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Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
Published on: October 16, 2018
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Inferring viral transmission time from phylogenies for known transmission pairs
Emma E Goldberg1, Erik J Lundgren1, Ethan O Romero-Severson1
1Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM, USA.
Biorxiv : the Preprint Server for Biology
|September 25, 2023
Summary
We developed a Markov model to estimate human immunodeficiency virus (HIV) transmission times using viral genetic data. This new method provides more accurate and precise estimates than previous approaches.
Area of Science:
- Virology
- Epidemiology
- Computational Biology
- Phylogenetics
Background:
- Determining the timing of human immunodeficiency virus (HIV) transmission is crucial for understanding transmission dynamics and implementing effective public health interventions.
- Existing methods for inferring transmission times from viral genetic data have limitations in accuracy and precision.
Conclusions:
- The developed Markov time-slice model offers an accurate and precise method for inferring HIV transmission times from phylogenetic data.
- Phylogenetic time-calibration accuracy is critical for reliable transmission time inference, highlighting a key area for methodological improvement.
- Comparable performance between the Markov and coalescent models suggests potential for developing new methods that integrate diverse phylogenetic information for enhanced transmission time estimation.
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