Development of a bioinformatic pipeline for identification of emerging infectious diseases among patients in regimen of chronic transfusion

• Grant number: 19/07861-8
• Support Opportunities: Scholarships in Brazil - Master
• Start date: June 01, 2019
• End date: May 31, 2021
• Field of knowledge: Biological Sciences - Genetics - Molecular Genetics and Genetics of Microorganisms
• Principal Investigator: Svetoslav Nanev Slavov
• Grantee: Ian Nunes Valença
• Host Institution: Hemocentro de Ribeirão Preto. Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto da USP (HCMRP). Secretaria da Saúde (São Paulo - Estado). Ribeirão Preto , SP, Brazil
• Associated research grant: 17/23205-8 - Evaluation of the impact of emerging and reemerging viruses in the field of hemotherapy and stem cell transplantation by multiple-research approach, AP.JP

Abstract

Studies in the field of viral metagenomics have increased its importance in the recent decades due to advances of the Next Generation Sequencing (SNG), mainly due to the possibility of identifying emerging viruses without any knowledge of their genomic characteristics. In this scenario, patients who receive multiple blood transfusions or continuous treatments with hemoderivatives (beta-thalassemia, sickle-cell disease and hemophilia) are especially vulnerable, because they show a higher risk of acquisition of parenterally transmitted infectious diseases. Moreover, these patients manifest specific immunological alterations which might be responsible for the development of chronic viral infections and subsequent viral carriage. Therefore, such patients are target of interest for the identification of emerging, re-emergent and non-suspected viral agents that may adversely affect the patient survival. At the same time viral metagenomics performed in this group can reveal non-suspected viruses which demonstrate transfusion-transmitted potential. One of the main challenges of viral metagenomics are the bioinformatic procedures. Some difficulties include the processing of large amounts of data, lack of qualified bioinformaticians in Brazil, the complexity of the bioinformatic tools and the clinical interpretation of the obtained data. Therefore, our objective is to develop a bioinformatic pipeline to analyze the virome in blood samples obtained from patients with thalassemia, sickle cell disease and hemophilia. In addition, analysis of the viral molecular evolution will be performed, including phylogenetic analysis, presence of viral subpopulations and genotyping. The development of this project counts with international collaborations of the Institute Pasteur, France and the National Institute of Blood Transfusion, France. (AU)

Scientific publications

(12)

(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)

BEZERRA, RAFAEL DOS SANTOS; BITENCOURT, HELLEN TAYANA; COVAS, DIMAS TADEU; KASHIMA, SIMONE; SLAVOV, SVETOSLAV NANEV. Molecular evolution pattern of Merkel cell polyomavirus identified by viral metagenomics in plasma of high-risk blood donors from the Brazilian Amazon. INFECTION GENETICS AND EVOLUTION, v. 85, NOV 2020. (19/08528-0, 17/23205-8, 18/15826-5, 19/07861-8)

VALENCA, IAN NUNES; BEZERRA, RAFAEL DOS SANTOS; DE OLIVEIRA, LUCIANA CORREA OLIVEIRA; COVAS, DIMAS TADEU; KASHIMA, SIMONE; SLAVOV, SVETOSLAV NANEV. Deep viral metagenomics in patients with haemophilia receiving plasma-derived coagulation factor concentrates. HAEMOPHILIA, v. 27, n. 5, JUL 2021. (20/13194-1, 17/23205-8, 19/08528-0, 19/07861-8)

BEZERRA, RAFAEL DOS SANTOS; DE MELO JORGE, DANIEL MACEDO; CASTRO, ITALO ARAUJO; MORETTO, EDSON LARA; DE OLIVEIRA, LEONARDO SCALON; AMORIM UBIALI, EUGENIA MARIA; COVAS, DIMAS TADEU; ARRUDA, EURICO; KASHIMA, SIMONE; SLAVOV, SVETOSLAV NANEV. Detection of Influenza A(H3N2) Virus RNA in Donated Blood. Emerging Infectious Diseases, v. 26, n. 7, p. 1621-1623, JUL 2020. (17/23205-8, 19/07861-8, 18/15826-5, 19/08528-0)

BEZERRA, RAFAEL DOS SANTOS; BUB, CAROLINA BONET; PERONNI, KAMILA CHAGAS; DE FIGIUEIREDO BARROS, BRUNA DURAES; DA COSTA LIRA, SANNY MARCELE; KUTNER, JOSE MAURO; COVAS, DIMAS TADEU; KASHIMA, SIMONE; SLAVOV, SVETOSLAV NANEV. Virome comparison of deferred blood donations obtained from different geographic regions in the Sao Paulo State, Brazil. TRANSFUSION AND APHERESIS SCIENCE, v. 60, n. 3, JUN 2021. (17/23205-8, 19/08528-0, 19/07861-8, 18/15826-5)

RAFAEL DOS SANTOS BEZERRA; KAMILA CHAGAS PERONNI; BRUNA DURÃES DE FIGUEIREDO BARROS; LEONARDO SCALON DE OLIVEIRA; EVANDRA STRAZZA RODRIGUES; ROCHELE AZEVEDO; EUGÊNIA MARIA AMORIM UBIALI; DIMAS TADEU COVAS; SIMONE KASHIMA; SVETOSLAV NANEV SLAVOV. Viral metagenomics in blood donors with post-donation diseases and negative tests for dengue and Zika viruses RNA detection during a major outbreak of arboviruses in Sao Paulo State in 2016. Revista do Instituto de Medicina Tropical de São Paulo, v. 62, p. -, 2020. (19/08528-0, 18/15826-5, 19/07861-8, 17/23205-8)

BEZERRA, RAFAEL S.; BITENCOURT, HELLEN T.; COVAS, DIMAS T.; KASHIMA, SIMONE; SLAVOV, SVETOSLAV N.. Metagenomic identification of human Gemykibivirus-2 (HuGkV-2) in parenterally infected blood donors from the Brazilian Amazon. INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, v. 98, p. 3-pg., 2020-09-01. (19/08528-0, 18/15826-5, 19/07861-8, 17/23205-8)

BEZERRA, RAFAEL DOS SANTOS; VALENCA, IAN N.; RUY, PATRICIA DE CASSIA; XIMENEZ, JOAO P. B.; SILVA JUNIOR, WILSON A.; COVAS, DIMAS T.; KASHIMA, SIMONE; SLAVOV, SVETOSLAV N.. The novel coronavirus SARS-CoV-2: From a zoonotic infection to coronavirus disease 2019. Journal of Medical Virology, v. 92, n. 11, JUN 2020. (19/08528-0, 18/15826-5, 19/07861-8)

I.N. VALENÇA; F.A. RÓS; V.S. ZUCHERATO; A.C. SILVA-PINTO; D.T. COVAS; S. KASHIMA; S.N. SLAVOV. Comparative metavirome analysis in polytransfused patients. Brazilian Journal of Medical and Biological Research, v. 54, n. 12, 2021-10-18. (20/13194-1, 19/22155-2, 18/15826-5, 17/23205-8, 19/07861-8)

BEZERRA, RAFAEL DOS SANTOS; DIEFENBACH, CRISTIANE FRACAO; PEREIRA, DALNEI VEIGA; KASHIMA, SIMONE; SLAVOV, SVETOSLAV NANEV. Viral metagenomics performed in patients with acute febrile syndrome during Toxoplasma gondii outbreak in south Brazil. Brazilian Journal of Infectious Diseases, v. 24, n. 3, p. 250-255, MAY-JUN 2020. (19/07861-8, 18/15826-5, 19/08528-0, 17/23205-8)

BEZERRA, RAFAEL DOS SANTOS; DE OLIVEIRA, LEONARDO SCALON; MORENO, EDSON L.; UBIALI, EUGENIA M. AMORIM; SILVEIRA, ROBERTA MARANINCHI; DA SILVA JUNIOR, WILSON A.; COVAS, DIMAS TADEU; KASHIMA, SIMONE; SLAVOV, SVETOSLAV N.. Viral metagenomics in blood donations with post-donation illness reports from Brazil. BLOOD TRANSFUSION, v. 19, n. 2, p. 93-101, MAR-APR 2021. (19/07861-8, 14/50947-7, 19/08528-0)

VALENCA, IAN NUNES; DOS SANTOS, RAFAEL BEZERRA; PERONNI, KAMILA CHAGAS; SAUVAGE, VIRGINIE; VANDENBOGAERT, MATHIAS; CARO, VALERIE; DA SILVA JUNIOR, WILSON ARAUJO; COVAS, DIMAS TADEU; SILVA-PINTO, ANA CRISTINA; LAPERCHE, SYRIA; et al. Deep sequencing applied to the analysis of viromes in patients with beta-thalassemia. Revista do Instituto de Medicina Tropical de São Paulo, v. 63, 2021. (19/07861-8, 18/15826-5, 19/08528-0, 17/23205-8)

NUNES VALENCA, I; SILVA-PINTO, A. C.; ARAUJO DA SILVA JUNIOR, W.; COVAS, D. TADEU; KASHIMA, S.; NANEV SLAVOV, S.. Viral metagenomics in Brazilian multiply transfused patients with sickle cell disease as an indicator for blood transfusion safety. TRANSFUSION CLINIQUE ET BIOLOGIQUE, v. 27, n. 4, p. 237-242, NOV 2020. (18/22009-3, 17/23205-8, 19/07861-8, 18/15826-5, 19/08528-0)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

VALENÇA, Ian Nunes. Development of a bioinformatics pipeline for the identification of emerging infectious diseases in patients submitted to chronic transfusion. 2021. Master's Dissertation - Universidade de São Paulo (USP). Faculdade de Medicina de Ribeirão Preto (PCARP/BC) Ribeirão Preto.