So far, the sequence diversity of H1N1 2009 influenza virus has been rather limited. From our analysis, it would be possible to resequence all the published isolates using this resequencing approach. However, as antigenic drift is expected to occur, it is likely that the resequencing array would need to be updated at least annually. Updating the array requires only bioinformatics input, and does not require any other additional manufacturing costs. Thus, this combination of sample amplification primers, low-cost multiplex array and robust interpretation software allows sustainable, rapid, large-scale biosurveillance of the influenza H1N1(2009) virus.