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

Author:

Róka Eszter1,Déri Dániel2ORCID,Khayer Bernadett1ORCID,Kis Zoltán2,Schuler Eszter1,Magyar Nóra2,Pályi Bernadett2,Pándics Tamás1,Vargha Márta1ORCID

Affiliation:

1. a Department of Public Health Laboratory, National Public Health Center, Albert Flórián út 2-6., H-1097 Budapest, Hungary

2. b National Biosafety Laboratory, Division of Microbiological Reference Laboratories, National Public Health Center, Albert Flórián út 2-6., H-1097 Budapest, Hungary

Abstract

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.

Publisher

IWA Publishing

Subject

Infectious Diseases,Microbiology (medical),Public Health, Environmental and Occupational Health,Waste Management and Disposal,Water Science and Technology

Reference20 articles.

1. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England;Science,2021

2. Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7;Nature,2021

3. European Commission 2021 Commission Recommendation of 17.3.2021 on a Common Approach to Establish a Systematic Surveillance of SARS-CoV-2 and Its Variants in Wastewaters in the EU. Available from: https://ec.europa.eu/environment/pdf/water/recommendation_covid19_monitoring_wastewaters.pdf (accessed 30 July 2021).

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