Triplet Entropy in H1N1 Virus

Laurita dos Santos, J.L. Rybarczyk, G.J.L. Gerhardt

Abstract


In this work we analyze triplet entropy in a set of H1N1 virus sequences.
We correlated measures of entropy and guanine and cytosine concentration with chronology sample for a set of more than 30,000 sequences. This description allowed us to draw a map of the virus organizational changes throughout the 20th century. The main conclusion of our analysis was to show that some virus segments are mutating with a higher rate than others over the years and, in some cases, they are clustering sequences into new subgroups. A higher changing rate was found precisely in PA and PB1 segments, which are parts of H1N1 replication machinery. This highlights that organizational measures, as presented here, partially reflect segment dynamics and corroborates some recent experimental findings, which showed that during the last virus outbreak there has been a major change in polymerase activity. This type of approach may help to optimize treatment targets for this disease.

References


D.A. Benson, I. Karsch-Mizrachi, D.J. Lipman, J. Ostell, D.L. Wheeler, GenBank Nucleic Acids Research, Jan 2008, 36 (Database issue): D25-30 (http://www.ncbi.nlm.nih.gov/genbank/).

G.J.L. Gerhardt, N. Lemke, G. Corso; Network Clustering Coefficient approach to DNA Sequence Analysis, Chaos, Solitons and Fractals, (2006), 1037–1045.

D. Jackson, M.J. Hossain, D. Hickman, D.R. Perez, R.A. Lamb, A new influenza virus virulence determinant: the NS1 protein four C-terminal residues modulate pathogenicity, Proc. Natl. Acad. Sci., 105 (2008), 43816. PubMed DOI: 10.1073 pnas.0800482105

S. Jameel, The 2009 influenza pandemic, Current Science, 98, No. 3 (2010), 306–311.

B. Lewin, “Genes VII”, Oxford University Press, Oxford, 2000.

J.A.T. Machado, A.C. Costa, M.D. Quelhas, Shannon, Rényie and Tsallis entropy analysis of DNA using phase plane, Nonlinear Analysis: Real World Applications, 12 (2011), 3135–3144.

M.I. Nelson, E.C. Holmes, The evolution of epidemic influenza, Nature Reviews Genetics, 8 (2007), 196–210.

C.P. Octaviani, H. Goto, Y. Kawaoka, Reassortment between Seasonal H1N1 and Pandemic (H1N1) 2009, Influenza viruses is restricted by limited compatibility among polymerase subunits, The Journal of Virology, 85, No. 16 (2011), 8449–8452.

H.H. Otu, Khalid Sayood, A new sequence distance measure for phylogenetic tree construction, Bioinformatics, 19, No. 16 (2003), 2122–2130.

A. Rambaut, O.G. Pybus, M.I. Nelson, C. Viboud, J.K. Taubenberger E.C. Holmes, The genomic and epidemiological dynamics of human influenza A virus, Nature, 453. No. 29 (2008), 615–620.

J.J. Sanz-Ezquerro, J. Fernandez-Santaren, T. Sierra, T. Aragon, J. Ortega, J. Ortin, G. L. Smith, A. Nieto, The PA influenza virus polymerase subunit is a phosphorylated protein, J. Gen. Virol., 79 (1998), 471–478.

Y. Shi, I. Kanter, D. Kessler, Distributions of triplets in genetic sequences, Physica A 252 (1998), 48–60.

M.P. Simmons, Potential use of host-derived genome signatures to root virus phylogenies, Molecular Phylogenetics and Evolution, 49 (2008), 969–978.

E.N. Trifonov, Elucidating sequence codes: three codes for evolution, Ann. NY Acad. Sci., 870 (1999), 330–338.

D. Zamarin, M.B. Ortigoza, P. Palese, Influenza A virus PB1-F2 protein contributes to viral pathogenesis in mice, J. Virol., 80 (2006), 7976 83. PubMed DOI: 10.1128/JVI.00415-06.




DOI: https://doi.org/10.5540/tema.2011.012.03.0253

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Trends in Computational and Applied Mathematics

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