The Spectre of SARS-CoV-2 in the Ambient Urban Natural Water in Ahmedabad and Guwahati: A Tale of Two Cities

COVID-19 positive patients can egest live SARS-CoV-2 virus through faecal matter and urine, raising concerns about viral transmission through faecal-oral route and/or contaminated aerosolized water. These worries are heightened in many low and middle income nations, where raw sewage is often dumped into surface waterways and open defecation betide. In this manuscript we attempt to discern the presence of SARS-CoV-2 genetic material (ORF-1ab, N and S genes) in two urban cities of India viz., Ahmedabad, in western India with ∼12 WWTPs and Guwahati, in north-east of the country with no such plants. 25.8% and 20% of the surface water samples had detectable SARS-CoV-2 RNA load in Ahmedabad and Guwahati. N-gene>S-gene>ORF-1ab-gene were readily detected in surface water of Ahmedabad, whereas, no such significant trend was found in the case of Guwahati. The high concentration of gene (ORF-1ab – 800 copies/L for Sabarmati river, Ahmedabad and S-gene – 565 copies/L for Bharalu urban river, Guwahati) found in natural waters indicates low sanitation and have various health and ecological consequences that should be investigated further. Graphical abstract Highlights Natural urban waters show the presence of SARS-CoV-2 RNA. Lake water receiving runoff containing SARS-CoV-2 genes reflected positive sign early Viral RNA in surface water reflects inadequate sanitation and wastewater management. Residence time and transmission owing to viral RNA in natural waters needs further research.