The three-country programme aims to immunize 360,000 children aged two years and under, partly to get a wider view on the vaccine's effectiveness but also to see whether the delivery process is feasible.
"The malaria vaccine has the potential to save tens of thousands of children's lives", said WHO Director-General Dr Tedros Adhanom Ghebreyesus.
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Mosquirix has been developed by British pharmaceutical giant GlaxoSmithKline in partnership with the PATH Malaria Vaccine Initiative.
"So, this vaccine is a huge plus to Malawi", he said.
These sentiments were echoed by Pedro Alonso, director of WHO's Global Malaria Programme.
Some experts warned the vaccination programs should not divert limited public health funds from low-cost and proven tools to curb malaria such as bed nets and insecticides.
The vaccine known as RTS, S has taken 30 years to develop and so far is the only vaccine proven to significantly reduce malaria in children.
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"There are over 250 000 deaths of children in Africa every year because of malaria", Mary Hamel, the coordinator for the Malaria Vaccine Implementation Programme at the World Health Organisation told the DPA news agency.
Preventive measures like use of insecticide-treated nets, mosquito repellents, eradicating mosquito breeding grounds, and anti-malaria drugs helped in reducing the disease incidence rate. The programme is created to throw up results about reduction in child deaths, vaccine uptake, and vaccine safety in the context of routine use. "It may not sound like much but we are talking about 40% reduction in severe malaria which unfortunately still has high mortality even when you have access to good treatment".
"We salute World Health Organization and Malawi for their leadership in realizing this historic milestone", said Steve Davis, President and CEO of PATH, "and we look forward to the start of vaccination in Ghana, and then Kenya later this year".
The vaccine works against the most deadly malarial parasite Plasmodium falciparum which is most prevalent in African countries.
As per a report by The Guardian, Gavi, the Vaccine Alliance, the Global Fund to Fight Aids, Tuberculosis and Malaria, and Unitaid are providing just under $50m (£38m) to fund the first phase of the pilots in Malawi, Kenya and Ghana. Alonso cited the need to understand where the vaccine would be adding benefit - whether it would be to all areas where malaria is endemic, or only the ones with the greatest need.
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