Large-scale evolutionary surveillance of the 2009 H1N1 influenza A virus using resequencing arrays

Lee, Charlie Wah Heng; Koh, Chee Wee; Chan, Yang Sun; Aw, Pauline Poh Kim; Loh, Kuan Hon; Han, Bing Ling; Thien, Pei Ling; Nai, Geraldine Yi Wen; Hibberd, Martin L.; Wong, Christopher W.; Sung, Wing-Kin

Besides a FASTA output of the virus sequence, EvolSTAR generates a visualization map of the sequence calls using a heat map based on the percentage identity of the called sequence to the reference sequence measured at 50 bp windows (Figure 8 ). The map template consists of all eight segments of the 2009 influenza A(H1N1) virus and the locations of known drug binding sites (marked with green lines) on the NA gene. Locations of all mutation calls are denoted by red triangles beneath the heat map bar. Sequences that are of low coverage (<90%) are automatically flagged, and the overall PM/ MM discrimination ratio for each segment is displayed. The heat map bar allows the technician to rapidly assess the quality of the sequence data obtained from the microarray and identify regions where PCR did not work well, or presence of potential recombination/ reassortment events. Mutations, especially those in close proximity to drug binding sites, can be quickly visualized. Other details such as coverage, number of base calls successfully made, number of mutations and number of 'N' calls for each sequence call are also shown on the visualization map.