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American Society for Microbiology NGS 2020 Aine O'Toole
- 1. Pandemic phylogenetics and reporting in 2020 Áine O’Toole Rambaut Group University of Edinburgh 200,001: A tree-space odyssey
- 2. Thank you!
- 7. Early 2020 outbreak investigations Royal Infirmary Edinburgh
- 8. Early 2020 outbreak investigations Royal Infirmary Edinburgh
- 9. Genomes actionable information Crucial for information to be fed back within a time frame useful to public health
- 11. Lineage Intro to distinct geographic area
- 12. Lineage Intro to distinct geographic area Evidence of onward transmission
- 13. ASM.org | 13 pangolin phylogenetic assignment of named global outbreak lineages
- 14. Representative guide tree - 1 basal representative - Maximise diversity - All SNPs > 10% frequency represented - Minimise N content Manually curated lineages JT McCrone pangolin 1.0 Maximum likelihood assignment
- 15. Emily Scher pangolin 2.0 Machine Learning assignment AKA pangoLEARN Train model: - Multinomial logistic regression - Decision tree - Hierarchical logistic regression Manually curated lineages
- 18. Early 2020 outbreak investigations B.1.5 B.1.47 B.1 B.1.1 B.2.1 Rebecca Dewar
- 19. Early 2020 outbreak investigations B.1.5 B.1.47 B.1 B.1.1 B.2.1 Rebecca Dewar
- 20. Phylogenetics of SARS-CoV-2 in DRC Placide Mbala Summary information about what lineages were circulating in DRC Pulled out local trees, ruled out linkage Early 2020 surveillance
- 21. Placide Mbala Downloading from GISAID QC filters Downsampling non DRC Masking UTRs Run pangolin Alignment Tree building w sensible outgroup Annotated tree with location Parsimony reconstruct ancestral states Introductions- manual and with parsimony for upper bound Phylogenetics of SARS-CoV-2 in DRC Early 2020 surveillance
- 22. Not real time This same analysis could be done locally and quickly with the right tools Placide Mbala Early 2020 surveillance Phylogenetics of SARS-CoV-2 in DRC
- 23. 126 countries with SARS-CoV-2 genome sequences
- 24. C llec i Da e bmi i n 20 , 4 1 1 33 1,175 ,6 15,617 35,6 3 57,450 75,551 3,0 0 131,417 24-D EC 31-D EC 31-JA 29-FEB 31- A 30-A 31- A 30-J 31-J L 31-A G 30- E 20- 209k
- 26. How do you get useful information out of >200,000 sequences?
- 27. Downsampling
- 29. Big tree model Flexible Best-practice Central resources No time lag
- 30. Big tree model Virus phylogenetics: SARS-CoV-2 Best-practices
- 31. Virus phylogenetics Low quality/ missing data Homoplasies Heuristic searching
- 32. Virus phylogenetics Low quality/ missing data Homoplasies Heuristic searching True tree
- 33. Virus phylogenetics SARS-CoV-2 lack of diversity Foregone bootstrapping
- 34. 34 Figure by Andrew Rambaut SARS-CoV-2 & bat/Yunnan/RaTG13
- 39. Ben Jackson
- 41. Local sequencing centres Local bioinformatics Local metadata/ patient linkage Majora Sam Nicholls ASMNGS TALK!
- 42. Local sequencing centres Local bioinformatics Local metadata/ patient linkage Majora Sam Nicholls Grapevine Ben Jackson Rachel Colquhoun
- 43. C llec i Da e bmi i n 20 , 1 1 1 33 1,175 ,6 15,617 35,6 3 57,450 75,551 3,0 0 131,417 24-D EC 31-D EC 31-JA 29-FEB 31- A 30-A 31- A 30-J 31-J 31-A G 30- E 17- 204kMany Grapevine D614G A222V Y453F
- 47. ASM.org | 47 civet cluster investigation & virus epidemiology tool
- 48. civet cluster investigation & virus epidemiology tool Verity Hill
- 52. Ben Jackson
- 58. Local trees
- 62. snipit
- 63. 63 civet –fm country=DRC Placide Mbala Phylogenetics of SARS-CoV-2 in DRC Summary of each local tree How many local subtrees Lineage assignment & summarize SNPs
- 64. 64 civet –fm country=DRC Placide Mbala Phylogenetics of SARS-CoV-2 in DRC Summary of each local tree How many local subtrees Lineage assignment & summarize SNPs llama: local lineage & monophyly assessment
- 66. ASM.org | 66 polecat phylogenetic overview & local epidemiological cluster analysis tool
- 67. Andrew Rambaut polecat phylogenetic overview & local epidemiological cluster analysis tool
- 68. Andrew Rambaut polecat phylogenetic overview & local epidemiological cluster analysis tool Summary statistics: - Recency - Growth rate - Age - Location count … and many more
- 71. Growth rate
- 80. University of Edinburgh Andrew Rambaut Verity Hill JT McCrone Ben Jackson Rachel Colquhoun Emily Scher Stefan Rooke Shawn Yu
- 81. Thank you!