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 (2024), 15(11):1365. doi: 10.3390/genes15111365.:.
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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 (2024), ():107262. doi: 10.1016/j.ijid.2024.107262.:.
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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 (2024), 30(11):. doi: 10.3201/eid3011.241132.:.
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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 (2024), 24(1):. doi: 10.1186/s12879-024-09658-6.:.
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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 (2024), 13(7):589. doi: 10.3390/pathogens13070589.:.
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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 (2024), 16(7):1143. doi: 10.3390/v16071143.:.
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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 (2024), 15(7):922. doi: 10.3390/genes15070922.:.
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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 (2024), 13(1):. doi: 10.1080/22221751.2024.2362941.:.
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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 (2024), 35():100786. doi: 10.1016/j.lana.2024.100786.:.
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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 (2024), 145():107090. doi: 10.1016/j.ijid.2024.107090.:.
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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 (2024), 17(7):102442. doi: 10.1016/j.jiph.2024.04.026.:.
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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 (2024), 13(1):. doi: 10.1080/22221751.2024.2332672.:.
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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 (2024), 4(28):2-9. doi: 10.22533/at.ed.1594282419035.:.
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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 (2024), 96(3):. doi: 10.1002/jmv.29526.:.
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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 (2024), 13(3):202. doi: 10.3390/pathogens13030202.:.
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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 (2024), 12(3):449. doi: 10.3390/microorganisms12030449.:.
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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 (2024), 30(2):. doi: 10.3201/eid3002.230122.:.
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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 (2024), 16(1):83. doi: 10.3390/v16010083.:.
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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 (2024), 22(9):e3002834. doi: 10.1371/journal.pbio.3002834.:.
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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), 2024.05.16.24307504. doi: 10.1101/2024.05.16.24307504:.
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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 (2023), 16(1):23. doi: 10.3390/v16010023.:.
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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 (2023), 9(35):eadg9204. doi: 10.1126/sciadv.adg9204:.
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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), 2023.01.13.23284525v1:.
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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 (2023), doi:10.1101/2023.04.16.23288635:.
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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 (2022), doi: 10.1038/s41564-022-01191-z:.
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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 (2022), 23(1):520. doi: 10.1186/s12864-022-08764-6:.
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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] (2022), 28:2021.10.07.21264644. doi: 10.1101/2021.10.07.21264644:.
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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 (2022), doi: 10.1093/ve/veac024:.
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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. (2022), e0015522. doi: 10.1128/spectrum.00155-22:.
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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 (2021), MEDRXIV-2021-264018v1:.
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A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
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West Nile Virus in Brazil.
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Short Report: Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil.
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Molecular surveillance of the on-going SARS-COV-2 epidemic in Ribeirao Preto City, Brazil.
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Promoting Responsible Research and Innovation (RRI) During Brazilian Activities of Genomic and Epidemiological Surveillance of Arboviruses.
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Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS-CoV-2 mitigation strategies.
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Short report: Introduction of chikungunya virus ECSA genotype into the Brazilian Midwest and its dispersion through the Americas.
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Genomic Evidence of SARS-CoV-2 Reinfection Involving E484K Spike Mutation, Brazil.
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Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil.
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SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy.
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Epidemiologic History and Genetic Diversity Origins of Chikungunya and Dengue Viruses, Paraguay.
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Genomic surveillance activities unveil the introduction of the SARS-CoV-2 B.1.525 variant of interest in Brazil: Case report.
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Genomic evidence of SARS-CoV-2 reinfection case with the emerging B.1.2 variant in Brazil.
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Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa.
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Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein.
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Epidemiology and evolution of Zika virus in Minas Gerais, Southeast Brazil.
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Dengue Virus Serotype 2 Intrahost Diversity in Patients with Different Clinical Outcomes.
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Chikungunya virus ECSA lineage reintroduction in the northeasternmost region of Brazil.
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Sixteen novel lineages of SARS-CoV-2 in South Africa.
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Co-Circulation of Two Independent Clades and Persistence of CHIKV-ECSA Genotype during Epidemic Waves in Rio de Janeiro, Southeast Brazil. .
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Pan-genomics of virus and its applications.
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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.
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High Resolution analysis of Transmission Dynamics of Sars-Cov-2 in Two Major Hospital Outbreaks in South Africa Leveraging Intrahost Diversity.
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Portable sequencing in the field and the classroom: a retrospective examination of the circulation of DENV1 and DENV2 in Brazil.
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Fatal outcome of chikungunya virus infection in Brazil.
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Yellow fever transmission in non-human primates, Bahia, Northeastern Brazil.
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Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic.
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Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report.
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Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region.
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Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes.
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Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls.
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Persistence of chikungunya ECSA genotype and local outbreak in an upper medium class neighborhood in Northeast Brazil.
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Return of the founder Chikungunya virus to its place of introduction into Brazil is revealed by genomic characterization of exanthematic disease cases..
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Analysis of the microarray gene expression for breast cancer progression after the application modified logistic regression.
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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 (2019), DOI: 10.5772/intechopen.88769:.
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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 (2019), 14(6):e0217871:.
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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 (2019), 13(5):e0007231: doi: 10.1371/journal.pntd.0007231.
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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 (2019), doi: 10.1093/bioinformatics/bty695:.
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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 (2018), DOI: 10.1126/science.aat7115:.
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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 (2017), : doi: 10.1093/ve/vew036.033.
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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 (2013), 7:1-11.
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