Detection of human noroviruses in sewage by next generation sequencing in Shandong Province, 2019-2021.

Publisher: BioMed Central Country of Publication: England NLM ID: 101231645 Publication Model: Electronic Cited Medium: Internet ISSN: 1743-422X (Electronic) Linking ISSN: 1743422X NLM ISO Abbreviation: Virol J Subsets: MEDLINE

Original Publication: [London] : BioMed Central, 2004-

Norovirus*/genetics ; Norovirus*/classification ; Norovirus*/isolation & purification ; Sewage*/virology ; High-Throughput Nucleotide Sequencing* ; Genotype* ; Phylogeny* ; Genetic Variation*; Humans ; China/epidemiology ; RNA, Viral/genetics ; Gastroenteritis/virology ; Gastroenteritis/epidemiology ; Caliciviridae Infections/virology ; Caliciviridae Infections/epidemiology ; Real-Time Polymerase Chain Reaction/methods

Competing Interests: Declarations. Ethics approval and consent to participate: The Ethics Review Committee of the Shandong Center for Disease Control and Prevention approved the current study (2017–01). Consent for publication: All authors agree to publish the research data. Competing interests: The authors declare no competing interests.
Background: Human noroviruses are the major cause of acute gastroenteritis and exhibit considerable genetic diversity. Next generation sequencing (NGS) analysis based on environmental surveillance has been proved to be an effective method in norovirus surveillance.
Methods: Between January 2019 and December 2021, 36 sewage samples were collected and analyzed using real-time quantitative PCR to detect noroviruses. Partial VP1 region was amplified and subjected to NGS analysis to assess the abundance and genetic characterization of various norovirus genotypes across different samples.
Results: A total of 23 norovirus genotypes were identified, including 9 genotypes of GI, 13 genotypes of GII and 1 genotype of GIX. The most frequently detected genotypes were GI.5 (86.11%), GII.2 (86.11%), GII.4 (63.89%), GII.17 (58.33%), and GII.13 (55.56%). Additionally, some rare genotypes, such as GI.7, GII.5, GII.9, and GII.16, which had not been previously reported in Shandong, were identified. No significant differences were observed in genotypic diversity or viral copy numbers in sewage samples when comparing pre- and post-COVID-19 periods. A total of 379 partial VP1 sequences were obtained, with the means sequence identity within a genotype of Shandong sequences ranging from 92.69 to 98.37% and a coefficient of variation ranging from 1.46 to 6.73%. Phylogenetic analysis indicated that local noroviruses within each genotype comprised multiple co-circulating lineages.
Conclusions: Our data demonstrate that sewage contains noroviruses with considerable high diversities. NGS based environmental surveillance greatly improves the understanding of norovirus circulation and should be encouraged.
(© 2025. The Author(s).)

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202012051301 Medical and Health Science and Technology Development Plan Program of Shandong; 202412051234 Medical and Health Science and Technology Development Plan Program of Shandong; tsqn.202103187 Taishan Scholar Program of Young Experts

Keywords: Diversity; Next generation sequencing (NGS); Noroviruses; Sewage

GENBANK OR994323-OR994497; OR994513-OR994520; OR999378-OR999385; PP000305-PP000492

0 (Sewage)
0 (RNA, Viral)

Date Created: 20250128 Date Completed: 20250128 Latest Revision: 20250424

20250425

PMC11773704

10.1186/s12985-025-02638-5

39871378