Quantifying Pathogen Surveillance Using Temporal Genomic Data

Chan, Joseph M.; Rabadan, Raul

Sequence collection, annotation, and alignment. Complete coding sequences of all influenza virus coding segments were collected from the NCBI influenza virus resource (43) and the GISAID database (20) downloaded as of October 2012 for human, avian, and swine hosts. Complete coding sequences for the envelope (env) gene of dengue virus subtypes 1, 2, and 3, as well as West Nile virus, were collected from the Virus Pathogen Resource and Broad Institute downloaded as of May 2012. All sequences were filtered for year and month information. If no day information was provided, isolation was assumed to have occurred on the 15th of the month. To avoid the effect of depositing duplicated sequences, only unique sequences were considered for each date and location. Sequences were then aligned using ClustalW2 v. 2.0.12, using default parameters, and then manually curated. Influenza virus sequences were annotated by transmission zones, defined by the WHO as geographically contiguous regions with similar peaks in the influenza season (27) . All alignments and the code used are available upon request.