Nphet considers asking all arrivals to give samples for Covid-19 genomic sequencing

Letter to Government warns of 33% increase in workplace outbreaks in one week

Dr Ronan Glynn, Prof Philip Nolan and Dr Cillian de Gascun of the National Public Health Emergency Team at a briefing last week. Photograph: Colin Keegan, Collins Dublin

All inbound travellers could be asked to provide samples for detailed laboratory analysis so researchers can detect Covid-19 variants amid concern around travel, it has emerged.

Whole genome sequencing provides critical information for the monitoring of variants of concern.

The National Public Health Emergency team (Nphet) has discussed pursuing a universal strategy where all inbound passengers would provide a sample and then be subjected to enhanced contact tracing.

Minister for Health Stephen Donnelly said on Tuesday there had already been a "significant increase" in genome sequencing of positive Covid-19 tests from 1 per cent of positive tests being genome sequenced to 15 per cent, and he said he hoped this can increase further.


Given that viruses evolve over time and can mutate into variants that can spread faster and make people sicker, and potentially affect how well vaccines work, genomic testing is considered to be crucial to efforts to control Covid-19. Whole genomic sequence testing will allow authorities to keep a closer eye on how the virus is changing and respond accordingly.

Minutes of a Nphet meeting in late January show that the team discussed the increasing concerns at a European level in relation to the importation of new variants of Covid-19. The growth of such variants has had a detrimental impact on the global effort to contain the virus due to increased transmissibility.

“Some members drew attention to the possible need for a broader approach to whole genome sequencing of inbound travellers. Reflecting on the experience of importation of cases due to international travel in March 2020, there may be merit in pursuing a universal strategy whereby all inbound travellers would give samples for analysis through whole-genome sequencing and be subject to enhanced contact tracing,” according to a note of Nphet’s discussion on January 28th.

“The Chair re-emphasised that in the first instance, adherence to basic public health measures at national level is necessary to significantly reduce community transmission. However, measures designed to curb non-essential international travel can significantly slow any possible importation of new variants once community transmission is at a more manageable level. This will be particularly important in the context of the rollout of the vaccination campaign.”

The team also discussed provisional data from the UK which showed a lower vaccine uptake across certain population groups.

"The need to look at similar data in Ireland and anticipate challenges will be necessary going forward; a one size fits all approach may not be feasible."

Separately, the deputy chief medical officer has warned the Government that there had been a 33 per cent week-on-week increase in the number of workplace outbreaks.

In a letter sent to the Minister for Health Stephen Donnelly last week, Mr Glynn said there were 10 outbreaks in commercial settings, nine related to food production settings, six in manufacturing settings, and five related to the construction industry.

The letter also says that the number of close contacts captured during the week had risen three per cent on the previous week. Furthermore, a small number of people were making up for a large increase.

“Indicators of mobility and contact across the population are low but continue to drift upwards, with the average number of close contacts per adult confirmed case now at 2.6. To note, this indicators is currently over-dispersed, meaning that a small number of cases with large numbers of contacts are inflating the mean.”

The letter said there were 195 open clusters associated with residential institutions with 23 linked deaths and 1,605 linked confirmed cases to these outbreaks. There were also three newly notified outbreaks associated with third-level institutions.

“A number of significant clusters in the community associated with students who attend third-level educational settings in the west and mid west are currently under investigation,” the letter said.

Separately, notes of the meeting also show that a different form of testing could be on the way. The National Virus Reference Laboratory told the meeting that “work on salivary testing in the community setting is now complete and has been returned to the HSE to inform planning”.

The current test involves swabbing the back of the nose and throat using a long cotton bud called a swab to collect the sample. The test in some other countries involves swabbing the front of the nose and collecting saliva in a test tube or on a sponge which may be more comfortable. Children in the Republic have been tested this way since late last year.

Jennifer Bray

Jennifer Bray

Jennifer Bray is a Political Correspondent with The Irish Times