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 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.