Jonathan M. Carlson
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View article: Large-scale statistical mapping of T-cell receptor β sequences to human leukocyte antigens
Large-scale statistical mapping of T-cell receptor β sequences to human leukocyte antigens Open
Introduction T-cell receptors (TCRs) interacting with peptides presented by human leukocyte antigens (HLAs) are the foundation of the adaptive immune system, but population-level analysis of TCR–HLA interactions is lacking. Methods We stat…
View article: A large-scale database of T-cell receptor beta sequences and binding associations from natural and synthetic exposure to SARS-CoV-2
A large-scale database of T-cell receptor beta sequences and binding associations from natural and synthetic exposure to SARS-CoV-2 Open
We describe the establishment and current content of the ImmuneCODE™ database, which includes hundreds of millions of T-cell Receptor (TCR) sequences from over 1,400 subjects exposed to or infected with the SARS-CoV-2 virus, as well as ove…
View article: HIV-1 adapts to HLA class II–associated selection pressure exerted by CD4 <sup>+</sup> and CD8 <sup>+</sup> T cells
HIV-1 adapts to HLA class II–associated selection pressure exerted by CD4 <sup>+</sup> and CD8 <sup>+</sup> T cells Open
Developing an effective HIV-1 vaccine is a global health priority, but HIV-1 mutational escape from T cells poses a challenge. While escape from human leukocyte antigen class I (HLA-I)–restricted CD8 + T cells is well characterized, less i…
View article: Magnitude and dynamics of the T-cell response to SARS-CoV-2 infection at both individual and population levels
Magnitude and dynamics of the T-cell response to SARS-CoV-2 infection at both individual and population levels Open
Introduction T cells are involved in the early identification and clearance of viral infections and also support the development of antibodies by B cells. This central role for T cells makes them a desirable target for assessing the immune…
View article: Large-scale statistical mapping of T-cell receptor<i>β</i>sequences to Human Leukocyte Antigens
Large-scale statistical mapping of T-cell receptor<i>β</i>sequences to Human Leukocyte Antigens Open
T-cell receptors (TCRs) interacting with peptides presented by human leukocyte antigens (HLAs) are the foundation of the adaptive immune system but population-level analysis of TCR-HLA interactions is lacking. Here we statistically associa…
View article: HLA-II-Associated HIV-1 Adaptation Decreases CD4 <sup>+</sup> T-Cell Responses in HIV-1 Vaccine Recipients
HLA-II-Associated HIV-1 Adaptation Decreases CD4 <sup>+</sup> T-Cell Responses in HIV-1 Vaccine Recipients Open
Despite decades of research, an effective HIV-1 vaccine remains elusive. Vaccine strategies leading to the generation of broadly neutralizing antibodies are likely needed to provide the best opportunity of generating a protective immune re…
View article: T cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibodies and disease severity
T cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibodies and disease severity Open
BACKGROUNDMeasuring the immune response to SARS-CoV-2 enables assessment of past infection and protective immunity. SARS-CoV-2 infection induces humoral and T cell responses, but these responses vary with disease severity and individual ch…
View article: Longitudinal analysis of T cell receptor repertoires reveals shared patterns of antigen-specific response to SARS-CoV-2 infection
Longitudinal analysis of T cell receptor repertoires reveals shared patterns of antigen-specific response to SARS-CoV-2 infection Open
T cells play a prominent role in orchestrating the immune response to viral diseases, but their role in the clinical presentation and subsequent immunity to SARS-CoV-2 infection remains poorly understood. As part of a population-based surv…
View article: LB17. Immunosequencing of the T-Cell Receptor Repertoire Reveals Signatures Specific for Diagnosis and Characterization of Early Lyme Disease
LB17. Immunosequencing of the T-Cell Receptor Repertoire Reveals Signatures Specific for Diagnosis and Characterization of Early Lyme Disease Open
Background Changing climate and demographic trends have led to recent increases in the incidence of tick-borne illnesses. Early diagnosis of Lyme disease (LD) is critical for initiation of antibiotics to mitigate symptoms and prevent late …
View article: 126. Magnitude and Dynamics of the T-Cell Response to SARS-CoV-2 Infection and Vaccination
126. Magnitude and Dynamics of the T-Cell Response to SARS-CoV-2 Infection and Vaccination Open
Background T cells are central to the early identification and clearance of viral infections and support antibody generation by B cells, making them desirable for assessing the immune response to SARS-CoV-2 infection and vaccines. We combi…
View article: Immunosequencing of the T-cell receptor repertoire reveals signatures specific for diagnosis and characterization of early Lyme disease
Immunosequencing of the T-cell receptor repertoire reveals signatures specific for diagnosis and characterization of early Lyme disease Open
Lyme disease, the most common tick-borne illness in the United States, is most frequently caused by infection with Borrelia burgdorferi . Although early antibiotic treatment can prevent development of severe illness and late manifestations…
View article: Elevated HIV Infection of CD4 T Cells in MRKAd5 Vaccine Recipients Due to CD8 T Cells Targeting Adapted Epitopes
Elevated HIV Infection of CD4 T Cells in MRKAd5 Vaccine Recipients Due to CD8 T Cells Targeting Adapted Epitopes Open
Despite the well-established contribution of CD8 T cells in HIV control, prior CD8 T cell-based HIV vaccines have failed to demonstrate any efficacy in preventing viral infection. One such vaccine, known as the MRKAd5 vaccine, showed a pot…
View article: Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein
Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein Open
The spike protein receptor-binding domain (RBD) of SARS-CoV-2 is the molecular target for many vaccines and antibody-based prophylactics aimed at bringing COVID-19 under control. Such a narrow molecular focus raises the specter of viral im…
View article: T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity
T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity Open
Measuring the adaptive immune response to SARS-CoV-2 can enable the assessment of past infection as well as protective immunity and the risk of reinfection. While neutralizing antibody (nAb) titers are one measure of protection, such assay…
View article: HLA-associated preadaptation in HIV Vif is associated with higher set point viral load and faster CD4+ decline in Zambian transmission pairs
HLA-associated preadaptation in HIV Vif is associated with higher set point viral load and faster CD4+ decline in Zambian transmission pairs Open
Objective (s): We investigated the relationship between human leukocyte antigen (HLA)-associated preadaptation for the entire subtype C HIV-1 proteome of the transmitted founder virus and subsequent HIV-1 disease progression in a cohort of…
View article: Pre-treatment integrase inhibitor resistance is uncommon in antiretroviral therapy-naive individuals with HIV-1 subtype A1 and D infections in Uganda
Pre-treatment integrase inhibitor resistance is uncommon in antiretroviral therapy-naive individuals with HIV-1 subtype A1 and D infections in Uganda Open
Objective: Dolutegravir (DTG) is now a preferred component of first-line antiretroviral therapy (ART). However, prevalence data on natural resistance to integrase inhibitors [integrase strand transfer inhibitors (INSTIs)] in circulating no…
View article: Risk of evolutionary escape from neutralizing antibodies targeting SARS-CoV-2 spike protein
Risk of evolutionary escape from neutralizing antibodies targeting SARS-CoV-2 spike protein Open
As many prophylactics targeting SARS-CoV-2 are aimed at the spike protein receptor-binding domain (RBD), we examined the risk of immune evasion from previously published RBD-targeting neutralizing antibodies (nAbs). Epitopes for RBD-target…
View article: Diagnosis and Tracking of SARS-CoV-2 Infection By T-Cell Receptor Sequencing
Diagnosis and Tracking of SARS-CoV-2 Infection By T-Cell Receptor Sequencing Open
In viral diseases T cells exert a prominent role in orchestrating the adaptive immune response and yet a comprehensive assessment of the T-cell repertoire, compared and contrasted with antibody response, after severe acute respiratory synd…
View article: HLA tapasin independence: broader peptide repertoire and HIV control
HLA tapasin independence: broader peptide repertoire and HIV control Open
Significance HLA class I molecules bind antigenic peptides and present them on the cell surface to cytotoxic T cells to initiate immune responses. The peptide selection process occurs intracellularly with the aid of a molecule called tapas…
View article: Magnitude and Dynamics of the T-Cell Response to SARS-CoV-2 Infection at Both Individual and Population Levels
Magnitude and Dynamics of the T-Cell Response to SARS-CoV-2 Infection at Both Individual and Population Levels Open
T cells are involved in the early identification and clearance of viral infections and also support the development of antibodies by B cells. This central role for T cells makes them a desirable target for assessing the immune response to …
View article: CD8 T cells targeting adapted epitopes in chronic HIV infection promote dendritic cell maturation and CD4 T cell trans-infection
CD8 T cells targeting adapted epitopes in chronic HIV infection promote dendritic cell maturation and CD4 T cell trans-infection Open
HIV-1 frequently escapes from CD8 T cell responses via HLA-I restricted adaptation, leading to the accumulation of adapted epitopes (AE). We previously demonstrated that AE compromise CD8 T cell responses during acute infection and are ass…
View article: Clinical and evolutionary consequences of HIV adaptation to HLA
Clinical and evolutionary consequences of HIV adaptation to HLA Open
Though adaptation represents a major challenge to HIV prevention and cure, achieving an in-depth understanding of this phenomenon can help move the design of such strategies forward.
View article: Genotypic and Mechanistic Characterization of Subtype-Specific HIV Adaptation to Host Cellular Immunity
Genotypic and Mechanistic Characterization of Subtype-Specific HIV Adaptation to Host Cellular Immunity Open
The identification of HIV polymorphisms reproducibly selected under pressure by specific HLA alleles and the elucidation of their impact on viral function can help identify immunogenic viral regions where immune escape incurs a fitness cos…
View article: Antisense-Derived HIV-1 Cryptic Epitopes Are Not Major Drivers of Viral Evolution during the Acute Phase of Infection
Antisense-Derived HIV-1 Cryptic Epitopes Are Not Major Drivers of Viral Evolution during the Acute Phase of Infection Open
Although prior studies demonstrated that cryptic epitopes of HIV-1 induce CD8 T cell responses, evidence that targeting these epitopes drives HIV escape mutations has been substantially limited, and no studies have addressed this question …
View article: Killer cell immunoglobulin–like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1
Killer cell immunoglobulin–like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1 Open
HLA-B*57 control of HIV involves enhanced CD8+ T cell responses against infected cells, but extensive heterogeneity exists in the level of HIV control among B*57+ individuals. Using whole-genome sequencing of untreated B*57+ HIV-1-infected…
View article: HLA-associated polymorphisms in the HIV-2 capsid highlight key differences between HIV-1 and HIV-2 immune adaptation
HLA-associated polymorphisms in the HIV-2 capsid highlight key differences between HIV-1 and HIV-2 immune adaptation Open
Greater constraints on evolution may exist in HIV-2, resulting in more purifying selection and different immune adaptation pathways in HIV-1 and HIV-2 capsids. This may allow CTL responses to persist in HIV-2.
View article: Elevated <i>HLA-A</i> expression impairs HIV control through inhibition of NKG2A-expressing cells
Elevated <i>HLA-A</i> expression impairs HIV control through inhibition of NKG2A-expressing cells Open
Inhibiting natural killer cells in AIDS The human leukocyte antigen (HLA) gene complex varies enormously among individuals and helps explain individual variation in immunity to infectious diseases. Ramsuran et al. examined data from almost…
View article: Weaker HLA Footprints on HIV in the Unique and Highly Genetically Admixed Host Population of Mexico
Weaker HLA Footprints on HIV in the Unique and Highly Genetically Admixed Host Population of Mexico Open
HIV circumvents HLA class I-restricted CD8 + T-cell responses through selection of escape mutations that leave characteristic mutational “footprints,” also known as HLA-associated polymorphisms (HAPs), on HIV sequences at the population le…