There have now been 72 cases of the so-called Indian variant detected in Ireland. The updated figure was provided by Dr Cillian De Gascun of the National Virus Reference Laboratory at Friday's NPHET briefing.
On Wednesday, the total number of cases confirmed was 59. That figure was up from 41 at the NPHET briefing one week ago.
A breakdown has been provided for when the 59 cases confirmed as of Wednesday were reported to laboratories.
Some 24 cases are linked to the week of 26 April to 2 May, the most recent week for which data is complete.
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All 72 cases of the variant reported by the laboratory have gone through a process called whole genome sequencing, which takes approximately two weeks to complete. For that reason, the current total is seen as a snapshot of the situation between two and three weeks ago.
Also known as B1617.2, the Indian variant has been spreading rapidly in parts of the UK, with the number of confirmed detections surging in the last two weeks.
Some 3,000 cases of the variant have now been reported there, where sequencing data is also time-lagged. It is now the dominant variant in the city of Bolton, and five or more cases have been reported in at least 86 local authority areas.
The first Indian variant case in England was detected in mid-March, three weeks before one was detected in the Republic of Ireland.
Public Health England data indicates B1617.2 has taken root and spread far more quickly than any other previously monitored variant. The British government’s scientific advisory group, SAGE, has said "with high confidence" that it’s likely it is more transmissible than the so-called UK variant, but definitive conclusions are awaited.
Some 1,000 cases of the Indian variant were documented in England within 40 days of initial reporting. No other monitored variant has broached the 200 case mark in the same time period.
The British government is now facing criticism for leaving India listed under the default 'amber’ category on its travel list until 23 April. Many of the early cases in England were linked to travel.
For months, the government here has advised against all non-essential travel to the Republic of Ireland. People who have been to India have been required to complete mandatory hotel quarantine since 4 May.
Variant monitoring stepped up in Ireland
The remarkable pace of the spread of the Indian variant in parts of the UK – combined with the comparably lengthy time needed to complete the genome sequencing process – has prompted scientists here to ramp-up use of a faster method for monitoring variants.
Until recently, a team led by Dr Cillian De Gascun had received weekly reports of what’s called "S-gene Target Failure" among positive Covid-19 swabs.
This data constitutes an early warning system on variants, indicating to scientists whether the proportion of variants among cases is stable or changing.
Dr De Gascun told Prime Time these reports will now be compiled more regularly.
While whole-genome sequencing is based on samples taken weeks prior, this early warning system is instead based on samples taken in the previous days. The downside is that it’s not definitive about which variants are present.
The Indian variant was categorised as a variant of concern on 10 May, in line with WHO guidance. This categorisation also means more public health resources will be assigned to the investigation of potential cases.
"I’m hopeful that the enhanced public health measures – now that it’s a variant of concern – will successfully control it," Dr De Gascun told Prime Time.
"They seem to have done so with the other variants of concern," he said. "We’re going to monitor the S-gene Target Failure rate more regularly as well, so we have more real time data."
Having asked Dr De Gascun about the S-gene Target Failure data at a recent NPHET press conference, Prime Time requested updated information, and was sent weekly reports covering to 17 May.
For comparison, the published whole genome sequencing data reliably covers to 2 May. Therefore the S-gene Target Failure provides an insight into the recent weeks, for which whole genome sequencing data is incomplete.
The early warning system data shows a slight dip in the proportion of samples considered to be the UK variant in the weeks since 26 April.
Between 22 February and 26 April, every weekly report bar one indicated that more than 92% of positive swabs were the UK variant. Most weeks, the proportion was between 94% and 96%.
In the three weeks since 27 April, 91%, 90% and 90% of swabs are considered to be the UK variant.
The last time two consecutive weeks of these reports indicated less than 92% of cases as the UK variant was in late February.
However, this early warning system can’t identify variants among the remaining percentages. Therefore, the data indicates a slight fall in the proportion of cases of the UK variant, but not specifically a corresponding increase of any single other variant.
The updated data will be watched closely in the coming days and weeks by the team in the National Virus Reference Laboratory, to see if the recent data constitutes the start of a trend, or whether the proportion of the UK variant reverts to the previous norm of 92% or more.
Whole genome sequencing reports will provide much more definitive conclusions, when they do come.
A lot remains unknown about the new variant
In the meantime, further reports on the characteristics of the Indian variant are expected to be published in the UK. A lot remains unknown about it – largely because it’s only come to the fore recently.
According to Cov-lineages.org, which tracks submissions to the GISAID virus database, there have been just 5,000 cases of the Indian variant sequenced and reported to it. More than half were completed in the UK in just the last three weeks.
It's not known whether it causes more severe disease, or if it will make vaccines any less effective.
On severity: "The number of hospitalisations remains low in the affected areas," minutes from the 13 May meeting of England’s scientific advisory group read, "though this could be because the number of infections has only recently increased."
On vaccines: British Health Secretary Matt Hancock said early data showed positive signs, while his deputy chief medical officer had a similar assessment. Prof Jonathan Van-Tam said his view was there is now "a straight race" between the spread of the variant and the roll-out of vaccines.
However, at Friday's NPHET briefing, Chief Medical Officer, Dr Tony Holohan said Public Health England is going to publish data "raising the possibility of effectiveness of the vaccine, particularly after first dose, being reduced in preventing transmission."
Dr Holohan said he'd been made aware of the forthcoming publication by his counterpart in Northern Ireland, but not seen the details.
Details on Irish cases
In Ireland, some details have been made available about the first 34 cases detected in the country. They’re contained in a Health Surveillance Protection Centre report dated 11 May. Other information was provided in press conferences.
Of the 34 cases for which details have been published by the HPSC, or provided later, 27 have been linked to other known cases of the variant.
That indicates the virus was transmitted from one contact-traced person to another, meaning that public health doctors have some understanding of the spread. Theoretically, such an understanding would allow public health teams to shut down further transmission.
However, four cases of the Indian variant here have been categorised as community transmission. That means public health doctors couldn’t trace how the virus was transmitted to the person infected.
Transmission details were not provided on the remaining three cases within the 34. It would appear they remain under investigation.
Two-thirds of the 34 cases were people between the ages of 18 and 45, and the largest outbreak was six cases.
It is likely more details will be published or provided on other cases soon.