Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand
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Date
2020
Journal Title
Journal ISSN
Volume Title
Publisher
PLoS Pathog
Abstract
Most HIV-1 infected individuals do not know their infection dates. Precise infection timing is
crucial information for studies that document transmission networks or drug levels at infection.
To improve infection timing, we used the prospective RV217 cohort where the window
when plasma viremia becomes detectable is narrow: the last negative visit occurred a
median of four days before the first detectable HIV-1 viremia with an RNA test, referred
below as diagnosis. We sequenced 1,280 HIV-1 genomes from 39 participants at a median
of 4, 32 and 170 days post-diagnosis. HIV-1 infections were dated by using sequencebased
methods and a viral load regression method. Bayesian coalescent and viral load
regression estimated that infections occurred a median of 6 days prior to diagnosis (IQR:
9–3 and 11–4 days prior, respectively). Poisson-Fitter, which analyzes the distribution of
hamming distances among sequences, estimated a median of 7 days prior to diagnosis
(IQR: 15–4 days) based on sequences sampled 4 days post-diagnosis, but it did not yield
plausible results using sequences sampled at 32 days. Fourteen participants reported a
high-risk exposure event at a median of 8 days prior to diagnosis (IQR: 12 to 6 days prior).
These different methods concurred that HIV-1 infection occurred about a week before
detectable viremia, corresponding to 20 days (IQR: 34–15 days) before peak viral load.
Description
Keywords
Molecular dating, Viral load growth rates, Eclipse phase, HIV-1 infected adults, East Africa and Thailand
Citation
Rolland M, Tovanabutra S, Dearlove B, Li Y, Owen CL, Lewitus E, et al. (2020) Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand. PLoS Pathog 16(2): e1008179. https://doi.org/10.1371/ journal.ppat.1008179