Illumina sequencing of HIV-1 plasmids to assess measurement error

Next-generation deep sequencing of viral genomes, particularly on the Illumina platform, is routinely applied in HIV research. Yet, there is no standard protocol or method used by the research community to account for measurement errors that arise during sample preparation and sequencing. To study measurement error in variant calling in the pol region, we sequenced mixtures of plasmids pNL4.3 (AF324493.2) and p89.6 (U39362) in 1:1 and 1:9 proportions on the Illumina MiSeq platform.