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Genomic Epidemiology and Evolution of Rhinovirus in Western Washington State, 2021-2022
Stephanie Goya1, Seffir T Wendm1, Hong Xie1
1Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington.
The Journal of Infectious Diseases
|July 4, 2024
Summary
Human rhinoviruses (RVs) show dynamic genomic diversity, with many genotypes co-circulating. Understanding these RV genetic patterns is key for future immunity and cross-protection strategies.
Area of Science:
- Virology
- Genomics
- Epidemiology
Background:
- Human rhinoviruses (RVs) cause the common cold, with varied outcomes from mild to severe, impacting immunocompromised individuals.
- High serotype diversity hinders therapeutic development.
- Traditional sequencing methods leave gaps in understanding RV genomic diversity.
Purpose of the Study:
- To explore human rhinovirus (RV) genomic evolution and diversity.
- To analyze RV epidemiology during distinct COVID-19 pandemic and post-pandemic periods.
- To characterize intragenotypic evolution and viral dynamics.
Main Methods:
- Sequenced 1078 RV genomes from symptomatic and asymptomatic individuals in Washington State (2021-2022).
- Constructed maximum likelihood and BEAST phylodynamic trees.
- Analyzed viral load, RV species, genotype, polyprotein selection pressure, and Shannon entropy.
Main Results:
- Detected 99 of 168 known RV genotypes, observing intergenotypic recombination and cluster swapping.
- Found a significant association between symptoms and viral load, but not RV species or genotype.
- Revealed co-circulation of divergent clades within genotypes with high amino acid constraints.
Conclusions:
- Human rhinovirus (RV) genomic epidemiology is dynamic, with over 20% of genotypes co-circulating monthly in a region.
- Findings highlight the need to investigate RV genotype-serotype correlations for immunity and cross-protection.
- Emphasizes the importance of comprehensive genomic surveillance for understanding RV evolution.
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