Quantifying the limits of accurate and reproducible SNP frequency estimates for influenza within-host sequencing. Influenza A virus (A/California/04/2009(H1N1))

Clinical viral isolates often contain very low genome copy numbers. To interrogate the limitations that viral copy number places on the ability to accurately and reproducibly quantify variants, we generated a dilution series of a 2009 pandemic influenza virus ranging from 102 to 107 DNA copies and sequenced the HA gene in triplicate on an Illumina MiSeq.