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Omicron: South Africa's treatment means scientists might balk at revealing next variants

Caught napping before, we must take basic precautions to slow spread of latest variant

A “wait and see” approach has taken hold internationally following the initial frenzy that followed the discovery of the Omicron variant of Covid-19 last week.

As the World Health Organisation made clear on Monday, there are huge gaps in our knowledge about the variant and it is likely to take several weeks for richer information to flow.

Much of the hysteria of the last week was driven by wilder voices in the international scientific community

Hospital Report

There are some reassuring noises coming from treating doctors in South Africa and Israel, who report seeing mostly mild cases with no substantial burden of disease so far. But again, these are early days and it might take longer for more serious problems to accumulate.

The media has been accused by some of hyping the threat posed by the new variant. But much of the hysteria of the last week was driven by wilder voices in the international scientific community, some of whom have been platformed in Ireland during the pandemic.


For the time being, it makes sense to take some basic precautions to slow the spread of the variant, though it may already be here.

At least five European countries have confirmed cases of Omicron, but Ireland was on Monday still at the stage of talking about “suspected” cases. In recent months, we have drastically reduced the proportion of cases sent for genetic sequencing – to allow the variant involved to be identified – thereby impairing our ability to track the movement of a new arrival.

Genome tracking

On Monday, Minister for Health Stephen Donnelly defended Ireland's level of genome tracking, saying it was the third-highest in Europe, with 10 per cent of samples being sequenced.

The latest figures for submitted data to Gisaid, an international data-sharing collaboration between scientists that is tracking the spread of variants, suggest a different story.

Over the past four weeks, Ireland has submitted the results of 344 sequenced Delta variant cases to Gisaid. This is a tiny figure compared to our neighbours, for which the equivalent numbers include the UK (120,818), Germany (9,539), Denmark (21,957) and Sweden (4,084).

Mexico, Lithuania, Chile and the Czech Republic all made more submissions than Ireland.

It could be argued that up to last week we didn’t need to sequence large number of cases because we knew the result would be the utterly dominant Delta variant. But if that were true, why would other countries, where Delta is also dominant, be investing so heavily in genetic sequencing?

Although the UK has developed techniques to process sequencing within days, it isn't clear Ireland has got faster at turning around samples

We have been caught napping before. The Alpha/UK variant was in the State for weeks at the end of 2020 before we confirmed its presence on the brink of Christmas. By then, it was too late to respond effectively to the arrival of a more transmissible variant and the die was cast.

Last year’s disaster

If we had been able to identify Alpha earlier through a more vigorous programme of genetic sequencing, control measures could have been brought in more quickly and the disaster that followed Christmas 2020 could have been mitigated.

Back then, it was taking over two weeks to get back the results of sequencing, often from overseas labs. Although the UK has developed techniques to process sequencing within days, it isn’t clear Ireland has got faster at turning around samples.

There is a way to use the standard PCR test as a marker for the Omicron variant, pending confirmation by sequencing. In some forms of PCR test, one of the three target genes is not detected – S-gene dropout or target failure – which can be indicative of the presence of Omicron (the Delta variant does not exhibit S-gene dropout).

There is only one centre in Ireland where this form of PCR test can be performed, so throughput is limited. In the UK, up to half of all labs have the requisite technology.

It seems daft that South Africa is being punished, through the imposition of unilateral travel bans, for the excellence of its scientists. In future, any researchers with a modicum of cop-on would think twice about revealing the discovery of the next new variant if it means their country ends up being treated as a pariah. And with early signs of community transmission in Europe, it could even turn out that the variant did not originate in southern Africa.