Development and application of bioinformatic pipelines for metagenomic analysis of clinical samples

• Grant number: 22/00910-6
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• Start date: March 01, 2022
• End date: December 31, 2022
• Field of knowledge: Biological Sciences - Genetics - Molecular Genetics and Genetics of Microorganisms
• Principal Investigator: Svetoslav Nanev Slavov
• Grantee: Gabriel Montenegro de Campos
• Host Institution: Hemocentro de Ribeirão Preto. Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto da USP (HCMRP). 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

The metagenomic approaches are one of the most sensitive tools to identify emerging viruses. With the emergence of the New Generation Sequencing (NGS) technologies, the software diversity used for data analysis has grown significantly. The bioinformatic analysis of the obtained NGS sequencing data represents still a significant challenge for the correct interpretation of the data due to the variability of the programs used for taxonomic classification. Therefore, this project aims to develop and optimize a pipeline for viral metagenomic analysis originating from NGS sequencing data obtained from several study groups (plasma samples obtained from patients with prostate cancer, undefined febrile illness, and waste pickers). At the same time, parallel comparisons with other bioinformatics programs and mainly viral taxonomy classifiers will be carried out. Adjustments will be performed to the classifiers' databases once they represent high variability of the available viral taxonomic data. Once this is performed, the identified viruses with clinical importance will be assembled and they will be subjected to phylogenetic analysis in order to investigate their molecular epidemiology. This proposal will allow a deeper insight into the metavirome of different groups of patients.(AU)

Scientific publications

(5)

(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)

DA SILVA, ANIELLY SARANA; DE CAMPOS, GABRIEL MONTENEGRO; ALTIZANI, GABRIELA MARENGONE; BARROS, ALICE CHAGAS; JUNQUEIRA, DENNIS MALETICH; KASHIMA, SIMONE; SAMPAIO, SANDRA COCCUZZO; ELIAS, MARIA CAROLINA; GIOVANETTI, MARTA; SCRIDELI, CARLOS ALBERTO; et al. Human pegivirus-1 (HPgV-1) RNA frequency and genotype distribution in pediatric oncology patients with febrile neutropenia. VIRUS RESEARCH, v. 350, p. 5-pg., 2024-10-11. (22/14958-0, 17/23205-8, 22/00910-6, 21/11944-6)

DE CAMPOS, GABRIEL MONTENEGRO; SANTOS, HAZERRAL DE OLIVEIRA; LIMA, ALEX RANIERI JERONIMO; LEITE, ANDERSON BRANDAO; RIBEIRO, GABRIELA; BERNARDINO, JARDELINA DE SOUZA TODAO; DO NASCIMENTO, JEAN PHELLIPE MARQUES; SOUZA, JULIANA VANESSA CAVALCANTE; DE LIMA, LOYZE PAOLA OLIVEIRA; LIMA, MARLON BRENO ZAMPIERI; et al. Unveiling viral pathogens in acute respiratory disease: Insights from viral metagenomics in patients from the State of Alagoas, Brazil. PLoS Neglected Tropical Diseases, v. 18, n. 9, p. 11-pg., 2024-09-01. (21/11944-6, 17/23205-8, 22/00910-6, 23/12155-0, 22/14958-0)

LIMA, MARLON BRENO ZAMPIERI; DANIEL, THUANY GIOVANA PEREIRA; BITENCOURT, HELLEN TAYANA OLIVEIRA; ALCANTARA, LUIZ CARLOS JUNIOR; HADDAD, RODRIGO; KASHIMA, SIMONE; ELIAS, MARIA CAROLINA; GIOVANETTI, MARTA; SAMPAIO, SANDRA COCCUZZO; SLAVOV, SVETOSLAV NANEV. Molecular frequency of human gemycircularvirus (GCYV) dna among blood donors from the Brazilian Amazon. TRANSFUSION CLINIQUE ET BIOLOGIQUE, v. 31, n. 2, p. 4-pg., 2024-04-17. (22/00910-6, 17/23205-8, 21/11944-6, 18/15826-5, 22/14958-0)

DE CAMPOS, GABRIEL MONTENEGRO; LIMA DE LA-ROQUE, DEBORA GLENDA; JERONIMO LIMA, ALEX RANIERI; ZUCHERATO, VICTORIA SIMIONATTO; DE CARVALHO, ENEAS; OLIVEIRA DE LIMA, LOYZE PAOLA; CATTONY NETO, PEDRO DE QUEIROZ; DOS SANTOS, MURILO MARCONI; CICCOZZI, MASSIMO; GIOVANETTI, MARTA; et al. Exploring Viral Metagenomics in Pediatric Patients with Acute Respiratory Infections: Unveiling Pathogens beyond SARS-CoV-2. MICROORGANISMS, v. 11, n. 11, p. 10-pg., 2023-11-01. (22/00910-6, 17/23205-8, 21/11944-6, 18/15826-5, 21/09446-8)

ZANETTE, DALILA LUCIOLA; COELHO, KAROLINE BRITO CAETANO ANDRADE; DE CARVALHO, ENEAS; AOKI, MATEUS NOBREGA; NARDIN, JEANINE MARIE; LALLI, LARISSA ARAUJO; BEZERRA, RAFAEL DOS SANTOS; GIOVANETTI, MARTA; ZUCHERATO, VICTORIA SIMIONATTO; DE CAMPOS, GABRIEL MONTENEGRO; et al. Metagenomic insights into the plasma virome of Brazilian patients with prostate cancer. MOLECULAR & CELLULAR ONCOLOGY, v. 10, n. 1, p. 9-pg., 2023-12-31. (19/08528-0, 22/00910-6, 17/23205-8, 20/13194-1)