Practices are to receive bonus payments for bringing forward the COVID and flu vaccination programme because of the risks of the new variant virus, it has been announced.

NHS England said the programme should begin on 11 September – three weeks earlier than the planned October start. The alarm has been caused by the identification of a new and rapidly mutating COVID variant, BA.2.86, in the UK. There was already concern about the virulence of the flu strain experienced in Australia and new, rapidly spreading variants of COVID.

UK Health Security Agency chief executive Dame Jenny Harries said: “There is limited information available at present on BA.2.86 so the potential impact of this particular variant is difficult to estimate. As with all emergent and circulating COVID-19 variants – both in the UK and internationally – we will continue to monitor BA.2.86 and to advise government and the public as we learn more.”

NHS England medical director Professor Stephen Powis said: “Vaccinations are our best defence against flu and COVID-19 ahead of what could be a very challenging winter, and with the potential for this new covid variant to increase the risk of infection, we are following the latest expert guidance and bringing the covid vaccination programme forward, with people able to get their flu vaccine at the same time to maximise protection. The NHS will work quickly to offer people protection against these nasty viruses as soon as possible, first going into adult care homes and inviting those most at risk including those with weakened immune systems.”

The British Medical Association said the decision had forced a climb-down over the level of payments to practices. It had objected to plans to reduce the payment per vaccine.

Dr Samira Anane, the deputy chair of the BMA GP committee for England, said: “Thankfully, many GP practices had already prepared to deliver the flu vaccination programme in September despite suggestions that NHS England would delay it, so practices are already on-track to deliver this before the end of October and make sure those who are eligible get the protection they need.”

Dr Anane added: “Making sure that GPs have the right resources is essential in helping them to deliver as many boosters as possible, and to ensure that communities are protected against this highly transmissible, new variant. While many practices may feel relieved that the vaccine programme may be more viable for them to deliver, the increased payments are only available until the end of October – at which point the base fee returns to the much lower rate, that made so many practices question if they could provide the COVID vaccines at all this year. This programme comes as an incredibly demanding piece of work, which will have an impact across general practice, generating significant workload as a result. The restrictions on not being able to use enhanced access services such as out-of-hours appointments to help vaccinate patients presents an additional barrier to helping protect our patients and will mean workforce will be stretched beyond capacity.”