Genomic evolution in a virus under specific selection for host recognition.

Area of Science:

• Virology
• Evolutionary Biology
• Genomics

Background:

• Viral genetic variation in structural proteins drives adaptation through mechanisms like immune evasion and host switching.
• Understanding viral surface protein evolution is crucial for developing interventions against emerging diseases.

Purpose of the Study:

• To investigate the predictability of viral genomic evolution in response to specific differences in host receptor structure.
• To explore the role of mutations in viral structural proteins during adaptation to new hosts.

Main Methods:

• Evolved bacteriophage PhiX174 on three strains of E. coli with specific mutations in lipopolysaccharides (host receptors).
• Utilized large phage populations to maximize mutation exploration and potential for parallel evolution.
• Assessed repeatability through genome sequencing of multiple isolates and fitness measurements relative to the ancestor.

Main Results:

• Consistent fitness increases were observed across different evolutionary lines.
• A single, repeatable mutation in the internal DNA pilot protein H was identified as a key intermediate for adaptation.
• Mutations in the major capsid protein F primarily affected capsid stability rather than specific host receptor interactions.

Conclusions:

• Non-specific alterations in capsid structure may be significant for adaptation to novel hosts.
• Synonymous mutations indicated selection on codon usage, with 33% of all mutations being synonymous.
• Evolving populations of small single-stranded DNA (ssDNA) viruses can maintain substantial genetic variation.