Inferring viral population structures using heteroduplex mobility and DNA sequence analyses

J Virol Methods. 2013 Dec;194(1-2):169-77. doi: 10.1016/j.jviromet.2013.08.012. Epub 2013 Aug 29.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Genetic Variation*
  • HIV Infections / virology
  • HIV-1 / classification*
  • HIV-1 / genetics*
  • HIV-1 / isolation & purification
  • Heteroduplex Analysis / methods*
  • Humans
  • Sequence Analysis, DNA / methods*
  • Virology / methods*