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Updated: Mar 29, 2026

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
Published on: October 16, 2018
Population genomics of intrapatient HIV-1 evolution
Fabio Zanini1, Johanna Brodin2, Lina Thebo2
1Evolutionary Dynamics and Biophysics, Max Planck Institute for Developmental Biology, Tübingen, Germany.
Human immunodeficiency virus (HIV) evolution was tracked using genome-wide sequencing in untreated patients. Findings reveal reproducible diversity patterns and frequent reversions, indicating universal fitness costs and recombination
Area of Science:
- Microbial evolution
- Virology
- Genomics
Background:
- Microbial populations exhibit rapid adaptation and competition in changing environments.
- Understanding in vivo evolutionary dynamics requires time-resolved, genome-wide data, including rare variants.
Purpose of the Study:
- To quantify complex in vivo evolutionary dynamics of HIV-1 populations.
- To analyze longitudinal, genome-wide sequence data from untreated HIV-1 infected patients.
Main Methods:
- Whole-genome deep sequencing of HIV-1 populations.
- Longitudinal sampling (6-12 samples per patient) over 5-8 years from 9 untreated patients.
- Development of an interactive web application for data exploration.
Main Results:
- Reproducible patterns of minor HIV-1 diversity observed across patients, mirroring global HIV-1 diversity.
- Reversions to the ancestral HIV-1 sequence constitute nearly one-third of all sequence changes, with rates dependent on sequence conservation.
- Frequent recombination limits linkage disequilibrium, while strong hitch-hiking restricts diversity.
Conclusions:
- A universal landscape of fitness costs governs HIV-1 diversity.
- Reversion dynamics are strongly influenced by sequence conservation.
- Recombination and hitch-hiking are key factors shaping HIV-1 genomic diversity during chronic infection.
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