Every week, a report that gives a strong indication as to whether the proportion of Covid variants present in Ireland is stable or changing is sent to Dr Cillian De Gascun, the Director of the National Virus Reference Laboratory.
For months, it’s been broadly stable, in that more than 90% of cases each week were showing up as the UK, or Alpha, variant.
The report is on what’s called S-gene positivity, which indicates whether a positive Covid-19 swab contains or does not contain the Alpha variant.
What it does not do is say which other variants are present, if the Alpha variant is not there. That requires whole-genome sequencing, a process that takes up to two-and-a-half weeks.
But because at least 90% of cases were showing up as the Alpha variant each week since February, it was clear that the country had a consistently low presence of other variants.
And in recent weeks, even as the Delta variant spread across the UK, the S-gene positivity numbers didn’t change.
With that and other data in mind, last Thursday, Professor Philip Nolan, the Chair of the NPHET Epidemiological Modelling Advisory Group, said it appeared the Delta variant had so far been contained in Ireland, thanks to the work of public health teams within the HSE.
Confirmed Delta cases no longer appeared to be growing week-on-week, he said. It was good news.
Chief Medical Officer Dr Tony Holohan noted that, while the whole-genome sequencing data came with a delay of almost three weeks, the S-gene positivity data was more up to date.
As of last Thursday, the most recent data covered the period 7 to 14 days beforehand. It was still showing more than 90% of cases were the UK variant, he said.
That was Thursday.
On Monday morning, updated S-gene positivity data was provided to Dr De Gascun. It covered the period from the previous Sunday – eight days before – to the Friday following the NPHET briefing.
It showed a sudden drop: just 78% of cases were the UK variant. That meant 22% were some other variant.
On Monday evening, based on this data, the Chief Medical Officer tweeted his concerns about the spread of the Delta variant.
"We estimate that Delta accounts for up to 20% of cases reported in the last week," he said.
The S-gene data is the most timely data available, and likely to be closely watched in the coming weeks by Dr De Gascun’s team and others in NPHET. But it’s important to note that Dr Holohan’s tweet contains the phrase "up to" and the word "estimate".
For that reason, it’s worth understanding the S-gene data – and what it does and does not show.
Why S-gene data matters
When a Covid swab is sent to a lab, the lab tests for the presence of certain genes associated with the SARS-CoV-2, the virus responsible for Covid-19. Each laboratory’s testing process is slightly different.
This was a simple and consistent process until the Alpha variant emerged in late 2020. Certain labs across the world began detecting positive Covid-19 results from swabs, but found their testing process was unable to detect the presence of the S-gene.
We later learned that the Alpha variant has a mutation that means that some PCR tests no longer detect the S-gene when it’s present.
Those tests will correctly return a positive result, but by detecting other genes.
As such, the non-detection of the S-gene in a positive swab – by happenstance – became a reliable indicator of the presence of the Alpha variant.
At the same time, the variant spread across the world.
In Ireland, only one lab in the country happened to use a testing process that would return positive results but not detect the S-gene: Backweston Laboratories in Co Kildare.
By early December, suspected cases of the Alpha variant were being sent to Backweston to try to get an understanding of the emergence of that variant here.
By January, Alpha had become the dominant strain in Ireland. By March, it made up more than 90% of cases.
At that point, other variants of concern began to emerge. Testing for the presence of the UK variant became almost redundant, since it was so ubiquitous.
However, positive cases of the South African and Brazilian variants would show up with the S-gene, so Dr De Gascun’s team began sending suspected cases of them to the same lab.
They inverted their presumption in relation to the test: If the S-gene appeared in Backweston in a positive swab, it meant the Alpha variant wasn’t present, and therefore it must be another variant.
Then Delta emerged and began spreading rapidly in India and the UK. Like the South African and Brazilian variants, it returned the S-gene in labs like Backweston.
As such, if the proportions of the Alpha cases dropped below 90% in the swabs sent to Backweston, it could indicate the silent emergence of Delta. Therefore, scientists have been keeping a close eye on the S-gene data since the first case emerged in early April.
The concern about the Delta variant has been growing ever since. In May, Delta exploded in the UK, and data emerged showing it’s likely be significantly more transmissible than Alpha.
On 30 May, guidance was issued here to public health teams, asking them to send the swabs from any suspected Delta cases to Backweston.
But the proportions within the S-gene data didn’t change significantly until Monday, when it indicated the Alpha variant had suddenly dropped to 78%.
In the meantime, scientists had also begun sending more and more suspected cases of the Delta variant for whole-genome sequencing.
The most recent whole-genome sequencing data is three weeks old. Just 5% of cases were the Delta variant. Yet, on foot of Dr Holohan’s tweet, news headlines say 20% of cases are now the Delta variant.
How much Delta?
Where does all this leave us? What percentage of cases are actually Delta now?
The reality is: it’s very unclear.
The S-gene data from the Backweston lab is the basis for Dr Holohan’s tweet about Delta. It’s the most timely data on variants, but limited.
Around 25% of all swabs go through the lab, but they tend to come from the Leinster region, so it’s not geographically representative.
Assuming public health teams are following the renewed guidance from 30 May, a disproportionate number of suspected Delta cases nationwide should pass through Backweston.
As a result of that, it’s also not clear how representative the S-gene data is now of the wider case numbers when it comes to variants.
The whole-genome sequencing data is more definitive, but it’s less timely. It’s three weeks old and had showed a stabilisation in the spread of the variant. Yet, as we all know, three weeks is a long time in this pandemic. It could easily be out of date by now.
The whole picture is very unclear. What is clear is that the Delta variant is spreading faster than was perceived as recently as last Thursday. How fast it’s spreading is still unknown. It’s now linked to a concerning cluster in Athlone, and increasing rates of community transmission.
When the whole-genome sequencing is completed for last week, it’s possible more than 100 Delta cases will be associated with it.
That’s a significant increase: As of last Thursday, there had been 188 cases of Delta in total confirmed in Ireland.
Yet, as with every other variant, testing, tracing and isolating can slow its spread, and mitigate its impact. Its increased transmissibility means it will eventually become the dominant variant.
We still don’t know what that will mean for the country – in particular the health services – given the number of vulnerable people who are now vaccinated.
The question is: when will we find out? This week, the answer seems, unfortunately: sooner than we thought.