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The First Minister insisted the country was still at a “delicate and fragile point” in the battle with the virus, in an announcement on restrictions which she described as a “mixed bag”.
And Jason Leitch warned the Indian variant “is causing us some challenge and is spreading quicker than we hoped”.
When asked by BBC Radio Scotland’s Drivetime if the country was at the start of a third wave he replied: “Yes, I think we are.
“The question is how big that third wave is – everybody, every modelling higher education institution… they all said, if you open you will get more cases.
“Now I’m not sure I needed a university to tell me that, I think people in the street would have told me that.
“The question is, whether you control that to a level that doesn’t cause enough severe disease to fill hospitals, and enough severe disease to cause misery and death to families.
“That’s the balance we’re now trying to strike and the advice we’ve given and the decisions the First Minister and the Cabinet have made today.”
As part of those decisions the First Minister confirmed Glasgow, which had been under the strictest restrictions in Scotland, will see these relaxed, with the city moving to Level 2 from Saturday.
On that date, many island communities will move to Level 0 – the lowest level there is under Scotland’s five tier system – while 15 council areas will step down to Level 1.
But 13 local authority areas, including Edinburgh, Dundee and Stirling, will remain in Level 2 for the time being.
It had been hoped most of Scotland would be able to move to Level 1, and the First Minister’s announcement means businesses in some areas, such as soft play centres, will not be able to reopen as planned.
Support will be provided for such companies, Ms Sturgeon said, with Finance Secretary Kate Forbes expected to set out more details of this on Wednesday.
Confirming the changes to MSPs at Holyrood, the First Minister said Scotland was “currently at a delicate and fragile point in what we hope is a transition to a different way of dealing with this virus”.
She said: “We believe that vaccinations are opening the path to a less restrictive way of dealing with Covid – one less driven by case numbers.
“But because not all adults have been fully vaccinated with two doses so far, we are not quite there yet.”
The latest figures show almost three quarters (72%) of adults have had their first vaccine, with less than half (46%) having now received both doses.
As a result Ms Sturgeon said the country was “in a transition phase”, adding that “vaccines make the outlook positive, but the new variant means the road ahead is still potentially bumpy”.
While she said “vaccines are changing the game”, she also stressed that for the moment “caution is necessary”.
But with the number of people vaccinated growing, the First Minister said: “We can still be optimistic, very optimistic, about our chances of much more normality over the summer and beyond.”
Her comments came as she announced Edinburgh, Midlothian, Dundee, East Dunbartonshire, Renfrewshire, East Renfrewshire, East Ayrshire, North Ayrshire, South Ayrshire, North and South Lanarkshire, Clackmannanshire and Stirling will all remain in Level 2.
However 15 council areas will move to Level 1 restrictions from Saturday: Highland, Argyll and Bute, Aberdeen City and Aberdeenshire, Moray, Angus, Perth and Kinross, Falkirk, Fife, Inverclyde, East and West Lothian, West Dunbartonshire, Dumfries and Galloway and the Borders.
The move will allow people to gather indoors and outdoors in larger groups, with the numbers allowed at weddings and funerals also increasing, while pubs can open slightly later indoors.
Scottish Labour leader Anas Sarwar said that “for many in those parts of Scotland that were expecting to move down a level, this news will come as a bitter blow”.
Both he and Scottish Conservative leader Douglas Ross welcomed the move to Level 2 for Glasgow – which will allow people to hug each other and visit friends and family in their homes for the first time since August, with pubs and restaurants also now allowed to sell alcohol indoors.
Mr Ross said the announcement would “bring to an end 277 days of our largest city living under some of the toughest restrictions”, but added that for other areas it was a “disappointing setback”.
He said: “Half of the country will move forward while the rest remains stuck in limbo, with no clear idea when the restrictions will ease.
“We understand the need for caution, but we also believe more emphasis needs to be placed on the impact of these restrictions on businesses, on jobs, and on people’s mental and physical health.”
Mr Ross argued ministers should be taking a more localised approach, with “targeted interventions to tackle local outbreaks instead of sweeping measures”.
But Ms Sturgeon told him: “We are taking all of the different factors into account, not least the progress with vaccination.”
She said if the decisions were based purely on public health advice “we would simply have held the whole of the country in the levels they are at right now” – adding the raw figures indicated some areas should have even stricter restrictions imposed.
And she said that with fewer than half of all adults having had both vaccine doses, the country was still “vulnerable to this new, faster-spreading variant”.
While Ms Sturgeon said the Level 2 restrictions, which will be in place in 14 council areas from Saturday, were “still tough” she also insisted it was “not lockdown”.
She added: “We can go into each other’s homes, we can see hospitality open, stay open indoors, so there are significant steps there.”