Quantifying Pathogen Surveillance Using Temporal Genomic Data

Chan, Joseph M.; Rabadan, Raul

Toward a measure that synthesizes both the absolute number of isolates and the evolutionary rate, we calculated the q2 coefficient as a function of time for each influenza virus strain in Fig. 1D as a representation of surveillance history. We also tabulated their final q2 coefficients (see Tables S2 and S3 in the supplemental material) and mapped these values among WHO transmission zones (27) in Fig. 2 (and Fig. S2 in the supplemental material) to denote the present state of surveillance around the world. We showed that our q2 coefficient calculations did not drastically change for different genetic distances (Ͻ0.035 difference in the q2 coefficient). Analysis of each strain reflects a different state of geographic and host surveillance. Overall, surveillance of human seasonal strains was high; the q2 coefficient values of both human seasonal H3N2 and seasonal H1N1 viruses, which had been sampled and sequenced long before 2003, approached 1 from 2003 to the present (Fig. 1D ). Clustering of sequences by transmission zone began to uncover weakness in the surveillance of seasonal H3N2, particularly in central Asia (see Fig. S1A and S2A in the supplemental material). In addition to central Asia, several parts of Europe, western Asia, and especially central Africa, yielded lower q2 coefficients of seasonal H1N1 (see Fig. S1B and S2B in the supplemental material). As a testament to the global response to the pandemic, human SOIV H1N1 shot up to a q2 coefficient of 1 shortly after its arrival in March 2009 in all transmission zones except central and southern Africa and central Asia ( Fig. 1D ; see Fig. S1C and S2C in the supplemental material).