The seasonal flu vaccine has provided low protection against one subtype, H3N2, which circulated this winter, research from PHE has found.
This is because of a mismatch between the A(H3N2) strain selected for the vaccine this year and the strain of influenza that has been circulating in the UK.
The research, based on results from 1314 patients presenting in primary care across the UK found that vaccine effectiveness in preventing influenza was estimate to be three per cent overall. This compares to approximately 50 per cent vaccine effectiveness typically seen in the UK over recent years.
This flu season has been dominated by a circulation of influenza A(H3N2) subtype viruses which cause problems for particular groups such as the elderly. This has resulted in care home outbreaks, hospitalisations and excess mortality in those over 65 years.
Dr Richard Pebody, study author and PHE's head of flu surveillance, said: 'The WHO monitors influenza globally and each year recommends the strains of flue virus that should be included in the flu vaccine for the forthcoming flu season.
'Throughout the last decade, there has generally been a good match between the strains of flu in the vaccine and those that subsequently circulate, so it's crucial that these results do not discourage people in at-risk groups from having flu vaccination now, or in the future.'
'Currently, we are seeing an uptake just in excess of 70 per cent for vaccinations in at-risk groups.'
Dr Pebody said that it is not always possible to fully predict strains that will circulate in any season and there is always a risk of a mismatch as seen this year.
The UK findings follow the publication of the US and Canada's mid-season vaccine effectiveness estimates, both of which also revealed the vaccine had provided little protection against circulating A9H3n2) viruses this season in these countries.
Dr Pebody added: 'Primary care nurses should continue to recommend vaccinations against flu for vulnerable groups, as the current vaccine is effective against other strains of flu that are circulating such as flu B and influenza AH1N1. Our findings from this season will inform the WHO's flu vaccine for next year.'
PHE's weekly flu report has shown that levels of flu activity were at similar or lower levels than the previous week, despite the fact this year has seen the highest levels of flu in the last three years.