Genome analysis of yellow fever virus of the ongoing outbreak in Brazil reveals polymorphisms

Bonaldo, Myrna C.; Gómez, Mariela Martínez; Santos, Alexandre Ac dos; Abreu, Filipe Vieira Santos de; Ferreira-de-Brito, Anielly; Miranda, Rafaella Moraes de; Castro, Márcia Gonçalves de; Lourenço‐de‐Oliveira, Ricardo

doi:10.1590/0074-02760170134

Cited by 73 publications

(96 citation statements)

References 13 publications

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“…All alignments were screened for recombination using the Phi-test available in SplitsTree v.4 (60); the null hypothesis of the absence of recombination could not be rejected (P<0.05) and lack of recombination was confirmed using the RDP4 package (61). The outbreak dataset comprises 52 genome isolates, 50 of which were generated by this study and 2 of which were published in (27) (clade c in figure S5; see also table S3).…”

Section: Curation Of Whole-genome Sequence Datasetsmentioning

confidence: 99%

Genomic and epidemiological monitoring of yellow fever virus transmission potential

Faria¹,

Kraemer²,

Hill³

et al. 2018

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The yellow fever virus (YFV) epidemic that began in Dec 2016 in Brazil is the largest in decades. The recent discovery of YFV in Brazilian Aedes sp. vectors highlights the urgent need to monitor the risk of re-establishment of domestic 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 in Brazil is characteristic of sylvatic transmission. Analysis of YFV cases combined with genomes generated locally using a new protocol reveals an early phase of sylvatic YFV transmission restricted to Minas Gerais, followed in late 2016 by a rise in viral spillover to humans, and the southwards spatial expansion of the epidemic towards previously YFV-free areas. Our results establish a framework for monitoring YFV transmission in real-time, contributing to the global strategy of eliminating future yellow fever epidemics.

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Section: Curation Of Whole-genome Sequence Datasetsmentioning

confidence: 99%

Genomic and epidemiological monitoring of yellow fever virus transmission potential

Faria¹,

Kraemer²,

Hill³

et al. 2018

Preprint

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“…Analysis of amino acid signatures showed the ubiquitous presence of the nine unique amino acid substitutions previously described (Bonaldo et al, 2017;Gomez et al, 2018) in almost all new YFV Brazilian genomes from the Southeastern region and in one sample from Goiás (GO27/2015) (Supplementary Table 3 and Supplementary Figure 3). Distinctly, the other YFV strain from Goiás (GO05/2017), exhibited an amino acid pattern more similar to older YFV sub-clade 1E strains sampled in Brazil and Venezuela between 2000 and 2010 (Supplementary Table 3 and Supplementary Figure 3).…”

Section: Resultsmentioning

confidence: 78%

“…Viral samples from 12 infected hosts from distinct biomes and river basins in the states of Goiás ( n = 2), Central-Western region, and Rio de Janeiro ( n = 2), Minas Gerais ( n = 3), Espírito Santo ( n = 3) and São Paulo ( n = 2), Southeastern region of Brazil, were analyzed (Table 1). Serum samples of human cases, liver samples of NHPs and homogenates of entire bodies of pooled adult female mosquitoes were collected and processed as previously described (Ferreira-de-Brito et al, 2016;Bonaldo et al, 2017;Gomez et al, 2018;Abreu et al, 2019). The YFV isolates ABR1005 and ABR1009 were obtained from the sera of a 64 and 30-year-old male patients, respectively.…”

Section: Methodsmentioning

confidence: 99%

“…Therefore, to define in greater detail the geographic origin and subsequent dissemination routes of the 2016-2018 Brazilian YFV clade, we generated and analyzed 12 YFV new genomes obtained from humans, NHPs and mosquitoes, between 2015 and 2018, from all Southeast Brazilian states (Minas Gerais, Espírito Santo, Rio de Janeiro e São Paulo) and from Central-West region (Goiás). Interestingly, we identified two YFV lineages circulating in Central-West (Goiás) during 2015-2017, one (GO27/2015) displaying the nine unique amino acid signatures characteristic of the 2016-2018 YFV Southeastern outbreak (Bonaldo et al, 2017) and the other (GO05/2017) isolated two year later that displayed an amino acid pattern typical of older YFV sub-clade 1E strains sampled in Brazil and Venezuela between 2000 and 2010 (de Souza et al, 2010). Besides, these 12 new YFV complete coding region sequences (CDS) were combined with previously described YFV CDS from Brazil (n = 67), Venezuela (n = 5) and Trinidad and Tobago (n = 1) and then subjected to phylogeographic analyses to get a better picture of the ongoing YFV epidemic in Brazil.…”

Section: Introductionmentioning

confidence: 99%

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Distinct YFV lineages co-circulated in the Central-Western and Southeastern Brazilian regions from 2015 to 2018

Delatorre

Abreu

Ribeiro

et al. 2019

Preprint

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28 29 30 Keywords: Yellow fever virus, Brazilian outbreak, lineages, amino acid changes, phylogeography. 31 32 33 34 35 Delatorre et al., 2019 -Distinct YFV lineages co-circulated in Brazil 2 Abstract 36The current outbreak of yellow fever virus (YFV) that is afflicting Brazil since the end of 2016 probably 37 originated from a re-introduction of YFV from endemic areas into the non-endemic Southeastern 38Brazil. However, the lack of genomic sequences from endemic regions hinders the tracking of YFV's 39 dissemination routes. We assessed the origin and spread of the ongoing YFV Brazilian outbreak 40 analyzing a new set of YFV strains infecting humans, non-human primates (NHP) and mosquitoes 41 sampled across five Brazilian states from endemic and non-endemic regions between 2015 and 2018. 42We found two YFV sub-clade 1E lineages circulating in NHP from Goiás state (GO), resulting from 43 independent viral introductions into the Araguaia tributary river basin: while the strain from 2017 44 clustered intermingled with Venezuelan YFV strains from 2000, the YFV strain sampled in 2015 45 clustered with sequences of the current YFV outbreak in the Brazilian Southeastern region (named 46 YFV2015-2018 lineage), displaying the same molecular signature associated to the current YFV outbreak. 47After its introduction in GO at around mid-2014, the YFV2015-2018 lineage followed two paths of 48 dissemination outside GO, originating two major YFV sub-lineages: 1) the YFVMG/ES/RJ sub-lineage 49 spread sequentially from the eastern area of Minas Gerais state to Espírito Santo and then to Rio de 50 Janeiro states, following the Southeast Atlantic basin; 2) the YFVMG/SP sub-lineage spread from the 51 southwestern area of Minas Gerais to the metropolitan region of São Paulo state, following the Paraná 52 basin. These results indicate the ongoing YFV outbreak in Southeastern Brazil originated from a 53 dissemination event from GO almost two years before its recognition at the end of 2016. From GO this 54 lineage was introduced in Minas Gerais state at least two times, originating two sub-lineages that 55 followed different routes towards densely populated areas. The spread of YFV outside endemic regions 56 for at least four years stresses the imperative importance of the continuous monitoring of YFV to aid 57 decision-making for effective control policies aiming the increase of vaccination coverage to avoid the 58 YFV transmission in densely populated urban centers. 59 60 Delatorre et al., 2019 -Distinct YFV lineages co-circulated in Brazil 3

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“…This uncommonly large epidemic is associated with YFV variants from the Modern sub-lineage 1E of South America genotype I. Most epidemic strains exhibited several amino acid substitutions within non-structural proteins at locations that are involved in both viral protease and polymerase activities [145,171]. The effect(s) of these changes on the fitness, pathogenicity, and transmissibility of the virus is not yet known.…”

Section: In South Americamentioning

confidence: 99%

What Does the Future Hold for Yellow Fever Virus? (I)

Klitting

Fischer

Drexler

et al. 2018

Preprint

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Abstract:The recent resurgence of yellow fever virus (YFV) activity in the tropical regions of Africa and South America has sparked renewed interest in this infamous arboviral disease. YFV had been a human plague for centuries prior to the identification of its urban transmission vector, the Aedes aegypti mosquito species, and the development of an efficient live-attenuated vaccine, the YF-17D strain. The combination of vector-control measures and vaccination campaigns drastically reduced YFV incidence in humans on many occasions, but the virus never ceased to circulate in the forest, through its sylvatic invertebrate vector(s) and vertebrate host(s). Outbreaks recently reported in Central Africa (2015)(2016) and Brazil (since late 2016), reached considerable proportions in terms of spatial distribution and total numbers of cases, with multiple exports, including to China. In turn, questions regarding the likeliness of occurrence of large urban YFV outbreaks in the Americas or of a successful import of YFV to Asia are currently resurfacing. This two-part review describes the current state of knowledge and gaps regarding the molecular biology and transmission dynamics of YFV, along with an overview of the tools that can be used to manage the disease at the individual, local and global levels.

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Genome analysis of yellow fever virus of the ongoing outbreak in Brazil reveals polymorphisms

Cited by 73 publications

References 13 publications

Genomic and epidemiological monitoring of yellow fever virus transmission potential

Genomic and epidemiological monitoring of yellow fever virus transmission potential

Distinct YFV lineages co-circulated in the Central-Western and Southeastern Brazilian regions from 2015 to 2018

What Does the Future Hold for Yellow Fever Virus? (I)

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