Coronavirus has pushed the death toll in England and Wales to its highest level since official weekly statistics began 15 years ago, with fatalities running at almost 40% above the average.

The Office for National Statistics said that in the week to 3 April, 16,387 people died in England and Wales, an increase of 5,246 deaths compared with the previous week and 6,082 more than the five-year average.

“The deaths that were registered in England and Wales during the week ending 3 April is the highest weekly total since we started compiling weekly deaths data in 2005,” said Nick Stripe, head of health analysis and life events at the ONS.

The figures also showed the increasing impact of Covid-19 on mortality in England and Wales, with 22% of all deaths relating to the disease in the week ending 3 April compared with 5% in the week ending 27 March.

In London, nearly half of deaths registered involved Covid-19 and the West Midlands also recorded one of the highest proportions of Covid-19 deaths, accounting for 22.1% of all deaths in the region.

However, the figures continued to show relatively low levels of deaths in care homes compared to reports from operators.

HC One, which operates around 350 homes, said that as of 8pm on Monday there had been 311 deaths from confirmed or suspected Covid-19. It said there had been outbreaks in two-thirds of its homes. MHA, a charitable operator, said there had now been 210 deaths across 131 homes and there were outbreaks in around half of its homes.

The care home figures contrast with the assertion by Prof Chris Whitty, the UK government’s chief medical adviser, that there are outbreaks in one in seven care homes in England. And the ONS figures showed that 237 people died in care homes in the two weeks to 3 April, all but 20 of them in the latest week. Nine of the 217 care home deaths recorded in the week ending 3 April were in Wales.

“The latest comparable data for deaths involving Covid-19 with a date of death up to 3 April, show there were 6,235 deaths in England and Wales. When looking at data for England, this is 15% higher than the NHS numbers as they include all mentions of Covid-19 on the death certificate, including suspected Covid-19, as well as deaths in the community.”