Illuminating early events in HIV infection using single genome amplification

Richard Jefferys, TAG

Two papers in the current Journal of Experimental Medicine offer unprecedented insight into the initial interactions between virus and host after HIV infection. An accompanying commentary by Zabrina Brumme and Bruce Walker eloquently articulates what these studies have achieved: “By identifying persons before seroconversion, pinpointing the transmitted virus, and assessing immune responses to that particular variant as it evolves, they provide a novel view of host and viral dynamics during the earliest stages of infection.” [1]

In both studies the researchers use an optimised version of a technique called Single Genome Amplification (SGA), originally developed by Sarah Palmer and colleagues at the National Cancer Institute. While costly and labour-intensive, this technique allows sequencing of the HIV genome without many of the potential confounding errors that can occur with standard PCR. The researchers also used the sequences obtained by SGA to synthesise peptides for CD8 T cell response assays; this allowed detailed tracking of the impact of CD8 T cell responses on the virus genome.

The study results echo prior work from these groups suggesting that most HIV transmission events involve a single isolate; in 11 out of 12 cases SGA showed that all detected sequences were related to a single infecting virus. The remaining individual was infected with two viruses that could be unambiguously identified based on their sequences. In terms of viral evolution after infection, the researchers found that between transmission and peak viraemia, diversification of HIV sequences was essentially random and showed no evidence of selection pressure from host immune responses. Subsequently, between 9-16 days later, the effects of selection became obvious, particularly effects attributable to HIV-specific CD8 T cell responses. By 32-45 days postinfection, almost the entire replicating virus population in each subject studied was replaced by viruses with mutations at two to five distinct loci in the genome, evincing selection pressure from both CD8 T cell and neutralizing antibody responses (and other unidentified sources also, perhaps innate and/or CD4 T cell immune responses).

The level of detail involved in the study also allowed the researchers to document virus escape from CD8 T cell responses earlier than has previously been reported. Mathematical modelling of the data indicated that HIV-specific CD8 T cells are more efficient at killing virus-infected cells during acute infection than prior estimates have suggested. Discussing the implications of their findings for T-cell-based vaccines, the authors state: “Modelling implied that a single T cell response was contributing as much as 15–35% of viral decline with multiple T cell responses. The implication of these observations is that vaccine-induced HIV-1–specific T cells will contribute to control of acute viraemia if they are activated early in subsequent HIV-1 infection. However, because of the very rapid escape that occurs within the first few weeks of infection, T cell vaccines will need to stimulate a considerable breadth of T cell responses, clearly greater than the median of three epitopes induced by the Merck vaccine.”

Source: TAG basic science project (22 Jun 2009).


  1. Brumme ZL and Walker BD. Tracking the culprit: HIV-1 evolution and immune selection revealed by single-genome amplification. Commentary. Journal of Experimental Medicine, Vol. 206, No. 6, 1215-1218. Published online 1 June 2009. doi:10.1084/jem.20091094.
  2. Goonetilleke N et al. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. Journal of Experimental Medicine, Vol. 206, No. 6, 1253-1272.

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