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Typing

Typing. Sequencing and Phylogeny. May 2007. Learning objectives. At the end of the presentation, participants should: Understand sequencing Interpret phylogenetic trees. Sequencing. Process to determine the exact order of nucleotides in DNA

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Typing

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  1. Typing Sequencing and Phylogeny May 2007

  2. Learning objectives At the end of the presentation, participants should: • Understand sequencing • Interpret phylogenetic trees

  3. Sequencing Process to determine the exact order of nucleotides in DNA Parts of the genome are compared with other sequenced samples • From a databank • By direct comparison

  4. Review of molecular biology Genes – DNA and RNA are made of nucleotides …AGCUAAAGCUA… Nucleotides code for amino acids (codons) …ala-lys-ala… Amino acids make proteins Proteins 'R' us; enzymes, cell membranes, etc. Genetic variation (mutation) breeds trial and error – evolution RNA based organisms mutate (evolve) much faster than DNA based ones e.g. influenza, HIV

  5. Evaluating organism similarity …AGCUAAAGCUA… Gene sequence #1 …AACUAAACCUG… Gene sequence #2 …AACUCCACCUA… Gene sequence #3 …GGUUGCACCGG… Gene sequence #4

  6. Algorithms & programs to compare genes Several available: http://research.amnh.org/~siddall/methods/ Different approaches and assumptions but all startcwith computer alignment e.g. Phylip, PAUP Parsimony is "a principle that states that the simplest explanation that explains the greatest number of observations is preferred to more complex explanations". #1…AGCUAAAGCUA… #1…AGCUAAAGCUA… #1…AGCUAAAGCUA… #1…AGCUAAAGCUA… #1…AGCUAAAGCUA… #2…AACUAAACCUG… #2…AACUAAACCUG… #2…AACUAAACCUG… #2…AACUAAACCUG… #2…AACUAAACCUG… 73% identity

  7. Comparing genes to evaluate similarity among organisms …AGCUAAAGCUA… Gene sequence #1 …AACUAAACCUG… Gene sequence #2 …AACUCCACCUA… Gene sequence #3 …GGUUGCACCGG… Gene sequence #4 Trees can be built with nucleic acid or protein sequences

  8. Sequence #1 Sequence #2 Sequence #3 Sequence #4 Sequence #1 Sequence #2 Sequence #3 Sequence #4 Unrooted phylogenetic tree by unweighted pair group method Distance in characters (nt/aa)

  9. Comparing genes to evaluate similarity among organisms …AGCUAAAGCUA… Gene sequence #1 Glutamate Lysine …AACUAAACCUG… Gene sequence #2 G G …AACUCCACCUA… Gene sequence #3 …GGUUGCACCGG… Gene sequence #4

  10. Molecular Phylogeny of H5 Avian Influenza viruses (HA and M genes) Source: Suarez et. al. 2000: J. Virology 74: 6592-6599

  11. Evolution of the 'Z genotype' Letters to Nature Nature430, 209-213 (8 July 2004) Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia K. S. Li1, Y. Guan1,2, J. Wang1,2, G. J. D. Smith1,2, K. M. Xu1,2, L. Duan1,2, A. P. Rahardjo3, P. Puthavathana4, C. Buranathai5, T. D. Nguyen6, A. T. S. Estoepangestie3, A. Chaisingh5, P. Auewarakul4, H. T. Long7, N. T. H. Hanh7, R. J. Webby8, L. L. M. Poon2, H. Chen1,2, K. F. Shortridge1,2, K. Y. Yuen2, R. G. Webster2,8 and J. S. M. Peiris1,2

  12. Conclusions A phylogenetic tree is a tool to be used under defined circumstances – it is not absolute Phylogenetic relationships offer useful information Phylogenetic relationships often match antigenic relationships, particularly with influenza viruses Phylogenetic relationships can not predict evolutionary pathways , specific mutations or likelihood of animal viruses becoming human viruses

  13. Typing Developed by the Department of Epidemic and Pandemic Alert and Response of the World Health Organization with assistance from: European Program for Intervention Epidemiology Training Canadian Field Epidemiology Program Thailand Ministry of Health Institut Pasteur

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