Tyson Graber
@rnaguru
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## wastewater plots automatically tweeted Tues-Fri. Data updated *once per week* ## Cell biologist and poopcaster. I do RNA biology with a side of SARS-CoV-2.
Ottawa
Joined November 2008
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Probable BF.7 in Ottawa wastewater in two of last week's samples. Surprisingly high proportion (>50%) of total signal. This is an omicron variant with an important mutation (S:R346T) that is known to confer immune evasion. Variant landscape is changing again.
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And the beat goes on! Ottawa wastewater surveillance🧪📉 will continue
@uOttawa
thanks to financial support from
@HealthOttawa
,
@CHEO
Hospital, and CHEO Research Institute. Thanks
@AlexMunter
@LabBerman
@VeraEtches
@RobDelatolla
for making this happen!
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Almost 2 years since Ottawa began looking for CoV-2 in its wastewaters. This plot shows a slightly different perspective of signal across time. Darker reds indicate speed of growth of a wave, while blue represents how fast it degrades...note how fast we are climbing in this wave.
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Anxiety in Ottawa rising because wastewater data from the last few days is delayed 😃. Apologies. Site will be updated Wednesday with data points from over the weekend. The signal has not peaked. There will also be a data correction. More information to follow Wednesday.
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COVID hospitalizations* have shot up in Ottawa in the last week. We haven't seen these numbers since Spring last major wave).
Hosp. data on is not plotted past June 30 as the open data is no longer published.
The plot below is from Ottawa public health
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Ottawa wastewater has flipped from all Delta to all Omicron in about 1 week. This is unprecedented. Alpha took 4 weeks to replace the ancestral variant. Delta took 2 weeks to supplant Alpha...
@AlexMunter
@OttawaHealth
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As
#Ottawa
enters its XBB wave, let’s take a closer look at
@TRyanGregory
's "rising tide” phenomemon in Ottawa. The story starts with our lowest hospitalization counts that occured in Summer 2021, not coincidentally following a successful vaccination campaign in the city...
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Ottawa wastewater CoV2 signals increasing significantly along with percent positivity. Similar trends in the rest of the province. Please take appropriate precautions to protect yourself and the community in which you live.
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Across this pandemic we have observed that an emerging variant reaching 50% of the WW signal is followed by a rapid increase in overall wastewater signal signalling the beginning of a wave. I suspect we are starting to see that now.
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Ottawa trajectory not looking good. Reaching heights not seen since Spring of this year when XBB entered the scene. VOC data from last week of AUG indicates a mixture of XBB flavours incl. EG.5, no BA.2.86. Bot plots coming near top of hour.
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Good morning Ottawa. As of last Thursday, wastewater CoV-2 RNA levels were observed to be as high as the peak levels seen in the first Winter omicron wave. Plots below show signal from 2 different gene regions (N1 and N2) normalized to pepper virus.
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Currently Ottawa WW at ~3 times the signal that was observed at the peak of the first Omicron wave.
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Ottawa Public Health just updated to this week’s hospitalizations. I’d say it’s a wave?
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#Ottawa
SARS-CoV-2 wastewater trends as of: January 02. (A) Pandemic overview with past year highlighted, (B) Past year with past 2 months highlighted, (C) past two months with most recent sample highlighted. Polyline =7 day mean normalized signal [:|] automated tweet. [|:]
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This is amazing news. However, scientists like
@RobDelatolla
@uottawa
shouldn't have to depend on funds earmarked for *research* -- an already scarce source of $ in Canada -- to carry out what is a now-established gold standard of public health surveillance.
Wastewater surveillance will continue - for now - in Ottawa. The
@uOttawa
lab that runs the program has found research funds to keep it going for a few months. Public health officials are seeking a longer term solution. Individuals use it, as do hospitals.
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Great interview with Dr. Delatolla explaining what Ontario residents will be losing. Some tough questions answered with aplomb.
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Key point... where we are now was forecasted back in August based on Ontario's disease surveillance intelligence and global intelligence. Based on wastewater and assuming current xmission pressure, we won't be out of this protracted wave until year's end.
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Adding some context…we are firmly in previous omicron wave territory now and it is absolutely no surprise. Europe seeing similar trend in wastewaters.
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Aggregated Canadian wastewater-based variant reporting is now live! Courtesy of the National Microbiology Labs. It'll be updated twice a month.
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Flu and RSV weekly average continues their climb in
#ottawa
as of last Friday. OPH reporting still increasing flu positivity (possibly a week or two behind the wastewater numbers).
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The data visualizations posted to this account rely 💯% on
@RobDelatolla
's lab generating datapoints and funding from the Ontario government. To answer your main question (from several rec'd): Yes, this directly affects Ottawa ww surveillance and when that goes, so do plots.
'I was shocked': Ontario to cancel widely used wastewater surveillance program via
@ottawacitizen
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#Ottawa
VOC update to 26JAN: After some tweaking, our K444.2 and L452.3 assays that pick up XBB* markers are in agreement with each other and show a growth in the last couple of weeks of Jan. There has been an uptick in SARS-CoV-2 wastewater signal in the first week of FEB...
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More wastewater-derived evidence that XBB* isn't contributing much to this wave yet in Ottawa: If XBB were here we would see a positive deflection of "N1/N2 sigma" which is measured daily in Ottawa (panel C). We see no indication of this in the last weeks...
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As of 16AUG
#Ottawa
variant landscape is a mixture of XBB.1.9*, EG.5* and XBB.1.5* hanging on. No evidence of BA.2.86 here or in sites across the Ontario network. Caveat is sampling frequency once a week which reduces detection sensitivity for this (still) rare variant...
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Welcome to 2023. I'll tweet updated Ottawa WW plots regularly (via a bot I hope). These tweets will post the following 3 timelines: Pandemic, past year, past 2 months. The min, median, max weekly average signal across the pandemic provides more context.
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Please note that there won't be any NEW wastewater datapoints from
#Ottawa
for the next week or so while students/staff are on holiday. Those days will indeed be sampled and analyzed retrospectively. Meantime, the poopbot from this account will continue to post.
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...I’ve plotted ww signal (A) and hosp. cases (B; patients in acute care because of COVID-19) and let my computer tag the epiwave peaks (red dots) and valleys (blue dots). In (C), I’ve plotted those blue minima for both ww and hosp. Regression lines for each are shown...
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#Ottawa
SARS-CoV-2 wastewater trends as of: October 19. Pandemic highlighting past year (A), blue line is weekly average, (B) Past year highlighting last 2 months, (C) Past 2 months, (D) inferred case incidence, (E) inferred Reff. D and E determined with phac-nml-phrsd/ern
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And now from Texas; wastewater-based influenza sequencing identifying H5N1 using a commercially available probe capture method (Twist).
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@culturaltutor
There's an abstract painting in our house that we turn 180⁰ twice a year. I'm sure Mondrian did the same.
#abstractarthasnorulez
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As of 2nd week of July it's clear from wastewater sequencing data that KP.3 has supplanted other variants in Ottawa wastewater and the rate of increase and time correlate well with the surge in CoV-2 signal.
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Does Germany know something that we don't on this side of the pond?
No.
Germany is reintroducing masks in schools and advocating
#N95s
. Here in the UK we are doing nothing this Autumn and leaving all at risk from
#LongCovid
and cev children at high risk. I don’t trust this government to make the right decision on schools.
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And just like that...clinical genomic surveillance in Ottawa is essentially gone. Wastewater genomic surveillance now standing watch for any emerging variants across Ontario and major population areas in Canada.
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BA.4/5 has taken over in Ottawa. Wastewater samples from July 2, 4, 5 indicate it's the winner, as BA.2.12.1 and BA.2 plummet as a proportion of total SARS-CoV-2 signal. Unlike in the US, BA.2.12.1 never had a chance in Ontario as BA.4/5. This was an interesting race to watch.
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Pumpkin spice RATs at the local library. Reminder that these are still available FREE in Ottawa. Follow link for locations.
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Canada's began its KP.3 a little later than most. That's a good thing because we can see into the future by looking at how others are coping. Here's a round-up of what's happening in wastewater in countries with national and public dashboards...
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Wastewater surveillance is great but beware that it's still a young science and there's a lot of overinterpretation going on out there.
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One of the most comprehensive articles out there; outlines what we as Ontarians built, what we use(d) it for, and what we are losing. If this were the US, it would have been successfully transitioned to the private sector. In Canada, any new leaf of innovation is left to wither.
Ontario has a globally praised system for monitoring diseases through wastewater. So why is the province shutting it down? by
@IvanSemeniuk
via
@globeandmail
#COVID19
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@jeffgilchrist
At least for CoV-2, toilet plumes are just not a route of transmission. Infectious particles in urine or feces are not there. Multiple studies including this prospective study show this. Is the risk zero? No. But exceedingly low.
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This plot shows the % of wastewater SARS-CoV-2 signal associated with Delta and Omicron in Ottawa. As of December 16 Omicron represented 50% of the signal. To measure omicron, we use a qRT-PCR test specific for a single nucleotide variation not present in Delta; C28311T) ...
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Moving the goalposts continues...
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#Ottawa
wastewater VOC update. Increased growth of S:K444T in the last weeks. Sequencing data from end of November suggests growth is due to BQ*. Samples from Monday indicate the mutation associated with these lineages now represents the majority of CoV-2 WW signal in the city.
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The latest Ottawa ww datapoint from Wednesday has been added. With more than a full week of new data, I think it’s safe to say that we’ve reached the peak of this wave. It will take awhile to get down the highest mountain that we’ve climbed so far.
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Especially important as clinical genome surveillance wanes. We need ways to anticipate unknown knowns (i.e., new, unknown variants).
The essentiality of wastewater surveillance
"Core component of infectious disease monitoring, providing a variant-specific, community-representative picture of public health trends that captures previously undetected spread and pathogen transmission links"
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Local media reporting that COVID numbers are stabilizing. There is no indication of this. It hasn't been "stable" since early summer. Expect increases as a new variant makes inroads in the next several weeks.
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Absolutely. Need randomized clinical testing of population in order to fully understand wastewater signal.
i’m no wastewater expert but it’s still shocking/telling that our reluctance to test has us sifting through sewers to tell us anything about this sixth wave.
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Way too late of a response, but every bit helps.
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Wisps of Delta have been reappearing in Ottawa wastewater of late after going below detection in late February. It doesn’t appear to be increasing but it clearly wasn’t extinguished and its embers are still burning. Please get vaccinated.
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Spring is coming. The melting snowpack creates *very* high flows in Ottawa sewers. We found out last March that this can break our local WW-based CoV2 surveillance system...
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BC reporting first clinical case of BA.2.86
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Boston and Dutch wastewater have been my go-to sentinel surveillance spots since Spring 2020. While there has been an uptick the last few weeks, the rate of growth is slower than in previous waves. Ottawa is looking similar.
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Proportion of omicron signal in Ottawa wastewater ending December 21.
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As total ww signal increases in Ottawa, the VOC landscape is shifting yet again as of June 13. BA.1; ancient history; BA.2 is already out of style.
@WalaaEidCanada
monitors BA.2.12.1 using a S:L452Q assay. BA.4/5 is monitored at the same locus with an S:L452R specific assay.
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Preliminary data from samples collected December 17-19 indicates that as of Sunday, Omicron is the totality of the ww signal. We will post that data soon via twitter and at . Thanks to the Ottawa WBE crew
@RobDelatolla
@emerc19
@PatrickAoust
@WalaaEidCanada
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#Ottawa
wastewater-derived VOC update: Samples tested up to last week (JAN5) indicate that K444T+ lineages (includes BQ*) represent majority of WW signal (figure panel B). JAN5 sample had weak positivity for L452 (L452.2 is an assay version #) which is indicative of XBB*...
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Ontario WW trending in the right direction, albeit still at a high baseline.
Unfortunately
@PublicHealthON
we only get to see the last year of data :-(
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If you look at case incidence dervied from wastewater across the entire pandemic it seems we’ve never been lower (Reff also the lowest ever at <0.4). Let’s see if it holds.
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Looks like Ontario has transitioned to XBB without a big wave which is great news. Baseline still very high though...
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As XBB.1.16 makes in-roads in Ontario, is the Omicron tide receding in Ottawa? WW signal remains high, hospitalizations trending down. In bottom plots, the “meta-epiwave” (tide) is assessed by following magnitude of valleys/troughs between individual epiwaves over time.
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Wastewater as of Monday showing decreased SARS-CoV-2 signal. Clinical test percent positivity also going down. If this decrease continues, cautiously optimistic that hospitalizations will peak later this week or early next week.
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Having fun translating Ottawa WW signal into case numbers and R(e) with the ern package from D. Champendron et al (). Take the case #'s with a grain of salt.
R(e) > 1 since July!
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Samples taken from this past weekend in Ottawa suggest a levelling off SARS-CoV-2. will be updated later today to include samples from 7,8,9 January.
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