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de Souza LM, de Oliveira ID, Sales FCS, da Costa AC, Campos KR, Abbud A, Guerra JM, Dos Santos Cirqueira Borges C, Takahashi CPFJ, de Araújo LJT. Technical comparison of MinIon and Illumina technologies for genotyping Chikungunya virus in clinical samples. J Genet Eng Biotechnol 2023; 21:88. [PMID: 37642827 PMCID: PMC10465416 DOI: 10.1186/s43141-023-00536-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 07/27/2023] [Indexed: 08/31/2023]
Abstract
New-generation sequencing (NGS) techniques have brought the opportunity for genomic monitoring of several microorganisms potentially relevant to public health. The establishment of different methods with different mechanisms provides a wide choice, taking into account several aspects. With that in mind, the present aim of the study was to compare basic genomic sequencing metrics that could potentially impact genotyping by nanopores from Oxford Nanopore Technologies and by synthesis from Illumina in clinical samples positive for Chikungunya (CHIKV). Among the metrics studied, running time, read production, and Q score were better represented in Illumina sequencing, while the MinIOn platform showed better response time and greater diversity of generated files. That said, it was possible to establish differences between the studied metrics in addition to verifying that the distinctions in the methods did not impact the identification of the CHIKV virus genotype.
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Affiliation(s)
- Leandro Menezes de Souza
- Centro de Patologia, Instituto Adolfo Lutz, Sao Paulo, Brazil
- Programa de Pós Graduação em Ciências da Saúde do Instituto de Assistência Médica ao Servidor Público Estadual - IAMSPE, Sao Paulo, Brazil
| | - Isabelle Dias de Oliveira
- Centro de Patologia, Instituto Adolfo Lutz, Sao Paulo, Brazil
- Programa de Pós Graduação em Ciências da Saúde do Instituto de Assistência Médica ao Servidor Público Estadual - IAMSPE, Sao Paulo, Brazil
| | - Flávia Cristina Silva Sales
- Departamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brazil
| | - Antonio Charlys da Costa
- Departamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brazil
| | | | - Adriano Abbud
- Centro de Respostas Rápidas, Instituto Adolfo Lutz, Sao Paulo, Brazil
| | | | | | | | - Leonardo José Tadeu de Araújo
- Centro de Patologia, Instituto Adolfo Lutz, Sao Paulo, Brazil.
- Programa de Pós Graduação em Ciências da Saúde do Instituto de Assistência Médica ao Servidor Público Estadual - IAMSPE, Sao Paulo, Brazil.
- Departamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brazil.
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