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Updated: Jun 14, 2026
09:40
Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
Published on: June 11, 2015
High-resolution mapping of evolutionary trajectories in a phage
Benjamin Dickins1, Anton Nekrutenko
1Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, USA. ben@bx.psu.edu
Genome Biology and Evolution
|March 25, 2010
Summary
This study uses short-read sequencing to observe viral evolution in real-time. We detected early genetic changes in bacteriophage PhiX174 within hours, revealing rapid adaptation dynamics.
Area of Science:
- Virology
- Evolutionary Biology
- Genomics
Background:
- Experimental evolution studies viral adaptation.
- Conventional methods limit detection of early genetic changes.
- Low-frequency mutations are often missed.
Purpose of the Study:
- To develop a method for observing early viral evolution dynamics.
- To analyze polymorphism dynamics in bacteriophage PhiX174.
- To provide a framework for real-time viral resequencing studies.
Main Methods:
- Utilized short-read sequencing technology.
- Employed binomial filtering with quality scores for nucleotide difference detection.
- Analyzed polymorphism dynamics in PhiX174 over short incubation periods (2-hour cultures).
Main Results:
- Observed significant genetic variation even in brief cultures.
- Detected rapid increases in polymorphism frequency within hours.
- Identified statistically significant linkage among polymorphic sites and parallels between replicate lineages.
- Found missense mutations to be more common than silent mutations.
Conclusions:
- Short-read sequencing enables real-time observation of viral substitution trajectories.
- Early stages of viral adaptation can be captured within hours.
- This approach offers a robust framework for future viral evolution studies.
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