The Rise and Fall of Omicron BA.1 Variant as Seen in Wastewater Supports Epidemiological Model Predictions

Abstract

The COVID-19 pandemic caused by the SARS-CoV-2 virus has inflicted significant mortality and morbidity worldwide. Continuous virus mutations have led to the emergence of new variants. The Omicron BA.1 sub-lineage prevailed as the dominant variant globally at the beginning of 2022 but was subsequently replaced by BA.2 in numerous countries. Wastewater-based epidemiology (WBE) offers an efficient tool for capturing viral shedding from infected individuals, enabling early detection of potential pandemic outbreaks without relying solely on community cooperation and clinical testing resources. This study integrated RT-qPCR assays for detecting general SARS-CoV-2 and its variants levels in wastewater into a modified triple susceptible-infected-recovered-susceptible (SIRS) model. The emergence of the Omicron BA.1 variant was observed, replacing the presence of its predecessor, the Delta variant. Comparative analysis between the wastewater data and the modified SIRS model effectively described the BA.1 and subsequent BA.2 waves, with the decline of the Delta variant aligning with its diminished presence below the detection threshold in wastewater. This study demonstrates the potential of WBE as a valuable tool for future pandemics. Furthermore, by analyzing the sensitivity of different variants to model parameters, we are able to deduce real-life values of cross-variant immunity probabilities, emphasizing the asymmetry in their strength.

Keywords: Omicron; RT-qPCR; SARS-CoV-2; SIR model; SIRS model; wastewater-based epidemiology.

Figure 1

RT-qPCR of SARS-CoV-2, Delta, and Omicron BA.1 variants in Beer Sheva wastewater from mid-December 2021 to July 2022. The gray area illustrates the overall SARS-CoV-2 variants using N gene sets. The blue columns indicate the detection of the Delta variant using the SΔ157 set, while the orange columns represent the detection of the Omicron variant of concern using the Ins214S set.

Figure 2

SARS-CoV-2 variants copy number from the model, scaled to the observed wastewater concentrations (Figure 1).