Covid caused at least 58,000 pupil absences last week amid rising fears over keeping schools open in the face of the surge in the Omicron variant.

The first national snapshot of post-Christmas attendance, which covers January 5 and 6, came as calls grew for an earlier decision on arrangements for this year’s exams.

While the vast majority of schools appear to be open as planned, unions are increasingly concerned about disruption and the hit to educational quality.

There are reports that staff shortages have resulted in large groups of pupils being herded into areas such as canteens or halls, with some establishments sending S4-6 students home.

One headteacher said he knew of schools where absences had forced senior management to ask entire year groups to learn at home for the remainder of January.

READ MORE: Pupils told to learn at home as Covid-linked teacher absences bite

The Herald has also been told that teachers, headteachers and specialist support staff are being pulled away from their normal duties to look after children or provide general supply cover.

Union leaders warned previously that keeping schools open at all costs when absence rates are high could damage education and create safety risks. They have also argued that short periods of remote learning can provide a more coherent learning experience.

Seamus Searson, general secretary at the Scottish Secondary Teachers’ Association (SSTA), said: “At the moment we’re in a bit of a crisis. We haven’t got enough bodies to put in front of classes.”

HeraldScotland: Seamus Searson said schools were experiencing a range of pressures.Seamus Searson said schools were experiencing a range of pressures.

The latest figures show 39,799 pupils were not in school for Covid-related reasons on January 6. This is one of the highest totals since September 8 last year, even though education establishments in a number of local authority areas had still to reopen following the Christmas break. There were 18,789 absences on January 5.

Statistics also reveal there was a huge leap in coronavirus-linked pupil absences between December 16 and 17 - from 43,163 to 83,414. 

The Scottish Government did not explain why it thought the number had increased so dramatically. However, rapidly rising infection rates fuelled by the Omicron variant are likely to have contributed. 

Anecdotal reports suggest that parents keeping children off to cut the risk of self-isolation over Christmas may also have been a factor.

Local authority data, including figures for teacher absences, will be available later this week. However, with fears growing that the return to school will create fresh chains of transmission, statistics obtained from individual councils suggest pressures are already significant.

ANALYSIS: Staff absence fears grow as schools reopen

In South Lanarkshire, schools were dealing with 236 Covid-linked teacher absences on January 5 – well over double the number recorded for December 14.

And, although most schools reopened as planned after the Christmas holiday, union bosses stressed that challenges on the ground were huge.

Mr Searson said the SSTA had become aware of reports that staffing pressures are leading to large groups of pupils being supervised together in facilities such as school halls.

He also warned some schools were sending senior phase students home and that teachers had been losing preparation and marking time so they could provide emergency cover.

“It’s been going on for a good while now, probably months, because the priority is to keep the schools open and keep the children in school,” Mr Searson added. “An emergency is one day or two days at the most. Emergency can’t be for weeks and months. 

“And our headteacher and depute members are losing all their management time – all the time they should be running the school, they’re using it to cover classes individually or grouping them together in a hall or a canteen.”

HeraldScotland: ASL staff in Edinburgh are to be used as supply cover in mainstream schools.ASL staff in Edinburgh are to be used as supply cover in mainstream schools.

The Herald has also learned that additional support for learning (ASL) staff in Edinburgh are set to be used as supply cover in mainstream council schools in an effort to alleviate strains caused by Covid-linked teacher shortages. Rotas for the measure are in place until the February holidays. 

It comes after we told how those working in the capital's ASL service were being redeployed to plug gaps in special schools. Council bosses said individuals would only be asked to cover if absolutely necessary and to avoid closures or asking pupils to learn at home.

Mr Searson said: "That’s been happening for a while – that’s exactly the same sort of measure that takes place already in secondary schools. If there’s a shortage of teachers and the class needs to be covered, then the ASL teachers are taken off their duties to do that. It’s very unfair on the youngsters that need that support.”

Concerns over disruption to education come amid increasing pressure for an early decision on holding exams and potentially providing additional help for preparation. Such assistance could include advance sight of some topics that will feature in question papers.

Critics say waiting until late March to make an announcement would be unacceptable.     

READ MORE: Education Secretary admits exams decision may not be made until end of March

Daniel Wyatt, rector of Kelvinside Academy in Glasgow, said: "I – as I’m sure many working in education in Scotland will be – am dismayed a decision on whether or not to go ahead with exams could be left until March. It’s far too late. 

"Put simply, it is not acceptable and shows complete disregard for the mental health of pupils and staff following two years of disruption, distraction, and disappointment, all against a backdrop of coping with the impact of the pandemic."

He added: "I appreciate it can never be 100%, particularly in this climate, but the educational community deserves more certainty in what the future holds, and there simply must be more positive messaging for pupils and indeed all involved in education in Scotland. 

“Exams must go ahead unless there is a significant health concern far greater than we are currently experiencing with the Omicron variant.”

HeraldScotland: There is growing pressure for early decisions on this year's exams.There is growing pressure for early decisions on this year's exams.

In a social media post, Rod Grant, headmaster at Clifton Hall School near Edinburgh, said: "We have learned that a decision regarding exams won’t potentially be made until the end of March.

"The Government needs to stop dithering on such issues because ultimately it is our children who suffer from being in a constant state of flux, as do our teachers. I appreciate the contextual difficulties within which we are operating but we need to put those difficulties to one side and make a decision.

"If the Government is worried that exams may not go ahead then just cancel them now. That would be fair to our children. Perhaps, however, our Government is waiting to see what England does – that seems to be the way political decisions in Scotland are currently being handled."

He added: "As a Head, I am really, really tired of the constantly shifting sands on which we are meant to operate... We already know of schools that have sent home entire year groups for the remainder of January because of the absence of teachers."

Echoing calls from School Leaders Scotland president Jon Reid, Mr Searson also said he favoured a speedy move towards adopting the contingency plan that would give teachers and pupils notice of some topics that will be assessed in exams.   

READ MORE: Teacher survey sparks fears over strain on schools

A Scottish Government spokesman said: “Our priority is to keep schools safely open and to minimise further disruption to education. We know the next few weeks will be challenging for pupils, staff and parents and we are monitoring the situation very closely.

“Safety guidance for schools was strengthened in light of Omicron and updated to reflect changes to self-isolation requirements. We are working with local authorities to keep a close eye on staffing levels in schools and we will keep the need for any further measures under close review.

“As set out in August last year, exams will go ahead if it is safe to do so. They will only be cancelled if public health advice says it isn’t safe for them to take place – for example, if there are restrictions on gatherings. If this were to happen, awards would be made on teachers’ judgements based on normal in-year assessment. 

“Due to the unpredictability of the pandemic, we cannot know now what the public health advice will be for exams in the spring, but learners, parents and teachers will be told of any changes to plans as soon as possible.”

HeraldScotland: Education Secretary Shirley-Anne Somerville is under pressure to make an earlier decision on the 2022 exams diet.Education Secretary Shirley-Anne Somerville is under pressure to make an earlier decision on the 2022 exams diet.

A Scottish Qualifications Authority spokeswoman said: “The clear intention is for exams to take place in 2022. They will only be cancelled by the Scottish Government if public health advice restricts physical gatherings at the time of the exams.

“The Covid-19 Education Recovery Group is closely monitoring levels of learner and teacher absences, and school closures, and SQA will be guided by these in deciding whether to provide learners with additional support for exam revision.

"It is important to remember that the significant modifications already made to courses this year are designed to address the ongoing disruption to learning and teaching.”