The rapid spread of SARS-COV-2 Omicron variant in Italy reflected early through wastewater surveillance

Abstract

The SARS-CoV-2 Omicron variant emerged in South Africa in November 2021, and has later been identified worldwide, raising serious concerns. A real-time RT-PCR assay was designed for the rapid screening of the Omicron variant, targeting characteristic mutations of the spike gene. The assay was used to test 737 sewage samples collected throughout Italy (19/21 Regions) between 11 November and 25 December 2021, with the aim of assessing the spread of the Omicron variant in the country. Positive samples were also tested with a real-time RT-PCR developed by the European Commission, Joint Research Centre (JRC), and through nested RT-PCR followed by Sanger sequencing. Overall, 115 samples tested positive for Omicron SARS-CoV-2 variant. The first occurrence was detected on 7 December, in Veneto, North Italy. Later on, the variant spread extremely fast in three weeks, with prevalence of positive wastewater samples rising from 1.0% (1/104 samples) in the week 5-11 December, to 17.5% (25/143 samples) in the week 12-18, to 65.9% (89/135 samples) in the week 19-25, in line with the increase in cases of infection with the Omicron variant observed during December in Italy. Similarly, the number of Regions/Autonomous Provinces in which the variant was detected increased from one in the first week, to 11 in the second, and to 17 in the last one. The presence of the Omicron variant was confirmed by the JRC real-time RT-PCR in 79.1% (91/115) of the positive samples, and by Sanger sequencing in 66% (64/97) of PCR amplicons. In conclusion, we designed an RT-qPCR assay capable to detect the Omicron variant, which can be successfully used for the purpose of wastewater-based epidemiology. We also described the history of the introduction and diffusion of the Omicron variant in the Italian population and territory, confirming the effectiveness of sewage monitoring as a powerful surveillance tool.

Keywords: Omicron; RT-qPCR; SARS-CoV-2; Sewage; Variant; Wastewater-based epidemiology.

Graphical abstract

Fig. 1

Number of Omicron positive samples detected in the three weeks of December (05.12.2021–25.12.2021) divided by Region/A.P. Samples negative for Omicron variant are reported in green; positive samples are represented in red.

Fig. 2

Geographic spread of the Omicron positive samples during the three weeks of December (05.12.2021–25.12.2021) by province Regions in which wastewater surveillance was not yet activated at the time of the study are reported in black. Provinces for which no samples were tested in the study are reported in grey. Detection of the Omicron variant is reported in orange.