One of the children infected attended services at the Iglesia de Cristo Fuente de Vida church in Sanford.
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Health officials said those who attended the church between July 6 and August 6 may have been exposed to the infection.
A second confirmed case is another sick child who is not connected to the first case.
Pertussis is an infection that affects the airways and lungs that can cause serious illness, especially in infants.
Symptoms usually develop within five to 10 days after exposure, but in some cases can take as long as three weeks to appear. The disease is easily spread from person to person by coughing or sneezing and can result in a severe cough that may last for weeks or months.
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Health officials said if you believe you may have been exposed to pertussis or feel you have symptoms, seek medical attention.
In some cases, antibiotics are provided to those who believe they have been exposed, but are not yet showing symptoms.
Individuals who have been diagnosed with pertussis should stay away from large crowds. The best way to protect yourself against the disease is to keep your vaccinations up-to-date.