- submitted 2022-10-21
(Popular Science/National Museum of Natural Science Foundation) as “Chronicles of New
Zealand Lavatory Detective Agency for SARS-CoV-2 Footprints”, accepted
2023-04-10,
- published 2023-05-06 [中文] @ https://foundation.nmns.edu.tw/writing/
- URI: https://details-or-fragments.blogspot.com/2023/05/NZwws.html
- DOIs: https://doi.org/10.6084/m9.figshare.23541075 ; https://doi.org/10.5281/zenodo.8054748
On Friday, October 21, 2022, the weather in Auckland, New Zealand (NZ) was cloudy and the temperature was 16 degrees C. Since this winter (June-August) was the peak of the COVID-19 pandemic in NZ, Ania and her family have not traveled for a while, so Ania was planning a weekend family trip, watching the weather report: sunny and fine weather with a temperature of 20 degrees.
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| Fig 1: ESR COVID-19 Wastewater Surveillance Dashboard |
Friday, October 21, 2022, the weather in Auckland, New Zealand (NZ) was cloudy and the temperature was 16 degrees C. Since this winter (June-August) was the peak of the COVID-19 pandemic in NZ, Ania and her family have not traveled for a while, so Ania was planning a weekend family trip, watching the weather report: sunny and fine weather with a temperature of 20 degrees.
Ania used to like to visit Lake Taupo the most, but at this moment she had to change her plan, even the pandemic in Auckland has generally slowed down. This time, Ania consulted the Environmental Research and Science (ESR)'s COVID-19 Wastewater Surveillance Dashboard, and she changed plans for her family.
Ania, who lives in Auckland (yellow circle area in Figure 1), learned from the website that the recent pandemic has slowed down (upper right in Figure 1), but many areas are still unstable (red triangle area in Figure 1). When checking the situation in Lake Taupo, the map showed a red triangle. Ania took a closer look at the trend chart and found that although the number of confirmed cases decreased, the wastewater data showed an increase. Therefore, she changed the location and decided to go to Kawakawa Bay, where the overall pandemic situation has declined. (Figure 1 map, blue triangle area).
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| Fig 2: Wastewater Variant Analysis |
Not only that, but Ania had older and younger members in her family, so she further checked the situation of SARS-CoV-2 variants across the country and east of Auckland (Figure 2).
Since NZ was in a state of competition for multiple variants of the COVID-19 , the scientific uncertainty at the time was high. Therefore, it was changed to an outdoor picnic to avoid indoor dining and group gatherings, in order to reducing the unknown risks of family travel.
However, these data about COVID-19 are different from the confirmed clinical data familiar to the public (i.e. confirmed cases, hospitalization, moderate to severe disease, death, etc. in the blue curve in Figure 1), and what is this kind of "additional" environmental data?
The green curve in Figure 1 covers 73% of the NZ population, and the average number of SARS-CoV-2 genomes detected in wastewater per person per day. This is from the surveillance results of wastewater samples from lavatory, sinks and drains in households in the community. Most of these shit & poops samples are regularly collected by an automatic sampler within 24 to 25 hours for testing. After estimating the number of viruses and analyzing the variants, a weekly wastewater surveillance report is provided, and finally published on the dashboard to inform the public of potential local COVID-19 risks. Wellington Laboratory's NZ National Wastewater Surveillance for COVID-19 footprint work is like the work of a Lavatory Detective Agency.
Taking a closer look at the work of the "Lavatory Detective Agency" in NZ, it can be roughly divided into three stages (Figure 3):
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| Fig 3: Chronicles of New Zealand Lavatory Detective Agency for SARS-CoV-2 Footprints |
The first stage of establishment & testing:
In 2020, when the pandemic broke out in the early stage, the COVID-19 wastewater surveillance project began to be established in April.
After the alert level was raised to level 4 in May, ESR and the National Health Coordination Center (NHCC) coordinated the prevention strategy and established a national clinical data repository (Clinical Data Repository, CDR) for all COVID-19 test reports in laboratories across the country.
From July to November, closed sampling research was carried out. On the one hand, it provided a "time snapshot" of wastewater viruses, and on the other hand, it provided the theoretical basis for NZ's wastewater surveillance task.
The second phase of verification & expansion:
During the "Zero COVID" in 2021, in areas with zero confirmed cases, the evidence of the SARS-CoV-2 footprints has been detected in wastewater. In Stratford, a small town in the Taranaki (where wastewater services cover 97%) since July 2021, it has joined the COVID-19 wastewater surveillance task. For the first time, virus fragments shed after infection with SARS-CoV-2 (or SARS-CoV-2 RNA fragments) were detected in the wastewater samples.
After the wastewater "disease detective" solved the case based on the above-mentioned closed sampling research, the Detective Agency continued to strengthen public health measures, such as community testing and vaccination, canceling some community activities, and increasing wastewater sampling and testing.
Subsequently, it was found in Stratford that 6 confirmed cases were all from the same family, and the pandemic was quickly brought under control. It was not until 3 months later that further community cases were found in the wastewater, so the results of the COVID-19 wastewater surveillance tasks were verified and has been reported in the World Health Organization as a case report.
The third stage of daily wastewater surveillance:
After NZ gave up Zero COVID, it provided new digital tools for the public to "living with the COVID", allowing the exploration of the COVID-19 wastewater surveillance report to be like checking the weather report, helping the public to manage their own safety.
“NZ’s move to self-reporting has made our official case numbers less reliable than ever before – and that’s where wastewater testing comes in”, microbiologist Siouxsie Wiles and ESR geneticist Mike Bunce, the ESR scientists explained.
July 2022, NZ launched an interactive COVID-19 wastewater dashboard, using new tools to track the COVID-19 footprints, assisting the public to be ware of national and regional pandemic trends, and providing temporal and spatial visual assistance, such as map area options and searches. It also supports the comparison of trends in different time periods as shown in Figure 1 and Figure 2.
So how does NZ's "Lavatory Detective Agency" establish the relationship between wastewater data and clinical data?
It was hard to detect SARS-CoV-2 cases during the time of Zero COVID in NZ. How could NZ solve the problem of wastewater sensitivity when the virus in wastewater was extremely low? Figure 4 illustrates the overall research landscape.
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| Fig 4: Relations between COVID19 clinical and wastewater data |
In July 2020, ESR selected a community with a population of about 120,000 to sample wastewater daily in two areas. They are the Managed Isolation and Quarantine Facility (MIQF) and the wastewater treatment plant (WWTP).
The left side of Figure 4 is the clinical analysis of COVID-19 that is familiar to the general public, and the right side is to illustrate the analysis process of COVID-19 wastewater-based epidemiology (WBE).
The main difference between the two methods lies
in the source of samples and sampling methods.
The follow-up quality control is based on the purpose of the researcher, and different viruses are used as the control group. For example, this study chose to use Feline Infectious Peritonitis Virus (FIPV) and Murine Norovirus Virus (MNV) as external process controls to monitor viral copies and evaluate inhibition by quantitative RT-qPCR.
Subsequent processes such as virus concentration, RNA extraction, use of PCR to test whether the sample is positive or negative, or further sequencing are the same as the process of people testing the virus from nasal swabs.
Finally, using the clinical data in the EpiSurv surveillance database of the Ministry of Health, four infectious models (Total Cases, Infectious Cases: reported symptomatic cases or imputed asymptomatic cases, Relative Infectious Cases, New Daily Cases), compared with the wastewater data for statistical analysis to confirm the relationship between clinical cases and wastewater data, and verified that in a low-infection environment, wastewater data can still help to detect about 10 positive cases in an area of 100,000 people.
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| Fig 5: COVIDPoops19 snapshot (20230507) |
"Lavatory Detective Agency"
detects SARS-CoV-2 footprints in the environment. In the near future,
regardless of whether the next super variant is discovered, this kind of work
to track the source of potential variants will help researchers understand the
biological factors that lead to the mutation, or help ordinary people like Ania
and her family: checking the COVID-19 wastewater data is like checking the
weather data, thus self-risk prevention has become a simple daily routine. And
if scientists or digital engineers want to further use the source data of the NZ
"Lavatory Detective Agency", the "Open Lavatory" provided
by ESR is available in the open database.
Reference:
[1] https://www.health.govt.nz/covid-19-novel-coronavirus/covid-19-health-advice-public/covid-19-wastewater-testing
[2] ESR News: https://www.esr.cri.nz/home/about-esr/media-releases/streamlining-covid-19-laboratory-data-to-ministry-of-health/ ; https://www.scoop.co.nz/stories/SC2005/S00024/sysmex-and-esr-collaborate-on-national-covid-19-results-cdr.htm. 2020/5/12
[3] Hewitt, Joanne, et al. "Sensitivity of wastewater-based epidemiology for detection of SARS-CoV-2 RNA in a low prevalence setting." Water Research 211 (2022): 118032.
[4] Harvey, Helen, "The riddle in the wastewater: Taranaki 'disease detectives' solved a Covid-19 mystery", https://www.stuff.co.nz/national/health/128983961/the-riddle-in-the-wastewater-taranaki-disease-detectives-solved-a-covid19-mystery. 2022/6/18
[5] Siouxsie Wiles and Mike Bunce, "As Covid case counts become less accurate, wastewater testing is riding to the rescue", https://thespinoff.co.nz/science/13-06-2022/as-covid-case-counts-rapidly-lose-accuracy-wastewater-testing-is-riding-to-the-rescue
[6] "ESR launches interactive COVID-19 wastewater dashboard to better track the virus's progress", https://thespinoff.co.nz/science/13-06-2022/as-covid-case-counts-rapidly-lose-accuracy-wastewater-testing-is-riding-to-the-rescue
[7] COVIDPoops19: Summary of Global SARS-CoV-2 Wastewater Monitoring Efforts by UC Merced Researchers Details: https://ucmerced.maps.arcgis.com/apps/dashboards/c778145ea5bb4daeb58d31afee389082
[8] Callaway, Ewen. "These scientists traced a new coronavirus lineage to one office-through sewage." Nature News. https://www.nature.com/articles/d41586-022-02996-y. 2022/9/26
[9] ESR Open Data: https://github.com/ESR-NZ/covid_in_wastewater