Detection of SARS-CoV-2 and Variants in Hospital Wastewater in a Developing Country

Abstract

Wastewater-based epidemiology (WBE) is a beneficial tool for comprehensive health information on communities, especially during the COVID-19 pandemic. In developing countries, including Thailand, the application of WBE is limited. Few SARS-CoV-2 detections and variants have been monitored in wastewater in these countries. This is because of the time-consuming, low recovery of viruses in the concentration techniques and difficulties in finding the proper primers and amplification kits. Therefore, this study aimed to quantify SARS-CoV-2 RNA concentration using a commercial clinical kit. We identified the SARS-CoV-2 variants and estimated the detection costs in the wastewater samples. One hundred and fifty hospital wastewater samples were filtered with commercial ultrafiltration (UF) and then detected for the SARS-CoV-2 concentration using a Sansure Biotech SARS-CoV-2 kit. The recovery of the virus concentration technique in UF was studied using a surrogate (porcine epidemic diarrhea virus). The virus detection in wastewater was quantified by RT-qPCR. In addition, the mutation sites in the partial spike glycoprotein (S) gene of SARS-CoV-2 were verified using short nested RT-PCR. The results showed a high recovery of the commercial UF (80.53%), and 24.6% of hospital wastewater contained SARS-CoV-2. The detection of SARS-CoV-2 in wastewater cost USD 35.43 per sample. The virus variants revealed V70del, H69del, and V144del mutations in the partial S gene of SARS-CoV-2 in B.1.1.7 (SARS-CoV-2 Alpha variant), and T95I and G142D mutations in B.1.617.2 (Delta variant).