Background: The magnitude of Omicron SARS-CoV-2 variant of concern (VOC) global spread necessitates reinforcement of surveillance implementation. Conventional VOC surveillance based on genotyping of clinical samples is characterized by certain challenges related to available sequencing capacity, population sampling methodologies, and demands in terms of time, labor, and resources. Wastewater-based SARS-CoV-2 VOC surveillance constitutes a valuable supplementary practice, since it does not require extensive sampling, and provides information on the prevalence of the disease in a timely and cost-effective manner.
Methods: A highly sensitive real-time RT-PCR assay was developed, for targeted Omicron VOC detection and quantification in wastewater samples. The assay exclusively amplifies sequences with the S:Δ69/70 deletion, thus its performance is not hampered by the presence of the Delta VOC. The method was incorporated in the analysis of composite daily samples taken from the main Wastewater Treatment Plant (WWTP) of Thessaloniki, Greece from 1 December 2021 to 9 January 2022.
Results: The Omicron VOC was detected for the first time in samples from the Thessaloniki WWTP on 19 December 2021. In the following 10-day period, a rapid increase in Omicron sewage viral load was observed with an estimated early doubling time of 1.86 days. The proportion of the total SARS-CoV-2 load attributed to Omicron reached 91.09% on 7 January, revealing a fast Delta-to-Omicron VOC transition pattern. The detection of Omicron in wastewater preceded the outburst of reported (presumable) Omicron cases in the city by approximately 7 days.
Conclusions: The proposed wastewater-based surveillance approach enables rapid, real-time data acquisition on the Omicron VOC prevalence and transmission dynamics. Timely provision of these results to State authorities can readily influence the decision-making process for targeted public health interventions, including control measures, awareness, and preparedness.