In the first quarter of 2011 Pakistani doctor Shakil Afridi began a hepatitis B vaccination programme in and around one of the poorer cities in Hazara in Northeastern Pakistan.

Abbottabad is similar to less fortunate Pakistani cities struggling with poverty and insufficient access to health services. Employed by the government and considered the top medic in the Khyber tribal area, Dr. Afridi’s vaccination programme was typical of such immunisation initiatives.

Dr. Shakil Afridi

However what is now well known is that Dr. Afridi had been recruited by the CIA. Provided with only minimal information from CIA operative “Peter”, he was to use the vaccination programme as cover for gathering blood samples from an Abbottabad compound.

The CIA believed Osama bin Laden may be hiding in the compound and were after a DNA sample from children to compare with his late sister. Dr. Afridi had two female staff working with him on the programme. One was able to access the compound and gather blood samples. Afridi and his staff had no idea who the CIA were targetting.

Ultimately the scheme failed and did not lead to the success of the USA confirming this was bin Laden’s hideout.

What is known is that the CIA’s use of this and other vaccination programmes has had a lasting negative effect on their implementation and success. As a result the control of dangerous diseases including polio, has likely been set back years.

Already regarded with suspicion in developing Islamic nations, Western backed and funded vaccine programmes are subject to anti-vaccination propaganda. Conspiracies linking polio vaccination to deliberate Western plots to spread HIV/AIDS or cause sterility have circulated for years. The incorrect claim that the vaccine is “unclean” under Islamic law has been thankfully countered by the global Islamic Advisory Group on polio.

Pakistan’s polio vaccination programmes have suffered significantly from the plot involving Dr. Afridi. The Pakistani Taliban have placed a “ban” on polio vaccine programmes. 350,000 children have missed out on polio vaccination and access to other health care. A spike in polio infection has seen 66 children diagnosed to date this year compared to a total of 14 for the whole of 2013.

60 health workers have been killed over the past three years due to enforcement of this ban by violent militant groups. Infection has spread across the border to Afghanistan.

On May 5th this year the World Health Organisation announced polio had “re-emerged as a public health emergency”. Some critics have argued 30 years of work to control the virus “could unravel”. The WHO is calling for all children in affected countries to be vaccinated or revaccinated, whilst anyone travelling from these countries should also be revaccinated, and carry proof of this with them.

A few days ago the CIA announced an end to the exploitation of vaccination programmes.

Lisa Monaco, a senior counterterrorism and homeland security adviser to President Obama, wrote in a letter addressed to the leaders of several prominent public health schools that the CIA would not use immunisation programs – or workers – as a means to collect intelligence. Such programs have prompted attacks on medical workers in Pakistan.

“The Director of the Central Intelligence Agency directed in August 2013 that the agency make no operational use of vaccination programs, which includes vaccination workers,” Monaco wrote in the letter, which was first obtained by Yahoo News.

“Similarly, the agency will not seek to obtain or exploit DNA or other genetic material acquired through such programs. This CIA policy applies worldwide and to US and non-US persons alike.”

Former CIA spy Micheal Scheuer, who was a senior adviser to the CIA’s bin Laden unit has criticised the decision. Speaking to the BBC he argued any tool that got the job done is justified.

MICHAEL SCHEUER: If it saves Americans it justifies the end. That’s what the agencies and business want.

BBC INTERVIEWER: Even though potentially thousands of people could die as a result of the spread now of polio?

MICHAEL SCHEUER: Well, you know, stuff happens, Sir.

WILL OCKENDEN: He says the use of vaccination programs by the CIA paid off in the hunt for and execution of Osama bin Laden.

MICHAEL SCHEUER: Without a doubt. It led directly to the killing of Osama bin Laden. It was too late in the war to make much of a difference but as long as he was alive he was involved in planning attacks against the United States and Britain and some of our other allies. It was very much worth the cost.

You can catch the full ABC News audio below, or download the mp3 file here.

Leaving the CIA behind it’s worth noting that logistical problems associated with conflict in Syria and the inexplicable apathy of the Syrian government have seen the resurgence of polio, measles and meningitis. In April it was reported polio had spread from Syria to Iraq.

In Somalia Al Shabaab had banned 16 humanitarian agencies by late 2011. Consequently 300,000 children went unvaccinated for three years. This led to a 2013 outbreak in polio, including 194 cases of paralysis and a spread to Ethiopia and Kenya. Existing Aid programmes managed to control this spread within six months. Large scale measles infection has also proven a problem across the Horn of Africa.

Boku Harem has attacked health facilities responsible for vaccination programmes in Nigeria. Ten polio workers were killed in February of 2013.

According to an editorial just published in Nigeria’s Leadership newspaper, ten countries currently report that polio is in circulation.

The action of the CIA in Pakistan (and apparently elsewhere) has been monumentally reckless. The consequent scattering of polio vaccination reduction, alongside global conflict has led to a global emergency.

The lesson then for the developed world is clear. Now, more than ever, there is no excuse for parents to question the validity of any vaccination.

Particularly polio.

• Below Professor Michael Toole, Deputy Director of Melbourne’s Burnet Institute discusses the problems facing some Islamic nations on ABC 24 (May 24th 2014).

Radical Islam Opposition To Polio Vaccination