Monitoring the Circulation of SARS-CoV-2 Variants by Genomic Analysis of Wastewater in Marseille, South-East France

Abstract

The monitoring of SARS-CoV-2 RNA in sewage has been proposed as a simple and unbiased means of assessing epidemic evolution and the efficiency of the COVID-19 control measures. The past year has been marked by the emergence of variants that have led to a succession of epidemic waves. It thus appears that monitoring the presence of SARS-CoV-2 in wastewater alone is insufficient, and it may be important in the future to also monitor the evolution of these variants. We used a real-time RT-PCR screening test for variants in the wastewater of our city to assess the effectiveness of direct SARS-CoV-2 sequencing from the same wastewater. We compared the genome sequencing results obtained over the large RS network and the smaller B7 network with the different distributions of the variants observed by RT-PCR screening. The prevalence of the “UK variant” in the RS and B7 networks was estimated to be 70% and 8% using RT-PCR screening compared to 95% and 64% using genome sequencing, respectively. The latter values were close to the epidemiology observed in patients of the corresponding area, which were 91% and 58%, respectively. Genome sequencing in sewage identified SARS-CoV-2 of lineage B.1.525 in B7 at 27% (37% in patients), whereas it was completely missed by RT-PCR. We thus determined that direct sequencing makes it possible to observe, in wastewater, a distribution of the variants comparable to that revealed by genomic monitoring in patients and that this method is more accurate than RT-PCR. It also shows that, rather than a single large sample, it would be preferable to analyse several targeted samples if we want to more appropriately assess the geographical distribution of the different variants. In conclusion, this work supports the wider surveillance of SARS-CoV-2 variants in wastewater by genome sequencing and targeting small areas on the condition of having a sequencing capacity and, when this is not the case, to developing more precise screening tests based on the multiplexed detection of the mutations of interest.

A State-of-the-Art Scoping Review on SARS-CoV-2 in Sewage Focusing on the Potential of Wastewater Surveillance for the Monitoring of the COVID-19 Pandemic

“…Also, SARS-CoV-2 VOCs have been detected in sewage (pango lineage B.1.1.7 and P.1), suggesting that tracking SARS-CoV-2 variants and their abundance in sewersheds could provide an early warning system for the emergence or spread of more infectious or virulent strains in the community. More recently, SARS-CoV-2 VOCs and VOIs were identified in wastewater samples matching those found in clinical isolates from the same time periods (Ai et al, 2021 ; Avgeris et al, 2021 ; Carcereny et al, 2021 ; Gregory et al, 2021 ; Heijnen et al, 2021 ; La Rosa et al, 2021c ; Lee et al, 2021 ; Mishra et al, 2021 ; Rios et al, 2021 ; Swift et al, 2021 ; Wurtz et al, 2021 ; Yaniv et al, 2021 ).…”

SARS-CoV-2 testing of aircraft wastewater shows that mandatory tests and vaccination pass before boarding did not prevent massive importation of Omicron variant in Europe

“…Reads of wastewater samples were analyzed as previously described [27]. Briefly, reads from pool1 and pool2 provided by the ARTIC procedure were mapped together against the Wuhan-Hu-1 SARS-CoV-2 isolate genome (GenBank accession number NC_045512.2) using the CLC genomics softwarev7.5 (Qiagen Digital Insights, Germany) with the default parameters.…”

“…After the first report of the detection of SARS-CoV-2 in wastewater by Medema et al in Netherlands [10], detection and monitoring in wastewater samples have been reported in many countries [11][12][13][14]. A few studies have performed SARS-CoV-2 genome sequencing from sewage to identify viral genotypes circulating in a community and study genetic diversity [14][15][16][17][18][19]. Some of them showed congruence bewteen variants found in clinical isolates during the same period, while others identified genotypes not yet reported in clinical samples.…”

SARS-CoV-2 Whole-Genome Sequencing Using Oxford Nanopore Technology for Variant Monitoring in Wastewaters

“…To date, several studies have demonstrated that SARS-CoV-2 RNA sequencing from wastewater could help to understand the city- or country-scale circulation of SARS-CoV-2 variants ( Nemudryi et al, 2020 ; Agrawal et al, 2021 ; Bar-Or et al, 2021 ; Crits-Christoph et al, 2021 ; Fontenele et al, 2021 ; Izquierdo-Lara et al, 2021 ; Jahn et al, 2021 ; Prado et al, 2021 ; Rouchka et al, 2021 ; Rubio-Acero et al, 2021 ; Wilton et al, 2021 ). SARS-CoV-2 WGS in sewage was conducted using multiplex PCR panels combined mostly with Illumina sequencing ( Ai et al, 2021 ; Bar-Or et al, 2021 ; Fontenele et al, 2021 ; Hillary et al, 2021 ; Izquierdo-Lara et al, 2021 ; Jahn et al, 2021 ; Mondal et al, 2021 ; Prado et al, 2021 ; Rouchka et al, 2021 ; Rubio-Acero et al, 2021 ; Wurtz et al, 2021 ), and more rarely with Oxford Nanopore Technology ( Nemudryi et al, 2020 ; Izquierdo-Lara et al, 2021 ; Rios et al, 2021 ). Here, we aimed to adapt a sequencing technique using the widely used and frequently updated ARTIC-400 panel of primers ( Tyson et al, 2020 ) and Oxford Nanopore Technology (ONT), initially designed for clinical samples, to apply it to the challenging wastewater matrix.…”