Parallel evolution of influenza across multiple spatiotemporal scales

Area of Science:

• Virology
• Evolutionary Biology
• Genetics

Background:

• Understanding how influenza virus variants emerge from within-host mutations to global diversity is crucial.
• The evolutionary dynamics transforming within-host variation to global genetic diversity remain poorly understood.

Purpose of the Study:

• To investigate whether influenza evolution within infected humans recapitulates global evolutionary dynamics.
• To analyze the origins and spread of viral mutations across different scales.

Main Methods:

• Deep sequencing of longitudinal samples from four immunocompromised patients with long-term H3N2 influenza infections.
• Analysis of parallel evolution within individual patients, across patients, and in the global influenza population.

Main Results:

• Identified parallel evolution across within-host, inter-patient, and global scales.
• Observed a small set of hemagglutinin mutations arising independently in multiple patients and repeatedly within single patients.
• Demonstrated clonal interference within hosts and found that recurrent within-host mutations frequently reach high global frequencies.

Conclusions:

• Influenza virus evolution within hosts surprisingly mirrors global evolutionary dynamics.
• Findings highlight the concordance of evolutionary processes across multiple spatiotemporal scales, from within a single host to the global population.