Ottawa covid-19 wastewater surveillance

People with covid-19 shed the causative SARS-CoV-2 virus in their stool, regardless of whether they have symptoms, receive a covid-19 test or ever are diagnosed. Thus, in contrast to assessing community covid-19 levels by measuring the number of active cases, which may miss asymptomatic infections as well as be subject to limited test availability, wastewater surveillance consistently captures most of the population with covid-19 given that everyone goes to the washroom. In addition to serving as a valuable confirmatory data source for covid-19 levels, wastewater can also serve as early indicator for possible outbreaks, as described below.


For mobile users, dragging the plot while in landscape mode will allow you to view current data. Using the display options at the top allows you to modify the view by zooming in and out of the plot.

*Midpoint mean viral signal omits dates (coloured in blue) flagged by wastewater researchers with potential data concerns. Data is currently being studied for effects of snow melt and other diluting factors on RNA signal.


The next plot illustrates the 7-day midpoint mean in daily covid-19 wastewater viral signal. This number is the average of a week’s readings; today’s reading, the previous 3 days, and the subsequent 3 days. Also on the graph are various comparators (e.g. reported daily covid-19 cases, hospitalization census), which can be individually selected by toggling the menu on the right.



Variant testing began late February for B.1.1.7 in the Ottawa wastewater system. The next plot illustrates the proportion of variant B.1.1.7 RNA signal detected in wastewater samples.

*Shaded area reflect the uncertainty of the midpoint rolling average.


Variants of Concern and Interest (VOC and VOI)

Summary

Analysis of COVID-19 wastewater RNA viral signal shows that the mean is changing direction.

Alpha (B.1.1.7) detected in low levels by sequencing and PCR, last reported on June 18, 2021.

B.1.617+ including Delta variant detected at low levels by sequencing, last reported on June 18, 2021.

B.1.351 detected at low levels by sequencing, last reported on June 18, 2021.

P.1 variant detected at low levels by sequencing, last reported on June 18, 2021.

No other VOC/VOI were identified by sequencing above the level of detection of the assay.

Detailed VOC/VOI report

  • Community genome analyses is in-progress research by the National Microbial Laboratory. The findings are presented for discussion only. Interpret with caution.

  • The assembled consensus community genome (i.e., most frequent metagenome observed) was consistent with genomes of B.1.1.7 lineage (aka the UK variant) with 11.05% genome coverage at >5X read depth. The mean depth of coverage across the community genome was 378X.

  • 6.0 mutations associated with B.1.1.7 genomes were present in the community genome.

  • Of every 100 reads that overlapped sites of B.1.1.7 mutations, approx. 30 were found to harbour B.1.1.7 mutations. This is consistent with a sample where the major proportion of contributing viral RNA can be assigned to the B.1.1.7 lineage.

  • There was insufficient evidence to support the presence of any other VOC/VOI above the level of detection of the assay.

Ottawa wastewater includes two VOC/VOI tests. See methods for more details. See the bottom of the page for detailed report, including the quality control summary.

  1. Thrice weekly tests for Alpha (B.1.1.7) using a qRT-PCR assay. These tests are performed by the uOttawa/CHEO laboratory beginning February 2021.

See plot above, “Proportion of variant, Alpha (B.1.1.7) RNA in wastewater, Ottawa”.

  1. Weekly test for all VOC/VOI using a metagenome assay, also known as the consensus community genome. These tests are performed by the National Microbiology Laboratory, Winnipeg beginning May 2021.

Quality control

Overall viral signal

  • Standard curves R 2 ≥ 0.95.

  • Primer efficiency between 90%-130%.

  • No template controls are negative

VOC/VOI

  • CDC N1 and N2 RT-qPCR assays yielded Cts of 36.6 and 36.2, respectively (Cts >35 will result in poor sensitivity).

  • Protocol: Tiled amplicon sequencing of SARS-CoV-2 meta-genomes 2(ArticV3) using an Illumina platform. See methods for details.

Interpretation cautions

The accuracy and thus reliability of SARS-CoV-2 wastewater testing is improving, as scientists understand more of the role of factors such as differences in sewage systems and laboratory protocols. Nonetheless, we recommend caution when interpreting daily and short-term variation in the viral signal. The level of detection for variant tests is unknown at this time but based on preliminary data, is estimated at more than 100 newly diagnosed or active cases. Research is underway to arrive at a more precise estimate sensitivity. Covid-19 wastewater signal is helpful when interpreted alongside other covid-19 surveillance measures, taking into consideration the strengths and limitations of each measure.


See the Methods page for more information on how the samples were collected, access to the data, and how the plots were created. The plots are currently for research only and presented to the public for discussion.

You can learn more about wastewater epidemiology and its role in covid-19 surveillance on Ottawa Public Health’s website.

Definitions

* A 7-day average is generated by averaging the levels from a given day with the three previous and three subsequent days. The average is termed “rolling” as it changes each day.

* For new cases, the reported date is the day the test result is reported by the laboratory. Episode date is the approximate date of covid-19 infection estimated from information available: the date of symptom onset, test date, or the reported date.

* A central question in wastewater epidemiology is determining the proportion of the wastewater that is actually from humans and the proportion that is rain water, snow melt etc. To address this issue, viral copy data is thus normalized using a seasonally stable fecal biomarker; pepper mild mottle virus (PMMoV). See methods for more details.

^ Percent change in 7-day average is calculated by comparing the 7-day average (previous day 1 to 7) with a lagged 7-day average (days 8 to 14).

Data to 2021-10-18