Scotch Matthew

Sequence-informed surveillance is now recognized as an important extension to the monitoring of rapidly evolving pathogens [2]. This includes phylogeography, a field that studies the geographical lineages of species including viruses [3] by using sequence data (and relevant metadata such as sampling location). This work relies on bioinformatics knowledge. For example, the user first needs to find a relevant sequence database, navigate through it, and use proper search parameters to obtain the desired data. They also must ensure that there is sufficient metadata such as collection date and sampling location. They then need to align the sequences and integrate everything into specific software for phylogeography. For example, BEAST [4] is a popular tool for discrete phylogeography. For proper use, the software requires knowledge of phylogenetics and utilization of BEAUti, its XML processing software. The user then needs to use other software, like TreeAnnotator [4], to produce a single (representative) maximum clade credibility (MCC) tree. Even then, the evolutionary spread of the virus can be difficult to interpret via a simple tree viewer. There is software (such as SpreaD3 [5]) for visualizing a tree within a geographic context, yet for novice users, it might not be easy to use. Currently, there are only a few systems designed to automate these types of tasks for virus surveillance and phylogeography.

Objective: We will describe the ZooPhy system for virus phylogeography and public health surveillance [1]. ZooPhy is designed for public health personnel that do not have expertise in bioinformatics or phylogeography. We will show its functionality by performing case studies of different viruses of public health concern including influenza and rabies virus. We will also provide its URL for user feedback by ISDS delegates.

Sewerage systems of villages, townships, cities and megacities convey the urine, stool, blood, and sputum of community members, enabling through analysis of community wastewater, a near real-time assessment of population health status and of emerging public health threats. Signature compounds and biomarkers targeted analytically for surveillance may include chemical and biological threat agents, transformation products of the same, human metabolites, biomarkers of exposure and other markers of interest. Additional information can be gleaned by analyzing, in a similar fashion, municipal sewage sludge resulting from wastewater treatment, a material that during treatment becomes enriched in persistent, hydrophobic and potentially bioaccumulative pollutants, while more biodegradable compounds are converted to methane mostly. When taken together, these multi-dimensional data sources promise to yield critical information on the health status, sustainability and resilience of rural and urban human populations in a new scientific approach termed population metabolism metrology, or for city environments, urban metabolism metrology.

Objective: To highlight the new science of population and urban metabolism metrology, for characterizing human exposures to biological agents, narcotics, antimicrobials and other contaminants of emerging concern using community wastewater as a diagnostic matrix.