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

Retrovirus Life Cycles01:10

Retrovirus Life Cycles

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 retrovirus to...
Size and Structure of Viral Genomes01:26

Size and Structure of Viral Genomes

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...
Chromosomal Theory of Inheritance01:39

Chromosomal Theory of Inheritance

In 1866, Gregor Mendel published the results of his pea plant breeding experiments, providing evidence for predictable patterns in the inheritance of physical characteristics. The significance of his findings was not immediately recognized. In fact, the existence of genes was unknown at the time. Mendel referred to hereditary units as “factors.”
Hardy-Weinberg Principle01:49

Hardy-Weinberg Principle

Diploid organisms have two alleles of each gene, one from each parent, in their somatic cells. Therefore, each individual contributes two alleles to the gene pool of the population. The gene pool of a population is the sum of every allele of all genes within that population and has some degree of variation. Genetic variation is typically expressed as a relative frequency, which is the percentage of the total population that has a given allele, genotype or phenotype.In the early 20th century,...
Retroviruses02:33

Retroviruses

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’...
Viral Recombination00:57

Viral Recombination

Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.

You might also read

Related Articles

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

Sort by
Same author

Genotypic challenges in implementing broadly neutralizing antibody-based long-acting HIV-1 therapies.

Communications medicine·2026
Same author

Accurate <i>ab initio</i> gene prediction in eukaryotes with Tiberius in multiple clades.

bioRxiv : the preprint server for biology·2026
Same author

Induction of broadly neutralizing HIV antibodies by a two-step mechanism informs vaccine design.

Science (New York, N.Y.)·2026
Same author

Oropouche virus: transmission, epidemiology, genetic diversity, and public health implications.

EClinicalMedicine·2026
Same author

Contemporary HIV-1 envelope pseudovirus panels for detecting and assessing B cell lineages with broadly neutralizing antibody potential.

PLoS pathogens·2026
Same author

Identification and genomic characterization of BA.3.2: a highly divergent BA.3-related SARS-CoV-2 lineage from southern Africa.

Virus evolution·2026
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
Same journal

EDEL: Enhancing Dense Retrievers for Curation of Biomedical Knowledge Bases.

Bioinformatics (Oxford, England)·2026
Same journal

Informative Relational Learning for Adverse Reaction Prediction with Enhanced Generalization to Novel Drugs.

Bioinformatics (Oxford, England)·2026
Same journal

An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.

Bioinformatics (Oxford, England)·2026
Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Jun 13, 2026

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
11:10

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Published on: December 27, 2010

HIV classification using the coalescent theory.

Ingo Bulla1, Anne-Kathrin Schultz, Fabian Schreiber

  • 1Abteilung Bioinformatik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Goldschmidtstrasse 1, 37077 Göttingen, Germany. ibulla@uni-goettingen.de

Bioinformatics (Oxford, England)
|April 20, 2010
PubMed
Summary
This summary is machine-generated.

A new program, ARGUS, can now accurately classify human immunodeficiency virus (HIV) sequences, including complex recombinant forms. This tool reconstructs ancestral recombination graphs (ARGs) to resolve subtype and circulating recombinant form (CRF) classifications, improving upon existing methods.

More Related Videos

A Restriction Enzyme Based Cloning Method to Assess the In vitro Replication Capacity of HIV-1 Subtype C Gag-MJ4 Chimeric Viruses
14:23

A Restriction Enzyme Based Cloning Method to Assess the In vitro Replication Capacity of HIV-1 Subtype C Gag-MJ4 Chimeric Viruses

Published on: August 31, 2014

Related Experiment Videos

Last Updated: Jun 13, 2026

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
11:10

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Published on: December 27, 2010

A Restriction Enzyme Based Cloning Method to Assess the In vitro Replication Capacity of HIV-1 Subtype C Gag-MJ4 Chimeric Viruses
14:23

A Restriction Enzyme Based Cloning Method to Assess the In vitro Replication Capacity of HIV-1 Subtype C Gag-MJ4 Chimeric Viruses

Published on: August 31, 2014

Area of Science:

  • Virology
  • Computational Biology
  • Genetics

Background:

  • Existing phylogenetic tools struggle with human immunodeficiency virus (HIV) sequence genealogy due to frequent recombination.
  • Ad hoc methods are currently used for classifying HIV subtypes and circulating recombinant forms (CRFs) owing to a lack of comprehensive models.
  • Complex recombination patterns in HIV necessitate advanced computational approaches for accurate sequence classification.

Purpose of the Study:

  • To develop a computational tool for accurate classification of HIV sequences, including complex recombinant forms.
  • To reconstruct ancestral recombination graphs (ARGs) that reflect the genealogy of HIV sequences.
  • To address ambiguities in HIV subtype and CRF classification.

Main Methods:

  • Developed ARGUS, a program that scores sequence classifications and reconstructs ancestral recombination graphs (ARGs).
  • Employed a Markov chain Monte Carlo approach to approximate the maximal probability ARG.
  • Utilized simulation studies with realistic parameters to evaluate ARGUS's performance.

Main Results:

  • ARGUS accurately distinguishes correct HIV sequence classifications from plausible alternatives with a low error rate.
  • The program successfully reconstructed ARGs reflecting sequence genealogy under various classification hypotheses.
  • Applied to CRF02 of HIV-1, ARGUS confirmed it as a recombinant of Subtypes A and G.

Conclusions:

  • ARGUS provides a robust computational solution for classifying complex HIV sequences and their genealogies.
  • The tool enhances the accuracy of HIV subtype and CRF determination, overcoming limitations of existing methods.
  • ARGUS's application to CRF02 provides definitive evidence for its recombinant origin from Subtypes A and G.