - Analia Rojas
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay; (C.V.); (A.G.d.l.F.); (S.G.); (F.F.); (A.R.); (T.A.); (C.C.); (J.B.); (S.V.); (M.J.O.); (J.T.); (M.L.G.); (C.A.)
| | - Tania Alfonso
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay; (C.V.); (A.G.d.l.F.); (S.G.); (F.F.); (A.R.); (T.A.); (C.C.); (J.B.); (S.V.); (M.J.O.); (J.T.); (M.L.G.); (C.A.)
| | - Cesar Cantero
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay; (C.V.); (A.G.d.l.F.); (S.G.); (F.F.); (A.R.); (T.A.); (C.C.); (J.B.); (S.V.); (M.J.O.); (J.T.); (M.L.G.); (C.A.)
| | - Julio Barrios
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay; (C.V.); (A.G.d.l.F.); (S.G.); (F.F.); (A.R.); (T.A.); (C.C.); (J.B.); (S.V.); (M.J.O.); (J.T.); (M.L.G.); (C.A.)
| | - Shirley Villalba
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay; (C.V.); (A.G.d.l.F.); (S.G.); (F.F.); (A.R.); (T.A.); (C.C.); (J.B.); (S.V.); (M.J.O.); (J.T.); (M.L.G.); (C.A.)
| | - Maria Jose Ortega
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay; (C.V.); (A.G.d.l.F.); (S.G.); (F.F.); (A.R.); (T.A.); (C.C.); (J.B.); (S.V.); (M.J.O.); (J.T.); (M.L.G.); (C.A.)
| | - Juan Torales
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay; (C.V.); (A.G.d.l.F.); (S.G.); (F.F.); (A.R.); (T.A.); (C.C.); (J.B.); (S.V.); (M.J.O.); (J.T.); (M.L.G.); (C.A.)
| | - Maria Liz Gamarra
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay; (C.V.); (A.G.d.l.F.); (S.G.); (F.F.); (A.R.); (T.A.); (C.C.); (J.B.); (S.V.); (M.J.O.); (J.T.); (M.L.G.); (C.A.)
| | - Carolina Aquino
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay; (C.V.); (A.G.d.l.F.); (S.G.); (F.F.); (A.R.); (T.A.); (C.C.); (J.B.); (S.V.); (M.J.O.); (J.T.); (M.L.G.); (C.A.)
| | - Leticia Franco
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization/World Health Organization (PAHO/WHO), Washington, DC 20037, USA; (L.F.); (J.M.R.)
| | - Jairo Mendez Rico
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization/World Health Organization (PAHO/WHO), Washington, DC 20037, USA; (L.F.); (J.M.R.)
| | - Luiz Carlos Junior Alcantara
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, Brazil
- Climate Amplified Diseases and Epidemics (CLIMADE), University of Washington, Seattle, WA 98195, USA
| | - Marta Giovanetti
- Climate Amplified Diseases and Epidemics (CLIMADE), University of Washington, Seattle, WA 98195, USA
- Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia 40296-710, Brazil
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico, 00128 Rome, Italy
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3
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Xavier J, Fonseca V, Adelino T, Iani FCM, Pereira GC, Duarte MM, Lima M, Castro E, Oliveira C, Fritsch H, Guimarães N, Lamounier LO, Barreto FK, Braga de Oliveira CMM, Maymone Gonçalves CC, Malta Lima D, de Oliveira EC, de Castro Lichs GG, Gomes I, Mazaro J, Rodrigues JTN, Abrantes J, Colares JKB, Luz KG, Barbosa da Silva L, Demarchi L, Câmara MCB, Umaki Zardin MCS, Sabatini Mello Pinheiro R, Barbosa Souza R, Haddad SK, Figueiredo da Silva S, Slavov SN, Rocha T, Morel N, Chiparelli H, Burgueño A, Bórmida V, Cortinas MN, Martín RS, Pereira AC, dos Santos MF, André Júnior W, Mendez Rico J, Franco L, Rosewell A, do Carmo Said RF, de Albuquerque CFC, Noia Maciel EL, Santini de Oliveira M, Venâncio da Cunha R, Vinhal Frutuoso LC, de Filippis AMB, Giovanetti M, Carlos Junior Alcantara L. A Multiplex Nanopore Sequencing Approach for the Detection of Multiple Arboviral Species. Viruses 2023; 16:23. [PMID: 38257724 PMCID: PMC10821003 DOI: 10.3390/v16010023] [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: 11/18/2023] [Revised: 12/08/2023] [Accepted: 12/10/2023] [Indexed: 01/24/2024] Open
Abstract
The emergence and continued geographic expansion of arboviruses and the growing number of infected people have highlighted the need to develop and improve multiplex methods for rapid and specific detection of pathogens. Sequencing technologies are promising tools that can help in the laboratory diagnosis of conditions that share common symptoms, such as pathologies caused by emerging arboviruses. In this study, we integrated nanopore sequencing and the advantages of reverse transcription polymerase chain reaction (RT-PCR) to develop a multiplex RT-PCR protocol for the detection of Chikungunya virus (CHIKV) and several orthoflaviviruses (such as dengue (Orthoflavivirus dengue), Zika (Orthoflavivirus zikaense), yellow fever (Orthoflavivirus flavi), and West Nile (Orthoflavivirus nilense) viruses) in a single reaction, which provides data for sequence-based differentiation of arbovirus lineages.
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Affiliation(s)
- Joilson Xavier
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Vagner Fonseca
- Organização Pan-Americana da Saúde, Organização Mundial da Saúde, Brasília 70800-400, Brazil
| | - Talita Adelino
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil (F.C.M.I.)
| | - Felipe C. M. Iani
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil (F.C.M.I.)
| | - Glauco C. Pereira
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil (F.C.M.I.)
| | - Myrian M. Duarte
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil (F.C.M.I.)
| | - Mauricio Lima
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, Brazil
| | - Emerson Castro
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, Brazil
| | - Carla Oliveira
- lnstituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
| | - Hegger Fritsch
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Natalia Guimarães
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil (F.C.M.I.)
| | - Ludmila O. Lamounier
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil (F.C.M.I.)
| | - Fernanda Khouri Barreto
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Brazil
| | | | | | - Danielle Malta Lima
- Faculty of the Graduate Program in Biotechnology (Renorbio), Universidade de Fortaleza, Fortaleza 60811-905, Brazil
| | | | | | - Iago Gomes
- Laboratório Central de Saúde Pública do Rio Grande do Norte, Natal 59037-170, Brazil
| | - Janaina Mazaro
- Secretaria Estadual de Saúde do estado do Acre, Rio Branco 69900-064, Brazil
| | | | - Jayra Abrantes
- Laboratório Central de Saúde Pública do Rio Grande do Norte, Natal 59037-170, Brazil
| | - Jeová K. B. Colares
- Faculty of the Graduate Program in Biotechnology (Renorbio), Universidade de Fortaleza, Fortaleza 60811-905, Brazil
| | - Kleber G. Luz
- Department of Infectious Diseases, Universidade Federal do Rio Grande do Norte, Natal 59078-900, Brazil
| | | | - Luiz Demarchi
- Laboratorio Central de Saúde Pública do Mato Grosso do Sul, Campo Grande 79074-460, Brazil
| | - Magaly C. B. Câmara
- Laboratório Central de Saúde Pública do Rio Grande do Norte, Natal 59037-170, Brazil
| | | | | | | | - Simone K. Haddad
- Fundação Hemocentro de Ribeirão Preto, Ribeirão Preto 14051-140, Brazil
| | | | | | - Themis Rocha
- Laboratório Central de Saúde Pública do Rio Grande do Norte, Natal 59037-170, Brazil
| | - Noelia Morel
- Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Montevideo 11200, Uruguay
| | - Hector Chiparelli
- Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Montevideo 11200, Uruguay
| | - Analía Burgueño
- Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Montevideo 11200, Uruguay
| | - Victoria Bórmida
- Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Montevideo 11200, Uruguay
| | - María N. Cortinas
- Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Montevideo 11200, Uruguay
| | - Rosario S. Martín
- Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Montevideo 11200, Uruguay
| | | | | | | | | | - Leticia Franco
- Pan American Health Organization, Washington, DC 20037, USA
| | - Alexander Rosewell
- Organização Pan-Americana da Saúde, Organização Mundial da Saúde, Brasília 70800-400, Brazil
| | | | | | - Ethel L. Noia Maciel
- Secretaria de Vigilância em Saúde e Ambiente, Ministério da Saúde, Brasília 70058-900, Brazil
| | | | | | | | | | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, Brazil
- Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di Roma, 00128 Roma, Italy
- Climate Amplified Diseases and Epidemics (CLIMADE), Fundação Oswaldo Cruz, Belo Horizonte 30190-002, Brazil
| | - Luiz Carlos Junior Alcantara
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, Brazil
- Climate Amplified Diseases and Epidemics (CLIMADE), Fundação Oswaldo Cruz, Belo Horizonte 30190-002, Brazil
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4
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Morel N, Giovanetti M, Fonseca V, Burgueño A, Lima M, Castro E, Guimarães NR, Iani FCM, Bormida V, Cortinas MN, Ramas V, Coppola L, Bento AI, Rosewell A, Franco L, Rico JM, Lourenço J, Alcantara LCJ, Chiparelli H. Genomics-based timely detection of Dengue Virus type I genotypes I and V in Uruguay. medRxiv 2023:2023.09.05.23295075. [PMID: 37732223 PMCID: PMC10508810 DOI: 10.1101/2023.09.05.23295075] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
We report the first whole-genome sequences of Dengue Virus type I genotypes I and V from Uruguay, including the first cases ever reported in the country. Through timely genomic analysis, identification of these genotypes was possible, aiding in timely public health responses and intervention strategies to mitigate the impact of dengue outbreaks.
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Affiliation(s)
- Noelia Morel
- Laboratorio de Virus Emergentes/reemergentes. Unidad de Virología, Departamento de Laboratorios de Salud Pública
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di Roma, Italy
- Climate Amplified Diseases And Epidemics (CLIMADE), Brazil, Americas
| | - Vagner Fonseca
- Climate Amplified Diseases And Epidemics (CLIMADE), Brazil, Americas
- Coordenação de Vigilância, Preparação e Resposta à Emergências e Desastres (PHE), Organização Pan-Americana da Saúde / Organização Mundial da Saúde (OPAS/OMS), Brasília DF, Brazil
- Department of Exact and Earth Sciences, University of the State of Bahia, Salvador, Brazil
| | - Analía Burgueño
- Laboratorio de Virus Emergentes/reemergentes. Unidad de Virología, Departamento de Laboratorios de Salud Pública
| | - Mauricio Lima
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Emerson Castro
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Natália R. Guimarães
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Felipe C. M. Iani
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Victoria Bormida
- Unidad de Genómica. Depto. De Laboratorios de Salud Pública, Uruguay
| | | | - Viviana Ramas
- Laboratorio de Virus Respiratorios, Unidad de Virología. Departamento de Laboratorios de Salud Pública, Uruguay
| | - Leticia Coppola
- Laboratorio de Virus Respiratorios, Unidad de Virología. Departamento de Laboratorios de Salud Pública, Uruguay
| | - Ana I. Bento
- Pandemic Prevention Initiative, The Rockefeller Foundation, Washington DC, USA
| | - Alexander Rosewell
- Coordenação de Vigilância, Preparação e Resposta à Emergências e Desastres (PHE), Organização Pan-Americana da Saúde / Organização Mundial da Saúde (OPAS/OMS), Brasília DF, Brazil
| | - Leticia Franco
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization / World Health Organization (PAHO/WHO), Washington DC, USA
| | - Jairo Mendez Rico
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization / World Health Organization (PAHO/WHO), Washington DC, USA
| | - José Lourenço
- BioISI (Biosystems and Integrative Sciences Institute), Faculdade de Ciências da Universidade de Lisboa
- Católica Biomedical Research Centre, Católica Medical School, Universidade Católica Portuguesa
- Climate Amplified Diseases And Epidemics (CLIMADE), Portugal, Europe
| | - Luiz Carlos Junior Alcantara
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Climate Amplified Diseases And Epidemics (CLIMADE), Brazil, Americas
| | - Hector Chiparelli
- Unidad de Virología. Depto. De Laboratorios de Salud Pública, Uruguay
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5
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Burgueño A, Giovanetti M, Fonseca V, Morel N, Lima M, Castro E, Guimarães NR, Iani FCM, Bormida V, Cortinas MN, Ramas V, Coppola L, Bento AI, Franco L, Rico JM, Lourenço J, Alcantara LCJ, Chiparelli H. Genomic and eco-epidemiological investigations in Uruguay reveal local Chikungunya virus transmission dynamics during its expansion across the Americas in 2023. medRxiv 2023:2023.08.17.23294156. [PMID: 37646000 PMCID: PMC10462220 DOI: 10.1101/2023.08.17.23294156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Uruguay experienced its first Chikungunya virus outbreak in 2023, resulting in a significant burden to its healthcare system. We conducted analysis based on real-time genomic surveillance (30 novel whole genomes) to offer timely insights into recent local transmission dynamics and eco-epidemiological factors behind its emergence and spread in the country.
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Affiliation(s)
- Analía Burgueño
- Laboratorio de Virus Emergentes/reemergentes. Unidad de Virología, Departamento de Laboratorios de Salud Pública
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, Italy
| | - Vagner Fonseca
- Department of Exact and Earth Sciences, University of the State of Bahia, Salvador, Brazil
- Coordenação de Vigilância, Preparação e Resposta à Emergências e Desastres (PHE), Organização Pan-Americana da Saúde / Organização Mundial da Saúde (OPAS/OMS), Brasilia DF, Brazil
| | - Noelia Morel
- Laboratorio de Virus Emergentes/reemergentes. Unidad de Virología, Departamento de Laboratorios de Salud Pública
| | - Mauricio Lima
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Emerson Castro
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Natália R. Guimarães
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Felipe C. M. Iani
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Victoria Bormida
- Laboratorio de Genómica Departamento de Laboratorios de Salud Pública, Uruguay
| | - Maria Noel Cortinas
- Laboratorio de Genómica Departamento de Laboratorios de Salud Pública, Uruguay
| | - Viviana Ramas
- Laboratorio de Virus Respiratorios, Unidad de Virología. Departamento de Laboratorios de Salud Pública, Uruguay
| | - Leticia Coppola
- Laboratorio de Virus Respiratorios, Unidad de Virología. Departamento de Laboratorios de Salud Pública, Uruguay
| | - Ana I. Bento
- Pandemic Prevention Initiative, The Rockefeller Foundation, Washington DC, USA
| | - Leticia Franco
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization / World Health Organization (PAHO/WHO), Washington DC, USA
| | - Jairo Mendez Rico
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization / World Health Organization (PAHO/WHO), Washington DC, USA
| | - José Lourenço
- BioISI (Biosystems and Integrative Sciences Institute), Faculdade de Ciências da Universidade de Lisboa
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Vazquez C, Alcantara LCJ, Fonseca V, Lima M, Xavier J, Adelino T, Fritsch H, Castro E, de Oliveira C, Schuab G, Lima ARJ, Villalba S, Gomez de la Fuente A, Rojas A, Cantero C, Fleitas F, Aquino C, Ojeda A, Sequera G, Torales J, Barrios J, Elias MC, Iani FCM, Ortega MJ, Gamarra ML, Montoya R, Rodrigues ES, Kashima S, Sampaio SC, Coluchi N, Leite J, Gresh L, Franco L, Lourenço J, Rico JM, Bispo de Filippis AM, Giovanetti M. Retrospective Spatio-Temporal Dynamics of Dengue Virus 1, 2 and 4 in Paraguay. Viruses 2023; 15:1275. [PMID: 37376575 DOI: 10.3390/v15061275] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 06/29/2023] Open
Abstract
Dengue virus (DENV) has been a major public health concern in Paraguay, with frequent outbreaks occurring since early 1988. Although control measures have been implemented, dengue remains a significant health threat in the country, and continued efforts are required for prevention and control. In response to that, in collaboration with the Central Public Health Laboratory in Asunción, we conducted a portable whole-genome sequencing and phylodynamic analysis to investigate DENV viral strains circulating in Paraguay over the past epidemics. Our genomic surveillance activities revealed the co-circulation of multiple DENV serotypes: DENV-1 genotype V, the emerging DENV-2 genotype III, BR4-L2 clade, and DENV-4 genotype II. Results additionally highlight the possible role of Brazil as a source for the international dispersion of different viral strains to other countries in the Americas emphasizing the need for increased surveillance across the borders, for the early detection and response to outbreaks. This, in turn, emphasizes the critical role of genomic surveillance in monitoring and understanding arbovirus transmission and persistence locally and over long distances.
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Affiliation(s)
- Cynthia Vazquez
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay
| | | | - Vagner Fonseca
- Organização Pan-Americana da Saúde, Organização Mundial da Saúde, Brasília 70-800400, SP, Brazil
| | - Mauricio Lima
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, MG, Brazil
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte 30510-010, MG, Brazil
| | - Joilson Xavier
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, MG, Brazil
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte 30510-010, MG, Brazil
| | - Talita Adelino
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte 30510-010, MG, Brazil
| | - Hegger Fritsch
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, MG, Brazil
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte 30510-010, MG, Brazil
| | - Emerson Castro
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte 30510-010, MG, Brazil
| | - Carla de Oliveira
- Laboratório de Arbovírus e Vírus Hemorrágicos (LARBOH), Instituto Osawldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Gabriel Schuab
- Laboratório de Arbovírus e Vírus Hemorrágicos (LARBOH), Instituto Osawldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Alex Ranieri Jerônimo Lima
- Butantan Institute, Center for Viral Surveillance and Serological Assessment (CeVIVAS), Sao Paulo 05507-000, SP, Brazil
| | | | | | - Analia Rojas
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay
| | - Cesar Cantero
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay
| | - Fatima Fleitas
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay
| | - Carolina Aquino
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay
| | - Andrea Ojeda
- Dirección General de Vigilancia de la Salud, Asunción 40556, Paraguay
| | - Guillermo Sequera
- Dirección General de Vigilancia de la Salud, Asunción 40556, Paraguay
| | - Juan Torales
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay
| | - Julio Barrios
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay
| | - Maria Carolina Elias
- Butantan Institute, Center for Viral Surveillance and Serological Assessment (CeVIVAS), Sao Paulo 05507-000, SP, Brazil
| | - Felipe C M Iani
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte 30510-010, MG, Brazil
| | | | | | - Romeo Montoya
- Enfermedades Trasmisibles y Determinantes Ambientales de la Salud CDE/HA/PHE, OPS/OMS, Asuncion 40126, Paraguay
| | - Evandra Strazza Rodrigues
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil
| | - Simone Kashima
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil
| | - Sandra Coccuzzo Sampaio
- Butantan Institute, Center for Viral Surveillance and Serological Assessment (CeVIVAS), Sao Paulo 05507-000, SP, Brazil
| | - Norma Coluchi
- Laboratorio Central de Salud Pública, Asunción 001535, Paraguay
| | - Juliana Leite
- Emergency Department, Infectious Hazards Management, Pan American Health Organization, Washington, DC 20037, USA
| | - Lionel Gresh
- Emergency Department, Infectious Hazards Management, Pan American Health Organization, Washington, DC 20037, USA
| | - Leticia Franco
- Emergency Department, Infectious Hazards Management, Pan American Health Organization, Washington, DC 20037, USA
| | - José Lourenço
- Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Jairo Mendez Rico
- Emergency Department, Infectious Hazards Management, Pan American Health Organization, Washington, DC 20037, USA
| | - Ana Maria Bispo de Filippis
- Laboratório de Arbovírus e Vírus Hemorrágicos (LARBOH), Instituto Osawldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, MG, Brazil
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico, 00128 Rome, Italy
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7
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Giovanetti M, Vazquez C, Lima M, Castro E, Rojas A, de la Fuente AG, Aquino C, Cantero C, Fleitas F, Torales J, Barrios J, Ortega MJ, Gamarra ML, Villalba S, Alfonzo T, Xavier J, Adelino T, Fritsch H, Iani FCM, Pereira GC, de Oliveira C, Schuab G, Rodrigues ES, Kashima S, Leite J, Gresh L, Franco L, Tegally H, Van Voorhis WC, Lessels R, de Filippis AMB, Ojeda A, Sequera G, Montoya R, Holmes EC, de Oliveira T, Rico JM, Lourenço J, Fonseca V, Alcantara LCJ. Rapid epidemic expansion of chikungunya virus-ECSA lineage in Paraguay. medRxiv 2023:2023.04.16.23288635. [PMID: 37131602 PMCID: PMC10153315 DOI: 10.1101/2023.04.16.23288635] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The spread of vector-borne viruses, such as CHIKV, is a significant public health concern in the Americas, with over 120,000 cases and 51 deaths in 2023, of which 46 occurred in Paraguay. Using a suite of genomic, phylodynamic, and epidemiological techniques, we characterized the ongoing large CHIKV epidemic in Paraguay. Article Summary Line Genomic and epidemiological characterization of the ongoing Chikungunya virus epidemic in Paraguay.
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Affiliation(s)
- Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico,Rome, Italy
| | | | - Mauricio Lima
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Emerson Castro
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Analia Rojas
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | | | | | - Cesar Cantero
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | - Fatima Fleitas
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | - Juan Torales
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | - Julio Barrios
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | | | | | | | - Tania Alfonzo
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | - Joilson Xavier
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Talita Adelino
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Hegger Fritsch
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Felipe C. M. Iani
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Glauco Carvalho Pereira
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Carla de Oliveira
- Laboratório de Arbovírus e Vírus Hemorrágicos (LARBOH), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Gabriel Schuab
- Laboratório de Arbovírus e Vírus Hemorrágicos (LARBOH), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Evandra Strazza Rodrigues
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Simone Kashima
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Juliana Leite
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization / World Health Organization (PAHO/WHO), Washington DC, USA
| | - Lionel Gresh
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization / World Health Organization (PAHO/WHO), Washington DC, USA
| | - Leticia Franco
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization / World Health Organization (PAHO/WHO), Washington DC, USA
| | - Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Wesley C. Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, USA
| | - Richard Lessels
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Ana Maria Bispo de Filippis
- Laboratório de Arbovírus e Vírus Hemorrágicos (LARBOH), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Andrea Ojeda
- Dirección General de Vigilancia de la Salud, Asunción, Paraguay
| | | | - Romeo Montoya
- Enfermedades Trasmisibles y Determinantes Ambientales de la Salud CDE/HA/PHE, Organización Panamericana de la Salud / Organización Mundial de la Salud (OPS/OMS), Asuncion, Paraguay
| | - 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
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Jairo Mendez Rico
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization / World Health Organization (PAHO/WHO), Washington DC, USA
| | - José Lourenço
- Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, 1749-016, Portugal
| | - Vagner Fonseca
- Coordenação de Vigilância, Preparação e Resposta à Emergências e Desastres (PHE), Organização Pan-Americana da Saúde / Organização Mundial da Saúde (OPAS/OMS), Brasilia DF, Brazil
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8
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Li SL, Acosta AL, Hill SC, Brady OJ, de Almeida MAB, Cardoso JDC, Hamlet A, Mucci LF, Telles de Deus J, Iani FCM, Alexander NS, Wint GRW, Pybus OG, Kraemer MUG, Faria NR, Messina JP. Mapping environmental suitability of Haemagogus and Sabethes spp. mosquitoes to understand sylvatic transmission risk of yellow fever virus in Brazil. PLoS Negl Trop Dis 2022; 16:e0010019. [PMID: 34995277 PMCID: PMC8797211 DOI: 10.1371/journal.pntd.0010019] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 01/28/2022] [Accepted: 11/23/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Yellow fever (YF) is an arboviral disease which is endemic to Brazil due to a sylvatic transmission cycle maintained by infected mosquito vectors, non-human primate (NHP) hosts, and humans. Despite the existence of an effective vaccine, recent sporadic YF epidemics have underscored concerns about sylvatic vector surveillance, as very little is known about their spatial distribution. Here, we model and map the environmental suitability of YF's main vectors in Brazil, Haemagogus spp. and Sabethes spp., and use human population and NHP data to identify locations prone to transmission and spillover risk. METHODOLOGY/PRINCIPAL FINDINGS We compiled a comprehensive set of occurrence records on Hg. janthinomys, Hg. leucocelaenus, and Sabethes spp. from 1991-2019 using primary and secondary data sources. Linking these data with selected environmental and land-cover variables, we adopted a stacked regression ensemble modelling approach (elastic-net regularized GLM, extreme gradient boosted regression trees, and random forest) to predict the environmental suitability of these species across Brazil at a 1 km x 1 km resolution. We show that while suitability for each species varies spatially, high suitability for all species was predicted in the Southeastern region where recent outbreaks have occurred. By integrating data on NHP host reservoirs and human populations, our risk maps further highlight municipalities within the region that are prone to transmission and spillover. CONCLUSIONS/SIGNIFICANCE Our maps of sylvatic vector suitability can help elucidate potential locations of sylvatic reservoirs and be used as a tool to help mitigate risk of future YF outbreaks and assist in vector surveillance. Furthermore, at-risk regions identified from our work could help disease control and elucidate gaps in vaccination coverage and NHP host surveillance.
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Affiliation(s)
- Sabrina L. Li
- School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
- * E-mail: (SLL); (JPM)
| | - André L. Acosta
- Departamento de Ecologia, Instituto de Biociências, Laboratório de Ecologia de Paisagens e Conservação—LEPAC, Universidade de São Paulo, São Paulo, Brazil
| | - Sarah C. Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, United Kingdom
| | - Oliver J. Brady
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Marco A. B. de Almeida
- State Centre of Health Surveillance, Rio Grande do Sul State Health Secretariat, Rio Grande do Sul, Brazil
| | - Jader da C. Cardoso
- State Centre of Health Surveillance, Rio Grande do Sul State Health Secretariat, Rio Grande do Sul, Brazil
| | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Luis F. Mucci
- Superintendence for Endemic Diseases Control, São Paulo State Health Secretariat, São Paulo, Brazil
| | - Juliana Telles de Deus
- Superintendence for Endemic Diseases Control, São Paulo State Health Secretariat, São Paulo, Brazil
| | | | - Neil S. Alexander
- Environmental Research Group Oxford, c/o Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - G. R. William Wint
- Environmental Research Group Oxford, c/o Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Oliver G. Pybus
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Nuno R. Faria
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Departamento de Molestias Infecciosas e Parasitarias & Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Jane P. Messina
- School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
- Oxford School of Global and Area Studies, University of Oxford, Oxford, United Kingdom
- * E-mail: (SLL); (JPM)
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9
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Iani FCM, Giovanetti M, Fonseca V, Souza WM, Adelino TER, Xavier J, Jesus JG, Pereira MA, Silva MVF, Costa AVB, Silva EC, Mendes MCO, Filippis AMB, Albuquerque CFC, Abreu AL, Oliveira MAA, Alcantara LCJ, Faria NR. Epidemiology and evolution of Zika virus in Minas Gerais, Southeast Brazil. Infect Genet Evol 2021; 91:104785. [PMID: 33652117 DOI: 10.1016/j.meegid.2021.104785] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 02/15/2021] [Accepted: 02/24/2021] [Indexed: 12/14/2022]
Abstract
Autochthonous Zika virus (ZIKV) transmission in Brazil was first identified in April 2015 in Brazil, with the first ZIKV-associated microcephaly cases detected in October 2015. Despite efforts on understanding ZIKV transmission in Brazil, little is known about the virus epidemiology and genetic diversity in Minas Gerais (MG), the second most populous state in the country. We report molecular and genomic findings from the main public health laboratory in MG. Until January 2020, 26,817 ZIKV suspected infections and 86 congenital syndrome cases were reported in MG state. We tested 8552 ZIKV and microcephaly suspected cases. Ten genomes were generated on-site directly from clinical samples. A total of 1723 confirmed cases were detected in Minas Gerais, with two main epidemic waves; the first and larger epidemic wave peaked in March 2016, with the second smaller wave that peaked in March 2017. Dated molecular clock analysis revealed that multiple introductions occurred in Minas Gerais between 2014 and 2015, suggesting that the virus was circulating unnoticed for at least 16 months before the first confirmed laboratory case that we retrospectively identified in December 2015. Our findings highlight the importance of continued genomic surveillance strategies combined with traditional epidemiology to assist public health laboratories in monitoring and understanding the diversity of circulating arboviruses, which might help attenuate the public health impact of infectious diseases.
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Affiliation(s)
- Felipe C M Iani
- Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil; Department of Zoology, University of Oxford, United Kingdom; Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marta Giovanetti
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Vagner Fonseca
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZuluNatal, Durban 4001, South Africa; Coordenação Geral dos Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - William M Souza
- Department of Zoology, University of Oxford, United Kingdom; Centro de Pesquisa em Virologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Talita E R Adelino
- Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Joilson Xavier
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Jaqueline G Jesus
- Centro de Pesquisa em Virologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Maira A Pereira
- Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Marcos V F Silva
- Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Alana V B Costa
- Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Erniria C Silva
- Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Brazil
| | - Márcia C O Mendes
- Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Brazil
| | - Ana M B Filippis
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - André L Abreu
- Coordenação Geral dos Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - Marluce A A Oliveira
- Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil.
| | - Luiz C J Alcantara
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
| | - Nuno R Faria
- Department of Zoology, University of Oxford, United Kingdom; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK.
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Faria NR, Kraemer MUG, Hill SC, Goes de Jesus J, Aguiar RS, Iani FCM, Xavier J, Quick J, du Plessis L, Dellicour S, Thézé J, Carvalho RDO, Baele G, Wu CH, Silveira PP, Arruda MB, Pereira MA, Pereira GC, Lourenço J, Obolski U, Abade L, Vasylyeva TI, Giovanetti M, Yi D, Weiss DJ, Wint GRW, Shearer FM, Funk S, Nikolay B, Fonseca V, Adelino TER, Oliveira MAA, Silva MVF, Sacchetto L, Figueiredo PO, Rezende IM, Mello EM, Said RFC, Santos DA, Ferraz ML, Brito MG, Santana LF, Menezes MT, Brindeiro RM, Tanuri A, Dos Santos FCP, Cunha MS, Nogueira JS, Rocco IM, da Costa AC, Komninakis SCV, Azevedo V, Chieppe AO, Araujo ESM, Mendonça MCL, Dos Santos CC, Dos Santos CD, Mares-Guia AM, Nogueira RMR, Sequeira PC, Abreu RG, Garcia MHO, Abreu AL, Okumoto O, Kroon EG, de Albuquerque CFC, Lewandowski K, Pullan ST, Carroll M, de Oliveira T, Sabino EC, Souza RP, Suchard MA, Lemey P, Trindade GS, Drumond BP, Filippis AMB, Loman NJ, Cauchemez S, Alcantara LCJ, Pybus OG. Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science 2018; 361:894-899. [PMID: 30139911 PMCID: PMC6874500 DOI: 10.1126/science.aat7115] [Citation(s) in RCA: 204] [Impact Index Per Article: 34.0] [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: 03/31/2018] [Accepted: 07/20/2018] [Indexed: 12/21/2022]
Abstract
The yellow fever virus (YFV) epidemic in Brazil is the largest in decades. The recent discovery of YFV in Brazilian Aedes species mosquitos highlights a need to monitor the risk of reestablishment of urban YFV transmission in the Americas. We use a suite of epidemiological, spatial, and genomic approaches to characterize YFV transmission. We show that the age and sex distribution of human cases is characteristic of sylvatic transmission. Analysis of YFV cases combined with genomes generated locally reveals an early phase of sylvatic YFV transmission and spatial expansion toward previously YFV-free areas, followed by a rise in viral spillover to humans in late 2016. Our results establish a framework for monitoring YFV transmission in real time that will contribute to a global strategy to eliminate future YFV epidemics.
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Affiliation(s)
- N R Faria
- Department of Zoology, University of Oxford, Oxford, UK.
| | - M U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK
- Computational Epidemiology Lab, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - S C Hill
- Department of Zoology, University of Oxford, Oxford, UK
| | - J Goes de Jesus
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - R S Aguiar
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - F C M Iani
- Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - J Xavier
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - J Quick
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - L du Plessis
- Department of Zoology, University of Oxford, Oxford, UK
| | - S Dellicour
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - J Thézé
- Department of Zoology, University of Oxford, Oxford, UK
| | - R D O Carvalho
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - G Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - C-H Wu
- Department of Statistics, University of Oxford, Oxford, UK
| | - P P Silveira
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - M B Arruda
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - M A Pereira
- Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil
| | - G C Pereira
- Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil
| | - J Lourenço
- Department of Zoology, University of Oxford, Oxford, UK
| | - U Obolski
- Department of Zoology, University of Oxford, Oxford, UK
| | - L Abade
- Department of Zoology, University of Oxford, Oxford, UK
- The Global Health Network, University of Oxford, Oxford, UK
| | - T I Vasylyeva
- Department of Zoology, University of Oxford, Oxford, UK
| | - M Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - D Yi
- Department of Statistics, Harvard University, Cambridge, MA, USA
| | - D J Weiss
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - G R W Wint
- Department of Zoology, University of Oxford, Oxford, UK
| | - F M Shearer
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - S Funk
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - B Nikolay
- Mathematical Modelling of Infectious Diseases and Center of Bioinformatics, Institut Pasteur, Paris, France
- CNRS UMR2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
| | - V Fonseca
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - T E R Adelino
- Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil
| | - M A A Oliveira
- Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil
| | - M V F Silva
- Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil
| | - L Sacchetto
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - P O Figueiredo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - I M Rezende
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - E M Mello
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - R F C Said
- Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - D A Santos
- Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - M L Ferraz
- Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - M G Brito
- Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - L F Santana
- Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - M T Menezes
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - R M Brindeiro
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - A Tanuri
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - F C P Dos Santos
- Núcleo de Doenças de Transmissão Vetorial, Instituto Adolfo Lutz, São Paulo, Brazil
| | - M S Cunha
- Núcleo de Doenças de Transmissão Vetorial, Instituto Adolfo Lutz, São Paulo, Brazil
| | - J S Nogueira
- Núcleo de Doenças de Transmissão Vetorial, Instituto Adolfo Lutz, São Paulo, Brazil
| | - I M Rocco
- Núcleo de Doenças de Transmissão Vetorial, Instituto Adolfo Lutz, São Paulo, Brazil
| | - A C da Costa
- Instituto de Medicina Tropical e Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - S C V Komninakis
- Retrovirology Laboratory, Federal University of São Paulo, São Paulo, Brazil
- School of Medicine of ABC (FMABC), Clinical Immunology Laboratory, Santo André, São Paulo, Brazil
| | - V Azevedo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - A O Chieppe
- Coordenação de Vigilância Epidemiológica do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - E S M Araujo
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - M C L Mendonça
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - C C Dos Santos
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - C D Dos Santos
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - A M Mares-Guia
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - R M R Nogueira
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - P C Sequeira
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - R G Abreu
- Departamento de Vigilância das Doenças Transmissíveis da Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília-DF, Brazil
| | - M H O Garcia
- Departamento de Vigilância das Doenças Transmissíveis da Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília-DF, Brazil
| | - A L Abreu
- Secretaria de Vigilância em Saúde, Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília-DF, Brazil
| | - O Okumoto
- Secretaria de Vigilância em Saúde, Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília-DF, Brazil
| | - E G Kroon
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - C F C de Albuquerque
- Organização Pan - Americana da Saúde/Organização Mundial da Saúde - (OPAS/OMS), Brasília-DF, Brazil
| | - K Lewandowski
- Public Health England, National Infections Service, Porton Down, Salisbury, UK
| | - S T Pullan
- Public Health England, National Infections Service, Porton Down, Salisbury, UK
| | - M Carroll
- NIHR HPRU in Emerging and Zoonotic Infections, Public Health England, London, UK
| | - T de Oliveira
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - E C Sabino
- Instituto de Medicina Tropical e Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - R P Souza
- Núcleo de Doenças de Transmissão Vetorial, Instituto Adolfo Lutz, São Paulo, Brazil
| | - M A Suchard
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, USA
- Department of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
| | - P Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - G S Trindade
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - B P Drumond
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - A M B Filippis
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - N J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - S Cauchemez
- Mathematical Modelling of Infectious Diseases and Center of Bioinformatics, Institut Pasteur, Paris, France
- CNRS UMR2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
| | - L C J Alcantara
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - O G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
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11
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Amâncio FF, Ferraz ML, Almeida MCDM, Pessanha JEM, Iani FCM, Fraga GL, Lambertucci JR, Carneiro M. Dengue virus serotype 4 in a highly susceptible population in Southeast Brazil. J Infect Public Health 2014; 7:547-52. [PMID: 25179890 DOI: 10.1016/j.jiph.2014.07.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 07/14/2014] [Accepted: 07/18/2014] [Indexed: 11/28/2022] Open
Abstract
In Minas Gerais, Brazil, almost 500,000 dengue fever cases were reported to the State Surveillance System between November 2012 and July 2013. An analysis of the laboratory-confirmed cases revealed a higher age-specific incidence in adults and a higher case fatality rate in people aged ≥50. Dengue virus serotypes 1 and 4 (the latter of which is an emerging serotype in Brazil) were responsible for the outbreak.
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Affiliation(s)
| | - Marcela L Ferraz
- Epidemiology Department of the State of Minas Gerais Health Secretariat, Minas Gerais, Brazil
| | | | | | | | - Gabriela L Fraga
- Epidemiology Department of the State of Minas Gerais Health Secretariat, Minas Gerais, Brazil
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