Correspondence of SARS-CoV-2 genomic sequences obtained from wastewater samples and COVID-19 patient at long-term care facilities

Abstract

Wastewater-based epidemiology (WBE) has been in the spotlight because of applicability of early detection of virus outbreak and new variants at the catchment area. However, there has been a notable absence of research directly confirming the association between SARS-CoV-2 in wastewater and patient specimens. In this study, we performed a quantitative and qualitative investigation with a genetic-level comparison of SARS-CoV-2 between COVID-19 patients and SARS-CoV-2 positive wastewater samples at long-term care facilities. Wastewater samples were collected via passive sampling from manholes, and SARS-CoV-2 load in wastewater was determined by qPCR. We performed correlation analysis between SARS-CoV-2 load and COVID-19 case number, which suggested that SARS-CoV-2 was detected from wastewater earlier than ascertainment of COVID-19 case. Six and six RNA samples from COVID-19 positive cases and wastewater, respectively, from two facilities were then applied for amplicon sequencing analysis. Mutation analysis revealed high sequence similarity of SARS-CoV-2 variants between wastewater and patient samples (>99 %). To the best of our knowledge, this is the first study demonstrating that WBE is also effective in predicting predominant SARS-CoV-2 variant at facility-level, which is helpful to develop early-warning system for outbreak occurrence with predominant variant.

Keywords: COVID-19 patient; Passive sampling; SARS-CoV-2; Sequence similarity; Variant; Wastewater-based epidemiology.