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High-throughput Detection Method for Influenza Virus
Published on: February 4, 2012
A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza
Sergei L Kosakovsky Pond1, Art F Y Poon, Andrew J Leigh Brown
1Department of Pathology, University of California, San Diego, CA, USA. spond@ucsd.edu
Molecular Biology and Evolution
|May 31, 2008
Summary
We developed a new method, directional evolution of protein sequences (DEPS), to detect directional selection in proteins. This approach accurately identifies sites and target residues under selection, revealing insights into viral evolution.
Area of Science:
- Evolutionary biology
- Molecular evolution
- Bioinformatics
Background:
- Detecting directional selection in protein evolution is challenging.
- Existing methods struggle with scenarios like selective sweeps and frequency-dependent selection.
- Understanding directional evolution is crucial for fields like virology and drug development.
Purpose of the Study:
- To develop a novel phylogenetic test for directional selection in protein sequences.
- To identify specific residues and sites evolving under directional selection.
- To apply this test to influenza A virus (IAV) evolution.
Main Methods:
- Developed a model-based phylogenetic maximum likelihood test: directional evolution of protein sequences (DEPS).
- DEPS identifies target residues and sites under directional evolution.
- Applied DEPS to avian (H5N1) and human (H3N2) influenza A virus genomic alignments.
Main Results:
- DEPS demonstrated good power and accuracy on simulated data.
- Identified multiple directionally evolving sites in 5/8 genomic segments of both H5N1 and H3N2 IAV.
- Proposed a 5-group classification for directionally evolving sites based on residue frequency dynamics.
Conclusions:
- DEPS is an effective tool for detecting directional selection in protein evolution.
- Directional evolution is evident in multiple genomic segments of IAV.
- Identified sites correlate with functional adaptations like immune escape and host adaptation.
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