SARS-CoV-2 surveillance of wastewater in small rural communities identifies lack of vaccine coverage as influence of omicron outbreak

Wastewater-based epidemiology (WBE) can provide critical early warnings to aid public health, which can be particularly beneficial in rural communities with limited access to health care. Spikes of SARS-CoV-2 RNA concentration in wastewater have been used to represent infections in a community, but wastewater holds a wealth of information that has not been explored yet. The objectives of this research were to expand the use of WBE to 1) determine the dynamic of SARS-CoV-2 variants in rural communities, and 2) evaluate the relationship between community vaccination status and the outbreak of a variant. We quantified the concentration of SARS-CoV-2 RNA, as well as specific mutations that are consistent with Delta and Omicron in influent raw wastewater samples collected from wastewater treatment facilities (WWTFs) for five populations with <1000 residents and one larger population in Latah County, ID. A binomial generalized linear model using the percent of the population with protection against Omicron from the initial vaccines and the booster shot was able to predict the probability of an uptick in Omicron concentration in wastewater with an accuracy of 0.96. Evaluation of vaccination data indicate that the spike in Omicron infections in December 2021 in the studied towns was linked to low levels of population protection from the initial shots of the COVID-19 vaccine against Omicron infection and limited uptake of booster shots in these communities. Despite difficulties with applying WBE in rural regions, this study shows that beyond evaluating spikes of viral infections, WBE can be used to evaluate the effect of a population’s vaccine coverage on SARS-CoV-2 variant dynamics.