10 research outputs found
Promoting Responsible Research and Innovation (RRI) During Brazilian Activities of Genomic and Epidemiological Surveillance of Arboviruses
Zika infectio
Circulation of chikungunya virus East/Central/South African lineage in Rio de Janeiro, Brazil.
The emergence of chikungunya virus (CHIKV) has raised serious concerns due to the virus' rapid dissemination into new geographic areas and the clinical features associated with infection. To better understand CHIKV dynamics in Rio de Janeiro, we generated 11 near-complete genomes by means of real-time portable nanopore sequencing of virus isolates obtained directly from clinical samples. To better understand CHIKV dynamics in Rio de Janeiro, we generated 11 near-complete genomes by means of real-time portable nanopore sequencing of virus isolates obtained directly from clinical samples. Our phylogenetic reconstructions indicated the circulation of the East-Central-South-African (ECSA) lineage in Rio de Janeiro. Time-measured phylogenetic analysis combined with CHIKV notified case numbers revealed the ECSA lineage was introduced in Rio de Janeiro around June 2015 (95% Bayesian credible interval: May to July 2015) indicating the virus was circulating unnoticed for 5 months before the first reports of CHIKV autochthonous transmissions in Rio de Janeiro, in November 2015. These findings reinforce that continued genomic surveillance strategies are needed to assist in the monitoring and understanding of arbovirus epidemics, which might help to attenuate public health impact of infectious diseases
Emergence of Dengue Virus Serotype 2 Cosmopolitan Genotype, Brazil
We used nanopore sequencing and phylogenetic analyses to identify a cosmopolitan genotype of dengue virus serotype 2 that was isolated from a 56-year-old male patient from the state of GoiĂĄs in Brazil. The emergence of a cosmopolitan genotype in Brazil will require risk assessment and surveillance to reduce epidemic potential
Persistence of chikungunya ECSA genotype and local outbreak in an upper medium class neighborhood in Northeast Brazil.
The chikungunya East/Central/South/Africa virus lineage (CHIKV-ECSA) was first detected in Brazil in the municipality of Feira de Santana (FS) by mid 2014. Following that, a large number of CHIKV cases have been notified in FS, which is the second-most populous city in Bahia state, northeastern Brazil, and plays an important role on the spread to other Brazilian states due to climate conditions and the abundance of competent vectors. To better understand CHIKV dynamics in Bahia state, we generated 5 complete genome sequences from a local outbreak raised in Serraria Brasil, a neighbourhood in FS, by next-generation sequencing using Illumina approach. Phylogenetic reconstructions revealed that the new FS genomes belongs to the ECSA genotype and falls within a single strongly supported monophyletic clade that includes other older CHIKV sequences from the same location, suggesting the persistence of the virus during distinct epidemic seasons. We also performed minor variants analysis and found a small number of SNPs per sample (b_29L and e_45SR = 16 SNPs, c_29SR = 29 and d_45PL and f_45FL = 21 SNPs). Out of the 93 SNPs found, 71 are synonymous, 21 are non-synonymous and one generated a stop codon. Although those mutations are not related to the increase of virus replication and/or infectivity, some SNPs were found in non-structural proteins which may have an effect on viral evasion from the mammal immunological system. These findings reinforce the needing of further studies on those variants and of continued genomic surveillance strategies to track viral adaptations and to monitor CHIKV epidemics for improved public health control
Retrospective Investigation in Horses with Encephalitis Reveals Unnoticed Circulation of West Nile Virus in Brazil
During these past years, several studies have provided serological evidence regarding the circulation of West Nile virus (WNV) in Brazil. Despite some reports, much is still unknown regarding the genomic diversity and transmission dynamics of this virus in the country. Recently, genomic monitoring activities in horses revealed the circulation of WNV in several Brazilian regions. These findings on the paucity of genomic data reinforce the need for prompt investigation of WNV infection in horses, which may precede human cases of encephalitis in Brazil. Thus, in this study, we retrospectively screened 54 suspicious WNV samples collected between 2017 and 2020 from the spinal cord and brain of horses with encephalitis and generated three new WNV genomes from the Ceará and Bahia states, located in the northeastern region of Brazil. The Bayesian reconstruction revealed that at least two independent introduction events occurred in Brazil. The first introduction event appears to be likely related to the North American outbreak, and was estimated to have occurred in March 2013.The second introduction event appears to have occurred in September 2017 and appears to be likely related to the South American outbreak. Together, our results reinforce the importance of increasing the priority of WNV genomic monitoring in equines with encephalitis in order to track the dispersion of this emerging pathogen through the country
Increased interregional virus exchange and nucleotide diversity outline the expansion of chikungunya virus in Brazil
Abstract The emergence and reemergence of mosquito-borne diseases in Brazil such as yellow fever, zika, chikungunya, and dengue have had serious impacts on public health. Concerns have been raised due to the rapid dissemination of the chikungunya virus across the country since its first detection in 2014 in Northeast Brazil. In this work, we carried out on-site training activities in genomic surveillance in partnership with the National Network of Public Health Laboratories that have led to the generation of 422 chikungunya virus genomes from 12 Brazilian states over the past two years (2021â2022), a period that has seen more than 312 thousand chikungunya fever cases reported in the country. These genomes increased the amount of available data and allowed a more comprehensive characterization of the dispersal dynamics of the chikungunya virus East-Central-South-African lineage in Brazil. Tree branching patterns revealed the emergence and expansion of two distinct subclades. Phylogeographic analysis indicated that the northeast region has been the leading hub of virus spread towards other regions. Increased frequency of Câ>âT transitions among the new genomes suggested that host restriction factors from the immune system such as ADAR and AID/APOBEC deaminases might be driving the genetic diversity of the chikungunya virus in Brazil
Genomic epidemiology reveals how restriction measures shaped the SARS-CoV-2 epidemic in Brazil
Abstract Brazil has experienced some of the highest numbers of COVID-19 infections and deaths globally and made Latin America a pandemic epicenter from May 2021. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of local virus transmission dynamics. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and an adjacent country - Paraguay. We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed, the absence of effective restriction measures led to the local emergence and international spread of Variants of Concern (VOC) and under monitoring (VUM), including the Gamma (P.1) and Zeta (P.2) variants. In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring and providing a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies
Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil
This work was supported by Decit, SCTIE, Brazilian
Ministry of Health, Conselho Nacional de Desenvolvimento CientĂfico - CNPq (440685/
2016-8, 440856/2016-7 and 421598/2018-2), Coordenação de Aperfeiçoamento de Pessoal de NĂvel Superior - CAPES - (88887.130716/2016-00), European Unionâs Horizon
2020 Research and Innovation Programme under ZIKAlliance Grant Agreement
(734548), STARBIOS (709517), Fundação de Amparo à Pesquisa do Estado do Rio de
Janeiro â FAPERJ (E-26/2002.930/2016), International Development Research Centre
(IDRC) Canada (108411-001), European Unionâs Horizon 2020 under grant agreements
ZIKACTION (734857) and ZIKAPLAN (734548).Fundação Ezequiel Dias. LaboratĂłrio Central de SaĂșde PĂșblica do Estado de Minas Gerais. Belo Horizonte, MG, Brazil / Latin American Genomic Surveillance Arboviral Network.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de FlavivĂrus. Rio de Janeiro, RJ, Brazil / Latin American Genomic Surveillance Arboviral Network.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de FlavivĂrus. Rio de Janeiro, RJ, Brazil Latin American Genomic Surveillance Arboviral Network.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de FlavivĂrus. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de FlavivĂrus. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Instituto LeĂŽnidas e Maria Deane. LaboratĂłrio de Ecologia de Doenças TransmissĂveis na AmazĂŽnia. Manaus, AM, Brazil.Secretaria de SaĂșde do Estado de Mato Grosso do Sul. LaboratĂłrio Central de SaĂșde PĂșblica. Campo Grande, MS, Brazil.Fundação Ezequiel Dias. LaboratĂłrio Central de SaĂșde PĂșblica do Estado de Minas Gerais. Belo Horizonte, MG, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica Dr. Giovanni Cysneiros. GoiĂąnia, GO, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica Professor Gonçalo Moniz. Salvador, BA, Brazil.Secretaria de SaĂșde do Estado da Bahia. Salvador, BA, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica Dr. Milton Bezerra Sobral. Recife, PE, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica do Estado de Mato Grosso. CuiabĂĄ, MT, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica do Distrito Federal. BrasĂlia, DF, Brazil.Fundação Ezequiel Dias. LaboratĂłrio Central de SaĂșde PĂșblica do Estado de Minas Gerais. Belo Horizonte, MG, Brazil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de FlavivĂrus. Rio de Janeiro, RJ, Brazil.MinistĂ©rio da SaĂșde. Secretaria de VigilĂąncia em SaĂșde. Coordenação Geral dos LaboratĂłrios de SaĂșde PĂșblica. BrasĂlia, DF, Brazil.MinistĂ©rio da SaĂșde. Secretaria de VigilĂąncia em SaĂșde. Coordenação Geral dos LaboratĂłrios de SaĂșde PĂșblica. BrasĂlia, DF, Brazil.Organização Pan-Americana da SaĂșde / Organização Mundial da SaĂșde. BrasĂlia, DF, Brazil.Organização Pan-Americana da SaĂșde / Organização Mundial da SaĂșde. BrasĂlia, DF, Brazil.Organização Pan-Americana da SaĂșde / Organização Mundial da SaĂșde. BrasĂlia, DF, Brazil.MinistĂ©rio da SaĂșde. Secretaria de VigilĂąncia em SaĂșde Coordenação Geral das Arboviroses. BrasĂlia, DF, Brazil.MinistĂ©rio da SaĂșde. Secretaria de VigilĂąncia em SaĂșde Coordenação Geral das Arboviroses. BrasĂlia, DF, Brazil.MinistĂ©rio da SaĂșde. Secretaria de VigilĂąncia em SaĂșde Coordenação Geral das Arboviroses. BrasĂlia, DF, Brazil.MinistĂ©rio da SaĂșde. Secretaria de VigilĂąncia em SaĂșde Coordenação Geral das Arboviroses. BrasĂlia, DF, Brazil.Fundação Hemocentro de RibeirĂŁo Preto. RibeirĂŁo Preto, SP, Brazil.Gorgas Memorial Institute for Health Studies. Panama, Panama.Universidade Federal da Bahia. VitĂłria da Conquista, BA, Brazil.Laboratorio Central de Salud PĂșblica. AsunciĂłn, Paraguay.Fundação Oswaldo Cruz. Bio-Manguinhos. Rio de Janeiro, RJ, Brazil.MinistĂ©rio da SaĂșde. Secretaria de VigilĂąncia em SaĂșde. Coordenação Geral dos LaboratĂłrios de SaĂșde PĂșblica. BrasĂlia, DF, Brazil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de FlavivĂrus. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de FlavivĂrus. Rio de Janeiro, RJ, BrazilFundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de FlavivĂrus. Rio de Janeiro, RJ, BrazilMinistĂ©rio da SaĂșde. Secretaria de VigilĂąncia em SaĂșde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de FlavivĂrus. Rio de Janeiro, RJ, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica do Estado de Mato Grosso do Sul. Campo Grande, MS, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica do Estado de Mato Grosso do Sul. Campo Grande, MS, Brazil.Instituto de Investigaciones en Ciencias de la Salud. San Lorenzo, Paraguay.Secretaria de Estado de SaĂșde de Mato Grosso do Sul. Campo Grande, MS, Brazil.Fundação Oswaldo Cruz. Campo Grande, MS, Brazil.Fundação Hemocentro de RibeirĂŁo Preto. RibeirĂŁo Preto, SP, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica Dr. Giovanni Cysneiros. GoiĂąnia, GO, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica Dr. Giovanni Cysneiros. GoiĂąnia, GO, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica Professor Gonçalo Moniz. Salvador, BA, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica Dr. Milton Bezerra Sobral. Recife, PE, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica do Distrito Federal. BrasĂlia, DF, Brazil.Secretaria de SaĂșde de Feira de Santana. Feira de Santana, Ba, Brazil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de FlavivĂrus. Rio de Janeiro, RJ, Brazil.Universidade Federal de Minas Gerais. Instituto de CiĂȘncias BiolĂłgicas. Belo Horizonte, MG, Brazil.Universidade Federal de Minas Gerais. Instituto de CiĂȘncias BiolĂłgicas. Belo Horizonte, MG, Brazil.Secretaria de SaĂșde do Estado de Minas Gerais. Belo Horizonte, MG, Brazil.Hospital das Forças Armadas. BrasĂlia, DF, Brazil.MinistĂ©rio da SaĂșde. Secretaria de VigilĂąncia em SaĂșde. BrasĂlia, DF, Brazil.MinistĂ©rio da SaĂșde. Secretaria de VigilĂąncia em SaĂșde. BrasĂlia, DF, Brazil.Universidade Nova de Lisboa. Instituto de Higiene e Medicina Tropical. Lisboa, Portugal.University of Sydney. School of Life and Environmental Sciences and School of Medical Sciences. Marie Bashir Institute for Infectious Diseases and Biosecurity. Sydney, NSW, Australia.University of KwaZulu-Natal. College of Health Sciences. KwaZulu-Natal Research Innovation and Sequencing Platform. Durban, South Africa.University of Oxford. Peter Medawar Building. Department of Zoology. Oxford, UK.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de FlavivĂrus. Rio de Janeiro, RJ, Brazil.Universidade Estadual de Feira de Santana. Salvador, BA, Brazil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, Brazil.Universidade de BrasĂlia. BrasĂlia, DF, Brazil.Universidade Salvador. Salvador, BA, Brazil.Fundação Ezequiel Dias. Belo Horizonte, MG, Brazil.Fundação Ezequiel Dias. Belo Horizonte, MG, Brazil.Fundação Ezequiel Dias. Belo Horizonte, MG, Brazil.Fundação Ezequiel Dias. Belo Horizonte, MG, Brazil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de FlavivĂrus. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de FlavivĂrus. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de FlavivĂrus. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de FlavivĂrus. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de FlavivĂrus. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de FlavivĂrus. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de FlavivĂrus. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de FlavivĂrus. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. LaboratĂłrio de Hantaviroses e Rickettsioses. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Instituto LeĂŽnidas e Maria Deane. LaboratĂłrio de Ecologia de Doenças TransmissĂveis na AmazĂŽnia. Manaus, AM, Brazil.Universidade Federal de Minas Gerais. Instituto de CiĂȘncias BiolĂłgicas. Belo Horizonte, MG, Brazil.Universidade Federal de Minas Gerais. Instituto de CiĂȘncias BiolĂłgicas. Belo Horizonte, MG, Brazil.Universidade Federal de Minas Gerais. Instituto de CiĂȘncias BiolĂłgicas. Belo Horizonte, MG, Brazil.Universidade Federal de Minas Gerais. Instituto de CiĂȘncias BiolĂłgicas. Belo Horizonte, MG, Brazil.Universidade Federal de Minas Gerais. Instituto de CiĂȘncias BiolĂłgicas. Belo Horizonte, MG, Brazil.Universidade Federal de Minas Gerais. Instituto de CiĂȘncias BiolĂłgicas. Belo Horizonte, MG, Brazil.Universidade Federal de Minas Gerais. Instituto de CiĂȘncias BiolĂłgicas. Belo Horizonte, MG, Brazil.Universidade Federal de Minas Gerais. Instituto de CiĂȘncias BiolĂłgicas. Belo Horizonte, MG, Brazil.Universidade Federal de Minas Gerais. Instituto de CiĂȘncias BiolĂłgicas. Belo Horizonte, MG, Brazil.Universidade Federal de Minas Gerais. Instituto de CiĂȘncias BiolĂłgicas. Belo Horizonte, MG, Brazil.Universidade Federal de Minas Gerais. Instituto de CiĂȘncias BiolĂłgicas. Belo Horizonte, MG, Brazil.Universidade Federal de Minas Gerais. Instituto de CiĂȘncias BiolĂłgicas. Belo Horizonte, MG, Brazil.Universidade Federal de Minas Gerais. Instituto de CiĂȘncias BiolĂłgicas. Belo Horizonte, MG, Brazil.Universidade Federal de Minas Gerais. Faculdade de Medicina VeterinĂĄria. Belo Horizonte, MG, Brazil.Universidade Federal de Minas Gerais. Faculdade de Medicina VeterinĂĄria. Belo Horizonte, MG, Brazil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, Brazil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, Brazil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica do Estado do ParanĂĄ. Curitiba, PR, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica do Estado de RondĂŽnia. Porto Velho, RO, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica do Estado do Amazonas. Manaus, AM, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica do Estado do Rio Grande do Norte. Natal, RN, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica do Estado de Mato Grosso. CuiabĂĄ, MT, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica Professor Gonçalo Moniz. Salvador, BA, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica Professor Gonçalo Moniz. Salvador, BA, Brazil.LaboratĂłrio Central de SaĂșde PĂșblica Noel Nutels. Rio de Janeiro, RJ, Brazil.Instituto Adolfo Lutz. SĂŁo Paulo, SP, Brazil.MinistĂ©rio da SaĂșde. Secretaria de VigilĂąncia em SaĂșde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.MinistĂ©rio da SaĂșde. Secretaria de VigilĂąncia em SaĂșde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.MinistĂ©rio da SaĂșde. Secretaria de VigilĂąncia em SaĂșde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.MinistĂ©rio da SaĂșde. Secretaria de VigilĂąncia em SaĂșde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Universidade de SĂŁo Paulo. Instituto de Medicina Tropical. SĂŁo Paulo, SP, Brazil.Universidade de SĂŁo Paulo. Instituto de Medicina Tropical. SĂŁo Paulo, SP, Brazil.Universidade de SĂŁo Paulo. Instituto de Medicina Tropical. SĂŁo Paulo, SP, Brazil.University of Oxford. Peter Medawar Building. Department of Zoology. Oxford, UK.Instituto Nacional de Enfermedades Virales Humanas Dr. Julio Maiztegui. Pergamino, Argentina.Gorgas Memorial Institute for Health Studies. Panama, Panama.Gorgas Memorial Institute for Health Studies. Panama, Panama.Gorgas Memorial Institute for Health Studies. Panama, Panama.Instituto de Salud PĂșblica de Chile. Santiago, Chile.Instituto de DiagnĂłstico y Referencia EpidemiolĂłgicos Dr. Manuel MartĂnez BĂĄez. Ciudad de MĂ©xico, MĂ©xico.Instituto Nacional de Enfermedades Infecciosas Dr Carlos G MalbrĂĄn. Buenos Aires, Argentina.Ministerio de Salud PĂșblica de Uruguay. Montevideo, Uruguay.Instituto Costarricense de InvestigaciĂłn y Enseñanza em NutriciĂłn y Salud. Tres RĂos, Costa Rica.Instituto Nacional de Investigacion en Salud Publica Dr Leopoldo Izquieta PĂ©rez. Guayaquil, Ecuador.Instituto Nacional de Investigacion en Salud Publica Dr Leopoldo Izquieta PĂ©rez. Guayaquil, Ecuador.Universidade Federal de Pernambuco. Recife, PE, Brazil.Secretaria de SaĂșde do Estado de Minas Gerais. Belo Horizonte. MG, Brazil.MinistĂ©rio da SaĂșde. Secretaria de VigilĂąncia em SaĂșde. BrasĂlia, DF, Brazil.MinistĂ©rio da SaĂșde. Secretaria de VigilĂąncia em SaĂșde. BrasĂlia, DF, Brazil.Universidade Federal do Rio de Janeiro. Rio de Janeiro, RJ, Brazil.Universidade Federal do Rio de Janeiro. Rio de Janeiro, RJ, Brazil.Universidade Federal do Rio de Janeiro. Rio de Janeiro, RJ, Brazil.Universidade Federal do Rio de Janeiro. Rio de Janeiro, RJ, Brazil.Universidade Federal de Ouro Preto. Ouro Preto, MG, Brazil.Universidade Federal de Ouro Preto. Ouro Preto, MG, Brazil.Universidade Federal de Ouro Preto. Ouro Preto, MG, Brazil.Universidade Federal de Ouro Preto. Ouro Preto, MG, Brazil.Fundação Hemocentro de RibeirĂŁo Preto. RibeirĂŁo Preto, SP, Brazil.Secretaria de SaĂșde de Feira de Santana. Feira de Santana, BA, Brazil.Universidade Federal de Minas Gerais. Instituto de CiĂȘncias BiolĂłgicas. Belo Horizonte, MG, Brazil.Brazil experienced a large dengue virus (DENV) epidemic in 2019, highlighting a continuous struggle with effective control and public health preparedness. Using Oxford Nanopore sequencing, we led field and classroom initiatives for the monitoring of DENV in Brazil, generating 227 novel genome sequences of DENV1-2 from 85 municipalities (2015â2019). This equated to an over 50% increase in the number of DENV genomes from Brazil available in public databases. Using both phylogenetic and epidemiological models we retrospectively reconstructed the recent transmission history of DENV1-2. Phylogenetic analysis revealed complex patterns of transmission, with both lineage co-circulation and replacement. We identified two lineages within the DENV2 BR-4 clade, for which we estimated the effective reproduction number and pattern of seasonality. Overall, the surveillance outputs and training initiative described here serve as a proof-of-concept for the utility of real-time portable sequencing for research and local capacity building in the genomic surveillance of emerging viruses
Open data from the first and second observing runs of Advanced LIGO and Advanced Virgo
Advanced LIGO and Advanced Virgo are monitoring the sky and collecting gravitational-wave strain data with sufficient sensitivity to detect signals routinely. In this paper we describe the data recorded by these instruments during their first and second observing runs. The main data products are gravitational-wave strain time series sampled at 16384 Hz. The datasets that include this strain measurement can be freely accessed through the Gravitational Wave Open Science Center at http://gw-openscience.org, together with data-quality information essential for the analysis of LIGO and Virgo data, documentation, tutorials, and supporting software
Search for intermediate-mass black hole binaries in the third observing run of Advanced LIGO and Advanced Virgo
International audienceIntermediate-mass black holes (IMBHs) span the approximate mass range 100â105âMâ, between black holes (BHs) that formed by stellar collapse and the supermassive BHs at the centers of galaxies. Mergers of IMBH binaries are the most energetic gravitational-wave sources accessible by the terrestrial detector network. Searches of the first two observing runs of Advanced LIGO and Advanced Virgo did not yield any significant IMBH binary signals. In the third observing run (O3), the increased network sensitivity enabled the detection of GW190521, a signal consistent with a binary merger of mass âŒ150âMâ providing direct evidence of IMBH formation. Here, we report on a dedicated search of O3 data for further IMBH binary mergers, combining both modeled (matched filter) and model-independent search methods. We find some marginal candidates, but none are sufficiently significant to indicate detection of further IMBH mergers. We quantify the sensitivity of the individual search methods and of the combined search using a suite of IMBH binary signals obtained via numerical relativity, including the effects of spins misaligned with the binary orbital axis, and present the resulting upper limits on astrophysical merger rates. Our most stringent limit is for equal mass and aligned spin BH binary of total mass 200âMâ and effective aligned spin 0.8 at 0.056 Gpcâ3 yrâ1 (90% confidence), a factor of 3.5 more constraining than previous LIGO-Virgo limits. We also update the estimated rate of mergers similar to GW190521 to 0.08 Gpcâ3 yrâ1.Key words: gravitational waves / stars: black holes / black hole physicsCorresponding author: W. Del Pozzo, e-mail: [email protected]â Deceased, August 2020