Comparative evaluation of MinION and Nanoporus nanopore sequencers in identification of pathogen nucleic acids

Introduction . Nanopore sequencing technologies have become routine methods in science and medicine, being widely used in the study of pathogen diversity and distribution and playing a key role in field epidemiology. Objective . Comparative evaluation of the functional capabilities of third-generation MinION and Nanoporus sequencers in the detection of pathogens in biological material, including comparison of the as-determined taxonomic composition with the results obtained using the second-generation MiSeq (Illumina) reference platform. Materials and methods. A total of 138 archival DNA samples with known taxonomic composition (14 families, 20 genus, and 43 species of viral and bacterial pathogens; altogether 169 pathogens) were analyzed. MinION and Nanoporus nanopore sequencers with original R9.4.1 and R10.4.1 flow cells (ONT), as well as the high-performance MiSeq (Illumina) platform were used for preliminary identification of the composition of samples containing different titers of pathogen nucleic acids belonging to various taxonomic groups. Comparative evaluation of the obtained data (number of sequences, average read quality scores (Qscore) for each nucleotide, GC-content of sequences, sequence length distribution, read duplication level) was performed using the MultiQC bioinformatics tool (version 1.20). Results. The MinION and Nanoporus devices identified 98.8% and 97.6% of pathogens, respectively, including understudied or new viruses. The use of the latest-version flow cell on both devices significantly reduced the share of low-quality reads. The findings demonstrate a high degree of correlation between the results obtained by the second- and third-generation sequencers, which confirms the comparability and interchangeability of these technologies for the purposes of pathogen nucleic acid identification. Conclusions . The study results demonstrate the potential of MinION and Nanoporus nanopore sequencers for epidemiologic surveillance. These devices are capable of identifying pathogens of different nature with high accuracy and, due to their compactness and portability, facilitating the diagnostics and monitoring of infectious diseases.