Mr Thomson goes on to say that Ms Sturgeon was concerned about the messaging coming from Mr Johnson.
He says: "At the end of that meeting she turned to me, possibly with some exasperation, and said: 'I can't stand in front of a television camera and tell people to stay alert to something that they can't see'.
"She was thinking about how does this work as a piece of public health communications?"
Sturgeon insisted she would decide Covid warning messaging in Scotland
Jamie Dawson KC refers to a meeting between Boris Johnson and Nicola Sturgeon in May 2020 and Mr Thomson replies that it was a four-nations ministerial call.
Mr Thomson remembers that the first minister was trying to warn the prime minister that a move to ease restrictions from Stay at Home to Stay Alert would be "catastrophic".
Sturgeon said she would decide the messaging in Scotland, not Johnson.
Who will be giving evidence this afternoon?
The afternoon session will begin with further questions to former senior civil servant Ken Thomson.
Then it will be Dr Jim McMenamin, who is the head of infections service and strategic incident director of Public Health Scotland.
Finally we'll hear from Dr Nick Phin, the current director of Public Health Science for Public Health Scotland.
Previously Dr Phin was the deputy director of Public Health England’s national infections service.
The headlines so far
The UK Covid Inquiry, sitting in Edinburgh, has broken for lunch and will return at 13:45. If you're just joining us, here's a brief recap of the main headlines this morning:
The inquiry heard official confirmation that the former First Minister Nicola Sturgeon did not keep any of her WhatsApp messages or texts during the Covid pandemic
The messages were deleted in routine tidying up of inboxes or changing of phones
Lesley Fraser, who is the director general corporate of the Scottish government, told the inquiry that she did not accept that the Scottish government's record retention policies were not fit for purpose during the pandemic
She did say she would accept the "hurt and frustration" about not being able to access WhatsApp messages and the policies should be reviewed
Former top civil servant Ken Thomson, the second witness this morning, said it was "very rare" for the first minister to message him
National Clinical Director Jason Leitch messaged that "WhatsApp deletion is a pre-bed ritual"
The relationship between Sturgeon and Johnson "had not been built up in peacetime"
'The relationship had not been built up in peacetime'
BBCCopyright: BBC
Ken Thomson says strained relations affected the quality of decisions made by both governmentsImage caption: Ken Thomson says strained relations affected the quality of decisions made by both governments
Ken Thomson goes on: "It is important for there to be a relationship of trust between heads of governments."
That did not happen between Ms Sturgeon and Mr Johnson.
"The relationship had not been built up in peacetime, " he adds.
The former civil servant says that did affect the quality of decisions being made.
He says there was a brief opportunity for tiers and levels to be brought together with clarity across the whole of the UK.
"In the event, that did not happen," he says.
England adopted a three tier coronavirus restrictions system and Scotland went with five levels, causing some confusion.
Tensions emerged over easing of restrictions in England
Back to the relationship between the Scottish and UK governments...
Mr Thomson tells the inquiry there was "serious engagement" between Scottish and UK ministers in the early stages of the pandemic.
He adds: "I didn't see party politics in those discussions at all."
But Mr Thomson says tensions emerged in May 2020 when Mr Johnson eased restrictions in England and Wales but Scotland did not follow suit.
Background: Boris Johnson says he has no 'ill will' towards Nicola Sturgeon
PA MediaCopyright: PA Media
Boris Johnson and Nicola Sturgeon had a "friendly" relationship, according to the former prime ministerImage caption: Boris Johnson and Nicola Sturgeon had a "friendly" relationship, according to the former prime minister
In December, Boris Johnson claimed he had a "friendly" relationship with Nicola Sturgeon during the coronavirus pandemic.
The ex-prime minister denied feelings of "ill will" but made jibes against the SNP.
He previously said he thought it was wrong to hold regular meetings with devolved leaders.
Ms Sturgeon has said Mr Johnson's reign was characterised by "chaos and complete lack of integrity".
Sturgeon's first impression of Johnson: 'You can have a debate with him'
Jamie Dawson KC asks Mr Thomson about the early relationship between former First Minister Nicola Sturgeon and former Prime Minister Boris Johnson.
Mr Thomson says after the two leaders met for the first time he had a discussion with Ms Sturgeon about how Mr Johnson contrasted with his predecessor, Theresa May.
He recalls Ms Sturgeon remarked: "You can have a debate with him."
Mr Thomson goes on to say that the Sturgeon/Johnson relationship was not "warm" due to their political differences but adds he was "more optimistic that it would become productive".
Mr Dawson asks: "Did it?"
Mr Thomson replies: "The short answer to that is no."
Relations between governments had deteriorated, says witness
The evidence now takes a turn to the relationship between the Scottish and UK governments.
Mr Thomson says the Delta variant was raised in a four nations ministerial call.
He did not feel there had been a useful exchange between the UK and Scottish governments at the time.
The former civil servant says intergovernmental relations had deteriorated at that time of the pandemic.
However, there were good exchanges in a different four nations ministerial call, he concedes.
Mr Thomson says he was responsible for intergovernmental relations and he highlights close working relationships with UK counterparts.
He used those contacts to put the case for more frequent liaison between the governments.
Prof Jason Leitch: 'WhatsApp deletion is a pre-bed ritual'
The inquiry is shown a series of WhatsApp group exchanges from 13 May 2021 in which Mr Thomson posts: "I feel moved at this point to tell you that this chat is FOI-recoverable."
He includes an emoji with a zipped mouth.
Two minutes later, Prof Jason Leitch responds: "WhatsApp deletion is a pre-bed ritual."
Analysis
Deletion goes against Sturgeon's commitment on WhatsApps
Kirsten Campbell
BBC Scotland political correspondent
We now have official confirmation that the
former First Minister Nicola Sturgeon did not keep any of her WhatsApp messages
or texts during the covid pandemic.
The messages were deleted in routine
tidying up of inboxes or changing of phones.
A Scottish government table
summarising the retained notebooks and messages of a variety of ministers
between 21 January 2020 and 30 April 2022 says starkly of Nicola Sturgeon “
Nothing to return”.
The document stresses that anything of significance would
have been recorded appropriately. But it can do nothing to reassure
bereaved families that insights into ministers’ thinking before decisions were
taken have not been lost.
And it goes against the commitment Nicola
Sturgeon made in August 2021 when she announced there would be a Scottish Covid
inquiry, that she would disclose her private messages.
Background: Jason Leitch deleted Covid WhatsApp messages - newspaper report
PA MediaCopyright: PA Media
Jason Leitch helped lead the Scottish government's handling of the Covid-19 pandemicImage caption: Jason Leitch helped lead the Scottish government's handling of the Covid-19 pandemic
Last October we reported that electronic messages sent by National Clinical Director Jason Leitch had been deleted, according to a newspaper report.
The Times said national clinical director Jason Leitch deleted his messages every day during the pandemic.
It means the messages cannot be handed to the UK or Scottish inquiries into how Covid was handled.
Were people encouraged to delete messages to defeat FOI requests?
Jamie Dawson KC turns to messages from the Covid outbreak group which included Deputy Chief Medical Officer Nicola Steedman and the National Clinical Director Jason Leitch, and shows Mr Thomson calling for messages to be cleared.
Mr Dawson asks if this is Mr Thomson encouraging people to delete messages in order to defeat FOI requests.
The former civil servant denies this and says he was reminding colleagues in an informal way that messages should not be kept, other than in relation to salient points.
'Very rare' for FM to message me, official says
Mr Thomson is being asked about the process of decision making in the Scottish government during the pandemic.
He says: "The first minister (Nicola Sturgeon at the time) did not take a decision in informal messaging.
"It would be very rare that she would message me at all, never mind to make a decision."
How government decisions were taken and recorded
Jamie Dawson KC runs through the CV of Ken Thomson and his responsibilities during the Covid pandemic.
Mr Thomson explains the use of electronic messaging grew very rapidly at the start of the pandemic as people worked from home.
He says where there was a salient point in messaging, that he would transfer it and record it and not retain the message.
The former Scottish government official, now retired, tells the inquiry the cabinet records were the "gold standard" for record retention.
He details the messaging that took place as the Delta variant emerged during the pandemic and the decisions that were taken were recorded.
Second Scottish government official gives evidence
Ken Thomson, the former director general for constitution and external affairs and manager of the Covid Co-ordination Directorate of the Scottish government, is next to give evidence.
Concerns about security around government phones
Claire Mitchell KC asks the witness what was the rationale behind the deletion policy?
Ms Fraser says there was concern about security around phones being used for government business.
Difference in Covid messaging between Scotland and England
Claire Mitchell, the KC for Scottish Covid Bereaved, is allowed the opportunity to intervene and she asks if there was any need for a correction of the UK government's public health messaging and was any action taken.
Ms Fraser says there were regular weekly meetings with communication counterparts in the UK to ensure there was not contradictory messages applied.
She refers to FACTS in Scotland and here's a reminder of that acronym:
Face coverings
Avoid crowded places
Clean your hands regularly
Two metre distance
Self-isolate and book a test if you have symptoms
The UK government chose to go with the message: "Hands Face Space".
Some WhatsApp messages drifted into 'banter', says official
Ms Fraser says some WhatsApp messages drifted into "banter" which was not relevant and should not be retained.
She points out three individuals lost their messages when government mobile phones were upgraded.
Mr Dawson asks: "Would you accept the Scottish government's record retention policies were simply not fit for purpose during the pandemic?"
Ms Fraser does not accept that, but says she would accept the "hurt and frustration" about not being able to access WhatsApp messages and the policies should be reviewed.
Live Reporting
Edited by Paul McLaren
All times stated are UK
How the UK government defended 'Stay Alert' advice amid backlash
In May 2020, the UK government's coronavirus message changed from "stay at home" to "stay alert", amid widespread criticism.
PM Boris Johnson announced the slogan for England, telling people to "stay alert, control the virus, save lives", ahead of his national address.
Scotland, Wales and Northern Ireland stuck with "stay at home".
Read more here
Sturgeon had concerns about 'Stay Alert' advice
Mr Thomson goes on to say that Ms Sturgeon was concerned about the messaging coming from Mr Johnson.
He says: "At the end of that meeting she turned to me, possibly with some exasperation, and said: 'I can't stand in front of a television camera and tell people to stay alert to something that they can't see'.
"She was thinking about how does this work as a piece of public health communications?"
Sturgeon insisted she would decide Covid warning messaging in Scotland
Jamie Dawson KC refers to a meeting between Boris Johnson and Nicola Sturgeon in May 2020 and Mr Thomson replies that it was a four-nations ministerial call.
Mr Thomson remembers that the first minister was trying to warn the prime minister that a move to ease restrictions from Stay at Home to Stay Alert would be "catastrophic".
Sturgeon said she would decide the messaging in Scotland, not Johnson.
Who will be giving evidence this afternoon?
The afternoon session will begin with further questions to former senior civil servant Ken Thomson.
Then it will be Dr Jim McMenamin, who is the head of infections service and strategic incident director of Public Health Scotland.
Finally we'll hear from Dr Nick Phin, the current director of Public Health Science for Public Health Scotland.
Previously Dr Phin was the deputy director of Public Health England’s national infections service.
The headlines so far
The UK Covid Inquiry, sitting in Edinburgh, has broken for lunch and will return at 13:45. If you're just joining us, here's a brief recap of the main headlines this morning:
'The relationship had not been built up in peacetime'
Ken Thomson goes on: "It is important for there to be a relationship of trust between heads of governments."
That did not happen between Ms Sturgeon and Mr Johnson.
"The relationship had not been built up in peacetime, " he adds.
The former civil servant says that did affect the quality of decisions being made.
He says there was a brief opportunity for tiers and levels to be brought together with clarity across the whole of the UK.
"In the event, that did not happen," he says.
England adopted a three tier coronavirus restrictions system and Scotland went with five levels, causing some confusion.
Tensions emerged over easing of restrictions in England
Back to the relationship between the Scottish and UK governments...
Mr Thomson tells the inquiry there was "serious engagement" between Scottish and UK ministers in the early stages of the pandemic.
He adds: "I didn't see party politics in those discussions at all."
But Mr Thomson says tensions emerged in May 2020 when Mr Johnson eased restrictions in England and Wales but Scotland did not follow suit.
Background: Boris Johnson says he has no 'ill will' towards Nicola Sturgeon
In December, Boris Johnson claimed he had a "friendly" relationship with Nicola Sturgeon during the coronavirus pandemic.
The ex-prime minister denied feelings of "ill will" but made jibes against the SNP.
He previously said he thought it was wrong to hold regular meetings with devolved leaders.
Ms Sturgeon has said Mr Johnson's reign was characterised by "chaos and complete lack of integrity".
Sturgeon's first impression of Johnson: 'You can have a debate with him'
Jamie Dawson KC asks Mr Thomson about the early relationship between former First Minister Nicola Sturgeon and former Prime Minister Boris Johnson.
Mr Thomson says after the two leaders met for the first time he had a discussion with Ms Sturgeon about how Mr Johnson contrasted with his predecessor, Theresa May.
He recalls Ms Sturgeon remarked: "You can have a debate with him."
Mr Thomson goes on to say that the Sturgeon/Johnson relationship was not "warm" due to their political differences but adds he was "more optimistic that it would become productive".
Mr Dawson asks: "Did it?"
Mr Thomson replies: "The short answer to that is no."
Relations between governments had deteriorated, says witness
The evidence now takes a turn to the relationship between the Scottish and UK governments.
Mr Thomson says the Delta variant was raised in a four nations ministerial call.
He did not feel there had been a useful exchange between the UK and Scottish governments at the time.
The former civil servant says intergovernmental relations had deteriorated at that time of the pandemic.
However, there were good exchanges in a different four nations ministerial call, he concedes.
Mr Thomson says he was responsible for intergovernmental relations and he highlights close working relationships with UK counterparts.
He used those contacts to put the case for more frequent liaison between the governments.
Prof Jason Leitch: 'WhatsApp deletion is a pre-bed ritual'
The inquiry is shown a series of WhatsApp group exchanges from 13 May 2021 in which Mr Thomson posts: "I feel moved at this point to tell you that this chat is FOI-recoverable."
He includes an emoji with a zipped mouth.
Two minutes later, Prof Jason Leitch responds: "WhatsApp deletion is a pre-bed ritual."
Deletion goes against Sturgeon's commitment on WhatsApps
Kirsten Campbell
BBC Scotland political correspondent
We now have official confirmation that the former First Minister Nicola Sturgeon did not keep any of her WhatsApp messages or texts during the covid pandemic.
The messages were deleted in routine tidying up of inboxes or changing of phones.
A Scottish government table summarising the retained notebooks and messages of a variety of ministers between 21 January 2020 and 30 April 2022 says starkly of Nicola Sturgeon “ Nothing to return”.
The document stresses that anything of significance would have been recorded appropriately. But it can do nothing to reassure bereaved families that insights into ministers’ thinking before decisions were taken have not been lost.
And it goes against the commitment Nicola Sturgeon made in August 2021 when she announced there would be a Scottish Covid inquiry, that she would disclose her private messages.
Background: Jason Leitch deleted Covid WhatsApp messages - newspaper report
Last October we reported that electronic messages sent by National Clinical Director Jason Leitch had been deleted, according to a newspaper report.
The Times said national clinical director Jason Leitch deleted his messages every day during the pandemic.
It means the messages cannot be handed to the UK or Scottish inquiries into how Covid was handled.
Were people encouraged to delete messages to defeat FOI requests?
Jamie Dawson KC turns to messages from the Covid outbreak group which included Deputy Chief Medical Officer Nicola Steedman and the National Clinical Director Jason Leitch, and shows Mr Thomson calling for messages to be cleared.
Mr Dawson asks if this is Mr Thomson encouraging people to delete messages in order to defeat FOI requests.
The former civil servant denies this and says he was reminding colleagues in an informal way that messages should not be kept, other than in relation to salient points.
'Very rare' for FM to message me, official says
Mr Thomson is being asked about the process of decision making in the Scottish government during the pandemic.
He says: "The first minister (Nicola Sturgeon at the time) did not take a decision in informal messaging.
"It would be very rare that she would message me at all, never mind to make a decision."
How government decisions were taken and recorded
Jamie Dawson KC runs through the CV of Ken Thomson and his responsibilities during the Covid pandemic.
Mr Thomson explains the use of electronic messaging grew very rapidly at the start of the pandemic as people worked from home.
He says where there was a salient point in messaging, that he would transfer it and record it and not retain the message.
The former Scottish government official, now retired, tells the inquiry the cabinet records were the "gold standard" for record retention.
He details the messaging that took place as the Delta variant emerged during the pandemic and the decisions that were taken were recorded.
Second Scottish government official gives evidence
Ken Thomson, the former director general for constitution and external affairs and manager of the Covid Co-ordination Directorate of the Scottish government, is next to give evidence.
Concerns about security around government phones
Claire Mitchell KC asks the witness what was the rationale behind the deletion policy?
Ms Fraser says there was concern about security around phones being used for government business.
Difference in Covid messaging between Scotland and England
Claire Mitchell, the KC for Scottish Covid Bereaved, is allowed the opportunity to intervene and she asks if there was any need for a correction of the UK government's public health messaging and was any action taken.
Ms Fraser says there were regular weekly meetings with communication counterparts in the UK to ensure there was not contradictory messages applied.
She refers to FACTS in Scotland and here's a reminder of that acronym:
Face coverings
Avoid crowded places
Clean your hands regularly
Two metre distance
Self-isolate and book a test if you have symptoms
The UK government chose to go with the message: "Hands Face Space".
Some WhatsApp messages drifted into 'banter', says official
Ms Fraser says some WhatsApp messages drifted into "banter" which was not relevant and should not be retained.
She points out three individuals lost their messages when government mobile phones were upgraded.
Mr Dawson asks: "Would you accept the Scottish government's record retention policies were simply not fit for purpose during the pandemic?"
Ms Fraser does not accept that, but says she would accept the "hurt and frustration" about not being able to access WhatsApp messages and the policies should be reviewed.