TY - GEN
T1 - A coding theoretical approach to predict sequence changes in H5N1 influenza a virus hemagglutinin
AU - Sato, Keiko
AU - Hara, Toshihide
AU - Ohya, Masanori
N1 - Publisher Copyright:
Copyright © 2016 by SCITEPRESS - Science and Technology Publications, Lda. All rights reserved.
PY - 2016
Y1 - 2016
N2 - The changes in the receptor binding domain of influenza A virus hemagglutinin lead to the appearance of new viral strains that evade the immune system. To prepare the future emergence of potentially dangerous outbreaks caused by divergent influenza strains including human-adapted H5N1 strains, it is imperative that we understand the rule stored in the sequence of the receptor binding domain. Information of life is stored as a sequence of nucleotides, and the sequence composed of four nucleotides seems to be a code. It is important to determine the code structure of the sequences. Once we know the code structure, we can make use of mathematical results concerning coding theory for research in life science. In this study, we applied various codes in coding theory to sequence analysis of the 220 loop in the receptor binding domain of H1, H3, H5 and H7 subtype viruses isolated from humans. Sequence diversity in the 220 loop has been observed even within the same hemagglutinin subtype. However, we found that the code structure of the 220 loop from the same subtype remains unchanged. Our results indicate that the sequences at the 220 loop have the structure of subtype-specific codes. In addition, in view of these finding, we predicted possible amino acid changes in the 220 loop of H5N1 strains that will emerge in the future. Our method will facilitate understanding of the evolutionary patterns of influenza A viruses, and further help the development of new antiviral drugs and vaccines.
AB - The changes in the receptor binding domain of influenza A virus hemagglutinin lead to the appearance of new viral strains that evade the immune system. To prepare the future emergence of potentially dangerous outbreaks caused by divergent influenza strains including human-adapted H5N1 strains, it is imperative that we understand the rule stored in the sequence of the receptor binding domain. Information of life is stored as a sequence of nucleotides, and the sequence composed of four nucleotides seems to be a code. It is important to determine the code structure of the sequences. Once we know the code structure, we can make use of mathematical results concerning coding theory for research in life science. In this study, we applied various codes in coding theory to sequence analysis of the 220 loop in the receptor binding domain of H1, H3, H5 and H7 subtype viruses isolated from humans. Sequence diversity in the 220 loop has been observed even within the same hemagglutinin subtype. However, we found that the code structure of the 220 loop from the same subtype remains unchanged. Our results indicate that the sequences at the 220 loop have the structure of subtype-specific codes. In addition, in view of these finding, we predicted possible amino acid changes in the 220 loop of H5N1 strains that will emerge in the future. Our method will facilitate understanding of the evolutionary patterns of influenza A viruses, and further help the development of new antiviral drugs and vaccines.
KW - Code structure
KW - H5N1
KW - Receptor binding domain
KW - Sequence prediction
UR - https://www.scopus.com/pages/publications/84969220198
U2 - 10.5220/0005659701590167
DO - 10.5220/0005659701590167
M3 - Conference contribution
AN - SCOPUS:84969220198
T3 - BIOINFORMATICS 2016 - 7th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 9th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2016
SP - 159
EP - 167
BT - BIOINFORMATICS 2016 - 7th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 9th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2016
A2 - Gilbert, James
A2 - Azhari, Haim
A2 - Ali, Hesham
A2 - Quintao, Carla
A2 - Sliwa, Jan
A2 - Ruiz, Carolina
A2 - Fred, Ana
A2 - Gamboa, Hugo
PB - SciTePress
T2 - 7th International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2016 - Part of 9th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2016
Y2 - 21 February 2016 through 23 February 2016
ER -