4 results on '"Loman, N"'
Search Results
2. Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 - 2018.
- Author
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Hill SC, de Souza R, Thézé J, Claro I, Aguiar RS, Abade L, Santos FCP, Cunha MS, Nogueira JS, Salles FCS, Rocco IM, Maeda AY, Vasami FGS, du Plessis L, Silveira PP, de Jesus JG, Quick J, Fernandes NCCA, Guerra JM, Réssio RA, Giovanetti M, Alcantara LCJ, Cirqueira CS, Díaz-Delgado J, Macedo FLL, Timenetsky MDCST, de Paula R, Spinola R, Telles de Deus J, Mucci LF, Tubaki RM, de Menezes RMT, Ramos PL, de Abreu AL, Cruz LN, Loman N, Dellicour S, Pybus OG, Sabino EC, and Faria NR
- Subjects
- Animals, Brazil epidemiology, Disease Outbreaks, Genomics, Humans, Phylogeny, Phylogeography, Primate Diseases epidemiology, Primate Diseases transmission, Primates virology, Yellow Fever epidemiology, Yellow Fever transmission, Yellow fever virus classification, Yellow fever virus isolation & purification, Zoonoses epidemiology, Zoonoses transmission, Genome, Viral, Primate Diseases virology, Yellow Fever veterinary, Yellow Fever virology, Yellow fever virus genetics, Zoonoses virology
- Abstract
São Paulo, a densely inhabited state in southeast Brazil that contains the fourth most populated city in the world, recently experienced its largest yellow fever virus (YFV) outbreak in decades. YFV does not normally circulate extensively in São Paulo, so most people were unvaccinated when the outbreak began. Surveillance in non-human primates (NHPs) is important for determining the magnitude and geographic extent of an epizootic, thereby helping to evaluate the risk of YFV spillover to humans. Data from infected NHPs can give more accurate insights into YFV spread than when using data from human cases alone. To contextualise human cases, identify epizootic foci and uncover the rate and direction of YFV spread in São Paulo, we generated and analysed virus genomic data and epizootic case data from NHPs in São Paulo. We report the occurrence of three spatiotemporally distinct phases of the outbreak in São Paulo prior to February 2018. We generated 51 new virus genomes from YFV positive cases identified in 23 different municipalities in São Paulo, mostly sampled from NHPs between October 2016 and January 2018. Although we observe substantial heterogeneity in lineage dispersal velocities between phylogenetic branches, continuous phylogeographic analyses of generated YFV genomes suggest that YFV lineages spread in São Paulo at a mean rate of approximately 1km per day during all phases of the outbreak. Viral lineages from the first epizootic phase in northern São Paulo subsequently dispersed towards the south of the state to cause the second and third epizootic phases there. This alters our understanding of how YFV was introduced into the densely populated south of São Paulo state. Our results shed light on the sylvatic transmission of YFV in highly fragmented forested regions in São Paulo state and highlight the importance of continued surveillance of zoonotic pathogens in sentinel species., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2020
- Full Text
- View/download PDF
3. Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region.
- Author
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Giovanetti M, Faria NR, Lourenço J, Goes de Jesus J, Xavier J, Claro IM, Kraemer MUG, Fonseca V, Dellicour S, Thézé J, da Silva Salles F, Gräf T, Silveira PP, do Nascimento VA, Costa de Souza V, de Melo Iani FC, Castilho-Martins EA, Cruz LN, Wallau G, Fabri A, Levy F, Quick J, de Azevedo V, Aguiar RS, de Oliveira T, Bôtto de Menezes C, da Costa Castilho M, Terra TM, Souza da Silva M, Bispo de Filippis AM, Luiz de Abreu A, Oliveira WK, Croda J, Campelo de Albuquerque CF, Nunes MRT, Sabino EC, Loman N, Naveca FG, Pybus OG, and Alcantara LC
- Subjects
- Brazil epidemiology, Epidemiological Monitoring, Female, Genomics methods, Humans, Male, Zika Virus Infection epidemiology, Zika Virus genetics, Zika Virus Infection virology
- Abstract
Zika virus (ZIKV) has caused an explosive epidemic linked to severe clinical outcomes in the Americas. As of June 2018, 4,929 ZIKV suspected infections and 46 congenital syndrome cases had been reported in Manaus, Amazonas, Brazil. Although Manaus is a key demographic hub in the Amazon region, little is known about the ZIKV epidemic there, in terms of both transmission and viral genetic diversity. Using portable virus genome sequencing, we generated 59 ZIKV genomes in Manaus. Phylogenetic analyses indicated multiple introductions of ZIKV from northeastern Brazil to Manaus. Spatial genomic analysis of virus movement among six areas in Manaus suggested that populous northern neighborhoods acted as sources of virus transmission to other neighborhoods. Our study revealed how the ZIKV epidemic was ignited and maintained within the largest urban metropolis in the Amazon. These results might contribute to improving the public health response to outbreaks in Brazil., Competing Interests: Declaration of Interests The authors declare no competing interests., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
4. Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon.
- Author
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Naveca FG, Claro I, Giovanetti M, de Jesus JG, Xavier J, Iani FCM, do Nascimento VA, de Souza VC, Silveira PP, Lourenço J, Santillana M, Kraemer MUG, Quick J, Hill SC, Thézé J, Carvalho RDO, Azevedo V, Salles FCDS, Nunes MRT, Lemos PDS, Candido DDS, Pereira GC, Oliveira MAA, Meneses CAR, Maito RM, Cunha CRSB, Campos DPS, Castilho MDC, Siqueira TCDS, Terra TM, de Albuquerque CFC, da Cruz LN, Abreu AL, Martins DV, Simoes DSMV, Aguiar RS, Luz SLB, Loman N, Pybus OG, Sabino EC, Okumoto O, Alcantara LCJ, and Faria NR
- Subjects
- Animals, Brazil epidemiology, Chikungunya Fever transmission, Chikungunya Fever virology, Chikungunya virus isolation & purification, Epidemiological Monitoring, Humans, Phylogeny, Whole Genome Sequencing, Zoonoses transmission, Zoonoses virology, Chikungunya Fever epidemiology, Chikungunya virus genetics, Disease Outbreaks prevention & control, Genome, Viral genetics, Zoonoses epidemiology
- Abstract
Background: Since its first detection in the Caribbean in late 2013, chikungunya virus (CHIKV) has affected 51 countries in the Americas. The CHIKV epidemic in the Americas was caused by the CHIKV-Asian genotype. In August 2014, local transmission of the CHIKV-Asian genotype was detected in the Brazilian Amazon region. However, a distinct lineage, the CHIKV-East-Central-South-America (ECSA)-genotype, was detected nearly simultaneously in Feira de Santana, Bahia state, northeast Brazil. The genomic diversity and the dynamics of CHIKV in the Brazilian Amazon region remains poorly understood despite its importance to better understand the epidemiological spread and public health impact of CHIKV in the country., Methodology/principal Findings: We report a large CHIKV outbreak (5,928 notified cases between August 2014 and August 2018) in Boa vista municipality, capital city of Roraima's state, located in the Brazilian Amazon region. We generated 20 novel CHIKV-ECSA genomes from the Brazilian Amazon region using MinION portable genome sequencing. Phylogenetic analyses revealed that despite an early introduction of the Asian genotype in 2015 in Roraima, the large CHIKV outbreak in 2017 in Boa Vista was caused by an ECSA-lineage most likely introduced from northeastern Brazil. Epidemiological analyses suggest a basic reproductive number of R0 of 1.66, which translates in an estimated 39 (95% CI: 36 to 45) % of Roraima's population infected with CHIKV-ECSA. Finally, we find a strong association between Google search activity and the local laboratory-confirmed CHIKV cases in Roraima., Conclusions/significance: This study highlights the potential of combining traditional surveillance with portable genome sequencing technologies and digital epidemiology to inform public health surveillance in the Amazon region. Our data reveal a large CHIKV-ECSA outbreak in Boa Vista, limited potential for future CHIKV outbreaks, and indicate a replacement of the Asian genotype by the ECSA genotype in the Amazon region., Competing Interests: The authors declare no competing interests.
- Published
- 2019
- Full Text
- View/download PDF
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