Inter Biorisks-EURLs WG on NGS
Published November 24, 2025 | Version 1
Standard Open

Guidelines for amplicon sequencing of the capsid region of noroviruses

Creators

  • 1. EDMO icon Swedish Food Agency

Contributors

  • 1. ROR icon Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail
  • 2. ROR icon Swedish Veterinary Agency
  • 3. ROR icon Istituto Superiore di Sanità
  • 4. EDMO icon Swedish Food Agency
  • 5. ROR icon Technical University of Denmark
  • 6. ROR icon National Institute for Public Health and the Environment

Description

In this document, methodologies for amplicon sequencing of the capsid region of human noroviruses (from now on, referred as norovirus) are described. The document comprises guidance for the wet laboratory work (i.e. RNA-extraction, reverse transcription, PCRs and sequencing) as well as sequence analysis and determination of genotypes (bioinformatics). These guidelines convey all steps generally required for implementation of next generation sequencing based norovirus typing and have been drafted to assist novices to implement NGS in their typing strategy. In addition, specific and complete
method descriptions are appended to these general guidelines.


For subtyping of norovirus the capsid-region is the most commonly used region and a nomenclature of genogroups and genotypes has been developed (Chhabra et al, 2019). Of all noroviruses, genogroups I, II and IV primarily affect humans. Norovirus genogroup I and II are causative of the majority of the disease burden worldwide. A region of about 300 bp is usually amplified using PCR and then sequenced.Traditionally, such sequencing was performed by Sanger sequencing but the use of Next Generation Sequencing (NGS) enables typing of several genotypes within the same sample (Ollivier et al, 2022). This is important for environmentally contaminated foods or waters that might contain more than one genotype. Due to genomic heterogeneity, typing of noroviruses is generally performed separately for each genogroup.


It is also possible to also sequence the polymerase region (Pol) of norovirus to further increase typing resolution. However, this is out of scope for the current version of this document.

Files

Biorisks EURLs WG on NGS - Del11_Guidelines_Norovirus_typing-Skarin-20251124-v1.pdf

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Additional details

Dates

Issued
2025-11-24