Quantifying Pathogen Surveillance Using Temporal Genomic Data

Chan, Joseph M.; Rabadan, Raul

Within H5N1, there is biased sampling in different transmission zones. Following particularly large outbreaks, H5N1 human surveillance is high, with q2 coefficients of roughly 0.9 in northern Africa and eastern and southeastern Asia. Over time, the q2 coefficient has decreased in eastern and southeastern Asia most likely because of a decline in the number of sporadic introductions into the local human populations compared to that in northern Africa, specifically Egypt (see Fig. S1E and S2D in the supplemental material). H5N1 avian influenza virus surveillance is high in northern and western Africa; eastern, southeastern, and southern Asia; and eastern, southwestern, and northern Europe. On the other hand, the q2 coefficient indicates less avian H5N1 influenza virus surveillance in North America. In the United States, for example, only until 2006 were the reporting and tracking of H5 in birds mandated by the USDA (28) . The smaller push for reporting stems from the low pathogenicity displayed by North American avian H5N1 influenza virus strains, which have antigenic and genetic differences from the Asian HPAI virus lineage (see Fig. S1F and S2E in the supplemental material) (29) .