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Volume 17
Issue 11
10.3390/v17111440
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

A Novel Nanopore-Based Genotyping System for Norovirus GII: Validation and Application to Pediatric Gastroenteritis Cases in Moscow, Russia

by
Ivan F. Stetsenko
1,†,
Vasilina K. Lapshina
1,†,
Polina A. Nikolaeva
1,
Boris S. Gukov
1,
Alexandr V. Chernitsov
1,
Andrey R. Luparev
1,
Ekaterina E. Davydova
1,
Maria A. Gordukova
2,
Elena V. Galeeva
2,
Alina D. Matsvay
1,* and
German A. Shipulin
1
1
Federal State Budgetary Institution «Centre for Strategic Planning and Management of Biomedical Health Risks» of the Federal Medical Biological Agency, 119121 Moscow, Russia
2
G. Speransky Children’s Hospital No. 9, 123317 Moscow, Russia
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Viruses 2025, 17(11), 1440; https://doi.org/10.3390/v17111440
Submission received: 1 October 2025 / Revised: 23 October 2025 / Accepted: 26 October 2025 / Published: 29 October 2025
(This article belongs to the Section Human Virology and Viral Diseases)
Versions Notes

Abstract

Norovirus is a leading cause of acute gastroenteritis, with genogroup II (NoV-GII) being predominant. This study presents a novel genotyping system for norovirus GII, combining long-range PCR to amplify the complete ~3.2 kb RdRp–VP1 region with Nanopore sequencing and a dedicated bioinformatics pipeline. This approach provides comprehensive, high-resolution genomic data, representing a significant advancement over conventional methods. Encompassing the recombination site and the full lengths of both genotyping regions in a single amplicon enables sensitive detection of mixed infections and recombinant variants, even at concentrations as low as 1% for minor genotypes. We validated the system through retrospective analysis of 115 pediatric acute gastroenteritis cases in Moscow, Russia (2021–2025) with a high viral load of NoV-GII, selected from 3061 screened stool samples. The analysis revealed the predominant circulation of GII.4[P16] norovirus strains, while GII.17[P17] emerged as the second most prevalent genotype after 2021. In contrast, previously common genotypes GII.4[P31] and GII.3[P12] sharply declined. Mixed infections were found in 4% of cases. With the data obtained, we are doubling the number of long (>3000 bp) NoV-GII genomic sequences from Russia available in public databases and providing unique surveillance data for the Moscow region covering the last five years. The results establish the system as a robust framework for high-resolution surveillance, supporting timely detection of emerging strains and informed public health response.
Keywords: norovirus; nanopore sequencing; retrospective studies; Russia; gastroenteritis; computational biology; polymerase chain reaction norovirus; nanopore sequencing; retrospective studies; Russia; gastroenteritis; computational biology; polymerase chain reaction

Share and Cite

MDPI and ACS Style

Stetsenko, I.F.; Lapshina, V.K.; Nikolaeva, P.A.; Gukov, B.S.; Chernitsov, A.V.; Luparev, A.R.; Davydova, E.E.; Gordukova, M.A.; Galeeva, E.V.; Matsvay, A.D.; et al. A Novel Nanopore-Based Genotyping System for Norovirus GII: Validation and Application to Pediatric Gastroenteritis Cases in Moscow, Russia. Viruses 2025, 17, 1440. https://doi.org/10.3390/v17111440

AMA Style

Stetsenko IF, Lapshina VK, Nikolaeva PA, Gukov BS, Chernitsov AV, Luparev AR, Davydova EE, Gordukova MA, Galeeva EV, Matsvay AD, et al. A Novel Nanopore-Based Genotyping System for Norovirus GII: Validation and Application to Pediatric Gastroenteritis Cases in Moscow, Russia. Viruses. 2025; 17(11):1440. https://doi.org/10.3390/v17111440

Chicago/Turabian Style

Stetsenko, Ivan F., Vasilina K. Lapshina, Polina A. Nikolaeva, Boris S. Gukov, Alexandr V. Chernitsov, Andrey R. Luparev, Ekaterina E. Davydova, Maria A. Gordukova, Elena V. Galeeva, Alina D. Matsvay, and et al. 2025. "A Novel Nanopore-Based Genotyping System for Norovirus GII: Validation and Application to Pediatric Gastroenteritis Cases in Moscow, Russia" Viruses 17, no. 11: 1440. https://doi.org/10.3390/v17111440

APA Style

Stetsenko, I. F., Lapshina, V. K., Nikolaeva, P. A., Gukov, B. S., Chernitsov, A. V., Luparev, A. R., Davydova, E. E., Gordukova, M. A., Galeeva, E. V., Matsvay, A. D., & Shipulin, G. A. (2025). A Novel Nanopore-Based Genotyping System for Norovirus GII: Validation and Application to Pediatric Gastroenteritis Cases in Moscow, Russia. Viruses, 17(11), 1440. https://doi.org/10.3390/v17111440

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