Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon

Naveca, Felipe Gomes; Claro, Ingra Morales; Giovanetti, Marta; Jesus, Jaqueline Góes de; Xavier, Joilson; Iani, Felipe Campos de Melo; Nascimento, Valdinete Alves do; Souza, Victor Costa de; Silveira, Paola Paz; Lourenço, José; Santillana, Mauricio; Kraemer, Moritz U. G.; Quick, Josh; Hill, Sarah C.; Thézé, Julien; Carvalho, Rodrigo Dias de Oliveira; Azevedo, Vasco; Salles, Flávia Cristina da Silva; Nunes, Márcio Roberto Teixeira; Lemos, Poliana da Silva; Cândido, Darlan da Silva; Pereira, Glauco de Carvalho; Oliveira, Marluce Aparecida Assunção; Meneses, Cátia Alexandra Ribeiro; Maito, Rodrigo Melo; Cunha, Claudeth Rocha Santa Brígida; Campos, Daniela Palha de Sousa; Castilho, Márcia da Costa; Siqueira, Thalita Caroline da Silva; Terra, Tiza Matos; Albuquerque, Carlos Frederico Campelo de; Cruz, Laura N.; Abreu, André Luiz de; Martins, Divino Valerio; Simoes, Daniele Silva de Moraes Vanlume; Aguiar, Renato Santana; Luz, Sérgio Luíz Bessa; Loman, Nicholas J.; Pybus, Oliver G.; Sabino, Éster Cerdeira; Okumoto, Osnei; Alcântara, Luíz Carlos Júnior; Faria, Nuno Rodrigues

doi:10.1371/journal.pntd.0007065

Cited by 83 publications

(90 citation statements)

References 75 publications

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“…Recent advances in third generation sequencing technologies have opened up new opportunities for infectious disease research. Pathogen genomics can be used to resolve crucial questions regarding origin, modes of transmission and ecology of emerging viral disease [31][32][33][34][35] . Therefore, we have sequenced 112 USUV genomes from blackbirds brain tissues on the Nanopore sequencing platform to analyse the emergence and spread of USUV throughout the Netherlands in 2016, 2017 and 2018.…”

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confidence: 99%

Genomic monitoring to understand the emergence and spread of Usutu virus in the Netherlands, 2016–2018

Munnink

Munger

Nieuwenhuijse

et al. 2020

Sci Rep

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Usutu virus (USUV) is a mosquito-borne flavivirus circulating in Western Europe that causes die-offs of mainly common blackbirds (Turdus merula).In the Netherlands, USUV was first detected in 2016, when it was identified as the likely cause of an outbreak in birds. In this study, dead blackbirds were collected, screened for the presence of USUV and submitted to nanopore-based sequencing. Genomic sequences of 112 USUV were obtained and phylogenetic analysis showed that most viruses identified belonged to the USUV Africa 3 lineage, and molecular clock analysis evaluated their most recent common ancestor to 10 to 4 years before first detection of USUV in the Netherlands. USUV Europe 3 lineage, commonly found in Germany, was less frequently detected. this analyses further suggest some extent of circulation of USUV between the netherlands, Germany and Belgium, as well as likely overwintering of USUV in the netherlands.Usutu virus (USUV) is a mosquito-borne arbovirus of the genus Flavivirus. The virus has a positive-stranded RNA genome with a genome length of around 11,000 nucleotides which encodes a single polyprotein. The polyprotein is processed by viral and host proteases into structural and non-structural proteins 1 . The life cycle of USUV involves mosquitoes (mainly Culex sp. 2,3 ) as vectors and wild birds as the main amplifying hosts. Humans and other mammals can be infected by mosquito bites and are generally considered dead-end hosts. Recent studies revealed that USUV can also be detected in small mammals such as bats 4 , rodents and shrews 5 .USUV was first identified from a Culex neavei mosquito in South Africa in 1959 6 . Over subsequent decades, it was sporadically reported in several mosquito and bird species, and twice in a human patient with fever and rash in African countries 7 . USUV was for first identified in Europe in 2001, when it was determined to be the causative agent of a mass mortality event in several bird species in Austria 8 . This prompted retrospective analysis of archived tissue samples from dead wild birds in Italy in 1996, which revealed an earlier presence of the virus in Europe 9 . Our understanding of the USUV geographical range has since expanded to include the majority of European countries 10 , where outbreaks are marked by mass die-offs of wild birds, with the heaviest toll on common blackbird (Turdus merula) populations. In Germany, it has been demonstrated that five years after the first detection of USUV in the southwest of the country, circulation of the virus was associated with a 15.7% decline in the common blackbird population in USUV-suitable areas 11 .The recent emergence of USUV epizootics among wild bird populations in Europe has been accompanied by reports of USUV infections in humans. Pathogenicity in humans appears to range from asymptomatic or mild symptoms, as shown in seroprevalence studies among healthy blood donors in Italy 12 , Germany 13 , Austria 14 and the Netherlands 15 to neuroinvasive infections associated with encephalitis or meningo-encephalitis, m...

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confidence: 99%

Genomic monitoring to understand the emergence and spread of Usutu virus in the Netherlands, 2016–2018

Munnink

Munger

Nieuwenhuijse

et al. 2020

Sci Rep

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“…mosquitoes, such as locations with tropical and subtropical climates [2]. Integration of routine serological, molecular, and genomic data along with improved digital surveillance [29], will help to anticipate the arrival and establishment of new virus lineages and other pathogens in the Americas.…”

Section: Resultsmentioning

confidence: 99%

Early identification of dengue virus lineage replacement in Brazil using portable genomic surveillance

Jesus

Dutra

Salles

et al. 2019

Preprint

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and 33 nuno.faria@zoo.ox.ac.uk 3 35 Abstract 36 Over 400 million people are estimated to be at risk of acquiring dengue virus (DENV). 37 Despite efforts to mitigate the impact of DENV epidemics, the virus remains a public health 38 problem in the Americas: more than one million DENV cases were reported in the continent 39 between January and July 2019 DENV was first detected in Brazil in 1982, and Brazil has 40 reported 88% (1,127,244 cases) of all DENV cases in the Americas during 2019 to date. São 41 Paulo state in the southeast of Brazil has reported nearly half of all DENV infections in the 42 country. Here we characterised the genetic diversity of DENV strains circulating in São 43 Paulo state in 2019, at the epicentre of the ongoing DENV epidemic. Using portable 44 nanopore sequencing we generated 20 new DENV genome sequences from viremic patients45 with suspected dengue infection residing in two of the most-affected municipalities, 46 Araraquara and São José do Rio Preto. We conducted a comprehensive phylogenetic analysis 47 with 1,630 global DENV strains to better understand the evolutionary history of the DENV 48 lineages that currently circulate in the region. The new outbreak strains were classified as 49 DENV2 genotype III (American/Asian genotype). Notably, phylogenetic analysis indicated 50 that the 2019 outbreak is the result of a novel DENV lineage that was recently introduced to 51 Brazil from the Caribbean region. Our genetic analysis further indicates that the introduction 52 and onwards spread of the outbreak lineage (named here DENV2-III BR-4) indicates a new 53 DENV2 lineage replacement in Brazil. Dating phylogeographic analysis suggests that 54 DENV2-III BR-4 was introduced to Brazil in or around early 2014, possibly from the 55 Caribbean region. Our study describes the early detection of a newly introduced and rapidly-56 expanding DENV2 virus lineage in Brazil. 57 58 Key words: dengue 2, outbreak, genomic surveillance, lineage replacement 4 60 Author Summary 61 Dengue is the most important mosquito-borne viral disease of humans. The disease is caused 62 by the dengue virus (DENV) that is classified within genus Flavivirus. DENV infections are 63 caused by 4 serotypes (DENV 1-4) that are genetically related but antigenically distinct. 64 Dengue infection results in a variety of symptoms that range from mild fever to dengue 65 hemorrhagic fever and/or dengue shock syndrome (DHF/DSS). Clinical outcomes are 66 associated with different types of infection, viral serotypes, genotypes, lineages, and host 67 genetic factors. As a re-emerging infectious disease, DENV has become a serious threat to 68 public health in the Americas, and particularly in Brazil, where it was introduced in the 1980s 69 and became well established due to the country-wide re-infestation of the Aedes aegypti 70 mosquito vector species. During the first six months of 2019, 1,282,183 DENV cases were 71 reported in the Americas, with Brazil reporting a staggering 1,127,244 (88%) of all dengue 72 cases in the continent. To dat...

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“…In addition, the system is simple to use, fast, high portability, thus, allows it to be used on real-time analysis of sequencing. MinION has been increasingly applied in the fields of virus detection, viral whole-genome sequencing, and viral evolution [19][20][21][22]. NGS was also successfully applied in response to the event described in this paper.…”

Section: Discussionmentioning

confidence: 99%

Identification of Histoplasma causing an unexplained disease cluster in Matthews Ridge, Guyana

Wang

Zhou

Ling³

et al. 2019

Biosafety and Health

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Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon

Cited by 83 publications

References 75 publications

Genomic monitoring to understand the emergence and spread of Usutu virus in the Netherlands, 2016–2018

Genomic monitoring to understand the emergence and spread of Usutu virus in the Netherlands, 2016–2018

Early identification of dengue virus lineage replacement in Brazil using portable genomic surveillance

Identification of Histoplasma causing an unexplained disease cluster in Matthews Ridge, Guyana

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