Table 1Currently available techniques to detail and quantify minority quasispecies of HIV-1

MethodAdvantagesDisadvantagesLicensed diagnostic kit availableReference
Direct sequencingComplete genotype;
Detection of unknown mutations;
Easy handling due to available kits;
Extensive experience
Minority quasispecies <20–25% are not detectable;
Inaccurate quantification of minority quasispecies
Yes[44,64]
Allele-specific real-time PCR (AS-PCR)Accurate quantification to levels ≥0.01%Each single mutation requires a separate assay;
Sensitive to polymorphisms;
No detection of unknown mutations;
Expensive;
Labour intensive
No[53,59,61,65]
Heteroduplex tracking assay (HTA)Quantification to levels ≥3–5%;
Simple handling
Inaccurate quantification of minority quasispecies;
Unknown location of mutation;
Sensitive to polymorphisms;
Limited fragment size;
Difficult interpretation
No[66,67]
Line probe assay (LiPA)Quantification to levels ≥4–8%;
Simple handling
Inaccurate quantification of minority quasispecies;
Sensitive to polymorphisms;
No detection of unknown mutations
No[6870]
Oligonucleotide ligase-based assay (OLA)Quantification to levels ≥5%Each single mutation requires a separate assay;
Sensitive to polymorphisms;
No detection of unknown mutations;
Expensive;
Labour intensive
No[71,72]
Single genome sequencingComplete genotypeTime-consuming;
Expensive;
Quantification of minority quasispecies depends on amount of clones analysed
Yes (for sequencing)[73,74]
Ty1/HIV-1 RT hybrid system (TyHRT)Quantification to levels ≥0.5%;
Detection of unknown mutations possible
Limitation to NNRTI-resistant mutations;
Labour intensive
No[75]

RT, reverse transcriptase; NNRTI, non-nucleoside reverse transcriptase inhibitor; Tyl, Saccharomyces cerevisiae retrotransposon Tyl.

From: Chapter 11, The significance of minority drug-resistant quasispecies

Cover of Antiretroviral Resistance in Clinical Practice
Antiretroviral Resistance in Clinical Practice.
Geretti AM, editor.
London: Mediscript; 2006.
Copyright © 2006, Mediscript.

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