Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium

Izquierdo-Lara, Ray; Elsinga, Goffe; Heijnen, Leo; Munnink, Bas B. Oude; Schapendonk, Claudia M. E.; Nieuwenhuijse, David F.; Kon, Matthijs; Lu, Lu; Aarestrup, Frank Møller; Lycett, Samantha; Medema, Gertjan; Koopmans, Marion; Graaf, Miranda de

doi:10.3201/eid2705.204410

Cited by 180 publications

(161 citation statements)

References 48 publications

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“…Especially as new SARS-CoV-2 variants emerge that have altered viral fitness and/or pathogenesis, it is important for health professionals and policy makers to have up-to-date information on the viral populations present in communities. Surveillance of wastewater by high-throughput sequencing has proven to be a cost effective and reliable method to obtain such information [ 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 ]. Sequencing of wastewater for SARS-CoV-2 relies on whole-genome sequencing, targeted amplicon sequencing, or some intermediate of the two; each approach has advantages and disadvantages.…”

Section: Discussionmentioning

confidence: 99%

“…However, early in the SARS-CoV-2 pandemic, wastewater was used to track community levels and spread of SARS-CoV-2 by Reverse Transcription-Quantitative Polymerase Chain Reaction (RT-qPCR) methods [ 4 , 5 ]. Investigators have also used high-throughput sequencing on wastewater samples to obtain full or partial SARS-CoV-2 genomic sequences which have been used for metagenomic and epidemiologic analysis [ 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 ]. Sequences identified in wastewater samples may reflect known lineages as well as lineages not reported from clinical samples.…”

Section: Introductionmentioning

confidence: 99%

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Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner

Gregory

Wieberg

Wenzel

et al. 2021

Viruses

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Sequencing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from wastewater has become a useful tool in monitoring the spread of viral variants. Approaches to this task have been varied, relying on differing sequencing methods and computational analyses. We used a novel computation workflow based on amplicon sequencing of SARS-CoV-2 spike domains in order to track viral populations in wastewater. As part of this workflow, we developed a program, SAM Refiner, that has a variety of outputs, including novel variant reporting as well as functions designed to remove polymerase chain reaction (PCR) generated chimeric sequences. With these methods, we were able to track viral population dynamics over time. We report here on the emergence of two variants of concern, B.1.1.7 (Alpha) and P.1 (Gamma), and their displacement of the D614G B.1 variant in a Missouri sewershed.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner

Gregory

Wieberg

Wenzel

et al. 2021

Viruses

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“…Variants surveillance done through whole genome sequencing of clinical samples is expensive and time-consuming. Therefore, genome sequencing of viral RNA isolated from sewage can rapidly detect and identify any sequence variation (Izquierdo-Lara et al, 2021 ). Thus, deep sequencing initiatives in sewage samples can help detect new and rare mutations from mixtures of SARS-CoV-2 lineages and identify VoC in sewage and subsequently their presence in the community (Heijnen et al, 2021 ).…”

Section: Wastewater-based Epidemiological Surveillance Of Coronavirusesmentioning

confidence: 99%

“…Thus, NGS analysis of wastewater could be used to study CoV-2 diversity in a community. Genome sequencing of sewage could be either used independently or with clinical surveillance to observe for changes in viral diversity and clinically relevant mutations (Izquierdo-Lara et al, 2021 ).…”

Section: Nucleic Acid-based Rt-qpcr and Metagenomics For Detection Of Cov-2 In Wastewatermentioning

confidence: 99%

Coronavirus: occurrence, surveillance, and persistence in wastewater

Basavaraju

Aswathanarayan

Madhu

et al. 2021

Environ Monit Assess

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it will help in knowing if there are asymptomatic carriers, as such people do not show any signs of symptoms but shed the viruses in feces. The present review focuses on the epidemiological surveillance of wastewater for coronaviruses, as in recent years these are increasingly causing global pandemics. In this review we have discussed, the four pertinent areas of coronavirus study: (1) occurrence of coronavirus in wastewater, (2) wastewater based epidemiological surveillance of coronaviruses, (3) epidemiological surveillance tools used for detection of coronaviruses in sewage, and (4) persistence and sustainability of coronaviruses in wastewater.

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“…The genetic diversity of SARS-CoV-2 has largely been determined via the sequencing of clinical samples obtained from infected individuals; however, changes in the viral genome have been shown to be detectable in wastewater samples [18][19][20][21][22][23]. Indeed, the presence of specific SARS-CoV-2 variants is often detectable in the wastewater of a community prior to detection in clinical samples [2,5,9,13,21,23,24].…”

Section: Introductionmentioning

confidence: 99%

The Rapid Assessment of Aggregated Wastewater Samples for Genomic Surveillance of SARS-CoV-2 on a City-Wide Scale

Rouchka

Chariker

Kumar

et al. 2021

Preprint

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Throughout the course of the ongoing SARS-CoV-2 pandemic there has been a need for approaches that enable rapid monitoring of public health using an unbiased and minimally invasive means. A major way this has been accomplished is through the regular assessment of wastewater samples by qRT-PCR to detect the prevalence of viral nucleic acid with respect to time and location. Further expansion of SARS-CoV-2 wastewater monitoring efforts to include the detection of variants of interest / concern through next-generation sequencing have enhanced the understanding of the SARS-CoV-2 outbreak. In this report we detail the results of a collaborative effort between public health and metropolitan wastewater management authorities and the University of Louisville to monitor the SARS-CoV-2 pandemic through the monitoring of aggregate wastewater samples over a period of 28 weeks. Our data indicates that wastewater monitoring of water quality treatment centers and smaller neighborhood-scale catchment areas is a viable means by which the prevalence and genetic variation of SARS-CoV-2 within a metropolitan community of approximately one million individuals may be monitored. Importantly, these efforts confirm that regional emergence and spread of variants of interest / concern may be detected as readily in aggregate wastewater samples as compared to the individual wastewater sheds.

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Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium

Cited by 180 publications

References 48 publications

Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner

Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner

Coronavirus: occurrence, surveillance, and persistence in wastewater

The Rapid Assessment of Aggregated Wastewater Samples for Genomic Surveillance of SARS-CoV-2 on a City-Wide Scale

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