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Speaking during PMQs on Wednesday, the prime minister praised the “astonishing” way in which the country has dealt with the outbreak.
Johnson has also said he was “very proud” of how his government reacted.
The government’s latest figures on those who have died after testing positive for coronavirus stand at 40,883.
According to the Office for National Statistics (ONS) the number of people who have died with coronavirus mentioned on their death certificate is now 51,089.
And the number of excess deaths – the number of deaths above the expected number for that time of year – stands at 63,000.
Keir Starmer, the Labour leader, told Johnson during PMQs: “These are amongst the highest numbers anywhere in the world.
“Last week, the prime minister said he was proud of the government’s record, but there’s no pride in those figures is there?”
Johnson said he would “mourn every one” of the deaths and “grieve for them and for their relatives and their friends”.
But he said the country had to “wait until the epidemic has been through its whole cycle” before it was fair to compare the death toll to other countries.
“As for what this country did to fight the epidemic, I must say I strongly disagree with the way he characterises it,” the prime minister told Starmer.
“I think it was an astonishing achievement by the NHS to build the Nightingale hospitals, I think it was an astonishing thing this country came together to drive down, to follow the social distancing rules in spite of all the doubt that was cast on the advice.”
The exchanges came as Johnson prepared to announce children will soon be able to visit zoos in the latest easing of lockdown measures – although their wait to go back to school could last months.
Johnson will face the nation at the Downing Street briefing on Wednesday and is expected to confirm zoos, safari parks and drive-in cinemas can reopen in England from June 15.
It comes a day after Business Secretary Alok Sharma confirmed shops would also be able to reopen on the same day.
But Education Secretary Gavin Williamson was forced to admit defeat over plans for all primary pupils in England to attend classes before the summer break.