Detection of the SARS-CoV-2 Delta Variant in the Transboundary Rivers of Yunnan, China

Abstract

Ruili and Longchuan, two border counties in southwestern China, are facing epidemic control challenges due to the high rate of COVID-19 infections originating from neighboring Myanmar. Here, we aimed to establish the applicability of wastewater and environmental water surveillance of SARS-CoV-2 and conduct whole-genome sequencing (WGS) to trace the possible infection origin. In August 2021, total 72 wastewater and river water samples were collected from 32 sampling sites. SARS-CoV-2 ORF1ab and N genes were measured by RT-qPCR. We found that 19 samples (26.39%) were positive, and the viral loads of ORF1ab and N genes were 6.62 × 102–2.55×105 and 1.86 × 103–2.32 × 105 copies/L, respectively. WGS further indicated the sequences in two transboundary river samples, and one hospital wastewater sample belonged to the delta variant, suggesting that the infection source might be areas with high COVID-19 delta variant incidence in Southeast Asia (e.g., Myanmar). We reported for the first time the detection and quantification of SARS-CoV-2 RNA in the transboundary rivers of Myanmar–China. Our findings demonstrate that wastewater and environmental water may provide independent and nonintrusive surveillance points to monitor the global spread of emerging COVID-19 variants of concern, particularly in high-risk regions or border areas with considerable epidemic challenges and poor wastewater treatment facilities.

Moving forward with COVID-19: Future research prospects of wastewater-based epidemiology methodologies and applications

“…Unlike conventional epidemiological surveillance techniques, WBE does not depend on access to clinical testing [ 7 ]. It can be implemented in many communities with a reticulated sewerage system, or even in developing countries with fragmented or open sewers [ 8 ] or even by sampling river/surface water instead [ 9 ].…”