Computational model for analyzing the evolutionary patterns of the neuraminidase gene of influenza A/H1N1.

Abstract

In this study, we performed computer simulations to evaluate the changes of selection potentials of codons in influenza A/H1N1 from 1999 to 2009. We artificially generated the sequences by using the transition matrices of positively selected codons over time, and their similarities against the database of influenzavirus A genus were determined by BLAST search. This is the first approach to predict the evolutionary direction of influenza A virus (H1N1) by simulating the codon substitutions over time. We observed that the BLAST results showed the high similarities with pandemic influenza A/H1N1 in 2009, suggesting that the classical human-origin influenza A/H1N1 isolated before 2009 might contain some selection potentials of swine-origin viruses. Computer simulations using the time series codon substitution patterns resulted dramatic changes of BLAST results in influenza A/H1N1, providing a possibility of developing a method for predicting the viral evolution in silico.

• Authors: Insung Ahn, Hyeon Seok Son
• Journal: Computational biology and chemistry (Comput Biol Chem) Vol. 36 Pg. 23-30 (Feb 2012) ISSN: 1476-928X [Electronic] England
• PMID: 22261151 (Publication Type: Journal Article)
• Copyright: Copyright © 2011 Elsevier Ltd. All rights reserved.

Chemical References

• Codon
• Viral Proteins
• Neuraminidase

Topics

• Animals
• Base Sequence
• Birds
• Codon
• Computer Simulation
• Databases, Genetic
• Evolution, Molecular
• Humans
• Influenza A Virus, H1N1 Subtype (genetics)
• Models, Genetic
• Neuraminidase (genetics)
• Orthomyxoviridae Infections (genetics)
• Swine
• Viral Proteins (genetics)