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Identifying SNP threshold from P2 sequences for investigating norovirus transmission
Luqiu Tao1, Xuan Wang2, Yan Yu2
1Nanjing Municipal Center for Disease Control and Prevention affiliated to Nanjing Medical University, Zizhulin 2, 210003 Nanjing, Jiangsu, China; School of Public Health, Nanjing Medical University, 101 Longmian Avenue, 211166 Nanjing, Jiangsu, China.
Virus Research
|May 26, 2024
Summary
Norovirus outbreaks are hard to track. This study created a simple genetic method using the P2 capsid protein region to identify norovirus transmission clusters, improving outbreak detection and control.
Area of Science:
- Virology
- Molecular Epidemiology
- Public Health
Background:
- Noroviruses, Caliciviridae family viruses, cause acute gastroenteritis via fecal-oral transmission from contaminated sources.
- Detecting and investigating norovirus outbreaks presents significant challenges.
- Effective molecular tools are needed for rapid norovirus outbreak identification and control.
Purpose of the Study:
- To develop a simple, accurate threshold detection approach for identifying norovirus transmission clusters.
- To utilize variations in the norovirus capsid protein P2 domain for molecular investigation.
Main Methods:
- Sanger sequencing of the norovirus hypervariable P2 region from epidemiologically-related and unrelated strains.
- Calculation of genetic distances between viral strains.
- Application of a Receiver Operating Characteristic (ROC) curve to establish a detection threshold with 80% sensitivity.
Main Results:
- A simple threshold detection method successfully identified transmission clusters in all tested norovirus outbreaks.
- Nucleotide diversity within outbreaks was significantly lower (67.5 times) than diversity between outbreaks.
- Accurate thresholds were established for three distinct norovirus genotypes.
Conclusions:
- The developed P2 domain variation threshold provides a streamlined approach for molecular investigation of norovirus outbreaks.
- This method enables rapid and efficient responses for controlling norovirus spread.
- The findings contribute to improved public health strategies for managing viral gastroenteritis outbreaks.
