Dryad
Published February 23, 2022 | Version v1
Dataset Open

Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/ Ya Tsie trial

Authors/Creators

  • 1. Harvard University
  • 2. University of Pittsburgh Medical Center
  • 3. University of Oxford
  • 4. University of Pennsylvania
  • 5. Centers for Disease Control and Prevention
  • 6. Ministry of Health, Republic of Botswana*
  • 7. Botswana Harvard AIDS Institute Partnership*
  • 8. Brigham and Women's Hospital

Description

Background: Mathematical models predict that community-wide access to HIV testing-and-treatment can rapidly and substantially reduce new HIV infections. Yet several large universal test-and-treat HIV prevention trials in high-prevalence epidemics demonstrated variable reduction in population-level incidence.

Methods: To elucidate patterns of HIV spread in universal test-and-treat trials we quantified the contribution of geographic-location, gender, age and randomized-HIV-intervention to HIV transmissions in the 30-community Ya Tsie trial in Botswana (estimated trial population: 175,664).

Results: Deep-sequence phylogenetic analysis revealed that most inferred HIV transmissions within the trial occurred within the same or between neighboring communities, and between similarly-aged partners. Transmissions into intervention communities from control communities were more common than the reverse post-baseline (30% [12.2 – 56.7] versus 3% [0.1 – 27.3]) than at baseline (7% [1.5 – 25.3] versus 5% [0.9 – 22.9]) compatible with a benefit from treatment-as-prevention.

Conclusion: Our findings suggest that population mobility patterns are fundamental to HIV transmission dynamics and to the impact of HIV control strategies.

Funding: This study was supported by the National Institute of General Medical Sciences (U54GM088558); the Fogarty International Center (FIC) of the U.S. National Institutes of Health (D43 TW009610); and the President's Emergency Plan for AIDS Relief through the Centers for Disease Control and Prevention (CDC) (Cooperative agreements U01 GH000447 and U2G GH001911).

Notes

Funding provided by: HHS | NIH | Fogarty International Center (FIC)
Crossref Funder Registry ID:
Award Number: D43 TW009610

Funding provided by: HHS | Centers for Disease Control and Prevention (CDC)
Crossref Funder Registry ID:
Award Number: U01 GH000447 and U2G GH001911

Funding provided by: HHS | National Institutes of Health (NIH)
Crossref Funder Registry ID:
Award Number:

Funding provided by: Bill and Melinda Gates Foundation (BMGF)
Crossref Funder Registry ID:
Award Number:

Files

metadata_bcpp_hiv_1c_viral_whole_genome_consensus_seqs_n382_magosi_etal_dryad_submission.csv

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Additional details

Related works

Is cited by
10.1101/2021.06.19.21259186 (DOI)