Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted Human Immunodeficiency Virus Type 1 Drug Resistance in a Large US Clinic Population.

Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America
Soo-Yon RheeRobert W Shafer

Abstract

There are few large studies of transmitted drug resistance (TDR) prevalence and the drug resistance mutations (DRMs) responsible for TDR in the United States. Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) and protease sequences were obtained from 4253 antiretroviral therapy (ART)-naive individuals in a California clinic population from 2003 to 2016. Phylogenetic analyses were performed to study linkages between TDR strains and selection pressure on TDR-associated DRMs. From 2003 to 2016, there was a significant increase in overall (odds ratio [OR], 1.05 per year [95% confidence interval {CI}, 1.03-1.08]; P < .001) and nonnucleoside RT inhibitor (NNRTI)-associated TDR (OR, 1.11 per year [95% CI, 1.08-1.15]; P < .001). Between 2012 and 2016, TDR rates to any drug class ranged from 15.7% to 19.2%, and class-specific rates ranged from 10.0% to 12.8% for NNRTIs, 4.1% to 8.1% for nucleoside RT inhibitors (NRTIs), and 3.6% to 5.2% for protease inhibitors. The thymidine analogue mutations, M184V/I and the tenofovir-associated DRMs K65R and K70E/Q/G/N/T accounted for 82.9%, 7.3%, and 1.4% of NRTI-associated TDR, respectively. Thirty-seven percent of TDR strains clustered with other TDR strains sharing the same D...Continue Reading

References

Jun 28, 2003·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Martin S HirschDouglas D Richman
Feb 11, 2005·Molecular Biology and Evolution·Sergei L Kosakovsky Pond, Simon D W Frost
Oct 6, 2005·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Paul E SaxKenneth A Freedberg
Nov 13, 2007·BMC Evolutionary Biology·Alexei J Drummond, Andrew Rambaut
Apr 17, 2010·AIDS·William H WheelerUNKNOWN Variant, Atypical, and Resistant HIV Surveillance Group
Jan 12, 2011·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Roger D KouyosUNKNOWN Swiss HIV Cohort Study
Apr 1, 2011·The Journal of Infectious Diseases·Vivek JainFrederick M Hecht
Sep 1, 2011·AIDS Research and Human Retroviruses·Toshibumi TaniguchiEdgar Turner Overton
Apr 16, 2013·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Emmi AnderssonMichael R Jordan
Aug 2, 2013·The Journal of Infectious Diseases·Hannah CastroUNKNOWN UK Collaborative Group on HIV Drug Resistance
Oct 23, 2013·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Sara M DrescherUNKNOWN Swiss HIV Cohort Study
Nov 7, 2013·BMC Bioinformatics·Manon Ragonnet-CroninUNKNOWN UK HIV Drug Resistance Database
Jan 17, 2014·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Christina GagliardoNatalie Neu
Nov 6, 2014·Molecular Biology and Evolution·Lam-Tung NguyenBui Quang Minh
Mar 24, 2015·PLoS Pathogens·Wan-Lin YangUNKNOWN Swiss HIV Cohort Study (SHCS)
Sep 12, 2015·AIDS·Raphaël MouradUNKNOWN UK HIV Drug Resistance Database & the Collaborative HIV, Anti-HIV Drug Resistance Network
Sep 29, 2015·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Theppharit PanichsillapakitSanjay R Mehta
Jun 17, 2016·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Seble G KassayeFrank Maldarelli
Sep 20, 2016·Scientific Reports·Manon L Ragonnet-CroninAndrew J Leigh Brown
Jun 28, 2017·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·G RocheleauP R Harrigan
Sep 13, 2017·BMC Research Notes·Annette M AldousUNKNOWN DC Cohort Executive Committee

❮ Previous
Next ❯

Citations

Oct 12, 2018·Journal of Clinical Microbiology·Ronit R DalmatAlexander L Greninger
Oct 22, 2019·AIDS·Jessica M FogelSusan H Eshleman
Nov 28, 2019·Expert Review of Clinical Pharmacology·Mary Clare MastersSusan E Cohn
Apr 18, 2020·American Journal of Transplantation : Official Journal of the American Society of Transplantation and the American Society of Transplant Surgeons·Marion Hemmersbach-MillerCameron R Wolfe
Oct 15, 2019·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Sara LodiMiguel A Hernán
May 6, 2019·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Emily P HyleRochelle P Walensky
Jun 7, 2019·AIDS Research and Human Retroviruses·Ron M KaganHarvey W Kaufman
Feb 17, 2021·International Journal of Infectious Diseases : IJID : Official Publication of the International Society for Infectious Diseases·Maria KantzanouAntigoni Katsoulidou
Apr 8, 2021·Current Infectious Disease Reports·Sarah M MichienziMelissa E Badowski
Sep 28, 2021·Antimicrobial Agents and Chemotherapy·Ernest Asante-AppiahJay A Grobler
Jun 28, 2021·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·R Paul McClungAngela L Hernandez
Aug 29, 2021·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·William A WerbelUNKNOWN HOPE in Action Investigators

❮ Previous
Next ❯

Software Mentioned

HyPhy
IQTREE
BEAST
FigTree
Tracer
BEAST ( Bayesian Evolutionary Analysis Sampling Trees )
ClusterPicker

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.