Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences

Tzou, P. L.; Kosakovsky Pond, S. L.; Avila-Rios, S.; Holmes, S. P.; Kantor, R.; Shafer, R. W.

doi:10.1101/831685

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bioRxiv · 10.1101/831685

Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences

Tzou, P. L.·Kosakovsky Pond, S. L.·Avila-Rios, S.·Holmes, S. P.·Kantor, R.·Shafer, R. W.

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Abstract

IntroductionAt low mutation-detection thresholds, next generation sequencing (NGS) for HIV-1 genotypic resistance testing is susceptible to artifactual detection of mutations arising from PCR error and APOBEC-mediated G-to-A hypermutation.\n\nMethodsWe analyzed published HIV-1 pol Illumina NGS data to characterize the distribution of mutations at eight NGS thresholds: 20%, 10%, 5%, 2%, 1%, 0.5%, 0.2%, and 0.1%. At each threshold, we determined the proportion of amino acid mutations that were unusual (defined as having a prevalence <0.01% in HIV-1 group M sequences) or were signature APOBEC mutations.\n\nResultsEight studies, containing 855 samples, in the NCBI Sequence Read Archive were analyzed. As detection thresholds were lowered, there was a progressive increase in the proportion of positions with both usual and unusual mutations and in the proportion of all mutations that were unusual. The median proportion of positions with an unusual mutation increased gradually from 0% at the 20% threshold to 0.3% at the 1% threshold and then exponentially to 1.3% (0.5% threshold), 6.9% (0.2% threshold), and 23.2% (0.1% threshold). In two of three studies with available plasma HIV-1 RNA levels, the proportion of positions with unusual mutations was negatively associated with virus levels. Although the complete set of signature APOBEC mutations was much smaller than that of unusual mutations, the former outnumbered the latter in one-sixth of the samples at the 0.5%, 1%, and 2% thresholds.\n\nConclusionsThe marked increase in the proportion of positions with unusual mutations at thresholds below 1% and in samples with lower virus loads suggests that, at low thresholds, many unusual mutations are artifactual, reflecting PCR error or G-to-A hypermutation. Profiling the numbers of unusual and signature APOBEC pol mutations at different NGS thresholds may be useful to avoid selecting a threshold that is too low and poses an unacceptable risk of identifying artifactual mutations.

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Tzou, P. L., Kosakovsky Pond, S. L., Avila-Rios, S., Holmes, S. P., Kantor, R., Shafer, R. W.. 2019-11-05. Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences. https://doi.org/10.1101/831685

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