Technical comparison of MinIon and Illumina technologies for genotyping Chikungunya virus in clinical samples

• Published in: Journal of Genetic Engineering and Biotechnology Vol. 21; no. 1; pp. 88 - 8
• Main Authors: de Souza, Leandro Menezes, de Oliveira, Isabelle Dias, Sales, Flávia Cristina Silva, da Costa, Antonio Charlys, Campos, Karoline Rodrigues, Abbud, Adriano, Guerra, Juliana Mariotti, dos Santos Cirqueira Borges, Cinthya, Takahashi, Carlos Pires Fernandes Júnior, de Araújo, Leonardo José Tadeu
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.12.2023; Springer; Springer Nature B.V; Elsevier
• Subjects: Bioinformatics; Biomedical Engineering and Bioengineering; Biotechnology; Chikungunya virus; Chikungunya virus genotype; Construction; Dengue fever; DNA sequencing; Engineering; Genetic Engineering; Genetics and Genomics; Genomes; Genomics; Genotypes; Genotyping; Metric MinION and Illumina; Next-generation sequencing; Nucleotide sequencing; Proteomics; Public health; Software; Surveillance; Viruses; Brazil; United Kingdom > UK; England; United States > US; Chikungunya virus genotype; Metric MinION and Illumina; Next-generation sequencing
• ISSN: 1687-157X; 2090-5920
• DOI: 10.1186/s43141-023-00536-3

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.