mesЭкстремальная биомедицинаExtreme Medicine3033-89643033-8972Centre for Strategic Planning of the Federal Medical and Biological Agency10.47183/mes.2024-242mes-242Research ArticleМОЛЕКУЛЯРНАЯ ЭПИДЕМИОЛОГИЯMOLECULAR EPIDEMIOLOGYСравнительный анализ нанопоровых секвенаторов MinION и Нанопорус в задаче идентификации нуклеиновых кислот патогеновComparative evaluation of MinION and Nanoporus nanopore sequencers in identification of pathogen nucleic acidshttps://orcid.org/0000-0001-9763-9879ГригорянД. А.GrigoryanD. A.

Григорян Диана Агароновна

Москва

Diana A. Grigoryan

Moscow

DGrigoryan@cspfmba.ruhttps://orcid.org/0000-0003-0979-3409СтеценкоИ. Ф.StetsenkoI. F.

Стеценко Иван Федорович

Москва

Ivan F. Stetsenko

Moscow

IStecenko@cspfmba.ruhttps://orcid.org/0000-0002-2587-0630ГуковБ. С.GukovB. S.

Гуков Борис Сергеевич

Москва

Boris S. Gukov

Moscow

BGukov@cspfmba.ruhttps://orcid.org/0000-0002-6301-9169МацвайА. Д.MatsvayA. D.

Мацвай Алина Дмитриевна - канд. биол. наук

Москва

Alina D. Matsvay

Moscow

AMatsvay@cspfmba.ruhttps://orcid.org/0000-0002-3668-6601ШипулинГ. А.ShipulinG. A.

Шипулин Герман Александрович - канд. мед. наук

Москва

German A. Shipulin

Moscow

Shipulin@cspfmba.ruЦентр стратегического планирования и управления медико-биологическими рисками здоровью Федерального медико-биологического агентстваРоссияCentre for Strategic Planning, of the Federal Medical and Biological AgencyRussian Federation2025230320252716473Copyright © Григорян Д.А., Стеценко И.Ф., Гуков Б.С., Мацвай А.Д., Шипулин Г.А., 20252025Григорян Д.А., Стеценко И.Ф., Гуков Б.С., Мацвай А.Д., Шипулин Г.А.Grigoryan D.A., Stetsenko I.F., Gukov B.S., Matsvay A.D., Shipulin G.A.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://www.extrememedicine.ru/jour/article/view/242Введение

Введение. Технологии нанопорового секвенирования стали рутинным инструментом в науке и медицине, широко применяются в исследовании разнообразия и распространения патогенов, играют ключевую роль в полевой эпидемиологии.

Цель

Цель. Проведение сравнительного анализа функциональных возможностей секвенаторов третьего поколения MinION и Нанопорус в задаче выявления патогенов в биологическом материале, включая сопоставление таксономического состава, определенного с их использованием, с результатами, полученными на референсной платформе второго поколения MiSeq (Illumina).

Материалы и методы

Материалы и методы. Проведено исследование 138 образцов архивной ДНК с известным таксономическим составом (исследованы 14 семейств, 20 родов и 43 вида патогенов вирусной и бактериальной природы, суммарно 169 возбудителей инфекций). В исследовании использовались нанопоровые секвенаторы MinION и Нанопорус с оригинальными проточными ячейками R9.4.1 и R10.4.1 от ONT, а также высокопроизводительная платформа MiSeq от Illumina для предварительной идентификации состава исследуемых образцов, содержащих различные титры нуклеиновых кислот возбудителей инфекций ряда таксономических групп. Сравнительный анализ полученных данных (количество последовательностей, средние показатели качества прочтений (Qscore) для каждого нуклеотида, GC-состав последовательностей, распределение длин последовательностей, уровень дупликаций прочтений) проводился биоинформатическим инструментом MultiQC (версия 1.20).

Результаты

Результаты. В ходе проведенных исследований на приборах MinION и Нанопорус было идентифицировано 98,8 и 97,6% патогенов соответственно, включая малоизученные или новые вирусы. Применение последней версии проточной ячейки на обоих приборах значительно снизило долю низкокачественных прочтений. Полученные данные продемонстрировали высокую степень корреляции между результатами секвенаторов второго и третьего поколений, что подтверждает сопоставимость и взаимозаменяемость этих технологий в задаче идентификации нуклеиновых кислот патогенов.

Выводы

Выводы. Результаты исследования демонстрируют потенциал нанопоровых секвенаторов MinION и Нанопорус для применения в эпидемиологическом надзоре. Приборы способны обеспечивать высокую точность идентификации патогенов различной природы и благодаря своей компактности и портативности могут существенно повысить скорость диагностики и мониторинга инфекционных заболеваний.

Introduction

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

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

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

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

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.

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The authors declare that there are no conflicts of interest present.