SARS-CoV-2 variant detection from wastewater: rapid spread of B.1.1.7 lineage in Hungary

Abstract

Wastewater-based epidemiology (WBE) is a recognised tool for tracking community transmission of COVID-19. From the second half of 2020, the emergence of new, highly infective, more pathogenic or vaccine-escape SARS-CoV-2 variants is the major public health concern. Variant analysis in sewage might assist the early detection of new mutations. Weekly raw sewage samples from 22 wastewater treatment plants (WWTPs) in Hungary (representing 40% of the population) were analysed between December 2020 and March 2021 for signature mutations N501Y and del H69/V70 of B.1.1.7 lineage by melting point genotyping and RT-digital droplet PCR (RT-ddPCR). The latter method proved to be more efficient in parallel detection of different variants and also provides quantitative information. Wastewater surveillance indicated that the B.1.1.7 variant first emerged in Budapest in early January 2021 and rapidly became dominant in the entire country. Results are in close agreement with the available clinical data (Pearson's correlation coefficient, R = 0.9153). RT-ddPCR was confirmed to be a reliable tool for tracking emerging variant ratios in wastewaters. It is a rapid and cost-effective method compared to whole-genome sequencing, but only applicable for the detection of known mutations. Efficient variant surveillance might require the combination of multiple methods. HIGHLIGHTS RT-digital droplet PCR was used to detect B.1.1.7 SARS-CoV-2 variant in sewage.; Signature mutations N501Y and del H69/V70 were detected in equal concentrations.; Signature mutations of B.1.1.7 became dominant within 6 weeks in Hungarian wastewater treatment plants.; Sewage data closely correlated with clinical emergence of B.1.1.7 cases.; Wastewater-based epidemiology is an efficient tool in tracing emerging SARS-CoV-2 variants of concern.;

Keywords

• digital droplet pcr
• sars-cov-2
• variants of concern
• wastewater-based epidemiology