Australian and New Zealand Laboratory Experience and Proposed Future Direction of Wastewater Pathogen Genomic Surveillance
Abstract
:1. Introduction
2. Materials and Methods
3. Analysis and Discussion
3.1. Sampling
3.2. Viral Concentration Methods
3.3. Extraction
3.4. Quantitative Detection
3.5. Sequencing
3.6. Reporting
3.7. Current Challenges, Limitations, and Strengths of Wastewater Surveillance
3.8. Future Recommendations and Considerations for Wastewater Surveillance
4. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
Appendix A. Questions Used to Survey Jurisdictions on Wastewater Surveillance
Survey Questions |
Which segments of the survey will you be completing? |
Does your jurisdiction undertake SARS-CoV-2 sequencing of wastewater? |
Does your jurisdiction issue wastewater reports? |
What is the name of the unit/service that collects the sample? |
What method of wastewater collection is used for general surveillance? |
Does the method vary between sites? Please explain. |
From how many sites are samples collected? |
How many sites of wastewater treatment plants do you collect samples from? |
How many times per month do you collect samples from wastewater treatment plants? |
How many sites from sewers do you collect samples from? |
How many sites from airports do you collect samples from? |
How many times per month do you collect samples from airports? |
How many sites from facility/building do you collect samples from? |
Please indicate the catchment sizes of wastewater treatment plant |
Please indicate the catchment sizes of sewer |
Please indicate the catchment sizes of facility/building |
Which type of sites are samples collected from? Other, please specify |
Please indicate the catchment type and sizes.—Other: please specify |
What is the make-up of the sites and how often are samples collected?—General population/community |
What is the make-up of the sites and how often are samples collected?—Targeted population/community e.g., facility |
How many wastewater samples are collected each week for SARS-CoV-2 quantification? |
Of these, for how many is sequencing undertaken on? |
Are pre-treatments performed on the sample prior to viral concentration (e.g., MgCl2, pre-acidification etc.)? If yes, please state which pre-treatments. |
What is the name of the unit/service where viral concentration is performed? |
What is the method used for viral concentration? |
What volume do you process? |
What is the name of the laboratory where RNA extraction is performed? |
What extraction platform and kit are used? |
Do you use an RNAase inhibitor? If yes, at what stage? |
Is quantitative SARS-CoV-2 PCR performed on all samples? |
Which RT-qPCR assay is used to perform quantitative SARS-CoV-2 PCR? Please describe. |
Is the sample transported to another laboratory after extraction and before amplification/sequencing? If yes, how long after extraction are they transported and what? |
What is the name of the laboratory where sequencing is performed? |
What sequencing method is used? |
What method/scheme is used for amplicon generation/library preparation? |
What sequencing platform is used |
What is the deconvolution tool for reporting of lineages? |
What are the QC criteria to allow reporting of a sample? |
Which of the following check controls do you use? |
Which components of the workflow have you validated and to what extent? |
What are you including in your reporting? |
What level are the lineages reported? |
If lineages are collapsed, what is your process for doing so? |
Who is the intended audience of the report? |
References
- Parkins Michael, D.; Lee Bonita, E.; Acosta, N.; Bautista, M.; Hubert Casey, R.J.; Hrudey Steve, E.; Frankowski, K.; Pang, X.-L. Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond. Clin. Microbiol. Rev. 2023, 37, e00103-22. [Google Scholar] [CrossRef] [PubMed]
- Sinclair, R.G.; Choi, C.Y.; Riley, M.R.; Gerba, C.P. Pathogen surveillance through monitoring of sewer systems. Adv. Appl. Microbiol. 2008, 65, 249–269. [Google Scholar] [PubMed]
- Levy, J.I.; Andersen, K.G.; Knight, R.; Karthikeyan, S. Wastewater surveillance for public health. Science 2023, 379, 26–27. [Google Scholar] [CrossRef] [PubMed]
- O’Keeffe, J. Wastewater-based epidemiology: Current uses and future opportunities as a public health surveillance tool. Environ. Health Rev. 2021, 64, 44–52. [Google Scholar] [CrossRef]
- Grassly, N.C.; Shaw, A.G.; Owusu, M. Global wastewater surveillance for pathogens with pandemic potential: Opportunities and challenges. Lancet Microbe 2025, 6, 100939. [Google Scholar] [CrossRef] [PubMed]
- Diamond, M.B.; Keshaviah, A.; Bento, A.I.; Conroy-Ben, O.; Driver, E.M.; Ensor, K.B.; Halden, R.U.; Hopkins, L.P.; Kuhn, K.G.; Moe, C.L.; et al. Wastewater surveillance of pathogens can inform public health responses. Nat Med. 2022, 28, 1992–1995. [Google Scholar] [CrossRef] [PubMed]
- Shrestha, S.; Yoshinaga, E.; Chapagain, S.K.; Mohan, G.; Gasparatos, A.; Fukushi, K. Wastewater-Based Epidemiology for Cost-Effective Mass Surveillance of COVID-19 in Low- and Middle-Income Countries: Challenges and Opportunities. Water 2021, 13, 2897. [Google Scholar] [CrossRef]
- Ali, S.; Gudina, E.K.; Gize, A.; Aliy, A.; Adankie, B.T.; Tsegaye, W.; Hundie, G.B.; Muleta, M.B.; Chibssa, T.R.; Belaineh, R.; et al. Community Wastewater-Based Surveillance Can Be a Cost-Effective Approach to Track COVID-19 Outbreak in Low-Resource Settings: Feasibility Assessment for Ethiopia Context. Int. J. Environ. Res. Public Health 2022, 19, 8515. [Google Scholar] [CrossRef]
- Leifels, M.; Lee, W.L.; Armas, F.; Gu, X.; Chandra, F.; Cheng, D.; Kwok, W.C.; Chua, F.J.D.; Kim, S.Y.; Ng, W.J.; et al. Surveillance of SARS-CoV-2 in Wastewater at the Population Level: Insights into the Implementation of Non-invasive Targeted Monitoring in Singapore and the USA. In Wastewater Surveillance for COVID-19 Management; Kumar, M., Kuroda, K., Mukherjee, S., Ngiehm, L.D., Vithanage, M., Tyagi, V.K., Eds.; Springer International Publishing: Cham, Switzerland, 2024; pp. 1–20. [Google Scholar]
- Hovi, T.; Shulman, L.M.; Van Der Avoort, H.; Deshpande, J.; Roivainen, M.; de Gourville, E.M. Role of environmental poliovirus surveillance in global polio eradication and beyond. Epidemiol. Infect. 2012, 140, 1–13. [Google Scholar] [CrossRef]
- Keshaviah, A.; Diamond, M.B.; Wade, M.J.; Scarpino, S.V.; Ahmed, W.; Amman, F.; Aruna, O.; Badilla-Aguilar, A.; Bar-Or, I.; Bergthaler, A.; et al. Wastewater monitoring can anchor global disease surveillance systems. Lancet Glob. Health 2023, 11, e976–e981. [Google Scholar] [CrossRef]
- Naughton, C.C.; Roman, F.A., Jr.; Alvarado, A.G.F.; Tariqi, A.Q.; Deeming, M.A.; Kadonsky, K.F.; Bibby, K.; Bivins, A.; Medema, G.; Ahmed, W.; et al. Show us the data: Global COVID-19 wastewater monitoring efforts, equity, and gaps. FEMS Microbes 2023, 4, xtad003. [Google Scholar] [CrossRef]
- Gawlik, B.; Tavazzi, S.; Mariani, G.; Skejo, H.; Sponar, M.; Higgins, T.; Medema, G.; Wintgens, T. SARS-CoV-2 Surveillance Employing Sewage—Towards a Sentinel System; European Union Publications Office: Luxembourg, 2021. [Google Scholar]
- Michie, A. Wastewater-based SARS-CoV-2 surveillance and sequencing. Microbiol. Aust. 2024, 45, 8–12. [Google Scholar] [CrossRef]
- Water Research Australia. Collaboration on Sewage Surveillance of SARS-CoV-2 (ColoSSoS); Water Research Australia: Adelaide, SA, Australia, 2022. [Google Scholar]
- Ahmed, W.; Tscharke, B.; Bertsch, P.M.; Bibby, K.; Bivins, A.; Choi, P.; Clarke, L.; Dwyer, J.; Edson, J.; Nguyen, T.M.H.; et al. SARS-CoV-2 RNA monitoring in wastewater as a potential early warning system for COVID-19 transmission in the community: A temporal case study. Sci. Total Environ. 2021, 761, 144216. [Google Scholar]
- Randazzo, W.; Truchado, P.; Cuevas-Ferrando, E.; Simón, P.; Allende, A.; Sánchez, G. SARS-CoV-2 RNA in wastewater anticipated COVID-19 occurrence in a low prevalence area. Water Res. 2020, 181, 115942. [Google Scholar] [PubMed]
- Medema, G.; Heijnen, L.; Elsinga, G.; Italiaander, R.; Brouwer, A. Presence of SARS-Coronavirus-2 RNA in Sewage and Correlation with Reported COVID-19 Prevalence in the Early Stage of the Epidemic in The Netherlands. Environ. Sci. Technol. Lett. 2020, 7, 511–516. [Google Scholar] [PubMed]
- La Rosa, G.; Iaconelli, M.; Mancini, P.; Bonanno Ferraro, G.; Veneri, C.; Bonadonna, L.; Lucentini, L.; Suffredini, E. First detection of SARS-CoV-2 in untreated wastewaters in Italy. Sci. Total Environ. 2020, 736, 139652. [Google Scholar]
- Levy, A.; Gazeley, J.; Lee, T.; Jardine, A.; Gordon, C.; Cooper, N.; Theobald, R.; Huppatz, C.; Sjollema, S.; Hodge, M.; et al. Whole genome sequencing of SARS-CoV-2 from wastewater links to individual cases in catchments. Sci. Total Environ. 2022, 851 Pt 2, 158266. [Google Scholar] [CrossRef] [PubMed]
- Hewitt, J.; Trowsdale, S.; Armstrong, B.A.; Chapman, J.R.; Carter, K.M.; Croucher, D.M.; Trent, C.R.; Sim, R.E.; Gilpin, B.J. Sensitivity of wastewater-based epidemiology for detection of SARS-CoV-2 RNA in a low prevalence setting. Water Res. 2022, 211, 118032. [Google Scholar] [PubMed]
- McMahan, C.S.; Self, S.; Rennert, L.; Kalbaugh, C.; Kriebel, D.; Graves, D.; Colby, C.; Deaver, J.A.; Popat, S.C.; Karanfil, T.; et al. COVID-19 wastewater epidemiology: A model to estimate infected populations. Lancet Planet. Health 2021, 5, e874–e881. [Google Scholar]
- Gazeley, J.; Lee, T.; Knight, D.R.; Shivarev, A.; Gordon, C.; Speers, D.; Barth, D.D.; Maticevic, J.; Hodge, M.; Armstrong, P.; et al. Correlating Quantitative and Genomic SARS-CoV-2 Wastewater Data with Clinical Metrics in Metropolitan Perth, Western Australia. Environments 2024, 11, 62. [Google Scholar] [CrossRef]
- Crits-Christoph, A.; Kantor, R.S.; Olm, M.R.; Whitney, O.N.; Al-Shayeb, B.; Lou, Y.C.; Flamholz, A.; Kennedy, L.C.; Greenwald, H.; Hinkle, A.; et al. Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants. mBio 2021, 12, 1. [Google Scholar] [CrossRef]
- Karthikeyan, S.; Levy, J.I.; De Hoff, P.; Humphrey, G.; Birmingham, A.; Jepsen, K.; Farmer, S.; Tubb, H.M.; Valles, T.; Tribelhorn, C.E.; et al. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Nature 2022, 609, 101–108. [Google Scholar] [CrossRef] [PubMed]
- Herold, M.; d’Hérouël, A.F.; May, P.; Delogu, F.; Wienecke-Baldacchino, A.; Tapp, J.; Walczak, C.; Wilmes, P.; Cauchie, H.-M.; Fournier, G.; et al. Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater. Water 2021, 13, 3018. [Google Scholar] [CrossRef]
- Merrett, J.E.; Nolan, M.; Hartman, L.; John, N.; Flynn, B.; Baker, L.; Schang, C.; McCarthy, D.; Lister, D.; Cheng, N.N.; et al. Highly sensitive wastewater surveillance of SARS-CoV-2 variants by targeted next-generation amplicon sequencing provides early warning of incursion in Victoria, Australia. Appl. Environ. Microbiol. 2024, 90, e01497-23. [Google Scholar]
- The Institute of Environmental Science and Research. Wastewater COVID-19 Surveillance 2025 [Updated 6 March 2025]. Available online: https://www.poops.nz/ (accessed on 13 March 2025).
- Wu, F.; Lee, W.L.; Chen, H.; Gu, X.; Chandra, F.; Armas, F.; Xiao, A.; Leifels, M.; Rhode, S.F.; Wuertz, S.; et al. Making waves: Wastewater surveillance of SARS-CoV-2 in an endemic future. Water Res. 2022, 219, 118535. [Google Scholar]
- Communicable Diseases Network Australia (CDNA). SARS-CoV-2 Wastewater Surveillance CDNA National Strategy; Australian Government—Department of Health and Aged Care: Canberra, ACT, Australia, 2022.
- Smith, M.F.; Holland, S.C.; Lee, M.B.; Hu, J.C.; Pham, N.C.; Sullins, R.A.; Holland, L.A.; Mu, T.; Thomas, A.W.; Fitch, R.; et al. Baseline Sequencing Surveillance of Public Clinical Testing, Hospitals, and Community Wastewater Reveals Rapid Emergence of SARS-CoV-2 Omicron Variant of Concern in Arizona, USA. mBio 2023, 14, e03101-22. [Google Scholar] [PubMed]
- Vo, V.; Tillett, R.L.; Papp, K.; Shen, S.; Gu, R.; Gorzalski, A.; Siao, D.; Markland, R.; Chang, C.-L.; Baker, H.; et al. Use of wastewater surveillance for early detection of Alpha and Epsilon SARS-CoV-2 variants of concern and estimation of overall COVID-19 infection burden. Sci. Total Environ. 2022, 835, 155410. [Google Scholar] [PubMed]
- Espinosa-Gongora, C.; Berg, C.; Rehn, M.; Varg, J.E.; Dillner, L.; Latorre-Margalef, N.; Székely, A.J.; Andersson, E.; Movert, E. Early detection of the emerging SARS-CoV-2 BA.2.86 lineage through integrated genomic surveillance of wastewater and COVID-19 cases in Sweden, weeks 31 to 38 2023. Eurosurveillance 2023, 28, 2300595. [Google Scholar] [PubMed]
- Health Emergency Preparedness and Response Authority. Launching GLOWACON: A Global Initiative for Wastewater Surveillance for Public Health; European Commission—Public Health: Brussels, Belgium, 2024.
- Council of the EU. Urban Wastewater: Council Adopts New Rules for More Efficient Treatment; European Council—Council of the European Union: Brussels, Belgium, 2024.
- National Academies of Sciences, Engineering, and Medicine. Increasing the Utility of Wastewater-Based Disease Surveillance for Public Health Action: A Phase 2 Report; National Academies Press: Washington, DC, USA, 2024. [Google Scholar]
- Adams, C.; Bias, M.; Welsh, R.M.; Webb, J.; Reese, H.; Delgado, S.; Person, J.; West, R.; Shin, S.; Kirby, A. The National Wastewater Surveillance System (NWSS): From inception to widespread coverage, 2020–2022, United States. Sci. Total Environ. 2024, 924, 171566. [Google Scholar] [CrossRef]
- United Nations. WHO Chief Declares End to COVID-19 as a Global Health Emergency. 2023. Available online: https://news.un.org/en/story/2023/05/1136367 (accessed on 13 March 2025).
- World Health Organization. WHO Director-General’s Opening Remarks at the Media Briefing—5 May 2023; World Health Organization: Geneva, Switzerland, 2023. [Google Scholar]
- Servetas, S.L.; Parratt, K.H.; Brinkman, N.E.; Shanks, O.C.; Smith, T.; Mattson, P.J.; Lin, N.J. Standards to support an enduring capability in wastewater surveillance for public health: Where are we? Case Stud. Chem. Environ. Eng. 2022, 6, 100247. [Google Scholar]
- Lu, D.; Huang, Z.; Luo, J.; Zhang, X.; Sha, S. Primary concentration—The critical step in implementing the wastewater based epidemiology for the COVID-19 pandemic: A mini-review. Sci. Total Environ. 2020, 747, 141245. [Google Scholar] [CrossRef]
- Ahmed, W.; Bivins, A.; Bertsch, P.M.; Bibby, K.; Choi, P.M.; Farkas, K.; Gyawali, P.; Hamilton, K.A.; Haramoto, E.; Kitajima, M.; et al. Surveillance of SARS-CoV-2 RNA in wastewater: Methods optimization and quality control are crucial for generating reliable public health information. Curr. Opin. Environ. Sci. Health 2020, 17, 82–93. [Google Scholar] [CrossRef] [PubMed]
- Ahmed, W.; Simpson, S.L.; Bertsch, P.M.; Bibby, K.; Bivins, A.; Blackall, L.L.; Bofill-Mas, S.; Bosch, A.; Brandão, J.; Choi, P.M.; et al. Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance. Sci. Total Environ. 2022, 805, 149877. [Google Scholar] [CrossRef] [PubMed]
- Kumblathan, T.; Liu, Y.; Uppal, G.K.; Hrudey, S.E.; Li, X.-F. Wastewater-Based Epidemiology for Community Monitoring of SARS-CoV-2: Progress and Challenges. ACS Environ. Au 2021, 1, 18–31. [Google Scholar] [CrossRef] [PubMed]
- Williams, R.C.; Perry, W.B.; Lambert-Slosarska, K.; Futcher, B.; Pellett, C.; Richardson-O’Neill, I.; Paterson, S.; Grimsley, J.M.; Wade, M.J.; Weightman, A.J.; et al. Examining the stability of viral RNA and DNA in wastewater: Effects of storage time, temperature, and freeze-thaw cycles. Water Res. 2024, 259, 121879. [Google Scholar] [CrossRef] [PubMed]
- Ferdous, J.; Kunkleman, S.; Taylor, W.; Harris, A.; Gibas, C.J.; Schlueter, J.A. A gold standard dataset and evaluation of methods for lineage abundance estimation from wastewater. Sci. Total Environ. 2024, 948, 174515. [Google Scholar] [CrossRef] [PubMed]
- World Health Organization. Updated Working Definitions and Primary Actions for SARS-CoV-2 Variants; World Health Organization: Geneva, Switzerland, 2023. [Google Scholar]
- Baaijens, J.A.; Zulli, A.; Ott, I.M.; Nika, I.; van der Lugt, M.J.; Petrone, M.E.; Alpert, T.; Fauver, J.R.; Kalinich, C.C.; Vogels, C.B.F.; et al. Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques. Genome Biol. 2022, 23, 236. [Google Scholar] [CrossRef] [PubMed]
- Yu, A.T.; Hughes, B.; Wolfe, M.K.; Leon, T.; Duong, D.; Rabe, A.; Kennedy, L.C.; Ravuri, S.; White, B.J.; Wigginton, K.R.; et al. Estimating Relative Abundance of 2 SARS-CoV-2 Variants through Wastewater Surveillance at 2 Large Metropolitan Sites, United States. Emerg. Infect. Dis. 2022, 28, 940–947. [Google Scholar] [CrossRef] [PubMed]
- Timme, R.E.; Woods, J.; Jones, J.L.; Calci, K.R.; Rodriguez, R.; Barnes, C.; Leard, E.; Craven, M.; Chen, H.; Boerner, C.; et al. SARS-CoV-2 wastewater variant surveillance: Pandemic response leveraging FDA’s GenomeTrakr network. mSystems 2024, 9, e01415-23. [Google Scholar] [CrossRef]
- Rakeman-Cagno, J.L.; Persing, D.H.; Loeffelholz, M.J. Maintaining point of care testing capacity and pandemic preparedness in the post-COVID-19 era. Expert Rev. Mol. Diagn. 2024, 24, 147–151. [Google Scholar] [CrossRef]
- Karami, H.; Soleimani, M.; Nayerain Jazi, N.; Navi, K.; Sajadi, R.; Fazeli, M.M.; Pagheh, G.; Dehkordi, S.O. The next viral pandemic: A call for global preparedness. J. Med. Surg. Public Health 2024, 4, 100150. [Google Scholar] [CrossRef]
- Yamey, G.; Schäferhoff, M.; Aars, O.K.; Bloom, B.; Carroll, D.; Chawla, M.; Dzau, V.; Echalar, R.; Gill, I.S.; Godal, T.; et al. Financing of international collective action for epidemic and pandemic preparedness. Lancet Glob. Health 2017, 5, e742–e744. [Google Scholar] [CrossRef] [PubMed]
- Valencia, D.; Yu, A.T.; Wheeler, A.; Hopkins, L.; Pray, I.; Horter, L.; Vugia, D.J.; Matzinger, S.; Stadler, L.; Kloczko, N.; et al. Notes from the Field: The National Wastewater Surveillance System’s Centers of Excellence Contributions to Public Health Action During the Respiratory Virus Season—Four U.S. Jurisdictions, 2022–2023. MMWR Morb. Mortal. Wkly. Rep. 2023, 72, 1309–1312. [Google Scholar] [CrossRef]
- Korfmacher, K.S.; Harris-Lovett, S.; Nelson, K.L. Campus Collaborations As a Model for Transforming SARS-CoV-2 Wastewater Surveillance Research into Public Health Action. Environ. Sci. Technol. 2021, 55, 12770–12772. [Google Scholar] [CrossRef] [PubMed]
- Hill, D.T.; Alazawi, M.A.; Moran, E.J.; Bennett, L.J.; Bradley, I.; Collins, M.B.; Gobler, C.J.; Green, H.; Insaf, T.Z.; Kmush, B.; et al. Wastewater surveillance provides 10-days forecasting of COVID-19 hospitalizations superior to cases and test positivity: A prediction study. Infect. Dis. Model. 2023, 8, 1138–1150. [Google Scholar] [CrossRef] [PubMed]
- Sheth, K.; Domakonda, K.; Short, K.; Stadler, L.; Ensor, K.B.; Johnson, C.D.; Williams, S.L.; Persse, D.; Hopkins, L. A Novel Framework for Internal Responses to Detection of Pathogens in Wastewater by Public Health Agencies. Public Health Rep. 2024, 140, 22–31. [Google Scholar] [CrossRef]
- Brosky, H.; Prasek, S.M.; Innes, G.K.; Pepper, I.L.; Miranda, J.; Brierley, P.E.; Slinski, S.L.; Polashenski, L.; Betancourt, W.Q.; Gronbach, K.; et al. A framework for integrating wastewater-based epidemiology and public health. Front. Public Health 2024, 12, 1418681. [Google Scholar] [CrossRef]
- Keshaviah, A.; Akram, A.; Rizmie, D.; Raxter, I.; Hasan, R.; Rahman, Z.; Jannat Suchana, A.; Jahan, F.; Rahman, A.; Rahman, M.; et al. A cost-benefit analysis of using wastewater monitoring to guide typhoid vaccine campaigns. Res. Sq. 2025; preprint. [Google Scholar] [CrossRef]
- Yoo, B.-K.; Iwamoto, R.; Chung, U.; Sasaki, T.; Kitajima, M. Economic Evaluation of Wastewater Surveillance Combined with Clinical COVID-19 Screening Tests, Japan. Emerg. Infect. Dis. 2023, 29, 1608–1617. [Google Scholar] [CrossRef]
- Foxman, B.; Salzman, E.; Gesierich, C.; Gardner, S.; Ammerman, M.; Eisenberg, M.; Wigginton, K. Wastewater surveillance of antibiotic resistant bacteria for public health action: Potential and Challenges. Am. J. Epidemiol. 2024, kwae419. [Google Scholar] [CrossRef]
- EU-WISH. Wastewater Surveillance of Antimicrobial Resistance Across Europe; EU-WISH: Online, 2025; Available online: https://www.eu-wish.eu/results?tx_news_pi1%5Baction%5D=detail&tx_news_pi1%5Bcontroller%5D=News&tx_news_pi1%5Bnews%5D=19&cHash=ee2b748d6620c0e1672128f8829f01ad (accessed on 26 March 2025).
- Qian, Q.; Fan, L.; Liu, W.; Li, J.; Yue, J.; Wang, M.; Ke, X.; Yin, Y.; Chen, Q.; Jiang, C. Direct Evidence of Active SARS-CoV-2 Replication in the Intestine. Clin. Infect. Dis. 2021, 73, 361–366. [Google Scholar] [CrossRef] [PubMed]
- Zhang, H.; Kang, Z.; Gong, H.; Xu, D.; Wang, J.; Li, Z.; Li, Z.; Cui, X.; Xiao, J.; Zhan, J.; et al. Digestive system is a potential route of COVID-19: An analysis of single-cell coexpression pattern of key proteins in viral entry process. Gut 2020, 69, 1010. [Google Scholar]
- Ciesielski, M.; Blackwood, D.; Clerkin, T.; Gonzalez, R.; Thompson, H.; Larson, A.; Noble, R. Assessing sensitivity and reproducibility of RT-ddPCR and RT-qPCR for the quantification of SARS-CoV-2 in wastewater. J. Virol. Methods 2021, 297, 114230. [Google Scholar] [PubMed]
- Ahmed, W.; Smith, W.J.M.; Metcalfe, S.; Jackson, G.; Choi, P.M.; Morrison, M.; Field, D.; Gyawali, P.; Bivins, A.; Bibby, K.; et al. Comparison of RT-qPCR and RT-dPCR Platforms for the Trace Detection of SARS-CoV-2 RNA in Wastewater. ACS ES&T Water 2022, 2, 1871–1880. [Google Scholar]
- Ding, J.; Xu, X.; Deng, Y.; Zheng, X.; Zhang, T. Comparison of RT-ddPCR and RT-qPCR platforms for SARS-CoV-2 detection: Implications for future outbreaks of infectious diseases. Environ. Int. 2024, 183, 108438. [Google Scholar] [PubMed]
- Robins, K.; Leonard, A.F.C.; Farkas, K.; Graham, D.W.; Jones, D.L.; Kasprzyk-Hordern, B.; Bunce, J.T.; Grimsley, J.M.S.; Wade, M.J.; Zealand, A.M.; et al. Research needs for optimising wastewater-based epidemiology monitoring for public health protection. J. Water Health 2022, 20, 1284–1313. [Google Scholar] [CrossRef]
- NSF Research Coordination Network. Wastewater Surveillance for SARS-CoV-2 and Emerging Public Health Threats. Available online: https://sites.nd.edu/rcn-wastewater-sarscov2/ (accessed on 13 March 2025).
- The Global Health Network—ODIN. Environmental and Wastewater Surveillance (EWS) Community of Practice and knowledge Exchange. 2025. Available online: https://odin-wsp.tghn.org/odin-consortium/unikin/ (accessed on 13 March 2025).
- Water Research Australia. Tag Archives: WBE Community of Practice. Available online: https://www.waterra.com.au/tag/wbe-community-of-practice/ (accessed on 13 March 2025).
- Communicable Diseases Genomics Network (CDGN). Working Groups—CDGN Working Groups. Available online: https://www.cdgn.org.au/working-groups (accessed on 13 March 2025).
- Minister for Health and Aged Care and Treasurer, Press Conference—29 October 2024 [Press Release]. 29 October 2024. Available online: https://www.health.gov.au/ministers/the-hon-mark-butler-mp/media/minister-for-health-and-aged-care-and-treasurer-press-conference-29-october-2024 (accessed on 13 March 2025).
- New Zealand Ministry of Business Innovation and Employment. Refocusing the Science, Innovation and Technology System. Online. 2025. Available online: https://www.mbie.govt.nz/science-and-technology/science-and-innovation/agencies-policies-and-budget-initiatives/refocusing-the-science-innovation-and-technology-system (accessed on 13 March 2025).
- Xiao, K.; Zhang, L. Wastewater pathogen surveillance based on One Health approach. Lancet Microbe 2023, 4, e297. [Google Scholar] [CrossRef] [PubMed]
- Hill, R.; Stentiford, G.D.; Walker, D.I.; Baker-Austin, C.; Ward, G.; Maskrey, B.H.; van Aerle, R.; Verner-Jeffreys, D.; Peeler, E.; Bass, D. Realising a global One Health disease surveillance approach: Insights from wastewater and beyond. Nat. Commun. 2024, 15, 5324. [Google Scholar] [CrossRef] [PubMed]
- Leifels, M.; Rahman, O.K.; Sam, I.-C.; Cheng, D.; Chua, F.J.D.; Nainani, D.; Kim, S.Y.; Ng, W.J.; Kwok, W.C.; Sirikanchana, K.; et al. The one health perspective to improve environmental surveillance of zoonotic viruses: Lessons from COVID-19 and outlook beyond. ISME Commun. 2022, 2, 107. [Google Scholar] [CrossRef] [PubMed]
- Yoo, B.-K.; Goto, R.; Kitajima, M.; Sasaki, T.; Himmler, S. Willingness to pay for nationwide wastewater surveillance system for infectious diseases in Japan. Environ. Sci. Water Res. Technol. 2025, 11, 29–38. [Google Scholar]
- Morales, D.; Rhodes, T.; O’Reilly, K. Stakeholder Interviews to Inform Best Practice for Public Facing COVID-19 Wastewater Dashboards [version 1; peer review: 2 approved with reservations]. Gates Open Res. 2024, 8, 61. [Google Scholar] [CrossRef]
- Parkinson, S.; Dawney, J.; Adams, A.; Senator, B. Data Collection and Sharing for Pathogen Surveillance: Making Sense of a Fragmented Global System. RAND Health Q. 2024, 11, 4. [Google Scholar] [PubMed]
Key Process | Number of Jurisdictions or Process Metric/Number of Responses |
---|---|
Sampling by single water utility | 4/8 |
Use of composite auto-sampling | 5/8 |
Use of passive samplers | 3/8 |
Fewer than 10 sampling locations | 5/8 |
Only collected from treatment plants | 5/8 |
Airport included in catchment site | 2/8 |
Treatment plant catchment population size | 50,000–2,000,000 |
Concentration by electronegative membrane filtration | 6/7 |
Concentration by polyethylene glycol precipitation | 1/7 |
Volume concentrated | 50–250 mL |
Use of the ThermoFisher MagMAX Microbiome Ultra extraction kit | 4/7 |
Purification by semi-automated magnetic bead platform | 4/7 |
Purification by silica spin column method | 4/7 |
Use of RNase inhibitor | 4/7 |
RT-PCR targeting nucleocapsid gene used | 5/7 |
Quantitative real-time RT-PCR used | 5/7 |
Validated PCR method in use | 3/6 |
DNA sequencing performed | 5/8 |
Whole genome tiled amplicon (Illumina) sequencing performed | 4/7 |
Inclusion of negative controls in sequencing | 4/6 |
SARS-CoV-2 lineage relative abundance determined | 5/6 |
Direct comparison of wastewater sequencing with clinical case lineages | 3/6 |
Data publicly available via online dashboard | 2/6 |
Control | Number Jurisdictions |
---|---|
Negative concentration control | 3 |
Negative extraction control | 3 |
Internal process control at extraction step | 2 |
Positive PCR control | 3 |
Internal process control at PCR step | 2 |
Negative sequencing control | 5 |
Positive sequencing control | 1 |
Jurisdiction | Number of Samples Tested by PCR per Week | Number of Samples Sequenced per Week (Proportion) | Sequencing Method |
---|---|---|---|
A | 4 | 4 (100%) | WGS |
B | 3 | 1.5 * (50%) | WGS |
C | 10 | 6 (60%) | amplicon |
D | 6 | 3 (50%) | WGS |
E | 19 | 19 ** (100%) | amplicon + WGS |
F | 45 | 20 (44%) | amplicon |
G | 15 | 0 (0%) | NA |
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Levy, A.; Crachi, C.; Gazeley, J.; Chapman, J.; Brischetto, A.; Speers, D.; Hewitt, J.; Jennison, A.V.; The Wastewater Surveillance Working Group, Communicable Diseases Genomics Network of Australia. Australian and New Zealand Laboratory Experience and Proposed Future Direction of Wastewater Pathogen Genomic Surveillance. Environments 2025, 12, 114. https://doi.org/10.3390/environments12040114
Levy A, Crachi C, Gazeley J, Chapman J, Brischetto A, Speers D, Hewitt J, Jennison AV, The Wastewater Surveillance Working Group, Communicable Diseases Genomics Network of Australia. Australian and New Zealand Laboratory Experience and Proposed Future Direction of Wastewater Pathogen Genomic Surveillance. Environments. 2025; 12(4):114. https://doi.org/10.3390/environments12040114
Chicago/Turabian StyleLevy, Avram, Christina Crachi, Jake Gazeley, Joanne Chapman, Anna Brischetto, David Speers, Joanne Hewitt, Amy V. Jennison, and The Wastewater Surveillance Working Group, Communicable Diseases Genomics Network of Australia. 2025. "Australian and New Zealand Laboratory Experience and Proposed Future Direction of Wastewater Pathogen Genomic Surveillance" Environments 12, no. 4: 114. https://doi.org/10.3390/environments12040114
APA StyleLevy, A., Crachi, C., Gazeley, J., Chapman, J., Brischetto, A., Speers, D., Hewitt, J., Jennison, A. V., & The Wastewater Surveillance Working Group, Communicable Diseases Genomics Network of Australia. (2025). Australian and New Zealand Laboratory Experience and Proposed Future Direction of Wastewater Pathogen Genomic Surveillance. Environments, 12(4), 114. https://doi.org/10.3390/environments12040114