Author details

Full Name

Jonathan M Carlson

Affiliation

ORCID

Career Start Year

2006

Papers

107

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36000845	HLA-II-Associated HIV-1 Adaptation Decreases CD4<sup>+</sup> T-Cell Responses in HIV-1 Vaccine Recipients.	J Virol	2022
35439174	Longitudinal analysis of T cell receptor repertoires reveals shared patterns of antigen-specific response to SARS-CoV-2 infection.	JCI Insight	2022
35439166	T cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibodies and disease severity.	JCI Insight	2022
33710015	HLA-associated preadaptation in HIV Vif is associated with higher set point viral load and faster CD4+ decline in Zambian transmission pairs.	AIDS	2021
34076482	Elevated HIV Infection of CD4 T Cells in MRKAd5 Vaccine Recipients Due to CD8 T Cells Targeting Adapted Epitopes.	Journal of Virology	2021
33909660	Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein.	PLoS One	2021
33635845	Pre-treatment integrase inhibitor resistance is uncommon in antiretroviral therapy-naive individuals with HIV-1 subtype A1 and D infections in Uganda.	AIDS	2021
33757299	Impact of Human Leukocyte Antigen-Associated Polymorphisms on Variability of HIV-1 Accessory and Regulatory Proteins.	AIDS Research and Human Retroviruses	2021
33173092	Impaired ability of Nef to counteract SERINC5 is associated with reduced plasma viremia in HIV-infected individuals.	Scientific Reports	2020
33097667	HLA tapasin independence: broader peptide repertoire and HIV control.	Proc Natl Acad Sci U S A	2020
32793896	A large-scale database of T-cell receptor beta (TCRÎ²) sequences and binding associations from natural and synthetic exposure to SARS-CoV-2.	Res Sq	2020
31398241	CD8 T cells targeting adapted epitopes in chronic HIV infection promote dendritic cell maturation and CD4 T cell trans-infection.	PLoS Pathog	2019
30925534	Clinical and evolutionary consequences of HIV adaptation to HLA: implications for vaccine and cure.		2019
29369160	HLA-associated polymorphisms in the HIV-2 capsid highlight key differences between HIV-1 and HIV-2 immune adaptation.	AIDS	2018
30021907	Antisense-Derived HIV-1 Cryptic Epitopes Are Not Major Drivers of Viral Evolution during the Acute Phase of Infection.	J Virol	2018
30305354	Genotypic and Mechanistic Characterization of Subtype-Specific HIV Adaptation to Host Cellular Immunity.	J Virol	2018
29093100	Weaker HLA Footprints on HIV in the Unique and Highly Genetically Admixed Host Population of Mexico.	Journal of Virology	2018
29302013	Elevated <i>HLA-A</i> expression impairs HIV control through inhibition of NKG2A-expressing cells.	Science	2018
29461980	Killer cell immunoglobulin-like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1.	J Clin Invest	2018
28797020	Brief Report: Selection of HIV-1 Variants With Higher Transmission Potential by 1% Tenofovir Gel Microbicide.	Journal of acquired immune deficiency syndromes (1999)	2017
28637761	Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-Driven Replication Capacity.	Journal of Virology	2017
28497124	PARV4 prevalence, phylogeny, immunology and coinfection with HIV, HBV and HCV in a multicentre African cohort.	Wellcome Open Research	2017
27608713	Paediatric non-progression following grandmother-to-child HIV transmission.	Retrovirology	2016
27183217	Impact of pre-adapted HIV transmission.	Nat Med	2016
26951820	Lower Viral Loads and Slower CD4+ T-Cell Count Decline in MRKAd5 HIV-1 Vaccinees Expressing Disease-Susceptible HLA-B*58:02.	J Infect Dis	2016
27163788	Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus.	PLoS Pathog	2016
26983786	HIV-1-Specific CD8 T Cells Exhibit Limited Cross-Reactivity during Acute Infection.	J Immunol	2016
26655301	HLA-A is a Predictor of Hepatitis B e Antigen Status in HIV-Positive African Adults.	J Infect Dis	2016
26595539	A strong association of human leukocyte antigen-associated Pol and Gag mutations with clinical parameters in HIV-1 subtype A/E infection.	AIDS	2016
26322665	Enhanced Recognition of HIV-1 Cryptic Epitopes Restricted by HLA Class I Alleles Associated With a Favorable Clinical Outcome.	Journal of acquired immune deficiency syndromes (1999)	2015
25589651	Immune screening identifies novel T cell targets encoded by antisense reading frames of HIV-1.	Journal of Virology	2015
25911754	CD8+ TCR Bias and Immunodominance in HIV-1 Infection.	J Immunol	2015
25613992	HIV-1 adaptation to HLA: a window into virus-host immune interactions.	Trends in Microbiology	2015
25646817	Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial.	PLoS Comput Biol	2015
25808313	A molecular switch in immunodominant HIV-1-specific CD8 T-cell epitopes shapes differential HLA-restricted escape.	Retrovirology	2015
26559841	Population-Level Immune-Mediated Adaptation in HIV-1 Polymerase during the North American Epidemic.	J Virol	2015
26218239	Prevalence and Characteristics of Hepatitis B Virus (HBV) Coinfection among HIV-Positive Women in South Africa and Botswana.	PLoS ONE	2015
26302050	HLA Class-II Associated HIV Polymorphisms Predict Escape from CD4+ T Cell Responses.	PLoS Pathog	2015
26575988	Selection of an HLA-C*03:04-Restricted HIV-1 p24 Gag Sequence Variant Is Associated with Viral Escape from KIR2DL3+ Natural Killer Cells: Data from an Observational Cohort in South Africa.	PLoS Med	2015
25165115	HIV control is mediated in part by CD8+ T-cell targeting of specific epitopes.	J Virol	2014
25453107	Impact of HLA-driven HIV adaptation on virulence in populations of high HIV seroprevalence.	Proc Natl Acad Sci U S A	2014
25350851	CD8 and CD4 epitope predictions in RV144: no strong evidence of a T-cell driven sieve effect in HIV-1 breakthrough sequences from trial participants.	PLoS ONE	2014
24227851	Increased sequence coverage through combined targeting of variant and conserved epitopes correlates with control of HIV replication.	J Virol	2014
24501417	Differential escape patterns within the dominant HLA-B*57:03-restricted HIV Gag epitope reflect distinct clade-specific functional constraints.	J Virol	2014
25212686	Early immune adaptation in HIV-1 revealed by population-level approaches.	Retrovirology	2014
24762668	Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic.	PLoS Genet	2014
24522911	Host-specific adaptation of HIV-1 subtype B in the Japanese population.	Journal of Virology	2014
25013080	HIV transmission. Selection bias at the heterosexual HIV-1 transmission bottleneck.	Science	2014
25193656	Nef-mediated down-regulation of CD4 and HLA class I in HIV-1 subtype C infection: association with disease progression and influence of immune pressure.	Virology	2014
23365420	Frequent and variable cytotoxic-T-lymphocyte escape-associated fitness costs in the human immunodeficiency virus type 1 subtype B Gag proteins.	Journal of Virology	2013