Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Size and Structure of Viral Genomes01:26

Size and Structure of Viral Genomes

1.0K
Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
1.0K
Retrovirus Life Cycles01:10

Retrovirus Life Cycles

50.5K
Retroviruses have a single-stranded RNA genome that undergoes a special form of replication. Once the retrovirus has entered the host cell, an enzyme called reverse transcriptase synthesizes double-stranded DNA from the retroviral RNA genome. This DNA copy of the genome is then integrated into the host’s genome inside the nucleus via an enzyme called integrase. Consequently, the retroviral genome is transcribed into RNA whenever the host’s genome is transcribed, allowing the...
50.5K
Viral Mutations00:36

Viral Mutations

40.7K
A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
40.7K
Retroviruses02:33

Retroviruses

15.7K
Retroviruses and retrotransposons both insert copies of their genetic elements into the genome of the host cell. Thus, the viral genes are passed on when the host genome is replicated or translated. A typical retroviral DNA sequence contains 3-4 genes that encode the different proteins required for its structural assembly and function as a molecular parasite. This DNA is transcribed into a single mRNA, which is very similar in structure to conventional mRNAs, i.e., it is capped at the 5’...
15.7K
Viruses with RNA Genomes01:29

Viruses with RNA Genomes

1.2K
RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
1.2K
LTR Retrotransposons03:08

LTR Retrotransposons

20.4K
LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
20.4K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Estimation of Prevention-Effective CAB-LA Concentrations Among Men Who Have Sex With Men (MSM) and Transgender Women (TGW) in HPTN 083.

The Journal of infectious diseases·2025
Same author

Fixed dosing versus weight-based dosing of HIV-1 prophylactic monoclonal antibodies in adults: a post-hoc, cross-protocol pharmacokinetics modelling study.

EBioMedicine·2025
Same author

Multilevel Intervention to Support Tailored and Responsive HIV Pre-Exposure Prophylaxis Care in Rural North Carolina: Protocol for a Randomized Controlled Trial.

JMIR research protocols·2025
Same author

Pharmacokinetic interaction assessment of an HIV broadly neutralizing monoclonal antibody VRC07-523LS: a cross-protocol analysis of three phase 1 trials in people without HIV.

BMC immunology·2025
Same author

Prevalence and Correlates of Hepatitis C Viremia Among People With Human Immunodeficiency Virus in the Direct-Acting Antiviral Era.

Open forum infectious diseases·2025
Same author

Safety, tolerability, pharmacokinetics, and neutralisation activities of the anti-HIV-1 monoclonal antibody PGT121.414.LS administered alone and in combination with VRC07-523LS in adults without HIV in the USA (HVTN 136/HPTN 092): a first-in-human, open-label, randomised controlled phase 1 trial.

The lancet. HIV·2024
Same journal

Something old, something new? Herpesvirus genome packaging examined in light of lessons from the tailed bacteriophages.

Journal of virology·2026
Same journal

Receptor profiling and growth assessment of influenza A virus in porcine mammary and non-mammary tissues and derived cells.

Journal of virology·2026
Same journal

Live human metapneumovirus vaccine candidates attenuated by temperature sensitivity mutations from human respiratory syncytial virus.

Journal of virology·2026
Same journal

Structure and functional analyses of vaccinia virus J5 protein reveal distinct determinants for entry-fusion complex assembly and activation.

Journal of virology·2026
Same journal

Coronavirus membrane protein with a fluorescent protein tag enables particle tracking for the study of virus assembly and egress in live cells.

Journal of virology·2026
Same journal

Disruption of the S1/S2 multibasic cleavage site attenuates infectious bronchitis virus, while S2' partially restores viral virulence and expands tissue tropism.

Journal of virology·2026
See all related articles

Related Experiment Video

Updated: Mar 22, 2026

Rapid Screening of HIV Reverse Transcriptase and Integrase Inhibitors
05:46

Rapid Screening of HIV Reverse Transcriptase and Integrase Inhibitors

Published on: April 9, 2014

18.5K

HIV-1 Protease, Reverse Transcriptase, and Integrase Variation.

Soo-Yon Rhee1, Kris Sankaran2, Vici Varghese3

  • 1Department of Medicine, Stanford University, Stanford, California, USA syrhee@stanford.edu.

Journal of Virology
|April 22, 2016
PubMed
Summary
This summary is machine-generated.

Characterizing HIV-1 protease, reverse transcriptase, and integrase variability is crucial for genotypic resistance testing. Understanding mutation prevalence and origins aids in quality control for dried blood spot and next-generation sequencing.

More Related Videos

Measurement of In Vitro Integration Activity of HIV-1 Preintegration Complexes
10:34

Measurement of In Vitro Integration Activity of HIV-1 Preintegration Complexes

Published on: February 22, 2017

8.1K
Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
10:18

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

12.8K

Related Experiment Videos

Last Updated: Mar 22, 2026

Rapid Screening of HIV Reverse Transcriptase and Integrase Inhibitors
05:46

Rapid Screening of HIV Reverse Transcriptase and Integrase Inhibitors

Published on: April 9, 2014

18.5K
Measurement of In Vitro Integration Activity of HIV-1 Preintegration Complexes
10:34

Measurement of In Vitro Integration Activity of HIV-1 Preintegration Complexes

Published on: February 22, 2017

8.1K
Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
10:18

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

12.8K

Area of Science:

  • Virology
  • Genetics
  • Molecular Biology

Background:

  • HIV-1 drug resistance testing relies on sequencing key viral proteins: protease (PR), reverse transcriptase (RT), and integrase (IN).
  • High variability in these proteins, influenced by drug pressure, APOBEC editing, and natural mutation, complicates accurate resistance profiling.
  • Emerging sequencing methods like next-generation sequencing (NGS) and analysis of proviral DNA (e.g., dried blood spots) necessitate a deeper understanding of HIV-1 variant prevalence.

Purpose of the Study:

  • To comprehensively characterize amino acid variation across HIV-1 PR, RT, and IN.
  • To identify and differentiate mutations arising from APOBEC-mediated G-to-A editing, drug selection pressure, and natural variation.
  • To provide essential data for improving the quality control of genotypic resistance testing, particularly with advanced sequencing technologies.

Main Methods:

  • Analysis of PR and RT sequences from over 100,000 individuals and IN sequences from over 10,000 individuals.
  • Quantification of amino acid variant prevalence at each position within PR, RT, and IN.
  • Classification of variants based on potential origins: APOBEC editing, drug selection, or natural polymorphism.

Main Results:

  • A significant proportion of amino acid positions in PR, RT, and IN exhibit common variants (≥1% prevalence) and rare variants (≥0.1% prevalence).
  • The majority of variants showed low inter-subtype prevalence ratios, suggesting limited widespread dominance.
  • Distinct sets of mutations were identified as indicative of APOBEC-mediated G-to-A editing (209 mutations) and non-polymorphic treatment selection (326 mutations).

Conclusions:

  • The study provides a detailed landscape of HIV-1 PR, RT, and IN variation, essential for interpreting genotypic resistance tests.
  • Identifying APOBEC-associated mutations aids in quality control for dried blood spot sequencing.
  • Characterizing rare mutations is critical for enhancing the reliability of next-generation sequencing-based HIV-1 variant detection.