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An Italian Single-Center Genomic Surveillance Study: Two-Year Analysis of SARS-CoV-2 Spike Protein Mutations
Riccardo Cecchetto1,2, Emil Tonon1,2, Asia Palmisano1
1Department of Diagnostic and Public Health, Division of Microbiology, University of Verona, 37134 Verona, Italy.
International Journal of Molecular Sciences
|August 14, 2025
Summary
Genomic surveillance tracked SARS-CoV-2 spike protein mutations over two years. Some mutations reappeared, highlighting the need for ongoing monitoring to guide public health strategies and vaccine development.
Area of Science:
- Virology
- Genomics
- Epidemiology
Background:
- The emergence of SARS-CoV-2 variants poses an ongoing public health threat.
- Spike protein mutations are key drivers of viral infectivity, transmissibility, and immune evasion.
Purpose of the Study:
- To analyze the evolution of SARS-CoV-2 spike protein mutations over a two-year period.
- To classify mutation dynamics and identify patterns of emergence and disappearance.
Main Methods:
- Conducted a local genomic surveillance program in Verona, Italy, from February 2022 to April 2024.
- Performed next-generation full-length genome sequencing on 1333 SARS-CoV-2 positive nasopharyngeal swabs.
- Classified spike protein mutations based on prevalence over time into fixed, emerging, fading, transient, and divergent categories.
Main Results:
- Identified dynamic patterns in spike protein mutations, including a
- Lazarus effect
- where some divergent mutations reappeared after initially disappearing.
- Observed potential adaptive advantages of certain mutations in specific genomic contexts.
- Highlighted the continuous evolution of SARS-CoV-2 through spike protein alterations.
Conclusions:
- Ongoing, mutation-focused genomic surveillance is crucial for early detection of new SARS-CoV-2 variants.
- Understanding mutation dynamics, including seemingly disadvantageous ones, is vital for public health responses.
- Findings inform future vaccine and therapeutic strategies by tracking viral evolution.
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