The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002–2020)

Phylogenetic Clustering among Asylum Seekers with New HIV-1 Diagnoses in Montreal, QC, Canada

(2021) Hyejin Park et al.   Viruses-Basel

Longitudinal typing of molecular HIV clusters in a statewide epidemic

(2021) Vlad Novitsky et al.   AIDS

Human Immunodeficiency Virus (HIV) Genetic Diversity Informs Stage of HIV-1 Infection Among Patients Receiving Antiretroviral Therapy in Botswana

(2021) Manon Ragonnet-Cronin et al.   JOURNAL OF INFECTIOUS DISEASES

Phylogenetic Networks and Parameters Inferred from HIV Nucleotide Sequences of High-Risk and General Population Groups in Uganda: Implications for Epidemic Control

(2021) Nicholas Bbosa et al.   Viruses-Basel

The Role of Phylogenetics in Discerning HIV-1 Mixing among Vulnerable Populations and Geographic Regions in Sub-Saharan Africa: A Systematic Review

(2021) George M. Nduva et al.   Viruses-Basel

Characterization of Molecular Cluster Detection and Evaluation of Cluster Investigation Criteria Using Machine Learning Methods and Statewide Surveillance Data in Washington State

(2020) Steven J. Erly et al.   Viruses-Basel

Phylodynamic Analysis Complements Partner Services by Identifying Acute and Unreported HIV Transmission

(2020) Ellsworth M. Campbell et al.   Viruses-Basel

Antiretroviral Drugs for Treatment and Prevention of HIV Infection in Adults

(2020) Michael S. Saag et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Assessing the role of transmission chains in the spread of HIV-1 among men who have sex with men in Quebec, Canada

(2019) Luc Villandré et al.   PLoS One

Cohort profile: l’Actuel Pre-Exposure Prophylaxis (PrEP) Cohort study in Montreal, Canada

(2019) Zoë R Greenwald et al.   BMJ Open

Global, regional and country-level 90–90–90 estimates for 2018

(2019) Kimberly Marsh et al.   AIDS

Natural selection favoring more transmissible HIV detected in United States molecular transmission network

(2019) Joel O. Wertheim et al.   Nature Communications

Substantial heterogeneity in progress towards reaching the 90-90-90 HIV target in the WHO European Region

(2018) Kholoud Porter et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Growth of HIV-1 Molecular Transmission Clusters in New York City

(2018) Joel O Wertheim et al.   JOURNAL OF INFECTIOUS DISEASES

HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens

(2018) Sergei L Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

(2018) Luc Villandré et al.   BMC BIOINFORMATICS

Identifying Clusters of Recent and Rapid HIV Transmission Through Analysis of Molecular Surveillance Data

(2018) Alexandra M. Oster et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

HIV-1 strains belonging to large phylogenetic clusters show accelerated escape from integrase inhibitors in cell culture compared with viral isolates from singleton/small clusters

(2017) Bluma G. Brenner et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Genotypic and Phylogenetic Insights on Prevention of the Spread of HIV-1 and Drug Resistance in “Real-World” Settings

(2017) Bluma Brenner et al.   Viruses-Basel

Assessment of Overlap of Phylogenetic Transmission Clusters and Communities in Simple Sexual Contact Networks: Applications to HIV-1

(2016) Luc Villandre et al.   PLoS One

Characteristics and spread to the native population of HIV-1 non-B subtypes in two European countries with high migration rate

(2015) Kenny Dauwe et al.   BMC INFECTIOUS DISEASES

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

(2015) Alex Marzel et al.   CLINICAL INFECTIOUS DISEASES

Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis

(2015) Daniela Bezemer et al.   PLOS MEDICINE

A Significant Reduction in the Frequency of HIV-1 Drug Resistance in Québec from 2001 to 2011 Is Associated with a Decrease in the Monitored Viral Load

(2014) Hugues Charest et al.   PLoS One

Phylogenetic inferences on HIV-1 transmission

(2013) Bluma Brenner et al.   AIDS

The increase in global HIV epidemics in MSM

(2013) Chris Beyrer et al.   AIDS

Evaluation of sequence ambiguities of the HIV-1 pol gene as a method to identify recent HIV-1 infection in transmitted drug resistance surveys

(2013) Emmi Andersson et al.   INFECTION GENETICS AND EVOLUTION

Future of Phylogeny in HIV Prevention

(2013) Bluma G. Brenner et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Genetic Diversity as a Marker for Timing Infection in HIV-Infected Patients: Evaluation of a 6-Month Window and Comparison With BED

(2012) Manon Ragonnet-Cronin et al.   JOURNAL OF INFECTIOUS DISEASES

Extended high viremics

(2011) Vladimir Novitsky et al.   AIDS

Ambiguous Nucleotide Calls From Population-based Sequencing of HIV-1 are a Marker for Viral Diversity and the Age of Infection

(2011) Roger D. Kouyos et al.   CLINICAL INFECTIOUS DISEASES

Transmission Clustering Drives the Onward Spread of the HIV Epidemic Among Men Who Have Sex With Men in Quebec

(2011) Bluma G. Brenner et al.   JOURNAL OF INFECTIOUS DISEASES

The Role of Migration and Domestic Transmission in the Spread of HIV-1 Non-B Subtypes in Switzerland

(2011) Viktor von Wyl et al.   JOURNAL OF INFECTIOUS DISEASES

Tracing the HIV-1 subtype B mobility in Europe: a phylogeographic approach

(2009) Dimitrios Paraskevis et al.   Retrovirology

Transmission networks of drug resistance acquired in primary/early stage HIV infection

(2008) Bluma G Brenner et al.   AIDS