Ireland’s first confirmed case of the Omicron variant was identified through “blind luck”, according to public health officials.

The case involved a person who recently returned from a country in southern Africa, where the new variant was first identified. Seven designated countries in the region are now the subject of travel restrictions.

The person had returned to Ireland before the restrictions were imposed and then developed symptoms which necessitated a PCR test in the past week.

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Outlining the case at a media briefing on Wednesday, Dr Cillian de Gascun, director of the National Virus Reference Laboratory, said he had no details on the severity of the case.

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Dr de Gascun said there was “an element of blind luck” involved in the identification of the case, as it was included in a regular 10 per cent sample of all cases that is referred to the NVRL’s lab at Backweston each week.

He said a review of cases involving S-gene failure, which can be used to identify potential Omicron cases, was carried out, dating back to the start of October.

This identified 14 recent samples with this characteristic, of which eight could be retrieved. These were sent for whole genome sequencing, but only one was confirmed as involving Omicron. Enhanced contact tracing around the case has since begun.

Seven other cases with S-gene dropout, which can be indicative of Omicron, were found not to involve this variant but a sub-lineage of the dominant Delta variant.

According to Dr de Gascun, the prevalence of S-gene dropout cases was well under 1 per cent. The vast majority of cases from October and November were no longer be available for sequencing.

Dr de Gascun said there was no evidence of community transmission of the variant in Ireland, and for this reason travel measures had been introduced to minimise spread. Once a variant gets into a country, it has to achieve a “critical mass”, after which dominance occurs over four to eight weeks.

About 1,500 cases a week can be genetically sequenced, or about 5 per cent of all cases, he told the briefing.

The NVRL had anticipated the S-gene dropout test could have been used as a proxy test for the presence of Omicron, prior to sequencing, but Dr de Gascun said the fact that only one out of eight samples identified in this way turned out to be the new variant showed it could not be used in isolation as a surveillance measure.

Officials are now working through what the best approach might be. Aside from travel-related cases and close contacts, they will be trying to find the best way of sampling that can “characterise what’s happening in the population at large”.

“We only found out about this lack of association between S-gene targeting and Omicron this morning.”

Omicron response

The emergence last week of the new variant prompted the Government on Friday to impose travel restrictions on passengers from seven southern African countries: South Africa, Botswana, Zimbabwe, Namibia, Lesotho, Eswatini and Mozambique.

People arriving in Ireland from these countries have to quarantine at home for 10 days after entering the State.

Although the number of travellers impacted will be small, the reintroduction of travel restrictions marks a further return to tighter restrictions to bring Covid under control.

Travellers from those countries will also have to present a “not-detected” pre-flight PCR test result, regardless of vaccination status, quarantine at home for 10 days and undergo a further two PCR tests.

The obligation is backdated for recent arrivals from these countries, who will be traced and contacted using the passenger locator form. The Garda will monitor compliance, initially.

Concerns over Omicron and the ongoing high level of Covid cases in the State has led to the Government approving a raft of measures.

These measures require travellers into Ireland from any country to show negative PCR or antigen test results, introduce mask-wearing for primary school children from third class upwards and ask parents to limit their children’s socialising.

Pandemic powers

Two pieces of legislation – one to extend several Covid powers and one specifically to revive mandatory hotel quarantine if needed – are to be brought to the Dáil and Seanad in the coming days.

The mandatory hotel legislation is necessary because those powers have already lapsed, while the other Covid powers – including those concerning masks, hospitality restrictions, Covid certificates, travel restrictions and others – are due to lapse early next year.

Officials are currently preparing orders to require travellers into the country to show a negative PCR or antigen test from Friday. There will be “spot checks” at the airport to ensure travellers are compliant, but officials said it would be mostly a matter for airlines and ferry companies to ensure that passengers could show a negative test.

The Government is considering fines for carriers that allow people without tests to board, while a spokesman confirmed there would be fines for passengers who could not show a negative test. There will be no checks for travellers from Northern Ireland.