It is the fifth week in a row that data from the Office for National Statistics (ONS) has shown infections in Scotland going up.
In the last full week of May, it was estimated that one in 50 Scots had the virus.
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But the latest ONS figures showed that in the week ending June 24, an estimated 288,200 people in Scotland had Covid-19.
This amounts to 5.47 per cent of the population in Scotland having the virus – the equivalent of around one in 18 people.
Infection rates in Scotland continue to be the highest in the UK, despite increases in the other three nations.
Around one in 30 people in both England and Wales were estimated to have Covid in the week ending June 24, while in Northern Ireland it is estimated one in 25 people had it.
Prof Pennington said he was not surprised by the surge in cases given less was being done to control the spread of the virus.
"There's a fair amount of chance involved – it depends on super-spreader events, where the virus was a few months ago and all these kind of things,” he told BBC Radio Scotland's Lunchtime Live.
"There's no simple explanation. You could say it's bad luck we've got higher figures than the rest of the UK.
"A lot of people don't have any symptoms, but are still infectious."
The Scottish Government is running a digital marketing campaign called Covid Sense that references mask wearing indoors, but Prof Pennington said there should be more public encouragement.
"[That’s] not necessarily to go back to the compulsory rules we had, but really have quite a good publicity campaign explaining why mask wearing is a good thing,” he said.
Sarah Crofts, head of analytical outputs for the Covid-19 infection survey at the ONS, said: “Across the UK we’ve seen a continued increase of over half a million infections, likely caused by the growth of BA.4 and BA.5 variants.
“This rise is seen across all ages, countries and regions of England.”
The figures were released the day after data from National Records of Scotland (NRS) showed by as of June 26, 14,953 deaths linked to Covid-19 had been registered in Scotland – with the total increasing by 51 in the most recent week.
With infection levels rising again, Labour health spokeswoman Jackie Baillie said the Scottish Government “must wake up to the reality and act urgently to keep people safe”.
Ms Baillie said: “Covid is far from over as these stark figures show.
“With our NHS still in crisis, we cannot allow this SNP Government to sit on its hands.
“Thousands of Scots who are immunosuppressed feel abandoned by the Scottish Government and remain in danger due to upsurge in the virus.
“Doing nothing is not an option and the health secretary must accelerate and extend the vaccination programme.
“We all agree that vaccination is one of the best forms of protection, but for far too many people that protection is waning, as it has been so long since their last booster. “