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Prado AF, Prist PR, Mucci LF, de Freitas PD. Ecological Requirements for Abundance and Dispersion of Brazilian Yellow Fever Vectors in Tropical Areas. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2024; 21:609. [PMID: 38791823 PMCID: PMC11120827 DOI: 10.3390/ijerph21050609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/01/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024]
Abstract
In the Americas, wild yellow fever (WYF) is an infectious disease that is highly lethal for some non-human primate species and non-vaccinated people. Specifically, in the Brazilian Atlantic Forest, Haemagogus leucocelaenus and Haemagogus janthinomys mosquitoes act as the major vectors. Despite transmission risk being related to vector densities, little is known about how landscape structure affects vector abundance and movement. To fill these gaps, we used vector abundance data and a model-selection approach to assess how landscape structure affects vector abundance, aiming to identify connecting elements for virus dispersion in the state of São Paulo, Brazil. Our findings show that Hg. leucocelaenus and Hg. janthinomys abundances, in highly degraded and fragmented landscapes, are mainly affected by increases in forest cover at scales of 2.0 and 2.5 km, respectively. Fragmented landscapes provide ecological corridors for vector dispersion, which, along with high vector abundance, promotes the creation of risk areas for WYF virus spread, especially along the border with Minas Gerais state, the upper edges of the Serra do Mar, in the Serra da Cantareira, and in areas of the metropolitan regions of São Paulo and Campinas.
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Affiliation(s)
- Amanda Francisco Prado
- Department of Genetics and Evolution, Center for Biological and Health Sciences, Federal University of São Carlos, Rodovia Washington Luis km 235, São Carlos 13565-905, SP, Brazil;
| | | | - Luis Filipe Mucci
- Taubaté Regional Lab., State Department of Health of São Paulo, Instituto Pasteur, Pça. Coronel Vitoriano, 23, Taubate 12020-020, SP, Brazil;
| | - Patrícia Domingues de Freitas
- Department of Genetics and Evolution, Center for Biological and Health Sciences, Federal University of São Carlos, Rodovia Washington Luis km 235, São Carlos 13565-905, SP, Brazil;
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Fernandes NCCDA, Cunha MS, Suarez PEN, Machado EF, Garcia JM, De Carvalho ACSR, Figueiredo KB, Ressio RA, Matsumoto PSS, Saad LDC, de Jesus IP, de Carvalho J, Ferreira CSDS, Spínola RMF, Maeda AY, Guerra JM. Phylogenetic analysis reveals a new introduction of Yellow Fever virus in São Paulo State, Brazil, 2023. Acta Trop 2024; 251:107110. [PMID: 38163515 DOI: 10.1016/j.actatropica.2023.107110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/27/2023] [Accepted: 12/24/2023] [Indexed: 01/03/2024]
Abstract
Yellow Fever (YF) is a viral arbovirosis of Public Health importance. In Brazil, surveillance is focused mainly on detecting epizootic events of Platyrrhini. Herein, we compared the detection and phylogenetic analysis of YF virus in two neotropical primates (NTP), a Callithrix detected in the previous epidemic period (2016-2020), and a Callicebus nigrifons, showing a new introduction of YF in 2023. This paper illustrates the importance of joint actions of laboratory and field teams to ensure quick response to Public Health emergencies, such as the intensification of vaccination of susceptible human populations.
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Affiliation(s)
| | | | | | - Eduardo Ferreira Machado
- Centro de Patologia, Instituto Adolfo Lutz, São Paulo, São Paulo, SP, Brazil; Laboratório de Patologia Comparada de Animais Selvagens (LAPCOM), Departamento de Patologia, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | | | | | | | | | - Julia de Carvalho
- Centro de Patologia, Instituto Adolfo Lutz, São Paulo, São Paulo, SP, Brazil
| | | | | | | | - Juliana Mariotti Guerra
- Centro de Patologia, Instituto Adolfo Lutz, São Paulo, São Paulo, SP, Brazil; Laboratório de Patologia Comparada de Animais Selvagens (LAPCOM), Departamento de Patologia, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
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3
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Dias JS, Beltrão-Mendes R, Bezerra TL, La Corte R. Parasites and Viruses in Callithrix in Brazil. Acta Parasitol 2024; 69:152-163. [PMID: 38184509 DOI: 10.1007/s11686-023-00766-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 11/22/2023] [Indexed: 01/08/2024]
Abstract
PURPOSE As a result of environmental imbalances of anthropogenic origin, the potential for transmission of parasites and viruses between different primates, including humans, might increase. Thus, parasitic studies have great relevance to primatology, which motivated us to conduct a literature review to synthesize the information available in American primates of the Callithrix genus. METHODS We carried out the bibliographic search on the main groups of parasites (protozoa, helminths, arthropods, ectoparasites) and viruses found in Callithrix in Brazil in search platforms and consider all manuscript that appeared in search engines, published between the years 1910 and December 2022. In each selected article, the following information was recorded: the host species; parasite taxa; scientific classification of the parasite; host habitat (free-living, captive); diagnostic technique; state; and bibliographic reference. Data were tabulated and arranged in a parasite-host table. RESULTS Some endemic genera, such as Callithrix, are widely distributed geographically across Brazil and have characteristics of adaptation to different habitats due to their flexibility in diet and behavior. These factors can make them subject to a greater diversity of parasites and viruses in the country. Here, we identified 68 parasitic taxa, belonging to the clades protozoa (n = 22), helminths (n = 34), ectoparasites (n = 7), and viruses (n = 5). Out of this total, 19 have zoonotic potential. Of the six existing marmoset species, Callithrix jacchus was the most frequent in studies, and Callithrix flaviceps did not have reports. All regions of the country had occurrences, mainly the Southeast, where 54% of the cases were reported. In 46% of the reported parasites and viruses, it was not possible to identify the corresponding species. CONCLUSION We conclude that in part of the works the identification methods are not being specific, which makes it difficult to identify the species that affects Callithrix spp. Furthermore, the studies present geographic disparities, being concentrated in the southeast of the country, making it impossible to have a more uniform analysis of the findings. Thus, it is observed that information about parasites and viruses is incipient in the genus Callithrix in Brazil.
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Affiliation(s)
- Jéssica Souza Dias
- Programa de Pós-Graduação em Biologia Parasitária, Universidade Federal de Sergipe, São Cristóvão, Sergipe, Brazil.
- Laboratory of Tropical Entomology and Parasitology, Federal University of Sergipe, Avenue Marechal Rondon, S/N, Jardim Rosa Elze, São Cristóvão, Sergipe, 49100-000, Brazil.
| | - Raone Beltrão-Mendes
- Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal de Sergipe, São Cristóvão, SE, Brazil
| | - Taynar Lima Bezerra
- Programa de Pós-Graduação em Ciência Animal nos Trópicos, Universidade Federal da Bahia, Salvador, BA, Brazil
| | - Roseli La Corte
- Programa de Pós-Graduação em Biologia Parasitária, Universidade Federal de Sergipe, São Cristóvão, Sergipe, Brazil
- Departamento de Morfologia, Universidade Federal de Sergipe, São Cristóvão, SE, Brazil
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de Carvalho Marques B, Sacchetto L, Banho CA, Estofolete CF, Dourado FS, da Silva Cândido D, Dutra KR, da Silva Salles FC, de Jesus JG, Sabino EC, Faria NR, Nogueira ML. Genetic differences of dengue virus 2 in patients with distinct clinical outcome. Braz J Microbiol 2023; 54:1411-1419. [PMID: 37178262 PMCID: PMC10485208 DOI: 10.1007/s42770-023-01006-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
The genetic diversity of the dengue virus is characterized by four circulating serotypes, several genotypes, and an increasing number of existing lineages that may have differences in the potential to cause epidemics and disease severity. Accurate identification of the genetic variability of the virus is essential to identify lineages responsible for an epidemic and understanding the processes of virus spread and virulence. Here, we characterize, using portable nanopore genomic sequencing, different lineages of dengue virus 2 (DENV-2) detected in 22 serum samples from patients with and without dengue warning signs attended at Hospital de Base of São José do Rio Preto (SJRP) in 2019, during a DENV-2 outbreak. Demographic, epidemiological, and clinical data were also analyzed. The phylogenetic reconstruction and the clinical data showed that two lineages belonging to the American/Asian genotype of DENV-2-BR3 and BR4 (BR4L1 and BR4L2)-were co-circulating in SJRP. Although preliminary, these results indicate no specific association between clinical form and phylogenetic clustering at the virus consensus sequence level. Studies with larger sample sizes and which explore single nucleotide variants are needed. Therefore, we showed that portable nanopore genome sequencing could generate quick and reliable sequences for genomic surveillance to monitor viral diversity and its association with disease severity as an epidemic unfolds.
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Affiliation(s)
- Beatriz de Carvalho Marques
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | - Lívia Sacchetto
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | - Cecília Artico Banho
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | - Cássia Fernanda Estofolete
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | - Fernanda Simões Dourado
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | | | - Karina Rocha Dutra
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | | | - Jaqueline Góes de Jesus
- Instituto de Medicina Tropical da Faculdade de Medicina - Universidade de São Paulo, São Paulo, Brazil
| | - Ester Cerdeira Sabino
- Instituto de Medicina Tropical da Faculdade de Medicina - Universidade de São Paulo, São Paulo, Brazil
| | - Nuno Rodrigues Faria
- Department of Zoology, University of Oxford, Oxford, UK
- Instituto de Medicina Tropical da Faculdade de Medicina - Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil.
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA.
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Urban L, Perlas A, Francino O, Martí‐Carreras J, Muga BA, Mwangi JW, Boykin Okalebo L, Stanton JL, Black A, Waipara N, Fontsere C, Eccles D, Urel H, Reska T, Morales HE, Palmada‐Flores M, Marques‐Bonet T, Watsa M, Libke Z, Erkenswick G, van Oosterhout C. Real-time genomics for One Health. Mol Syst Biol 2023; 19:e11686. [PMID: 37325891 PMCID: PMC10407731 DOI: 10.15252/msb.202311686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to our future relationship with our planet. While the concept of One Health describes how human health is inextricably linked with environmental health, many of these complex interdependencies are still not well-understood. Here, we describe how the advent of real-time genomic analyses can benefit One Health and how it can enable timely, in-depth ecosystem health assessments. We introduce nanopore sequencing as the only disruptive technology that currently allows for real-time genomic analyses and that is already being used worldwide to improve the accessibility and versatility of genomic sequencing. We showcase real-time genomic studies on zoonotic disease, food security, environmental microbiome, emerging pathogens, and their antimicrobial resistances, and on environmental health itself - from genomic resource creation for wildlife conservation to the monitoring of biodiversity, invasive species, and wildlife trafficking. We stress why equitable access to real-time genomics in the context of One Health will be paramount and discuss related practical, legal, and ethical limitations.
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Affiliation(s)
- Lara Urban
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Albert Perlas
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
| | - Olga Francino
- Nano1Health SL, Parc de Recerca UABCampus Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Joan Martí‐Carreras
- Nano1Health SL, Parc de Recerca UABCampus Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Brenda A Muga
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
| | | | | | | | - Amanda Black
- Bioprotection AotearoaLincoln UniversityLincolnNew Zealand
| | | | - Claudia Fontsere
- Center for Evolutionary HologenomicsThe Globe Institute, University of CopenhagenCopenhagenDenmark
| | - David Eccles
- Hugh Green Cytometry CentreMalaghan Institute of Medical ResearchWellingtonNew Zealand
| | - Harika Urel
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Tim Reska
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Hernán E Morales
- Center for Evolutionary HologenomicsThe Globe Institute, University of CopenhagenCopenhagenDenmark
- Department of Biology, Ecology BuildingLund UniversityLundSweden
| | - Marc Palmada‐Flores
- Institute of Evolutionary BiologyUniversitat Pompeu Fabra‐CSIC, PRBBBarcelonaSpain
| | - Tomas Marques‐Bonet
- Institute of Evolutionary BiologyUniversitat Pompeu Fabra‐CSIC, PRBBBarcelonaSpain
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
- CNAGCentre of Genomic AnalysisBarcelonaSpain
- Institut Català de Paleontologia Miquel CrusafontUniversitat Autònoma de BarcelonaBarcelonaSpain
| | | | - Zane Libke
- Instituto Nacional de BiodiversidadQuitoEcuador
- Fundación Sumak Kawsay In SituCantón MeraEcuador
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Wilk-da-Silva R, Prist PR, Medeiros-Sousa AR, Laporta GZ, Mucci LF, Marrelli MT. The role of forest fragmentation in yellow fever virus dispersal. Acta Trop 2023:106983. [PMID: 37419378 DOI: 10.1016/j.actatropica.2023.106983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/26/2023] [Accepted: 07/04/2023] [Indexed: 07/09/2023]
Abstract
The intense process of deforestation in tropical forests poses serious challenges for the survival of biodiversity, as well as for the human species itself. This scenario is supported by the increase in the incidence of epidemics of zoonotic origin observed over the last few decades. In the specific case of sylvatic yellow fever (YF), it has already been shown that an increase in the transmission risk of the causative agent (yellow fever virus - YFV) is associated with areas with a high degree of forest fragmentation, which can facilitate the spread of the virus. In this study we tested the hypothesis that areas with more fragmented landscapes and a higher edge density (ED) but a high degree of connectivity between forest patches favor YFV spread. To this end, we used YF epizootics in non-human primates (NHPs) in the state of São Paulo to build direct networks, and used a multi-selection approach to analyze which landscape features could facilitate YFV spread. Our results showed that municipalities with the potential to spread the virus exhibited a higher amount of forest edge. Additionally, the models with greater empirical support showed a strong association between forest edge density and the risk of occurrence of epizootic diseases, as well as the need for a minimum threshold of native vegetation cover to restrict their transmission. These findings corroborate our hypothesis that more fragmented landscapes with a higher degree of connectivity favor the spread of YFV, while landscapes with fewer connections tend to act as dead zones for the circulation of the virus.
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Affiliation(s)
- Ramon Wilk-da-Silva
- Institute of Tropical Medicine, University of São Paulo, Av. Dr. Eneas Carvalho de Aguiar 470, São Paulo, SP, Brazil.
| | | | - Antônio Ralph Medeiros-Sousa
- Department of Epidemiology, School of Public Health, University of São Paulo, Av. Dr. Arnaldo 715, São Paulo, SP, Brazil
| | - Gabriel Zorello Laporta
- Graduate Studies, Research and Innovation Center, FMABC University Center, ABC Foundation, Av. Laure Gomes, 2000, Santo André, SP, Brazil
| | - Luis Filipe Mucci
- Institute Pasteur, São Paulo State Department of Health, PA. Cal. Victorian 23, Taubaté, SP, Brazil
| | - Mauro Toledo Marrelli
- Institute of Tropical Medicine, University of São Paulo, Av. Dr. Eneas Carvalho de Aguiar 470, São Paulo, SP, Brazil; Department of Epidemiology, School of Public Health, University of São Paulo, Av. Dr. Arnaldo 715, São Paulo, SP, Brazil
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7
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Silva NIO, Albery GF, Arruda MS, Oliveira GFG, Costa TA, de Mello ÉM, Moreira GD, Reis EV, da Silva SA, Silva MC, de Almeida MG, Becker DJ, Carlson CJ, Vasilakis N, Hanley KA, Drumond BP. Ecological drivers of sustained enzootic yellow fever virus transmission in Brazil, 2017-2021. PLoS Negl Trop Dis 2023; 17:e0011407. [PMID: 37276217 PMCID: PMC10270639 DOI: 10.1371/journal.pntd.0011407] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 06/15/2023] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
Beginning December 2016, sylvatic yellow fever (YF) outbreaks spread into southeastern Brazil, and Minas Gerais state experienced two sylvatic YF waves (2017 and 2018). Following these massive YF waves, we screened 187 free-living non-human primate (NHPs) carcasses collected throughout the state between January 2019 and June 2021 for YF virus (YFV) using RTqPCR. One sample belonging to a Callithrix, collected in June 2020, was positive for YFV. The viral strain belonged to the same lineage associated with 2017-2018 outbreaks, showing the continued enzootic circulation of YFV in the state. Next, using data from 781 NHPs carcasses collected in 2017-18, we used generalized additive mixed models (GAMMs) to identify the spatiotemporal and host-level drivers of YFV infection and intensity (an estimation of genomic viral load in the liver of infected NHP). Our GAMMs explained 65% and 68% of variation in virus infection and intensity, respectively, and uncovered strong temporal and spatial patterns for YFV infection and intensity. NHP infection was higher in the eastern part of Minas Gerais state, where 2017-2018 outbreaks affecting humans and NHPs were concentrated. The odds of YFV infection were significantly lower in NHPs from urban areas than from urban-rural or rural areas, while infection intensity was significantly lower in NHPs from urban areas or the urban-rural interface relative to rural areas. Both YFV infection and intensity were higher during the warm/rainy season compared to the cold/dry season. The higher YFV intensity in NHPs in warm/rainy periods could be a result of higher exposure to vectors and/or higher virus titers in vectors during this time resulting in the delivery of a higher virus dose and higher viral replication levels within NHPs. Further studies are needed to better test this hypothesis and further compare the dynamics of YFV enzootic cycles between different seasons.
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Affiliation(s)
| | - Gregory F. Albery
- Department of Biology, Georgetown University, Washington, DC, United States of America
| | - Matheus Soares Arruda
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Thaís Alkifeles Costa
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Érica Munhoz de Mello
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Laboratório de Zoonoses—Centro de Controle de Zoonoses, Prefeitura de Belo Horizonte, Belo Horizonte, Minas Gerais, Brazil
| | - Gabriel Dias Moreira
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Erik Vinícius Reis
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Simone Agostinho da Silva
- Laboratório de Zoonoses—Centro de Controle de Zoonoses, Prefeitura de Belo Horizonte, Belo Horizonte, Minas Gerais, Brazil
| | - Marlise Costa Silva
- Laboratório de Zoonoses—Centro de Controle de Zoonoses, Prefeitura de Belo Horizonte, Belo Horizonte, Minas Gerais, Brazil
| | - Munique Guimarães de Almeida
- Laboratório de Zoonoses—Centro de Controle de Zoonoses, Prefeitura de Belo Horizonte, Belo Horizonte, Minas Gerais, Brazil
| | - Daniel J. Becker
- Department of Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Colin J. Carlson
- Department of Biology, Georgetown University, Washington, DC, United States of America
- Center for Global Health Science and Security, Georgetown University, Washington, D.C., United States of America
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Vector-Borne and Zoonotic Diseases, The University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kathryn A. Hanley
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Betânia Paiva Drumond
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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de Oliveira CH, Andrade MS, Campos FS, da C. Cardoso J, Gonçalves-dos-Santos ME, Oliveira RS, Aquino-Teixeira SM, Campos AAS, Almeida MAB, Simonini-Teixeira D, da P. Sevá A, Temponi AOD, Magalhães FM, da Silva Menezes AS, Lopes BT, Almeida HP, Pedroso AL, Gonçalves GP, Chaves DCC, de Menezes GG, Bernal-Valle S, Müller NFD, Janssen L, dos Santos E, Mares-Guia MA, Albuquerque GR, Romano APM, Franco AC, Ribeiro BM, Roehe PM, Lourenço-de-Oliveira R, de Abreu FVS. Yellow Fever Virus Maintained by Sabethes Mosquitoes during the Dry Season in Cerrado, a Semiarid Region of Brazil, in 2021. Viruses 2023; 15:757. [PMID: 36992466 PMCID: PMC10058068 DOI: 10.3390/v15030757] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
In recent decades, waves of yellow fever virus (YFV) from the Amazon Rainforest have spread and caused outbreaks in other regions of Brazil, including the Cerrado, a savannah-like biome through which YFV usually moves before arriving at the Atlantic Forest. To identify the vectors involved in the maintenance of the virus in semiarid environments, an entomological survey was conducted after confirmation of yellow fever (YF) epizootics at the peak of the dry season in the Cerrado areas of the state of Minas Gerais. In total, 917 mosquitoes from 13 taxa were collected and tested for the presence of YFV. Interestingly, mosquitoes of the Sabethes genus represented 95% of the diurnal captured specimens, displaying a peak of biting activity never previously recorded, between 4:30 and 5:30 p.m. Molecular analysis identified three YFV-positive pools, two from Sabethes chloropterus-from which near-complete genomes were generated-and one from Sa. albiprivus, whose low viral load prevented sequencing. Sa. chloropterus was considered the primary vector due to the high number of copies of YFV RNA and the high relative abundance detected. Its bionomic characteristics allow its survival in dry places and dry time periods. For the first time in Brazil, Sa. albiprivus was found to be naturally infected with YFV and may have played a role as a secondary vector. Despite its high relative abundance, fewer copies of viral RNA were found, as well as a lower Minimum Infection Rate (MIR). Genomic and phylogeographic analysis showed that the virus clustered in the sub-lineage YFVPA-MG, which circulated in Pará in 2017 and then spread into other regions of the country. The results reported here contribute to the understanding of the epidemiology and mechanisms of YFV dispersion and maintenance, especially in adverse weather conditions. The intense viral circulation, even outside the seasonal period, increases the importance of surveillance and YFV vaccination to protect human populations in affected areas.
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Affiliation(s)
- Cirilo H. de Oliveira
- Insect Behavior Laboratory, Federal Institute of Northern Minas Gerais, Salinas 39560-000, MG, Brazil
| | - Miguel S. Andrade
- Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, DF, Brazil
- Department of Molecular Biology, Sabin Diagnóstico e Saúde, Brasília 70632-340, DF, Brazil
| | - Fabrício S. Campos
- Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi 77410-570, TO, Brazil
- Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, RS, Brazil
| | - Jader da C. Cardoso
- State Center of Health Surveillance, Rio Grande do Sul State Health Department, Porto Alegre 90610-000, RS, Brazil
| | | | - Ramon Silva Oliveira
- Insect Behavior Laboratory, Federal Institute of Northern Minas Gerais, Salinas 39560-000, MG, Brazil
| | | | - Aline AS Campos
- State Center of Health Surveillance, Rio Grande do Sul State Health Department, Porto Alegre 90610-000, RS, Brazil
| | - Marco AB Almeida
- Pan American Health Organization, World Health Organization Office in Brazil, Brasília 70800-400, DF, Brazil
| | - Danilo Simonini-Teixeira
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil
| | - Anaiá da P. Sevá
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil
| | - Andrea Oliveira Dias Temponi
- Health Department of the State of Minas Gerais, State Coordination for Arbovirus Surveillance, Belo Horizonte 31630-901, MG, Brazil
| | - Fernando Maria Magalhães
- Health Department of the State of Minas Gerais, State Coordination for Arbovirus Surveillance, Belo Horizonte 31630-901, MG, Brazil
| | - Agna Soares da Silva Menezes
- Health Department of the State of Minas Gerais, State Coordination for Arbovirus Surveillance, Belo Horizonte 31630-901, MG, Brazil
| | - Bartolomeu Teixeira Lopes
- Health Department of the State of Minas Gerais, State Coordination for Arbovirus Surveillance, Belo Horizonte 31630-901, MG, Brazil
| | - Hermes P. Almeida
- Health Department of the State of Minas Gerais, State Coordination for Arbovirus Surveillance, Belo Horizonte 31630-901, MG, Brazil
| | - Ana Lúcia Pedroso
- Health Department of the State of Minas Gerais, State Coordination for Arbovirus Surveillance, Belo Horizonte 31630-901, MG, Brazil
| | - Giovani Pontel Gonçalves
- Health Department of the State of Minas Gerais, State Coordination for Arbovirus Surveillance, Belo Horizonte 31630-901, MG, Brazil
| | - Danielle Costa Capistrano Chaves
- Health Department of the State of Minas Gerais, State Coordination for Arbovirus Surveillance, Belo Horizonte 31630-901, MG, Brazil
| | - Givaldo Gomes de Menezes
- Health Department of the State of Minas Gerais, State Coordination for Arbovirus Surveillance, Belo Horizonte 31630-901, MG, Brazil
| | - Sofía Bernal-Valle
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil
| | - Nicolas FD Müller
- Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, RS, Brazil
| | - Luis Janssen
- Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, DF, Brazil
| | - Edmilson dos Santos
- State Center of Health Surveillance, Rio Grande do Sul State Health Department, Porto Alegre 90610-000, RS, Brazil
| | - Maria A. Mares-Guia
- Flavivirus Laboratory, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
| | - George R. Albuquerque
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil
| | - Alessandro PM Romano
- General Coordination of Arbovirus Surveillance, Ministry of Health, Brasília 70058-900, DF, Brazil
| | - Ana C. Franco
- Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, RS, Brazil
| | - Bergmann M. Ribeiro
- Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, DF, Brazil
| | - Paulo M. Roehe
- Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, RS, Brazil
| | - Ricardo Lourenço-de-Oliveira
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
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9
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Kipp EJ, Lindsey LL, Milstein MS, Blanco CM, Baker JP, Faulk C, Oliver JD, Larsen PA. Nanopore adaptive sampling for targeted mitochondrial genome sequencing and bloodmeal identification in hematophagous insects. Parasit Vectors 2023; 16:68. [PMID: 36788607 PMCID: PMC9930342 DOI: 10.1186/s13071-023-05679-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/19/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND Blood-feeding insects are important vectors for an array of zoonotic pathogens. While previous efforts toward generating molecular resources have largely focused on major vectors of global medical and veterinary importance, molecular data across a large number of hematophagous insect taxa remain limited. Advancements in long-read sequencing technologies and associated bioinformatic pipelines provide new opportunities for targeted sequencing of insect mitochondrial (mt) genomes. For engorged hematophagous insects, such technologies can be leveraged for both insect mitogenome genome assembly and identification of vertebrate blood-meal sources. METHODS We used nanopore adaptive sampling (NAS) to sequence genomic DNA from four species of field-collected, blood-engorged mosquitoes (Aedes and Culex spp.) and one deer fly (Chrysops sp.). NAS was used for bioinformatical enrichment of mtDNA reads of hematophagous insects and potential vertebrate blood-meal hosts using publically available mt genomes as references. We also performed an experimental control to compare results of traditional non-NAS nanopore sequencing to the mt genome enrichment by the NAS method. RESULTS Complete mitogenomes were assembled and annotated for all five species sequenced with NAS: Aedes trivittatus, Aedes vexans, Culex restuans, Culex territans and the deer fly, Chrysops niger. In comparison to data generated during our non-NAS control experiment, NAS yielded a substantially higher proportion of reference-mapped mtDNA reads, greatly streamlining downstream mitogenome assembly and annotation. The NAS-assembled mitogenomes ranged in length from 15,582 to 16,045 bp, contained between 78.1% and 79.0% A + T content and shared the anticipated arrangement of 13 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs. Maximum likelihood phylogenies were generated to further characterize each insect species. Additionally, vertebrate blood-meal analysis was successful in three samples sequenced, with mtDNA-based phylogenetic analyses revealing that blood-meal sources for Chrysops niger, Culex restuans and Aedes trivittatus were human, house sparrow (Passer domesticus) and eastern cottontail rabbit (Sylvilagus floridanus), respectively. CONCLUSIONS Our findings show that NAS has dual utility to simultaneously molecularly identify hematophagous insects and their blood-meal hosts. Moreover, our data indicate NAS can facilitate a wide array of mitogenomic systematic studies through novel 'phylogenetic capture' methods. We conclude that the NAS approach has great potential for broadly improving genomic resources used to identify blood-feeding insects, answer phylogenetic questions and elucidate complex pathways for the transmission of vector-borne pathogens.
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Affiliation(s)
- Evan J. Kipp
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN USA
| | - Laramie L. Lindsey
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN USA
| | - Marissa S. Milstein
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN USA
| | - Cristina M. Blanco
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN USA
| | - Julia P. Baker
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN USA
| | - Christopher Faulk
- Department of Animal Science, University of Minnesota, St. Paul, MN USA
| | - Jonathan D. Oliver
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN USA
| | - Peter A. Larsen
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN USA
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10
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Ribeiro IP, Delatorre E, de Abreu FVS, dos Santos AAC, Furtado ND, Ferreira-de-Brito A, de Pina-Costa A, Neves MSAS, de Castro MG, Motta MDA, Brasil P, Lourenço-de-Oliveira R, Bonaldo MC. Ecological, Genetic, and Phylogenetic Aspects of YFV 2017-2019 Spread in Rio de Janeiro State. Viruses 2023; 15:v15020437. [PMID: 36851651 PMCID: PMC9961572 DOI: 10.3390/v15020437] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/23/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
In Brazil, a yellow fever (YF) outbreak was reported in areas considered YF-free for decades. The low vaccination coverage and the increasing forest fragmentation, with the wide distribution of vector mosquitoes, have been related to yellow fever virus (YFV) transmission beyond endemic areas since 2016. Aiming to elucidate the molecular and phylogenetic aspects of YFV spread on a local scale, we generated 43 new YFV genomes sampled from humans, non-human primates (NHP), and primarily, mosquitoes from highly heterogenic areas in 15 localities from Rio de Janeiro (RJ) state during the YFV 2016-2019 outbreak in southeast Brazil. Our analysis revealed that the genetic diversity and spatial distribution of the sylvatic transmission of YFV in RJ originated from at least two introductions and followed two chains of dissemination, here named the YFV RJ-I and YFV RJ-II clades. They moved with similar dispersal speeds from the north to the south of the RJ state in parallel directions, separated by the Serra do Mar Mountain chain, with YFV RJ-I invading the north coast of São Paulo state. The YFV RJ-I clade showed a more significant heterogeneity across the entire polyprotein. The YFV RJ-II clade, with only two amino acid polymorphisms, mapped at NS1 (I1086V), present only in mosquitoes at the same locality and NS4A (I2176V), shared by all YFV clade RJ-II, suggests a recent clustering of YFV isolates collected from different hosts. Our analyses strengthen the role of surveillance, genomic analyses of YVF isolated from other hosts, and environmental studies into the strategies to forecast, control, and prevent yellow fever outbreaks.
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Affiliation(s)
- Ieda Pereira Ribeiro
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Edson Delatorre
- Laboratório de Genômica Evolutiva e Ambiental, Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre 29500-000, ES, Brazil
| | - Filipe Vieira Santos de Abreu
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
- Instituto Federal do Norte de Minas Gerais, Salinas 39560-000, MG, Brazil
| | - Alexandre Araújo Cunha dos Santos
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Nathália Dias Furtado
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Anielly Ferreira-de-Brito
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Anielle de Pina-Costa
- Laboratório de Doenças Febris Agudas, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
- Faculdade de Medicina de Teresópolis, Centro Universitário Serra dos Órgãos, UNIFESO, Teresópolis 25955-001, RJ, Brazil
| | | | - Márcia Gonçalves de Castro
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Monique de Albuquerque Motta
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Patricia Brasil
- Laboratório de Doenças Febris Agudas, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Ricardo Lourenço-de-Oliveira
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
- Correspondence: (R.L.-d.-O.); (M.C.B.)
| | - Myrna Cristina Bonaldo
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
- Correspondence: (R.L.-d.-O.); (M.C.B.)
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11
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Laiton-Donato K, Quintero-Cortés P, Franco-Salazar JP, Peláez-Carvajal D, Navas MC, Junglen S, Parra-Henao G, Usme-Ciro JA. Usefulness of an in vitro-transcribed RNA control for the detection and quantification of Yellow fever virus through real-time reverse transcription-polymerase chain reaction. Infect Dis Now 2023; 53:104654. [PMID: 36709865 DOI: 10.1016/j.idnow.2023.104654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/09/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023]
Abstract
INTRODUCTION Unvaccinated individuals in endemic areas with proven enzootic transmission of Yellow fever virus are at risk of infection due to a dramatic shift in the epidemiology of the disease over recent years. For this reason, epidemiological surveillance and laboratory confirmation of cases have become mandatory. OBJECTIVE To develop and test a control RNA for YFV detection through real-time RT-PCR. METHODS A 437-bp insert containing the T7 promoter and the target sequences for two different in-house protocols was designed in the context of the pUC57 vector and obtained through gene synthesis. After T7-driven in vitro transcription, standard curves were developed for Log10 serial dilutions of the YFV control RNA with 8 replicates. RESULTS A dynamic range of quantification of 10 orders of magnitude was observed with a limit of detection of 6.3 GCE/µL (95% CI, 2.6 to 139.4 GCE/µL). CONCLUSION The plasmid construct is available for YFV molecular test validation on clinical, entomological, and epizootic samples.
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Affiliation(s)
- Katherine Laiton-Donato
- Grupo de Genómica de Microorganismos Emergentes. Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia; CIST-Centro de Investigación en Salud para el Trópico, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta, Colombia
| | - Paula Quintero-Cortés
- CIST-Centro de Investigación en Salud para el Trópico, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta, Colombia
| | - Juan P Franco-Salazar
- CIST-Centro de Investigación en Salud para el Trópico, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta, Colombia
| | - Dioselina Peláez-Carvajal
- Grupo de Genómica de Microorganismos Emergentes. Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Maria-Cristina Navas
- Grupo de Gastrohepatología, Facultad de Medicina, Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Gabriel Parra-Henao
- CIST-Centro de Investigación en Salud para el Trópico, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta, Colombia
| | - Jose A Usme-Ciro
- Grupo de Genómica de Microorganismos Emergentes. Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia; CIST-Centro de Investigación en Salud para el Trópico, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta, Colombia.
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12
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Salgado Á, de Melo-Minardi RC, Giovanetti M, Veloso A, Morais-Rodrigues F, Adelino T, de Jesus R, Tosta S, Azevedo V, Lourenco J, Alcantara LCJ. Machine learning models exploring characteristic single-nucleotide signatures in yellow fever virus. PLoS One 2022; 17:e0278982. [PMID: 36508435 PMCID: PMC9744328 DOI: 10.1371/journal.pone.0278982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
Yellow fever virus (YFV) is the agent of the most severe mosquito-borne disease in the tropics. Recently, Brazil suffered major YFV outbreaks with a high fatality rate affecting areas where the virus has not been reported for decades, consisting of urban areas where a large number of unvaccinated people live. We developed a machine learning framework combining three different algorithms (XGBoost, random forest and regularized logistic regression) to analyze YFV genomic sequences. This method was applied to 56 YFV sequences from human infections and 27 from non-human primate (NHPs) infections to investigate the presence of genetic signatures possibly related to disease severity (in human related sequences) and differences in PCR cycle threshold (Ct) values (in NHP related sequences). Our analyses reveal four non-synonymous single nucleotide variations (SNVs) on sequences from human infections, in proteins NS3 (E614D), NS4a (I69V), NS5 (R727G, V643A) and six non-synonymous SNVs on NHP sequences, in proteins E (L385F), NS1 (A171V), NS3 (I184V) and NS5 (N11S, I374V, E641D). We performed comparative protein structural analysis on these SNVs, describing possible impacts on protein function. Despite the fact that the dataset is limited in size and that this study does not consider virus-host interactions, our work highlights the use of machine learning as a versatile and fast initial approach to genomic data exploration.
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Affiliation(s)
- Álvaro Salgado
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- * E-mail: (AS); (LCJA); (JL)
| | - Raquel C. de Melo-Minardi
- Departamento de Ciência da Computação, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marta Giovanetti
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Adriano Veloso
- Departamento de Ciência da Computação, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Francielly Morais-Rodrigues
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Talita Adelino
- Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Ronaldo de Jesus
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, DF, Brazil
| | - Stephane Tosta
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - José Lourenco
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail: (AS); (LCJA); (JL)
| | - Luiz Carlos J. Alcantara
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- * E-mail: (AS); (LCJA); (JL)
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13
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Moreira Salles AP, de Seixas Santos Nastri AC, Ho YL, Vilas Boas Casadio L, Emanuel Amgarten D, Justo Arévalo S, Soares Gomes-Gouvea M, Jose Carrilho F, de Mello Malta F, Rebello Pinho JR. Updating the Phylodynamics of Yellow Fever Virus 2016-2019 Brazilian Outbreak With New 2018 and 2019 São Paulo Genomes. Front Microbiol 2022; 13:811318. [PMID: 35633726 PMCID: PMC9132216 DOI: 10.3389/fmicb.2022.811318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/16/2022] [Indexed: 11/19/2022] Open
Abstract
The recent outbreak of yellow fever (YF) in São Paulo during 2016-2019 has been one of the most severe in the last decades, spreading to areas with low vaccine coverage. The aim of this study was to assess the genetic diversity of the yellow fever virus (YFV) from São Paulo 2016-2019 outbreak, integrating the available genomic data with new genomes from patients from the Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP). Using phylodynamics, we proposed the existence of new IE subclades, described their sequence signatures, and determined their locations and time of origin. Plasma or urine samples from acute severe YF cases (n = 56) with polymerase chain reaction (PCR) positive to YFV were submitted to viral genome amplification using 12 sets of primers. Thirty-nine amplified genomes were subsequently sequenced using next-generation sequencing (NGS). These 39 sequences, together with all the complete genomes publicly available, were aligned and used to determine nucleotide/amino acids substitutions and perform phylogenetic and phylodynamic analysis. All YFV genomes generated in this study belonged to the genotype South American I subgroup E. Twenty-one non-synonymous substitutions were identified among the new generated genomes. We analyzed two major clades of the genotypes IE, IE1, and IE2 and proposed the existence of subclades based on their sequence signatures. Also, we described the location and time of origin of these subclades. Overall, our findings provide an overview of YFV genomic characterization and phylodynamics of the 2016-2019 outbreak contributing to future virological and epidemiological studies.
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Affiliation(s)
- Ana Paula Moreira Salles
- Department of Gastroenterology (LIM07), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- Clinical Laboratory of Hospital Israelita Albert Einstein, São Paulo, Brazil
| | | | - Yeh-Li Ho
- Department of Infectious and Parasitic Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Luciana Vilas Boas Casadio
- Department of Infectious and Parasitic Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Deyvid Emanuel Amgarten
- Clinical Laboratory of Hospital Israelita Albert Einstein, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Santiago Justo Arévalo
- Clinical Laboratory of Hospital Israelita Albert Einstein, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Facultad de Ciencias Biológicas, Universidad Ricardo Palma, Lima, Peru
| | | | - Flair Jose Carrilho
- Department of Gastroenterology (LIM07), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Fernanda de Mello Malta
- Department of Gastroenterology (LIM07), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- Clinical Laboratory of Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - João Renato Rebello Pinho
- Department of Gastroenterology (LIM07), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- Clinical Laboratory of Hospital Israelita Albert Einstein, São Paulo, Brazil
- Division of Clinical Laboratories (LIM 03), Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
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14
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Wilke ABB, Vasquez C, Carvajal A, Moreno M, Petrie WD, Beier JC. Evaluation of the effectiveness of BG-Sentinel and CDC light traps in assessing the abundance, richness, and community composition of mosquitoes in rural and natural areas. Parasit Vectors 2022; 15:51. [PMID: 35135589 PMCID: PMC8822692 DOI: 10.1186/s13071-022-05172-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/21/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Vector-borne diseases are a major burden to public health. Controlling mosquitoes is considered the most effective way to prevent vector-borne disease transmission. Mosquito surveillance is a core component of integrated vector management, as surveillance programs are often the cornerstone for the development of mosquito control operations. Two traps are the most commonly used for the surveillance of adult mosquitoes: Centers for Disease Control and Prevention miniature light trap (CDC light trap) and BG-Sentinel trap (BioGents, Regensburg, Germany). However, despite the importance of the BG-Sentinel trap in surveillance programs in the United States, especially in the Southern states, its effectiveness in consistently and reliably collecting mosquitoes in rural and natural areas is still unknown. We hypothesized that BG-Sentinel and CDC light traps would be more attractive to specific mosquito species present in rural and natural areas. Therefore, our objective was to compare the relative abundance, species richness, and community composition of mosquitoes collected in natural and rural areas by BG-Sentinel and CDC light traps. METHODS Mosquitoes were collected from October 2020 to March 2021 using BG-Sentinel and CDC light traps baited with dry ice, totaling 105 trap-nights. RESULTS The BG-Sentinel traps collected 195,115 mosquitoes comprising 23 species from eight genera, and the CDC light traps collected 188,594 mosquitoes comprising 23 species from eight genera. The results from the permutational multivariate analysis of variance (PERMANOVA) and generalized estimating equation model for repeated measures indicate the BG-Sentinel and CDC light traps had similar sampling power. CONCLUSION Even though BG-Sentinel traps had a slightly better performance, the difference was not statistically significant indicating that both traps are suitable to be used in mosquito surveillance in rural and natural areas.
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Affiliation(s)
- André B B Wilke
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, 1120 Northwest 14th Street, Miami, FL, 33136, USA.
| | | | | | - Maday Moreno
- Miami-Dade County Mosquito Control Division, Miami, FL, USA
| | | | - John C Beier
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, 1120 Northwest 14th Street, Miami, FL, 33136, USA
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15
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Li SL, Acosta AL, Hill SC, Brady OJ, de Almeida MAB, Cardoso JDC, Hamlet A, Mucci LF, Telles de Deus J, Iani FCM, Alexander NS, Wint GRW, Pybus OG, Kraemer MUG, Faria NR, Messina JP. Mapping environmental suitability of Haemagogus and Sabethes spp. mosquitoes to understand sylvatic transmission risk of yellow fever virus in Brazil. PLoS Negl Trop Dis 2022; 16:e0010019. [PMID: 34995277 PMCID: PMC8797211 DOI: 10.1371/journal.pntd.0010019] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 01/28/2022] [Accepted: 11/23/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Yellow fever (YF) is an arboviral disease which is endemic to Brazil due to a sylvatic transmission cycle maintained by infected mosquito vectors, non-human primate (NHP) hosts, and humans. Despite the existence of an effective vaccine, recent sporadic YF epidemics have underscored concerns about sylvatic vector surveillance, as very little is known about their spatial distribution. Here, we model and map the environmental suitability of YF's main vectors in Brazil, Haemagogus spp. and Sabethes spp., and use human population and NHP data to identify locations prone to transmission and spillover risk. METHODOLOGY/PRINCIPAL FINDINGS We compiled a comprehensive set of occurrence records on Hg. janthinomys, Hg. leucocelaenus, and Sabethes spp. from 1991-2019 using primary and secondary data sources. Linking these data with selected environmental and land-cover variables, we adopted a stacked regression ensemble modelling approach (elastic-net regularized GLM, extreme gradient boosted regression trees, and random forest) to predict the environmental suitability of these species across Brazil at a 1 km x 1 km resolution. We show that while suitability for each species varies spatially, high suitability for all species was predicted in the Southeastern region where recent outbreaks have occurred. By integrating data on NHP host reservoirs and human populations, our risk maps further highlight municipalities within the region that are prone to transmission and spillover. CONCLUSIONS/SIGNIFICANCE Our maps of sylvatic vector suitability can help elucidate potential locations of sylvatic reservoirs and be used as a tool to help mitigate risk of future YF outbreaks and assist in vector surveillance. Furthermore, at-risk regions identified from our work could help disease control and elucidate gaps in vaccination coverage and NHP host surveillance.
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Affiliation(s)
- Sabrina L. Li
- School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
- * E-mail: (SLL); (JPM)
| | - André L. Acosta
- Departamento de Ecologia, Instituto de Biociências, Laboratório de Ecologia de Paisagens e Conservação—LEPAC, Universidade de São Paulo, São Paulo, Brazil
| | - Sarah C. Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, United Kingdom
| | - Oliver J. Brady
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Marco A. B. de Almeida
- State Centre of Health Surveillance, Rio Grande do Sul State Health Secretariat, Rio Grande do Sul, Brazil
| | - Jader da C. Cardoso
- State Centre of Health Surveillance, Rio Grande do Sul State Health Secretariat, Rio Grande do Sul, Brazil
| | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Luis F. Mucci
- Superintendence for Endemic Diseases Control, São Paulo State Health Secretariat, São Paulo, Brazil
| | - Juliana Telles de Deus
- Superintendence for Endemic Diseases Control, São Paulo State Health Secretariat, São Paulo, Brazil
| | | | - Neil S. Alexander
- Environmental Research Group Oxford, c/o Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - G. R. William Wint
- Environmental Research Group Oxford, c/o Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Oliver G. Pybus
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Nuno R. Faria
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Departamento de Molestias Infecciosas e Parasitarias & Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Jane P. Messina
- School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
- Oxford School of Global and Area Studies, University of Oxford, Oxford, United Kingdom
- * E-mail: (SLL); (JPM)
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16
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Haslwanter D, Lasso G, Wec AZ, Furtado ND, Raphael LMS, Tse AL, Sun Y, Stransky S, Pedreño-Lopez N, Correia CA, Bornholdt ZA, Sakharkar M, Avelino-Silva VI, Moyer CL, Watkins DI, Kallas EG, Sidoli S, Walker LM, Bonaldo MC, Chandran K. Genotype-specific features reduce the susceptibility of South American yellow fever virus strains to vaccine-induced antibodies. Cell Host Microbe 2022; 30:248-259.e6. [PMID: 34998466 PMCID: PMC10067022 DOI: 10.1016/j.chom.2021.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/01/2021] [Accepted: 12/10/2021] [Indexed: 12/13/2022]
Abstract
The resurgence of yellow fever in South America has prompted vaccination against the etiologic agent, yellow fever virus (YFV). Current vaccines are based on a live-attenuated YF-17D virus derived from a virulent African isolate. The capacity of these vaccines to induce neutralizing antibodies against the vaccine strain is used as a surrogate for protection. However, the sensitivity of genetically distinct South American strains to vaccine-induced antibodies is unknown. We show that antiviral potency of the polyclonal antibody response in vaccinees is attenuated against an emergent Brazilian strain. This reduction was attributable to amino acid changes at two sites in central domain II of the glycoprotein E, including multiple changes at the domain I-domain II hinge, which are unique to and shared among most South American YFV strains. Our findings call for a reevaluation of current approaches to YFV immunological surveillance in South America and suggest approaches for updating vaccines.
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Affiliation(s)
- Denise Haslwanter
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, The Bronx, NY 10461, USA
| | - Gorka Lasso
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, The Bronx, NY 10461, USA
| | | | - Nathália Dias Furtado
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, 21040-360 Rio de Janeiro, Brazil
| | - Lidiane Menezes Souza Raphael
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, 21040-360 Rio de Janeiro, Brazil
| | - Alexandra L Tse
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, The Bronx, NY 10461, USA
| | - Yan Sun
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Núria Pedreño-Lopez
- Department of Pathology, The George Washington University, Washington, DC 20037, USA
| | - Carolina Argondizo Correia
- Laboratório de Imunologia Clínica e Alergia, Faculdade de Medicina, Universidade de São Paulo, 01246-903 São Paulo, Brazil
| | | | | | - Vivian I Avelino-Silva
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, 01246-903 São Paulo, Brazil
| | | | - David I Watkins
- Department of Pathology, The George Washington University, Washington, DC 20037, USA
| | - Esper G Kallas
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, 01246-903 São Paulo, Brazil
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laura M Walker
- Adimab, LLC, Lebanon, NH 03766, USA; Adagio Therapeutics Inc., Waltham, MA 02451, USA
| | - Myrna C Bonaldo
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, 21040-360 Rio de Janeiro, Brazil.
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, The Bronx, NY 10461, USA.
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17
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Ribeiro Prist P, Reverberi Tambosi L, Filipe Mucci L, Pinter A, Pereira de Souza R, Lara Muylaert R, Roger Rhodes J, Henrique Comin C, Fontoura Costa L, Lang D'Agostini T, Telles de Deus J, Pavão M, Port‐Carvalho M, Del Castillo Saad L, Mureb Sallum MA, Fernandes Spinola RM, Metzger JP. Roads and forest edges facilitate yellow fever virus dispersion. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.14031] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Paula Ribeiro Prist
- Department of Ecology Institute of Bioscience University of São Paulo São Paulo Brazil
| | - Leandro Reverberi Tambosi
- Department of Ecology Institute of Bioscience University of São Paulo São Paulo Brazil
- Center for Engineering, Modelling and Applied Social Sciences Federal University of ABC Santo André Brazil
| | | | | | | | - Renata Lara Muylaert
- Molecular Epidemiology and Public Health Laboratory Hopkirk Research InstituteMassey University Palmerston North New Zealand
| | - Jonathan Roger Rhodes
- School of Earth and Environmental Sciences The University of Queensland Brisbane QLD Australia
| | - César Henrique Comin
- Department of Computer Science Federal University of São Carlos São Carlos Brazil
| | | | - Tatiana Lang D'Agostini
- Center for Epidemiology Surveillance ‘Dr Alexandre Vranjac’ Coordination for Disease ControlPublic Health Branch São Paulo Brazil
| | | | - Mônica Pavão
- Geoprocessing and Spatial Analysis Core Environment Research Institute. Infrastructure and Environment Secretariat of São Paulo São Paulo Brazil
| | - Márcio Port‐Carvalho
- Conservation Biodiversity Nucleus, Environmental Research Institute, Infrastructure and Environment Secretariat of São Paulo São Paulo SP Brazil
- Post Graduated Program in Biodiversity of Conservations UnitsNational School of Tropical Botanical—Rio de Janeiro Botanical Garden Rio de Janeiro Brazil
| | - Leila Del Castillo Saad
- Center for Epidemiology Surveillance ‘Dr Alexandre Vranjac’ Coordination for Disease ControlPublic Health Branch São Paulo Brazil
| | | | - Roberta Maria Fernandes Spinola
- Center for Epidemiology Surveillance ‘Dr Alexandre Vranjac’ Coordination for Disease ControlPublic Health Branch São Paulo Brazil
| | - Jean Paul Metzger
- Department of Ecology Institute of Bioscience University of São Paulo São Paulo Brazil
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18
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Berthet M, Mesbahi G, Duvot G, Zuberbühler K, Cäsar C, Bicca-Marques JC. Dramatic decline in a titi monkey population after the 2016-2018 sylvatic yellow fever outbreak in Brazil. Am J Primatol 2021; 83:e23335. [PMID: 34609763 DOI: 10.1002/ajp.23335] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 09/03/2021] [Accepted: 09/25/2021] [Indexed: 11/07/2022]
Abstract
Platyrrhini are highly vulnerable to the yellow fever (YF) virus. From 2016 to 2018, the Atlantic Forest of southeast Brazil faced its worst sylvatic YF outbreak in about a century, thought to have killed thousands of primates. It is essential to assess the impact of this epidemic on threatened primate assemblages to design effective conservation strategies. In this study, we assessed the impact of the 2016-2018 YF outbreak on a geographically isolated population of Near Threatened black-fronted titi monkeys (Callicebus nigrifrons) in two Atlantic Forest patches of the Santuário do Caraça, MG, Brazil. Extensive preoutbreak monitoring, conducted between 2008 and 2016, revealed that the home range and group sizes of the population remained stable. In 2016, the population size was estimated at 53-57 individuals in 11-12 groups. We conducted monitoring and playback surveys in 2019 and found that the population had decreased by 68% in one forest patch and completely vanished in the other, resulting in a combined decline of 80%. We discuss this severe loss of a previously stable population and conclude that it was highly likely caused by the YF outbreak. The remaining population is at risk of disappearing completely because of its small size and geographic isolation. A systematic population surveys of C. nigrifrons, along other sensible Platyrrhini species, is needed to re-evaluate their current conservation status.
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Affiliation(s)
- Mélissa Berthet
- Département d'études cognitives, Institut Jean Nicod, ENS, EHESS, CNRS, PSL Research University, Paris, France
| | - Geoffrey Mesbahi
- Université de Lorraine, INRAE, LAE, Nancy, France.,Parc Naturel Régional des Vosges du Nord, La Petite Pierre, France
| | - Guilhem Duvot
- Département d'études cognitives, Institut Jean Nicod, ENS, EHESS, CNRS, PSL Research University, Paris, France
| | - Klaus Zuberbühler
- School of Psychology & Neurosciences, University of St Andrews, Scotland, UK.,Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | | | - Júlio Cèsar Bicca-Marques
- Escola de Ciências da Saúde e da Vida, Laboratório de Primatologia, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
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19
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Andrade MDS, Campos FS, Campos AAS, Abreu FVS, Melo FL, Sevá ADP, Cardoso JDC, Dos Santos E, Born LC, da Silva CMD, Müller NFD, de Oliveira CH, da Silva AJJ, Simonini-Teixeira D, Bernal-Valle S, Mares-Guia MAMM, Albuquerque GR, Romano APM, Franco AC, Ribeiro BM, Roehe PM, de Almeida MAB. Real-Time Genomic Surveillance during the 2021 Re-Emergence of the Yellow Fever Virus in Rio Grande do Sul State, Brazil. Viruses 2021; 13:v13101976. [PMID: 34696408 PMCID: PMC8539658 DOI: 10.3390/v13101976] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 02/06/2023] Open
Abstract
The 2021 re-emergence of yellow fever in non-human primates in the state of Rio Grande do Sul (RS), southernmost Brazil, resulted in the death of many howler monkeys (genus Alouatta) and led the state to declare a Public Health Emergency of State Importance, despite no human cases reported. In this study, near-complete genomes of yellow fever virus (YFV) recovered from the outbreak were sequenced and examined aiming at a better understanding of the phylogenetic relationships and the spatio-temporal dynamics of the virus distribution. Our results suggest that the most likely sequence of events involved the reintroduction of YFV from the state of São Paulo to RS through the states of Paraná and Santa Catarina, by the end of 2020. These findings reinforce the role of genomic surveillance in determining the pathways of distribution of the virus and in providing references for the implementation of preventive measures for populations in high risk areas.
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Affiliation(s)
- Miguel de S. Andrade
- Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, Distrito Federal, Brazil; (M.d.S.A.); (F.L.M.); (B.M.R.)
| | - Fabrício S. Campos
- Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi 77410-570, Tocantins, Brazil;
| | - Aline A. S. Campos
- State Center of Health Surveillance, Rio Grande do Sul State Health Department, Porto Alegre 90610-000, Rio Grande do Sul, Brazil; (A.A.S.C.); (J.d.C.C.); (E.d.S.); (L.C.B.); (C.M.D.d.S.)
| | - Filipe V. S. Abreu
- Insect Behavior Laboratory, Federal Institute of Northern Minas Gerais, Salinas 39560-000, Minas Gerais, Brazil; (F.V.S.A.); (C.H.d.O.); (A.J.J.d.S.)
| | - Fernando L. Melo
- Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, Distrito Federal, Brazil; (M.d.S.A.); (F.L.M.); (B.M.R.)
| | - Anaiá da P. Sevá
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus 45662-900, Bahia, Brazil; (A.d.P.S.); (D.S.-T.); (S.B.-V.); (G.R.A.)
| | - Jader da C. Cardoso
- State Center of Health Surveillance, Rio Grande do Sul State Health Department, Porto Alegre 90610-000, Rio Grande do Sul, Brazil; (A.A.S.C.); (J.d.C.C.); (E.d.S.); (L.C.B.); (C.M.D.d.S.)
| | - Edmilson Dos Santos
- State Center of Health Surveillance, Rio Grande do Sul State Health Department, Porto Alegre 90610-000, Rio Grande do Sul, Brazil; (A.A.S.C.); (J.d.C.C.); (E.d.S.); (L.C.B.); (C.M.D.d.S.)
| | - Lucas C. Born
- State Center of Health Surveillance, Rio Grande do Sul State Health Department, Porto Alegre 90610-000, Rio Grande do Sul, Brazil; (A.A.S.C.); (J.d.C.C.); (E.d.S.); (L.C.B.); (C.M.D.d.S.)
| | - Cláudia M. D. da Silva
- State Center of Health Surveillance, Rio Grande do Sul State Health Department, Porto Alegre 90610-000, Rio Grande do Sul, Brazil; (A.A.S.C.); (J.d.C.C.); (E.d.S.); (L.C.B.); (C.M.D.d.S.)
| | - Nicolas F. D. Müller
- Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90050-170, Rio Grande do Sul, Brazil; (N.F.D.M.); (A.C.F.); (P.M.R.)
| | - Cirilo H. de Oliveira
- Insect Behavior Laboratory, Federal Institute of Northern Minas Gerais, Salinas 39560-000, Minas Gerais, Brazil; (F.V.S.A.); (C.H.d.O.); (A.J.J.d.S.)
| | - Alex J. J. da Silva
- Insect Behavior Laboratory, Federal Institute of Northern Minas Gerais, Salinas 39560-000, Minas Gerais, Brazil; (F.V.S.A.); (C.H.d.O.); (A.J.J.d.S.)
| | - Danilo Simonini-Teixeira
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus 45662-900, Bahia, Brazil; (A.d.P.S.); (D.S.-T.); (S.B.-V.); (G.R.A.)
| | - Sofía Bernal-Valle
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus 45662-900, Bahia, Brazil; (A.d.P.S.); (D.S.-T.); (S.B.-V.); (G.R.A.)
| | - Maria A. M. M. Mares-Guia
- Flavivirus Laboratory, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Rio de Janeiro, Brazil;
| | - George R. Albuquerque
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus 45662-900, Bahia, Brazil; (A.d.P.S.); (D.S.-T.); (S.B.-V.); (G.R.A.)
| | - Alessandro P. M. Romano
- General Coordination of Arbovirus Surveillance, Ministry of Health, Brasília 70058-900, Distrito Federal, Brazil;
| | - Ana C. Franco
- Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90050-170, Rio Grande do Sul, Brazil; (N.F.D.M.); (A.C.F.); (P.M.R.)
| | - Bergmann M. Ribeiro
- Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, Distrito Federal, Brazil; (M.d.S.A.); (F.L.M.); (B.M.R.)
| | - Paulo M. Roehe
- Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90050-170, Rio Grande do Sul, Brazil; (N.F.D.M.); (A.C.F.); (P.M.R.)
| | - Marco A. B. de Almeida
- State Center of Health Surveillance, Rio Grande do Sul State Health Department, Porto Alegre 90610-000, Rio Grande do Sul, Brazil; (A.A.S.C.); (J.d.C.C.); (E.d.S.); (L.C.B.); (C.M.D.d.S.)
- Correspondence:
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20
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Diffusion of sylvatic yellow fever in the state of São Paulo, Brazil. Sci Rep 2021; 11:16277. [PMID: 34381111 PMCID: PMC8358007 DOI: 10.1038/s41598-021-95539-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/26/2021] [Indexed: 11/08/2022] Open
Abstract
We investigated the sylvatic yellow fever (SYF) diffusion process in São Paulo (SP) between 2016 and 2019. We developed an ecological study of SYF through autochthonous human cases and epizootics of non-human primates (NHPs) that were spatiotemporally evaluated. We used kriging to obtain maps with isochrones representative of the evolution of the outbreak and characterized its diffusion pattern. We confirmed 648 human cases of SYF in SP, with 230 deaths and 843 NHP epizootics. Two outbreak waves were identified: one from West to East (2016 and 2017), and another from the Campinas region to the municipalities bordering Rio de Janeiro, Minas Gerais, and Paraná and those of the SP coast (2017-2019). The SYF outbreak diffusion process was by contagion. The disease did not exhibit jumps between municipalities, indicating that the mosquitoes and NHPs were responsible for transmitting the virus. There were not enough vaccines to meet the population at risk; hence, health authorities used information about the epizootic occurrence in NHPs in forest fragments to identify priority populations for vaccination.
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21
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Giovanetti M, Alcantara LCJ, Dorea AS, Ferreira QR, Marques WDA, Junior Franca de Barros J, Adelino TER, Tosta S, Fritsch H, Iani FCDM, Mares-Guia MA, Salgado A, Fonseca V, Xavier J, Lopes EN, Soares GC, de Castro Amarante MF, Azevedo V, Kruger A, Correa Matta G, Paineiras-Domingos LL, Colonnello C, Bispo de Filippis AM, Montesano C, Colizzi V, Barreto FK. Promoting Responsible Research and Innovation (RRI) During Brazilian Activities of Genomic and Epidemiological Surveillance of Arboviruses. Front Public Health 2021; 9:693743. [PMID: 34277552 PMCID: PMC8282202 DOI: 10.3389/fpubh.2021.693743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 06/07/2021] [Indexed: 12/29/2022] Open
Affiliation(s)
- Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luiz Carlos Junior Alcantara
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Qesya Rodrigues Ferreira
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista, Brazil
| | | | | | - Talita Emile Ribeiro Adelino
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Brazil
| | - Stephane Tosta
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Hegger Fritsch
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Felipe Campos de Melo Iani
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Brazil
| | | | - Alvaro Salgado
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vagner Fonseca
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Joilson Xavier
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Elisson Nogueira Lopes
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gilson Carlos Soares
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Instituto de Ciencia Biologica (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Alícia Kruger
- Departamento Nacional de IST/AIDS/Hepatites Virais, Brasília, Brazil
| | - Gustavo Correa Matta
- Escola Nacional de Saúde Pública Sergio Arouca, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | | | | | - Carla Montesano
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Vittorio Colizzi
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Fernanda Khouri Barreto
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista, Brazil
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22
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Ellwanger JH, Chies JAB. Zoonotic spillover: Understanding basic aspects for better prevention. Genet Mol Biol 2021; 44:e20200355. [PMID: 34096963 PMCID: PMC8182890 DOI: 10.1590/1678-4685-gmb-2020-0355] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 04/05/2021] [Indexed: 01/07/2023] Open
Abstract
The transmission of pathogens from wild animals to humans is called “zoonotic spillover”. Most human infectious diseases (60-75%) are derived from pathogens that originally circulated in non-human animal species. This demonstrates that spillover has a fundamental role in the emergence of new human infectious diseases. Understanding the factors that facilitate the transmission of pathogens from wild animals to humans is essential to establish strategies focused on the reduction of the frequency of spillover events. In this context, this article describes the basic aspects of zoonotic spillover and the main factors involved in spillover events, considering the role of the inter-species interactions, phylogenetic distance between host species, environmental drivers, and specific characteristics of the pathogens, animals, and humans. As an example, the factors involved in the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic are discussed, indicating what can be learned from this public health emergency, and what can be applied to the Brazilian scenario. Finally, this article discusses actions to prevent or reduce the frequency of zoonotic spillover events.
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Affiliation(s)
- Joel Henrique Ellwanger
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Laboratório de Imunobiologia e Imunogenética, Porto Alegre, RS, Brazil
| | - José Artur Bogo Chies
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Laboratório de Imunobiologia e Imunogenética, Porto Alegre, RS, Brazil
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Guerra JM, Ferreira CSDS, Díaz-Delgado J, Takahashi JPF, Kimura LM, de Araújo LJT, Réssio RA, Dos Santos Cirqueira C, Ozahatar CH, Cunha MS, Luchs A, Fernandes NCCDA. Concurrent yellow fever and pulmonary aspergillosis due to Aspergillus fumigatus in a free-ranging howler monkey (Alouatta sp). J Med Primatol 2021; 50:201-204. [PMID: 33817795 DOI: 10.1111/jmp.12522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/17/2021] [Accepted: 03/21/2021] [Indexed: 11/29/2022]
Abstract
Herein, we describe a unique case of concomitant angioinvasive pulmonary aspergillosis due to Aspergillus fumigatus and yellow fever in a free-ranging howler monkey (Alouatta sp). Lung samples were negative for influenza viruses A and B.
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Affiliation(s)
- Juliana Mariotti Guerra
- Quantitative Pathology Department, Pathology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | | | - Josué Díaz-Delgado
- Texas A&M Veterinary Medical Diagnostic Laboratory (TVMDL), College Station, TX, USA
| | | | - Lidia Midori Kimura
- Quantitative Pathology Department, Pathology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | | | | | | | | | - Mariana Sequetin Cunha
- Vector-Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | - Adriana Luchs
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
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25
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Dengue-2 and Guadeloupe Mosquito Virus RNA Detected in Aedes ( Stegomyia) spp. Collected in a Vehicle Impound Yard in Santo André, SP, Brazil. INSECTS 2021; 12:insects12030248. [PMID: 33809477 PMCID: PMC8001461 DOI: 10.3390/insects12030248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 11/17/2022]
Abstract
In 2018-2019, we conducted mosquito collections in a municipal vehicle impound yard, which is 10 km from the Serra do Mar Environmental Protection Area in Santo André, SP, Brazil. Our aim is to study arboviruses in the impound yard, to understand the transmission of arboviruses in an urban environment in Brazil. We captured the mosquitoes using human-landing catches and processed them for arbovirus detection by conventional and quantitative RT-PCR assays. We captured two mosquito species, Aedes aegypti (73 total specimens; 18 females and 55 males) and Ae. albopictus (34 specimens; 27 females and 7 males). The minimum infection rate for DENV-2 was 11.5 per 1000 (CI95%: 1-33.9). The detection of DENV-2 RNA in an Ae. albopictus female suggests that this virus might occur in high infection rates in the sampled mosquito population and is endemic in the urban areas of Santo André. In addition, Guadeloupe mosquito virus RNA was detected in an Ae. aegypti female. To our knowledge, this was the first detection of the Guadeloupe mosquito virus in Brazil.
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Coding-Complete Genome Sequence of a Yellow Fever Virus Isolated from a Baby Howler Monkey ( Alouatta caraya) from São Paulo State, Brazil, in 2016. Microbiol Resour Announc 2021; 10:10/1/e01244-20. [PMID: 33414341 PMCID: PMC8407717 DOI: 10.1128/mra.01244-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report a coding-complete sequence of a yellow fever virus, strain JabSPM02, containing the 3′ untranslated region and all coding regions. The virus was recovered from an infected howler monkey from a rural area in São Paulo State, Brazil. Our findings show that it belongs to the South America 1E genotype. We report a coding-complete sequence of a yellow fever virus, strain JabSPM02, containing the 3′ untranslated region and all coding regions. The virus was recovered from an infected howler monkey from a rural area in São Paulo State, Brazil. Our findings show that it belongs to the South America 1E genotype.
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27
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Tyson JR, James P, Stoddart D, Sparks N, Wickenhagen A, Hall G, Choi JH, Lapointe H, Kamelian K, Smith AD, Prystajecky N, Goodfellow I, Wilson SJ, Harrigan R, Snutch TP, Loman NJ, Quick J. Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.09.04.283077. [PMID: 32908977 DOI: 10.1101/2020.09.04.283077v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Genome sequencing has been widely deployed to study the evolution of SARS-CoV-2 with more than 90,000 genome sequences uploaded to the GISAID database. We published a method for SARS-CoV-2 genome sequencing ( https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w ) online on January 22, 2020. This approach has rapidly become the most popular method for sequencing SARS-CoV-2 due to its simplicity and cost-effectiveness. Here we present improvements to the original protocol: i) an updated primer scheme with 22 additional primers to improve genome coverage, ii) a streamlined library preparation workflow which improves demultiplexing rate for up to 96 samples and reduces hands-on time by several hours and iii) cost savings which bring the reagent cost down to £10 per sample making it practical for individual labs to sequence thousands of SARS-CoV-2 genomes to support national and international genomic epidemiology efforts.
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28
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Tyson JR, James P, Stoddart D, Sparks N, Wickenhagen A, Hall G, Choi JH, Lapointe H, Kamelian K, Smith AD, Prystajecky N, Goodfellow I, Wilson SJ, Harrigan R, Snutch TP, Loman NJ, Quick J. Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.09.04.283077. [PMID: 32908977 PMCID: PMC7480024 DOI: 10.1101/2020.09.04.283077] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Genome sequencing has been widely deployed to study the evolution of SARS-CoV-2 with more than 90,000 genome sequences uploaded to the GISAID database. We published a method for SARS-CoV-2 genome sequencing (https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w) online on January 22, 2020. This approach has rapidly become the most popular method for sequencing SARS-CoV-2 due to its simplicity and cost-effectiveness. Here we present improvements to the original protocol: i) an updated primer scheme with 22 additional primers to improve genome coverage, ii) a streamlined library preparation workflow which improves demultiplexing rate for up to 96 samples and reduces hands-on time by several hours and iii) cost savings which bring the reagent cost down to £10 per sample making it practical for individual labs to sequence thousands of SARS-CoV-2 genomes to support national and international genomic epidemiology efforts.
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Affiliation(s)
- John R Tyson
- Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada
| | | | | | - Natalie Sparks
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Grant Hall
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ji Hyun Choi
- Division of AIDS, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Hope Lapointe
- Division of AIDS, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Kimia Kamelian
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
| | - Andrew D Smith
- Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada
- Oxford Nanopore Technologies Ltd., Oxford, UK
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
- Division of AIDS, Faculty of Medicine, University of British Columbia, Vancouver, Canada
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Natalie Prystajecky
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Sam J Wilson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Richard Harrigan
- Division of AIDS, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Terrance P Snutch
- Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Joshua Quick
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
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