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. 2025 Apr 30:16:1570161.
doi: 10.3389/fmicb.2025.1570161. eCollection 2025.

Genomic characterization of norovirus and Sapovirus from a diarrhea outbreak in a school linked to heavy rainfall

Zhongyan Fu #  1   2 , Changjing Wu #  3   4 , Yinghui Yu  5 , Jian Zhao  3   4 , Yan Dong  6 , Wei Liu  2   3 , Huixin Dou  2   3 , Xuezhen Shi  7 , Chengzhi Cai  8 , Baihai Jiao  9 , Tiantian Liu  10 , Boyan Jiao  3   4
Affiliations

Genomic characterization of norovirus and Sapovirus from a diarrhea outbreak in a school linked to heavy rainfall

Zhongyan Fu et al. Front Microbiol. .

Abstract

Background: Diarrhea poses a serious threat to human health, and rainfall is known to increase the incidence of diarrheal diseases. On July 7, 2024, a diarrhea outbreak occurred in a school in Sishui County, Jining City, Shandong Province, China, following heavy rainfall. This study aimed to identify the pathogens responsible for the outbreak and characterize their whole genomes.

Methods: On July 8, 2024, a total of 21 stool samples from diarrhea cases, 2 water samples from private wells, and 1 drinking water sample from the school cafeteria were collected. Real-time quantitative PCR was used to detect Rotavirus A (RV-A), Norovirus genogroup I (NV GI), Norovirus genogroup II (NV GII), Sapovirus (SaV), Human Astrovirus (HAstV), and Human Adenovirus (HAdV). Whole-genome sequencing was performed for NV GI and SaV-positive samples to determine their genotypes, construct phylogenetic trees, and analyze amino acid variation sites in encoded proteins.

Results: Among the 21 case stool samples, 7 tested positive for both NV GI and SaV, 10 were positive for NV GI only, and 1 was positive for SaV only. Of the 2 private well water samples, one was positive for NV GI and the other for SaV. Whole-genome sequences were obtained for 11 NV GI strains and 2 SaV strains. The 11 NV GI sequences from the outbreak exhibited high homology, with whole-genome similarity ranging from 99.96% to 100%, and were all identified as the NV GI.6 [P11] genotype. Phylogenetic analysis showed that these 11 sequences clustered within the same evolutionary branch. Similarly, the 2 SaV sequences were highly homologous, with 99.97% similarity, and were identified as the SaV GI.6 genotype, clustering within the same phylogenetic branch.

Conclusions: This diarrhea outbreak was caused by the combined presence of NV GI and SaV following heavy rainfall. These findings provide valuable reference data for the prevention and control of diarrhea outbreaks caused by heavy rainfall or multiple pathogens.

Keywords: Norovirus; Sapovirus; diarrhea outbreak; heavy rainfall; whole genome.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Epidemiological characteristics of the diarrheal outbreak. (A) Distribution of onset times; a total of 12 cases were reported on July 7, 2024, 9 cases on July 8, 2024, and 5 cases on July 9, 2024. (B) Distribution of affected populations; there were 24 students and 2 restaurant staff members. (C) Gender distribution; there were 16 male cases and 10 female cases. (D) Pathogen detection results indicated that among 19 student cases, the positivity rate for both NVGI and SaV viruses was 36.84% (7/19), the positivity rate for NVGI only was 52.63% (10/19), and the positivity rate for SaV only was 5.26% (1/19). Both samples from restaurant staff and the cafeteria's drinking water tested negative. However, self-supplied well A tested positive for SaV, and self-supplied well B tested positive for NVGI.
Figure 2
Figure 2
Phylogenetic tree of NV GI full genes. The phylogenetic tree was constructed using the maximum likelihood method with 1,000 bootstrap replicates, employing MEGA version 7.0.14 software. The yellow lines represent the NV GI sequences associated with this diarrheal outbreak.
Figure 3
Figure 3
Phylogenetic tree of the ORF1 region of NV GI. The tree was constructed using the maximum likelihood method with 1,000 bootstrap replicates in MEGA 7.0.14 software. The yellow branches represent the NV GI sequences associated with the current diarrheal outbreak.
Figure 4
Figure 4
Phylogenetic tree of the ORF2 region of NV GI. The tree was constructed using the maximum likelihood method with 1,000 bootstrap replicates in MEGA 7.0.14 software. The yellow branches represent the NV GI sequences associated with the current diarrheal outbreak.
Figure 5
Figure 5
Phylogenetic tree of the ORF3 region of NV GI. The tree was constructed using the maximum likelihood method with 1,000 bootstrap replicates in MEGA 7.0.14 software. The yellow branches represent the NV GI sequences associated with the current diarrheal outbreak.
Figure 6
Figure 6
Phylogenetic tree of the complete genome of SaV GI. The tree was constructed using the maximum likelihood method with 1,000 bootstrap replicates in MEGA 7.0.14 software. The green branches represent the SaV sequences associated with the current diarrheal outbreak.
Figure 7
Figure 7
Phylogenetic tree of ORF1 for SaV GI. The tree was constructed using the maximum likelihood method with 1,000 bootstrap replicates in MEGA 7.0.14 software. The green branches indicate the SaV sequences associated with the current diarrheal outbreak.
Figure 8
Figure 8
Phylogenetic tree of ORF2 for SaV GI. The tree was constructed using the maximum likelihood method with 1,000 bootstrap replicates in MEGA 7.0.14 software. The green branches represent the SaV sequences associated with the current diarrheal outbreak.
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References

    1. Azage M., Kumie A., Worku A., C Bagtzoglou A., Anagnostou E. (2017). Effect of climatic variability on childhood diarrhea and its high risk periods in northwestern parts of Ethiopia. PLoS ONE 12:e0186933. 10.1371/journal.pone.0186933 - DOI - PMC - PubMed
    1. Cheng C. C., Ke G. M., Chu P. Y., Ke L. Y. (2023). Elucidating the implications of norovirus N- and O-Glycosylation, O-GlcNAcylation, and phosphorylation. Viruses 15:798. 10.3390/v15030798 - DOI - PMC - PubMed
    1. Chhabra P., de Graaf M., Parra G. I., Chan M. C., Green K., Martella V., et al. . (2019). Updated classification of norovirus genogroups and genotypes. Journal of general virology 100, 1393–1406. 10.1099/jgv.0.001318 - DOI - PMC - PubMed
    1. Chigor V. N., Digwo D. C., Adediji A., Chidebelu P. E., Chigor C. B., Ugwu K. O., et al. . (2024). Epidemiology of norovirus infection in Nigeria: a systematic review and meta-analysis. Arch. Virol. 169:138. 10.1007/s00705-024-06056-w - DOI - PubMed
    1. Cohen A. L., Platts-Mills J. A., Nakamura T., Operario D. J., Antoni S., Mwenda J. M., et al. . (2022). Aetiology and incidence of diarrhoea requiring hospitalisation in children under 5 years of age in 28 low-income and middle-income countries: findings from the Global Pediatric Diarrhea Surveillance network. BMJ Global Health 7:e009548. 10.1136/bmjgh-2022-009548 - DOI - PMC - PubMed

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