TEAM
Dr Vagner Fonseca
CERI Team

Dr Vagner
Fonseca

Post-Doctoral Fellow
// Affiliations
Primary
CERI - Centre for Epidemic Response and Innovation, Stellenbosch University, Stellenbosch, South Africa
Also at
KRISP - KwaZulu-Natal Research and Innovation Sequencing Platform, UKZN, Durban, South Africa
Also at
Department of Exact and Earth Sciences, University of the State of Bahia
// Education
PhD in Virology
Nelson R. Mandela School of Medicine, University of KwaZulu-Natal (UKZN), South Africa, 2022
PhD in Bioinformatics
Federal University of Minas Gerais (UFMG), Brazil, 2022
Master of Biotechnology in Health and Investigative Medicine
Oswaldo Cruz Foundation, 2016
Bachelor of Information Systems
University of the State of Bahia, 2013

Dr Vagner Fonseca is a bioinformatician in viral evolution and a data scientist. He has a PhD in medicine, majoring in Virology at the UKZN and a PhD in Bioinformatics at the UFMG. He has developed abilities to work with teams and setting up very advanced bioinformatics systems in the laboratory and in the field. He has been working with the genomic surveillance of Zika, Dengue, Chikungunya, HIV, Yellow Fever Virus, West Nile Virus SARS-CoV-2 and Rift Valley Fever Viruses. Dr Fonseca isn’t afraid of going into the field to set up mobile genomic laboratories to respond to the epidemics as they are ongoing. His primary skills are Bioinformatics Software Development, Databases, BigData, Pipelines Development, Next Generation Sequence data Management and Analysis, Genomic Epidemiology, Phylogenetics, Phylogeography, Transmission Clusters, Recombination analysis and High Performance and Cloud Computing for Data Intensive Projects.

Besides that, Dr Fonseca has been active in Information Technology sector since 2004 with: Systems Analysis and Development, Project Management and IT Infrastructure Projects. I am experienced in large projects and high complexity, covering the following areas of activity: Analysis and systems development (Web/Desktop/Mobile), Analysis and Development for Databases (Administration, Modeling, Data Migration, Tuning SQL, Optimization, Functions, Triggers and Stored Procedures), Development team manager, identification of functional prerequisites (APF, RUP, UML), Systems Auditing, Software Quality, Agile Methods, Configuration and Windows/Linux Servers Maintenance, Configuration Management and Continuous Integration Servers.

// Research Output

Publications

2026
Cross-platform protocol for HTLV-1 whole-genome sequencing using nanopore and Illumina technologies

Lima A, de Moraes L, Amorim R, Cucco M, Silva R, Giovanetti M, Rego F, Araújo T, Fonseca V, Khouri R, Alcantara L, Santos L, Barreto F

Next Research
3:101110
2026
Re-emergence of DENV-3 in Paraguay After Two Decades: A Genomic and Epidemiological Investigation

Cantero C, Vazquez C, Gonzalez S, Rojas A, Fleitas F, Barrios J, Gomez de la Fuente A, Villalba S, Torales M, Ijeda A, Fonseca V, Junior Alcantara L, Giovanetti M

Emerging Microbes & Infections
2025
Reemergence of yellow fever virus in forest and periurban settings in Brazil

das Graças Dantas Andrade V, Ribeiro Adelino T, Fonseca V, Melo Farias Moreno K, Ribeiro Tomé L, Pereira L, Lima de La-Roque D, Bispo de Filippis A, Garkauskas Ramos D, Brock Ramalho D, de Lima Furtado K, Borges G, Martins L, Frutuoso L, Oliveira Lamounier L, Guimarães N, Sayuri Sato Barros P, Souza de Almeida P, de Souza da Silva P, Giesbrecht Pinheiro R, Guerino Stabeli R, Moreira da Silva Chagas S, Sousa Pietra Pedroso S, Kashima S, Gonçalves Penante S, Santini de Oliveira M, Lemes da Silva V, Van Voorhis W, Holmes E, Lourenço J, de Melo Iani F, Simões Jorge Júnior A, Giovanetti M, Junior Alcantara L

Communications Medicine
6:35
2025
Detection of Lymphocytic Choriomeningitis Virus in House Mouse (Mus musculus) in Brazil

Cavalcanti G, Fernandes J, Santos F, Teixeira B, Guterres A, Brignone J, Levis S, Lucio C, Costa-Neto S, Fonseca V, Giovanetti M, Alcantara L, D’Andrea P, de Lemos E, Oliveira R

Viruses
17:1544
2025
VAMPIRE: ALGORITMO PARA ANÁLISE DE DADOS DE NGS E IDENTIFICAÇÃO DE VARIANTES GENÉTICAS DO SISTEMA SANGUÍNEO RH

Galdino D, Rodrigues E, Lenz A, Chagas L, Laroque D, Santos F, Kashima S, Calado R, Fonseca V, Frias D

Hematology, Transfusion and Cell Therapy
47:105690
2025
Genomic surveillance of SARS-CoV-2 in the State of Mato Grosso, Midwest Brazil

da Silva S, Vasconcelos K, Almeida J, Guimarães N, Tomé L, Fonseca V, Júnior D, Giovanetti M, de Oliveira E, Alcântara L

Gene Reports
41:102361
2025
Uncovering DENV, CHIKV, and ZIKV in Urban Wastewater in Brazil Through Genomic and Molecular Screening

de Araujo J, Carvalho A, Adelino T, Iani F, Guimaraes N, Santos S, Leal C, Natividade M, Lima M, Almada M, Bertuce A, Guerra A, Costa M, Saia F, Fonseca V, Giovanetti M, Frutuoso L, Alcantara L

Microorganisms
13:2164
2025
Identifying genomic surveillance gaps in Africa for the global public health response to West Nile virus: a systematic review

Moir M, Sitharam N, Hofstra L, Dor G, Mwanyika G, Ramphal Y, Reichmuth M, San J, Gifford R, Wilkinson E, Tshiabuila D, Preiser W, Konou A, Bitew M, Onoja A, Paganotti G, Abera A, Maror J, Kayiwa J, Abuelmaali S, Lusamaki E, de Oliveira T, Alcantara L, Holmes E, Padane A, Musa A, Abera A, Campbell A, Ssemaganda A, Ahouidi A, Muianga A, Samson A, Onoja A, Alemu B, Foka C, Baxter C, van Zyl D, de Castro Silva D, Martin D, Wilkinson E, Kouma E, Simo F, Mwanyika G, Godebo G, D’or G, Tegally H, Omara I, Maror J, Poonagavan J, Juma J, Oludele J, Xavier J, Lourenco J, Fokam J, Maeka K, Singh L, Chabuka L, Issaka M, Hofstra M, Giovanetti M, Faye M, Koffi M, Owusu M, Dikongo M, Alimohamed M, Bitew M, Moir M, Kraemer M, Sitharam N, Jerome N, Mbhele N, Miantsatian Andry N, Tomori O, Magalutcheemee R, Guimaraes R, Oyola S, Abuelmaali S, Golubchik T, Fonseca V, Preiser W, Ramphal Y, Venter M, Burt F, Baxter C, Lessells R, de Oliveira T, Tegally H

The Lancet Microbe
6:101176
2025
Understanding the emergence expansion and impact of oropouche virus

Santos S, Adelino T, Cella E, Slavov S, Kashima S, Ciccozzi M, Tomé L, Guimarães N, Iani F, Alcantara L, Fonseca V, Giovanetti M

Discover Viruses
2
2025
Anellovirus abundance as an indicator for viral metagenomic classifier utility in plasma samples

de Campos G, Clemente L, Lima A, Cella E, Fonseca V, Ximenez J, Nishiyama M, de Carvalho E, Sampaio S, Giovanetti M, Elias M, Slavov S

Virology Journal
22
2025
Establishing a dengue genomic monitoring in Cuba: uncovering virus dynamics to enhance local response

Pérez M, Álvarez M, Perez L, Benitez A, Serrano S, Adelino T, Fonseca V, Resik S, Kouri V, Gresh L, Franco L, Rico J, Lourenço J, Alcantara L, Giovanetti M, Guzman M

IJID Regions
16:100683
2025
Spatiotemporal disease suitability prediction for Oropouche virus and the role of vectors across the Americas

Poongavanan J, Dunaiski M, D’or G, Kraemer M, Giovanetti M, Lim A, Brady O, Baxter C, Fonseca V, Alcantara L, de Oliveira T, Tegally H

medRxiv
doi: 10.1101/2025.02.28.25323068.
2025
Travel-associated international spread of Oropouche virus beyond the Amazon

de Melo Iani F, Pereira F, de Oliveira E, Rodrigues J, Machado M, Fonseca V, Adelino T, Guimarães N, Tomé L, Gómez M, Nardy V, Ribeiro A, Rosewell A, Ferreira, Silva de Mello A, Fernandes B, de Albuquerque C, dos Santos Pereira D, Pimentel E, Lima F, Silva F, de Carvalho Pereira G, Tegally H, Almeida J, Moreno K, Vasconcelos K, Santos L, Silva L, Frutuoso L, Lamounier L, Costa M, de Oliveira M, dos Anjos M, Ciccozzi M, Lima M, Pereira M, Rocha M, de Souza da Silva P, Rabinowitz P, de Almeida P, Lessells R, Gazzinelli R, da Cunha R, Gonçalves S, dos Santos S, de Alcântara Belettini S, Pedroso S, Araújo S, da Silva S, Croda J, Maciel E, Van Voorhis W, Martin D, Holmes E, de Oliveira T, Lourenço J, Alcantara L, Giovanetti M

Journal of Travel Medicine
doi: 10.1093/jtm/taaf018.
2024
Dynamics and ecology of a multi-stage expansion of Oropouche virus in Brazil

Tegally H, Dellicour S, Poongavanan J, Mavian C, Dor G, Fonseca V, Tagliamonte M, Dunaiski M, Moir M, Wilkinson E, de Albuquerque C, Frutuoso L, , Holmes E, Baxter C, Lessells R, Kraemer M, Lourenço J, Alcantara L, de Oliveira T, Giovanetti M

doi: 10.1101/2024.10.29.24316328.
2024
North–south pathways, emerging variants, and high climate suitability characterize the recent spread of dengue virus serotypes 2 and 3 in the Dominican Republic

Miguel I, Feliz E, Agramonte R, Martinez P, Vergara C, Imbert Y, De la Cruz L, de Castro N, Cedano O, De la Paz Y, Fonseca V, Santiago G, Muñoz-Jordán J, Peguero A, Paulino-Ramírez R, Grubaugh N, de Filippis A, Alcantara L, Rico J, Lourenço J, Franco L, Giovanetti M

BMC Infectious Diseases
24(1):. doi: 10.1186/s12879-024-09658-6.
2024
Genomics-based timely detection of dengue virus type I genotypes I and V in Uruguay

Morel N, Giovanetti M, Fonseca V, Burgueño A, Lima M, Castro E, Guimarães N, Iani F, Bormida V, Cortinas M, Ramas V, Coppola L, Bento A, Rosewell A, Franco L, Mendez Rico J, Lourenço J, Junior Alcantara L, Chiparelli H

Heliyon
10(22):e39246. doi: 10.1016/j.heliyon.2024.e39246.
2024
Unraveling the Complexity of Chikungunya Virus Infection Immunological and Genetic Insights in Acute and Chronic Patients

Fritsch H, Giovanetti M, Clemente L, da Rocha Fernandes G, Fonseca V, de Lima M, Falcão M, de Jesus N, de Cerqueira E, Venâncio da Cunha R, de Oliveira Francisco M, de Siqueira I, de Oliveira C, Xavier J, Ferreira J, Queiroz F, Smith E, Tisoncik-Go J, Van Voorhis W, Rabinowitz P, Wasserheit J, Gale M, de Filippis A, Alcantara L

Genes
15(11):1365. doi: 10.3390/genes15111365.
2024
Integrated analyses of the transmission history of SARS-CoV-2 and its association with molecular evolution of the virus underlining the pandemic outbreaks in Italy, 2019-2023

Cella E, Fonseca V, Branda F, Tosta S, Moreno K, Schuab G, Ali S, Slavov S, Scarpa F, Santos L, Kashima S, Wilkinson E, Tegally H, Mavian C, Borsetti A, Caccuri F, Salemi M, de Oliveira T, Azarian T, de Filippis A, Alcantara L, Ceccarelli G, Caruso A, Colizzi V, Marcello A, Lourenço J, Ciccozzi M, Giovanetti M

International Journal of Infectious Diseases
():107262. doi: 10.1016/j.ijid.2024.107262.
2024
Fatal Oropouche Virus Infections in Nonendemic Region, Brazil, 2024

Bandeira A, Pereira F, Leal A, Santos S, Barbosa A, Souza M, de Souza D, Guimaraes N, Fonseca V, Giovanetti M, Alcantara L, Lessa A, Saavedra R, Tomé L, Iani F, Barros R, Purificação S, de Jesus J, Fonseca R, Araújo M

Emerging Infectious Diseases
30(11):. doi: 10.3201/eid3011.241132.
2024
North–south pathways, emerging variants, and high climate suitability characterize the recent spread of dengue virus serotypes 2 and 3 in the Dominican Republic

Miguel I, Feliz E, Agramonte R, Martinez P, Vergara C, Imbert Y, De la Cruz L, de Castro N, Cedano O, De la Paz Y, Fonseca V, Santiago G, Muñoz-Jordán J, Peguero A, Paulino-Ramírez R, Grubaugh N, de Filippis A, Alcantara L, Rico J, Lourenço J, Franco L, Giovanetti M

BMC Infectious Diseases
24(1):. doi: 10.1186/s12879-024-09658-6.
2024
Detection of Multiple Human Viruses, including Mpox, Using a Wastewater Surveillance Approach in Brazil

Calabria de Araujo J, Carvalho A, Leal C, Natividade M, Borin M, Guerra A, Carobin N, Sabino A, Almada M, Costa M, Saia F, Frutuoso L, Iani F, Adelino T, Fonseca V, Giovanetti M, Alcantara L

Pathogens
13(7):589. doi: 10.3390/pathogens13070589.
2024
Insights into SARS-CoV-2 Surveillance among Prison Populations in Mato Grosso do Sul, Brazil, in 2022

Ferreira da Silva L, Alcantara L, Fonseca V, Frias D, Umaki Zardin M, de Castro Lichs G, Esposito A, Xavier J, Fritsch H, Lima M, de Oliveira C, Castilho de Arruda L, Maziero L, Rodrigues Barretos E, Tsuha Oshiro P, Gimenes Mendes Menezes E, de Freitas Cardoso L, Ferreira Lemos E, Lourenço J, de Albuquerque C, do Carmo Said R, Rosewell A, Ferraz Demarchi L, Croda J, Giovanetti M, Maymone Gonçalves C

Viruses
16(7):1143. doi: 10.3390/v16071143.
2024
Exploring Microorganisms Associated to Acute Febrile Illness and Severe Neurological Disorders of Unknown Origin: A Nanopore Metagenomics Approach

Moreno K, de Andrade V, de Melo Iani F, Fonseca V, Lima M, de Castro Barbosa E, Tomé L, Guimarães N, Fritsch H, Adelino T, Oliveira Fereguetti T, Aspahan M, Gamarano Barros T, Alcantara L, Giovanetti M

Genes
15(7):922. doi: 10.3390/genes15070922.
2024
Tracing the evolution of the chikungunya virus in Argentina, 2016-2023: independent introductions and prominence of Latin American lineages

Fabbri C, Giovanetti M, Luppo V, Fonseca V, Garcia J, Barulli C, Feroci M, Perrone S, Casoni D, Giamperetti S, Alvarez Lopez M, Foussal M, Figueredo M, Salvatierra K, Lejona S, Ruiz Diaz N, Castro G, Bravo G, Jackel N, Sen C, Poklepovich Caride T, Franco L, Giovachini C, Mendez Rico J, Alcantara L, Morales M

Emerging Microbes & Infections
13(1):. doi: 10.1080/22221751.2024.2362941.
2024
Exploring the urban arbovirus landscape in Rio de Janeiro, Brazil: transmission dynamics and patterns of disease spread

Schuab G, Tosta S, Moreno K, Fonseca V, Santos L, Slavov S, Kashima S, Ciccozzi M, Lourenço J, Cella E, de Oliveira C, Cavalcanti A, Junior Alcantara L, de Bruycker-Nogueira F, Bispo de Filippis A, Giovanetti M

The Lancet Regional Health - Americas
35():100786. doi: 10.1016/j.lana.2024.100786.
2024
Detection of encephalitis-causing viruses reveals predominance of chikungunya virus in the state of Bahia, Brazil

Sampaio M, do Rosário M, Martins L, Trindade L, Francisco M, Costa B, Vasconcelos G, Lima I, Macêdo Y, Carvalho F, de Santana M, Khouri R, Fritsch H, Xavier J, Fonseca V, Giovanetti M, de Mello A, Pereira F, Campos G, de Jesus P, Farias D, de Souza M, Galvão A, Costa F, Bessa M, Chagas J, Silvany C, Teles J, de Lima M, Farias T, Gräf T, de Siqueira I

International Journal of Infectious Diseases
145():107090. doi: 10.1016/j.ijid.2024.107090.
2024
Exploring the Chikungunya virus landscape in a dengue-endemic Brazilian area

de La Roque D, Santos E, Policastro L, da Costa P, Evaristo M, Yamamoto A, Giomo D, Torres P, Gentil D, Minto E, Slavov S, Fonseca V, dos Santos Barros C, Martins A, Calado R, Passos L, Elias M, Sampaio S, Giovanetti M, Covas D, Alcântara L, Kashima S

Journal of Infection and Public Health
17(7):102442. doi: 10.1016/j.jiph.2024.04.026.
2024
Genomic and eco-epidemiological investigations in Uruguay reveal local Chikungunya virus transmission dynamics during its expansion across the Americas in 2023

Burgueño A, Giovanetti M, Fonseca V, Morel N, Lima M, Castro E, Guimarães N, Iani F, Bormida V, Cortinas M, Ramas V, Coppola L, Bento A, Franco L, Rico J, Lourenço J, Junior Alcantara L, Chiparelli H

Emerging Microbes & Infections
13(1):. doi: 10.1080/22221751.2024.2332672.
2024
Mapping the Dynamics of Dengue Serotypes in the 2023 Epidemic: Insights from Spatial-Temporal Analysis and Emergence of the Cosmopolitan DENV-2 Genotype in Ribeirão Preto, São Paulo, Brazil

Carmo S, Torres P, Roque D, Santos E, Elias M, Sampaio S, Giovanetti M, Fonseca V, Alcantara L, Gentil D, Giomo D, Kashima S, Passos L

International Journal of Health Science
4(28):2-9. doi: 10.22533/at.ed.1594282419035.
2024
DENV-1 genotype V circulation during the nonepidemic period in the Northeast of São Paulo State endemic area

de La-Roque D, Santos E, Oliveira R, Slavov S, Rodrigues E, Fonseca V, Martins A, Giomo D, Torres P, Gentil D, Catoia E, Chiquito N, Medeiros A, Yamamoto A, Passos L, Calado R, Barros C, Elias M, Sampaio S, Giovanetti M, Junior Alcantara L, Covas D, Kashima S

Journal of Medical Virology
96(3):. doi: 10.1002/jmv.29526.
2024
Resurgence of Dengue Virus Serotype 3 in Minas Gerais, Brazil: A Case Report

Adelino T, Lima M, Guimarães N, Xavier J, Fonseca V, Tomé L, Pereira M, Machado V, Alcantara L, Iani F, Giovanetti M

Pathogens
13(3):202. doi: 10.3390/pathogens13030202.
2024
Epidemiology of the SARS-CoV-2 Omicron Variant Emergence in the Southeast Brazilian Population

Rodrigues E, Slavov S, de La Roque D, Santos E, Borges J, Evaristo M, da Costa P, de Matos Maçonetto J, Marques A, Baccarin A, Oliveira R, Junior W, Benincasa B, de Andrade da Cruz L, Lima A, Ribeiro G, Viala V, de Lima L, Martins A, dos Santos Barros C, Marqueze E, de Souza Todao Bernardino J, Grotto R, Souza-Neto J, Fonseca V, Nogueira M, Fukumasu H, Coutinho L, Calado R, Covas D, Giovanetti M, Alcantara L, Sampaio S, Elias M, Kashima S

Microorganisms
12(3):449. doi: 10.3390/microorganisms12030449.
2024
Evidence of Zika Virus Reinfection by Genome Diversity and Antibody Response Analysis, Brazil

da Costa Castilho M, de Filippis A, Machado L, de Lima Calvanti T, Lima M, Fonseca V, Giovanetti M, Docena C, Neto A, Bôtto-Menezes C, Kara E, de La Barrera R, Modjarrad K, Giozza S, Pereira G, Alcantara L, Broutet N, Calvet G, Wallau G, Franca R

Emerging Infectious Diseases
30(2):. doi: 10.3201/eid3002.230122.
2024
Exploring the Genomic Dynamics of the Monkeypox Epidemic in Paraguay

Vazquez C, Fonseca V, de la Fuente A, Gonzalez S, Fleitas F, Lima M, Guimarães N, Iani F, Rojas A, Alfonso T, Cantero C, Barrios J, Villalba S, Ortega M, Torales J, Gamarra M, Aquino C, Franco L, Rico J, Alcantara L, Giovanetti M

Viruses
16(1):83. doi: 10.3390/v16010083.
2024
A new lineage nomenclature to aid genomic surveillance of dengue virus

Hill V, Cleemput S, Pereira JS, Gifford RJ, Fonseca V, Tegally H, Brito AF, Ribeiro G, de Souza VC, Brcko IC, Ribeiro IS, De Lima ITT, Slavov SN, Sampaio SC, Elias MC, Tran VT, Kien DTH, Huynh T, Yacoub S, Dieng I, Salvato R, Wallau GL, Gregianini TS, Godinho FMS, Vogels CBF, Breban MI, Leguia M, Jagtap S, Roy R, Hapuarachchi C, Mwanyika G, Giovanetti M, Alcantara LCJ, Faria NR, Carrington CVF, Hanley KA, Holmes EC, Dumon W, Lima ARJ, de Oliveira T, Grubaugh ND.

PLoS Biology
22(9):e3002834. doi: 10.1371/journal.pbio.3002834.
2024
A new lineage nomenclature to aid genomic surveillance of dengue virus

Hill V, Cleemput S, Fonseca V, Tegally H, Brito AF, Gifford R, Tran VT, Kien DTH, Huynh T, Yacoub S, Dieng I, Ndiaye M, Balde D, Diagne MM, Faye O, Salvato R, Wallau GL, Gregianini TS, Godinho FMS, Vogels CBF, Breban MI, Leguia M, Jagtap S, Roy R, Hapuarachchi C, Mwanyika G, Giovanetti M, Alcantara LCJ, Faria NR, Carrington CVF, Hanley KA, Holmes EC, Dumon W, de Oliveira T, Grubaugh ND

medRxiv [Preprint]
2024.05.16.24307504. doi: 10.1101/2024.05.16.24307504
2023
Global SARS-CoV-2 genomic surveillance: What we have learned (so far)

Tosta S, Moreno K, Schuab G, Fonseca V, Segovia F, Kashima S, Elias M, Sampaio S, Ciccozzi M, Alcantara L, Slavov S, Lourenço J, Cella E, Giovanetti M

Infection, Genetics and Evolution
108():105405. doi: 10.1016/j.meegid.2023.105405.
2023
SARS-CoV-2 Spillback to Wild Coatis in Sylvatic–Urban Hotspot, Brazil

Stoffella-Dutra A, de Campos B, Bastos e Silva P, Dias K, da Silva Domingos I, Hemetrio N, Xavier J, Iani F, Fonseca V, Giovanetti M, de Oliveira L, Teixeira M, Lobato Z, Ferreira H, Arns C, Durigon E, Drumond B, Alcantara L, de Carvalho M, de Souza Trindade G

Emerging Infectious Diseases
29(3):664-667. doi: 10.3201/eid2903.221339.
2023
Phylogenetic Reconstructions Reveal the Circulation of a Novel Dengue Virus-1V Clade and the Persistence of a Dengue Virus-2 III Genotype in Northeast Brazil

Fritsch H, Moreno K, Lima I, Santos C, Costa B, de Almeida B, dos Santos R, Francisco M, Sampaio M, de Lima M, Pereira F, Fonseca V, Tosta S, Xavier J, de Oliveira C, Adelino T, de Mello A, Gräf T, Alcantara L, Giovanetti M, de Siqueira I

Viruses
15(5):1073. doi: 10.3390/v15051073.
2023
Genomic Surveillance of Monkeypox Virus, Minas Gerais, Brazil, 2022

Guimarães N, Tomé L, Lamounier L, Silva M, Lima M, da Costa A, Luiz K, de Jesus R, Trindade G, Oliveira D, da Fonseca F, Fernandes A, de Oliveira J, Moura J, Kroon E, Giovanetti M, Fonseca V, Alcantara L, Adelino T, de Milo Iani F

Emerging Infectious Diseases
29(6):. doi: 10.3201/eid2906.230113.
2023
Retrospective Spatio-Temporal Dynamics of Dengue Virus 1, 2 and 4 in Paraguay

Vazquez C, Alcantara L, Fonseca V, Lima M, Xavier J, Adelino T, Fritsch H, Castro E, de Oliveira C, Schuab G, Lima A, Villalba S, Gomez de la Fuente A, Rojas A, Cantero C, Fleitas F, Aquino C, Ojeda A, Sequera G, Torales J, Barrios J, Elias M, Iani F, Ortega M, Gamarra M, Montoya R, Rodrigues E, Kashima S, Sampaio S, Coluchi N, Leite J, Gresh L, Franco L, Lourenço J, Rico J, Bispo de Filippis A, Giovanetti M

Viruses
15(6):1275. doi: 10.3390/v15061275.
2023
Potential use of high-resolution melting analyses for SARS-CoV-2 genomic surveillance

de Souza Andrade A, Freitas E, de Castro Barbosa E, Guimarães N, de Melo Iani F, da Costa A, Bernardes A, Adelino T, Ataide A, Gregianini T, Nunes J, Stringari L, Riediger I, Fernandes S, de Jesus R, Fonseca V, Caldas S

Journal of Virological Methods
317():114742. doi: 10.1016/j.jviromet.2023.114742.
2023
The Importance of Entomo-Virological Investigation of Yellow Fever Virus to Strengthen Surveillance in Brazil

Cruz A, Hernández L, Aragão C, da Paz T, da Silva S, da Silva F, de Aquino A, Cereja G, Nascimento B, Rosa Junior J, Elias C, Nogueira C, Ramos D, Fonseca V, Giovanetti M, Alcantara L, Nunes B, Vasconcelos P, Martins L, Nunes-Neto J

Tropical Medicine and Infectious Disease
8(6):329. doi: 10.3390/tropicalmed8060329.
2023
Molecular Characterization of Salmonella Phage Wara Isolated from River Water in Brazil

Romero-Calle D, Pedrosa-Silva F, Ribeiro Tomé L, Fonseca V, Guimarães Benevides R, de Oliveira Santos L, de Oliveira T, da Costa M, Alcantara L, de Carvalho Azevedo V, Brenig B, Venancio T, Billington C, Góes-Neto A

Microorganisms
11(7):1837. doi: 10.3390/microorganisms11071837.
2023
Increased interregional virus exchange and nucleotide diversity outline the expansion of chikungunya virus in Brazil

Xavier J, Alcantara L, Fonseca V, Lima M, Castro E, Fritsch H, Oliveira C, Guimarães N, Adelino T, Evaristo M, Rodrigues E, Santos E, de La-Roque D, de Moraes L, Tosta S, Neto A, Rosewell A, Mendonça A, Leite A, Vasconcelos A, Silva de Mello A, Vasconcelos B, Montalbano C, Zanluca C, Freitas C, de Albuquerque C, Duarte dos Santos C, Santos C, dos Santos C, Gonçalves C, Teixeira D, Neto D, Cabral D, de Oliveira E, Noia Maciel E, Pereira F, Iani F, de Carvalho F, Andrade G, Bezerra G, de Castro Lichs G, Pereira G, Barroso H, Franz H, Ferreira H, Gomes I, Riediger I, Rodrigues I, de Siqueira I, Silva J, Rico J, Lima J, Abrantes J, do Nascimento J, Wasserheit J, Pastor J, de Magalhães J, Luz K, Lima Neto L, Frutuoso L, da Silva L, Sena L, de Sousa L, Pereira L, Demarchi L, Câmara M, Astete M, Almiron M, Lima M, Umaki Zardin M, Presibella M, Falcão M, Gale M, Freire N, Marques N, de Moura N, Almeida Da Silva P, Rabinowitz P, da Cunha R, Trinta K, do Carmo Said R, Kato R, Stabeli R, de Jesus R, Hans Santos R, Kashima S, Slavov S, Andrade T, Rocha T, Carneiro T, Nardy V, da Silva V, Carvalho W, Van Voorhis W, Araujo W, de Filippis A, Giovanetti M

Nature Communications
14(1):. doi: 10.1038/s41467-023-40099-y.
2023
Unveiling the Impact of the Omicron Variant: Insights from Genomic Surveillance in Mato Grosso do Sul, Midwest Brazil

de Mello Almeida Maziero L, Giovanetti M, Fonseca V, Zardin M, de Castro Lichs G, de Rezende Romera G, Tsuha D, Frias D, Escandolhero V, Demarchi L, Domingues Castilho L, Barbosa K, Tebet D, Xavier J, Fritsch H, Lima M, de Oliveira C, Santos E, Kashima S, Said R, Rosewell A, Croda J, Alcantara L, Cavalheiro Maymone Gonçalves C

Viruses
15(7):1604. doi: 10.3390/v15071604.
2023
Case report: Urbanized non-human primates as sentinels for human zoonotic diseases: a case of acute fatal toxoplasmosis in a free-ranging marmoset in coinfection with yellow fever virus

Sousa D, Wilson T, Macêdo I, Romano A, Ramos D, Passos P, Costa G, Fonseca V, Mares-Guia M, Giovanetti M, Alcantara L, de Filippis A, Paludo G, Melo C, Castro M

Frontiers in Public Health
11():. doi: 10.3389/fpubh.2023.1236384.
2023
Rapid Epidemic Expansion of Chikungunya Virus East/Central/South African Lineage, Paraguay

Giovanetti M, Vazquez C, Lima M, Castro E, Rojas A, Gomez de la Fuente A, Aquino C, Cantero C, Fleitas F, Torales J, Barrios J, Ortega M, Gamarra M, Villalba S, Alfonzo T, Xavier J, Adelino T, Fritsch H, Iani F, Pereira G, de Oliveira C, Schuab G, Rodrigues E, Kashima S, Leite J, Gresh L, Franco L, Tegally H, Van Voorhis W, Lessels R, de Filippis A, Ojeda A, Sequera G, Montoya R, Holmes E, de Oliveira T, Rico J, Lourenço J, Fonseca V, Alcantara L

Emerging Infectious Diseases
29(9):. doi: 10.3201/eid2909.230523.
2023
Dengue Fever Surveillance in Mato Grosso do Sul: Insights from Genomic Analysis and Implications for Public Health Strategies

Castilho de Arruda L, Giovanetti M, Fonseca V, Zardin M, Lichs G, Asato S, Esposito A, Tokeshi Müller M, Xavier J, Fritsch H, Lima M, de Oliveira C, Santos E, Maziero L, Frias D, Ahad das Neves D, Ferreira da Silva L, Rodrigues Barretos E, Tsuha Oshiro P, Modafari Goday B, Lemos dos Santos J, Kashima S, Albuquerque C, Said R, Rosewell A, Demarchi L, Croda J, Alcantara L, Cavalheiro Maymone Gonçalves C

Viruses
15(9):1790. doi: 10.3390/v15091790.
2023
Technology transfer during the COVID-19 pandemic: report on the first face-to-face practical training course in Brazil

Barreto F, Santos L, Giovanetti M, Fonseca V, Aburjaile F, Silva J, Freitas C, Peterka C, Rico J, Almiron M, Melo C, Alcântara L

Epidemiologia e Serviços de Saúde
32(2):. doi: 10.1590/s2237-96222023000200017.
2023
Genomic Epidemiology and Lineage Dynamics of SARS-CoV-2 in Bulgaria: Insights from a Three-Year Pandemic Analysis

Giovanetti M, Cella E, Ivanov I, Grigorova L, Stoikov I, Donchev D, Dimitrova R, Slavov S, Mavian C, Fonseca V, Scarpa F, Borsetti A, Korsun N, Trifonova I, Dobrinov V, Kantardjiev T, Christova I, Ciccozzi M, Alexiev I

Viruses
15(9):1924. doi: 10.3390/v15091924.
2023
Genomic characterization of SARS-CoV-2 from an indigenous reserve in Mato Grosso do Sul, Brazil

de Oliveira L, de Rezende I, Navarini V, Marchioro S, Torres A, Croda J, Croda M, Gonçalves C, Xavier J, de Castro E, Lima M, Iani F, Adelino T, Aburjaile F, Ferraz Demarchi L, Taira D, Zardin M, Fonseca V, Giovanetti M, Andrews J, Alcantara L, Simionatto S

Frontiers in Public Health
11():. doi: 10.3389/fpubh.2023.1195779.
2023
Strengthening Genomic Surveillance Capacity for Epidemic-Prone Pathogens by Training Personnel From Public Health Laboratories in Brazil and Paraguay

Giovanetti M, Fonseca V, Navegantes W, Abreu AL, Stabeli R, Vazquez CC, Albuquerque CFC, Rico JM, Galiano SG, Almiron M, Alcantara LCJ

Weekly Epidemiological Record
v. 98, p. 63-68
2023
A Multiplex Nanopore Sequencing Approach for the Detection of Multiple Arboviral Species

Xavier J, Fonseca V, Adelino T, Iani F, Pereira G, Duarte M, Lima M, Castro E, Oliveira C, Fritsch H, Guimarães N, Lamounier L, Barreto F, Braga de Oliveira C, Maymone Gonçalves C, Malta Lima D, de Oliveira E, de Castro Lichs G, Gomes I, Mazaro J, Rodrigues J, Abrantes J, Colares J, Luz K, Barbosa da Silva L, Demarchi L, Câmara M, Umaki Zardin M, Sabatini Mello Pinheiro R, Barbosa Souza R, Haddad S, Figueiredo da Silva S, Slavov S, Rocha T, Morel N, Chiparelli H, Burgueño A, Bórmida V, Cortinas M, Martín R, Pereira A, dos Santos M, André Júnior W, Mendez Rico J, Franco L, Rosewell A, do Carmo Said R, de Albuquerque C, Noia Maciel E, Santini de Oliveira M, Venâncio da Cunha R, Vinhal Frutuoso L, de Filippis A, Giovanetti M, Carlos Junior Alcantara L

Viruses
16(1):23. doi: 10.3390/v16010023.
2023
Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil

Giovanetti M, Pinotti F, Zanluca C, Fonseca V, Nakase T, Koishi AC, Tscha M, Soares G, Dorl GG, Marques AEML, Sousa R, Adelino TER, Xavier J, de Oliveira C, Patroca S, Guimaraes NR, Fritsch H, Mares-Guia MA, Levy F, Passos PH, da Silva VL, Pereira LA, Mendonça AF, de Macêdo IL, Ribeiro de Sousa DE, Rodrigues de Toledo Costa G, Botelho de Castro M, de Souza Andrade M, de Abreu FVS, Campos FS, Iani FCM, Pereira MA, Cavalcante KRLJ, de Freitas ARR, Campelo de Albuquerque CF, Macário EM, Dos Anjos MPD, Ramos RC, Campos AAS, Pinter A, Chame M, Abdalla L, Riediger IN, Ribeiro SP, Bento AI, de Oliveira T, Freitas C, Oliveira de Moura NF, Fabri A, Dos Santos Rodrigues CD, Dos Santos CC, Barreto de Almeida MA, Dos Santos E, Cardoso J, Augusto DA, Krempser E, Mucci LF, Gatti RR, Cardoso SF, Fuck JAB, Lopes MGD, Belmonte IL, Mayoral Pedroso da Silva G, Soares MRF, de Castilhos MMS, de Souza E Silva JC, Bisetto Junior A, Pouzato EG, Tanabe LS, Arita DA, Matsuo R, Dos Santos Raymundo J, Silva PCL, Santana Araújo Ferreira Silva A, Samila S, Carvalho G, Stabeli R, Navegantes W, Moreira LA, Ferreira AGA, Pinheiro GG, Nunes BTD, de Almeida Medeiros DB, Cruz ACR, Venâncio da Cunha R, Van Voorhis W, Bispo de Filippis AM, Almiron M, Holmes EC, Ramos DG, Romano A, Lourenço J, Alcantara LCJ, Duarte Dos Santos CN

Science Advances
9(35):eadg9204. doi: 10.1126/sciadv.adg9204
2023
Genomic epidemiology sheds light on the recent spatio-temporal dynamics of Yellow Fever virus and the spatial corridor that fueled its ongoing emergence in southern Brazil

Giovanetti M, Pinotti F, Zanluca C, Fonseca V, Nakase T, Koishi A, Tscha M, Soares G, Dorl G, Marques AE, Sousa RS, Adelino TER, Xavier J, Oliveira C, Patroca S, Guimaraes NR, Fritsch H, Mares-Guia MA, Levy F, Passos PH, da Silva VL, Pereira LA, Mendonca AF, de Macedo IL, de Souze DER , Costa GRT, de Castro MB, Iani FCM, Pereira MA, Cavalcante KRLJ, Freitas ARR, de Albuquerque CFC, Macario EM, dos Anjos MPD, Ramos RC, Campos AAS, Pinter A, Chame M, Abdalla L, Riediger IN, Ribeiro SP, Bento AI, de Oliveira T, Freitas C, de Moura NFB, Fabri A, Rodrigues CDS, dos Santos CC, de Almeida MAB, dos Santos E, Cardoso J, Augusto DA, Krempser E, Mucci LF, Gatti RR, Cardoso SF, Fuck JAB, Lopes MGD, Belmonte IL, da Silva GMP, Soares MRF, de Castilhos MMS, Silva JCS, Junior AB, Pouzato EG, Tanabe LS, Arita DA, Matsuo RM, Raymundo JS, Silva PCL, Silva ASAF, Samila S, Pereira GC, Stabeli R, Navegantes W, Moreira LA, Ferreira AGA, Pinheiro GG, Nunes BTD, Medeiros DBA, Cruz ACR, Cunha RV, Voorhis WV, de Filippis AMB, Almiron MA, Holmes EC, Ramos DG, Martins AP, Lourenco JL, Alcantara LCJ, dos Santos CND

medRxiv
2023.01.13.23284525v1
2023
Rapid epidemic expansion of chikungunya virus-ECSA lineage in Paraguay

Giovanetti M, Vazquez C, Lima M, Castro E, Rojas A, de la Fuente AG, Aquino C, Cantero C, Fleitas F, Torales J, Barrios J, Ortega MJ, Gamarra ML, Villalba S, Alfonzo T, Xavier J, Adelino T, Fritsch H, Iani FCM, Pereira GC, de Oliveira C, Schuab G, Rodrigues ES, Kashima S, Leite J, Gresh L, Franco L, Tegally H, Van Voorhis WC, Lessels R, de Filippis AMB, Ojeda A, Sequera G, Montoya R, Holmes EC, de Oliveira T, Rico JM, Lourenço J, Fonseca V, Junior Alcantara LC

medRXiV
doi:10.1101/2023.04.16.23288635
2022
Fast surveillance response reveals the introduction of a new yellow fever virus sub-lineage in 2021, in Minas Gerais, Brazil

Andrade M, Campos F, Oliveira C, Oliveira R, Campos A, Almeida M, Fonseca V, Simonini-Teixeira D, Seva A, Temponi A, Magalhaes F, Chaves D, Pereira M, Lamounier L, Menezes G, Aquino-Teixeira S, Goncalves-dos-Santos M, Bernal-Valle S, Muller N, Cardoso J, Santos E, Mares-Guia M, Albuquerque G, Romano A, Franco A, Ribeiro B, Roehe P, Abreu F

Memórias do Instituto Oswaldo Cruz
117():. doi: 10.1590/0074-02760220127.
2022
Retrospective Analysis of the SARS-CoV-2 Infection Profile in COVID-19 Positive Patients in Vitoria da Conquista, Northeast Brazil

Dantas A, Oliveira H, Gomes C, Alves D, Infante P, Caitite R, Fritsch H, Cucco M, Silva L, Oliveira C, Bittencourt R, Amorim A, Nascimento A, Marinho F, de Medeiros D, de Oliveira M, Mistro S, de Melo F, Pereira T, Guimaraes A, Timenetsky J, Moreira P, de Oliveira S, Alcantara L, Giovanetti M, Santos L, Fonseca V, Barreto F, Campos G, Marques L

Viruses
14(11):2424. doi: 10.3390/v14112424.
2022
Emergence of Dengue Virus Serotype 2 Cosmopolitan Genotype, Brazil

Giovanetti M, Pereira L, Santiago G, Fonseca V, Mendoza M, de Oliveira C, de Moraes L, Xavier J, Tosta S, Fristch H, de Castro Barbosa E, Rodrigues E, Figueroa-Romero D, Padilla-Rojas C, Cáceres-Rey O, Mendonça A, de Bruycker Nogueira F, Venancio da Cunha R, de Filippis A, Freitas C, Peterka C, de Albuquerque C, Franco L, Méndez Rico J, Muñoz-Jordán J, Lemes da Silva V, Alcantara L

Emerging Infectious Diseases
28(8):1725-1727. doi: 10.3201/eid2808.220550.
2022
Dynamics of SARS-CoV-2 Variants of Concern in Vaccination Model City in the State of Sao Paulo, Brazil

Slavov S, de La-Roque D, da Costa P, Rodrigues E, Santos E, Borges J, Evaristo M, de Matos Maçonetto J, Marques A, Milhomens J, Rós F, Fonseca V, Lima A, Ribeiro G, Lima L, Garibaldi P, Ferreira N, Moraes G, Marqueze E, Barros C, Martins A, Coutinho L, Calado R, Borges M, Elias M, Sampaio S, Giovanetti M, Alcantara L, Covas D, Kashima S

Viruses
14(10):2148. doi: 10.3390/v14102148.
2022
Retrospective Genomic Surveillance of Chikungunya Transmission in Minas Gerais State, Southeast Brazil

Fritsch H, Giovanetti M, Xavier J, Adelino T, Fonseca V, de Jesus J, de Jesus R, Freitas C, Peterka C, Campelo de Albuquerque C, Bispo de Filippis A, da Cunha R, Silva E, Alcantara L, Iani F

Microbiology Spectrum
10(5):. doi: 10.1128/spectrum.01285-22.
2022
Molecular dynamics simulations of the SARS-CoV-2 Spike protein and variants of concern: structural evidence for convergent adaptive evolution

Neto D, Fonseca V, Jesus R, Dutra L, Portela L, Freitas C, Fillizola E, Soares B, Abreu A, Twiari S, Azevedo V, Goes-Neto A, de Medeiros A, Lopes N, Zanotto P, Kato R

Journal of Biomolecular Structure and Dynamics
41(12):5789-5801. doi: 10.1080/07391102.2022.2097955.
2022
Retrospective Investigation in Horses with Encephalitis Reveals Unnoticed Circulation of West Nile Virus in Brazil

Fritsch H, Pereira F, Costa E, Fonseca V, Tosta S, Xavier J, Levy F, Oliveira C, Menezes G, Lima J, Santos L, Silva L, Nardy V, Astete M, Santos B, Aguiar N, Guedes M, Faria G, Furtini R, Drumond S, Cunha G, Souza M, Jesus R, Guimarães S, Nuno I, Santana I, Sá J, Santos G, Silva W, Guedes T, Araújo E, Said R, Albuquerque C, Peterka C, Romano A, Cunha R, Filippis A, Leal e Silva de Mello A, Giovanetti M, Alcantara L

Viruses
14(7):1540. doi: 10.3390/v14071540.
2022
SARS-CoV-2 epidemic in Brazil: how the displacement of variants has driven distinct epidemic waves

Alcantara L, Nogueira E, Shuab G, Tosta S, Fristch H, Pimentel V, Souza-Neto J, Coutinho L, Fukumasu H, Sampaio S, Elias M, Kashima S, Slavov S, Ciccozzi M, Cella E, Lourenco J, Fonseca V, Giovanetti M

Virus Research
315():198785. doi: 10.1016/j.virusres.2022.198785.
2022
Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil

Giovanetti M, Slavov SN, Fonseca V, Wilkinson E, Tegally H, Patané JSL, Viala VL, San EJ, Rodrigues ES, Santos EV, Aburjaile F, Xavier J, Fritsch H, Adelino TER, Pereira F, Leal A, Iani FCM, de Carvalho Pereira G, Vazquez C, Sanabria GME, Oliveira EC, Demarchi L, Croda J, Dos Santos Bezerra R, Paola Oliveira de Lima L, Martins AJ, Renata Dos Santos Barros C, Marqueze EC, de Souza Todao Bernardino J, Moretti DB, Brassaloti RA, de Lello Rocha Campos Cassano R, Mariani PDSC, Kitajima JP, Santos B, Proto-Siqueira R, Cantarelli VV, Tosta S, Nardy VB, Reboredo de Oliveira da Silva L, Gómez MKA, Lima JG, Ribeiro AA, Guimarães NR, Watanabe LT, Barbosa Da Silva L, da Silva Ferreira R, da Penha MPF, Ortega MJ, de la Fuente AG, Villalba S, Torales J, Gamarra ML, Aquino C, Figueredo GPM, Fava WS, Motta-Castro ARC, Venturini J, do Vale Leone de Oliveira SM, Gonçalves CCM, do Carmo Debur Rossa M, Becker GN, Giacomini MP, Marques NQ, Riediger IN, Raboni S, Mattoso G, Cataneo AD, Zanluca C, Duarte Dos Santos CN, Assato PA, Allan da Silva da Costa F, Poleti MD, Lesbon JCC, Mattos EC, Banho CA, Sacchetto L, Moraes MM, Grotto RMT, Souza-Neto JA, Nogueira ML, Fukumasu H, Coutinho LL, Calado RT, Neto RM, Bispo de Filippis AM, Venancio da Cunha R, Freitas C, Peterka CRL, de Fátima Rangel Fernandes C, Navegantes W, do Carmo Said RF, Campelo de A E Melo CF, Almiron M, Lourenço J, de Oliveira T, Holmes EC, Haddad R, Sampaio SC, Elias MC, Kashima S, Junior de Alcantara LC, Covas DT

Nature Microbiology
doi: 10.1038/s41564-022-01191-z
2022
Genomic surveillance of Rift Valley fever virus: from sequencing to lineage assignment

Juma J, Fonseca V, Konongoi SL, van Heusden P, Roesel K, Sang R, Bett B, Christoffels A, de Oliveira T, Oyola SO

BMC Genomics
23(1):520. doi: 10.1186/s12864-022-08764-6
2022
Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil

Giovanetti M, Slavov SN, Fonseca V, Wilkinson E, Tegally H, Patané JSL, Viala VL, San JE, Rodrigues ES, Vieira Santos E, Aburjaile F, Xavier J, Fritsch H, Ribeiro Adelino TE, Pereira F, Leal A, Campos de Melo Iani F, de Carvalho Pereira G, Vazquez C, Mercedes Estigarribia Sanabria G, de Oliveira EC, Demarchi L, Croda J, Dos Santos Bezerra R, Oliveira de Lima LP, Martins AJ, Dos Santos Barros CR, Marqueze EC, de Souza Todao Bernardino J, Moretti DB, Brassaloti RA, de Lello Rocha Campos Cassano R, Drummond Sampaio Corrêa Mariani P, Kitajima JP, Santos B, Proto-Siqueira R, Cantarelli VV, Tosta S, Brandão Nardy V, Reboredo de Oliveira da Silva L, Astete Gómez MK, Lima JG, Ribeiro AA, Guimarães NR, Watanabe LT, Barbosa Da Silva L, da Silva Ferreira R, F da Penha MP, Ortega MJ, Gómez de la Fuente A, Villalba S, Torales J, Gamarra ML, Aquino C, Martínez Figueredo GP, Fava WS, Motta-Castro ARC, Venturini J, do Vale Leone de Oliveira SM, Cavalheiro Maymone Gonçalves C, Debur Rossa MDC, Becker GN, Presibella MM, Marques NQ, Riediger IN, Raboni S, Coelho GM, Cataneo AHD, Zanluca C, Dos Santos CND, Assato PA, Allan da Silva da Costa F, Poleti MD, Chagas Lesbon JC, Mattos EC, Banho CA, Sacchetto L, Moraes MM, Tommasini Grotto RM, Souza-Neto JA, Nogueira ML, Fukumasu H, Coutinho LL, Calado RT, Neto RM, Bispo de Filippis AM, Venancio da Cunha R, Freitas C, Leonel Peterka CR, Rangel Fernandes CF, de Araújo WN, do Carmo Said RF, Almiron M, Campelo de Albuquerque E Melo CF, Lourenço J, de Oliveira T, Holmes EC, Haddad R, Sampaio SC, Elias MC, Kashima S, de Alcantara LCJ, Covas DT

medRxiv [Preprint]
28:2021.10.07.21264644. doi: 10.1101/2021.10.07.21264644
2022
Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic

Giovanetti M, Fonseca V, Wilkinson E, Tegally H, San EJ, Althaus CL, Xavier J, Nanev Slavov S, Viala VL, Ranieri Jerônimo Lima A, Ribeiro G, Souza-Neto JA, Fukumasu H, Lehmann Coutinho L, Venancio da Cunha R, Freitas C, Campelo de A E Melo CF, Navegantes de Araújo W, Do Carmo Said RF, Almiron M, de Oliveira T, Coccuzzo Sampaio S, Elias MC, Covas DT, Holmes EC, Lourenço J, Kashima S, de Alcantara LCJ

Virus Evolution
doi: 10.1093/ve/veac024
2022
A Retrospective Overview of Zika Virus Evolution in the Midwest of Brazil.

Giovanetti M, Pereira LA, Adelino TÉR, Fonseca V, Xavier J, de Araújo Fabri A, Slavov SN, da Silva Lemos P, de Almeida Marques W, Kashima S, Lourenço J, de Oliveira T, Campelo de Albuquerque CF, Freitas C, Peterka CRL, da Cunha RV, Mendonça AF, Lemes da Silva V, Alcantara LCJ

Microbiol Spectr.
e0015522. doi: 10.1128/spectrum.00155-22
2021
Rapid replacement of the Beta variant by the Delta variant in South Africa

Tegally H, Wilkinson E, Althaus C, Giovanetti M, San J, Giandhari J, Pillay S, Naidoo Y, Ramphal U, Msomi N, Mlisana K, Amoako D, Everatt J, Mohale T, Nguni A, Mahlangu B, Ntuli N, Khumalo Z, Makatini Z, Wolter N, Scheepers C, Ismail A, Doolabh D, Joseph R, Strydom A, Mendes A, Davids M, Mayaphi S, Ramphal Y, Maharaj A, Karim W, Tshiabuila D, Anyaneji U, Singh L, Engelbrecht S, Fonseca V, Marais K, Korsman S, Hardie D, Hsiao N, Maponga T, van Zyl G, Marais G, Iranzadeh A, Martin D, Alcantara L, Bester P, Nyaga M, Subramoney K, Treurnicht F, Venter M, Goedhals D, Preiser W, Bhiman J, vonGottberg A, Williamson C, Lessells R, de Oliveira T

medRxiv
MEDRXIV-2021-264018v1
2021
A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

Wilkinson E, Giovanetti M, Tegally H, San JE, Lessells R, Cuadros D, Martin DP, Rasmussen DA, Zekri AN, Sangare AK, Ouedraogo AS, Sesay AK, Priscilla A, Kemi AS, Olubusuyi AM, Oluwapelumi AOO, Hammami A, Amuri AA, Sayed A, Ouma AEO, Elargoubi A, Ajayi NA, Victoria AF, Kazeem A, George A, Trotter AJ, Yahaya AA, Keita AK, Diallo A, Kone A, Souissi A, Chtourou A, Gutierrez AV, Page AJ, Vinze A, Iranzadeh A, Lambisia A, Ismail A, Rosemary A, Sylverken A, Femi A, Ibrahimi A, Marycelin B, Oderinde BS, Bolajoko B, Dhaala B, Herring BL, Njanpop-Lafourcade BM, Kleinhans B, McInnis B, Tegomoh B, Brook C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Peyrefitte C, Daubenberger C, Morang'a CM, Nokes DJ, Amoako DG, Bugembe DL, Park D, Baker D, Doolabh D, Ssemwanga D, Tshiabuila D, Bassirou D, Amuzu DSY, Goedhals D, Omuoyo DO, Maruapula D, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong'era EM, Ngabana EN, Shumba E, El Fahime E, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Leendertz F, Ajili F, Enoch FO, Wasfi F, Abdelmoula F, Mosha FS, Takawira FT, Derrar F, Bouzid F, Onikepe F, Adeola F, Muyembe FM, Tanser F, Dratibi FA, Mbunsu GK, Thilliez G, Kay GL, Githinji G, van Zyl G, Awandare GA, Schubert G, Maphalala GP, Ranaivoson HC, Lemriss H, Anise H, Abe H, Karray HH, Nansumba H, Elgahzaly HA, Gumbo H, Smeti I, Ayed IB, Odia I, Ben Boubaker IB, Gaaloul I, Gazy I, Mudau I, Ssewanyana I, Konstantinus I, Lekana-Douk JB, Makangara JC, Tamfum JM, Heraud JM, Shaffer JG, Giandhari J, Li J, Yasuda J, Mends JQ, Kiconco J, Morobe JM, Gyapong JO, Okolie JC, Kayiwa JT, Edwards JA, Gyamfi J, Farah J, Nakaseegu J, Ngoi JM, Namulondo J, Andeko JC, Lutwama JJ, O'Grady J, Siddle K, Adeyemi KT, Tumedi KA, Said KM, Hae-Young K, Duedu KO, Belyamani L, Fki-Berrajah L, Singh L, Martins LO, Tyers L, Ramuth M, Mastouri M, Aouni M, El Hefnawi M, Matsheka MI, Kebabonye M, Diop M, Turki M, Paye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina M, Nwando M, Owusu M, Wiley MR, Youtchou MT, Ayekaba MO, Abouelhoda M, Seadawy MG, Khalifa MK, Sekhele M, Ouadghiri M, Diagne MM, Mwenda M, Allam M, Phan MVT, Abid N, Touil N, Rujeni N, Kharrat N, Ismael N, Dia N, Mabunda N, Hsiao NY, Silochi NB, Nsenga N, Gumede N, Mulder N, Ndodo N, Razanajatovo NH, Iguosadolo N, Judith O, Kingsley OC, Sylvanus O, Peter O, Femi O, Idowu O, Testimony O, Chukwuma OE, Ogah OE, Onwuamah CK, Cyril O, Faye O, Tomori O, Ondoa P, Combe P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Dussart P, Bester PA, Mbala PK, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Carr RAA, El Kabbaj S, Gargouri S, Masmoudi S, Sankhe S, Lawal SB, Kassim S, Trabelsi S, Metha S, Kammoun S, Lemriss S, Agwa SHA, Calvignac-Spencer S, Schaffner SF, Doumbia S, Mandanda SM, Aryeetey S, Ahmed SS, Elhamoumi S, Andriamandimby S, Tope S, Lekana-Douki S, Prosolek S, Ouangraoua S, Mundeke SA, Rudder S, Panji S, Pillay S, Engelbrecht S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Aanniz T, Mohale T, Le-Viet T, Schindler T, Anyaneji UJ, Chinedu U, Ramphal U, Jessica U, George U, Fonseca V, Enouf V, Gorova V, Roshdy WH, Ampofo WK, Preiser W, Choga WT, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR, Sall AA, Rebai A, von Gottberg A, Kouriba B, Williamson C, Bridges DJ, Chikwe I, Bhiman JN, Mine M, Cotten M, Moyo S, Gaseitsiwe S, Saasa N, Sabeti PC, Kaleebu P, Tebeje YK, Tessema SK, Happi C, Nkengasong J, de Oliveira T

Science
DOI: 10.1126/science.abj4336
2021
West Nile Virus in Brazil

Costa WE, Giovanetti M, Silva Catenacci L, Fonseca V, Aburjaile FF, Chalhoub FLL, Xavier J, Campos de Melo Iani F, da Cunha E Silva Vieira MA, Freitas Henriques D, Medeiros DBA, Guedes MIMC, Senra Álvares da Silva Santos B, Gonçalves Silva AS, de Pino Albuquerque Maranhão R, da Costa Faria NR, Farinelli de Siqueira R, de Oliveira T, Ribeiro Leite Jardim Cavalcante K, Oliveira de Moura NF, Pecego Martins Romano A, Campelo de Albuquerque CF, Soares Feitosa LC, Martins Bayeux JJ, Bertoni Cavalcanti Teixeira R, Lisboa Lobato O, da Costa Silva S, Bispo de Filippis AM, Venancio da Cunha R, Lourenco J, Alcantara LCJ

Pathogens
10(7):896. doi: 10.3390/pathogens10070896
2021
Short Report: Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil

Tosta S, Giovanetti M, Brandão Nardy V, Reboredo de Oliveira da Silva L, Kelly Astete Gomez M, Gomes Lima J, Wanderley Cardoso C, Oliveira Silva T, Sao Pedro Leal de Souza M, Presta Dia PH, Fonseca V, de Oliveira T, Lourenco J, Carlos Junior Alcantara L, Pereira F, Leal A

PLoS Negl Trop Dis.
15(7):e0009591. doi: 10.1371/journal.pntd.0009591
2021
Molecular surveillance of the on-going SARS-COV-2 epidemic in Ribeirao Preto City, Brazil

Slavov SN, Giovanetti M, Bezerra RS, Fonseca V, Santos EV, Rodrigues ES, Adelino T, Xavier J, Borges JS, Evaristo M, Pereira GC, Yamamoto AY, Clé DV, Calado RT, Covas DT, Alcantara LCJ, Kashima S

Infect Genet Evol
2021; Volume 93, September 2021, 104976
2021
Promoting Responsible Research and Innovation (RRI) During Brazilian Activities of Genomic and Epidemiological Surveillance of Arboviruses

Giovanetti M, Alcantara LCJ, Dorea AS, Ferreira QR, Marques WA, Barros JJF, Adelino TER, Tosta S, Fritsch H, Iani FCM, Mares-Guia MA, Salgado A, Fonseca V, Xavier J, Lopes EN, Soares GC, Amarante MFC, Azevedo V, Kruger A, Matta GC, Paineiras-Domingos LL, Colonnello C, Filippis AMB, Montesano C, Colizzi V, Barreto FK

Front. Public Health
v. 9, p. 1, 2021.
2021
Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS-CoV-2 mitigation strategies

Lopes EN, Fonseca V, Frias D, Tosta S, Salgado A, Vialle RA, Toscano PES, Barreto FK, Azevedo VA, Guarino M, Angeletti S, Ciccozzi M, Alcantara LCJ, Giovanetti M

J Med Virol
2021; 1- 5. DOI: 10.1002/jmv.27056
2021
Short report: Introduction of chikungunya virus ECSA genotype into the Brazilian Midwest and its dispersion through the Americas

de Oliveira EC, Fonseca V, Xavier J, Adelino T, Morales Claro I, Fabri A, Macario EM, Viniski AE, Souza CLC, Costa ESG, Sousa CS, Duarte FGD, Medeiros AC, Albuquerque CFC, Cunha RV, Moura NFO, Filippis AMB, de Oliveira T, Lourenço J, Abreu AL, Alcantara LCJ, Giovanetti M

PLoS Negl Trop Dis
2021; 15(4): e0009290. https://doi.org/10.1371/journal.pntd.0009290
2021
Genomic Evidence of SARS-CoV-2 Reinfection Involving E484K Spike Mutation, Brazil

Nonaka CV, Franco M, Gräf T, Lorenzo BC, Avila MR, Sousa K, Neiva LMC, Fonseca V, Mendes AVA, Aguiar RS, Giovanetti M, Freitas BS.

Emerg Infect Dis
2021;27(5):1522-1524.
2021
Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil

Adelino TÉR, Giovanetti M, Fonseca V, Xavier J, de Abreu ÁS, do Nascimento VA, Demarchi LHF, Oliveira MAA, da Silva VL, de Mello ALES, Cunha GM, Santos RH, de Oliveira EC, Júnior JAC, de Melo Iani FC, de Filippis AMB, de Abreu AL, de Jesus R, de Albuquerque CFC, Rico JM, do Carmo Said RF, Silva JA, de Moura NFO, Leite P, Frutuoso LCV, Haddad SK, Martínez A, Barreto FK, Vazquez CC, da Cunha RV, Araújo ELL, de Oliveira Tosta SF, de Araújo Fabri A, Chalhoub FLL, da Silva Lemos P, de Bruycker-Nogueira F, de Castro Lichs GG, Zardin MCSU, Segovia FMC, Gonçalves CCM, Grillo ZDCF, Slavov SN, Pereira LA, Mendonça AF, Pereira FM, de Magalhaes JJF, Dos Santos Júnior ACM, de Lima MM, Nogueira RMR, Góes-Neto A, de Carvalho Azevedo VA, Ramalho DB, Oliveira WK, Macario EM, de Medeiros AC, Pimentel V; Latin American Genomic Surveillance Arboviral Network, Holmes EC, de Oliveira T, Lourenco J, Alcantara LCJ

Nature Communications
12(1):2296. doi: 10.1038/s41467-021-22607-0.
2021
SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy

Giovanetti M, Cella E, Benedetti F, Rife Magalis B, Fonseca V, Fabris S, Campisi G, Ciccozzi A, Angeletti S, Borsetti A, Tambone V, Sagnelli C, Pascarella S, Riva A, Ceccarelli G, Marcello A, Azarian T, Wilkinson E, de Oliveira T, Alcantara LCJ, Cauda R, Caruso A, Dean NE, Browne C, Lourenco J, Salemi M, Zella D, Ciccozzi M

Communications Biology
4(1):489. doi: 10.1038/s42003-021-02025-0.
2021
Epidemiologic History and Genetic Diversity Origins of Chikungunya and Dengue Viruses, Paraguay

Graf T, Vazquez C, Giovanetti M, de Bruycker-Nogueira F, Fonseca V, Claro IM, de Jesus JG, Gómez A, Xavier J, de Mendonça MCL, Villalba S, Torales J, Gamarra ML, Thézé J, de Filippis AMB, Azevedo V, de Oliveira T, Franco L, de Albuquerque CFC, Irala S, Holmes EC, Méndez Rico JA, Alcantara LCJ

Emerg Infect Dis
27(5):1393-1404. doi: 10.3201/eid2705.204244
2021
Genomic surveillance activities unveil the introduction of the SARS-CoV-2 B.1.525 variant of interest in Brazil: Case report

Pereira F, Tosta S, Lima MM, Reboredo de Oliveira da Silva L, Nardy VB, Gomez MKA, Lima JG, Fonseca V, de Oliveira T, Lourenco J, Alcantara LC Jr, Giovanetti M, Leal A

J Med Virol
doi: 10.1002/jmv.27086
2021
Genomic evidence of SARS-CoV-2 reinfection case with the emerging B.1.2 variant in Brazil

Fonseca V, de Jesus R, Adelino T, Reis AB, de Souza BB, Ribeiro AA, Guimaraes NR, Livorati MTFP, Neto DFL, Kato RB, Portela LMO, Dutra LH, Freitas C, de Abreu AL, Filizzola ERM, de Medeiros AC, Iani FCM, Carvalho G, Lourenco J, de Oliveira T, Alcantara LCJ, Giovanetti M

Journal of Infection
DOI:https://doi.org/10.1016/j.jinf.2021.05.014
2021
Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa

San JE, Ngcapu S, Kanzi AM, Tegally H, Fonseca V, Giandhari J, Wilkinson E, Nelson CW, Smidt W, Kiran AM, Chimukangara B, Pillay S, Singh L, Fish M, Gazy I, Martin DP, Khanyile K, Lessells R, de Oliveira T.

Virus Evolution
7(1):veab041. doi: 10.1093/ve/veab041. eCollection 2021 Jan
2021
Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein

Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, Doolabh D, Pillay S, San E, Msomi N, Mlisana K, Gottberg A, Walaza S, Allam M, Ismail A, Mohale T, Glass A, Engelbrecht S, Zyl G, Preiser W, Petruccione F, Sigal A, Hardie D, Marais G, Hsiao M, Korsman S, Davies M, Tyers L, Mudau I, York D, Maslo C, Goedhals D, Abrahams S, Laguda-Akingba O, Alisoltani-Dehkordi A, Godzik A, Wibmer Cos, Sewell B, Lourenco J, Alcantara Ls, Kosakovsky Pond S, Weaver S, Martin D, Lessells R, Bhiman J, Williamson C, de Oliveira T

Nature
https://doi.org/10.1038/s41586-021-03402-9
2021
Epidemiology and evolution of Zika virus in Minas Gerais, Southeast Brazil

Iani FCM, Giovanetti M, Fonseca V, Souza WM, Adelino TER, Xavier J, Jesus JG, Pereira MA, Silva MVF, Costa AVB, Silva EC, Mendes MCO, Filippis AMB, Albuquerque CFC, Abreu AL, Oliveira MAA, Alcantara LCJ, Faria NR.

Infect Genet Evol
S1567-1348(21)00082-4
2021
Dengue Virus Serotype 2 Intrahost Diversity in Patients with Different Clinical Outcomes

Torres MC, Lima de Mendonça MC, Damasceno dos Santos Rodrigues C, Fonseca V, Ribeiro MS, Brandão AP, Venâncio da Cunha R, Dias AI, Santos Vilas Boas L, Felix AC, Alves Pereira M, de Oliveira Pinto LM, Sakuntabhai A, Bispo de Filippis AM, on behalf of ZikAction Consortium.

Viruses
13(2), 349
2021
Chikungunya virus ECSA lineage reintroduction in the northeasternmost region of Brazil

Xavier J, Fonseca V, Bezerra JF, Do Monte Alves M, Mares-Guia NA, Claro IM, De Jesus R, Adelino T, Araujo E, Cavalcante KRLJ, Tosta S, De Souza TR, Moreira Da Cruz FE, De Araujo Fabri A, de Oliveira EC, De Moura NFO, Do Carmo Said RF, De Albuquerque CFC, Azevedo V, de Oliveira T, De Filippis AMB, Venancio Da Cunha R, Luz KG, Giovanetti M, Alcantara L

IJID
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2021
Sixteen novel lineages of SARS-CoV-2 in South Africa

Tegally H, Wilkinson E, Lessells R, Giandhari J, Pillay S, Msomi N, Mlisana K, Bhiman J, Gottberg A, Walaza S, Fonseca V, Allam M, Ismail A, Engelbrecht S, Van Zyl G, Preiser W, Williamson C, Pettruccione F, Sigal A, Gazy I, Hardie D, Hsiao M, Martin D, York D, Goedhals D, San EJ, Giovanetti M, Lourenco J, Alcantara LCJ, de Oliveira T

Nature Medicine
https://doi.org/10.1038/s41591-021-01255-3
2020
Co-Circulation of Two Independent Clades and Persistence of CHIKV-ECSA Genotype during Epidemic Waves in Rio de Janeiro, Southeast Brazil.

Fabri AA, Rodrigues CDS, Santos CC, Chalhoub FLL, Sampaio AS, Faria NRC, Torres MC, Fonseca V, Brasil P, Calvet G, Alcantara LCJ, Filippis AMB, Giovanetti M, Bruycker-Nogueira F.

Pathogens
2020, 9(12), 984
2020
Pan-genomics of virus and its applications

Giovanetti M, Salgado A, Fonseca V, Tosta SFO, Xavier J, de Jesus JG, Iani FCM, Adelino TER, Barreto FK, Faria NR, De Oliveira T, Alcantara LCJ.

Academic Press
2020; Pages 237-250
2020
Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa

Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, Doolabh D, Pillay S, San E, Msomi N, Mlisana K, Gottberg A, Walaza S, Allam M, Ismail A, Mohale T, Glass A, Engelbrecht S, Zyl G, Preiser W, Petruccione F, Sigal A, Hardie D, Marais G, Hsiao M, Korsman S, Davies M, Tyers L, Mudau I, York D, Maslo C, Goedhals D, Abrahams S, Laguda-Akingba O, Alisoltani-Dehkordi A, Godzik A, Wibmer Cos, Sewell B, Lourenço J, Alcantara Ls, Kosakovsky Pond S, Weaver S, Martin D, Lessells R, Bhiman J, Williamson C, de Oliveira T

medRxiv
https://doi.org/10.1101/2020.12.21.20248640
2020
High Resolution analysis of Transmission Dynamics of Sars-Cov-2 in Two Major Hospital Outbreaks in South Africa Leveraging Intrahost Diversity

San EJ, Ngcapu S, Kanzi A, Tegally H, Fonseca V, Giandhari J, Wilkinson E, Chimukangara B, Pillay S, Singh L, Fish M, Gazy I, Khanyile KS, Lessells R, de Oliveira T

medRxiv
https://doi.org/10.1101/2020.11.15.20231993
2020
Portable sequencing in the field and the classroom: a retrospective examination of the circulation of DENV1 and DENV2 in Brazil

Adelino TER, Giovanetti M, Fonseca V, Xavier J, Salgado A, Nascimento V, Demarchi LH, Oliveira M, Silva V, Mello A, Muricy G, Santos R, Oliveira E, Junior JAC, Iani F, de Filippis AMB, Abreu AL, de Jesus R, Albuquerque CF, Rico J, Said R, Silva J, Moura N, Leite P, Vinhal L, Kashima S, Martinez AA, Khouri F, Vazquez C, Cunha R, Araujo E, Tosta S, Fabri A, Chalhoub F, Lemos P, de Bruycker-Nogueira F, Lichs G, Zardin M, Cardozo F, Goncalves C, Fernandez Z, Slavov S, Pereira LA, Mendonca AF, Pereira F, Magalhaes J, de Castro A, Lima M, Nogueira R, Goes A, Azevedo V, Ramalho D, Oliveira W, Medeiros A, Pimentel V, Latin American Genomic Surveillance Arboviral Network, Holmes EC, de Oliveira T, Lourenco J, Alcantara LCJ

medRxiv
https://doi.org/10.1101/2020.09.01.20183301
2020
Fatal outcome of chikungunya virus infection in Brazil

Lima STS, Souza WM, Cavalcante JW, Candido DS, Fumagalli MJ, Carrera JP, Mello LMS, Araújo FMC, Ramalho ILC, Barreto FKA, Braga DNM, Simião AR, Silva MJM, Oliveira RMAB, Lima CPS, Lins CS, Barata RR, Melo MNP, Souza MPC, Franco LM, Távora FRF, Lemos DRQ, Alencar CHM, Jesus R, Fonseca V, Dutra LH, Abreu AL, Araújo ELL, Freitas ARR, Júnior JLSGV, Pybus OG, Figueiredo LTM, Faria NR, Nunes MRT, Cavalcanti LPG, Miyajima F.

Clinical Infectious Diseases
ciaa1038 DOI: https://doi.org/10.1093/cid/ciaa1038
2020
Yellow fever transmission in non-human primates, Bahia, Northeastern Brazil

Goes de Jesus J, Gräf T, Giovanetti M, Mares-Guia MA, Xavier J, Lima Maia M, Fonseca V, Fabri A, Santos RF, Pereira FM, Santos LFO, Silva LRO, Maia ZPG, Cerqueira JXG, Thèze J, Abade L, Cordeiro MCS, Torquato SSC, Santana EB, Silva NSJ, Dourado RSO, Alves AB, Guedes AS, Filho PMC, Faria NR, Campelo de Albuquerque CF, Abreu AL, Romano APM, Croda J, Said RFC, Cunha GM, Cerqueira JMF, Mello ALS, Filippis AMB, Alcantara LCJ.

PLoS Negl Trop Dis
14(8): e0008405. https://doi.org/10.1371/journal.pntd.0008405:14(8): e0008405
2020
Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic

Pillay S, Giandhari J, Tegally H, Wilkinson E, Chimukangara B, Lessells R, Mattison S, Moosa Y, Gazy I, Fish M, Singh L, Khanyile KS, Fonseca V, Giovanetti M, Alcantara LCJ, de Oliveira T

Genes
doi: https://doi.org/10.3390/genes11080949:11(8), 949
2020
Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report

Giandhari J, Pillay S, Wilkinson E, Tegally H, Sinayskiy I, Schuld M, Lourenço J, Chimukangara B, Lessells R, Moosa Y, Gazy I, Fish M, Singh L, Khanyile KS, Fonseca V, Giovanetti M, Alcantara LCJ, Petruccione F, de Oliveira T

IJID
doi: https://doi.org/10.1016/j.ijid.2020.11.128
2020
The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing

Xavier J, Giovanetti M, Adelino T, Fonseca V, da Costa AVB, Ribeiro AA, Felicio KN, Duarte CG, Silva MVF, Salgado A, Lima MT, de Jesus D, Fabri A, Zoboli CFS, Santos TGS, Iani F,de Filippis AMB, de Siqueira AMNT, de Abreu AL, de Azevedo V, Ramalho DBR, de Albuquerque CFC, de Oliveira T, Holmes EC, Lourenco J, Alcantara CLJ, Oliveira MAA

Emerging Microbes & Infections
vol 9
2020
Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region

Giovanetti M, Faria NR, Lourenco J, Goes de Jesus J, Xavier J, Claro IM, Kraemer MUG, Fonseca V, Dellicour S, Theze J, da Silva Salles F, Graef T, Silveira PP, Costa de Souza V, Alves do Nascimento V, Campos de Melo Iani F, Castilho-Martins EA, Cruz LN, Wallau G, Fabri A, Levy F, Quick J, de Azevedo V, Santana Aguiar R, de Oliveira T, Botto de Menezes C, da Costa Castilho M, Matos Terra T, Souza da Silva M, Bispo de Filippis M, Luiz de Abreu A, Kleber Oliveira W, Croda J, Campelo de Albuquerque CF, Nunes MRT, Cerdeira Sabino E, Loman N, Gomes Naveca F, Pybus O, Alcantara LC.

Cell Reports
https://doi.org/10.1016/j.celrep.2020.01.085
2020
Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes

Cleemput S, Dumon W, Fonseca V, Abdool Karim W, Giovanetti M, Alcantara LCJ, Deforche K, de Oliveira T

Bioinformatics
btaa145, https://doi.org/10.1093/bioinformatics/btaa145
2020
Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls

San EJ, Baichoo S, Kanzi A, Moosa Y, Lessells R, Fonseca V, Mogaka J, Power R, de Oliveira T

Front. Microbiol.
https://doi.org/10.3389/fmicb.2019.03119
2020
Persistence of chikungunya ECSA genotype and local outbreak in an upper medium class neighborhood in Northeast Brazil

Goes de Jesus J, da Luz Wallau G, Lima Maia M, Xavier J, Oliveira Lima MA, Fonseca V, Salgado de Abreu A, Fraga de Oliveira Tosta S, Ramos do Amaral H, Andrade Barbosa Lima I, Viana Silva P, Carlos Dos Santos D, Sousa de Oliveira A, Campos de Souza S, Barreto Falcão M, Cerqueira E, Ceschini Machado L, Sobral MC, Teodoro Rezende TM, Ribeiro Pereira M, Mota Pereira F, Pereira Gusmão Maia Z, Freitas de Oliveira França R, Luiz de Abreu A, Campelo de Albuquerque E Melo CF, Rodrigues Faria N, Venâncio da Cunha R, Giovanetti M, Alcantara LCJ

PLoS ONE
15(1):e0226098. doi: 10.1371/journal.pone.0226098
2020
Return of the founder Chikungunya virus to its place of introduction into Brazil is revealed by genomic characterization of exanthematic disease cases.

Pereira Gusmão Maia Z, Mota Pereira F, do Carmo Said RF, Fonseca V, Gräf T, de Bruycker Nogueira F, Brandão Nardy V, Xavier J, Lima Maia M, Abreu AL, Campelo de Albuquerque CF, Kleber Oliveira W, Croda J, de Filippis AMB, Venancio Cunha R, Lourenço J, de Oliveira T, Faria NR, Junior Alcantara LC, Giovanetti M

Emerg Microbes Infect.
9(1):53-57. doi: 10.1080/22221751.2019.1701954
2020
Analysis of the microarray gene expression for breast cancer progression after the application modified logistic regression

Morais-Rodrigues F, Silv Erio-Machado R, Kato RB, Rodrigues DLN, Valdez-Baez J, Fonseca V, San EJ, Gomes LGR, Dos Santos RG, Vinicius Canário Viana M, da Cruz Ferraz Dutra J, Teixeira Dornelles Parise M, Parise D, Campos FF, de Souza SJ, Ortega JM, Barh D, Ghosh P, Azevedo VAC, Dos Santos MA

Gene
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2019
Yellow fever virus re-emergence and spread in Southeast Brazil, 2016-2019

Giovanetti M, Lima de Mendonça MC, Fonseca V, Mares-Guia MA, Fabri A, Xavier J, Goes de Jesus J, Gräf T, Damasceno Dos Santos Rodrigues C, Cardoso Dos Santos C, Alves Sampaio S, Lowen Levy Chalhoub F, Bruycker Nogueira F, Theze J, Pecego Martins Romano A, Garkauskas Ramos D, Luiz de Abreu A, Kleber Oliveira W, do Carmo Said RF, Campelo de Alburque CF, de Oliveira T, Fernandes CA, Ferreira Aguiar S, Chieppe A, Carvalho Sequeira P, Rodrigues Faria N, Venâncio Cunha R, Alcantara LCJ, Bispo de Filippis AM.

Journal of Virology
JVI.01623-19. doi: 10.1128/JVI.01623-19
2019
Mosquito-Borne Viral Diseases: Control and Prevention in the Genomics Era

Fonseca V, Xavier J, San EJ, de Oliveira T, de Filippis AMB, Alcantara LCJ, Giovanetti M

Current Topics in the Epidemiology of Vector-Borne
DOI: 10.5772/intechopen.88769
2019
Circulation of chikungunya virus East/Central/South African lineage in Rio de Janeiro, Brazil

Xavier J, Giovanetti M, Fonseca V, Thézé J, Gräf T, Fabri A, Goes de Jesus J, Lima de Mendonça MC, Damasceno Dos Santos Rodrigues C, Mares-Guia MA, Cardoso Dos Santos C, Fraga de Oliveira Tosta S, Candido D, Ribeiro Nogueira RM, Luiz de Abreu A, Kleber Oliveira W, Campelo de Albuquerque CF, Chieppe A, de Oliveira T, Brasil P, Calvet G, Carvalho Sequeira P, Rodrigues Faria N, Bispo de Filippis AM, Alcantara LCJ

PLoS One
14(6):e0217871
2019
A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes

Fonseca V, Libin PJK, Theys K, Faria NR, Nunes MRT, Restovic MI, Freire M, Giovanetti M, Cuypers L, Nowé A, Abecasis A, Deforche K, Santiago GA, Siqueira IC, San EJ, Machado KCB, Azevedo V, Filippis AMB, Cunha RVD, Pybus OG, Vandamme AM, Alcantara LCJ, de Oliveira T

PLoS Negl Trop Dis
13(5):e0007231: doi: 10.1371/journal.pntd.0007231
2019
Genome Detective: An Automated System for Virus Identification from High-throughput sequencing data.

Vilsker M, Moosa Y, Nooij S, Fonseca V, Ghysens Y, Dumon K, Pauwels R, Alcantara LC, Vanden Eynden E, Vandamme AM, Deforche K, de Oliveira T

Bioinformatics
doi: 10.1093/bioinformatics/bty695
2018
Genomic and epidemiological monitoring of yellow fever virus transmission potential

Faria NR, Kraemer MUG, S C Hill, J Goes de Jesus, R S Aguiar, F C M Iani, J Xavier, J Quick, L du Plessis, S Dellicour, J Thézé, R D O Carvalho, G Baele, C-H Wu, P P Silveira, M B Arruda, M A Pereira, G C Pereira, J Lourenço1, U Obolski, L Abade, T I Vasylyeva, M Giovanetti, D Yi, D J Weiss, G R W Wint, F M Shearer, S Funk, B Nikolay, Fonseca V, T E R Adelino, M A A Oliveira, M V F Silva, L Sacchetto, P O Figueiredo, I M Rezende, E M Mello, R F C Said, D A Santos, M L Ferraz, M G Brito, L F Santana, M T Menezes, R M Brindeiro, A Tanuri, F C P dos Santos, M S Cunha, J S Nogueira, I M Rocco, A C da Costa, S C V Komninakis, V Azevedo, A O Chieppe, E S M Araujo, M C L Mendonça, C C dos Santos, C D dos Santos, A M Mares-Guia, R M R Nogueira, P C Sequeira, R G Abreu, M H O Garcia, A L Abreu, O Okumoto, E G Kroon, C F C de Albuquerque, K Lewandowski, S T Pullan, M Carroll, de Oliveira T, E C Sabino, R P Souza, M A Suchard, P Lemey, G S Trindade, B P Drumond, A M B Filippis, N J Loman, S Cauchemez, Alcantara LCJ, Pybus OG

Science
DOI: 10.1126/science.aat7115
2017
Automated profiling of the human virome from raw metagenomic data

Moosa Y, Vilsker M, Vanden Eyden E, Fonseca V, Nooij S, Deforche K, de Oliveira T

Virus Evolution
doi: 10.1093/ve/vew036.033
2013
Human Retrovirus Codon Usage from tRNA Point of View: Therapeutic Insights

Frias D, Monteiro-Cunha JP, Mota-Miranda AC, Fonseca V, de Oliveira T, Galvao-Castro B Alcantara LCJ

Bioinformatics and Biology Insights
7:1-11