EVOLUTIONARY TRAJECTORY ANALYSIS: RECENT ENHANCEMENTS. R. Burke Squires
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1 EVOLUTIONARY TRAJECTORY ANALYSIS: RECENT ENHANCEMENTS R. Burke Squires
2 Pandemic H1N Origin? April / May 2009 Cases of an Influenza-like Illness (ILI) occurred in California, Texas and Mexico New strain of influenza was found to be the cause. Pandemic H1N influenza virus - 1 st pandemic strain of the 21 st Century Like many, we also wondered what the origin of the virus and its segments were. Our analysis Different conclusions More accurate description of virus lineage
3 Original Analysis Reference strain A/California/04/2009 BLAST Each segment against all flu sequences in IRD Return top 1000 hits (June 2009) Graph Nucleotide differences vs. isolation year differences
4 Nucleotide Diff. vs Isolation Year Diff. Seg 5 (NP) 300 Nucleotide Difference (Normalized) C B A Isolation Year Difference (from 2009)
5 The Pattern Repeats Segment 4 (HA) Segment 8 (NS) Segment 7 (M) Segment 6 (NA)
6 Characterizing Groups: Seg 5 (NP) Group A Group B
7 Evolutionary Trajectory Similar, Distantly Related Evolutionary Trajectory (E.T.)
8 Evolutionary Trajectory Slopes vs. Mutation Rate Segment E. T. Slope S.U.R. Slope Mutation Rate PB PB PA HA NP NA M NS
9 Recent Enhancements Dynamic BLAST of reference sequence Alignment of BLAST hits Distance matrix scoring of aligned sequences Estimation of genetic distance Selection of ancestral sequences
10 Dynamic BLASTing 1000 BLAST Results overkill BLAST reference sequence with increasing 50 hit results Use default BLAST options BLAST against all influenza sequences isolated before 2009 Extract the oldest year of isolation from hits Stop when the oldest year of isolation does not change between iterations Using CDS sequences; not full length sequences
11 Alignment of BLAST Hits Align all of the BLAST hits using MAFFT Order alignment by year of isolation
12 Distance Matrix Calculate distance matrix aligned sequences Utilizing Criscuolo & Michel codon model DNAdistree X X X X X X X X Y 2 X X X X X X X X X 3 X X X X X X X X X 4 X X X X X X X X X 5 X X X X X X X X X 6 X X X X X X X X X 7 X X X X X X X X X 8 X X X X X X X X X 9 Y X X X X X X X X Criscuolo, A., & Michel, C. J. (2009). Phylogenetic Inference with Weighted Codon Evolutionary Distances. Journal of Molecular Evolution, 68(4), doi: /s y
13 Genetic Distance Estimation Find lowest slope of genetic distance / isolation year difference when compared to reference sequence (2009) Use that genetic distance as a cut off, eliminating all sequences with greater genetic distance Use remaining sequences to estimate slope with exponential curve fit
14 Estimation of Genetic Distance / Year Genetic Distance Isolation Year Differences
15 Estimation of Genetic Distance / Year Genetic Distance Isolation Year Differences
16 Estimation of Genetic Distance / Year Genetic Distance Isolation Year Differences
17 Estimation of Genetic Distance / Year Genetic Distance Isolation Year Differences
18 Estimation of Genetic Distance / Year Genetic Distance Isolation Year Differences
19 Genetic Distance Per Year - Actual Genetic Distance (Codon model) y = x R² = Isolation Year Differences
20 Eliminate Non-ancestral Sequences Use genetic distance per year curve fit to eliminate sequences in distance matrix X X X X X Y 2 X X X 3 X X X X X X X 4 X X X X X 5 X X 6 X X X 7 X X X X 8 9 Y X X X X
21 Determine Ancestral Sequences Sum number of sequences in a row of matrix Examine distribution of sums to determine ancestral sequences Fill-in gaps with hypothetical ancestor for each nucleotide change X X X X X Y 2 X X X 3 X X X X X X X 4 X X X X X 5 X X 6 X X X 7 X X X X 8 9 Y X X X X
22 Final Analysis Unfortunately, we will have to wait for the publication Prospectively linked 2009 H1N1 Pandemic sequence to 1918 Spanish Flu pandemic
23 Summary Developed the Evolutionary Trajectory Analysis Data-driven approach to ancestry Ancestry = similarity component + time component
24 Acknowledgements JCVI / Influenza Research Database (IRD) Richard H Scheuermann Brett Picket UT Southwestern / IRD Jyothi Noronha Victoria Hunt Erasmus MC / SMU Elizabeth McClellan My thanks to JCVI / IRD for travel support
25 Q & A R. Burke Squires NIAID, Bioinformatics & Computational Biosciences Branch (BCBB) richard.squires@nih.gov
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