SARS-CoV-2 genome quantification in wastewaters at regional and city scale allows precise monitoring of the whole outbreaks dynamics and variants spreading in the population

Abstract

SARS-CoV-2 is a coronavirus causing a globalized outbreak called COVID-19. SARS-CoV-2 transmission is associated with inhalation of contaminated respiratory droplets and could causes severe complications. Until today several “waves” of infections have been observed despite implementation of strict health policies. Decisions for such sanitary measures are based on population health monitoring. Unfortunately, for COVID-19, a significant proportion of individuals are asymptomatic but play a role in the virus transmission. To overcome these limitations, several strategies were developed including genome quantification in wastewater that could allow monitoring of the health status of population, since shedding of SARS-CoV-2 in patient stool is frequent. Wastewater-based epidemiology (WBE) was established and several countries implemented this approach to allow COVID-19 outbreak monitoring. In France, the OBEPINE project performed a quantitative analysis of SARS-CoV-2 in raw wastewater samples collected from major wastewater treatment plants (WWTP) since March 2020. In the greater Paris area 1101 samples (507 for five WWTP and 594 for sewer) were collected. This 16 months monitoring allows us to observe the outbreak dynamics. Comparison of WBE indicators with health data lead to several important observation; the good level of correlation with incidence rates, the average 3 days lead time, and the sensitivity (WBE change when incidence is > to 7/100000 inhabitants). We also compared the local monitoring (city level) with the regional monitoring, to help cluster identification. Moreover, variants of concern (VOC) emerged due to the selection pressure. We developed a specific RT-qPCR method targeting the deletion H69-V70 in the spike protein, using this deletion as a proxy of the B.1.1.7 presence in the wastewater. With this data we demonstrate the predominant role played by this strain in the third wave. All these results allow a better description and understanding of the pandemic and highlight the role of such WBE indicators.

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

“…The recovery rate of methods was estimated using bovine coronavirus spiked and the repeatability of the measurement was also evaluated on endogenous PMMoV as previously described (Wurtzer et al, 2022).…”

“…Even if the data quantity generated by sequencing is relevant, this methodology is also expensive and time-consuming. To overcome these limitations, targeted and specific RT-qPCR approaches have been proposed to detect certain mutations suggestive of variant presence or functional mutations whose evolution could reveal the spread of variants designated as VOC (Wurtzer et al, 2022). Different RT-PCR methods have been proposed based on either relative quantification of mutations to the total SARS-CoV-2 genomes (Erster et al, 2022; Wurtzer et al, 2022; Yaniv et al, 2021), either on wild-type and mutated allelic discrimination (Graber et al, 2021), quantification of mutations and total genomes by digital PCR (Boogaerts et al, 2022; Caduff et al, 2022; Heijnen et al, 2021; Lou et al, 2022).…”

“pySewage”: a hybrid approach to predict the number of SARS-CoV-2-infected people from wastewater in Brazil

“…Therefore, in addition to studies of SARS-CoV-2 monitoring by experimental techniques such as RT-qPCR and genomic sequencing, it is extremely important to develop web applications to automate the SARS-CoV-2 detection combined with COVID-19 monitoring (Pérez-Cataluña et al 2022 ). Moreover, the use of our web application can provide early prediction in wastewater, potentially identifying new variants for recurrent outbreaks (Peterson et al 2022 ; Wurtzer et al 2022 ).…”

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

“…Coronavirus disease-2019 (COVID- 19), caused by the Severe Acute Respiratory Syndrome -Coronavirus 2 (SARS-COV-2), emerged in Wuhan (China) in December 2019 and since then became a pandemic with more than 336 million confirmed cases globally and 5.5 million deaths as of January 20, 2022 . Most SARS-CoV-2 epidemics that occurred successively or concurrently at the level of countries resulted from the importation from abroad of emerging viral variants [1].…”

“…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.…”