Successful detection of the presence of the Delta variant through Wasterwater sequencing by CERTH and AUth
[12 July 2021

(top) The quantification of two mutations unique to the Alpha variant (B.1..7) by the analysis of the wastewater sequencing data, compared to the respective percentage of the variant in clinical samples.

(bottom) The quantification of three mutations unique to the Alpha (B.1.1.7), Beta (B.1.315) and Delta (B.1.617.2) respectively, as identified by the bioinformatics analysis.

Monday, 12 July 2021

The current phase of the SARS-CoV-2 pandemic is shaping into an era of genomic surveillance in order to track the genomic changes in the virus genome. Using NGS sequencing techniques, and according to the PANGO lineages, there are currently over 1500 known SARS-CoV-2 variants since the initial detection. In the last few months, clinical sequencing has revealed some fast-spreading and highly virulent variants, characterizing them as Variants of Concern (VoC). This development underlines the importance of sequencing analyses – however, scaling such efforts is a costly and time-consuming process.

Wastewater-based epidemiology (WBE) is an emerging paradigm for monitoring the circulation of SARS-CoV-2 in a community. The Institute of Applied Biosciences (INAB) at the Centre for Research and Technology Hellas (CERTH), and in collaboration with the Aristotle University of Thessaloniki (AUTH), developed a novel bioinformatic method for WBE based on NGS data. The method is capable of identifying and quantifying the individual mutations that are present in wastewater samples, and infer the overall presence of particular SARS-CoV-2 variants. Notably, INAB-CERTH was able to detect the presence of the Delta variant (B.1.617.2) in extremely low frequencies (1-3%) in the first three weeks of June 2021, as well as quantify its increase across the same time period.

“Wastewater sequencing will become more and more important as a large scale and passive detection scheme. For example, correlating wastewater reads across geographic regions and event countries could provide a unique view of the transmission of the virus and its variants”, noted Fotis Psomopoulos, the researcher leading the bioinformatics activities at INAB-CERTH. “Wastewater analysis is in an extend the equivalent of blood analysis in humans, but instead of monitoring the health of a human being we monitor the health of an entire city. Through wastewater analysis we can estimated and monitor not only SARS-CoV-2 but also other viruses and pathogens as well as the presence of antibiotics, drugs and human pollutants”, noted Anagnostis Argiriou, Deputy Director of INAB-CERTH.