Application of portable minion sequencing technology for viral metagenomics analysis

• Grant number: 21/09446-8
• Support Opportunities: Scholarships in Brazil - Master
• Start date: April 01, 2022
• End date: March 31, 2023
• Field of knowledge: Biological Sciences - Genetics - Molecular Genetics and Genetics of Microorganisms
• Principal Investigator: Svetoslav Nanev Slavov
• Grantee: Victória Simionatto Zucherato
• 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

Next Generation Sequencing (NGS) technologies have shown accelerated growth in the recent years, thus allowing for massive generation of genomic data in a simultaneous, impartial and rapid way. One of the main applications of NGS is metagenomics, which contributes to the identification of emerging pathogens and genomic signatures, thus transforming the medical history. Although the world's main platform for obtaining metagenomic data is represented by Illumina, this equipment is expensive, requires trained human resources and highly sophisticated infrastructure. Given this scenario, a technique that has been gaining ground in the scientific field is the portable MinION platform, which has a low cost, does not require improved infrastructure and, therefore, can be used for field studies in remote regions that are affected in most cases by emerging outbreaks. However, the MinION platform rarely has been applied for metagenomic studies due to the lack of adequate optimization of both the process of obtaining metagenome and the steps of sample pre-preparation, viral concentration and extraction. Therefore, the objective of this project is to optimize the MinION technology in order to obtain and analyze the metavirome of blood donors from three Brazilian regions: Southeast (São Paulo), Central-West (Federal District) and the Amazon region (Amapá), previously infected with viral agents such as HBV, HIV and HCV. The results of this study will provide information on the composition of the viroma of high-risk Brazilian donors, and will also enable the application of MinION technology in the area of viral metagenomics and molecular epidemiological surveillance. (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)

CAVALCANTE SOUZA, JULIANA VANESSA; SANTOS, HAZERRAL DE OLIVEIRA; LEITE, ANDERSON BRANDAO; GIOVANETTI, MARTA; BEZERRA, RAFAEL DOS SANTOS; DE CARVALHO, ENEAS; TODAO BERNARDINO, JARDELINA DE SOUZA; VIALA, VINCENT LOUIS; HADDAD, RODRIGO; CICCOZZI, MASSIMO; et al. Viral Metagenomics for the Identification of Emerging Infections in Clinical Samples with Inconclusive Dengue, Zika, and Chikungunya Viral Amplification. Viruses-Basel, v. 14, n. 9, p. 8-pg., 2022-09-01. (17/23205-8, 18/15826-5, 21/09446-8, 21/11944-6, 20/13194-1, 19/08528-0)

Academic Publications

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

ZUCHERATO, Victória Simionatto. Optimization of portable MinION sequencing technology for viral metagenome analysis. 2023. Master's Dissertation - Universidade de São Paulo (USP). Faculdade de Medicina de Ribeirão Preto (PCARP/BC) Ribeirão Preto.