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Human outbreaks of a novel reassortant Oropouche virus in the Brazilian Amazon region
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  • Article
  • Published: 18 September 2024

Human outbreaks of a novel reassortant Oropouche virus in the Brazilian Amazon region

  • Felipe Gomes Naveca  ORCID: orcid.org/0000-0002-2888-10601,2,
  • Tatiana Amaral Pires de Almeida  ORCID: orcid.org/0009-0007-9086-85301,3,
  • Victor Souza1,
  • Valdinete Nascimento1,
  • Dejanane Silva1,
  • Fernanda Nascimento1,
  • Matilde Mejía1,
  • Yasmin Silva de Oliveira1,
  • Luisa Rocha4,
  • Natana Xavier4,
  • Janis Lopes4,
  • Rodrigo Maito4,
  • Cátia Meneses4,
  • Tatyana Amorim5,
  • Luciana Fé5,
  • Fernanda Sindeaux Camelo  ORCID: orcid.org/0000-0002-1680-23105,
  • Samyly Coutinho de Aguiar Silva5,
  • Alexsandro Xavier de Melo5,
  • Leíse Gomes Fernandes5,
  • Marco Aurélio Almeida de Oliveira6,
  • Ana Ruth Arcanjo6,
  • Guilherme Araújo6,
  • Walter André Júnior6,
  • Renata Lia Coragem de Carvalho6,
  • Rosiane Rodrigues7,
  • Stella Albuquerque7,
  • Cristiane Mattos7,
  • Ciciléia Silva7,
  • Aline Linhares7,
  • Taynã Rodrigues8,
  • Francy Mariscal8,
  • Márcia Andréa Morais9,
  • Mayra Marinho Presibella10,
  • Nelson Fernando Quallio Marques10,
  • Anne Paiva11,
  • Karina Ribeiro11,
  • Deusilene Vieira12,
  • Jackson Alves da Silva Queiroz12,
  • Ana Maísa Passos-Silva12,
  • Lígia Abdalla13,
  • João Hugo Santos14,
  • Regina Maria Pinto de Figueiredo15,
  • Ana Cecília Ribeiro Cruz16,
  • Livia Neves Casseb16,
  • Jannifer Oliveira Chiang16,
  • Livia Vinhal Frutuoso17,
  • Agata Rossi18,
  • Lucas Freitas  ORCID: orcid.org/0000-0002-8766-089019,
  • Túlio de Lima Campos20,
  • Gabriel Luz Wallau  ORCID: orcid.org/0000-0002-1419-571320,21,
  • Emerson Moreira22,
  • Roberto Dias Lins Neto  ORCID: orcid.org/0000-0002-3983-802520,
  • Laura W. Alexander23,
  • Yining Sun24,
  • Ana Maria Bispo de Filippis2,
  • Tiago Gräf  ORCID: orcid.org/0000-0003-4921-797525,
  • Ighor Arantes2,
  • Ana I. Bento  ORCID: orcid.org/0000-0001-7728-007X24,
  • Edson Delatorre18 &
  • …
  • Gonzalo Bello  ORCID: orcid.org/0000-0002-2724-27932 

Nature Medicine (2024)Cite this article

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We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

Subjects

  • Viral epidemiology
  • Viral infection

Abstract

The Brazilian western Amazon is experiencing its largest laboratory-confirmed Oropouche virus (OROV) outbreak, with more than 6,300 reported cases between 2022 and 2024. Here, we sequenced and analyzed 382 OROV genomes from human samples collected in Amazonas, Acre, Rondônia, and Roraima states, between August 2022 and February 2024, to uncover the origin and genetic evolution of OROV in the current outbreak. Genomic analyses revealed that the upsurge of OROV cases in the Brazilian Amazon coincides with spread of a novel reassortant lineage containing the M segment of viruses detected in the eastern Amazon region (2009-2018) and the L and S segments of viruses detected in Peru, Colombia, and Ecuador (2008-2021). The novel reassortant likely emerged in the Amazonas state between 2010 and 2014 and spread through long-range dispersion events during the second half of the 2010s. Phylodynamics reconstructions showed that the current OROV spread was mainly driven by short-range (< 2 km) movements consistent with the flight range of vectors. Nevertheless, a substantial proportion (22%) of long-range (> 10 km) OROV migrations were also detected, consistent with viral dispersion by humans. Our data provides a view of the unprecedented spread and evolution of OROV in Brazilian western Amazon region.

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Author information

Authors and Affiliations

  1. Núcleo de Vigilância de Vírus Emergentes, Reemergentes ou Negligenciados – ViVER/EDTA. Instituto Leônidas e Maria Deane, Fiocruz, Manaus, AM, Brazil

    Felipe Gomes Naveca, Tatiana Amaral Pires de Almeida, Victor Souza, Valdinete Nascimento, Dejanane Silva, Fernanda Nascimento, Matilde Mejía & Yasmin Silva de Oliveira

  2. Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil

    Felipe Gomes Naveca, Ana Maria Bispo de Filippis, Ighor Arantes & Gonzalo Bello

  3. Diretoria de Ensino e Pesquisa, Fundação Centro de Controle de Oncologia do Estado do Amazonas, FCecon, Manaus, AM, Brazil

    Tatiana Amaral Pires de Almeida

  4. Laboratório Central de Saúde Pública de Roraima, Boa Vista, RR, Brazil

    Luisa Rocha, Natana Xavier, Janis Lopes, Rodrigo Maito & Cátia Meneses

  5. Fundação de Vigilância em Saúde – Dra. Rosemary Costa Pinto, Manaus, AM, Brazil

    Tatyana Amorim, Luciana Fé, Fernanda Sindeaux Camelo, Samyly Coutinho de Aguiar Silva, Alexsandro Xavier de Melo & Leíse Gomes Fernandes

  6. Laboratório Central de Saúde Pública do Amazonas, Manaus, AM, Brazil

    Marco Aurélio Almeida de Oliveira, Ana Ruth Arcanjo, Guilherme Araújo, Walter André Júnior & Renata Lia Coragem de Carvalho

  7. Laboratório Central de Saúde Pública de Rondônia, Porto Velho, RO, Brazil

    Rosiane Rodrigues, Stella Albuquerque, Cristiane Mattos, Ciciléia Silva & Aline Linhares

  8. Laboratório Central de Saúde Pública do Acre, Rio Branco, AC, Brazil

    Taynã Rodrigues & Francy Mariscal

  9. Núcleo de Doenças de Transmissão Vetorial, Secretaria Estadual de Saúde do Acre, Rio Branco, AC, Brazil

    Márcia Andréa Morais

  10. Laboratório Central de Saúde Pública do Paraná, Curitiba, PR, Brazil

    Mayra Marinho Presibella & Nelson Fernando Quallio Marques

  11. Coordenação Geral de Laboratórios de Saúde Pública – CGLAB, Ministério da Saúde, Brasília, DF, Brazil

    Anne Paiva & Karina Ribeiro

  12. Laboratório de Virologia Molecular, Fiocruz Rondônia, Porto Velho, RO, Brazil

    Deusilene Vieira, Jackson Alves da Silva Queiroz & Ana Maísa Passos-Silva

  13. Universidade do Estado do Amazonas, Manaus, AM, Brazil

    Lígia Abdalla

  14. Universidade Federal do Amazonas, Manaus, AM, Brazil

    João Hugo Santos

  15. Gerência de Virologia, Fundação de Medicina Tropical – Dr. Heitor Vieira Dourado, Manaus, AM, Brazil

    Regina Maria Pinto de Figueiredo

  16. Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua, PA, Brazil

    Ana Cecília Ribeiro Cruz, Livia Neves Casseb & Jannifer Oliveira Chiang

  17. Coordenação-Geral de Vigilância de Arboviroses – CGARB, Departamento de Doenças Transmissíveis, Secretaria de Vigilância em Saúde e Ambiente, Ministério da Saúde, Brasília, DF, Brazil

    Livia Vinhal Frutuoso

  18. Laboratório de Genômica e Ecologia Viral, Departamento de Patologia, Centro de Ciências da Saúde, Universidade Federal do Espírito Santo, Vitória, ES, Brazil

    Agata Rossi & Edson Delatorre

  19. GISAID Global Data Science Initiative, Munich, Germany

    Lucas Freitas

  20. Instituto Aggeu Magalhães, Fiocruz, Recife, PE, Brazil

    Túlio de Lima Campos, Gabriel Luz Wallau & Roberto Dias Lins Neto

  21. Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research. National Reference Center for Tropical Infectious Diseases. Bernhard-Nocht-Straße 74, Hamburg, Germany

    Gabriel Luz Wallau

  22. Universidade Federal de Pernambuco, Recife, PE, Brazil

    Emerson Moreira

  23. Department of Integrative Biology, University of California, Berkeley, CA, USA

    Laura W. Alexander

  24. Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA

    Yining Sun & Ana I. Bento

  25. Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fiocruz, Curitiba, PR, Brazil

    Tiago Gräf

Authors
  1. Felipe Gomes Naveca
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  2. Tatiana Amaral Pires de Almeida
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  3. Victor Souza
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  4. Valdinete Nascimento
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  5. Dejanane Silva
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  6. Fernanda Nascimento
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  7. Matilde Mejía
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  8. Yasmin Silva de Oliveira
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  9. Luisa Rocha
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  10. Natana Xavier
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  15. Luciana Fé
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  16. Fernanda Sindeaux Camelo
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  17. Samyly Coutinho de Aguiar Silva
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  20. Marco Aurélio Almeida de Oliveira
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  24. Renata Lia Coragem de Carvalho
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  28. Ciciléia Silva
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  30. Taynã Rodrigues
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  32. Márcia Andréa Morais
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  38. Jackson Alves da Silva Queiroz
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  39. Ana Maísa Passos-Silva
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  40. Lígia Abdalla
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  42. Regina Maria Pinto de Figueiredo
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  43. Ana Cecília Ribeiro Cruz
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  47. Agata Rossi
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  50. Gabriel Luz Wallau
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  51. Emerson Moreira
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  52. Roberto Dias Lins Neto
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  53. Laura W. Alexander
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  54. Yining Sun
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  56. Tiago Gräf
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  60. Gonzalo Bello
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Corresponding authors

Correspondence to Felipe Gomes Naveca or Gonzalo Bello.

Supplementary information

Supplementary Information

Supplementary tables 1–2.

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Cite this article

Naveca, F.G., de Almeida, T.A.P., Souza, V. et al. Human outbreaks of a novel reassortant Oropouche virus in the Brazilian Amazon region. Nat Med (2024). https://doi.org/10.1038/s41591-024-03300-3

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  • Received: 30 July 2024

  • Accepted: 15 September 2024

  • Published: 18 September 2024

  • DOI: https://doi.org/10.1038/s41591-024-03300-3

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