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Donor-Recipient Identification in Para- and Poly-phyletic Trees Under Alternative HIV-1 Transmission Hypotheses Using
Ethan O Romero-Severson1, Ingo Bulla2,3, Nick Hengartner2
1Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, New Mexico 87545 eoromero@lanl.gov.
Genetics
|September 16, 2017
Summary
Multiple variants in Human Immunodeficiency Virus Type 1 (HIV-1) transmissions complicate understanding infection origins. A new Bayesian method analyzes phylogenetic data to reconstruct transmission histories and identify multiple transmitted lineages, revealing complex infection dynamics.
Area of Science:
- Virology and Epidemiology
- Computational Biology and Phylogenetics
Background:
- Multiple founding variants in Human Immunodeficiency Virus Type 1 (HIV-1) transmissions are common (up to 40% of sexual infections).
- This genetic diversity complicates understanding transmission chains, reconstructing epidemiological histories, and assessing prevention efficacy.
Purpose of the Study:
- To develop a computational framework for inferring transmission origins and scenarios.
- To explicitly account for phylogenetic uncertainty and genetic diversity in Human Immunodeficiency Virus Type 1 (HIV-1) transmission events.
Main Methods:
- Developed an approximate Bayesian computation (ABC) method utilizing phylogenetic topology, branch lengths, and genetic diversity statistics.
- Applied the ABC method to a suspected heterosexual HIV-1 transmission case involving three individuals with complex phylogenetic relationships.
Main Results:
- Detected transmission of at least seven phylogenetic lineages between two individuals, suggesting extensive unsampled transmission.
- Evidence pointed towards an ongoing superinfection process over several years, rather than a single transmission event.
- Analysis revealed non-intuitive transmission dynamics where the primary donor was not readily identifiable through standard phylogenetic rooting, emphasizing the importance of epidemiological context.
Conclusions:
- The developed ABC framework provides a robust method for analyzing HIV-1 transmission, incorporating infection and sampling times.
- The study highlights the complexity of HIV-1 transmission, often involving multiple lineages and prolonged infection periods.
- Integrating epidemiological data with phylogenetic analysis is crucial for accurate reconstruction of transmission histories and identifying transmission sources.
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