List of works - Chanson J Brumme

"Test-and-treat" strategy for control of HIV and AIDS can lead to a decrease, not an increase, of multidrug-resistant viruses

scientific article published on 26 April 2013

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

scientific article published on 29 October 2013

Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes

scientific article

Adaptation of HIV-1 to human leukocyte antigen class I

scientific article published on 25 February 2009

Aminopeptidase substrate preference affects HIV epitope presentation and predicts immune escape patterns in HIV-infected individuals

scientific article published on 14 May 2012

Antigen load and viral sequence diversification determine the functional profile of HIV-1-specific CD8+ T cells

scientific article (publication date: 6 May 2008)

Automating HIV drug resistance genotyping with RECall, a freely accessible sequence analysis tool

scientific article published on 7 March 2012

CD4-dependent characteristics of coreceptor use and HIV type 1 V3 sequence in a large population of therapy-naive individuals

scientific article published in February 2008

Characteristics and Outcomes of Initial Virologic Suppressors during Analytic Treatment Interruption in a Therapeutic HIV-1 gag Vaccine Trial ⬇️

scientific article published on March 30, 2012

Competitive fitness assays indicate that the E138A substitution in HIV-1 reverse transcriptase decreases in vitro susceptibility to emtricitabine

scientific article

Correction: Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1

article

Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1.

scientific article

Definition of the viral targets of protective HIV-1-specific T cell responses

scientific article published on 7 December 2011

Development and Validation of Two Screening Assays for the Hepatitis C Virus NS3 Q80K Polymorphism Associated with Reduced Response to Combination Treatment Regimens Containing Simeprevir

scientific article published on July 2015

Direct non-productive HIV-1 infection in a T-cell line is driven by cellular activation state and NFκB.

scientific article published on 7 February 2014

Early selection in Gag by protective HLA alleles contributes to reduced HIV-1 replication capacity that may be largely compensated for in chronic infection

scientific article

Effects of Human Leukocyte Antigen Class I Genetic Parameters on Clinical Outcomes and Survival after Initiation of Highly Active Antiretroviral Therapy

article

Efficacious early antiviral activity of HIV Gag- and Pol-specific HLA-B 2705-restricted CD8+ T cells

scientific article (publication date: October 2010)

Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control

scientific article

Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of HIV-1

scientific article

Factors Associated With Viral Rebound in HIV-1-Infected Individuals Enrolled in a Therapeutic HIV-1 gag Vaccine Trial ⬇️

scientific article published on April 1, 2011

Gag-protease-mediated replication capacity in HIV-1 subtype C chronic infection: associations with HLA type and clinical parameters

scientific article

Genetic characterization of human immunodeficiency virus type 1 in elite controllers: lack of gross genetic defects or common amino acid changes

scientific article published on 18 June 2008

Genotypic analysis of the V3 region of HIV from virologic nonresponders to maraviroc-containing regimens reveals distinct patterns of failure

scientific article published on 30 September 2013

Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic

scientific article

HIV VprR77Q mutation does not influence clinical response of individuals initiating highly active antiretroviral therapy

scientific article published on July 2006

HIV drug resistance testing by high-multiplex "wide" sequencing on the MiSeq instrument

scientific article

HIV-1 drug resistance: degree of underestimation by a cross-sectional versus a longitudinal testing approach

scientific article published on 16 March 2005

HLA-B57/B*5801 human immunodeficiency virus type 1 elite controllers select for rare gag variants associated with reduced viral replication capacity and strong cytotoxic T-lymphocyte [corrected] recognition

scientific article published on 30 December 2008

HLA-associated alterations in replication capacity of chimeric NL4-3 viruses carrying gag-protease from elite controllers of human immunodeficiency virus type 1.

scientific article published on 29 October 2008

HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins

scientific article

HLA-associated viral mutations are common in human immunodeficiency virus type 1 elite controllers

scientific article published on 19 January 2009

High Levels of Dual-Class Drug Resistance in HIV-Infected Children Failing First-Line Antiretroviral Therapy in Southern Ethiopia

scientific article published in February 2018

Human immunodeficiency virus type 1-specific CD8+ T-cell responses during primary infection are major determinants of the viral set point and loss of CD4+ T cells

scientific article published on 20 May 2009

Human leukocyte antigen-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection

article

Impact of select immunologic and virologic biomarkers on CD4 cell count decrease in patients with chronic HIV-1 subtype C infection: results from Sinikithemba Cohort, Durban, South Africa

scientific article published on September 2009

Impaired replication capacity of acute/early viruses in persons who become HIV controllers

scientific article

Increasingly successful highly active antiretroviral therapy delays the emergence of new HLA class I-associated escape mutations in HIV-1.

scientific article published on 28 March 2012

Influence of Gag-protease-mediated replication capacity on disease progression in individuals recently infected with HIV-1 subtype C.

scientific article

Influence of HLA-C expression level on HIV control

scientific article published on April 2013

Lack of a significant impact of Gag-Protease-mediated HIV-1 replication capacity on clinical parameters in treatment-naive Japanese individuals

scientific article

Limited evolution of inferred HIV-1 tropism while viremia is undetectable during standard HAART therapy

scientific article

Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection

scientific article published on 9 July 2008

Minor contribution of HLA class I-associated selective pressure to the variability of HIV-1 accessory protein Vpu.

scientific article published on 7 April 2012

Molecular and Clinical Epidemiology of CXCR4‐Using HIV‐1 in a Large Population of Antiretroviral‐Naive Individuals

article

Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-Driven Replication Capacity

scientific article

Multi-Laboratory Comparison of Next-Generation to Sanger-Based Sequencing for HIV-1 Drug Resistance Genotyping

scientific article published on 27 June 2020

No inherent association between minor mutations in HIV protease at baseline and selection of the L90M mutation at the time of the first virological failure.

scientific article

Performance of a World Health Organization first-line regimen (stavudine/lamivudine/nevirapine) in antiretroviral-naïve individuals in a Western setting

scientific article published on July 2007

Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag.

scientific article

Population-based sequencing of the V3-loop can predict the virological response to maraviroc in treatment-naive patients of the MERIT trial

scientific article published in November 2012

Predictors of HIV drug-resistance mutations in a large antiretroviral-naive cohort initiating triple antiretroviral therapy

scientific article

Prevalence and Correlates of Pre-Treatment HIV Drug Resistance among HIV-Infected Children in Ethiopia

scientific article published on 19 September 2019

Prevalence and virologic consequences of transmitted HIV-1 drug resistance in Uganda

scientific article

Promises and pitfalls of Illumina sequencing for HIV resistance genotyping

scientific article published on 16 December 2016

Quantitative trait loci for CD4:CD8 lymphocyte ratio are associated with risk of type 1 diabetes and HIV-1 immune control

scientific article

Rates and Correlates of Short Term Virologic Response among Treatment-Naïve HIV-Infected Children Initiating Antiretroviral Therapy in Ethiopia: A Multi-Center Prospective Cohort Study

scientific article published on 24 September 2019

Rates of antiretroviral resistance among HIV-infected patients with and without a history of injection drug use.

scientific article published in July 2005

Reduced replication capacity of NL4-3 recombinant viruses encoding reverse transcriptase-integrase sequences from HIV-1 elite controllers

scientific article published on February 2011

Replication fitness of multiple nonnucleoside reverse transcriptase-resistant HIV-1 variants in the presence of etravirine measured by 454 deep sequencing

scientific article published on 29 May 2013

Short communication. Association of the CCR5delta32 mutation with clinical response and >5-year survival following initiation of first triple antiretroviral regimen

article

Short-term variation of HIV tropism readouts in the absence of CCR5 antagonists

article

Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection

scientific article

Suboptimal biological sampling as a probable cause of false-negative COVID-19 diagnostic test results

scientific article published on 08 May 2020

T-cell responses to sequentially emerging viral escape mutants shape long-term HIV-1 population dynamics

scientific article published on 28 December 2020

Technical and regulatory shortcomings of the TaqMan version 1 HIV viral load assay

scientific article

The impact of clinical, demographic and risk factors on rates of HIV transmission: a population-based phylogenetic analysis in British Columbia, Canada

scientific article

The major genetic determinants of HIV-1 control affect HLA class I peptide presentation

scientific article

The relationship between resistance and adherence in drug-naive individuals initiating HAART is specific to individual drug classes

scientific article published on November 2008

Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing

scientific article published on 7 May 2014

Transmission and long-term stability of compensated CD8 escape mutations

scientific article published on 17 December 2008

Transmission of drug-resistant HIV-1 from an infected individual to a caregiver

article

Trends in plasma HIV-RNA suppression and antiretroviral resistance in British Columbia, 1997-2010

scientific article

Uncommon pathways of immune escape attenuate HIV-1 integrase replication capacity

scientific article

Variation in HIV-1 Nef function within and among viral subtypes reveals genetically separable antagonism of SERINC3 and SERINC5

scientific article published on 14 September 2020

Viral adaptation to immune selection pressure by HLA class I-restricted CTL responses targeting epitopes in HIV frameshift sequences

scientific article

Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection

scientific article published on 8 March 2012

List of works by Chanson J Brumme

"Test-and-treat" strategy for control of HIV and AIDS can lead to a decrease, not an increase, of multidrug-resistant viruses

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes

Adaptation of HIV-1 to human leukocyte antigen class I

Aminopeptidase substrate preference affects HIV epitope presentation and predicts immune escape patterns in HIV-infected individuals

Antigen load and viral sequence diversification determine the functional profile of HIV-1-specific CD8+ T cells

Automating HIV drug resistance genotyping with RECall, a freely accessible sequence analysis tool

CD4-dependent characteristics of coreceptor use and HIV type 1 V3 sequence in a large population of therapy-naive individuals

Characteristics and Outcomes of Initial Virologic Suppressors during Analytic Treatment Interruption in a Therapeutic HIV-1 gag Vaccine Trial ⬇️

Competitive fitness assays indicate that the E138A substitution in HIV-1 reverse transcriptase decreases in vitro susceptibility to emtricitabine

Correction: Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1

Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1.

Definition of the viral targets of protective HIV-1-specific T cell responses

Development and Validation of Two Screening Assays for the Hepatitis C Virus NS3 Q80K Polymorphism Associated with Reduced Response to Combination Treatment Regimens Containing Simeprevir

Direct non-productive HIV-1 infection in a T-cell line is driven by cellular activation state and NFκB.

Early selection in Gag by protective HLA alleles contributes to reduced HIV-1 replication capacity that may be largely compensated for in chronic infection

Effects of Human Leukocyte Antigen Class I Genetic Parameters on Clinical Outcomes and Survival after Initiation of Highly Active Antiretroviral Therapy

Efficacious early antiviral activity of HIV Gag- and Pol-specific HLA-B 2705-restricted CD8+ T cells

Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control

Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of HIV-1

Factors Associated With Viral Rebound in HIV-1-Infected Individuals Enrolled in a Therapeutic HIV-1 gag Vaccine Trial ⬇️

Gag-protease-mediated replication capacity in HIV-1 subtype C chronic infection: associations with HLA type and clinical parameters

Genetic characterization of human immunodeficiency virus type 1 in elite controllers: lack of gross genetic defects or common amino acid changes

Genotypic analysis of the V3 region of HIV from virologic nonresponders to maraviroc-containing regimens reveals distinct patterns of failure

Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic

HIV VprR77Q mutation does not influence clinical response of individuals initiating highly active antiretroviral therapy

HIV drug resistance testing by high-multiplex "wide" sequencing on the MiSeq instrument

HIV-1 drug resistance: degree of underestimation by a cross-sectional versus a longitudinal testing approach

HLA-B57/B*5801 human immunodeficiency virus type 1 elite controllers select for rare gag variants associated with reduced viral replication capacity and strong cytotoxic T-lymphocyte [corrected] recognition

HLA-associated alterations in replication capacity of chimeric NL4-3 viruses carrying gag-protease from elite controllers of human immunodeficiency virus type 1.

HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins

HLA-associated viral mutations are common in human immunodeficiency virus type 1 elite controllers

High Levels of Dual-Class Drug Resistance in HIV-Infected Children Failing First-Line Antiretroviral Therapy in Southern Ethiopia

Human immunodeficiency virus type 1-specific CD8+ T-cell responses during primary infection are major determinants of the viral set point and loss of CD4+ T cells

Human leukocyte antigen-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection

Impact of select immunologic and virologic biomarkers on CD4 cell count decrease in patients with chronic HIV-1 subtype C infection: results from Sinikithemba Cohort, Durban, South Africa

Impaired replication capacity of acute/early viruses in persons who become HIV controllers

Increasingly successful highly active antiretroviral therapy delays the emergence of new HLA class I-associated escape mutations in HIV-1.

Influence of Gag-protease-mediated replication capacity on disease progression in individuals recently infected with HIV-1 subtype C.

Influence of HLA-C expression level on HIV control

Lack of a significant impact of Gag-Protease-mediated HIV-1 replication capacity on clinical parameters in treatment-naive Japanese individuals

Limited evolution of inferred HIV-1 tropism while viremia is undetectable during standard HAART therapy

Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection

Minor contribution of HLA class I-associated selective pressure to the variability of HIV-1 accessory protein Vpu.

Molecular and Clinical Epidemiology of CXCR4‐Using HIV‐1 in a Large Population of Antiretroviral‐Naive Individuals

Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-Driven Replication Capacity

Multi-Laboratory Comparison of Next-Generation to Sanger-Based Sequencing for HIV-1 Drug Resistance Genotyping

No inherent association between minor mutations in HIV protease at baseline and selection of the L90M mutation at the time of the first virological failure.

Performance of a World Health Organization first-line regimen (stavudine/lamivudine/nevirapine) in antiretroviral-naïve individuals in a Western setting

Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag.

Population-based sequencing of the V3-loop can predict the virological response to maraviroc in treatment-naive patients of the MERIT trial

Predictors of HIV drug-resistance mutations in a large antiretroviral-naive cohort initiating triple antiretroviral therapy

Prevalence and Correlates of Pre-Treatment HIV Drug Resistance among HIV-Infected Children in Ethiopia

Prevalence and virologic consequences of transmitted HIV-1 drug resistance in Uganda

Promises and pitfalls of Illumina sequencing for HIV resistance genotyping

Quantitative trait loci for CD4:CD8 lymphocyte ratio are associated with risk of type 1 diabetes and HIV-1 immune control

Rates and Correlates of Short Term Virologic Response among Treatment-Naïve HIV-Infected Children Initiating Antiretroviral Therapy in Ethiopia: A Multi-Center Prospective Cohort Study

Rates of antiretroviral resistance among HIV-infected patients with and without a history of injection drug use.

Reduced replication capacity of NL4-3 recombinant viruses encoding reverse transcriptase-integrase sequences from HIV-1 elite controllers

Replication fitness of multiple nonnucleoside reverse transcriptase-resistant HIV-1 variants in the presence of etravirine measured by 454 deep sequencing

Short communication. Association of the CCR5delta32 mutation with clinical response and >5-year survival following initiation of first triple antiretroviral regimen

Short-term variation of HIV tropism readouts in the absence of CCR5 antagonists

Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection

Suboptimal biological sampling as a probable cause of false-negative COVID-19 diagnostic test results

T-cell responses to sequentially emerging viral escape mutants shape long-term HIV-1 population dynamics

Technical and regulatory shortcomings of the TaqMan version 1 HIV viral load assay

The impact of clinical, demographic and risk factors on rates of HIV transmission: a population-based phylogenetic analysis in British Columbia, Canada

The major genetic determinants of HIV-1 control affect HLA class I peptide presentation

The relationship between resistance and adherence in drug-naive individuals initiating HAART is specific to individual drug classes

Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing

Transmission and long-term stability of compensated CD8 escape mutations

Transmission of drug-resistant HIV-1 from an infected individual to a caregiver

Trends in plasma HIV-RNA suppression and antiretroviral resistance in British Columbia, 1997-2010

Uncommon pathways of immune escape attenuate HIV-1 integrase replication capacity

Variation in HIV-1 Nef function within and among viral subtypes reveals genetically separable antagonism of SERINC3 and SERINC5

Viral adaptation to immune selection pressure by HLA class I-restricted CTL responses targeting epitopes in HIV frameshift sequences

Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection