Abstract
Aim: Wastewater-based epidemiology (WBE) is increasingly used to monitor pandemics. In this manuscript, we review methods and limitations of WBE, as well as their online dashboards. Materials & methods: Online dashboards were retrieved using PubMed and search engines, and annotated for timeliness, availability of English version, details on SARS-CoV-2 sublineages, normalization by population and PPMoV load, availability of case/hospitalization count charts and of raw data for export. Results: We retrieved 51 web portals, half of them from Europe. Africa is represented from South Africa only, and only seven portals are available from Asia. Conclusion: WBS provides near-real-time cost-effective monitoring of analytes across space and time in populations. However, tremendous heterogeneity still persists in the SARS-CoV-2 WBE literature.
Plain language summary
Monitoring the amount of a virus in the sewage system provides a way to work out the circulation of the virus among a population at a given time. Standard procedures are needed to produce data that can be compared across countries. Timely sharing of wastewater surveillance data across publicly accessible web portals is important to inform researchers and plan public health policies. This study shows that we are still far away from standardization and timely and transparent reporting.
Plain language summary
Summary points.
Wastewater based epidemiology has been boosted by the COVID-19 pandemic.
Wastewater based epidemiology anticipates clinical case counts and can inform public health policies.
Timely disclosure of publicly accessible datasets is crucial.
Too few countries have implemented user friendly online dashboards.
Standards for better collection and representation of WBS are urgently needed.
Several tools have been put in place during the COVID-19 pandemic to monitor, nowcast and forecast waves of different types (e.g., cases, hospitalization, work absenteeism) with better accuracy and lower cost than positivity rates in laboratory tests of individual citizens [1,2]. In fact, laboratory tests are expensive and time consuming, suffer from selection biases and fatigue. Testing rates in individual symptomatic patients has largely declined along the pandemic course, and most healthcare institutions have dismissed surveillance for asymptomatic infections for both professionals and patients. Strategies for ‘collective’ virological surveillance strategies have then been increasingly deployed to surrogate and integrate traditional individual testing. For example, infosurveillance consists in studying trends in user queries of publicly accessed web search engines (e.g., Google Trends) across local geographies: it can be informative at the beginning of a pandemic, but at the steady state of the pandemic (endemicity) infosurveillance suffers from aspecificity, with many queried symptoms and signs being redundant across co-circulating human pathogens [3]. Then the need for alternative ‘collective’ virological surveillance approaches.
Wastewaters can be used to monitor pharmaceutical ingredients (e.g., antivirals or over-the-counter anti-inflammatories [4,5]), which represent indirect proxies of the number of infected cases. However, wastewaters are especially suit to directly monitoring pathogens. Wastewater monitoring in sewage networks has advantages over monitoring of river waters, since sunlight photolysis [6] and contamination by animal excrements is much lower: as such, river surveillance is currently restricted to settings with limited formal sewage systems [7]. When the investigated pathogen is a RNA virus, the frail RNA should be extracted and concentrated from the highly diluted wastewater matrix. Wastewater-based epidemiology (WBE) has been successfully applied at different scales, ranging from limited settings (e.g., aircrafts [8], long-term care facilities [9], correctional facilities or academic campuses [10]) to whole nations. Monitoring via PCR is a specific and quantitative tool to estimate case counts [11,12], since each sewage node (treatment facility) corresponds to a defined population. Normalization strategies have been developed relying over pepper mild mottle virus (PMMov), the most abundant virus found in a metagenomic survey of RNA viruses from human feces [13]. In addition, viral genome sequencing can identify the relative abundance of specific viral sublineages.
On 17 March 2021, the European Union Commission issued Recommendation 2021/472, soliciting systematic surveillance of SARS-CoV-2 variants in wastewater across member countries. In the Fall 2021, the Rockefeller Foundation created the Wastewater Action Group – a network of researchers across USA and the UK – to share best practices in WBS [14]. Those tools have acquired much importance at times of reduced nasopharyngeal swab testing [15,16]. Wastewater-based surveillance (WBS) can function as an early warning system for COVID-19 in low-incidence settings. Novel data-sharing tools [17] allow immediate release of this data [18] enabling evidence-based local policy making [19].
In this review, we will collect publicly accessible online dashboards for wastewater monitoring around the globe.
Methods
A literature search through MEDLINE and PubMed electronic databases was performed for publications during the period from 1 December 2019, to 18 December 2023, using the following Medical Subject Heading (MeSH) and keywords: ‘COVID-19’, ‘SARS-CoV-2’, ‘wastewater’, ‘wastewater-based epidemiology’, ‘wastewater-based surveillance’.
We also screened the reference lists of the most relevant review articles for additional studies not captured in our initial literature search. We started from web portals listed in Table 1 and those listed at the EU Wastewater Observatory for Public Health by the European Commission (https://wastewater-observatory.jrc.ec.europa.eu/#/dashboards/2). Only web portals that could be reached (working URLs) were included. For each URL we collected data on timeliness (ongoing vs halted), availability of English version, availability of SARS-CoV-2 sublineage shares, normalization by population, normalization by PPMoV load, availability (overlap) of case/hospitalization count chart and availability of raw data for export.
Table 1.
Main international consortia investigating wastewater-based surveillance.
| Name | URL | Hosted by | Ref. |
|---|---|---|---|
| COVID-19 WBE Collaborative | https://www.covid19wbec.org/ | ||
| COVIDPoops19 | https://ucmerced.maps.arcgis.com/apps/dashboards/c778145ea5bb4daeb58d31afee389082 | Center for Information Technology Research in the Interest of Society and the Banatao Institute (CITRIS) in California | [24] |
| Sewage Analysis CORe group Europe (SCORE) Network | https://score-network.eu/ | European Universities | |
| Wastewater Surveillance for SARS-CoV-2 National Science Foundation Research Coordination Network (RCN) | https://sites.nd.edu/rcn-wastewater-sarscov2/ | University of Notre Dame, USA | |
| Global Water Pathogen Project | https://www.waterpathogens.org/ | Michigan State University, USA |
We retrieved further web portals using Google and to overcome language barriers we asked citizens and scientists on Twitter/X to report local wastewater web portals.
Results
Tables 2–4 summarizes the online dashboards that we have been able to retrieve in our search. While many countries have WBS programs in place, only a few are regularly disclosing data on publicly accessible online dashboards.
Table 2.
Publicly accessible online dashboards reporting European SARS-CoV-2 wastewater surveillance. ‘EN’ refers to availability of translation into English language.
Table 3.
Publicly accessible online dashboards reporting European (continued), American and African SARS-CoV-2 wastewater surveillance. ‘EN’ refers to availability of translation into English language.
Table 4.
Publicly accessible online dashboards reporting Asian or Oceanian SARS-CoV-2 wastewater surveillance. ‘EN’ refers to availability of translation into English language.
We were able to retrieve 51 web portals, half of them from Europe, and none ongoing from South America. Africa is represented from South Africa only, and only 7 portals are available from Asia. Large countries such as USA, Canada and Australia often have data reported at a state level, without a nation-wide aggregator. Nine web portals (England, Czech Republic, Slovenja, Wales, Fortaleza (Brazil), Cyprus, Israel, Bangalore (India) and Dhaka (Bangladesh)) are reporting historical data for programs that have since been discontinued: the case of England is notable, being one of the countries with the largest viral genome sequencing capabilities in the world [20]. SARS-CoV-2 concentration is usually reported in copies (or genome equivalents) or log10 copies per liter, as rolling average along a 7- or 14-day period. The viral load is often standardized per 100,000 inhabitants (or per capita in Hong Kong and New Zealand). Many portals provide regional or wastewater plant-specific data, which we believe are marginally informative during a pandemic. The majority of web portals are overlying case or hospitalization count curves to wastewater SARS-CoV-2 levels, which shows perfect correlation. A relevant amount of web-portals is reporting, in addition to cumulative SARS-CoV-2 levels in wastewater, the relative share of SARS-CoV-2 sublineages, which is incredibly informative for forecasting waves.
Unfortunately, the vast majority of web portals are not allowing direct export of raw data in accessible formats, with .pdf files (1-star in the Berners-Lee schema of linked open data) remaining a widely used standard for periodic bulletins, without any accompanying dataset. This is dismal in cases where only current geographical charts are represented, and there is instead no availability of historical charts.
Several countries have reported their experiences in peer-reviewed literature such as Norway [21], Denmark [22] and the Netherlands [23]. Several countries, despite issuing regular bulletins have a median delay of 4 months between sampling and publication, and never had an online dashboard for WBS. The case of Portugal is notable since the COVIDetect project (https://www.adp.pt/en/covidetect/?id=222) there never launched a web portal. The poor accessibility to these data makes it difficult to reuse data for elaborations, while the delay makes them almost useless for predictive models.
Discussion
In too many examples around the globe, WBS programs were just local (without an equitable distribution of monitoring sites), limited in duration, and failed to timely report data publicly: that has translated in a failure to further inform public health actions and perform meta-analysis [24]. Most importantly, there has never been an international consortium dictating operational standards and procedures, or even just gathering the URLs of national portals, thus creating unprecedented heterogeneity and hurdling the efforts of researchers.
In order for WBE to be feasible, the pathogen has to be excreted in urine and/or stools. The pathogen should not necessarily be specific to humans (i.e., anthroponoses) since modern wastewater plants have reduced infestation by other potential host species (notably, rodents) which can hardly contribute to the viral bulk: nevertheless, at times of low-level circulation, the relative contribution of other animal hosts cannot be ruled out. Adjustments in models are needed: e.g., the shedding of virus from the convalescing population can exceed the shedding from the infectious population after the peak, weakening the correlation between wastewater viral loads and case counts and delaying the detection of novel lineages [17].
WBS has the potential to provide near-real-time cost-effective, objective measures of analytes in a given population at a certain time. However, tremendous heterogeneity still persists in the SARS-CoV-2 WBS literature [19]. Variables to take into account include sampling sites and timing (time-weighted vs flow-weighted [12]), solid versus liquid fractions, enrichment using adsorptive surfaces) normalization (based on chemical, viral, bacterial or other human analyte), concentration (ultrafiltration, PEG precipitation, electronegative membrane filtration, flocculation, magnetic-based methods [25]), extraction, target gene and assay (NAAT, rt-qPCR, digital droplet PCR, RT-LAMP), and variant seeking (both in methods and software packages). Methods are expecially crucial, with tiled PCR metagenomic sequencing [26] being favored, and many ad hoc softwares developed so far (Table 5) [27]. The presence of encapsidated and potentially infectious SARS-CoV-2 in wastewaters can be excluded by performing RT-qPCR after treatment with photo-reactive monoazide dyes (‘capsid-integrity PCR’) [28]. WBS has been shown to inform variant introduction during major international sport and political events [29].
Table 5.
Main softwares for SARS-CoV-2 variant calling and relative abundance estimation in wastewaters.
| Software | URL | Ref. |
|---|---|---|
| Alcov | https://github.com/Ellmen/alcov | |
| Basic | https://github.com/arnaud00013/Wastewater_surveillance_pipeline | [42] |
| ASPICov | https://gitlab.com/vtilloy/aspicov | [43] |
| COJAC | https://github.com/cbg-ethz/cojac | [44] |
| Freyja | https://github.com/andersen-lab/Freyja | [29] |
| Gromstole | https://github.com/PoonLab/gromstole | n.a. |
| Kallisto | https://pachterlab.github.io/kallisto/ | [45] |
| LCS | http://github.com/rvalieris/LCS | [46] |
| Lineagespot | https://github.com/BiodataAnalysisGroup/lineagespot/blob/master/inst/scripts/raw-data-analysis.md | [47] |
| Pipes | https://zenodo.org/records/6999441 | [48] |
| VaQueRo | https://github.com/fabou-uobaf/VaQuERo | [45] |
| Viral Lineage Quantification (VLQ) | https://github.com/baymlab/wastewater_analysis | [48] |
| V-pipe | https://github.com/cbg-ethz/V-pipe | [37] |
Limitations of the current study mostly stem from language barriers: automated translation (as provided by web browsers) do not translate text in images (such as axis legends), which could have misled our interpretations. Second, we could have missed some national web portals, and encourage readers to report them to the corresponding author.
Notably, many large countries such as India, Brazil and Japan are still lacking a nation-wide dashboard and are sporadic initiatives by regional bodies are only in place. In many countries (detailed at the COVIDPoops19 web portal), individual investigators have published papers detailing local WBS at a certain time, without any follow-up at a national level. Another scenario is countries that discontinued their programs exactly at a time when it was most needed (e.g., UK, Scotland or Portugal). Not all dashboards present clinical case data, variant monitoring or downloadable source data [30].
Conclusion
WBS has been proven useful at tracking minoritarian variants at time of dominance from other variants, including reintroductions not detected by clinical surveillance [31], and at tracking cryptic sublineages [32,33] isolated with dedicated softwares that differentiate them from artifacts (e.g., Crykey [34]). WBS has been proven useful at identifying cryptic sublineage shedding by persistent infections in immunocompromised patients [35], which notably have often anticipated convergent evolution in the general population [36]. The positive experience gathered with SARS-CoV-2 has led to implementation of WBS for different pathogens, such as MPXV [37,38], influenza, parainfluenza, rhinovirus, metapneumovirus respiratory syncytial virus, enteroviruses and measles virus [39,40].
Exposure of WBS data on publicly accessible online dashboards represents a major advance for public health, and gains increased relevance at times of reduced clinical surveillance. While EU and USA have made consistent effort at disclosing accessible data, much remains to be done by the WHO to encourage similar platforms in other continents.
Author contributions
D Focosi performed online searches and wrote the first draft. PG Spezia supervised the project. F Maggi revised the manuscript.
Financial disclosure
The authors have no financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.
Competing interests disclosure
The authors have no competing interests or relevant affiliations with any organization or entity with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.
Writing disclosure
No writing assistance was utilized in the production of this manuscript.
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