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Updated: Mar 31, 2026

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

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.

Journal of Biomedical Informatics

|October 24, 2015

Summary

This summary is machine-generated.

APOBEC3 editing enzymes cause G-to-A hypermutation in viral genomes. Insertions/deletions (indels) disrupt sequence alignment, leading to misidentification of APOBEC3 targets and flawed biological conclusions.

Keywords:

APOBEC3 Alignment Hypermutation Indels (insertions/deletions)Viral sequences

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Last Updated: Mar 31, 2026

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Area of Science:

Genetics
Molecular Biology
Virology

Background:

The APOBEC3 (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like3) family comprises human editing enzymes.
These enzymes induce G-to-A changes, termed "hypermutation," in viral genomes like HIV, SIV, HBV, and endogenous retroviruses.

Purpose of the Study:

To investigate the impact of sequence variations on APOBEC3 hypermutation analysis.
To identify potential sources of error in identifying APOBEC3-targeted sites.

Main Methods:

Sequence alignment analysis.
Evaluation of APOBEC3 editing patterns in the presence of indels.

Main Results:

Insertions/deletions (indels) in sequences lead to incorrect assignment of APOBEC3 targeted and non-target sites.
This misassignment can result in the incorrect identification of hypermutated sequences.

Conclusions:

Indels pose a significant challenge to accurate APOBEC3 hypermutation analysis.
Erroneous biological inferences can arise from hypermutation data affected by indels, necessitating careful sequence analysis.