Related Experiment Video
Updated: Mar 31, 2026

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
Published on: June 16, 2011
A method to avoid errors associated with the analysis of hypermutated viral sequences by alignment-based methods
Hamid Alinejad-Rokny1, Diako Ebrahimi2
1Infection Analytics, Kirby Institute, UNSW Australia, Sydney, Australia.
Abstract:
The human genome encodes for a family of editing enzymes known as APOBEC3 (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like3). They induce context dependent G-to-A changes, referred to as "hypermutation", in the genome of viruses such as HIV, SIV, HBV and endogenous retroviruses. Hypermutation is characterized by aligning affected sequences to a reference sequence. We show that indels (insertions/deletions) in the sequences lead to an incorrect assignment of APOBEC3 targeted and non-target sites. This can result in an incorrect identification of hypermutated sequences and erroneous biological inferences made based on hypermutation analysis.
Related Concept Videos
Viral Mutations
Mismatch Repair
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
Mismatch Repair
Evolutionary Relationships through Genome Comparisons

