Introducing SARS-CoV-2 wastewater surveillance in Lebanon

Wastewater surveillance (WWS) gained global attention during the COVID-19 pandemic as an early warning system to continuously monitor SARS-CoV-2 and its evolving variants. The aim of this study is to detect and sequence SARS-CoV-2 in wastewater from an area in Lebanon that hosts vulnerable groups of Lebanese residents and refugees. A total of 188 wastewater samples were collected from 18 manholes between 20 February 2023 and 31 May 2023. Viral RNA extraction, RT-PCR, and genomic sequencing were performed. Eighteen percent of collected samples were SARS-CoV-2-positive. Omicron BA.2 was the only circulating variant in February. An overlap between Omicron BA.2 (33.33%) and B.1.1-like sublineages, including C.26 (16.67%), B.1.1.207 (16.67%), B.1.1.214 (16.67%), and C.2.1 (16.67%) was detected in March. In April, while Omicron circulation decreased to 12.5%, a BA.1 and BA.2 recombinant (XM) was detected. The lack of disaggregated data sets and case-specific SARS-CoV-2 reports from the study site residents limited our ability to perform correlation and comparative analyses between wastewater and national clinical data. However, wastewater samples showed higher positivity rates during most of the months prior to national surges of cases. These findings underscore the importance of incorporating WWS in public health interventions to complement clinical and epidemiologic surveillance. IMPORTANCE: Wastewater surveillance (WWS) is a valuable environmental surveillance tool that facilitates the real-time detection of circulating viruses and emerging variants. The COVID-19 pandemic has led to significant acceleration in the use of WWS as an early warning system for detecting SARS-CoV-2 and monitoring community transmission. This is the first study introducing SARS-CoV-2 community-based WWS in Lebanon. The findings of this study highlight the importance and feasibility of implementing WWS in a limited-resource setting to complement epidemiological surveillance in monitoring trends of SARS-CoV-2 at the population/community level.