Inferring viral population structures using heteroduplex mobility and DNA sequence analyses

Abstract

Heteroduplex mobility (HMA) and tracking assays (HTA) are used to assess genetic relationships between DNA molecules. While distinguishing relationships between clonal or nearly clonal molecules is relatively straightforward, inferring population structures is more complex. To address this issue, HIV-1 quasispecies with varying levels of diversity were studied using both HTA and DNA sequencing. Viral diversity estimates and the temporal features of virus evolution were found to be generally concordant between HTA and DNA sequencing. In addition, the distribution of pairwise differences and the rates of virus divergence were similar between the two methods. These findings support the use of HTA to characterize variant populations of DNA and strengthen previous inferences concerning the evolution of HIV-1 over the course of infection.

Keywords: DNA sequencing; HIV-1; Heteroduplex mobility assay; Heteroduplex tracking assay; Viral diversity; Viral evolution.

Figure 1. Assessment of genetic changes in HIV-1 over the course of infection using HTA and DNA sequence data

The gel images of the heteroduplexes formed between variants present at each time point and heteroduplex tracking probes derived from early, founder sequences (panel A), or late (final time point) sequences (panel D) are shown for each individual. Rox dye labeled molecular size markers were incorporated into each HTA and their sizes in basepairs are indicated on the left. Genetic distances estimated using heteroduplex mobilities (HTA-distance) are plotted in panels B and E for the probes derived from the founder and final sequences, respectively. Panels C and F illustrate the profile of pairwise DNA distances between sequences sampled at each time point and the founder (panel C) or final (panel F) sequence populations. For DNA distances, each pairwise distance value is plotted as an open diamond with the average values connected by a line. X-axes show the years following seroconversion (not plotted to scale).

Figure 2. Comparison of genetic distances estimated using HTA and DNA sequences according to the individual, time following infection, and the type of probe used in HTA experiments

Panel A illustrates the genetic distances plotted with respect to time following seroconversion, separately for each subject. Panel B shows the scatter plots of HTA- versus DNA-distance data, derived using the founder sequence (upper graph) and the final sequence probes (lower graph).

Figure 3. Temporal features in the evolution of HIV-1 assessed using HTA and DNA sequence data

Panel A illustrates intra-time point diversity and the HTA using probes as indicated at the top and driver sequences from each sample. The upper and middle sections of panel A illustrate the HTA distances and the source heteroduplexes, respectively, and the bottom section illustrates the DNA distances. Each pairwise DNA distance is depicted as an open diamond with a line connecting the average values. The purple colored open bar spanning all three sections of Panel A identifies the sample from which the probe sequences were derived. Panel B illustrates heteroduplexes formed between the labeled cloned probe DNA sequence from V14 (2.9 years post-seroconversion) and V15 (3.4 years post-seroconversion) and the driver virus population in samples over the course of infection. Highlighted lanes identify the sample from which cloned probes were derived.