The first report of SARS-CoV-2 genome in the groundwater of Tehran, Iran: A call to action for public health

Abstract

A pandemic of acute respiratory disease referred to as COVID-19 has been caused by the highly infectious and transmissible Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which threatened human health. Although the SARS-CoV-2 RNA has been found in wastewater from numerous regions in different countries due to fecal shedding of infected individuals, there is still little information available regarding how prevalent it is in other water matrices especially groundwater, where some areas still rely on it to supply drinking water, irrigation of farmlands, and other purposes. This study attempted to assess the presence of this virus genome in groundwater samples in Tehran, Iran. These samples were collected seasonally from 12 sites over 2 years period (2021–2023). At first, a virus adsorption-elution (VIRADEL) concentration procedure was tested utilizing an avian coronavirus (infectious bronchitis virus, IBV) as a process control followed by RNA extraction. Subsequently, SARS-CoV-2 was quantified using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect the E and S genes. As a result, SARS-CoV-2 RNA was detected in 1 out of 96 groundwater samples with a concentration of 2/53 × 103 and 3/16 × 103 genome copies/l for E and S genes, respectively. Furthermore, the SARS-CoV-2 positive sample was subjected to semi-nested PCR targeting the partial S gene, followed by direct sequencing, phylogenetic and mutation analysis. BA.1 Omicron was the only identified variant during this study. These findings show how important water-based epidemiology is to monitor SARS-CoV-2 at the community-level and subsequent human exposure, even when COVID-19 prevalence is low.