Silent emergence of Mayaro and Oropouche viruses in humans in Central Brazil

Costa, Vivaldo Gomes da; Féres, Valéria Christina de Rezende; Saivish, Marielena Vogel; Gimaque, João Bosco de Lima; Moreli, Marcos Lázaro

doi:10.1016/j.ijid.2017.07.016

Cited by 32 publications

(22 citation statements)

References 9 publications

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“…vectors [58], but has also been identified in Culex quinquefasciatus and Aedes aegypti mosquitoes [59]. MAYV has been detected in the north [60-64] and centre-west [21, 59, 65-68] regions of Brazil. Moderate to high prevalence of MYV IgM have been found in urban northern areas [60], which could explain the limited spread of CHIKV in Manaus compared to Roraima.…”

Section: Discussionmentioning

confidence: 99%

Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage

Naveca

Claro

Giovanetti

et al. 2018

Preprint

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48 49 50 51 52 Corresponding authors: luiz.alcantara@ioc.fiocruz.br and nuno.faria@zoo.ox.ac.uk 3 53 Abstract 54 Background 55 Since its first detection in the Caribbean in late 2013, chikungunya virus (CHIKV) has 56 affected 51 countries in the Americas. The CHIKV epidemic in the Americas was 57 caused by the CHIKV-Asian genotype. In August 2014, local transmission of the 58 CHIKV-Asian genotype was detected in the Brazilian Amazon region. However, a 59 distinct lineage, the CHIKV-East-Central-South-America (ECSA)-genotype, was 60 detected nearly simultaneously in Feira de Santana, Bahia state, northeast Brazil. The 61 genomic diversity and the dynamics of CHIKV in the Brazilian Amazon region 62 remains poorly understood despite its importance to better understand the 63 epidemiological spread and public health impact of CHIKV in the country. 64 65 Methodology/Principal Findings 66 We report a large CHIKV outbreak (5,928 notified cases between August 2014 and 67 August 2018) in Boa vista municipality, capital city of Roraima's state, located in the 68 Brazilian Amazon region. In just 48 hours, we generated 20 novel CHIKV-ECSA 69 genomes from the Brazilian Amazon region using MinION portable genome 70 sequencing. Phylogenetic analyses revealed that despite an early introduction of the 71 Asian genotype in 2015 in Roraima, the large CHIKV outbreak in 2017 in Boa Vista 72 was caused by an ECSA-lineage most likely introduced from northeastern Brazil. 73 Epidemiological analyses suggest a basic reproductive number of R 0 of 1.66, which 74 translates in an estimated 39 (95% CI: 36 to 45) % of Roraima's population infected 75 with CHIKV-ECSA. Finally, we find a strong association between Google search 76 activity and the local laboratory-confirmed CHIKV cases in Roraima. 77 78 Conclusions/Significance 79 This study highlights the potential of combining traditional surveillance with portable 80 genome sequencing technologies and digital epidemiology to inform public health 81 surveillance in the Amazon region. Our data reveal a large CHIKV-ECSA outbreak in 82 Boa Vista, limited potential for future CHIKV outbreaks, and indicate a replacement 83 of the Asian genotype by the ECSA genotype in the Amazon region. 84 85 4 86 Author Summary 87 Until the end of 2017, Brazil notified the highest number of infections caused by 88 chikungunya virus (CHIKV) in the Americas. We investigated a large CHIKV 89 outbreak in Boa vista municipality in the Brazilian Amazon region. Rapid portable 90 genome sequencing of 20 novel isolates and subsequent genetic analysis revealed that 91 ECSA lineage was introduced from northeastern Brazil to Roraima around July 2016. 92 Epidemiological analyses suggest a basic reproductive number of R 0 of 1.66, which 93 suggests that approximately 39% of Roraima's population was infected with CHIKV-94 ECSA. Given the dominance of the CHIKV-Asian genotype in the Americas, our data 95 highlights the rapid spread of a less understood and poorly characterized CHIKV-96 ECSA genotype in Brazil. Investigations on p...

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Section: Discussionmentioning

confidence: 99%

Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage

Naveca

Claro

Giovanetti

et al. 2018

Preprint

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“…Since its first description in 1961 in Trinidad and Tobago (5), OROV has caused several outbreaks and sporadic infections in the Brazilian Amazon, particularly in the states of Pará, Amapá, Rondônia, Maranhão, Acre, Amazonas, Minas Gerais, Mato Grosso, and Tocantins (6)(7)(8)(9), and evidence suggests the circulation of OROV in other Brazilian states (10). Since the late 1980s, additional cases and outbreaks of OROV have been reported in Panama, Peru (11)(12)(13), and, more recently, Ecuador (14).…”

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Evolutionary Dynamics of Oropouche Virus in South America

Gutierrez

Wise

Pullan

et al. 2020

J Virol

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The Amazon basin is home to numerous arthropod-borne viral pathogens that cause febrile disease in humans. Among these, Oropouche orthobunyavirus (OROV) is a relatively understudied member of the genus Orthobunyavirus, family Peribunyaviridae, that causes periodic outbreaks in human populations in Brazil and other South American countries. Although several studies have described the genetic diversity of the virus, the evolutionary processes that shape the OROV genome remain poorly understood. Here, we present a comprehensive study of the genomic dynamics of OROV that encompasses phylogenetic analysis, evolutionary rate estimates, inference of natural selective pressures, recombination and reassortment, and structural analysis of OROV variants. Our study includes all available published sequences, as well as a set of new OROV genome sequences obtained from patients in Ecuador, representing the first set of genomes from this country. Our results show differing evolutionary processes on the three segments that comprise the viral genome. We infer differing times of the most recent common ancestors of the genome segments and propose that this can be explained by cryptic reassortment. We also present the discovery of previously unobserved putative N-linked glycosylation sites, as well as codons that evolve under positive selection on the viral surface proteins, and discuss the potential role of these features in the evolution of OROV through a combined phylogenetic and structural approach. IMPORTANCE The emergence and reemergence of pathogens such as Zika virus, chikungunya virus, and yellow fever virus have drawn attention toward other cocirculating arboviruses in South America. Oropouche virus (OROV) is a poorly studied pathogen responsible for over a dozen outbreaks since the early 1960s and represents a public health burden to countries such as Brazil, Panama, and Peru. OROV is likely underreported since its symptomatology can be easily confounded with other febrile illnesses (e.g., dengue fever and leptospirosis) and point-of-care testing for the virus is still uncommon. With limited data, there is a need to optimize the information currently available. Analysis of OROV genomes can help us understand how the virus circulates in nature and can reveal the evolutionary forces that shape the genetic diversity of the virus, which has implications for molecular diagnostics and the design of potential vaccines.

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Section: Introductionmentioning

confidence: 99%

The evolutionary dynamics of Oropouche Virus (OROV) in South America

Gutierrez

Wise

Pullan

et al. 2019

Preprint

View full text Add to dashboard Cite

The Amazon basin is host to numerous arthropod-borne viral pathogens that cause febrile disease in humans. Among these, Oropouche orthobunyavirus (OROV) is a relatively understudied member of the Peribunyavirales that causes periodic outbreaks in human populations in Brazil and other South American countries. Although several studies have described the genetic diversity of the virus, the evolutionary processes that shape the viral genome remain poorly understood. Here we present a comprehensive study of the genomic dynamics of OROV that encompasses phylogenetic analysis, evolutionary rate estimates, inference of natural selective pressures, recombination and reassortment, and structural analysis of OROV variants. Our study includes all available published sequences, as well as a set of new OROV genomes sequences obtained from patients in Ecuador, representing the first set of viral genomes from this country. Our results show that differing evolutionary processes on the three segments that encompass the viral genome lead to variable evolutionary rates and TMRCAs that could be explained by cryptic reassortment. We also present the discovery of previously unobserved putative N-linked glycosylation sites, and codons which evolve under positive selection on the viral surface proteins, and discuss the potential role of these features in the evolution of the virus through a combined phylogenetic and structural approach.

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Silent emergence of Mayaro and Oropouche viruses in humans in Central Brazil

Cited by 32 publications

References 9 publications

Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage

Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage

Evolutionary Dynamics of Oropouche Virus in South America

The evolutionary dynamics of Oropouche Virus (OROV) in South America

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