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THE NUMBER OF Covid-19 cases in Ireland is likely higher than what has been reported over the last number of days.
The National Public Health Emergency Team (NPHET) last night confirmed a further 1,620 new cases. A total of 3,263 cases were reported on Tuesday and Wednesday.
These daily cases figures are extracted from the HPSC’s Computerised Infectious Disease Reporting (CIDR) system and then reported to the public by NPHET.
However, officials have warned of a significant delay between positive test results being processed through CIDR due to delays in people presenting for testing over Christmas.
As many as 4,000 additional positive results have been received which are not yet included in the official case count.
Chair of NPHET’s Irish Epidemiological Modelling Advisory Group Professor Philip Nolan said yesterday that the CIDR system was never designed to process the amount of cases Ireland is currently experiencing.
In the days preceding Christmas, Nolan explained, the number of cases reported using CIDR was “very close” to the number of positive test results reported in laboratories on each previous day.
Between 24 and 26 of December, however, very few people presented for testing.
This resulted in a significantly reduced number of laboratory confirmed cases over that three-day period.
The number of positive cases in laboratories rose sharply “immediately” after Christmas, according to Nolan, resulting in the current backlog of cases to be reported via CIDR.
Around 2,000 positive tests were reported by laboratories on 28 December. This rose to 2,860 on 29 December, Nolan said last night, and to 4,363 on 30 December.
Not all of these positive tests, however, will be reported as cases, they need to be validated first. However, “many of them” will be, Nolan said last night.
“It is going to take several days to confirm all of those cases,” he said. “This in no way interferes with the process of identifying those cases or of contact tracing those cases or managing those cases. It’s simply a question of delays in formal reporting.”
He added that these cases will gradually be included in NPHET’s daily figures over the coming days.
Nolan said that given the level of backlog in reporting cases, Ireland’s epidemiological is “somewhat worse” than daily case counts this week suggest.
HSE Chief Clinical Officer Dr Colm Henry this morning said that essential Public Health actions like notification of close contacts and Contact Tracing is taking place despite the lag in reporting cases.
Meanwhile, the HSE has said close contacts of confirmed cases of Covid-19 are no longer being advised to get tested for the coronavirus due to current widespread levels of infection and should instead restrict movements for 14 days. This is a temporary measure.
Chief Medical Officer Dr Tony Holohan said this change was made to “support the testing system through this surge”.
On Wednesday, the HSE processed over 26,000 swabs. More than 2,300 calls were made to people who tested positive for Covid-19 and nearly 11,000 calls were made to close contacts.
“Testing and tracing is an exercise in containment and we are no longer in a containment phase,” Holohan said.
However, he stressed that it is “imperative” for close contacts to restrict movements and contact a GP if they develop symptoms.
“The average number of contacts per case has risen from 2.5 in November to an average in recent days of 6.3.
This is very far from where we need to be and I am appealing to everyone at every age to adhere to the mandated restrictions that the government has introduced – stay at home, except for essential reasons, other than for exercise up to 5km.
Speaking today, HSE CEO Paul Reid said 15,000 people with symptoms of Covid-19 are being referred for testing per day and warned that the virus is “rampant” across the country.
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We’re really only seeing the numbers that the rest of Europe we’re seeing in November/December. Most of whom are over the hump now.
According to WHO lockdowns give you time to get your house in order, we took 6 weeks of it, and guess what, the HSE yet again didn’t get their house in order.
@Christy: With our third lockdown to give the HSE so much time to fix everything, it’ll be tip top on 31st January!
@Christy: sorry, but why are you not blaming fcuking ppl who are not taking personal responsibility, why is it the test and trace system and the hse that’s at fault
@tweet-freek: Our public health officials have taken personal responsibility out of our hands when they lock us down.
They regularly shift the blame between foreign travel, young people, alcohol etc. which only serves to distract from allowing people to make reasoned choices about risk.
How many times have you forgotten to wash your hands, re used the same mask twice, touch your face without washing your hands, not given people 2m’s etc etc?
It’s shouldn’t be a blame game, if our public health drilled home the basics it would have a lot more affect than sowing seeds of division amongst different sectors of our society.
@Christy: So it shouldn’t be a blame game but peoples personal responsibilities are the reason that the HSE is at fault. What kind of logic are you working off there?
@Christy: what do you propose the HSE do to “get their house in order”. If people can’t discipline themselves to do simple things despite the authorities messaging advice and guidance ad-nauseam then what more do you expect the HSE do?
@tweet-freek: Exactly
@GrumpyAulFella: well given the numbers of cases and fatalities they themselves were forecasting back in March and the WHO emphasis on test and trace being the key tool I would have expected them to invest in a suitable IT infrastructure to support those endeavours especially after receiving a huge boost in financing. It seems that the HSE struggle to do the simple things right also, but let’s continue to blame the public for the continuing failure of the authorities.
@Declan McArdle: We only had half a lockdown last time, to be fair
What’s behind enificiency???? Civil servants and unions. But watch everyone blame IT . IT that they paid top money for.
@john s: enificiency?! And that’s all civil servants and unions John is it?!
@john s: Efficiency and effectiveness presumably begin with good communication both of which seem to be sadly lacking in this case. I’m not sure though how you would tackle enificiency whatever that is…
@john s: What have unions to do with it? it wasn’t a staffing issue. They clearly say that the IT system wasn’t designed for that capacity, that’s not blaming IT, that’s acknowledging that the current situation wasn’t anticipated and that the system in place wasn’t made to cope with it. Calm down and don’t be so hypersensitive, I’d guess you were an IT worker yourself but they could spell “inefficiency” properly
@john s: I work in a testing centre. There’s LITERALLY only so many time slots the computer can’t fill and also so many staff and so much time to swab the people who are booked in. This isn’t a “civil servant and union” issue.
@Becca: *can
@john s: the CIDR system is years old and goes to show effects the lack of funding into public health in the preceding years.
@Lynn Perry: We’ve spent over 200 billion on healthcare in Ireland between 2011 and 2020, average 20 billion per annum. Lack of funding has not been the problem.
https://www.statista.com/statistics/433207/current-healthcare-expenditure-ireland/
@Brian Lilly: Ur right 20bn but It’s not spent on docs and nurses but on nicotine patches, leaflets, agency , free GP for all
@john s: how exactly are civil servants and Unions responsible? Or of this your stock reply to life
Refusal to carry out Antigen testing is a big missed opportunity.
@John O’Brien: Way too many false negatives with antigen testing.
@John O’Brien: The UK antigen testing was failure, with over half of infections missed.
Wise, J. 2020. Covid-19: Lateral flow tests miss over half of cases, Liverpool pilot data show. BMJ, 371, m4848, https://doi.org/10.1136/bmj.m4848.
@▪️: It’s another rapid way to test, https://www.ecdc.europa.eu/sites/default/files/documents/Options-use-of-rapid-antigen-tests-for-COVID-19.pdf
PCR test produces as many false positives
@John O’Brien: false positives are preferable to false negatives.
only if testing is being carried out in the first place!
@John O’Brien: “PCR test produces as many false positive”
Wrong. That is Misinformation from the “casedemic” conspiracy theory.
“A false positive result occurred in two of 2981 PCR negative people—a specificity of 99.93% (99.76% to 99.99%). But lateral flow tests missed 23 of the 45 PCR positive participants, giving a sensitivity of 48.89% (33.70% to 64.23%).”
So there were 2 false positives RT-PCR results out of 2981 PCR negative people.
https://doi.org/10.1136/bmj.m4848.
https://www.realclearscience.com/2020/11/24/there_is_no_covid-19_casedemic_650809.html
@Hundredth Idiot: The antigen false negatives are based on the PCR false positives. Antigen will pick up a high viral load, so the chances of you being infectious and getting a negative antigen results is very low.
The danger is that you have just caught the virus and you are pre infectious. The PCR is more likely to catch it than the antigen.
@John O’Brien: That link says that PCR is the gold standard of testing.
@David Jordan: if the PCR is picking up dead RNA you are not infectious.
It’s a positive test but you’re neither infectious nor do you have Covid 19.
@David Jordan: Even if the functional PCR FP is only ~.1%, detecting zero or more than zero cells of SARS-COV-2 doesn’t show if you are at the beginning or the end of an infection, doesn’t tell you if you are infectious or contagious or not to others, doesn’t tell you how sick you are or are not. The list of what it doesn’t show goes on…
@Declan McArdle:”doesn’t tell you if you are infectious or contagious or not to other”
This nonsense really must stop.
Wrong, the Ct score tells you if you are infectious.
Yes, The RT-PCR test amplifies small amounts of viral RNA, not the virus itself. So, we needed to know the amount of RNA detected, as it correlates with the probability of infectiousness.
The number of amplification steps needed for an RT-PCR test returns a positive result is expressed as a Ct value (Cycle Threshold value). The higher the Ct value, the more cycles were needed to amplify initially low levels of RNA to a detectable level.
According to HSE guidance, if a Ct is 31 to 39, a person is considered a Weak Positive / Suspected Positive / Borderline case. They will be asked to get tested again 2 days later.
They are not counted as True Positive, their uncertain test results are not added to the infection figures.
However,…
1. By the second test, if their virus levels increased (resulting in a lower Ct value i.e. 31 and they are symptom free, they are counted as True Negative.
Work has been carried out into Ct values (RNA levels) and the probability a person is infectious (see Jaafar et al., 2020).
They found, for a Ct >34, there’s a <3% chance a person is infectious; RT-PCR results above Ct 34 (if positive) are either detecting residual dead virus particles and their viral RNA (low and falling) or a person incubating the virus (low viral levels and rising). However, if a person's Ct value is well below 34, that are likely to be infectious and must isolate.
However, most people who have symptoms and are infectious have a Ct of <25.
By the way, Antigen tests in Liverpool missed 33% of people with a Ct <25, so about a third of infectious cases were missed. This is very poor.
Reference:
Jaafar, R., Aherfi, S., et al. 2020. Correlation Between 3790 Quantitative Polymerase Chain Reaction–Positives Samples and Positive Cell Cultures, Including 1941 Severe Acute Respiratory Syndrome Coronavirus 2 Isolates. Clinical Infectious Diseases, https://doi.org/10.1093/cid/ciaa1491.
Guidance on the management of weak positive (high Ct value) PCR results in the setting of testing individuals for SARS-CoV-2
https://www.hpsc.ie/a-z/respiratory/coronavirus/novelcoronavirus/guidance/outbreakmanagementguidance/PCR%20weak%20results%20guidance.pdf
@Christy: This is the whole point. But to quote Michael Caine: “Not a lot of people know that.” People are focusing on this new definition of a positive Q-tip being a clinical case.
@Christy: I think that finding small amounts of dead RNA is the reason the HSE protocol is set for tests at or above 35 cycles… and whether they are reported as cases or not.
From memory of reading the document if the test is positive after 35 cycles then the test is rerun in the sample… and if the result is lower then it is marked as negative, if it is the same then it is marked as possible unless a previous test (e.g. close contact test one) had a higher load in which case it is marked negative. If no previous test result is available then a second sample may be needed (and this is the close contact second test that many fail to turn up to) and if the virus load is lower it is a negative test and if higher then it is a positive test….. the protocol is published and available but I do not have the link… but it is designed to cover exactly what you describe.
@David Jordan: It’s not nonsense at all when the public are not informed of the CT associated with their test. If it’s positive at a low CT then there is a high viral load, yes. De Gascun says HSE use 45 CT. (see his tweet of Sep 13). I’ll look at v1.2 of that doc. HSE received FOI requests to ask if they had taken then HPSC’s advice based on v1.1 of that doc. No reply as of November I believe.
@David Jordan: Sorry part of my post went missing:
1. By the second test, if their virus levels increased (Ct 31 and they are still symptom free, they are counted as a True Negative.
I really want to rip the Num Lock key out of my keyboard and burn it. I sometimes accidentally touch the Num Lock, so when I think I’m typing numbers I actually deleting text.
@David Jordan: There’s no denying that Covid is virulent but would we be treating asymptomatic flu patients the same way. It has the same effect on people with underlying conditions as covid has, it may not be as virulent but we don’t test for flu every year like we do for covid and there is no standard to compare the PCR test to for covid as yet has not been isolated. You are talking about casedemics but asymptomatic people with the flu if there’s such a thing, do not come under any scrutiny whatsoever. Yes we have a vaccine for the flu and that controls the numbers but I think(and hope) we will find in the long term that covid with vaccine will be no better or worse than the seasonal flu. https://bpa-pathology.com/covid19-pcr-tests-are-scientifically-meaningless/
@Declan McArdle: Wrong again…
Here’s the results of RT-PCR testing of Irish test samples (100 people tested).
Most people tested positive with a Ct of about 20 for Gene E, and a Ct of about 19.9 for gene S. This is well below Ct 45, and well below 31 that the HSE calls a weak positive. Max Ct was 34.7 (target S gene). Testing carried out onusing RealStar test kit made by Altona in Germany, it is also the most frequently used kit in Ireland.
“The median Ct value for the B-βCoV specific RNA (target E gene) was 20 (range 12.9–34.5). The median Ct value of SARS-CoV-2 specific RNA (target S gene) was 19.9 (range 12.6–34.7). ”
Chan, G.Y., Rajan, L., De Gascun, C. and O’Flaherty, N. 2020. Partial compliance with symptom-based testing pathways reveals asymptomatic carriage of SARS-CoV-2 in Ireland. Irish Journal of Medical Science, 1–5.
Also,…
“Dr De Gascun says the true false positive rate is between 0.1 and 0.2%.”
https://www.thejournal.ie/factcheck-pcr-tests-irish-video-5304097-Dec2020/
Three laboratories were assessed here, they used several RT-PCR machines including the RealStar test kit. There was no false positives.
“By testing 3 positive (CT values: S1, 28.4; S2, 33.6; S3, 38.5) and 1 negative sample, no false-positive results were obtained by any of the laboratories.”
Görzer, I., Buchta, Ch., et al. 2020. First results of a national external quality assessment scheme for the detection of SARS-CoV-2 genome sequences. Journal of Clinical Virology, 129, 104537, https://doi.org/10.1016/j.jcv.2020.104537.
@Michael McGrath: I see you are posting a link to a trash journal that quotes AIDS denier Kary Mullis, eccentric inventor of the PCR test who melted his brain with LSD and went hunting for UFOs in his latter years, who claimed the HIV virus did not exist and RT-PCR tests for HIV were bunk. I noticed a few months back that casedemic conspiracy theorists were wrangling his mutterings to fit their narrative.
I see like many conspiracy screeds it a fluff piece with no facts to justify his it avowed conclusions, it just waffles on and on about RT-PCR is a religion and a faith what not.
@David Jordan: Careful now – its dangerous to use actual scientific evidence around these parts! Jokes aside, thanks for posting some evidence based information. Sick to death of reading these finger in the wind understandings based on tweets and YouTube videos.
@Sean: never said it wasn’t, just another weapon against the spread of the virus.
@David Jordan: That’s all well and good but if you’re not carrying out the pcr tests in the first place how is it better?
@David Jordan:That’s your opininion it’s thrash your using a journal fact check to back up what your saying.And sorry no matter what you say the fact that 80 to 90 p.c of people are asymptomatic means it is a casedemic and it makes the claim that vaccinating the vulnerable and front line heath staff is the way to go like what we do for the normal flu not mass vaccinations.Now if your a doctor or a physician or a professor with a masters in infectious diseases then I bow to your education and superior knowledge other than that I am just as entitled as you to look up articles on the Internet an post them up here your opinion on those articles is just as valid as mine or anyone else’s here.The person the whole medical world is basing the covid test on is hardly the best person to be slagging
folks
often I have posted links to the hub underlying data pages
https://covid-19.geohive.ie/datasets/f6d6332820ca466999dbd852f6ad4d5a_0/data?page=29
these get updated with lab test counts and positive test results at 11am each working day (and after weekends and Public holidays) –
Is this the unvalidated data or data between processing…
I had been making notes on the difference in positive tests and cases reported in the evening as is often the case as the evening report should have more up to date figures -but over days these do balance out
It should be stressed that the figures for 31/12 below were obtained early afternoon on the 31/12 from the link above as were the figures for the 30/12 retrieved on the 30/12 before the evening reports.
22/12 – 13216 – 698 – 5.28% positive ( 970)
23/12 – 20660 – 1077 – 5.21% positive ( 938)
24/12 – 22884 – 1269 – 5.54% positive ( 922)
25/12 – 21270 – 1637 – 7.69% positive (1025)
26/12 – 11995 – 1207 – 10.0% positive (1296)
27/12 – 3536 – 343 – 9.70% positive ( 744)
28/12 – 9177 – 1159 – 12.6% positive ( 756)
29/12 – 13802 – 2007 – 14.5% positive (1546)
30/12 – 17484 – 2867 – 16.3% positive (1718)
31/12 – 26238 – 3363 – 12.8% positive (1620)
This gives 14586 positive test results but just (11535) reported after validation which leaves 3052 as the number of cases yet to be validated from the above (assuming I can count and add correctly).
We can also see that the case numbers up to the 27th are more of less spot on 6231 positive tests and 5895 cases reported. We must remember that on the the 11am figures above and the even report figures appear to be compiled at a different time – so some numbers may come from earlier or later in the day and the numbers never match. Some days the positive test results are higher then the cases and sometimes the cases are higher than the positive test results.. but they tend to balance out over time.
The Northern Ireland test reports show the total number of tests, the total number of positive tests and the total number of positive individual…
I suppose the question needs to be asked – do we accept the “raw” data or wait for the verification? Regardless, scary as it might be, I think we should have been told that 31/12 we had 26238 tests with 3363 positive and not just 1620 positive. This information was there and available to me and everyone in Ireland – so the process for briefing NPHET seems to have failed – but also our journalists as surely someone was looking at the data other than me and the question should have been asked.
@Niall Ó Cofaigh: for what it is worth I did flag this discrepancy on the 14th December 2020
https://www.thejournal.ie/coronavirus-figures-deaths-cases-5299343-Dec2020/
and when I review what I posted then (figures in brackets show the reported cases )
Cases Date and Time Tests Prev Totol + Pos = New Total
(301) 12/6/2020, 11:00 AM 9413 78255 +292 = 78547
(242) 12/7/2020, 11:00 AM 9623 78547 +234 = 78781
(215) 12/8/2020, 11:00 AM 10421 78781 +224 = 79005
(227) 12/9/2020, 11:00 AM 12203 79005 +198 = 79279
(310) 12/10/2020, 11:00 AM 12685 79279 +284 = 79563
(313) 12/11/2020, 11:00 AM 12582 79563 +325 = 79888
(248) 12/12/2020, 11:00 AM 12600 79888 +332 = 80220
(1856) +1965
(429) 13/12/2020, 11:00 AM 10728 80220 +359 = 80579
(246) 14/12/2020, 11:00 AM 10220 80579 +292 = 80871
(2531) +2616
The positive tests (with the + sign) and reported new cases (in brackets) never did match. and at the time it was put down to validation and the timings of the statistics but still over 8 days we had old 85 in the difference and not the 3000 we have now and the 85 might have balanced out over the previous and next days..
“We are no longer in a containment phase”
That’s right, we have entered an “arse covering phase” in which computer system shortcomings will be blamed over everything else.
It begs the question what kind of computer system is unable to handling tens of thousands of case/data inputs?
This is one of the most basic of functions for all desktop computer systems since the 1980′s, and it’s not exactly something which drains processing power.
Even if you accept as reality this claim of computer system shortcomings, the obvious solution is simple…
A small stand alone high specification network could be set up in hours to process any numbers of cases, using just basic office software that the HSE already licences.
People lying about symptoms just to get a test for Christmas so they could see family. That has happened a lot
All these people complaining about the HSE. Have you never been in a work environment where you were totally overwhelmed by the volume of work. HSE staff have been at the coal face since March 2020. So stop deflecting blame from people who havnt bothered to take the necessary precautions and trying to blame everyone else except them.
@Anne Busher Collins: Arguably, thanks to failings in management, they’ve been at the coal face for far longer than March 2020… The complaints against the HSE didn’t just materialise out of nowhere over the past year; every Christmas they come under fire for some mishap or another, waiting lists/trolleys/etc. I’d say that is in no small way the reason so many are finding them hard to trust.
@Anne Busher Collins: Nobody but nobody is giving out about front line staff. When people give out about the HSE they are talking about the overpaid political appointees that are allegedly running the HSE
Total shambolic HSE highly inefficient
@Jonnie Marre: Saved my daughter’s life so I’d disagree there
“Nolan said that given the level of backlog in reporting cases, Ireland’s epidemiological is “somewhat worse” than daily case counts this week suggest.”
That means that in the next few days, when numbers include the backlog, Ireland’s epidemiological will be “somewhat better” than daily case counts will suggest… Somehow, I think they will forget to state it and will try to use it as a justification for Level 5, and then, when the backlog ends and numbers drops they’ll say it was Level 5 restrictions that did it…
@David Lloyd: actually the case was that no medical doctor made a diagnosis and therefore the law was not complied with. The reliability of the test was questioned – but had nothing to do with the outcome of the case which was, from memory, that the law required an authorised medical doctor to certify cases that were to have enforced quarantine.. and this did not happen so the detention was illegal
It is worth noting that this would also apply in Irish law as far as I know as the detention of individuals is authorised by the local medical officer and not the gardai – if my memory of the 1947 Health Acts are correct.
spurious evidence was presented on the test – but then we had people trying to get off speeding and drink driving charges here for years by trying to discredit the various machines used… this case was not about the PCR test even if one judge, like yourself, seems to think that maybe they are not reliable contrary to all the scientific evidence which was not even presented in court.
Of course one has to read a lot more than an headline or biased reported to get to the bottom of this one.
Here are some extracts – noting that the case was won because there was no diagnosis by a doctor regardless of whether the test were reliable or not.
According to the process: “There is no evidence that this diagnosis was actually carried out by a professional qualified under the Law and who had acted in accordance with good medical practices”. These acts are reserved for the exclusive competence of a doctor.
The judges concluded by stating that: “The problem is that this reliability is shown, in terms of scientific evidence (and in this field, the judge will have to rely on the knowledge of experts in the field), as being more than debatable.
“Thus, with so many scientific doubts, expressed by experts in the field, which are the ones that matter here, as to the reliability of such tests, ignoring the parameters of their performance and there being no diagnosis made by a doctor, in the sense of existence of infection and risk, it would never be possible for this court to determine that C … had the SARS-CoV-2 virus, nor that A., B … and D … had high risk exposure,”
For anyone interested, here’s some PowerShell code that you can run from almost any Windows PC to get the data easily. You could plug this into something very easily to graph the data or use it for other automated purposes.
$RawCovidTestData = invoke-RestMethod https://opendata.arcgis.com/datasets/f6d6332820ca466999dbd852f6ad4d5a_0.geojson
$TestFeatures = $RawCovidTestData.Features
$TestResults = $TestFeatures.Properties
2021/01/01 11:00:00+00
$TestResults | Where-object {$_.Date_HPSC -eq ’2021/01/01 11:00:00+00′}
$CovidByCounty = invoke-RestMethod https://opendata.arcgis.com/datasets/4779c505c43c40da9101ce53f34bb923_0.geojson
$FeaturesByCounty = $CovidByCounty.Features
$CovidCountyDetails = $FeaturesByCounty.Properties
$CovidCountyDetails | Where-Object {$_.CountyName -eq ‘Dublin’}
Anyone who believe the figures to be true in the first place is naive! The figures from the start have be grossly overrated. Death figures are less than flu for 2017 2018 and 2019. Gov. Are scaremongering and gaslighting the public!
If Close contacts not being tested are they being traced?
@Albert Brennerman: yes, they are directed to contact tracing.
have your say