病毒在亚马逊流域以外迅速扩展:奥罗普切病毒在美洲各地的流行活动加剧

Felipe Campos de Melo Iani, Felicidade Mota Pereira, Elaine Cristina de Oliveira, Janete Tayna Nascimento Rodrigues, Mariza Hoffmann Machado, Vagner Fonseca, Talita Emile Ribeiro Adelino, Natalia Rocha Guimaraes, Luiz Marcelo Ribeiro Tome, Marcela Kelly Astete Gomez, Vanessa Brandao Nardy, Adriana Aparecida Ribeiro, Alexander Rosewell, Alvaro Gil A. Ferreira, Arabela Leal e Silva de Mello, Brenda Machado Moura Fernandes, Carlos F. Campelo de Albuquerque, Dejanira dos Santos Pereira, Eline Carvalho Pimentel, Fabio Guilherme Mesquita Lima, Fernanda Viana Moreira Silva, Glauco de Carvalho Pereira, Houriiyah Tegally, Julia Deffune Profeta Cidin Almeida, Keldenn Melo Farias Moreno, Klaucia Rodrigues Vasconcelos, Leandro Cavalcante Santos, Livia Cristina Machado Silva, Livia C. V. Frutuoso, Ludmila Oliveira Lamounier, Mariana Araujo Costa, Marilia Santini de Oliveira, Marlei Pickler Dediasi dos Anjos, Massimo Ciccozzi, Mauricio Teixeira Lima, Maira Alves Pereira, Marilia Lima Cruz Rocha, Paulo Eduardo de Souza da Silva, Peter Rabinowitz, Priscila Souza de Almeida, Richard Lessels, Ricardo T. Gazzinelli, Rivaldo Venancio Cunha, Sabrina Goncalves, Sara Candida Ferreira dos Santos, Senele Ana de Alcantara Belettini, Silvia Helena Sousa Pietra Pedroso, Sofia Isabel Rotulo Araujo, Stephanni Figueiredo da Silva, Julio Croda, Ethel Maciel, Wes Van Voorhis, Darren Martin, Edward C Holmes, Tulio de Oliveira, Jose Lourenco, Luiz Carlos Junior Alcantara, Marta Giovanetti
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Frutuoso, Ludmila Oliveira Lamounier, Mariana Araujo Costa, Marilia Santini de Oliveira, Marlei Pickler Dediasi dos Anjos, Massimo Ciccozzi, Mauricio Teixeira Lima, Maira Alves Pereira, Marilia Lima Cruz Rocha, Paulo Eduardo de Souza da Silva, Peter Rabinowitz, Priscila Souza de Almeida, Richard Lessels, Ricardo T. Gazzinelli, Rivaldo Venancio Cunha, Sabrina Goncalves, Sara Candida Ferreira dos Santos, Senele Ana de Alcantara Belettini, Silvia Helena Sousa Pietra Pedroso, Sofia Isabel Rotulo Araujo, Stephanni Figueiredo da Silva, Julio Croda, Ethel Maciel, Wes Van Voorhis, Darren Martin, Edward C Holmes, Tulio de Oliveira, Jose Lourenco, Luiz Carlos Junior Alcantara, Marta Giovanetti","doi":"10.1101/2024.08.02.24311415","DOIUrl":null,"url":null,"abstract":"Summary: Oropouche virus (OROV), initially detected in Trinidad and Tobago in 1955, has been historically confined to the Amazon Basin. However, since late 2022, OROV has been reported in northern Brazil as well as urban centers in Bolivia, Colombia, Cuba, and Peru. Herein, we describe the doubling of publicly available full genomes by generating 133 new entries. We show how the virus evolved via genome component reassortment and how it rapidly spread across multiple states in Brazil, causing the largest outbreak ever recorded outside the Amazon basin including the first ever detected deaths. This work highlights the need for heightened epidemiological and genomic surveillance and the implementation of adequate measures in order to mitigate transmission and the impacts on the population. Background: Oropouche virus was first identified in 1955 in Trinidad and Tobago and later found in Brazil in 1960. Historically, it has been reported to have caused around 30 outbreaks, mostly within the Amazon Basin, where it circulates among forest animals, but also in urban areas where it is known to be transmitted by the midge Culicoides paraensis. Recently, Brazil has seen a surge in cases, with more than 7000 reported by mid-2024 alone.\nMethods: In a collaboration with Central Public Health Laboratories across Brazilian regions, we integrated epidemiological metadata with genomic analyses of recently sampled cases. This initiative resulted in the generation of 133 whole genome sequences from the three genomic segments (L, M, and S) of the virus, including the first genomes obtained from regions outside the Amazon and from the first ever recorded fatal cases.\nFindings: All of the 2024 genomes form a monophyletic group in the phylogenetic tree with sequences from the Amazon Basin sampled since 2022. 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引用次数: 0

摘要

摘要:奥罗波切病毒(OROV)最初于 1955 年在特立尼达和多巴哥发现,历来局限于亚马逊盆地。然而,自 2022 年末以来,巴西北部以及玻利维亚、哥伦比亚、古巴和秘鲁的城市中心都报告了奥罗普切病毒。在本文中,我们描述了通过生成 133 个新条目而使公开的全基因组增加一倍的情况。我们展示了该病毒是如何通过基因组成分重组进化的,以及它是如何在巴西多个州迅速传播的,造成了亚马逊流域以外有记录以来最大的一次疫情爆发,包括首次发现死亡病例。这项工作凸显了加强流行病学和基因组监测以及实施适当措施的必要性,以减轻传播和对人口的影响。背景:奥罗普切病毒于 1955 年首次在特立尼达和多巴哥被发现,随后于 1960 年在巴西被发现。据报道,该病毒已造成约 30 起疫情爆发,主要发生在亚马逊流域,在森林动物中传播,但也发生在城市地区,已知由蠓虫 Culicoides paraensis 传播。最近,巴西的病例激增,仅到 2024 年年中报告的病例就超过了 7000 例:我们与巴西各地区的中央公共卫生实验室合作,将流行病学元数据与最近采样病例的基因组分析相结合。这一举措产生了 133 个来自病毒三个基因组片段(L、M 和 S)的全基因组序列,包括首次从亚马逊以外地区获得的基因组和首次记录的死亡病例的基因组:所有 2024 个基因组在系统发生树中与 2022 年以来从亚马逊流域采样的序列形成一个单系群。我们的分析表明,病毒从北向南迅速从亚马逊盆地转移到历史上的非流行地区。我们发现了21个重配事件,但仍不清楚病毒的基因组进化是否使病毒能够适应当地的生态条件并进化出对公共卫生具有重要意义的新表型:最近的快速空间扩展和首次报告的与奥罗普切病毒相关的死亡病例(以及正在调查的其他结果)都强调了在整个地区加强对这种不断演变的病原体的监控的重要性。在过去的两年中,人类人口没有发生任何明显的变化,病毒的适应性、森林砍伐和最近的气候变化有可能单独或共同将奥罗普切病毒带出亚马逊盆地。
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Rapid Viral Expansion Beyond the Amazon Basin: Increased Epidemic Activity of Oropouche Virus Across the Americas
Summary: Oropouche virus (OROV), initially detected in Trinidad and Tobago in 1955, has been historically confined to the Amazon Basin. However, since late 2022, OROV has been reported in northern Brazil as well as urban centers in Bolivia, Colombia, Cuba, and Peru. Herein, we describe the doubling of publicly available full genomes by generating 133 new entries. We show how the virus evolved via genome component reassortment and how it rapidly spread across multiple states in Brazil, causing the largest outbreak ever recorded outside the Amazon basin including the first ever detected deaths. This work highlights the need for heightened epidemiological and genomic surveillance and the implementation of adequate measures in order to mitigate transmission and the impacts on the population. Background: Oropouche virus was first identified in 1955 in Trinidad and Tobago and later found in Brazil in 1960. Historically, it has been reported to have caused around 30 outbreaks, mostly within the Amazon Basin, where it circulates among forest animals, but also in urban areas where it is known to be transmitted by the midge Culicoides paraensis. Recently, Brazil has seen a surge in cases, with more than 7000 reported by mid-2024 alone. Methods: In a collaboration with Central Public Health Laboratories across Brazilian regions, we integrated epidemiological metadata with genomic analyses of recently sampled cases. This initiative resulted in the generation of 133 whole genome sequences from the three genomic segments (L, M, and S) of the virus, including the first genomes obtained from regions outside the Amazon and from the first ever recorded fatal cases. Findings: All of the 2024 genomes form a monophyletic group in the phylogenetic tree with sequences from the Amazon Basin sampled since 2022. Our analyses revealed a rapid north-to-south viral movement from the Amazon Basin into historically non-endemic regions. We identified 21 reassortment events, although it remains unclear if genomic evolution of the virus enabled the virus to adapt to local ecological conditions and evolve new phenotypes of public health importance. Interpretation: Both the recent rapid spatial expansion and the first reported fatalities associated with Oropouche (and other outcomes under investigation) underscore the importance of enhancing surveillance for this evolving pathogen across the Region. Without any obvious changes in the human population over the past 2 years, it is possible that viral adaptation, deforestation and recent climate change, either alone or in combination, have propelled Oropouche virus beyond the Amazon Basin.
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