DNA sequences (base order randomized) of NA, HA, and PB2 genes of samples taken from farms during the Dutch avian influenza (H7N7) epidemic in 2003. The dataset contains 241 farms, of which 231 were sampled and sequenced (for the other 10, identified by the prefix UNK, only the detection day + 2 days is given, as in Klinkenberg et al (2017)). The labels of the sequences refer to the labels in GISAID (www.gisaid.org), where the sequences in correct base order can be found.
AvianFluH7N7_2003A list with four elements:
the HA gene
the NA gene
the PB2 gene
the days at which the samples were taken (or the detection day + 2 days, for the 10 unsampled farms)
Bataille et al. (2011) Evolutionary analysis of inter-farm transmission dynamics in a highly pathogenic avian influenza epidemic. PLoS Pathog, 7(6): e1002094.
Klinkenberg et al. (2017) Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks. PLoS Comput Biol, 13(5): e1005495.