1887
  1. Home
  2. Eurosurveillance
  3. Volume 27, Issue 10, 10/Mar/2022
  4. Article
Research Open Access
Like 0
Download

Abstract

Background

Throughout the COVID-19 pandemic, SARS-CoV-2 genetic variants of concern (VOCs) have repeatedly and independently arisen. VOCs are characterised by increased transmissibility, increased virulence or reduced neutralisation by antibodies obtained from prior infection or vaccination. Tracking the introduction and transmission of VOCs relies on sequencing, typically whole genome sequencing of clinical samples. Wastewater surveillance is increasingly used to track the introduction and spread of SARS-CoV-2 variants through sequencing approaches.

Aim

Here, we adapt and apply a rapid, high-throughput method for detection and quantification of the relative frequency of two deletions characteristic of the Alpha, Beta, and Gamma VOCs in wastewater.

Methods

We developed drop-off RT-dPCR assays and an associated statistical approach implemented in the R package WWdPCR to analyse temporal dynamics of SARS-CoV-2 signature mutations (spike Δ69–70 and ORF1a Δ3675–3677) in wastewater and quantify transmission fitness advantage of the Alpha VOC.

Results

Based on analysis of Zurich wastewater samples, the estimated transmission fitness advantage of SARS-CoV-2 Alpha based on the spike Δ69–70 was 0.34 (95% confidence interval (CI): 0.30–0.39) and based on ORF1a Δ3675–3677 was 0.53 (95% CI: 0.49–0.57), aligning with the transmission fitness advantage of Alpha estimated by clinical sample sequencing in the surrounding canton of 0.49 (95% CI: 0.38–0.61).

Conclusion

Digital PCR assays targeting signature mutations in wastewater offer near real-time monitoring of SARS-CoV-2 VOCs and potentially earlier detection and inference on transmission fitness advantage than clinical sequencing.

© Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Loading

Article metrics loading...

/content/10.2807/1560-7917.ES.2022.27.10.2100806
2022-03-10
2024-12-23
/content/10.2807/1560-7917.ES.2022.27.10.2100806
Loading
Loading full text...

Full text loading...

/deliver/fulltext/eurosurveillance/27/10/eurosurv-27-10-4.html?itemId=/content/10.2807/1560-7917.ES.2022.27.10.2100806&mimeType=html&fmt=ahah

References

  1. Vogels CBF, Breban MI, Ott IM, Alpert T, Petrone ME, Watkins AE, et al. Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. PLoS Biol. 2021;19(5):e3001236.  https://doi.org/10.1371/journal.pbio.3001236  PMID: 33961632 
  2. Bedotto M, Fournier P-E, Houhamdi L, Levasseur A, Delerce J, Pinault L, et al. Implementation of an in-house real-time reverse transcription-PCR assay for the rapid detection of the SARS-CoV-2 Marseille-4 variant. J Clin Virol. 2021;139:104814.  https://doi.org/10.1016/j.jcv.2021.104814  PMID: 33836314 
  3. Wang W, Xu Y, Gao R, Lu R, Han K, Wu G, et al. Detection of SARS-CoV-2 in different types of clinical specimens. JAMA. 2020;323(18):1843-4.  https://doi.org/10.1001/jama.2020.3786  PMID: 32159775 
  4. Jones DL, Baluja MQ, Graham DW, Corbishley A, McDonald JE, Malham SK, et al. Shedding of SARS-CoV-2 in feces and urine and its potential role in person-to-person transmission and the environment-based spread of COVID-19. Sci Total Environ. 2020;749:141364.  https://doi.org/10.1016/j.scitotenv.2020.141364  PMID: 32836117 
  5. Crits-Christoph A, Kantor RS, Olm MR, Whitney ON, Al-Shayeb B, Lou YC, et al. Genome sequencing of sewage detects regionally prevalent sARS-CoV-2 Variants. MBio. 2021;12(1):e02703-20.  https://doi.org/10.1128/mBio.02703-20  PMID: 33468686 
  6. Jahn K, Dreifuss D, Topolsky I, Kull A, Ganesanandamoorthy P, Fernandez-Cassi X, et al. Detection of SARS-CoV-2 variants in Switzerland by genomic analysis of wastewater samples. medRxiv. 2021.01.08.21249379.  https://doi.org/10.1101/2021.01.08.21249379  https://doi.org/10.1101/2021.01.08.21249379 
  7. Wilton T, Bujaki E, Klapsa D, Majumdar M, Zambon M, Fritzsche M, et al. Rapid increase of SARS-CoV-2 variant B.1.1.7 detected in sewage samples from England between October 2020 and January 2021. mSystems. 2021;6(3):e0035321.  https://doi.org/10.1128/mSystems.00353-21  PMID: 34128696 
  8. Chaintoutis SC, Chassalevris T, Tsiolas G, Balaska S, Vlatakis I, Mouchtaropoulou E, et al. A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions. J Virol Methods. 2021;296:114242.  https://doi.org/10.1016/j.jviromet.2021.114242  PMID: 34274369 
  9. Wurtzer S, Waldman P, Levert M, Mouchel JM, Gorgé O, Boni M, et al. Monitoring the propagation of SARS CoV2 variants by tracking identified mutation in wastewater using specific RT-qPCR. medRxiv.2021.03.10.21253291  https://doi.org/10.1101/2021.03.10.21253291  https://doi.org/10.1101/2021.03.10.21253291 
  10. Lee WL, Imakaev M, Armas F, McElroy KA, Gu X, Duvallet C, et al. Quantitative SARS-CoV-2 Alpha variant B.1.1.7 tracking in wastewater by allele-specific RT-qPCR. Environ Sci Technol Lett. 2021;8(8):675-82.  https://doi.org/10.1021/acs.estlett.1c00375 
  11. Heijnen L, Elsinga G, de Graaf M, Molenkamp R, Koopmans MPG, Medema G. Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Sci Total Environ. 2021;799:149456.  https://doi.org/10.1016/j.scitotenv.2021.149456  PMID: 34371414 
  12. Chen C, Nadeau SA, Topolsky I, Manceau M, Huisman JS, Jablonski KP, et al. Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland. Epidemics. 2021;37:100480.  https://doi.org/10.1016/j.epidem.2021.100480  PMID: 34488035 
  13. Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, Harrison EM, et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol. 2021;19(7):409-24.  https://doi.org/10.1038/s41579-021-00573-0  PMID: 34075212 
  14. Meng B, Kemp SA, Papa G, Datir R, Ferreira IATM, Marelli S, et al. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Cell Rep. 2021;35(13):109292.  https://doi.org/10.1016/j.celrep.2021.109292  PMID: 34166617 
  15. Bechtold P, Wagner P, Hosch S, Siegrist D, Ruiz-Serrano A, Gregorini M, et al. Rapid identification of SARS-CoV-2 variants of concern using a portable peakPCR Platform. Anal Chem. 2021;93(49):16350-9.  https://doi.org/10.1021/acs.analchem.1c02368  PMID: 34852455 
  16. Zhu K, Suttner B, Pickering A, Konstantinidis KT, Brown J. A novel droplet digital PCR human mtDNA assay for fecal source tracking. Water Res. 2020;183:116085.  https://doi.org/10.1016/j.watres.2020.116085  PMID: 32750535 
  17. Fernandez-Cassi X, Scheidegger A, Bänziger C, Cariti F, Tuñas Corzon A, Ganesanandamoorthy P, et al. Wastewater monitoring outperforms case numbers as a tool to track COVID-19 incidence dynamics when test positivity rates are high. Water Res. 2021;200:117252.  https://doi.org/10.1016/j.watres.2021.117252  PMID: 34048984 
  18. Huisman JS, Scire J, Caduff L, Fernandez-Cassi X, Ganesanandamoorthy P, Kull A, et al. Wastewater-based estimation of the effective reproductive number of SARS-CoV-2. medRxiv.2021.04.29.21255961.  https://doi.org/10.1101/2021.04.29.21255961 . https://doi.org/10.1101/2021.04.29.21255961 
  19. Huggett JF, dMIQE Group. The digital MIQE guidelines update: minimum information for publication of quantitative digital PCR experiments for 2020. Clin Chem. 2020;66(8):1012-29.  https://doi.org/10.1093/clinchem/hvaa125  PMID: 32746458 
  20. Dube S, Qin J, Ramakrishnan R. Mathematical analysis of copy number variation in a DNA sample using digital PCR on a nanofluidic device. PLoS One. 2008;3(8):e2876.  https://doi.org/10.1371/journal.pone.0002876  PMID: 18682853 
  21. Basu AS. Digital assays part I: partitioning statistics and digital PCR. SLAS Technol. 2017;22(4):369-86.  https://doi.org/10.1177/2472630317705680  PMID: 28448765 
  22. Dorazio RM, Hunter ME. Statistical models for the analysis and design of digital polymerase chain reaction (dPCR) experiments. Anal Chem. 2015;87(21):10886-93.  https://doi.org/10.1021/acs.analchem.5b02429  PMID: 26436653 
  23. Whale AS, Huggett JF, Tzonev S. Fundamentals of multiplexing with digital PCR. Biomol Detect Quantif. 2016;10:15-23.  https://doi.org/10.1016/j.bdq.2016.05.002  PMID: 27990345 
  24. Milbury CA, Zhong Q, Lin J, Williams M, Olson J, Link DR, et al. Determining lower limits of detection of digital PCR assays for cancer-related gene mutations. Biomol Detect Quantif. 2014;1(1):8-22.  https://doi.org/10.1016/j.bdq.2014.08.001  PMID: 27920993 
  25. Baker FB, Kim S-H. Item response theory: parameter estimation techniques, second edition. CRC Press. 2nd ed. Boca Raton: CRC Press; 2004 https://doi.org/10.1201/9781482276725
  26. McCullagh P, Nelder JA. Generalized linear models. 2nd ed. New York: Routledge; 2019. https://doi.org/10.1201/9780203753736
  27. Held L, Sabanés Bové D. Applied statistical inference: likelihood and bayes. Berlin, Heidelberg: Springer; 2014. http://dx.doi.org/10.1007/978-3-642-37887-4
  28. Chen C, Nadeau S, Yared M, Voinov P, Xie N, Roemer C, et al. CoV-spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants. Bioinformatics. 2021;btab856.
  29. Jones TC, Biele G, Mühlemann B, Veith T, Schneider J, Beheim-Schwarzbach J, et al. Estimating infectiousness throughout SARS-CoV-2 infection course. Science. 2021;373(6551):eabi5273.  https://doi.org/10.1126/science.abi5273  PMID: 34035154 
  30. Philo SE, Keim EK, Swanstrom R, Ong AQW, Burnor EA, Kossik AL, et al. A comparison of SARS-CoV-2 wastewater concentration methods for environmental surveillance. Sci Total Environ. 2021;760:144215.  https://doi.org/10.1016/j.scitotenv.2020.144215  PMID: 33340739 
  31. Huggett JF, Novak T, Garson JA, Green C, Morris-Jones SD, Miller RF, et al. Differential susceptibility of PCR reactions to inhibitors: an important and unrecognised phenomenon. BMC Res Notes. 2008;1(1):70.  https://doi.org/10.1186/1756-0500-1-70  PMID: 18755023 
Inferring transmission fitness advantage of SARS-CoV-2 variants of concern from wastewater samples using digital PCR, Switzerland, December 2020 through March 2021
<p class="citation"> <span>Citation style for this article:</span> <span class="meta-value authors"> <a href="/search?value1=Lea+Caduff&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Caduff Lea</a>, <a href="/search?value1=David+Dreifuss&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Dreifuss David</a>, <a href="/search?value1=Tobias+Schindler&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Schindler Tobias</a>, <a href="/search?value1=Alexander+J+Devaux&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Devaux Alexander J</a>, <a href="/search?value1=Pravin+Ganesanandamoorthy&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Ganesanandamoorthy Pravin</a>, <a href="/search?value1=Anina+Kull&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Kull Anina</a>, <a href="/search?value1=Elyse+Stachler&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Stachler Elyse</a>, <a href="/search?value1=Xavier+Fernandez-Cassi&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Fernandez-Cassi Xavier</a>, <a href="/search?value1=Niko+Beerenwinkel&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Beerenwinkel Niko</a>, <a href="/search?value1=Tamar+Kohn&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Kohn Tamar</a>, <a href="/search?value1=Christoph+Ort&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Ort Christoph</a>, <a href="/search?value1=Timothy+R+Julian&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Julian Timothy R</a></span>. Inferring transmission fitness advantage of SARS-CoV-2 variants of concern from wastewater samples using digital PCR, Switzerland, December 2020 through March 2021. <a href="/content/ecdc">Euro Surveill.</a> 2022;27(10):pii=2100806. <a href="https://doi.org/10.2807/1560-7917.ES.2022.27.10.2100806" title="doi link" target="_blank">https://doi.org/10.2807/1560-7917.ES.2022.27.10.2100806</a> <span class="ES_Article_citation"> <span class="generated">Received</span>: 02 Aug 2021;&nbsp;&nbsp; <span class="generated">Accepted</span>: 21 Jan 2022 </span> </p>
/content/10.2807/1560-7917.ES.2022.27.10.2100806
/content/10.2807/1560-7917.ES.2022.27.10.2100806
Loading

Data & Media loading...

Supplementary data

Submit comment
Close
Comment moderation successfully completed
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error