Only Texas with nine and Oklahoma at 4 exceed Missouri's death toll from the disease.
But the figures have led to a dispute between the local and state health agencies.
The St. Louis Bureau Chief for Environmental Health Services Jeanine Arrighi said the number is significant.
"That is certainly more than we've had in past years and we suspect it's because we've had a particularly wet summer and so the availability of standing water in the community contributes to the number of mosquitoes."
But a spokesperson for Missouri's Health Department, Ryan Hobart, downplayed the significance of the numbers.
"The amount of cases that have been reported this year trend with some of years past. This isn't more cases or a significant amount more than would've happened in past years and people just need to be taking care of themselves and using insect repellent," Hobart said.
The website for the federal Centers for Disease Control reports that there "are no medications to treat or vaccines to prevent WNV infection. Fortunately, most people infected with WNV will have no symptoms."
Of 708 cases the CDC reports in the country this year, 13 are in Missouri.
But the fatality rate percentage is highe for Missouri.
Nationwide, the CDC connects West Nile to 29 deaths this year. Only two states exceeded Missouri's three-death total with Texas at nine and Oklahoma at 4.
The CDC figures are based on both confirmed and probable West Nile cases.
The CDC reports that most suffering from the West Nile virus disease will recover completely "but fatigue and weakness can last for weeks or months."
About ten percent of those infected who develop neurological infection from West Nile will die, according to the CDC.
According to the CDC, the West Nile disease was first identified in Africa in 1937. The first known case in the U.S. was in Brooklyn, New York in 1999.
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