1. Phylodynamically Estimated HIV Diversification Rates Reveal Prevention of HIV-1 by Antiretroviral Therapy Jeffrey B. Joy, Richard H. Liang, Rosemary M. McCloskey, Thuy Nguyen, Chanson J. Brumme, Guillaume Colley, Robert S. Hogg, Julio S.G. Montaner, P. Richard Harrigan, and Art F.Y. Poon

2. Conflict of Interest I have no conflict of interest to declare.

3. What is Phylodynamics? How epidemiological, and immunological processes act to shape viral phylogenies Complementary approach to epidemiological data Utilizing only viral sequence data When combined with clinical and demographic attribute data can yield insights into epidemic dynamics

4. What is a virus phylogeny? A virus phylogeny is a family tree of virus sequences

5. What is a virus phylogeny? A virus phylogeny is a family tree of virus sequences TimePastPresent

6. TimePastPresent Phylogenetic Epidemiological Inferences HIV.Seq.1 HIV.Seq.2 HIV.Seq.3 HIV.Seq.4 HIV.Seq.5 HIV.Seq.7 HIV.Seq.8 HIV.Seq.9 HIV.Seq.10 HIV.Seq.11 HIV.Seq. 12 HIV.Seq. 13 HIV.Seq. 14 HIV.Seq.6 Temporal Distribution of Nodes (branching points) 1 5 1023 Distribution Branch Lengths

7. Treatment Prevents HIV Transmission Antiretroviral treatment reduces individual plasma viral loads to undetectable levels Reduces HIV related morbidity and mortality Reduces the risk of HIV transmission

8. IAS 2015 We’ve heard strong evidence that treatment, especially early treatment, is highly beneficial UN 90-90-90 workshop Results of HPTN 052 trial

9. Quantifying Treatment Success at Preventing Transmission Remains a Significant Challenge

10. Can we use methods of analyzing viral sequence data to make inferences about the effectiveness of treatment at reducing HIV transmission rates?

11. Diversification Rate Slow Diversification Rate Rapid Diversification Rate Time Diversification rate is the rate of splitting of branches in a phylogenetic tree relative to time In a virus phylogeny diversification rate approximates transmission rate

12. Treatment and Diversification Rate Can uniquely assign an integrated diversification rate of a lineage to a tip in the tree We test the hypothesis that treated HIV lineages will display slower diversification (transmission) rates relative to untreated HIV lineages Slow Diversification Rate Rapid Diversification Rate Time

13. British Columbia HIV Sequences from the BC CfE Database 27,296 sequences (RT and Protease) 7,747 unique patients Annotated with patient and sequence attributes e.g. Sampling time Date of commencement of antiretroviral therapy Gender and age

14. Dataset Curation Censored cases of transmitted drug resistance - defined as presence of resistance in pre therapy sample Treatment experienced - defined as sequences collected after initiation of antiretroviral therapy Treatment inexperienced - defined as sequences collected before initiation of antiretroviral therapy

15. Distribution of Risk Factors

16. Phylogenetic Trees Generated a distribution of 1000 phylogenetic trees using approximate Maximum Likelihood (FastTree2) Price, M.N., et al. 2010. FastTree 2 approximately maximum-likelihood trees for large alignments. PloS One 5.3: e9490.

17. Diversification Rates of BC HIV Epidemic Calculated lineage specific diversification rates for each HIV lineage in each of 1000 trees Calculated the mean for each lineage Mapped associated rates onto phylogenetic trees Compared treated lineages to untreated lineages

18. BC HIV Diversification Rate

19. Treated Infections Transmit HIV Significantly Less Untreated Treated N=562 N=1626 N=1028 N=831 N=116 N=332 N=2049 N=3546

20. Phylogenetics Shows Reduced Transmission in Treated Lineages Measure derived directly from secondary analysis of sequence data provides independent confirmation that treatment significantly reduces HIV transmission Lineage rather than group level Replicated across risk exposure categories

21. Acknowledgements BC Centre for Excellence Molecular Lab