County Health Departments


  • Surveillance: CHDs should apply the definition of person under investigation (PUI) for COVID-19 to determine if laboratory testing and public health investigation is needed.
  • Investigations: Investigations should occur for individuals meeting the definition of PUI for COVID-19 within the same day of CHD notification, including weekends and holidays.
    • County epidemiology staff should alert their regional epidemiologist and laboratory liaison, or BOE on-call epidemiologist if after-hours, of all PUIs for COVID-19.
  • Reporting PUIs and Cases: PUIs or persons meeting the confirmed or probable case definition for COVID-19 should be entered into Merlin within 24 hours (including weekends and holidays).
  • CHD Laboratory Results Notification Process for 2019-nCoV: Emailed from Bureau of Public Health Laboratories.
  • Documents on this topic dated after January 31, 2020, supersede this one.

Laboratory Testing and Specimen Collection

  • If PUI criteria are met, or if you have questions about a patient, contact your Regional Epidemiologist and Laboratory Liaison or the after-hours BOE on-call epidemiologist (850-245-4401) to arrange for specimens to be submitted to the Bureau of Public Health Laboratories (BPHL).
  • BPHL will ship specimens to CDC for testing until testing is made available at state public health laboratories.
  • Specimens should be collected as soon as possible once a PUI is identified regardless of symptom onset.
  • To increase the likelihood of detecting COVID-19, CDC recommends collecting three specimen types, lower respiratory, upper respiratory, and serum:
    • Upper respiratory: nasopharyngeal and oropharyngeal swabs in viral transport media, each in a separate container; nasopharyngeal wash/aspirate or nasal aspirate may be used as well.
    • Lower respiratory: sputum (induced if necessary), bronchial alveolar lavage/tracheal aspirate, in a sterile container
    • Serum (red top or tiger top tube)
  • If additional specimen types such as stool, urine, or whole blood are collected, they can be stored for potential future use.
  • Ship specimens overnight for arrival to BPHL in Jacksonville, Miami, or Tampa following notification to the appropriate BPHL location.
  • Shipments arriving on the weekend must be pre-authorized by BPHL and BOE.
  • Ship specimens using category B shipping containers.
  • Notification Process of Laboratory Results for Specimens Tested by CDC: Emailed from Bureau of Public Health Laboratories

Reporting COVID-19 PUIs and Cases in Merlin

  • Individuals meeting the confirmed, probable, or PUI (suspect) case definition for COVID-19 should be entered into Merlin.
    • Use the disease code “COVID-19 – 00342” when entering PUIs in Merlin.
  • Enter PUIs within 24 hours of CHD notification.
  • PUI will be listed as suspect DX status until laboratory results have been returned.
  • Attach all available medical records, laboratory results, and paper PUI form (if available) to the Merlin case.
  • Attach CDC laboratory results to the case and submit.

The Florida Department of Health is actively working with private and public partners to monitor COVID-19. The Florida Department of Health has set up testing sites throughout the state and is assisting with vaccine distribution. 

The Florida Department of Health is communicating regularly with the public and health care providers with updates on COVID-19 and other respiratory illnesses. The COVID-19 Call Center is available 24/7 at 1-866-779-6121.


The Centers for Disease Control and Prevention and World Health Organization are reliable and up-to-date sources of information about this evolving outbreak.

For Florida specific information, please consult the Florida Department of Health website.