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.
 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.
 McClure MA, Vasi TK, Fitch WM, "Comparative analysis of multiple
protein sequence alignment methods", Mol Biol Evol, Vol. 4, 1994, pp.
 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.
 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.