Wastewater based epidemiology in countries with poor wastewater treatment - SARS-CoV-2 RNA in surface waters

Abstract

Background Wastewater-based epidemiology surveillance of COVID-19 and other outbreaks in the future is a challenge for developing countries, as the majority of households are not connected to sewerage systems. In December 2019, we have detected SARS-CoV-2 RNA in the Danube River at a site that is severely affected by wastewater of Belgrade. Considering that rivers are much more complex systems in comparison to wastewater, additional efforts are needed to address all the factors which might influence the adoption of WBE as an alternative of targeting raw wastewater. Objectives The major objective of this study was to provide a more detailed insight in the potential of SARS-CoV-2 surveillance in Serbian surface waters under consideration of epidemiological, microbiological, physico-chemical and hydro-morphological parameters for epidemiological purposes. Methodology Water samples were collected at 12 sites at Sava and Danube Rivers in the Belgrade city area during the fourth COVID-19 wave in Serbia that started in late February 2021. SARS-CoV-2 RNA was quantified using RT-qPCR with primer sets targeting nucleocapsid (N1 and N2) and envelope (E) protein genes. Microbiological (standard fecal indicator bacteria and microbial faecal source tracking markers), epidemiological, physico-chemical and hydro-morphological parameters were analysed in parallel. Results Out of 44 samples analyzed, 31 were positive for at least one of the target regions of SARS-CoV-2. The results indicated that surveillance of SARS-CoV-2 RNA in surface waters in context with the large amount of epidemiological and environmental metadata can be used as epidemiological early-warning tool in countries with poor wastewater treatment.