Photo Credit: Andrew Chappell

Introduction
ESR tests wastewater for the presence of SARS-CoV-2 (the virus that causes COVID-19) across the country. From 2020-2022, this aided Aotearoa's ability to identify outbreaks, and is now used to understand disease trends in communities and to monitor variants.

This dashboard is designed to share our wastewater science and help the public track potential COVID-19 risks in their local areas with easy-to-digest data visualisation. It is mobile-optimised, which means you can bookmark it on your phone and easily come back to check the weekly updates in your area.

Site Locations
Wastewater sites are selected based on several factors including population and geographic coverage. Typically, samples are collected twice per week. Sites and frequency may change over time.

Sampling Method
Most samples are collected by an autosampler, which collects a small volume of wastewater at regular intervals over the course of a 24-hour period to produce a 'composite' samples that is representative of the inputs into the catchment over the preceding 24-hr period. When composite samples are not available, ‘grab’ samples are collected. These range from a sample being taken at a single point in time, to 3 samples taken over 30 minutes. Grab samples represent only the composition of the source at that time of collection and may not be as representative as a composite sample. More variation may be expected with grab samples, samples collected from smaller catchments (an individual case can have a disproportionately large effect on overall viral level in small catchments) and from sites that are only sampled once per week.

Laboratory and data analysis
Samples are sent from each wastewater treatment plant to ESR. Processing first involves separating the solids from liquid by centrifugation, followed by recovering the virus from the solids. The virus from the solids is then combined with that in the liquid phase and concentrated to a small volume by polyethylene glycol (PEG) precipitation. The viral RNA is extracted using a commercial viral nucleic acid extraction kit. The presence of SARS-CoV-2 RNA in the sample is then determined using RT-qPCR (reverse transcription-quantitative polymerase chain reaction) with the N-gene of the SARS-CoV-2 viral genome. SARS-CoV-2 is considered detected when any of the RT-qPCR replicates are positive. A result of not detected means that SARS-CoV-2 RNA is either absent from the sample, or at a level in the wastewater that is too low to be detected.

When SARS-CoV-2 RNA is detected by RT-qPCR, the concentration in the sample is calculated and converted from genome copy per reaction into genome copies per litre of wastewater (i.e., raw data). Low amounts of SARS-CoV-2 RNA in a sample may not be able to be accurately quantified and are recorded as 500 genome copies/L.

These methods are well established for the identification of SARS-CoV-2 in wastewater, and are described in detail in Hewitt et al 2022.


Reporting Metrics
Genome copies per person per day
The raw data (genome copies per litre of wastewater) is converted to a viral load of genome copies per person per day (GC/person/day) (green line in charts) This conversion considers the flow of wastewater entering the treatment plant and the population in the wastewater catchment (please note that this will not necessarily be the same as the population of the town/city). At the site level, GC/person/day is the average value of all samples collected within that week. When a site is sampled only once per week, the value of that sample is shown (as there is no average for the week). This approach allows for aggregation at regional and national levels, and avoids small catchments being over-represented and large catchments being under-represented. This dashboard provides linear and log₁₀ unit options for data presentation.

Limitations: Caution should be taken when interpreting data. Overall, general trends are more informative than data from individual samples on any given day. This is because of the inherent variability in wastewater samples that may result in ‘noisy’ data. Less variation may be expected when case numbers are higher, in samples collected from larger catchments (because an individual case can have disproportionate effects in small catchments) and for composite samples compared to grab samples. Other variations and uncertainties may be introduced from other factors including specific sample collection method, transportation (time and conditions that may affect viral/RNA stability), wastewater flows, rainfall and temperature in the catchment, laboratory concentration protocol and analysis, etc.


New cases reported per day
Case numbers reported per day (blue line in charts) is calculated by summing up all the new cases reported to the Ministry of Health for the week and dividing by 7 days. Cases are reported on a per-day basis because wastewater samples are generally representative of the viral load in the catchment for the preceding 24-hrs. The report date is aligned with what the Ministry of Health publishes on their website.

Results for each week (GC/person/day and new cases) are presented on the charts on the Sunday of that week. Thus, a result listed as e.g., 7 January represents the average results for the period 1-7 January.

Linear/log₁₀ scale
The amount of virus in a wastewater catchment can vary across a very broad scale and depends on the number of people infected at any one time and the amount of virus they are shedding. During periods where COVID cases are spreading rapidly in the community, the amount of virus detected in the wastewater can increase 10-fold, 100-fold, or more, week to week. The opposite can be true as case numbers decline, although declines are often more gradual.

Plotting data on a graph with a linear axis (e.g. 1000, 2000, 3000 etc increments) is difficult when there is a broad range of data to encompass. Hence a log₁₀ scale (e.g., 100, 1000, 10000 etc increments) is offered in this dashboard to improve data visualisation during periods of rapidly changing levels. Large fluctuations are better visualised on a log₁₀ scale, whereas a linear scale is more useful for visualising small changes.

Estimated variant prevalence
SARS-CoV-2 variants such as Delta or Omicron, and subvariants such as CH.1.1 and XBB, have genetic mutations that can be used to identify them. For wastewater samples, ESR sequences a variable section of the Spike gene (specifically, the receptor binding domain, or RBD). To better resolve variants (such differentiating the subvariants XBB, XBB.1.5 and XBB.1.16), an alternative method is now used that covers a larger part of the spike gene. This new method has been implemented since 5 February 2023. The transition between the two methodologies (referred as ‘old’ and ‘new’) is denoted by a dashed line in Figure 4 on the Summary page.

Wastewater samples contain a mixture of SARS-CoV-2 variants from many infected individuals. The results show the proportion of variants detected. The proportion of each variant in wastewater is a proxy for the proportion of each variant in the community. Variant analysis is only performed on a subset of samples from select wastewater sites - referred to as 'sentinel sites'. National variant proportion each week is calculated as the mean of the sentinel sites used that week weighted by site populations. This approach (coupled with ESR's whole genome sequencing) allows tracking of variant composition across Aotearoa.

RNA in wastewater can be degraded. Therefore, there are benefits to sequencing the Spike gene amplicon, rather than the whole genome. The upside to this is enhanced sensitivity to detect emerging variants (often at low concentrations), the downside is that the method can lack the resolution to differentiate some variants – for example subvariants may not be able to be differentiated from their ‘parental’ variant. While variant analysis within wastewater is a valuable tool, it is best used in combination with whole genome sequencing, reporting of which can be found here


In the figure above, the left plot shows if a variant was detected at sentinel sites monitored in the latest week. The stacked bar plot on the right shows how the proportion of each variant has changed over time nationally. The transition between the two methodologies used to identify variants (see above) is denoted by a dashed line. Hovering your mouse/pointer on each bar shows the variant name and percentage.

Note: 'The ‘Recombinants’ category describes recombinant lineages that are not the focus of current surveillance efforts. Formerly tracked recombinant variants XBC and XBF are reported under this label.

Dashboard Layout
Summary Tab
Data can be viewed on a log₁₀ or linear scale (top right-hand corner of each chart). Select date range - either 6 weeks, 6 months and 12 months.

On the regional trend graphs, selected region can be changed using the toggle button above the time period bar.


Map Tab
The coloured symbols on the map illustrate changes in wastewater viral quantity (GC/person/day) for that site in comparison to the quantity detected at a prior time period. The default comparison is between the current reporting week and a week prior. To change the comparison period, click the filter located on the bottom right corner of the map.

Due to the variations in wastewater samples, thresholds are set to determine whether changes in viral load are noted. When the viral quantity is 30% or more higher in the current week than it was in the chosen prior time-period, this is labelled as increased (red up arrow on map). When the viral quantity is 30% or more lower in the current week than it was in the selected prior time-period, this is labelled as decreased (blue down arrow on map). If viral levels have changed less than this in the two compared weeks, this is labelled as no change (yellow circle on map).

If a site was not tested in the current week, or the comparison week, no symbol will appear on the map for that site.


Clicking/tapping on a map symbol brings up results for that site. As with national and regional graphs, results can be viewed on log₁₀ or linear scales, and across time periods . Tapping on ‘view catchment’ shows the area covered by wastewater testing (black line), individual sewer pipes in the catchment (blue lines) and the location where the sample was collected(triangle/circle symbol). This can also be achieved using the search button.

Resources
Have questions or curious to know more? Please visit our website where you can find more content related to our wastewater science:

ESR Homepage
COVID-19 research and services
Wastewater Surveillance Report
Wastewater (FAQs)

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