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Explainer: Why our positive Covid-19 numbers from Irish labs and those from a German lab are reported separately

Health officials say including the results from a German lab in ‘new cases’ would skew the curve.

Image: Shutterstock

THERE WAS CONFUSION at the end of last week when health officials here revealed more than 1,000 positive Covid-19 test results had come back from a Germany laboratory we had sent swabs to – but these positive results were not to be included in their daily reports of ‘new’ cases of the disease.

These swabs are part of the massive backlog that built up after officials broadened the testing criteria. The backlog should be cleared by the end of this week, but until then the Department of Health will be issuing two separate figures each evening.

So here’s why…

The backlog

In the early days of the outbreak in Ireland, when it was clear that the virus was spreading in the community, the case definition for testing was changed and anyone with symptoms (even just one of the symptoms) could be put forward by their GP for an appointment.

This led to a massive increase in the demand for testing. After this change to the case definition, the health service experienced supply shortages – first with the swab kits used in testing centres and hospitals and then with the chemicals (reagents) needed for the testing process in laboratories.

Both of these supply shortages created delays and the restricted access to reagents in particular led to a significant backlog of 35,000 swabs waiting to be tested in laboratories.

As an interim measure, while they worked to source a regular supply of reagents for Irish laboratories, officials came to an agreement with a German lab to send these backlog swabs there to be tested.

Meanwhile, Irish laboratories have been focusing on testing newer swabs. The reason for this is a second change in the case definition for testing which came two weeks after it had been expanded to include anyone with symptoms.

The huge demand for testing was unsustainable, and health officials reported just a 6% postivity rate, which meant most of the people who were being tested under this very broad definition did not have Covid-19.

As things currently stand, in order to get a test for Covid-19, a person must be in a priority group, such as healthcare workers, residents or staff at nursing homes and those who are medically vulnerable and have been advised to cocoon.

Since the case definition was changed, the positivity rate has increased – around 21% of Covid-19 tests done in Irish labs this week had positive results. 

This means those who are being tested now are more likely to have the coronavirus. These people are either in a vulnerable group or working in the healthcare system and there is a higher priority placed – in particular with healthcare workers – on a quick turnaround for those tests. 

German lab results

At the Department of Health’s daily press conference last Friday, Chief Medical Officer Dr Tony Holohan told reporters that a total of 1,035 positive results had come back so far from the overall number of swabs sent to Germany. 

Separately, he reported 480 new confirmed cases.

There was confusion Friday about why the German results were not added to the positives from Irish labs for an overall total of ‘new confirmed cases’. The CMO has said the majority of these samples (or swabs) are older – some dating back to the middle of March.

If everything had worked the way it was meant to – health officials could successfully ramp up testing capacity and there were no supply shortages – those test results would have come back within a week of the sample being taken.

And those figures would have been included in some of the daily figures in March and at the beginning of this month.

On Friday, Holohan said officials were not attempting to “obscure” figures. 

“If we reported them [as 'new cases'] it would give a false sense of how the disease is increasing day-on-day,” he said.

Yesterday the CMO presented a number of charts to explain why it was important not to report the Irish lab positives and the ones from the backlog together as one number.

chart1 Source: Michelle Hennessy via TheJournal.ie

[Apologies for the quality of the images - we asked the department for the original slides, but had to settle for our own pictures taken from a safe distance at the briefing]

The first line shows all cases at the times they were confirmed as positive. The second shows only the Irish laboratory results. 

Dr Holohan explained that if the cases were recorded according to the dates on which they were confirmed as positive, it would make it appear as though we had a significant growth in cases in recent days, which is not the case.

The second chart shows cases by the date the sample was taken.

“This is by date of occurrence. As you can see, the cases per day in the red line [the top line] occurring much earlier, they were older cases which is what the data would show us. This is them properly represented on the chart according to time.”

chart2 Source: Michelle Hennessy via TheJournal.ie

So when reading news reports, or if you have been watching or listening to the daily briefings this week and hearing two figures, that is why.

Yesterday, the CMO confirmed an additional 527 new cases of Covid-19 reported by Irish laboratories and an additional 465 cases reported by a laboratory in Germany.

Today, he confirmed an additional 548 new cases of Covid-19 reported by Irish laboratories and an additional 284 cases reportd by a laboratory in Germany.

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The 100 invalid tests from Germany

The HSE’s chief executive Paul Reid also this week revealed around 100 people  had been incorrectly informed their test for coronavirus was negative when they had actually contracted Covid-19. These were all results that had come back from Germany. 

Today, Dr Cillian DeGascun, chair of the HSE’s coronavirus expert advisory group, explained exactly what had happened with those cases.

A positive Covid-19 test will have detected the genetic material of the virus. De Gascun said the result can be either reported as detected/not detected but that there may “not infrequently” be results that are reported as ‘indeterminate or invalid’.

“What that means is that the assay or the assay platform hasn’t managed to generate enough information to decide whether the sample is positive or negative,” he explained.

Source: RollingNews.ie

He said in the ordinary course of events where there is an invalid result, a follow-up sample would be requested and taken from the patient.

“However, given the date of these samples in particular, and given the fact that the majority of individuals would now no longer have been symptomatic, we felt that it was not really terribly helpful to go back and recall these individuals for repeat testing.”

He said the raw data from the tests was reviewed as well as the original samples from the National Virus Reference Laboratory in UCD and they were able to reassign the majority of those tests either “positive, weak positive or negative” results.

However, due to what he described as “an IT glitch”, the computer system for managing this data as it came back from laboratories did not recognise the ‘invalid’ option and had recorded them automatically as negative. This is the system used by public health and by contact tracing teams, which is why people were originally given negative results. 

He said this issue has now been fixed and all of the cases identified as being affected by this have been resolved. 

HSE chief executive Paul Reid said yesterday that it was due to the assistance of the German laboratory that the backlog has now been reduced to 11,000.

He said it is expected that, between lab testing in Ireland and in Germany, this backlog will be eliminated this week. 

So for the rest of this week, you will continue to hear two figures; the results back from Irish labs – new cases – and the results from Germany – older samples from our backlog. After that, it will (hopefully) be back to one figure. 

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