The RIVM health institute said it found Omicron in samples dating from November 19 and 23.
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The Omicron variant of the coronavirus was already in the Netherlands when South Africa alerted the World Health Organisation (WHO) about it last week, Dutch health authorities have said.
The announcement adds to fear and confusion over the new version of the coronavirus in a world hoping it had left the worst of the pandemic behind.
The RIVM health institute said it found Omicron in samples dating from November 19 and 23.
Those findings pre-date the positive cases found among passengers who came from South Africa last Friday and were tested at Amsterdam’s Schiphol airport. The WHO said South Africa first reported the Omicron variant to the UN agency on November 24.
It remains unclear where or when the variant first emerged – but that has not stopped wary nations from rushing to impose travel restrictions, especially on visitors coming from southern Africa.
Those moves have been criticised by South Africa and the WHO has urged against them, noting their limited effect.
Japan and France also confirmed their first cases of the new variant on Tuesday as countries around the world scrambled to close their doors or find ways to limit its spread while scientists study how damaging it might be.
The WHO has warned that the global risk from the Omicron variant is “very high” based on early evidence, saying it could lead to surges with “severe consequences”.
French authorities confirmed the first case of the Omicron variant in the French island territory of Reunion in the Indian Ocean.
Patrick Mavingui, a microbiologist at the island’s research clinic for infectious diseases, said the person who has tested positive for the new variant is a 53-year-old man who had travelled to Mozambique and stopped in South Africa before returning to Reunion.