Real-time, rapid detection and sequencing of arboviruses in Brazil: Zika, Dengue, Chikungunya and Yellow Fever

• Grant number: 18/17176-8
• Support type: Scholarships in Brazil - Doctorate (Direct)
• Effective date (Start): January 01, 2019
• Effective date (End): October 31, 2021
• Field of knowledge: Health Sciences - Medicine - Medical Clinics
• Principal researcher: Ester Cerdeira Sabino
• Grantee: Ingra Morales Claro
• Home Institution: Faculdade de Medicina (FM). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated scholarship(s): 19/25047-6 - Establishing a rapid and mobile approach to detect new epidemics, BE.EP.DD

Abstract

Arbovirus infections in Brazil including Zika, Chikungunya, Dengue and Yellow Fever result inconsiderable morbidity and mortality and are pressing public health concerns. However ourunderstanding of these outbreaks is hampered by limited availability of epidemiological surveillance data. Typically these data are generated by molecular diagnostic assays that are expensive to setup and lack specificity. Consequently we have limited understanding of the interplay and interactions between arboviruses in both human and mosquito populations in Brazil, as demonstrated by Zika Virus in Brazil where detection was delayed by at least a year from the true start of the outbreak. Recently we pioneered a new approach to surveillance of arboviruses using portable, real-time nanopore sequencing - so-called 'genomic epidemiology'. This permits sensitive detection and assignment of viruses into genotypes. However, at present, the costs and complexity of this powerful technique (around $100) currently precludes its use as a routine surveillance tool in research and public health laboratory environments. In this proposal we aim to solve three pressing problems with portable sequencing for arbovirusdetection. This continues a highly productive collaboration between the University of São Paulo, the University of Birmingham and the University of Nottingham that has already resulted in very high impact publications in Nature and Nature Protocols (Faria et al. 2017; Quick et al. 2017). This project will have an immediate impact on the surveillance of arboviruses in Brazil and our understanding of this pressing public health problem. (AU)

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

IANI, FELIPE C. M.; GIOVANETTI, MARTA; FONSECA, VAGNER; SOUZA, WILLIAM M.; ADELINO, TALITA E. R.; XAVIER, JOILSON; JESUS, JAQUELINE G.; PEREIRA, MAIRA A.; SILVA, MARCOS V. F.; COSTA, ALANA V. B.; SILVA, ERNIRIA C.; MENDES, MARCIA C. O.; FILIPPIS, ANA M. B.; ALBUQUERQUE, CARLOS F. C.; ABREU, ANDRE L.; OLIVEIRA, MARLUCE A. A.; ALCANTARA, LUIZ C. J.; FARIA, NUNO R. Epidemiology and evolution of Zika virus in Minas Gerais, Southeast Brazil. INFECTION GENETICS AND EVOLUTION, v. 91, JUL 2021. Web of Science Citations: 0.

FARIA, NUNO R.; MELLAN, THOMAS A.; WHITTAKER, CHARLES; CLARO, INGRA M.; CANDIDO, DARLAN DA S.; MISHRA, SWAPNIL; CRISPIM, MYUKI A. E.; SALES, FLAVIA C.; HAWRYLUK, IWONA; MCCRONE, JOHN T.; HULSWIT, RUBEN J. G.; FRANCO, LUCAS A. M.; RAMUNDO, MARIANA S.; DE JESUS, JAQUELINE G.; ANDRADE, PAMELA S.; COLETTI, THAIS M.; FERREIRA, GIULIA M.; SILVA, CAMILA A. M.; MANULI, ERIKA R.; PEREIRA, RAFAEL H. M.; PEIXOTO, PEDRO S.; KRAEMER, MORITZ U.; GABURO, JR., NELSON; CAMILO, CECILIA DA C.; HOELTGEBAUM, HENRIQUE; SOUZA, WILLIAM M.; ROCHA, ESMENIA C.; DE SOUZA, LEANDRO M.; DE PINHO, MARIANA C.; ARAUJO, LEONARDO J. T.; MALTA, V, FREDERICO S.; DE LIMA, ALINE B.; SILVA, JOICE DO P.; ZAULI, DANIELLE A. G.; FERREIRA, ALESSANDRO C. DE S.; SCHNEKENBERG, RICARDO P.; LAYDON, DANIEL J.; WALKER, PATRICK G. T.; SCHLUETER, HANNAH M.; DOS SANTOS, ANA L. P.; VIDAL, MARIA S.; DEL CARO, VALENTINA S.; FILHO, ROSINALDO M. F.; DOS SANTOS, HELEM M.; AGUIAR, RENATO S.; PROENCA-MODENA, JOSE L. P.; NELSON, BRUCE; HAY, JAMES A.; MONOD, MELODIE; MISCOURIDOU, XENIA; COUPLAND, HELEN; SONABEND, RAPHAEL; VOLLMER, MICHAELA; GANDY, AXEL; PRETE, JR., CARLOS A.; NASCIMENTO, VITOR H.; SUCHARD, MARC A.; BOWDEN, THOMAS A.; POND, SERGEI L. K.; WU, CHIEH-HSI; RATMANN, OLIVER; FERGUSON, NEIL M.; DYE, CHRISTOPHER; LOMAN, NICK J.; LEMEY, PHILIPPE; RAMBAUT, ANDREW; FRAIJI, NELSON A.; CARVALHO, MARIA DO P. S. S.; PYBUS, OLIVER G.; FLAXMAN, SETH; BHATT, SAMIR; SABINO, ESTER C. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science, v. 372, n. 6544, p. 815+, MAY 21 2021. Web of Science Citations: 36.

CANDIDO, DARLAN S.; CLARO, INGRA M.; DE JESUS, JAQUELINE G.; SOUZA, WILLIAM M.; MOREIRA, FILIPE R. R.; DELLICOUR, SIMON; MELLAN, THOMAS A.; DU PLESSIS, LOUIS; PEREIRA, RAFAEL H. M.; SALES, FLAVIA C. S.; MANULI, ERIKA R.; THEZE, JULIEN; ALMEIDA, LUIZ; MENEZES, MARIANE T.; VOLOCH, CAROLINA M.; FUMAGALLI, MARCILIO J.; COLETTI, THAIS M.; SILVA, CAMILA A. M.; RAMUNDO, MARIANA S.; AMORIM, MARIENE R.; HOELTGEBAUM, HENRIQUE H.; MISHRA, SWAPNIL; GILL, MANDEV S.; CARVALHO, LUIZ M.; BUSS, LEWIS F.; PRETE JR, CARLOS A.; ASHWORTH, JORDAN; NAKAYA, I, HELDER; PEIXOTO, PEDRO S.; BRADY, OLIVER J.; NICHOLLS, SAMUEL M.; TANURI, AMILCAR; ROSSI, ATILA D.; BRAGA, V, CARLOS K.; GERBER, ALEXANDRA L.; GUIMARAES, ANA PAULA DE C.; GABURO JR, NELSON; ALENCAR, CECILA SALETE; FERREIRA, ALESSANDRO C. S.; LIMA, CRISTIANO X.; LEVI, JOSE EDUARDO; GRANATO, CELSO; FERREIRA, GIULIA M.; FRANCISCO JR, RONALDO S.; GRANJA, FABIANA; GARCIA, MARCIA T.; MORETTI, MARIA LUIZA; PERROUD JR, MAURICIO W.; CASTINEIRAS, TEREZINHA M. P. P.; LAZARI, CAROLINA S.; HILL, SARAH C.; DE SOUZA SANTOS, ANDREZA ARUSKA; SIMEONI, CAMILA L.; FORATO, JULIA; SPOSITO, ANDREI C.; SCHREIBER, ANGELICA Z.; SANTOS, MAGNUN N. N.; DE SA, CAMILA ZOLINI; SOUZA, RENAN P.; RESENDE-MOREIRA, LUCIANA C.; TEIXEIRA, MAURO M.; HUBNER, JOSY; LEME, PATRICIA A. F.; MOREIRA, RENNAN G.; NOGUEIRA, MAURICIO L.; FERGUSON, NEIL M.; COSTA, SILVIA F.; PROENCA-MODENA, JOSE LUIZ; VASCONCELOS, ANA TEREZA R.; BHATT, SAMIR; LEMEY, PHILIPPE; WU, CHIEH-HSI; RAMBAUT, ANDREW; LOMAN, NICK J.; AGUIAR, RENATO S.; PYBUS, OLIVER G.; SABINO, ESTER C.; FARIA, NUNO RODRIGUES; DISCOVERY, BRAZIL-UK CTR ARBOVIRUS. Evolution and epidemic spread of SARS-CoV-2 in Brazil. Science, v. 369, n. 6508, SI, p. 1255+, SEP 4 2020. Web of Science Citations: 1.