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.
Highlights
In the context of the COVID-19 pandemic caused by the Severe Acute RespiratorySyndrome CoronaVirus 2 (SARS-CoV-2), which appeared at the end of 2019 in China, global health situation is of great concern [1]
In the large separate sewer (RS) and its subset (B7), wastewater networks, the distribution of the SARS-CoV-2 variants analysed using the Bio-T Kit® showed that 70% of the SARS-CoV-2 detected in the RS network should correspond to the United Kingdom (UK) variant and 30% to other SARS-CoV-2 variants that did not have the mutation N501Y
During their routine survey of the distribution of SARS-CoV-2 variants in wastewater in different city districts using the Bio-T Kit® SARS-CoV-2, BMPM identified that one district of the city had a different profile compared to that of the general Marseille sewage network (RS)
Summary
In the context of the COVID-19 pandemic caused by the Severe Acute RespiratorySyndrome CoronaVirus 2 (SARS-CoV-2), which appeared at the end of 2019 in China, global health situation is of great concern [1]. The main symptoms of COVID-19 are respiratory symptoms such as a cough or runny nose that can, in severe cases, result in acute respiratory distress syndrome, as well as gastrointestinal symptoms such as diarrhoea and vomiting, in 2–10% of cases [3,4]. Of the gastrointestinal symptoms, several recent studies have reported the presence of SARS-CoV-2 RNA in stool samples and in anal/rectal swabs, in symptomatic and in asymptomatic patients and, in wastewater [5,6,7,8]. The detection and monitoring of SARS-CoV-2 in wastewater samples has already been reported in many countries [11,12,13,14,15,16,17,18,19,20,21]
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