Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC

Jahn, Katharina; Dreifuss, David; Topolsky, Ivan; Kull, Anina; Ganesanandamoorthy, Pravin; Fernández-Cassi, Xavier; Bänziger, Carola; Devaux, Alexander J.; Stachler, Elyse; Caduff, Lea; Cariti, Federica; Corzón, Álex Tuñas; Fuhrmann, Lara; Chen, Chaoran; Jablonski, Kim Philipp; Nadeau, Sarah; Feldkamp, Mirjam; Beisel, Christian; Aquino, Catharine; Stadler, Tanja; Ort, Christoph; Kohn, Tamar; Julian, Timothy R.; Beerenwinkel, Niko

doi:10.1038/s41564-022-01185-x

Cited by 92 publications

(71 citation statements)

References 34 publications

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“…Wastewater monitoring of the SARS-CoV-2 variant emergence and spread offers unique benefits based on the early detection of the variant arrival prior to the clinical data 3,34,35,15,25 , and broad surveillance coverage of the population 20,34,36,37 . QuaID offers a highly sensitive pipeline for VoC detection using wastewater SARS-CoV-2 sequencing data.…”

Section: Discussionmentioning

confidence: 99%

“…This is particularly important given that the underlying sample quality varies and the depth and breadth of coverage of amplicon sequencing data can vary widely across samples 18 . Furthermore, the ability to leverage indel information in the inference process makes QuaID overall more robust than approaches that rely solely on SNVs 9,15 . Methods that currently rely on phylogenetic placement or utilize phylogenetic trees inferred by tools like UShER 33 will likely continue to lack support for indel based detection.…”

Section: Discussionmentioning

confidence: 99%

“…Wastewater monitoring is an invaluable tool for SARS-CoV-2 surveillance [1][2][3][4][5][6][7][8] . Despite multiple recent successes in VoC monitoring and detection from wastewater sequencing data [9][10][11][12][13][14][15] , there are multiple challenges associated with the nature of the environmental data. Since wastewater represents a pooled sample of multiple hosts, it harbors a diversity of SARS-CoV-2 variants that are currently circulating in the population 1,2,10,13 , including potentially previously unreported genotypes 16 .…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

QuaID: Enabling Earlier Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater

Sapoval¹,

Lou

Hopkins

et al. 2021

Preprint

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SARS-CoV-2 RNA shedding in stool enabled wastewater surveillance for the genetic material of the virus. With the emergence of novel variants of concern and interest it becomes increasingly important to track arrival and spread of these variants. However, most current approaches rely on the manually curated lists of mutations phenotypically associated with the variants of concern. The resulting data has many overlaps between distinct variants leading to less specific characterization of complex sample mixtures that result from wastewater monitoring. In our work we propose a simple and specific method for characterization of wastewater samples by introducing the concept of quasi-unique mutations. Our approach is data driven and results in earlier detection and higher resolution of variants of concern emergence patterns in wastewater data.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

QuaID: Enabling Earlier Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater

Sapoval¹,

Lou

Hopkins

et al. 2021

Preprint

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“…Similar amplicon dropout issues were previously reported for a few amplicons using the ARTIC V3 panel. 32, 33 We used ARTIC V4.0 primers, which address the V3 coverage issues but do not include all the mutations in SARS-CoV-2 Delta and Omicron lineages in the primer design. 34 Other wastewater factors may also explain the low-depth coverage within certain regions of SARS-CoV-2 genome.…”

Section: Resultsmentioning

confidence: 99%

Improved Robustness of SARS-CoV-2 Whole-Genome Sequencing from Wastewater with a Nonselective Virus Concentration Method

Segelhurst

Bard

Pillsbury

et al. 2022

Preprint

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The sequencing of human virus genomes from wastewater samples is an efficient method for tracking viral transmission and evolution at the community level. However, this requires the recovery of viral nucleic acids of high quality. We developed a reusable tangential-flow filtration system to concentrate and purify viruses from wastewater for whole-genome sequencing. A pilot study was conducted with 94 wastewater samples from four local sewersheds, from which viral nucleic acids were extracted, and the whole genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was sequenced using the ARTIC V4.0 primers. Our method yielded a high probability (0.9) of recovering complete or near-complete SARS-CoV-2 genomes (>90% coverage at 10× depth) from wastewater when the COVID-19 incidence rate exceeded 33 cases per 100 000 people. The relative abundances of sequenced SARS-CoV-2 variants followed the trends observed from patient-derived samples. We also identified SARS-CoV-2 lineages in wastewater that were underrepresented or not present in the clinical whole-genome sequencing data. The developed tangential-flow filtration system can be easily adopted for the sequencing of other viruses in wastewater, particularly those at low concentrations.

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“…Sample intrinsic features such as fragmented RNA template are unavoidable. In fact, reports of fragmented wastewater SARS-CoV-2 sequencing results from whole genome amplification are not uncommon 9,18,19 ; for example, Amman et al applied a criteria of 40% genome breadth of coverage for a wastewater sample to be “passed” for downstream sequencing analysis 18 .…”

Section: Introductionmentioning

confidence: 99%

Intensity of sample processing methods impacts wastewater SARS-CoV-2 whole genome amplicon sequencing outcomes

Feng

Owens

Shrestha³

et al. 2022

Preprint

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Wastewater SARS-CoV-2 surveillance has been deployed since the beginning of the COVID-19 pandemic to monitor dynamics in virus burden in local communities. Genomic surveillance of SARS-CoV-2 in wastewater, particularly the efforts for whole genome sequencing for variant tracking or identification, are comparatively challenging due to low target concentration, complex microbial and chemical background, and lack of robust nucleic acid recovery experimental procedures. The intrinsic sample limitations are inherent to wastewater. In this study, we evaluated impacts from sample types, certain sample intrinsic features, and processing and sequencing methods on sequencing outcomes with a specific focus on the breadth of genome coverage. We collected 184 composite and grab wastewater samples from the Chicago area between March to October 2021 for SARS-CoV-2 quantification and genomic surveillance. Samples were processed using a mixture of processing methods reflecting different homogenization intensities (HA+Zymo beads, HA+glass beads, and Nanotrap), and were sequenced using two sequencing library preparation kits (the Illumina COVIDseq kit and the QIAseq DIRECT kit). A synthetic SARS-CoV-2 RNA experiment was performed to validate the potential impacts of processing methods on sequencing outcomes. Our findings suggested that 1) SARS-CoV-2 whole genome sequencing outcomes were associated with sample types and processing methods 2) in less intensive method processed samples (HA+glass beads), higher genome breadth of coverage in sequencing (over 80%) was associated with N1 concentration > 105 cp/L, while in intensive method (HA+Zymo beads), qPCR results were inconsistent with sequencing outcomes, and 3) sample processing methods and sequencing kits, rather than the extraction methods or intrinsic features of wastewater samples, played important roles in wastewater SARS-CoV-2 amplicon sequencing. Overall, extra attention should be paid to wastewater sample processing (e.g., concentration and homogenization) for sufficient, good quality RNA yield for downstream sequencing.

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Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC

Cited by 92 publications

References 34 publications

QuaID: Enabling Earlier Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater

QuaID: Enabling Earlier Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater

Improved Robustness of SARS-CoV-2 Whole-Genome Sequencing from Wastewater with a Nonselective Virus Concentration Method

Intensity of sample processing methods impacts wastewater SARS-CoV-2 whole genome amplicon sequencing outcomes

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