Related Experiment Video
Updated: Dec 5, 2025

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
Published on: October 16, 2018
Viral variant visualizer (VVV): A novel bioinformatic tool for rapid and simple visualization of viral genetic
Alexandre Flageul1, Pierrick Lucas2, Edouard Hirchaud2
1Agence National de Sécurité Sanitaire, de l'environnement et du travail (ANSES) Laboratory of Ploufragan-Plouzané-Niort, Virology, Immunology and Parasitology in Poultry and Rabbit (VIPAC) Unit, Université Bretagne Loire (UBL), France.
Abstract:
Here a bioinformatic pipeline VVV has been developed to analyse viral populations in a given sample from Next Generation Sequencing (NGS) data. To date, handling large amounts of data from NGS requires the expertise of bioinformaticians, both for data processing and result analysis. Consequently, VVV was designed to help non-bioinformaticians to perform these tasks. By providing only the NGS data file, the developed pipeline generated consensus sequences and determined the composition of the viral population for an avian Metapneumovirus (AMPV) and three different animal coronaviruses (Porcine Epidemic Diarrhea Virus (PEDV), Turkey Coronavirus (TCoV) and Infectious Bronchitis Virus (IBV)). In all cases, the pipeline produced viral consensus genomes corresponding to known consensus sequence and made it possible to highlight the presence of viral genetic variants through a single graphic representation. The method was validated by comparing the viral populations of an AMPV field sample, and of a copy of this virus produced from a DNA clone. VVV demonstrated that the cloned virus population was homogeneous (as designed) at position 2934 where the wild-type virus demonstrated two variant populations at a ratio of almost 50:50. A total of 18, 10, 3 and 28, viral genetic variants were detected for AMPV, PEDV, TCoV and IBV respectively. The simplicity of this pipeline makes the study of viral genetic variants more accessible to a wide variety of biologists, which should ultimately increase the rate of understanding of the mechanisms of viral genetic evolution.
More Related Videos
Related Concept Videos
Size and Structure of Viral Genomes
Viral Mutations
Genetic Variation
Genes exist in different versions called alleles,...
Viral Recombination
Viruses with RNA Genomes
Comparing Copy Number Variations and SNPs
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

