According to the latest genomic sequencing results of the Regional Reference Laboratory for polio, 83 of 91 polio cases in Pakistan in 2013 were genetically linked to the virus circulating in Peshawar.
Moreover, 12 of the 13 cases reported from Afghanistan last year were directly linked to Peshawar.
"With more than 90 percent of the current polio cases in the country genetically linked to Peshawar, the (city) is now the largest reservoir of endemic poliovirus in the world," WHO said in a statement.
Pakistan was the only polio-endemic country where cases of the crippling disease increased last year. Nigeria and Afghanistan are the only other countries where polio is endemic.
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During the last four years, samples of sewage water from across Pakistan were tested for the presence of polio virus.
A total of 86 samples were collected from different locations of Peshawar in this period, and 72 samples showed the presence of highly contagious and paralytic wild polio virus strain.
Khyber-Pakhtunkhwa province, of which Peshawar is the capital, and adjoining tribal districts are polio hotspots.
An explosive polio outbreak in the tribal areas, which left 65 children paralysed last year, was sustained by Peshawar.
WHO recommended that repeated, high-quality vaccination campaigns and strong monitoring should be organised in Peshawar to stop polio transmission and protect children.
The anti-polio campaign hit a wall in June 2012, when the Pakistani Taliban banned vaccinations in parts of the lawless tribal belt, saying the restriction would last till US drone strikes cease.
Pakistan registered 85 new polio cases last year.