Estimating time since infection in early homogeneous HIV-1 samples using a poisson model

Background: The occurrence of a genetic bottleneck in HIV sexual or mother-to-infant transmission has been well documented. This results in a majority of new infections being homogeneous, i.e., initiated by a single genetic strain. Early after infection, prior to the onset of the host immune response, the viral population grows exponentially. In this simple setting, an approach for estimating evolutionary and demographic parameters based on comparison of diversity measures is a feasible alternative to the existing Bayesian methods (e.g., BEAST), which are instead based on the simulation of genealogies. Results: We have devised a web tool that analyzes genetic diversity in acutely infected HIV-1 patients by comparing it to a model of neutral growth. More specifically, we consider a homogeneous infection (i.e., initiated by a unique genetic strain) prior to the onset of host-induced selection, where we can assume a random accumulation of mutations. Previously, we have shown that such a ...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Elena E. Giorgi, Bob Funkhouser, Gayathri Athreya, Alan S. Perelson, Bette T. Korber, Tanmoy Bhattacharya
• Keywords: BMCBI 2010, Genetic Strain, Homogeneous Infection, Infection