ArticlePLoS genetics2014
Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic.
Article in PLoS genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 46 citations in OpenAlex.
- HLA-I Associated Adaptation Dampens CD8 T-Cell Responses in HIV Ad5-Vectored Vaccine Recipients.The Journal of infectious diseases · 2019Trial
- Multistep coevolution of HIV-1 and human leukocyte antigen-C-restricted HIV-1-specific CD8PNAS nexus · 2026Article
- A genomic platform for surveillance and antigen discovery in Plasmodium spp. using long-read amplicon sequencing.Cell reports methods · 2023Article
- Article
- Analysis of Mycotoxin and Secondary Metabolites in Commercial and Traditional Slovak Cheese Samples.Toxins · 2022Article
- Collaboration of a Detrimental HLA-B*35:01 Allele with HLA-A*24:02 in Coevolution of HIV-1 with T Cells Leading to Poorer Clinical Outcomes.Journal of virology · 2021Article
- An Amino Acid Polymorphism within the HIV-1 Nef Dileucine Motif Functionally Uncouples Cell Surface CD4 and SERINC5 Downregulation.Journal of virology · 2021Article
- Risk compensation after HIV-1 vaccination may accelerate viral adaptation and reduce cost-effectiveness: a modeling study.Scientific reports · 2021Article
- T-cell responses to sequentially emerging viral escape mutants shape long-term HIV-1 population dynamics.PLoS pathogens · 2020Article
- Variation in HIV-1 Nef function within and among viral subtypes reveals genetically separable antagonism of SERINC3 and SERINC5.PLoS pathogens · 2020Article
- HIV-1 p24Gag adaptation to modern and archaic HLA-allele frequency differences in ethnic groups contributes to viral subtype diversification.Virus evolution · 2020Article
- Clinical and evolutionary consequences of HIV adaptation to HLA: implications for vaccine and cure.Current opinion in HIV and AIDS · 2019Review
- HIV peptidome-wide association study reveals patient-specific epitope repertoires associated with HIV control.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Extensive host immune adaptation in a concentrated North American HIV epidemic.AIDS (London, England) · 2018Article
- HLA-DQB1*06 and breadth of Nef core region-specific T-cell response are associated with slow disease progression in antiretroviral therapy-naive Chinese HIV-1 subtype B patients.Human vaccines & immunotherapeutics · 2017Article
- Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model.PLoS biology · 2017Article
- Balance between transmitted HLA preadapted and nonassociated polymorphisms is a major determinant of HIV-1 disease progression.The Journal of experimental medicine · 2016Article
- Impact of pre-adapted HIV transmission.Nature medicine · 2016Article
- Population-Level Immune-Mediated Adaptation in HIV-1 Polymerase during the North American Epidemic.Journal of virology · 2016Observational
- Consequences of HLA-B*13-Associated Escape Mutations on HIV-1 Replication and Nef Function.Journal of virology · 2015Article
Corrections and comments
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Authors and funding
29 authors at 9 institutions in 3 countries.
Funding
Abstract
HLA-restricted immune escape mutations that persist following HIV transmission could gradually spread through the viral population, thereby compromising host antiviral immunity as the epidemic progresses. To assess the extent and phenotypic impact of this phenomenon in an immunogenetically diverse population, we genotypically and functionally compared linked HLA and HIV (Gag/Nef) sequences from 358 historic (1979-1989) and 382 modern (2000-2011) specimens from four key cities in the North American epidemic (New York, Boston, San Francisco, Vancouver). Inferred HIV phylogenies were star-like, with approximately two-fold greater mean pairwise distances in modern versus historic sequences. The reconstructed epidemic ancestral (founder) HIV sequence was essentially identical to the North American subtype B consensus. Consistent with gradual diversification of a "consensus-like" founder virus, the median "background" frequencies of individual HLA-associated polymorphisms in HIV (in individuals lacking the restricting HLA[s]) were ∼ 2-fold higher in modern versus historic HIV sequences, though these remained notably low overall (e.g. in Gag, medians were 3.7% in the 2000s versus 2.0% in the 1980s). HIV polymorphisms exhibiting the greatest relative spread were those restricted by protective HLAs. Despite these increases, when HIV sequences were analyzed as a whole, their total average burden of polymorphisms that were "pre-adapted" to the average host HLA profile was only ∼ 2% greater in modern versus historic eras. Furthermore, HLA-associated polymorphisms identified in historic HIV sequences were consistent with those detectable today, with none identified that could explain the few HIV codons where the inferred epidemic ancestor differed from the modern consensus. Results are therefore consistent with slow HIV adaptation to HLA, but at a rate unlikely to yield imminent negative implications for cellular immunity, at least in North America. Intriguingly, temporal changes in protein activity of patient-derived Nef (though not Gag) sequences were observed, suggesting functional implications of population-level HIV evolution on certain viral proteins.
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