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.”
In both studies the researchers use an optimized version of a technique called Single Genome Amplification (SGA), originally developed by Sarah Palmer and colleagues at the National Cancer Institute. While costly and labor-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 synthesize 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 viremia, 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 modeling 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: “Modeling 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 viremia 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.”
Both papers are the work of researchers supported by the Center for HIV/AIDS Vaccine Immunology (CHAVI); without the substantial funding committed to this project by the National Institutes of Health, this work would not have been possible.
Published online June 1, 2009
doi:10.1084/jem.20091094
The Journal of Experimental Medicine, Vol. 206, No. 6, 1215-1218
COMMENTARY
Tracking the culprit: HIV-1 evolution and immune selection revealed by single-genome amplification
Zabrina L. Brumme and Bruce D. Walker
Z.L. Brumme and B.D. Walker are at the Ragon Institute of MGH, MIT and Harvard, Charlestown MA 02129; Z.L. Brumme is at the Faculty of Health Sciences, Simon Fraser University, Burnaby BC V5A 1S6, Canada
ABSTRACT
Early control of HIV-1 infection is determined by a balance between the host immune response and the ability of the virus to escape this response. Studies using single-genome amplification now reveal new details about the kinetics and specificity of the CD8+ T cell response and the evolution of the virus during early HIV infection.
Published online June 1, 2009
doi:10.1084/jem.20090365
The Journal of Experimental Medicine, Vol. 206, No. 6, 1253-1272
ARTICLE
Nilu Goonetilleke1, Michael K.P. Liu1, Jesus F. Salazar-Gonzalez2, Guido Ferrari3, Elena Giorgi4, Vitaly V. Ganusov4, Brandon F. Keele2, Gerald H. Learn2, Emma L. Turnbull5, Maria G. Salazar2, Kent J. Weinhold3, Stephen Moore1, CHAVI Clinical Core B, Norman Letvin6, Barton F. Haynes3, Myron S. Cohen7, Peter Hraber4, Tanmoy Bhattacharya4,8, Persephone Borrow5, Alan S. Perelson4, Beatrice H. Hahn2, George M. Shaw2, Bette T. Korber4,8, and Andrew J. McMichael1
1 Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, England, UK
2 Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294
3 Duke University Medical Research, Duke University, Durham, NC 27710
4 Los Alamos National Laboratory, Theoretical Division, Los Alamos, NM 87545
5 The Jenner Institute, Oxford University, Compton RG20 7NN, England, UK
6 BIDMC, Harvard University, Boston, MA 02115
7 HIV Prevention Trials Unit, University of North Carolina, Chapel Hill, NC 27599
8 The Santa Fe Institute, Santa Fe, NM 87501
Identification of the transmitted/founder virus makes possible, for the first time, a genome-wide analysis of host immune responses against the infecting HIV-1 proteome. A complete dissection was made of the primary HIV-1–specific T cell response induced in three acutely infected patients. Cellular assays, together with new algorithms which identify sites of positive selection in the virus genome, showed that primary HIV-1–specific T cells rapidly select escape mutations concurrent with falling virus load in acute infection. Kinetic analysis and mathematical modeling of virus immune escape showed that the contribution of CD8 T cell–mediated killing of productively infected cells was earlier and much greater than previously recognized and that it contributed to the initial decline of plasma virus in acute infection. After virus escape, these first T cell responses often rapidly waned, leaving or being succeeded by T cell responses to epitopes which escaped more slowly or were invariant. These latter responses are likely to be important in maintaining the already established virus set point. In addition to mutations selected by T cells, there were other selected regions that accrued mutations more gradually but were not associated with a T cell response. These included clusters of mutations in envelope that were targeted by NAbs, a few isolated sites that reverted to the consensus sequence, and bystander mutations in linkage with T cell–driven escape.
Published online June 1, 2009
doi:10.1084/jem.20090378
The Journal of Experimental Medicine, Vol. 206, No. 6, 1273-1289
ARTICLE
Jesus F. Salazar-Gonzalez1, Maria G. Salazar1, Brandon F. Keele1, Gerald H. Learn1, Elena E. Giorgi2,3, Hui Li1, Julie M. Decker1, Shuyi Wang1, Joshua Baalwa1, Matthias H. Kraus1, Nicholas F. Parrish1, Katharina S. Shaw1, M. Brad Guffey1, Katharine J. Bar1, Katie L. Davis1, Christina Ochsenbauer-Jambor1, John C. Kappes1, Michael S. Saag1, Myron S. Cohen4, Joseph Mulenga5, Cynthia A. Derdeyn6, Susan Allen6, Eric Hunter6, Martin Markowitz7,8, Peter Hraber2, Alan S. Perelson2, Tanmoy Bhattacharya2,9, Barton F. Haynes10, Bette T. Korber2,9, Beatrice H. Hahn1, and George M. Shaw1
1 University of Alabama at Birmingham, Birmingham, AL 35294
2 Los Alamos National Laboratory, Los Alamos, NM 87545
3 University of Massachusetts, Amherst, MA 01002
4 The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
5 Zambia-Emory HIV Research Project, Lusaka, Zambia
6 Emory University, Atlanta, GA 30329
7 Aaron Diamond AIDS Research Center, New York, NY 10016
8 The Rockefeller University, New York, NY 10065
9 Santa Fe Institute, Santa Fe, NM 87501
10 Duke University Medical Center, Durham, NC 27710
Identification of full-length transmitted HIV-1 genomes could be instrumental in HIV-1 pathogenesis, microbicide, and vaccine research by enabling the direct analysis of those viruses actually responsible for productive clinical infection. We show in 12 acutely infected subjects (9 clade B and 3 clade C) that complete HIV-1 genomes of transmitted/founder viruses can be inferred by single genome amplification and sequencing of plasma virion RNA. This allowed for the molecular cloning and biological analysis of transmitted/founder viruses and a comprehensive genome-wide assessment of the genetic imprint left on the evolving virus quasispecies by a composite of host selection pressures. Transmitted viruses encoded intact canonical genes (gag-pol-vif-vpr-tat-rev-vpu-env-nef) and replicated efficiently in primary human CD4+ T lymphocytes but much less so in monocyte-derived macrophages. Transmitted viruses were CD4 and CCR5 tropic and demonstrated concealment of coreceptor binding surfaces of the envelope bridging sheet and variable loop 3. 2 mo after infection, transmitted/founder viruses in three subjects were nearly completely replaced by viruses differing at two to five highly selected genomic loci; by 12–20 mo, viruses exhibited concentrated mutations at 17–34 discrete locations. These findings reveal viral properties associated with mucosal HIV-1 transmission and a limited set of rapidly evolving adaptive mutations driven primarily, but not exclusively, by early cytotoxic T cell responses.
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