Virome Metagenomics

Virome metagenomic sequencing reads all viral genetic material present in a wastewater sample, rather than testing for one pathogen at a time. In partnership with Baylor College of Medicine, this assay is deployed across select WC26 sites to broaden detection across respiratory, gastrointestinal, vector-borne, and emerging viruses.

Data generated using proven, cutting-edge methodology

The assay employed for this program has been tremendously successful for monitoring viruses throughout the state of Texas over the last four years (see the TexWEB dashboard). This vetted approach has been used to identify changes in seasonal pathogen abundances and identify public health relevant outbreaks. It has proven itself as an early warning system for newly emerged (Avian Flu) or remerged viruses (measles). This assay represents the next leap forward in wastewater epidemiology.

Methodology

Samples are collected from wastewater treatment plants on a weekly basis. Samples represent wastewater from approximately the past 24 hours. Once the samples are back in the lab, we extract the nucleic acids from them and capture the majority of the viruses present. Viral capture uses nanoparticle baits that are mixed into the sample and bind to viruses. We then sequence these captured viruses. Sequencing lets one understand the genetic code for a given virus. Each virus has its own specific genetic code so sequencing allows for precise identification and also allows monitoring of viral evolution.

After sequencing, we analyze the data and generate a metric of viral abundance called RPKMF (reads per kilobase of transcript per million filtered reads). This metric accounts for observation effort during the sequencing process (sequencing depth) and how easy it is to observe a given virus (genome size, larger viruses could be easier to observe via sequencing than smaller ones). RPKMF shows quantitative patterns expected of seasonal viruses. For more details, see Tisza et al. 2023.