About Vagner Fonseca

vagner.fonseca@gmail.com +27 (0) 79 623 3560

Background:

PhD student in Virology at the Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, South Africa. My research interests are the ongoing development of the NGS assembly, phylogenetic analsysis and in the built of a more stable JAVA environment to pre-process host and pathogen sequence data for MicroGWAS, ViroGWAS and GWAS.

Vagner is active in Information Technology sector since 2004 with: Systems Analysis and Development, Project Management and IT Infrastructure Projects. 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



Affiliations:

KRISP - KwaZulu-Natal Research and Innovation Sequencing Platform, UKZN, Durban, South Africa.

Department of Virology, National Health Laboratory Service (NHLS), Durban, South Africa (PhD student).



Education:

Master of Biotechnology in Health and Investigative Medicine, Oswaldo Cruz Foundation, 2016

Bachelor of Information Systems, University of the State of Bahia, 2013


PUBLICATIONS


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:.


A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa .
Wilkinson E, Giovanetti M, Tegally H, San EJ, Lessells R, Abdoul K. Sangare, Abdoul-Salam Ouedraogo, Abdul K. Sesay, Abechi Priscilla, Adedotun-Sulaiman Kemi, Adewunmi M. Olubusuyi, Adeyemi O.O. Oluwapelumi, Adnène Hammami, Adrienne A. Amuri, Ahmad Sayed, Ahmed E.O. Ouma, Aida Elargoubi, Ajayi N. Anthony, Ajogbasile F. Victoria, Akano Kazeem, Akpede George, Alexander J. Trotter, Ali A. Yahaya, Alpha K. Keita, Amadou Diallo, Amadou Kone, Amal Souissi, Amel Chtourou, Ana V. Gutierrez, Andrew J. Page, Anika Vinze, Arash Iranzadeh, Arnold Lambisia, Arshad Ismail, Audu Rosemary, Augustina Sylverken, Ayoade Femi, Azeddine Ibrahimi, Baba Marycelin, Bamidele S. Oderinde, Bankole Bolajoko, Beatrice Dhaala, Belinda L. Herring, Berthe-Marie Njanpop-Lafourcade, Bronwyn Kleinhans, Bronwyn McInnis, Bryan Tegomoh, Cara Brook, Catherine B. Pratt, Cathrine Scheepers, Chantal G. Akoua-Koffi, Charles N. Agoti, Christophe Peyrefitte, Claudia Daubenberger, Collins M. Morang’a, D. James Nokes, Daniel G. Amoako, Daniel L. Bugembe, Danny Park, David Baker, Deelan Doolabh, Deogratius Ssemwanga, Derek Tshiabuila, Diarra Bassirou, Dominic S.Y. Amuzu, Dominique Goedhals, Donwilliams O. Omuoyo, Dorcas Maruapula, Ebenezer Foster-Nyarko, Eddy K. Lusamaki, Edgar Simulundu, Edidah M. Ong'era, Edith N. Ngabana, Edwin Shumba, Elmostafa El Fahime, Emmanuel Lokilo, Enatha Mukantwari, Eromon Philomena, Essia Belarbi, Etienne Simon-Loriere, Etilé A. Anoh, Fabian Leendertz, Faida Ajili, Fakayode O. Enoch, Fares Wasfi, Fatma Abdelmoula, Fausta S. Mosha, Faustinos T. Takawira, Fawzi Derrar, Feriel Bouzid, Folarin Onikepe, Fowotade Adeola, Francisca M. Muyembe, Frank Tanser, Fred A. Dratibi, Gabriel K. Mbunsu, Gaetan Thilliez, Gemma L. Kay, George Githinji, Gert van Zyl, Gordon A. Awandare, Grit Schubert, Gugu P. Maphalala, Hafaliana C. Ranaivoson, Hajar Lemriss, Happi Anise, Haruka Abe, Hela H. Karray, Hellen Nansumba, Hesham A. Elgahzaly, Hlanai Gumbo, Ibtihel Smeti, Ikhlas B. Ayed, Ikponmwosa Odia, Ilhem Boutiba-Ben Boubaker, Imed Gaaloul, Inbal Gazy, Innocent Mudau, Isaac Ssewanyana, Iyaloo Konstantinus, Jean B. Lekana-Douk, Jean-Claude C. Makangara, Jean-Jacques M. Tamfum, Jean-Michel Heraud, Jeffrey G. Shaffer, Giandhari J, Jingjing Li, Jiro Yasuda, Joana Q. Mends, Jocelyn Kiconco, John M. Morobe, John O. Gyapong, Johnson C. Okolie, John T. Kayiwa, Johnathan A. Edwards, Jones Gyamfi, Jouali Farah, Joweria Nakaseegu, Joyce M. Ngoi, Joyce Namulondo, Julia C. Andeko, Julius J. Lutwama, Justin O’Grady, Katherine Siddle, Kayode T. Adeyemi, Kefentse A. Tumedi, Khadija M. Said, Kim Hae-Young, Kwabena O. Duedu, Lahcen Belyamani, Lamia Fki-Berrajah, Lavanya Singh, Leonardo de O. Martins, Lynn Tyers, Magalutcheemee Ramuth, Maha Mastouri, Mahjoub Aouni, Mahmoud el Hefnawi, Maitshwarelo I. Matsheka, Malebogo Kebabonye, Mamadou Diop, Manel Turki, Marietou Paye, Martin M. Nyaga, Mathabo Mareka, Matoke-Muhia Damaris, Maureen W. Mburu, Maximillian Mpina, Mba Nwando, Michael Owusu, Michael R. Wiley, Mirabeau T. Youtchou, Mitoha O. Ayekaba, Mohamed Abouelhoda, Mohamed G. Seadawy, Mohamed K. Khalifa, Mooko Sekhele, Mouna Ouadghiri, Moussa M. Diagne, Mulenga Mwenda, Mushal Allam, My V.T. Phan, Nabil Abid, Nadia Touil, Nadine Rujeni, Najla Kharrat, Nalia Ismael, Ndongo Dia, Nedio Mabunda, Nei-yuan Hsiao, Nelson B. Silochi, Ngoy Nsenga, Nicksy Gumede, Nicola Mulder, Nnaemeka Ndodo, Norosoa H Razanajatovo, Nosamiefan Iguosadolo, Oguzie Judith, Ojide C. Kingsley, Okogbenin Sylvanus, Okokhere Peter, Oladiji Femi, Olawoye Idowu, Olumade Testimony, Omoruyi E. Chukwuma, Onwe E. Ogah, Onwuamah Chika, Oshomah Cyril, Ousmane Faye, Oyewale Tomori, Pascale Ondoa, Patrice Combe, Patrick Semanda, Paul E. Oluniyi, Paulo Arnaldo, Peter K. Quashie, Philippe Dussart, Phillip A. Bester, Placide K. Mbala, Reuben Ayivor-Djanie, Richard Njouom, Richard O. Phillips, Richmond Gorman, Robert A. Kingsley, Rosina A.A. Carr, Saâd El Kabbaj, Saba Gargouri, Saber Masmoudi, Safietou Sankhe, Salako B. Lawal, Samar Kassim, Sameh Trabelsi, Samar Metha, Sami Kammoun, Sanaâ Lemriss, Sara H.A. Agwa, Sébastien Calvignac-Spencer, Stephen F. Schaffner, Seydou Doumbia, Sheila M. Mandanda, Sherihane Aryeetey, Shymaa S. Ahmed, Siham Elhamoumi, Soafy Andriamandimby, Sobajo Tope, Sonia Lekana-Douki, Sophie Prosolek, Soumeya Ouangraoua, Steve A. Mundeke, Steven Rudder, Sumir Panji, Sureshnee Pillay, Susan Engelbrecht, Susan Nabadda, Sylvie Behillil, Sylvie L. Budiaki, Sylvie van der Werf, Tapfumanei Mashe, Tarik Aanniz, Thabo Mohale, Thanh Le-Viet, Tobias Schindler, Ugochukwu J. Anyaneji, Ugwu Chinedu, Ramphal U, Uwanibe Jessica, Uwem George, Fonseca V, Vincent Enouf, Vivianne Gorova, Wael H. Roshdy, William K. Ampofo, Wolfgang Preiser, Wonderful T. Choga, Yaw Bediako, Yeshnee Naidoo, Yvan Butera, Zaydah R. de Laurent, Amadou A. Sall, Ahmed Rebai, Anne von Gottberg, Bourema Kouriba, Carolyn Williamson, Daniel J. Bridges, Ihekweazu Chikwe, Jinal Bhiman, Madisa Mine, Matthew Cotten, Sikhulile Moyo, Simani Gaseitsiwe, Ngonda Saasa, Pardis C. Sabeti, Pontiano Kaleebu, Yenew K. Tebeje, Sofonias K. Tessema, Happi Christian, John Nkengasong, de Oliveira T, Science (2021), DOI: 10.1126/science.abj4336:.


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 (2021), 10(7):896. doi: 10.3390/pathogens10070896:.


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. (2021), 15(7):e0009591. doi: 10.1371/journal.pntd.0009591:.


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), 2021; Volume 93, September 2021, 104976:.


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 (2021), v. 9, p. 1, 2021.:.


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), 2020, 9(12), 984:.


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), 2020; Pages 237-250:.


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), 2021; 1- 5. DOI: 10.1002/jmv.27056:.


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), 2021; 15(4): e0009290. https://doi.org/10.1371/journal.pntd.0009290:.


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), 2021;27(5):1522-1524.:.


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 (2021), 12(1):2296. doi: 10.1038/s41467-021-22607-0.:.


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 (2021), 4(1):489. doi: 10.1038/s42003-021-02025-0.:.


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 (2021), 27(5):1393-1404. doi: 10.3201/eid2705.204244:.


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 (2021), doi: 10.1002/jmv.27086:.


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 (2021), DOI:https://doi.org/10.1016/j.jinf.2021.05.014:.


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 (2021), 7(1):veab041. doi: 10.1093/ve/veab041. eCollection 2021 Jan:.


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 (2021), https://doi.org/10.1038/s41586-021-03402-9:.


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 (2021), S1567-1348(21)00082-4:.


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 (2021), 13(2), 349:.


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 (2021), S1201-9712(21)00037-0:.


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 (2021), https://doi.org/10.1038/s41591-021-01255-3:.


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 (2020), https://doi.org/10.1101/2020.12.21.20248640:.


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 (2020), https://doi.org/10.1101/2020.09.01.20183301:.


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 (2020), ciaa1038 DOI: https://doi.org/10.1093/cid/ciaa1038:.


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 (2020), 14(8): e0008405. https://doi.org/10.1371/journal.pntd.0008405:14(8): e0008405.


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 (2020), doi: https://doi.org/10.1016/j.ijid.2020.11.128:.


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 (2020), vol 9:.


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 (2020), https://doi.org/10.1016/j.celrep.2020.01.085:.


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 (2020), btaa145, https://doi.org/10.1093/bioinformatics/btaa145:.


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. (2020), https://doi.org/10.3389/fmicb.2019.03119:.


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 (2020), 15(1):e0226098. doi: 10.1371/journal.pone.0226098:.


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. (2020), 9(1):53-57. doi: 10.1080/22221751.2019.1701954:.


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 (2020), 144168. doi: 10.1016/j.gene.2019.144168.:.


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 (2019), JVI.01623-19. doi: 10.1128/JVI.01623-19:.


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:.


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:.


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.


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:.


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:.


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.


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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KRISP has been created by the coordinated effort of the University of KwaZulu-Natal (UKZN), the Technology Innovation Agency (TIA) and the South African Medical Research Countil (SAMRC).


Location: K-RITH Tower Building
Nelson R Mandela School of Medicine, UKZN
719 Umbilo Road, Durban, South Africa.
Director: Prof. Tulio de Oliveira