Surveillance of SARS-CoV-2 in extensive monitoring of municipal wastewater: key issues to yield reliable results

Cutrupi, Francesca; Cadonna, Maria; Manara, Serena; Foladori, P.

doi:10.2166/wst.2021.469

Cited by 9 publications

(3 citation statements)

References 20 publications

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“…WWS has been used for identifying increasing trends of community-level infections and predicting epidemic peaks with a reasonable anticipation time, thus providing opportune public health interventions [17][18][19][20][21]. Furthermore, by the introduction of genome sequencing methodologies, WWS has expanded from detecting traces of viral RNA by RT-qPCR to tracking the introduction and prevalence of mutations associated with VOCs circulating in the community [22].…”

Section: Introductionmentioning

confidence: 99%

Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing

et al. 2023

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SARS-CoV-2 surveillance of viral populations in wastewater samples is recognized as a useful tool for monitoring epidemic waves and boosting health preparedness. Next generation sequencing of viral RNA isolated from wastewater is a convenient and cost-effective strategy to understand the molecular epidemiology of SARS-CoV-2 and provide insights on the population dynamics of viral variants at the community level. However, in low- and middle-income countries, isolated groups have performed wastewater monitoring and data has not been extensively shared in the scientific community. Here we report the results of monitoring the co-circulation and abundance of variants of concern (VOCs) of SARS-CoV-2 in Uruguay, a small country in Latin America, between November 2020—July 2021 using wastewater surveillance. RNA isolated from wastewater was characterized by targeted sequencing of the Receptor Binding Domain region within the spike gene. Two computational approaches were used to track the viral variants. The results of the wastewater analysis showed the transition in the overall predominance of viral variants in wastewater from No-VOCs to successive VOCs, in agreement with clinical surveillance from sequencing of nasal swabs. The mutations K417T, E484K and N501Y, that characterize the Gamma VOC, were detected as early as December 2020, several weeks before the first clinical case was reported. Interestingly, a non-synonymous mutation described in the Delta VOC, L452R, was detected at a very low frequency since April 2021 when using a recently described sequence analysis tool (SAM Refiner). Wastewater NGS-based surveillance of SARS-CoV-2 is a reliable and complementary tool for monitoring the introduction and prevalence of VOCs at a community level allowing early public health decisions. This approach allows the tracking of symptomatic and asymptomatic individuals, who are generally under-reported in countries with limited clinical testing capacity. Our results suggests that wastewater-based epidemiology can contribute to improving public health responses in low- and middle-income countries.

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Section: Introductionmentioning

confidence: 99%

Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing

et al. 2023

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“…The detection and monitoring of SARS-CoV-2 in wastewater samples has been reported in many countries [ 15 , 17 , 18 , 19 , 20 , 21 ]. Nevertheless, few studies have performed SARS-CoV-2 genome sequencing on sewage samples in order to determine the strains circulating within a community and to study their genetic diversity [ 16 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 ]. Unexpectedly, some sequences were not identified in clinical samples [ 20 , 22 , 23 , 24 , 25 , 26 , 30 , 31 ].…”

Section: Introductionmentioning

confidence: 99%

“…Wastewater surveillance of SARS-CoV-2 comprises several phases, starting with the sampling of wastewater and possibly storing wastewater before processing, followed by virus concentration, RNA extraction, SARS-CoV-2 RNA detection, and quantification (qPCR) as well as the potential sequencing of any variants present. Although most studies agree that collected wastewater must be stored at low temperatures (usually at 4 °C) to preserve the viral load [ 27 , 28 ], a large panel of procedures is available that has been proposed to concentrate viruses. Numerous studies have evaluated procedures concentrating on enveloped viruses from wastewater including ultracentrifugation [ 24 , 32 ], ultrafiltration [ 32 , 33 , 34 , 35 , 36 , 37 ], polyethylene glycol (PEG) and salt-based precipitation [ 32 , 35 , 36 , 38 ], skimmed milk flocculation [ 36 , 37 ], sludge extraction [ 36 ], bag-mediated filtration [ 36 ], and magnesium- and aluminium-based adsorption [ 34 , 38 ].…”

Section: Introductionmentioning

confidence: 99%

Simple Wastewater Preparation Protocol Applied to Monitor the Emergence of the Omicron 21L/BA.2 Variant by Genome Sequencing

Wurtz

Boussier

Souville

et al. 2023

Viruses

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Detecting and monitoring viruses in wastewater samples have been reported as useful ways of tracking SARS-CoV-2 epidemic trends. However, there is currently no unanimously recognised method of processing samples to identify and quantify SARS-CoV-2 variants in wastewater. We aimed to implement a method that was as simple as possible in order to be used universally. In a study performed between January 2022 and June 2022 in the city of Marseille, France, we first evaluated the impact of the sample preservation strategy. We then compared ultracentrifugation to ultrafiltration and several steps of filtration to determine the optimal approach for virus concentration. As a proof-of-concept, the definitive protocol was applied to next-generation sequencing of SARS-CoV-2 in wastewater to monitor the emergence of the Omicron variant in the city. For sewage water to be processed in the week following the sampling, storage at +4 °C is sufficient, with less than 1 Ct loss. Filtration with a 5 µm syringe filter, then with a 0.8 µm filtration unit, followed by ultrafiltration was the optimal protocol, leading to an average increase of 3.24 Ct when the starting Ct was on average 38 in the wastewater. This made it possible to observe the emergence of the Omicron 21L/BA.2 variant after Omicron 21K/BA.1 by genome sequencing over a period ranging from 20 February to 10 April 2022 in agreement with observations based on patient data. To conclude, by using a simple method requiring only basic filters and a centrifuge as equipment, it is possible to accurately track the relative incidence rates and the emergence of SARS-CoV-2 variants based on sewage samples.

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Destiny of emerging viruses: a systematic review

Mobarak Qamsari,

Mohammadi

2024

Int. J. Environ. Sci. Technol.

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Surveillance of SARS-CoV-2 in extensive monitoring of municipal wastewater: key issues to yield reliable results

Cited by 9 publications

References 20 publications

Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing

Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing

Simple Wastewater Preparation Protocol Applied to Monitor the Emergence of the Omicron 21L/BA.2 Variant by Genome Sequencing

Destiny of emerging viruses: a systematic review

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