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Scotland's chief medical officer told colleagues to delete WhatsApp messages "every day" during the pandemic, the UK Covid Inquiry had heard.
Prof Gregor Smith said he erased his own messages "on a frequent basis" in line with government policy.
He said any "pertinent" information about "definitive" decision making was recorded via email.
The Scottish government has said it is satisfied "all steps are being taken to meet the inquiry's requests".
Prof Smith was deputy chief medical officer at the beginning of the pandemic but took over as interim chief medical officer in April 2020 following the resignation of Catherine Calderwood after she broke Covid rules by visiting her holiday home. The appointment was made permanent in December 2020.
Ms Calderwood has been excused from giving evidence at this stage on medical grounds.
The inquiry was shown WhatsApp messages from July 2021 between Prof Smith by Prof Graham Ellis, an expert in geriatric medicine who worked as clinical adviser to the chief medical officer. Prof Ellis was appointed deputy chief medical officer the following month.
In a WhatsApp chat called "CMO weekly", Prof Ellis asked: "Hope this isn't FOI able?"
Prof Smith replied: "Delete at the end of every day…"
Prof Ellis replied with crying with laughter and thumbs up emojis.
Prof Smith told the inquiry it was his "practice" was to capture any important information on the email system, to ensure it was an "auditable trail", as well as to "exhort" colleagues to do the same.
Asked if he deleted WhatsAppp messages every day, the chief medical officer said: "If not at the end of every day then certainly on a frequent basis I deleted information which was no longer needed to be kept."
He said information recorded on the official system related to "definitive" information once a consensus had been reached and would not be a "verbatim account" of a conversation but rather the "essence of any decision" that was recorded on the corporate system.
Prof Smith told the inquiry advice had been given to Scottish government officials to regularly delete informal messages, "partly for security purposes".
FOI concerns
Earlier, the official in charge of enforcing freedom of information (FOI) laws in Scotland told BBC Radio's Good Morning Scotland that the principles of the freedom information rules "appear to have been subverted" based on the messages that have been published by the inquiry.
Information Commissioner David Hamilton called the messages "quite concerning" and said he could launch a probe.
"Some of the material that came out last week, I think many people would say beggars belief," he said.
The commissioner described FOI rules - which give anyone the right to request access to information held by public bodies - as "absolutely critical to democracy and accountability" and showing how the government makes decisions.
"And when I see the types of things that I've seen, then I've got to question is that being done and if I need to act I will act," Mr Hamilton said.
He stressed that his responsibilities would only relate to an appeal regarding any information that had been held or deleted.
Mr Hamilton said his investigatory powers were "tightly limited" but that his office was looking back through old appeals to see if any covered the period of time covered by the pandemic.
He added: "What has surfaced through the inquiry, that's what's giving me concern that the public may not be getting the rights which they are entitled to."
If the commissioner rules against the government, he can order it to reconsider an FOI request.
The Scottish government published mobile messaging guidance for officials and ministers in November 2021.
It said they were allowed to use WhatsApp and other messaging services to conduct business, with the guidance stating "you must transcribe the salient points of any business discussions and/or decisions in a mobile messaging app into an email or text document" before saving the information centrally.
The Scottish government's records management policy, published in February 2021, said records should be kept as long as necessary to fulfil the Scottish government's business and legal obligations. It defined a record as something "which can provide evidence of activities, transactions and decisions made for, or on behalf of, the organisation".
It said the purpose of these records "is to provide reliable evidence of, and information about, 'who, what, when, and why' something happened".
On Friday, counsel to the UK Covid Inquiry, Jamie Dawson KC, said former first minister Nicola Sturgeon appeared to "have retained no messages whatsoever".
The hearing in Edinburgh was also told that her then-deputy John Swinney's WhatsApp messaging was set to auto-delete.
On Sunday, Ms Sturgeon said copies of some of her messages had been retrieved and were handed to the inquiry last year.
The inquiry was also shown messages from a "Covid outbreak group" WhatsApp chat which included Prof Leitch and retired civil servant Ken Thomson.
'Pre-bed ritual'
In one post from May 2021, Mr Thomson wrote: "I feel moved at this point to tell you that this chat is FOI-recoverable." He included an emoji with a zipped mouth.
Two minutes later Prof Leitch responded: "WhatsApp deletion is a pre-bed ritual."
Mr Thomson denied there was a culture among Covid decision-makers of deleting messages to prevent them coming into the public domain.
A spokesperson for the Scottish government said it had accepted the recommendations of the information commissioner's most recent FOI performance report, and "welcomed the progress it showed".
They said ministers are "committed to responding to both the UK and Scottish Covid-19 inquiries, as learning lessons from the pandemic is vital to prepare for the future".
The spokesperson added: "It would be inappropriate to comment on the detail of evidence being considered by the UK Covid Inquiry while hearings are ongoing."
Scotland's Information Commissioner has said that he will take action if he suspects Scottish government officials have been deliberately withholding information to "subvert" freedom of information laws. David Hamilton told BBC Scotland News that excerpts of conversations published between the national clinal director, Jason Leitch, and other officials gave him "cause for concern that people were not abiding by the spirit, if not the law, of freedom of information." Messages published by the UK Covid inquiry last week showed government officials discussing freedom of information laws in relation to Whatsapp chats. Prof Leitch responded by saying "WhatsApp deletion is a pre-bed ritual". The Scottish government has said that it believes all legal obligations have been met. However, Mr Hamilton told BBC Scotland News that "information may have been deleted that shouldn't have been deleted." He added that his office would take action if there was "any suggestion that people have been deliberately trying to withhold that, to subvert that policy of freedom of information." Mr Hamilton said he had concerns about the "attitude" some officials had displayed towards freedom of information laws, and that he planned to consider if there was a "systemic problem". The Information Commissioner said that some published conversations suggested a culture of "actively instructing people to delete conversations" as their content could be requested by the public. He added that there was a lack of "corporate oversight" on informal messaging apps, and that blended personal and professional conversations were leading to problems.