Prevalence and circulation patterns of SARS-CoV-2 variants in European sewage mirror clinical data of 54 European cities

Abstract

For community-level monitoring, the European Commission under the EU Sewage Sentinel System recommends wastewater-based SARS-CoV-2 surveillance. Tracking SARS-CoV-2 variants in a community is pivotal for appropriate public health response. Genome sequencing of SARS-CoV-2 in wastewater samples for tracking variants is challenging, often resulting in low coverage genome sequences, thereby impeding the detection of the SARS-CoV-2 mutations. Therefore, we aimed at high-coverage SARS-CoV-2 genome sequences from sewage samples which we successfully accomplished. This first pan-European surveillance compared the mutation profiles associated with the variants of concerns: B.1.1.7, P.1, B.1.351 and B.1.617.2 across 20 European countries, including 54 municipalities. The results highlight that SARS-CoV-2 variants detected in the wastewater samples mirror the variants profiles reported in clinical data. This study demonstrated that >98% coverage of SARS-CoV-2 genomic sequences is possible and can be used to track SARS-CoV-2 mutations in wastewater to support identifying variants circulating in a city at the community level.

Genetic sequencing detected the SARS-CoV-2 delta variant in wastewater a month prior to the first COVID-19 case in Ahmedabad (India)

“…D1118H, D614G, H69del, N501Y, P681H, S982A, and T716I) were present in all the samples A570D and Y144del were identified in 53 samples. Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2), and Gamma (P.1) Agrawal et al (2022) Pune, India Dec 2020 to Mar 2021 Wastewater cDNA synthesis/nanopore library preparation (MinION sequencing) P1140del, L452R E484Q, D614G; Q1071H, C480R, D950N, N801, P681R Delta (B.1.617.1) Dharmadhikari et al (2022) Spain Apr 2020 to Jan 2021 Sewage (76 samples) cDNA synthesis/Illumina MiSeq platform by paired-end reads (2 × 200) A total of 627 nucleotide substitutions and 20 deletions. During first and second wave: 8 deletions detected, with 5 of them in the (Δ21–23, Δ82–84, Δ84–86, Δ141–143, and Δ682); one in the spike glycoprotein (Δ385); and two in the ORF3a (Δ80 and Δ11–20).…”

Monitoring of SARS-CoV-2 variant dynamics in wastewater by digital RT-PCR : from Alpha to Omicron BA.2 VOC

“…The monitoring of variants, especially VOC, can also be performed in raw wastewater but with some limitations. Sequencing, the most frequently described method (Agrawal et al, 2022a; Crits-Christoph et al, 2021; Fontenele et al, 2021; Pérez-Cataluña et al, 2021; Rios et al, 2021), is complex to perform in wastewater due to the relatively low viral load compared to clinical samples and the potentially degradation and/or fragmentation of the viral RNA in such samples. In addition, the presence of multiple lineages in raw wastewater does not allow the proper assembly of reads to determine the complete sequences of circulating genomes and correct lineage assignment without a complex workflow.…”

SARS-CoV-2 in Environmental Samples of Quarantined Households

“…The presence of the viral RNA in the wastewater, even at low levels, indicates that SARS-CoV-2 can remain detectable in sewage for days or weeks [ 64 , 65 , 66 ]. Thus, the wastewater system is serving as a surveillance system for the circulation of the virus within several environments [ 35 , 67 , 68 ].…”

“…Following the wastewater pathway, SARS-CoV-2 RNA has already been found in wastewater [ 26 ], which has been demonstrated to be a reliable way of monitoring COVID-19 infections and variant spread [ 35 , 36 ]. Moreover, when SARS-CoV-2 infected persons with gastrointestinal symptoms excrete urine and faeces, SARS-CoV-2 can be identified in the immediate surroundings, such as the sanitary facilities.…”