List of works - Jürg Böni

A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland

scientific article published on 19 September 2016

A Lead-In with Silibinin Prior to Triple-Therapy Translates into Favorable Treatment Outcomes in Difficult-To-Treat HIV/Hepatitis C Coinfected Patients

scientific article

Adaptation of the ultrasensitive HIV-1 p24 antigen assay to dried blood spot testing

scientific article

Adherence as a predictor of the development of class-specific resistance mutations: the Swiss HIV Cohort Study

scientific article (publication date: 2013)

African descent is associated with slower CD4 cell count decline in treatment-naive patients of the Swiss HIV Cohort Study

scientific article published in June 2009

Ambiguous nucleotide calls from population-based sequencing of HIV-1 are a marker for viral diversity and the age of infection

scientific article published on 10 January 2011

An international collaboration to standardize HIV-2 viral load assays: results from the 2009 ACHI(E)V(2E) quality control study

scientific article

Assessing efficacy of different nucleos(t)ide backbones in NNRTI-containing regimens in the Swiss HIV Cohort Study

scientific article published on 11 September 2015

Assessing predicted HIV-1 replicative capacity in a clinical setting

scientific article published in November 2011

Assessing the Paradox Between Transmitted and Acquired HIV Type 1 Drug Resistance Mutations in the Swiss HIV Cohort Study From 1998 to 2012.

scientific article published on 9 January 2015

Assessing the danger of self-sustained HIV epidemics in heterosexuals by population based phylogenetic cluster analysis

scientific article published on 12 September 2017

CD4 cell count response to first-line combination ART in HIV-2+ patients compared with HIV-1+ patients: a multinational, multicohort European study

article

Characterization of human immunodeficiency virus type 1 (HIV-1) diversity and tropism in 145 patients with primary HIV-1 infection

scientific article published on 12 October 2011

Clustering of HCV coinfections on HIV phylogeny indicates domestic and sexual transmission of HCV.

scientific article published on 22 January 2014

Combined effect of zidovudine (ZDV), lamivudine (3TC) and abacavir (ABC) antiretroviral therapy in suppressing in vitro FIV replication

scientific article

Comparison of HIV-1 viral load based on RNA or reverse transcriptase activity in patients with suspected viral load underestimation.

scientific article published on 25 May 2012

Correction to: Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples

scientific article published on 12 October 2017

Correction: Long-Lasting Protection of Activity of Nucleoside Reverse Transcriptase Inhibitors and Protease Inhibitors (PIs) by Boosted PI Containing Regimens

scientific article (publication date: 25 July 2013)

Detection of low copy numbers of HIV-1 proviral DNA in patient PBMCs by a high-input, sequence-capture PCR (Mega-PCR).

scientific article

Detection of reverse transcriptase activity in human melanoma cell lines and identification of a murine leukemia virus contaminant.

scientific article

Determinants of HIV-1 broadly neutralizing antibody induction.

scientific article

Direct evidence for natural transmission of small-ruminant lentiviruses of subtype A4 from goats to sheep and vice versa

scientific article

Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T-Cell Decline, and Per-Parasite Pathogenicity

scientific article published in January 2018

Efficient suppression of minority drug-resistant HIV type 1 (HIV-1) variants present at primary HIV-1 infection by ritonavir-boosted protease inhibitor-containing antiretroviral therapy

scientific article published in April 2010

Emergence of Acquired HIV-1 Drug Resistance Almost Stopped in Switzerland: A 15-Year Prospective Cohort Analysis

scientific article published on 8 March 2016

Emergence of HIV-1 drug resistance in previously untreated patients initiating combination antiretroviral treatment: a comparison of different regimen types

scientific article published on September 2007

Epidemiological and biological evidence for a compensatory effect of connection domain mutation N348I on M184V in HIV-1 reverse transcriptase

scientific article

Estimating the basic reproductive number from viral sequence data.

scientific article

Factors associated with the emergence of K65R in patients with HIV-1 infection treated with combination antiretroviral therapy containing tenofovir

scientific article published in April 2008

Gammaretrovirus-specific antibodies in free-ranging and captive Namibian cheetahs

scientific article published on 25 March 2015

Generation of a recombinant Gag virus-like-particle panel for the evaluation of p24 antigen detection by diagnostic HIV tests

scientific article

Genotypic Resistance Tests Sequences Reveal the Role of Marginalized Populations in HIV-1 Transmission in Switzerland

scientific article published on 14 June 2016

HIV rebounds from latently infected cells, rather than from continuing low-level replication

scholarly article

HIV-1 Transmission During Recent Infection and During Treatment Interruptions as Major Drivers of New Infections in the Swiss HIV Cohort Study

scientific article published on 19 September 2015

HIV-1 p24 antigen is a significant inverse correlate of CD4 T-cell change in patients with suppressed viremia under long-term antiretroviral therapy

scientific article published in July 2003

HIV-1 reverse transcriptase connection domain mutations: dynamics of emergence and implications for success of combination antiretroviral therapy

scientific article published on September 2010

HIV-1 superinfection in an HIV-2-infected woman with subsequent control of HIV-1 plasma viremia

scientific article published in June 2009

HIV-1 transmission after cessation of early antiretroviral therapy among men having sex with men.

scientific article published in May 2010

HIV-specific cellular immune response is inversely correlated with disease progression as defined by decline of CD4+ T cells in relation to HIV RNA load

scientific article published on 17 March 2004

High Frequency of Non-B Subtypes in Newly Diagnosed HIV-1 Infections in Switzerland

article

Higher risk of incident hepatitis C virus coinfection among men who have sex with men, in whom the HIV genetic bottleneck at transmission was wide

scientific article

Identification and characterization of two closely related unclassifiable endogenous retroviruses in pythons (Python molurus and Python curtus)

scientific article

Importance of an Early HIV Antibody Differentiation Immunoassay for Detection of Dual Infection with HIV-1 and HIV-2

scientific article

Improved virological outcome in White patients infected with HIV-1 non-B subtypes compared to subtype B.

scientific article published on 13 October 2011

Incidence of HIV-1 Drug Resistance Among Antiretroviral Treatment–Naive Individuals Starting Modern Therapy Combinations ⬇️

scientific article published on November 4, 2011

Induced prion protein controls immune-activated retroviruses in the mouse spleen

scientific article

Inferring epidemic contact structure from phylogenetic trees

scientific article published on 8 March 2012

Inferring the age difference in HIV transmission pairs by applying phylogenetic methods on the HIV transmission network of the Swiss HIV Cohort Study

article

Lack of evidence for PERV expression after apoptosis-mediated horizontal gene transfer between porcine and human cells

scientific article published on January 2007

Large-scale inference of conjunctive Bayesian networks

scientific article

Limited clinical benefit of minority K103N and Y181C-variant detection in addition to routine genotypic resistance testing in antiretroviral therapy-naive patients

scientific article published on September 2014

Long-lasting protection of activity of nucleoside reverse transcriptase inhibitors and protease inhibitors (PIs) by boosted PI containing regimens

scientific article

Low human immunodeficiency virus envelope diversity correlates with low in vitro replication capacity and predicts spontaneous control of plasma viremia after treatment interruptions

scientific article

Metagenomic sequencing complements routine diagnostics in identifying viral pathogens in lung transplant recipients with unknown etiology of respiratory infection

scientific article

MinVar: A rapid and versatile tool for HIV-1 drug resistance genotyping by deep sequencing

scientific article published on 17 November 2016

Minor protease inhibitor mutations at baseline do not increase the risk for a virological failure in HIV-1 subtype B infected patients

scientific article (publication date: 2012)

Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland

scientific article published in May 2010

Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples

scientific article published on 8 August 2017

Optimized virus disruption improves detection of HIV-1 p24 in particles and uncovers a p24 reactivity in patients with undetectable HIV-1 RNA under long-term HAART.

scientific article published in August 2006

Origin of minority drug-resistant HIV-1 variants in primary HIV-1 infection

scientific article published on 11 July 2013

Parent-offspring regression to estimate the heritability of an HIV-1 trait in a realistic setup

scientific article

Partial rescue of V1V2 mutant infectivity by HIV-1 cell-cell transmission supports the domain's exceptional capacity for sequence variation

scientific article

Performance of Five Different Assays for the Quantification of Viral Load in Persons Infected With Various Subtypes of HIV-1

article published in 2000

Persistence of transmitted HIV-1 drug resistance mutations associated with fitness costs and viral genetic backgrounds

scientific article (publication date: March 2015)

Phylogenetic analysis and reclassification of caprine and ovine lentiviruses based on 104 new isolates: evidence for regular sheep-to-goat transmission and worldwide propagation through livestock trade

scientific article published in February 2004

Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load

scientific article published on 30 September 2010

Polymorphic mutations associated with the emergence of the multinucleoside/tide resistance mutations 69 insertion and Q151M.

scientific article published in February 2012

Positive in vivo selection of the HIV-1 envelope protein gp120 occurs at surface-exposed regions

scientific article published on 5 June 2007

Predictors for the emergence of the 2 multi-nucleoside/nucleotide resistance mutations 69 insertion and Q151M and their impact on clinical outcome in the Swiss HIV cohort study

scientific article published in February 2011

Prevalence of human T-cell leukemia virus types I and II in Switzerland

scientific article published on February 2004

Quality control assessment of human immunodeficiency virus type 2 (HIV-2) viral load quantification assays: results from an international collaboration on HIV-2 infection in 2006.

scientific article published on 23 April 2008

Quantification of HIV-1 p24 by a highly improved ELISA: an alternative to HIV-1 RNA based treatment monitoring in patients from Abidjan, Côte d'Ivoire

scientific article published on 14 September 2006

Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics

scientific article published on 20 February 2018

Replicative phenotyping adds value to genotypic resistance testing in heavily pre-treated HIV-infected individuals--the Swiss HIV Cohort Study

scientific article

Resolution of plasma sample mix-ups through comparison of patient antibody patterns to E. coli

scientific article published on 24 October 2015

Sensitive detection and quantification of particle-associated reverse transcriptase in plasma of HIV-1-infected individuals by the product-enhanced reverse transcriptase (PERT) assay

article

Sensitive detection and quantification of particle‐associated reverse transcriptase in plasma of HIV‐1‐infected individuals by the product‐enhanced reverse transcriptase (PERT) assay

article

Social meets molecular: Combining phylogenetic and latent class analyses to understand HIV-1 transmission in Switzerland

scientific article published on 12 May 2014

Successful Prevention of Transmission of Integrase Resistance in the Swiss HIV Cohort Study

scientific article published on 29 April 2016

The Cumulative Impact of Harm Reduction on the Swiss HIV Epidemic: Cohort Study, Mathematical Model, and Phylogenetic Analysis

article

The individualized genetic barrier predicts treatment response in a large cohort of HIV-1 infected patients

scientific article (publication date: 2013)

The role of migration and domestic transmission in the spread of HIV-1 non-B subtypes in Switzerland

scientific article published in October 2011

Therapeutic Immune Recovery and Reduction of CXCR4-Tropic HIV-1.

scientific article

Tracing HIV-1 strains that imprint broadly neutralizing antibody responses

scientific article published in Nature

Tracing HIV-1 transmission: envelope traits of HIV-1 transmitter and recipient pairs

scientific article published on 05 September 2016

Transmission of HIV-1 drug resistance in Switzerland: a 10-year molecular epidemiology survey

scientific article published in October 2007

Treatment-naive individuals are the major source of transmitted HIV-1 drug resistance in men who have sex with men in the Swiss HIV Cohort Study

scientific article published on 21 October 2013

Ultra-sensitive and specific detection of porcine endogenous retrovirus (PERV) using a sequence-capture real-time PCR approach

scientific article published on May 2003

Use of reverse-transcriptase-based HIV-1 viral load assessment to confirm low viral loads in newly diagnosed patients in Switzerland

scientific article

Viral Suppression Rates in Salvage Treatment With Raltegravir Improved With the Administration of Genotypic Partially Active or Inactive Nucleoside/Tide Reverse Transcriptase Inhibitors

List of works by Jürg Böni

A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland

A Lead-In with Silibinin Prior to Triple-Therapy Translates into Favorable Treatment Outcomes in Difficult-To-Treat HIV/Hepatitis C Coinfected Patients

Adaptation of the ultrasensitive HIV-1 p24 antigen assay to dried blood spot testing

Adherence as a predictor of the development of class-specific resistance mutations: the Swiss HIV Cohort Study

African descent is associated with slower CD4 cell count decline in treatment-naive patients of the Swiss HIV Cohort Study

Ambiguous nucleotide calls from population-based sequencing of HIV-1 are a marker for viral diversity and the age of infection

An international collaboration to standardize HIV-2 viral load assays: results from the 2009 ACHI(E)V(2E) quality control study

Assessing efficacy of different nucleos(t)ide backbones in NNRTI-containing regimens in the Swiss HIV Cohort Study

Assessing predicted HIV-1 replicative capacity in a clinical setting

Assessing the Paradox Between Transmitted and Acquired HIV Type 1 Drug Resistance Mutations in the Swiss HIV Cohort Study From 1998 to 2012.

Assessing the danger of self-sustained HIV epidemics in heterosexuals by population based phylogenetic cluster analysis

CD4 cell count response to first-line combination ART in HIV-2+ patients compared with HIV-1+ patients: a multinational, multicohort European study

Characterization of human immunodeficiency virus type 1 (HIV-1) diversity and tropism in 145 patients with primary HIV-1 infection

Clustering of HCV coinfections on HIV phylogeny indicates domestic and sexual transmission of HCV.

Combined effect of zidovudine (ZDV), lamivudine (3TC) and abacavir (ABC) antiretroviral therapy in suppressing in vitro FIV replication

Comparison of HIV-1 viral load based on RNA or reverse transcriptase activity in patients with suspected viral load underestimation.

Correction to: Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples

Correction: Long-Lasting Protection of Activity of Nucleoside Reverse Transcriptase Inhibitors and Protease Inhibitors (PIs) by Boosted PI Containing Regimens

Detection of low copy numbers of HIV-1 proviral DNA in patient PBMCs by a high-input, sequence-capture PCR (Mega-PCR).

Detection of reverse transcriptase activity in human melanoma cell lines and identification of a murine leukemia virus contaminant.

Determinants of HIV-1 broadly neutralizing antibody induction.

Direct evidence for natural transmission of small-ruminant lentiviruses of subtype A4 from goats to sheep and vice versa

Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T-Cell Decline, and Per-Parasite Pathogenicity

Efficient suppression of minority drug-resistant HIV type 1 (HIV-1) variants present at primary HIV-1 infection by ritonavir-boosted protease inhibitor-containing antiretroviral therapy

Emergence of Acquired HIV-1 Drug Resistance Almost Stopped in Switzerland: A 15-Year Prospective Cohort Analysis

Emergence of HIV-1 drug resistance in previously untreated patients initiating combination antiretroviral treatment: a comparison of different regimen types

Epidemiological and biological evidence for a compensatory effect of connection domain mutation N348I on M184V in HIV-1 reverse transcriptase

Estimating the basic reproductive number from viral sequence data.

Factors associated with the emergence of K65R in patients with HIV-1 infection treated with combination antiretroviral therapy containing tenofovir

Gammaretrovirus-specific antibodies in free-ranging and captive Namibian cheetahs

Generation of a recombinant Gag virus-like-particle panel for the evaluation of p24 antigen detection by diagnostic HIV tests

Genotypic Resistance Tests Sequences Reveal the Role of Marginalized Populations in HIV-1 Transmission in Switzerland

HIV rebounds from latently infected cells, rather than from continuing low-level replication

HIV-1 Transmission During Recent Infection and During Treatment Interruptions as Major Drivers of New Infections in the Swiss HIV Cohort Study

HIV-1 p24 antigen is a significant inverse correlate of CD4 T-cell change in patients with suppressed viremia under long-term antiretroviral therapy

HIV-1 reverse transcriptase connection domain mutations: dynamics of emergence and implications for success of combination antiretroviral therapy

HIV-1 superinfection in an HIV-2-infected woman with subsequent control of HIV-1 plasma viremia

HIV-1 transmission after cessation of early antiretroviral therapy among men having sex with men.

HIV-specific cellular immune response is inversely correlated with disease progression as defined by decline of CD4+ T cells in relation to HIV RNA load

High Frequency of Non-B Subtypes in Newly Diagnosed HIV-1 Infections in Switzerland

Higher risk of incident hepatitis C virus coinfection among men who have sex with men, in whom the HIV genetic bottleneck at transmission was wide

Identification and characterization of two closely related unclassifiable endogenous retroviruses in pythons (Python molurus and Python curtus)

Importance of an Early HIV Antibody Differentiation Immunoassay for Detection of Dual Infection with HIV-1 and HIV-2

Improved virological outcome in White patients infected with HIV-1 non-B subtypes compared to subtype B.

Incidence of HIV-1 Drug Resistance Among Antiretroviral Treatment–Naive Individuals Starting Modern Therapy Combinations ⬇️

Induced prion protein controls immune-activated retroviruses in the mouse spleen

Inferring epidemic contact structure from phylogenetic trees

Inferring the age difference in HIV transmission pairs by applying phylogenetic methods on the HIV transmission network of the Swiss HIV Cohort Study

Lack of evidence for PERV expression after apoptosis-mediated horizontal gene transfer between porcine and human cells

Large-scale inference of conjunctive Bayesian networks

Limited clinical benefit of minority K103N and Y181C-variant detection in addition to routine genotypic resistance testing in antiretroviral therapy-naive patients

Long-lasting protection of activity of nucleoside reverse transcriptase inhibitors and protease inhibitors (PIs) by boosted PI containing regimens

Low human immunodeficiency virus envelope diversity correlates with low in vitro replication capacity and predicts spontaneous control of plasma viremia after treatment interruptions

Metagenomic sequencing complements routine diagnostics in identifying viral pathogens in lung transplant recipients with unknown etiology of respiratory infection

MinVar: A rapid and versatile tool for HIV-1 drug resistance genotyping by deep sequencing

Minor protease inhibitor mutations at baseline do not increase the risk for a virological failure in HIV-1 subtype B infected patients

Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland

Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples

Optimized virus disruption improves detection of HIV-1 p24 in particles and uncovers a p24 reactivity in patients with undetectable HIV-1 RNA under long-term HAART.

Origin of minority drug-resistant HIV-1 variants in primary HIV-1 infection

Parent-offspring regression to estimate the heritability of an HIV-1 trait in a realistic setup

Partial rescue of V1V2 mutant infectivity by HIV-1 cell-cell transmission supports the domain's exceptional capacity for sequence variation

Performance of Five Different Assays for the Quantification of Viral Load in Persons Infected With Various Subtypes of HIV-1

Persistence of transmitted HIV-1 drug resistance mutations associated with fitness costs and viral genetic backgrounds

Phylogenetic analysis and reclassification of caprine and ovine lentiviruses based on 104 new isolates: evidence for regular sheep-to-goat transmission and worldwide propagation through livestock trade

Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load

Polymorphic mutations associated with the emergence of the multinucleoside/tide resistance mutations 69 insertion and Q151M.

Positive in vivo selection of the HIV-1 envelope protein gp120 occurs at surface-exposed regions

Predictors for the emergence of the 2 multi-nucleoside/nucleotide resistance mutations 69 insertion and Q151M and their impact on clinical outcome in the Swiss HIV cohort study

Prevalence of human T-cell leukemia virus types I and II in Switzerland

Quality control assessment of human immunodeficiency virus type 2 (HIV-2) viral load quantification assays: results from an international collaboration on HIV-2 infection in 2006.

Quantification of HIV-1 p24 by a highly improved ELISA: an alternative to HIV-1 RNA based treatment monitoring in patients from Abidjan, Côte d'Ivoire

Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics

Replicative phenotyping adds value to genotypic resistance testing in heavily pre-treated HIV-infected individuals--the Swiss HIV Cohort Study

Resolution of plasma sample mix-ups through comparison of patient antibody patterns to E. coli

Sensitive detection and quantification of particle-associated reverse transcriptase in plasma of HIV-1-infected individuals by the product-enhanced reverse transcriptase (PERT) assay

Sensitive detection and quantification of particle‐associated reverse transcriptase in plasma of HIV‐1‐infected individuals by the product‐enhanced reverse transcriptase (PERT) assay

Social meets molecular: Combining phylogenetic and latent class analyses to understand HIV-1 transmission in Switzerland

Successful Prevention of Transmission of Integrase Resistance in the Swiss HIV Cohort Study