Quantifying Pathogen Surveillance Using Temporal Genomic Data

Chan, Joseph M.; Rabadan, Raul

Analysis of H5N1 influenza virus describes the effects of implementing international sequencing initiatives like GISAID. Immediately following the second outbreak of HPAI virus among humans in 2003, the q2 coefficient of H5N1 in both human and avian hosts rose to approximately 0.7 to 0.85. With the establishment of GISAID in 2006, both human and avian H5N1 influenza virus q2 coefficients increased further to high levels of around 0.9, affirming the effectiveness of the global consortium. Beyond 2007, however, the surveillance of human H5N1 influenza virus has waned compared to that of avian H5N1 influenza virus (Fig. 1D ). This discrepancy is most likely due to the fact that human HPAI cases represent a subsampling of avian H5N1 influenza virus genotypes, as reflected by the slight drop in human H5N1 entropy compared to that in birds (Fig. 1C) .