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

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Viral Mutations00:36

Viral Mutations

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 for adaptive...
Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...

You might also read

Related Articles

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

Sort by
Same author

Pervasive HIV recombination limits the utility of circulating recombinant form nomenclature.

PLoS pathogens·2026
Same author

Carbapenem-resistant Enterobacterales across the UK: a nationwide study of carbapenemase testing and novel antimicrobial activity.

International journal of antimicrobial agents·2026
Same author

<i>ATG16L1</i> and <i>OPTN</i> as a novel prognostic gene expression signature in acute myeloid leukemia survival.

Frontiers in oncology·2026
Same author

A comparison of methods for the optimal recovery of the human fecal virome.

ISME communications·2026
Same author

Leveraging generative AI to transform statistical analysis plan authoring in clinical trials.

Clinical trials (London, England)·2026
Same author

Homologous recombination deficiency and hemizygosity drive resistance in breast cancer.

Nature·2026

Related Experiment Video

Updated: Jun 18, 2026

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

An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1.

Sergei L Kosakovsky Pond1, David Posada, Eric Stawiski

  • 1Department of Medicine, University of California San Diego, La Jolla, California, USA. spond@ucsd.edu

Plos Computational Biology
|December 4, 2009
PubMed
Summary

Accurate subtype classification of Human Immunodeficiency virus type 1 (HIV-1) is crucial for surveillance and treatment. A new phylogenetic method, SCUEAL, accurately identifies HIV-1 subtypes and recombinant strains, improving upon existing approaches.

More Related Videos

An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings
19:57

An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings

Published on: March 30, 2014

Prediction of HIV-1 Coreceptor Usage (Tropism) by Sequence Analysis using a Genotypic Approach
07:06

Prediction of HIV-1 Coreceptor Usage (Tropism) by Sequence Analysis using a Genotypic Approach

Published on: December 1, 2011

Related Experiment Videos

Last Updated: Jun 18, 2026

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

An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings
19:57

An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings

Published on: March 30, 2014

Prediction of HIV-1 Coreceptor Usage (Tropism) by Sequence Analysis using a Genotypic Approach
07:06

Prediction of HIV-1 Coreceptor Usage (Tropism) by Sequence Analysis using a Genotypic Approach

Published on: December 1, 2011

Area of Science:

  • * Virology
  • * Bioinformatics
  • * Evolutionary Biology

Background:

  • * Genetically diverse pathogens like Human Immunodeficiency virus type 1 (HIV-1) require subtype classification for surveillance and epidemiological analysis.
  • * Existing computational methods for HIV-1 subtyping have limitations, with no universally optimal approach.
  • * Accurate subtyping is increasingly important for studies on treatment, clinical outcomes, pathogenicity, and vaccine design.

Purpose of the Study:

  • * To present a model-based phylogenetic method for automatic subtyping of viral and bacterial sequences, including Human Immunodeficiency virus type 1 (HIV-1).
  • * To develop a procedure that maps breakpoints and assigns parental sequences in recombinant strains, with confidence levels.
  • * To provide a robust and accurate tool that complements existing subtyping methods.

Main Methods:

  • * Development of the Subtype Classification Using Evolutionary ALgorithms (SCUEAL) procedure, a model-based phylogenetic method.
  • * Application of SCUEAL to Human Immunodeficiency virus type 1 (HIV-1) polymerase (pol) sequences from the Stanford Drug Resistance and UK HIV Drug Resistance databases.
  • * Evaluation of SCUEAL's performance in simulation scenarios and comparison with existing approaches on empirical data.

Main Results:

  • * SCUEAL demonstrated high performance in simulations and matched or exceeded existing methods on empirical cases.
  • * Analysis revealed that approximately 5% of previously classified pure subtype Human Immunodeficiency virus type 1 (HIV-1) sequences may be recombinants.
  • * SCUEAL accurately identifies breakpoints and parental sequences in recombinant strains, providing confidence levels.

Conclusions:

  • * The SCUEAL procedure offers an accurate, robust, and extensible method for automatic viral and bacterial sequence subtyping.
  • * The method is particularly useful for accurate classification of unknown strains and detecting recombinant forms.
  • * SCUEAL is freely available as a module for the HyPhy package and the Datamonkey web server, facilitating its use in research and surveillance.