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Channel 4 won five awards amid uncertainty over its future with the government planning a shake up of public funding for TV.
The event at the Royal Festival Hall on Southbank, which featured its first full audience in two years, also saw the BBC claim nine awards and ITV take home seven.
Comer, who won her first award for her role in Killing Eve, thanked Channel 4 for “believing in the script”.
In Help she played a young carer at a Liverpool home who forms a bond with a patient struggling with early onset Alzheimer’s disease.
The plot sees the emergence of the COVID-19 pandemic which has terrible consequences for the people she cares for.
In her acceptance speech at the awards hosted by actor Richard Ayoade, she thanked carers who helped the show with their research and who were “incredibly gracious” with their time.
“The biggest reward is that they felt truly represented with the telling of this story,” she added.
Sean Bean won best leading actor at the Bafta TV awards for his role in BBC’s prison drama Time.
Simon Maloney, producer of Time, read a letter on the actor’s behalf which said he was “overwhelmed” to receive the award.
He also praised his “inspirational” cast members including Stephen Graham. Time also scooped the award for best mini series.
Cast member Lee took to the stage, accepting the prize for “past and present families who have been on Googlebox, it is an honour to get it for them,” he said.
The chief executive of production company which produces the show, Stephen Lambert, used his speech to voice opposition to the Government’s plans to pull public funding to the channel.
He said: “Gogglebox might have ended when it started nine years ago as it got modest ratings, but a publicly owned risk-taking Channel 4 believed in it and they stuck with it.
“If the Government goes ahead with its destructive plan to end Channel 4, these kind of risks will not be taken and a big part of what makes British TV great will have ended for no good reason.”
Meanwhile Ant & Dec’s Saturday Night Takeaway won the award for best entertainment programme while Coronation Street scooped the prize for best soap.
Controversially, It’s a Sin, the Russell T Davies’ series exploring the Aids virus and its impact on society, won no awards despite having 11 nominations, including best mini series.
The Duke of Cambridge also appeared at the awards sharing his hope that programme creators will continue their “invaluable work” and keep “environmental issues high up on the agenda of programming”.
William spoke to the audience at the ceremony as part of a pre-recorded video highlighting “planet placement”, referring to the inclusion of environmental messaging in TV shows.
He cited the “unique role” of programme creators who can “ensure climate change and sustainability remain at the forefront of our collective consciousness”.
He added: “By creating innovative, educational and emotive content for television, writers and producers are playing a unique role in ensuring the future of our planet is something that we all want to talk about.
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“Over the past year, we’ve seen some fantastic examples of this across a wide variety of programmes and genres.
“I hope you will all continue to carry on your invaluable work, keeping environmental issues high up on the agenda of programming in these years ahead.”