Oregon Wastewater Surveillance

County visits. This summer, we started meeting in-person with both utilities that participate in wastewater surveillance in Oregon and the county public health departments in which they reside to discuss the use of wastewater surveillance data, tour local wastewater treatment plants, and promote interfacing between utility and public health staff. We have visited 7 counties to date: Lincoln, Wasco, Hood River, Deschutes, Linn, Benton and Malheur Counties.  (See photo below of The Dalles Wastewater Treatment Plant Tour!) We plan to visit every participating utility and county and will contact you via email to discuss dates. We look forward to meeting you!

Influenza Testing Continues. We continued influenza A testing, per CDC request, throughout the summer, even though traditionally that is not flu season. This is because Oregon had uniquely late flu activity. In addition, the CDC is interested in understanding flu A that may be a result of the potential presence of H5N1.

H5N1 Highly Pathogenic Influenza Detection Challenges in Wastewater. Recall that H5N1 is a subtype of influenza A causing recent outbreaks in poultry and US dairy cows (https://www.cdc.gov/bird-flu/situation-summary/index.html).  Using dPCR, it is possible to detect both the H5 gene and the N1 gene.  However, it is not currently possible to use dPCR to definitively identify the presence of the H5N1 subtype.

Gene structure   This is because Influenza A viruses have 8 separate gene segments.  These segments are not attached to one another but rather float around independently inside the virus membrane.  For highly pathogenic avian influenza, the H5 gene is on one segment while the N1 gene is on a different gene segment (see figure below). In wastewater, gene segments from other subtypes of influenza may also be present. There are 18 known H gene segments and 11 known N gene segments, resulting in 131 subtype combinations being detected in nature.

dPCR Identification   Thus, a positive identification of H5 could be the result of one of nine currently known H5-containing Influenza subtypes being present in the wastewater.  Similarly, identification of N1 could be due to the presence of H5N1 but could also be due to the most common human-infecting influenza subtype, H1N1.  Even so, monitoring for influenza A and/or H5 trends in wastewater using dPCR is still a valuable tool as it can alert to increases in a community. 

Sequencing Development   Additionally, newer sequencing-based methods are being developed to more accurately detect the specific subtype from wastewater samples with a much higher degree of certainty.

(Influenza virus base figure from Biorender.)