publication . Other literature type . Preprint . 2018

Mutational dynamics of influenza A viruses: a principal component analysis of hemagglutinin sequences of subtype H1

Sanejouand, Yves-Henri;
Open Access English
  • Published: 09 Jan 2018
  • Publisher: Zenodo
Abstract
A principal component analysis of a multiple sequence alignement of hemagglutinin sequences of subtype H1 has been performed, the sequences being encoded using the amino-acid property that maximizes the weight of the major component. In the case of this alignment, it happens to be a well-known hydrophobicity scale. Interestingly, sequences coming from human have large positive amplitudes along the major component before 2009, and large negative ones afterwards. This means that the 2009 pandemic was associated to a major change in the hydrophobicity pattern of hemagglutinin. The present analysis also highlights the high variability of viral sequences coming from ...
Subjects
free text keywords: principal component analysis, multiple sequence aligment, hydrophobicity, hemagglutinin, influenza, pandemic, Quantitative Biology - Biomolecules, Quantitative Biology - Populations and Evolution
Download fromView all 4 versions
Zenodo
Other literature type . 2018
Provider: Datacite
Zenodo
Other literature type . 2018
Provider: Datacite
ZENODO
Preprint . 2018
Provider: ZENODO
34 references, page 1 of 3

[1] Ringne´r, M (2008) What is principal component analysis? Nature biotechnology 26:303.

[2] Van Heel, M (1991) A new family of powerful multivariate statistical sequence analysis techniques. Journal of molecular biology 220:877-887.

[3] Casari, G, Sander, C, Valencia, A (1995) A method to predict functional residues in proteins. Nature structural biology 2:171. [OpenAIRE]

[4] Vinga, S, Almeida, J (2003) Alignment-free sequence comparison: a review. Bioinformatics 19:513-523. [OpenAIRE]

[5] Clamp, M, Cu , J, Searle, SM, Barton, GJ (2004) The jalview java alignment editor. Bioinformatics 20:426-427.

[6] Cocco, S, Monasson, R, Weigt, M (2013) From principal component to direct coupling analysis of coevolution in proteins: Low-eigenvalue modes are needed for structure prediction. PLoS Comput Biol 9:e1003176. [OpenAIRE]

[7] Suhre, K, Claverie, JM (2003) Genomic correlates of hyperthermostability, an update. Journal of Biological Chemistry 278:17198-17202. [OpenAIRE]

[8] Kawashima, S, Kanehisa, M (2000) Aaindex: amino acid index database. Nucleic acids research 28:374-374.

[9] Kawashima, S et al. (2008) AAindex: amino acid index database, progress report 2008. Nucleic acids research 36:D202-D205.

[10] Reid, AH, Fanning, TG, Hultin, JV, Taubenberger, JK (1999) Origin and evolution of the 1918 ”spanish” influenza virus hemagglutinin gene. Proceedings of the National Academy of Sciences 96:1651-1656. [OpenAIRE]

[11] Johnson, NP, Mueller, J (2002) Updating the accounts: global mortality of the 1918-1920 ”spanish” influenza pandemic. Bulletin of the History of Medicine 76:105-115.

[12] Smith, GJ et al. (2009) Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459:1122-1125.

[13] Neumann, G, Noda, T, Kawaoka, Y (2009) Emergence and pandemic potential of swine-origin H1N1 influenza virus. Nature 459:931-939.

[14] Bao, Y et al. (2008) The influenza virus resource at the national center for biotechnology information. Journal of virology 82:596-601.

[15] Sanejouand, YH (2017) A singular mutation in the hemagglutinin of the 1918 pandemic virus. Archives of biochemistry and biophysics 625:13-16. [OpenAIRE]

34 references, page 1 of 3
Abstract
A principal component analysis of a multiple sequence alignement of hemagglutinin sequences of subtype H1 has been performed, the sequences being encoded using the amino-acid property that maximizes the weight of the major component. In the case of this alignment, it happens to be a well-known hydrophobicity scale. Interestingly, sequences coming from human have large positive amplitudes along the major component before 2009, and large negative ones afterwards. This means that the 2009 pandemic was associated to a major change in the hydrophobicity pattern of hemagglutinin. The present analysis also highlights the high variability of viral sequences coming from ...
Subjects
free text keywords: principal component analysis, multiple sequence aligment, hydrophobicity, hemagglutinin, influenza, pandemic, Quantitative Biology - Biomolecules, Quantitative Biology - Populations and Evolution
Download fromView all 4 versions
Zenodo
Other literature type . 2018
Provider: Datacite
Zenodo
Other literature type . 2018
Provider: Datacite
ZENODO
Preprint . 2018
Provider: ZENODO
34 references, page 1 of 3

[1] Ringne´r, M (2008) What is principal component analysis? Nature biotechnology 26:303.

[2] Van Heel, M (1991) A new family of powerful multivariate statistical sequence analysis techniques. Journal of molecular biology 220:877-887.

[3] Casari, G, Sander, C, Valencia, A (1995) A method to predict functional residues in proteins. Nature structural biology 2:171. [OpenAIRE]

[4] Vinga, S, Almeida, J (2003) Alignment-free sequence comparison: a review. Bioinformatics 19:513-523. [OpenAIRE]

[5] Clamp, M, Cu , J, Searle, SM, Barton, GJ (2004) The jalview java alignment editor. Bioinformatics 20:426-427.

[6] Cocco, S, Monasson, R, Weigt, M (2013) From principal component to direct coupling analysis of coevolution in proteins: Low-eigenvalue modes are needed for structure prediction. PLoS Comput Biol 9:e1003176. [OpenAIRE]

[7] Suhre, K, Claverie, JM (2003) Genomic correlates of hyperthermostability, an update. Journal of Biological Chemistry 278:17198-17202. [OpenAIRE]

[8] Kawashima, S, Kanehisa, M (2000) Aaindex: amino acid index database. Nucleic acids research 28:374-374.

[9] Kawashima, S et al. (2008) AAindex: amino acid index database, progress report 2008. Nucleic acids research 36:D202-D205.

[10] Reid, AH, Fanning, TG, Hultin, JV, Taubenberger, JK (1999) Origin and evolution of the 1918 ”spanish” influenza virus hemagglutinin gene. Proceedings of the National Academy of Sciences 96:1651-1656. [OpenAIRE]

[11] Johnson, NP, Mueller, J (2002) Updating the accounts: global mortality of the 1918-1920 ”spanish” influenza pandemic. Bulletin of the History of Medicine 76:105-115.

[12] Smith, GJ et al. (2009) Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459:1122-1125.

[13] Neumann, G, Noda, T, Kawaoka, Y (2009) Emergence and pandemic potential of swine-origin H1N1 influenza virus. Nature 459:931-939.

[14] Bao, Y et al. (2008) The influenza virus resource at the national center for biotechnology information. Journal of virology 82:596-601.

[15] Sanejouand, YH (2017) A singular mutation in the hemagglutinin of the 1918 pandemic virus. Archives of biochemistry and biophysics 625:13-16. [OpenAIRE]

34 references, page 1 of 3
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