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

Michal Liddor Naim; Yu Fu; Marilou Shagan; Itay Bar-Or; Robert Marks; Qun Sun; Rony Granek; Ariel Kushmaro

doi:10.3390/v15091862

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

Viruses. 2023 Aug 31;15(9):1862. doi: 10.3390/v15091862.

Authors

Michal Liddor Naim¹, Yu Fu^{1

2}, Marilou Shagan¹, Itay Bar-Or³, Robert Marks^{1

4}, Qun Sun², Rony Granek^{1

4}, Ariel Kushmaro^{1

4

5}

Affiliations

¹ Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
² Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China.
³ Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel.
⁴ The Ilse Katz Center for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
⁵ School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.

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.

Grants and funding

We would like to acknowledge funding from Ben Gurion University through The Corona Challenge COVID-19 funding number 87793711 and funding from the Israeli Ministry of Health grant number 3-0000-17151.