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. 2009 Apr;47(4):1238-40.
doi: 10.1128/JCM.02204-08. Epub 2009 Feb 4.

Single-point mutations causing more than 100-fold underestimation of human immunodeficiency virus type 1 (HIV-1) load with the Cobas TaqMan HIV-1 real-time PCR assay

Klaus Korn  1 , Benedikt Weissbrich, Cornelia Henke-Gendo, Albert Heim, Christin Mariel Jauer, Ninon Taylor, Josef Eberle
Affiliations

Single-point mutations causing more than 100-fold underestimation of human immunodeficiency virus type 1 (HIV-1) load with the Cobas TaqMan HIV-1 real-time PCR assay

Klaus Korn et al. J Clin Microbiol. 2009 Apr.

Abstract

Systematic sequence analysis of human immunodeficiency virus type 1 (HIV-1) variants with RNA levels underestimated by the Cobas TaqMan HIV-1 assay demonstrated that mutations at a single position of the downstream primer can lead to the underestimation of HIV-1 RNA levels by more than 2 log and to false-negative results in minipool screening of blood donors. Mutations at this position are found in about 2% of all HIV-1 M gag sequences.

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Figures

FIG. 1.
FIG. 1.
The 157-nucleotide sequence of the CTM HIV-1 amplicon shown corresponds to nucleotides 1359 to 1515 of the HXB2 reference sequence (GenBank accession no. K03455). The localization of the primers and probe of the Cobas Amplicor Monitor HIV-1 v1.5 assay is indicated by the lines above the consensus sequence. The position highlighted in bold in the alignment corresponds to nucleotide 1488.
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References

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