Bats: epidemiological surveillance, high-resolution phylodynamics, search and design of peptides of biotechnological interest in emergent and reemerging viruses

• Grant number: 19/01255-9
• Support Opportunities: Research Grants - Young Investigators Grants
• Start date: May 01, 2021
• End date: April 30, 2026
• Field of knowledge: Agronomical Sciences - Veterinary Medicine - Preventive Veterinary Medicine
• Principal Investigator: Ricardo Durães de Carvalho
• Grantee: Ricardo Durães de Carvalho
• Host Institution: Escola Paulista de Medicina (EPM). Universidade Federal de São Paulo (UNIFESP). Campus São Paulo. São Paulo , SP, Brazil
• City of the host institution: São Paulo
• Associated scholarship(s): 25/23404-7 - Principles of data management, data mining, and analysis of viral RNA-Seq data obtained from bats, BP.IC; 25/15040-5 - In silico approach and molecular Validation for the design of oligonucleotides targeting Mayaro virus, BP.IC; 25/05535-7 - Coronaviruses and Orthomyxoviruses in bats: screening of evolutionary dynamics and surveillance of emerging viruses with zoonotic potential, BP.TT; + associated scholarships 25/05645-7 - Epidemiological and molecular analysis and screening of caliciviruses and viral hepatitis in bats from Northeastern Brazil., BP.IC; 24/09079-3 - Investigation of emerging and reemerging viruses in bat specimens captured in different regions of the State of São Paulo, BP.TT; 24/03914-8 - Investigation of emerging and reemerging viruses in swab samples (oral/rectal) from bats captured in different regions of the State of São Paulo, BP.TT; 23/04038-4 - Epidemiological surveillance and principles of viral molecular evolution in the investigation of Coronavirus, Influenza A and Arbovirus in bats from different regions of the State of São Paulo, BP.MS; 22/12858-9 - Phylogeny and molecular evolution of Chikungunya (CHIKV), Dengue (DENVs) and Zika (ZIKV) viruses: identification, design and validation of peptides of biotechnological interest, BP.DD; 22/12861-0 - High-resolution phylodynamics and its translational application in the biotechnological context: identification, design and validation of peptides from Mayaro (MAYV), Oropouche (OROV) and Yellow Fever (YFV) viruses, BP.DD; 22/08748-3 - Investigation of emerging and reemerging viruses in bat specimens captured in different regions of the State of São Paulo, BP.TT; 22/09684-9 - Investigation of emerging and reemerging viruses in swab samples (oral/rectal) from bats captured in different regions of the State of São Paulo, BP.TT; 21/03684-4 - Bats: epidemiological surveillance, high-resolution phylodynamics, search and design of peptides of biotechnological interest in emergent and reemerging viruses, BP.JP - associated scholarships

Abstract

RNA viruses are important agents involved in emerging and reemerging zoonoses, representing an important public health concern. This scenario has been constantly monitored through the discovery of new pathogens, in which it comes into line and international interest to identify new agents in order to respond to new diseases before they reach the human population. In this context, bats, with a viroma still to be intensively explored, are increasingly receiving notorious attention for harbor several viral pathogens of medical importance (eg Nipah, Ebola, SARS-CoV, MERS-CoV and now SARS- CoV-2 [COVID-19] pandemic). On the other hand, arboviruses, also detected in bats, stand out. Namely, Chikungunya (CHIKV), Dengue 1-4 (DENVs), Mayaro (MAYV), Oropouche (OROV), Yellow Fever (YFV) and Zika (ZIKV), are responsible for more than 95% of infection cases in the whole Brazilian territory. Noteworthy, researches shows that commercially available diagnostic kits for the detection of CHIKV, DENV and ZIKV have serious limitations and the issue is aggravated when it comes to reemerging agents: MAYV, OROV and YFV. The present proposal will focus on investigating the presence of RNA viruses in bats and on approaches involving metagenomics and New Generation Sequencing (NGS) technologies aiming to identify new virus of zoonotic importance as well as new arboviral agents. In parallel, a pioneering approach will be implemented through the State-of-the-art phylodynamics using High Performance Computing (HPC), thus providing strategies for the development of platforms and workflows for the mapping and validation of target-specific peptides for diagnostic and therapeutics purposes. (AU)

Scientific publications

(16)

(The scientific publications listed on this page originate from the Web of Science or SciELO databases. Their authors have cited FAPESP grant or fellowship project numbers awarded to Principal Investigators or Fellowship Recipients, whether or not they are among the authors. This information is collected automatically and retrieved directly from those bibliometric databases.)

GARCIA, AMANDA BARBOSA; DE MORAES, ANA PAULA; RODRIGUES, DANIELE MASSELLI; GILIOLI, ROVILSON; DE OLIVEIRA-FILHO, EDMILSON FERREIRA; DURAES-CARVALHO, RICARDO; ARNS, CLARICE WEIS. Coding-Complete Genome Sequence of Murine Hepatitis Virus Strain 3 from Brazil. MICROBIOLOGY RESOURCE ANNOUNCEMENTS, v. 10, n. 15, APR 2021. (19/01255-9)

LOEFFLER, FELIX F.; VIANA, ISABELLE F. T.; FISCHER, NICO; COELHO, DANILO F.; SILVA, CAROLINA S.; PURIFICACAO, JR., ANTONIO F.; ARAUJO, CATARINA M. C. S.; LEITE, BRUNO H. S.; DURAES-CARVALHO, RICARDO; MAGALHAES, TEREZA; et al. Identification of a Zika NS2B epitope as a biomarker for severe clinical phenotypes. RSC MEDICINAL CHEMISTRY, v. 12, n. 9, JUL 2021. (19/01255-9)

ANDREATA-SANTOS, ROBERT; JANINI, LUIZ M. R.; DURAES-CARVALHO, RICARDO. From Alpha to Omicron SARS-CoV-2 variants: What their evolutionary signatures can tell us?. Journal of Medical Virology, JAN 2022. (21/03684-4, 19/01255-9, 21/05661-1, 20/08943-5)

DE SOUSA, LARISSA LEAO F.; GUILARDI, MARIANA DIAS; MARTINS, JUNIOR OLIMPIO; ALVES, BRUNA STEFANIE S.; TIBO, LUIZ HENRIQUE S.; DA SILVA-ANTUNES, PATRICIA; CABRAL-MIRANDA, GUSTAVO; CALDEIRA, DEBORA BELLINI; BRANDAO, PAULO EDUARDO; CAMPOS, FABRICIO SOUZA; et al. Phylogenetic inferences reveal multiple intra- and interhost genetic diversity among bat rabies viruses circulating in northeastern Brazil. ONE HEALTH OUTLOOK, v. 7, n. 1, p. 11-pg., 2025-01-06. (21/03684-4, 19/01255-9)

DE MELO, BRUNA A. G.; MUNDIM, MAYARA, V; LEMES, ROBERTHA M. R.; CRUZ, ELISA M.; RIBEIRO, TAIS N.; SANTIAGO, CAROLINA F.; DA FONSECA, JESSICA H. L.; BENINCASA, JULIA C.; STILHANO, ROBERTA S.; MANTOVANI, NATHALIA; et al. 3D Bioprinted Neural-Like Tissue as a Platform to Study Neurotropism of Mouse-Adapted SARS-CoV-2. ADVANCED BIOLOGY, v. 6, n. 8, p. 16-pg., 2022-05-06. (21/03684-4, 20/05289-2, 18/23039-3, 19/01255-9, 18/12605-8)

PRATES-SYED, WASIM ALUISIO; FONSECA, DENNYSON LEANDRO MATHIAS DA; POUR, SHAHAB ZAKI; LIRA, ALINE; CORTES, NELSON; SILVA, JAQUELINE DINIS QUEIROZ; CARVALHO, EVELYN; FILGUEIRAS, IGOR SALERNO; VINCES, TANIA GERALDINE CHURASCARI; SCHIMKE, LENA F.; et al. COVID-19 vaccination atlas using an integrative systems vaccinology approach. NPJ VACCINES, v. 10, n. 1, p. 12-pg., 2025-06-02. (18/18886-9, 23/07806-2, 19/01255-9, 19/14526-0, 21/03684-4, 20/16246-2, 23/13356-0, 20/05146-7)

SILVA JR, JOSE VALTER JOAQUIM; LOPES, THAISA REGINA ROCHA; PEDROSO, NATALIA HETTWER; DURAES-CARVALHO, RICARDO; WEIBLEN, RUDI; FLORES, EDUARDO FURTADO; GIL, LAURA HELENA VEGA GONZALES. Unprecedented Oropouche Fever Outbreak in Brazil: Could the M Segment-Encoded Proteins Provide Clues to Possible Insights?. Journal of Medical Virology, v. 96, n. 12, p. 4-pg., 2024-12-01. (21/03684-4, 19/01255-9)

SILVERIO, BRUNA STEFANIE; DURO, RODRIGO LOPES SANZ; DE SOUSA, LARISSA LEAO F.; GUILARDI, MARIANA DIAS; CABRAL-MIRANDA, GUSTAVO; JANINI, LUIZ MARIO RAMOS; DURAES-CARVALHO, RICARDO. Detection and Phylogenetic Analysis of Emerging Human-Associated Gemykibivirus-2 in Molossus molossus Bat From Brazil. Journal of Medical Virology, v. 97, n. 1, p. 4-pg., 2025-01-01. (19/14526-0, 20/05146-7, 23/04038-4, 21/03684-4, 24/09079-3, 19/01255-9, 20/08943-5)

CORTES, NELSON; LIRA, ALINE; SILVA, JAQUELINE D. Q.; CARVALHO, EVELYN; PRATES-SYED, WASIM A.; HAMAGUCHI, BARBARA; DURAES-CARVALHO, RICARDO; BALAN, ANDREA; CAMARA, NIELS O. S.; CABRAL-MARQUES, OTAVIO; et al. A VLPs based vaccine protects against Zika virus infection and prevents cerebral and testicular damage. NPJ VACCINES, v. 10, n. 1, p. 12-pg., 2025-05-27. (23/13991-7, 20/04667-3, 21/03508-1, 19/01255-9, 19/14526-0, 21/03684-4, 21/03102-5, 21/08468-8, 24/13269-2)

DA COSTA, ANDERSON LUIS; PRIETO-OLIVEIRA, PAULA; DUARTE-BARBOSA, MARCIA; ANDREATA-SANTOS, ROBERT; PETER, CRISTINA M.; DE BRITO, THAMIRES PROLO; ANTONELI, FERNANDO; DURAES-CARVALHO, RICARDO; BRIONES, MARCELO R. S.; MARICATO, JULIANA T.; et al. The Relationship between HERV, Interleukin, and Transcription Factor Expression in ZIKV Infected versus Uninfected Trophoblastic Cells. CELLS, v. 13, n. 17, p. 15-pg., 2024-09-01. (23/07287-5, 23/10230-5, 21/03684-4, 20/08943-5, 21/05661-1, 19/01255-9)

DE SOUSA, LARISSA L. F.; DE SOUZA, TATIANE L.; TIBO, LUIZ H. S.; MOURA, FRANCISCO B. P.; JUNIOR, FRANCISCO A. S.; DE OLIVEIRA-FILHO, EDMILSON F.; LUDWIG-BEGALL, LOUISA F.; CABRAL-MIRANDA, GUSTAVO; ANDREATA-SANTOS, ROBERT; JANINI, LUIZ M. R.; et al. Rabies virus variants from bats closely related to variants found in marmosets (Callithrix jacchus), a neglected source of human rabies infection in Brazil. Journal of Medical Virology, v. 95, n. 8, p. 8-pg., 2023-08-01. (19/01255-9, 22/09684-9, 21/03684-4, 22/08748-3)

NUNES, DANILO ROSA; BRACONI, CARLA TORRES; LUDWIG-BEGALL, LOUISA F.; ARNS, CLARICE WEIS; DURAES-CARVALHO, RICARDO. Deep phylogenetic-based clustering analysis uncovers new and shared mutations in SARS-CoV-2 variants as a result of directional and convergent evolution. PLoS One, v. 17, n. 5, p. 14-pg., 2022-05-24. (19/01255-9, 21/03684-4)

DOS SANTOS, DEBORA REGINA LOPES; DURAES-CARVALHO, RICARDO; GARDINALI, NOEMI ROVARIS; MACHADO, LAIS CESCHINI; DE PAULA, VANESSA SALETE; WALLAU, GABRIEL DA LUZ; DE OLIVEIRA, JAQUELINE MENDES; PENA, LINDOMAR JOSE; PINTO, MARCELO ALVES; GIL, LAURA HELENA VEGA GONZALEZ; et al. Uncovering neglected subtypes and zoonotic transmission of Hepatitis E virus (HEV) in Brazil. VIROLOGY JOURNAL, v. 20, n. 1, p. 7-pg., 2023-05-02. (19/01255-9, 21/03684-4)

JOAQUIM SILVA JUNIOR, JOSE VALTER; DURAES-CARVALHO, RICARDO; DE SOUZA, JOELMA RODRIGUES; RAMOS JANINI, LUIZ MARIO; WEIBLEN, RUDI; FLORES, EDUARDO FURTADO. Emergence of SARS-CoV-2 serotype(s): Is it a matter of time?. VIROLOGY, v. 585, p. 4-pg., 2023-06-13. (19/01255-9, 20/08943-5, 21/03684-4)

PINHEIRO, JOSILENE R.; DOS REIS, ESTHER C.; FARIAS, JESSICA P.; FOGACA, MAYANNA M. C.; DA SILVA, PATRICIA DE S.; SANTANA, ITANA VIVIAN R.; ROCHA, ANA LUIZA S.; VIDAL, PALOMA O.; SIMOES, RAFAEL DA C.; LUIZ, WILSON B.; et al. Impact of Early Pandemic SARS-CoV-2 Lineages Replacement with the Variant of Concern P.1 (Gamma) in Western Bahia, Brazil. Viruses-Basel, v. 14, n. 10, p. 12-pg., 2022-10-01. (19/01255-9, 21/03684-4)

DOS SANTOS PEREIRA ANDRADE, ANA CLAUDIA; CAMPOLINA-SILVA, GABRIEL HENRIQUE; QUEIROZ-JUNIOR, CELSO MARTINS; DE OLIVEIRA, LEONARDO CAMILO; LACERDA, LARISSE DE SOUZA BARBOSA; PIMENTA GAGGINO, JORDANE CLARISSE; OLIVEIRA DE SOUZA, FILIPE RESENDE; CHAVES, IAN DE MEIRA; PASSOS, INGREDY BEATRIZ; TEIXEIRA, DANIELLE CUNHA; et al. A Biosafety Level 2 Mouse Model for Studying Betacoronavirus- Induced Acute Lung Damage and Systemic Manifestations. Journal of Virology, v. 95, n. 22, NOV 2021. (19/01255-9)