Supplementary Materials

Supplementary Material for:

Sources of HIV infection among men having sex with men and implications for prevention

Oliver Ratmann,* Ard van Sighem, Daniela Bezemer, Alexandra Gavryushkina, Suzanne Jurriaans, Annemarie Wensing, Frank de Wolf, Peter Reiss, Christophe Fraser, ATHENA observational cohort

*Corresponding author. E-mail: oliver.ratmann{at}imperial.ac.uk

Published 6 January 2016, Sci. Transl. Med. 8, 320ra2 (2016)
DOI: 10.1126/scitranslmed.aad1863

This PDF file includes:

  • Extended acknowledgments
  • Materials and Methods
  • Fig. S1. Number of identified recipient MSM by 3-month intervals.
  • Fig. S2. Duration of infection windows of recipient MSM.
  • Fig. S3. Snapshot of the reconstructed viral phylogeny.
  • Fig. S4. Uncertainty in the estimated genetic distance between sequences from the transmitter and recipient of potential transmission pairs.
  • Fig. S5. Genetic distance between sequence pairs from previously published, epidemiologically confirmed transmitter-recipient pairs, and sequence pairs from the phylogenetically probable transmission pairs in this study.
  • Fig. S6. Right censoring at past, hypothetical database closure times.
  • Fig. S7. Sequence sampling probabilities by stage in the infection and care continuum.
  • Fig. S8. Individual-level variation in phylogenetically derived transmission probabilities by infection/care stages.
  • Fig. S9. Frequency of infection/care stages among phylogenetically probable transmitters.
  • Fig. S10. Phylogenetically derived transmission probabilities of observed transmission intervals.
  • Fig. S11. Transmission risk ratio from men after ART start compared to diagnosed untreated men with CD4 >500 cells/ml.
  • Fig. S12. Sensitivity analysis on the impact of PrEP with lower efficacy.
  • Fig. S13. Sensitivity analysis on the impact of lower or higher PrEP coverage.
  • Fig. S14. Impact of sampling and censoring adjustments on the estimated proportion of transmissions from stages in the infection and care continuum.
  • Fig. S15. Impact of phylogenetic transmission probabilities on the estimated proportion of transmissions from stages in the infection and care continuum.
  • Fig. S16. Impact of infection time estimates on the estimated proportion of transmissions from stages in the infection and care continuum.
  • Fig. S17. Impact of phylogenetic clustering criteria on the estimated proportion of transmissions from stages in the infection and care continuum.
  • Fig. S18. Impact of additional genetic distance criteria on the estimated proportion of transmissions from stages in the infection and care continuum.
  • Fig. S19. Impact of sequence sampling and censoring adjustments on the estimated proportion of averted infections.
  • Fig. S20. Impact of phylogenetic transmission probabilities on the estimated proportion of averted infections.
  • Fig. S21. Impact of infection time estimates and phylogenetic exclusion criteria on the estimated proportion of averted infections.
  • Fig. S22. Impact of additional genetic distance criteria on the estimated proportion of averted infections per biomedical intervention.
  • Fig. S23. Differences in transmission networks with and without a recipient MSM.
  • Fig. S24. Exploratory local polynomial regression fits to the time to diagnosis of MSM with a last negative test in the ATHENA cohort.
  • Fig. S25. Multivariable gamma regression model fitted to the time between the midpoint of the seroconversion interval and diagnosis of MSM with a last negative test in the ATHENA cohort.
  • Fig. S26. Estimated probability that the time between the midpoint of the seroconversion interval and diagnosis among MSM with a last negative test is larger than t years.
  • Fig. S27. Time to diagnosis estimates.
  • Fig. S28. Genetic distance among sequence pairs from transmitter-recipient pairs in the Belgium and Swedish transmission chains.
  • Fig. S29. Approximate type I error of the phylogenetic clustering criterion as a function of the clade frequency threshold.
  • Fig. S30. Type I error and power of the coalescence compatibility test.
  • Fig. S31. Estimated fraction of noncensored potential transmission intervals.
  • Fig. S32. Time between last negative test and diagnosis among MSM diagnosed in July 2009 to December 2010 and probable transmitters of recipients diagnosed in July 2009 to December 2010.
  • Table S1. Clinical and viral sequence data used in this study.
  • Table S2. Potential transmitters and potential transmission pairs to the recipient MSM.
  • Table S3. Identified phylogenetically probable transmitters and phylogenetically probable transmission pairs to the recipient MSM.
  • Table S4. Demographic and clinic characteristics of the 3025 MSM with a last negative test, which were used to fit the multivariable regression model.
  • References (4852)

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