The DOI matches its Crossref record; 54 of the 54 references it cites were found in a registry or an index.
Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection
Open accessAbstract
Deep sequencing technologies have the potential to transform the study of highly variable viral pathogens by providing a rapid and cost-effective approach to sensitively characterize rapidly evolving viral quasispecies. Here, we report on a high-throughput whole HIV-1 genome deep sequencing platform that combines 454 pyrosequencing with novel assembly and variant detection algorithms. In one subject we combined these genetic data with detailed immunological analyses to comprehensively evaluate viral evolution and immune escape during the acute phase of HIV-1 infection. The majority of early, low frequency mutations represented viral adaptation to host CD8+ T cell responses, evidence of strong immune selection pressure occurring during the early decline from peak viremia. CD8+ T cell responses capable of recognizing these low frequency escape variants coincided with the selection and evolution of more effective secondary HLA-anchor escape mutations. Frequent, and in some cases rapid, reversion of transmitted mutations was also observed across the viral genome. When located within restricted CD8 epitopes these low frequency reverting mutations were sufficient to prime de novo responses to these epitopes, again illustrating the capacity of the immune response to recognize and respond to low frequency variants. More importantly, rapid viral escape from the most immunodominant CD8+ T cell responses coincided with plateauing of the initial viral load decline in this subject, suggestive of a potential link between maintenance of effective, dominant CD8 responses and the degree of early viremia reduction. We conclude that the early control of HIV-1 replication by immunodominant CD8+ T cell responses may be substantially influenced by rapid, low frequency viral adaptations not detected by conventional sequencing approaches, which warrants further investigation. These data support the critical need for vaccine-induced CD8+ T cell responses to target more highly constrained regions of the virus in order to ensure the maintenance of immunodominant CD8 responses and the sustained decline of early viremia.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Genome sequencing in microfabricated high-density picolitre reactors
Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693
Self-citationPrognosis in HIV-1 Infection Predicted by the Quantity of Virus in Plasma
Mellors, J. W., Rinaldo, C. R., Gupta, P., White, R. M., Todd, J. A., & Kingsley, L. A. (1996) · Science · doi:10.1126/science.272.5265.1167 · Cited by 2,660
Keele, B. F., Giorgi, E. E., Salazar-Gonzalez, J. F., Decker, J. M., Pham, K. T., Salazar, M. G., Sun, C., Grayson, T., Wang, S., Li, H., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0802203105 · Cited by 1,912
Fiebig, E. W., Wright, D. J., Rawal, B. D., Garrett, P. E., Schumacher, R. T., Peddada, L., Heldebrant, C., Smith, R., Conrad, A., Kleinman, S. H., et al. (2003) · AIDS · doi:10.1097/00002030-200309050-00005 · Cited by 1,305
Rapid evolution of the neutralizing antibody response to HIV type 1 infection
Richman, D. D., Wrin, T., Little, S. J., & Petropoulos, C. J. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0630530100 · Cited by 1,200
Borrow, P., Lewicki, H., Wei, X., Horwitz, M. S., Peffer, N., Meyers, H., Nelson, J. A., Gairin, J. E., Hahn, B. H., Oldstone, M. B. A., et al. (1997) · Nature Medicine · doi:10.1038/nm0297-205 · Cited by 1,183
Goulder, P. J. R., Phillips, R. E., Colbert, R. A., McAdam, S., Ogg, G., Nowak, M. A., Giangrande, P., Luzzi, G., Morgana, B., Edwards, A., et al. (1997) · Nature Medicine · doi:10.1038/nm0297-212 · Cited by 1,116
An SNP map of the human genome generated by reduced representation shotgun sequencing
Altshuler, D., Pollara, V. J., Cowles, C. R., Van Etten, W. J., Baldwin, J., Linton, L., & Lander, E. S. (2000) · Nature · doi:10.1038/35035083 · Cited by 729
Positive selection of HIV-1 cytotoxic T lymphocyte escape variants during primary infection
Price, D. A., Goulder, P. J. R., Klenerman, P., Sewell, A. K., Easterbrook, P. J., Troop, M., Bangham, C. R. M., & Phillips, R. E. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.5.1890 · Cited by 688
Allen, T. M., O'Connor, D. H., Jing, P., Dzuris, J. L., Mothé, B. R., Vogel, T. U., Dunphy, E., Liebl, M. E., Emerson, C., Wilson, N., et al. (2000) · Nature · doi:10.1038/35030124 · Cited by 680
Self-citation
Cited by
Grubaugh, N. D., Gangavarapu, K., Quick, J., Matteson, N. L., De Jesus, J. G., Main, B. J., Tan, A. L., Paul, L. M., Brackney, D. E., Grewal, S., et al. (2019) · Genome Biology · doi:10.1186/s13059-018-1618-7 · Cited by 1,014
The epigenetic landscape of T cell exhaustion
Sen, D. R., Kaminski, J., Barnitz, R. A., Kurachi, M., Gerdemann, U., Yates, K. B., Tsao, H.-W., Godec, J., LaFleur, M. W., Brown, F. D., et al. (2016) · Science · doi:10.1126/science.aae0491 · Cited by 986
Self-citationExtremely High Mutation Rate of HIV-1 In Vivo
Cuevas, J. M., Geller, R., Garijo, R., López-Aldeguer, J., & Sanjuán, R. (2015) · PLOS Biology · doi:10.1371/journal.pbio.1002251 · Cited by 371
MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping
Lee, W.-P., Stromberg, M. P., Ward, A., Stewart, C., Garrison, E. P., & Marth, G. T. (2014) · PLoS ONE · doi:10.1371/journal.pone.0090581 · Cited by 279
Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis
Bull, R. A., Adikari, T. N., Ferguson, J. M., Hammond, J. M., Stevanovski, I., Beukers, A. G., Naing, Z., Yeang, M., Verich, A., Gamaarachchi, H., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-20075-6 · Cited by 269
Metadata
- Authors
- Henn, M. R., Boutwell, C. L., Charlebois, P., Lennon, N. J., Power, K. A., Macalalad, A. R., Berlin, A. M., Malboeuf, C. M., Ryan, E. M., Gnerre, S., Zody, M. C., Erlich, R. L., Green, L. M., Berical, A., Wang, Y., Casali, M., Streeck, H., Bloom, A. K., Dudek, T., Tully, D., Newman, R., Axten, K. L., Gladden, A. D., Battis, L., Kemper, M., Zeng, Q., Shea, T. P., Gujja, S., Zedlack, C., Gasser, O., Brander, C., Hess, C., Günthard, H. F., Brumme, Z. L., Brumme, C. J., Bazner, S., Rychert, J., Tinsley, J. P., Mayer, K. H., Rosenberg, E., Pereyra, F., Levin, J. Z., Young, S. K., Jessen, H., Altfeld, M., Birren, B. W., Walker, B. D., & Allen, T. M.
- Venue
- PLoS Pathogens
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-03-08
- Volume
- 8
- Issue
- 3
- Pages
- e1002529
- ISSN
- 1553-7366 (ISSN-L)
- 1553-7374
- OpenAlex
- W2148686896
- Cited by
- 317
- References
- 54
- FWCI
- 20.29
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection. https://app.cochat.ai/papers/10.1371/journal.ppat.1002529
- The paper
- Henn, M. R., Boutwell, C. L., Charlebois, P., Lennon, N. J., Power, K. A., Macalalad, A. R., Berlin, A. M., Malboeuf, C. M., Ryan, E. M., Gnerre, S., Zody, M. C., Erlich, R. L., Green, L. M., Berical, A., Wang, Y., Casali, M., Streeck, H., Bloom, A. K., Dudek, T., . . . Allen, T. M. (2012). Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection. PLoS Pathogens. https://doi.org/10.1371/journal.ppat.1002529
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
