Commenced in January 2007
Paper Count: 30855
Sequence Relationships Similarity of Swine Influenza a (H1N1) Virus
Abstract:In April 2009, a new variant of Influenza A virus subtype H1N1 emerged in Mexico and spread all over the world. The influenza has three subtypes in human (H1N1, H1N2 and H3N2) Types B and C influenza tend to be associated with local or regional epidemics. Preliminary genetic characterization of the influenza viruses has identified them as swine influenza A (H1N1) viruses. Nucleotide sequence analysis of the Haemagglutinin (HA) and Neuraminidase (NA) are similar to each other and the majority of their genes of swine influenza viruses, two genes coding for the neuraminidase (NA) and matrix (M) proteins are similar to corresponding genes of swine influenza. Sequence similarity between the 2009 A (H1N1) virus and its nearest relatives indicates that its gene segments have been circulating undetected for an extended period. Nucleic acid sequence Maximum Likelihood (MCL) and DNA Empirical base frequencies, Phylogenetic relationship amongst the HA genes of H1N1 virus isolated in Genbank having high nucleotide sequence homology. In this paper we used 16 HA nucleotide sequences from NCBI for computing sequence relationships similarity of swine influenza A virus using the following method MCL the result is 28%, 36.64% for Optimal tree with the sum of branch length, 35.62% for Interior branch phylogeny Neighber – Join Tree, 1.85% for the overall transition/transversion, and 8.28% for Overall mean distance.
Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1056454Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1781
 Saul B. Needleman, Christlan D. Wunsch, "A General Applicable to the Search for Similarities in the Amino Acid Sequence of two Proteins", J Mol. Biol, Vol. 48, 1970, pp. 443-453.
 David Sankoff, "Simultaneous solution of the RNA folding alignment and protosequence problems", Siam J. Appl Math, Vol. 45, 1985, pp. 810-825.
 McClure MA, Vasi TK, Fitch WM, "Comparative analysis of multiple protein sequence alignment methods", Mol Biol Evol, Vol. 4, 1994, pp. 571-592.
 Makoto Hirosawa, Yasushi Totoki, Masaki Hoshida, Masaro Ishikawa, "Comprehensive study on iterative algorithms of multiple sequence alignment", Comput. Appl. Biosci, Vol. 11, 1995, pp. 13-18.
 Ramana M. Idury, Michael S. Waterman, "A New Algorithm for DNA Sequence Assembly", Computer Biology, Vol. 2, 1995, pp. 291-306.
 Dan Gusfield, Jens Stoye, "Linear time algorithms for finding and representing all the tandem repeats in a string", Computer and Stem Sciences, Vol. 69, 2004, pp. 525-546.
 Thompson JD, Higgins DG, Gibson TJ, "CLUSTALW improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice", NucleicAcids Res, Vol. 22, 1994, pp. 4673-80.
 Edgar, Batzoglou, "Multiple sequence alignment", Curr Opin Struct Biol, Vol. 3, 2006, pp. 368-373.
 Saiki, Gelfand, Stoffel, Scharf, Higuchi, Horn, Hullis, Erlich, "Primer directed enzymatic amplification of DNA with a thermostable DNA polymerase", Science, Vol. 239, 1988, pp. 487-491.
 Kocher T., Thomas K., Meyer, Edwards V., P├ä├äbo, Villablanca X., Wilson, "Dynamics of mitochondrial DNA evolution in animals Amplification and sequencing with conserved primers", Proc. Natl. Acad. Sci. USA, Vol. 86, 1989, pp. 6196-6200.
 Pietro L├¼├▓, Nick Goldman, "Models of Molecular Evolution and Phylogeny", Genome Res, Vol. 8, 1998, pp. 1233-1244.
 Erpenbeck, Breeuwer, Soest, "Implications from a 28S rRNA gene fragment for the phylogenetic relationships of halichondrid sponges", Zoological Systematics and Evolutionary Research, Vol. 43, 2005, pp. 93-99.
 Sudhir Kumar, Masatoshi Nei, Joel Dudley, Koichiro Tamura, "MEGA A biologist-centric software for evolutionary analysis of DNA and protein sequences", Bioinformatics, Vol. 9, 2008, pp. 299-306.
 Robert G. Webster, "Influenza AN Emerging Disease", Emerging infectious diseases, Vol. 4, 1998, pp. 436-441.
 Hidenori Meguro, David Bryant, Anne E. Torrence, Peter F. Wright, "Canine Kidney Cell Line for Isolation of Respiratory Viruses", Clinical Microbiology, Vol. 9, 1997, pp. 175-179.
 Y.K.Choi, Goyal, Kang, Farnham, Joo, "Detection and subtyping of swine influenza H1N1 H1N2 and H3N2 viruses in clinical samples using two multiplex RT-PCR assays", Virological Methods, Vol. 102, 2002, pp. 53-59.
 Eric C.J. Claas, "Pandemic influenza is a zoonosis as it requires introduction of avian-like gene segments in the human population", Veterinary microbiology, Vol. 74, 2000, pp. 133-139.
 Brockwell Stats C, Webster RG, Webby RJ, "Diversity of InfluenzaViruses in Swine and the Emergence of a Novel Human Pandemic InfluenzaA (H1N1)", Influenza Other Respi Viruses, Vol. 3, 2009, pp. 207-213.
 M Panning, M Eickmann, O Landt, M Monazahian, S ├ûlschl├ñger, S Baumgarte, U Reischl, J J Wenzel, H H Niller, S G├£nther, B Hollmann, D Huzly, J F Drexler, A Helmer, S Becker, B Matz, A M Eis-H├╝binger, C Drosten, "Detechtion of influenza A(H1N1) virus by real-time RTPCR", Eurosurveillance, Vol. 14, 2009, pp. 1-6.
 Tamura K, Dudley J, Nei M, Kumar S, "MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0", Molecular Biology and Evolution, Vol. 24, 2007, pp. 1596-1599.