Influenza infects 9 to 45 million people in the United States each year and results in 300,000 to 500,000 deathsworldwide. Vaccination is the foundation of the global response to control and reduce the spread of Influenza;however, seasonal influenza vaccine efficacy ranged from non-statistically significant to 60% between 2011and 2019.Vaccine efficacy is largely contingent upon properly matching strains in circulation to the stainsselected for inclusion in the seasonal vaccine. History provides examples of mismatches that rendered vaccineineffective, thus highlighting the need to revisit the strain selection paradigm. In depth viral surveillance andgenomic characterization of circulating strains and the monitoring of viral spread dynamics across geographicareas throughout the year are paramount to select strains with the highest probability of circulation. However,with the current influenza surveillance network, < 0.2% of all influenza cases in the United States undergogenomic characterization, making it highly possible that a circulating strain would not be characterized.Additionally, there are several inherent challenges within the current swab-based surveillance approach thatcould bias the data coming out of this program and thus result in the incorrect selection of viruses for inclusionin the yearly vaccine. To improve vaccine-strain selection, we propose a macro-scale influenza and SARS-CoV-2 surveillance approach through monitoring community wastewater. Nearly all community membersunintentionally provide their wastewater treatment facilities with regular fecal samples, and both SARS-CoV-2and influenza have been shown to be shed in human feces. GT Molecular already developed and deployed astate-of-the-art viral quantification methodology for SARS-CoV-2 in wastewater monitoring used by over 100communities around the country. In the proposed work, we will expand our wastewater monitoring capabilitiesto include (i) monitoring influenza prevalence, in addition to SARS-CoV-2, for observation of viral spreaddynamics across geographic regions (Aim 1) and (ii) providing macroscale strain surveillance and genomiccharacterization of influenza and SARS-CoV-2 circulating strains found in wastewater (Aim 2). We will achieveSpecific Aim 1 through optimization of our current SARS-CoV-2 workflow for simultaneous concentration,extraction, and quantification of SARS-CoV-2 and influenza. We will achieve Specific Aim 2 throughoptimization of our previously described tiled amplicon sequencing approach for genomic characterization ofviral genomes in wastewater. Many vaccine experts expect SARS-CoV-2 to become endemic and potentiallyrequire a seasonal vaccine, like influenza. Therefore, this work could serve as a foundation for the surveillanceof both viruses, providing a robust dataset for international surveillance programs to use in their yearly straininclusion discussion and decision making.
Public Health Relevance Statement: NARRATIVE
Seasonal flu vaccines are our society's first line of defense against flu-related deaths. The current flu
surveillance program for monitoring strains in circulation and ultimately for selecting strains for the seasonal
vaccine relies on a very small number of samples, thus potentially missing relevant strains. We aim to translate
our successful SARS-CoV-2 wastewater monitoring service to include influenza, as well as develop a
wastewater sequencing pipeline to monitor both SARS-CoV-2 and influenza mutations and identify circulating
strains to ultimately fine-tune vaccine design strategies and monitor disease prevalence.
Project Terms: <2019-nCoV><2019 novel corona virus><2019 novel coronavirus><2019-nCoV vaccine> 