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Detection and Genogrouping of Noroviruses from Children's Stools By Taqman One-step RT-PCR
Published on: July 22, 2012
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Using molecular methods to delineate norovirus outbreaks: a systematic review.
Luqiu Tao1,2, Xinyang Zhang1,2, Xuan Wang1
1Nanjing Municipal Center for Disease Control and Prevention affiliated to Nanjing Medical University, Zizhulin 2, 210003, Nanjing, Jiangsu, China.
Archives of Virology
|January 3, 2024
Summary
This study suggests using single-nucleotide polymorphism (SNP) rates to define norovirus outbreaks. SNP rates below 0.20% indicate rigorous similarity, while rates under 0.50% suggest relaxed similarity for norovirus strains.
Area of Science:
- Epidemiology
- Virology
- Genomics
Background:
- Noroviruses are a leading cause of acute gastroenteritis globally.
- Assessing norovirus outbreak relationships relies on single-nucleotide polymorphism (SNP) analysis.
- A standardized threshold for clustering outbreak strains is currently lacking.
Approach:
- A systematic literature search was conducted in PubMed and Web of Science.
- SNP rates were calculated as (SNPs/sequence length) × 100%.
- Statistical analysis, including the Mann-Whitney U-test, compared SNP rates across various factors.
Key Points:
- 99.1% of analyzed norovirus outbreaks had SNP rates below 0.50%, with 89.8% below 0.20%.
- Higher SNP rates were observed when using the P2 domain or Next-Generation Sequencing (NGS) methods.
- No significant differences in SNP rates were found between different norovirus genotypes.
Conclusions:
- SNP rates under 0.20% and 0.50% can serve as rigorous and relaxed thresholds for norovirus strain similarity within outbreaks, respectively.
- Further research is needed to refine these thresholds and understand variations within and between outbreaks.
Keywords:
Genomic variationNorovirusOutbreak surveillanceOutbreak tracingSingle-nucleotide polymorphismsMore Related Videos
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