Clinical COVID-19 (Coronavirus Disease 2019)

 

Information updated: 5/16/2023 10:30 AM

 

The Wisconsin State Laboratory of Hygiene (WSLH) Communicable Disease Division is currently testing for the virus that causes COVID-19 (Coronavirus Disease 2019). We use multiple assays including the Real-Time amplified probe-based CDC Flu SC2 multiplex PCR assay to detect SAR-CoV-2 nucleic acid in patient respiratory specimen. These assays have Emergency Use Authorization (EUA) from the U.S. Food and Drug Administration. We currently only accept specimens that fit the testing criteria outlined by Department of Health and Human Services.

 

Contents:

• Contact Information
• Testing Guidance
• Wisconsin Reference Laboratories
• Acceptable Specimen Types
• Sequencing
• Swab Snapping Instructional Videos
• Ordering Collection Kits from SEOC Distribution Center
• Packaging and Shipping
• Specimen Rejection Criteria
• Test Results
• Biosafety Considerations
• Testing in Your Clinical Lab
• FAQs
• Other Resources (including WCLN webinar links)

 

CDD Customer Service Hours:

• Monday-Friday: 7:45 AM – 4:30 PM

CDD Specimen Receiving Hours:

• Monday-Friday: 6:00 AM – 4:30 PM
  
• Saturday: 6:30 AM – 12:30 PM

Contact Information:

• CDD Customer Service: 1-800-862-1013
• Clinical Orders: 1-800-862-1088
• Emergency Pager: 1-608-263-3280
• Gold Cross Courier: 1-715-839-9989

Testing Guidance:

The Wisconsin Department of Health Services set guidelines for specimen types acceptable for testing at Wisconsin public health laboratories. We will test patients that meet one or more of the criteria below. We encourage labs to use in-house testing whenever possible. Patients that do not meet the high priority testing criteria below may still warrant testing at another facility.

 

Patients tested for COVID-19 by WSLH: Update letter (effective June 12th, 2023)

• Surveillance samples requested by the WSLH
  • WSLH currently requests that each clinical laboratory submit 5 positive SARS-CoV-2 samples per week
• Post-mortem cause of death investigations
• Public Health outbreak investigations as directed by state, local, and tribal public health departments. Pre-approval is required.
• Other testing as directed by public health departments

Note: Please use a separate WSLH COVID-19 requisition form for each specimen. Req forms need to be pre-populated with submitter information by WSLH. To get this individualized req form call CDD Customer Service 1-800-862-1013.

Note: If testing is needed on a patient without these indicators, please consider testing in-house or sending specimens to a reference laboratory. These specimens will not be tested or forwarded by WSLH.

 

If you have questions about COVID-19 or patient prioritization, or if you feel your patient needs urgent testing, contact a Wisconsin State Epidemiologist at WDHS.

• During normal business hours, call 608-267-9003
• After hours, for urgent matters, call the 608-258-0099 emergency pager and ask for the epidemiologist on call.

 

Acceptable Specimen Types:

If you have questions about what specimen to collect for testing, or how to submit them, contact WSLH Customer Service at 800-862-1013

• Recommended: Nasopharyngeal (NP) swab (Flocked, Dacron-tipped with a plastic or aluminum shaft) in viral transport media (VTM). (Clinician collected)
• Oropharyngeal (OP) swabs (Dacron-tipped with a plastic or aluminum shaft), in VTM. (Clinician collected)
• Nasal swabs (Dacron-tipped with a plastic or aluminum shaft), in VTM if other swabs are not available. (Clinician collected or clinician observed self-collected)
• Sputum or other lower respiratory specimen such as bronchoalveolar lavage or aspirate. (Induction of sputum is not indicated) (Does not need VTM)
• For postmortem testing, collect an NP swab in viral transport media (VTM). If autopsy is performed also swab the bronchioles of each lung and place in a single VTM tube. CDC Postmortem testing guidance is available at https://www.cdc.gov/coronavirus/2019-ncov/hcp/guidance-postmortem-specimens.html

Note: If VTM is unavailable UTM, Amies, or sterile RNAse free Saline or PBS may be substituted. Please note this on the Requisition form.

Note: If you do not have VTM collection kits they are available for order from WSLH (limited) or from the DHS COVID ordering portal (see below).

Note: The CDC has a protocol for making your own VTM. https://www.cdc.gov/coronavirus/2019-ncov/downloads/Viral-Transport-Medium.pdf

 

Specimen Rejection Criteria:

• Specimens received at room temperature
• Swabs not submitted in approved liquid (dry swabs)
• Specimens without 2 patient identifiers
• Unvalidated specimen types (mid-turbinate swab, tongue swab, saliva, calcium alginate swabs, cotton tips, or wood shafts)

 

Whole Genome Sequencing

The WSLH performs whole genome sequencing surveillance to monitor the SARS-CoV-2 strains circulating in Wisconsin. Viral mutations are common and expected; however, it is important to monitor these mutations as they could impact disease severity or our ability to detect the virus in patient samples. We are asking for the submission of the following types of samples for our surveillance efforts:

• A subset of residual molecular positive samples (5 per week)
• Residual molecular positive samples from patients meeting the criteria below, outlined in HAN #25. Questions related to these criteria should be sent to DHS at DHSDPHBCD@dhs.wisconsin.gov
  • Traveled to another country within the previous 30 days
  • Known close contact with a person who tested positive for COVID-19 after traveling to another country in the previous 30 days.
  • Prolonged clinical illnesses, including those who are suspected of having protracted SARS-CoV-2 viral replication, are immunocompromised, or who have a recurrence of COVID-19 disease after an initial period of recovery.
  • Suspected repeat infection occurring in patients who received monoclonal antibody therapy, convalescent plasma therapy, or antiviral drugs including remdesivir.
  • Any SARS-CoV-2 infection in an individual who has received a COVID-19 vaccine.

Sequencing results will not be reported to the submitter or patient. Sequencing is performed strictly for public health surveillance purposes and is not meant to advise patient care. Submitters will not be billed for this testing.

Sequencing can be performed on residual specimen in viral transport media (VTM, PBS, or saline) from molecular positive specimens (1 mL is optimal).

Please include a COVID-19 requisition form for each specimen and mark “sequencing”. Req forms need to be pre-populated with submitter information by WSLH. To get this individualized req form please call CDD Customer Service 1-800-862-1013.

Contact Gold Cross Courier (715-839-9989) for transport of specimens to the WSLH.

Sequencing cannot be performed on residual rapid test test specimens (antigen tests, ID NOW, self-tests, etc.)

Please direct testing and submission question to CDD Customer Service 1-800-862-1013

 

Sequencing Data

WSLH has created a live Sequencing data dashboard to help visualize variant tracking in WI. Data includes sequences generated by WSLH and all other labs uploading data to GISAID.

https://dataportal.slh.wisc.edu/sc2dashboard

 

Collection Kits available for order from DHS COVID Web Portal

The DHS COVID Testing Team has collection kits and shipping supplies available to medical systems throughout Wisconsin. The supplies are available at no charge. To order supplies go to the ordering web portal. You cannot bill for these supplies. For questions contact their email WICOVIDTEST@wi.gov

 

Swab Snapping Instructional Videos

It is important to leave the tip of the swab in the transport tube after collecting a sample. Printable instructions and short videos of swab snapping are available for 3 common swab types.

Swab with score mark

Swab with no score mark

Swab thinner near the top

 

 

Packaging and Shipping:

If you have questions about how to submit specimens for testing, contact WSLH Customer Service at 800-862-1013

Submit specimens with a completed WSLH COVID-19 Requisition Form. If your laboratory doesn’t already have this form, please call WSLH Clinical Orders at 800-862-1088 during normal business hours (Monday – Friday 7:45 AM – 2:45 PM). Please leave a message outside of normal business hours.

• If the specimen will Arrive at WSLH <72 hours after collection: Store specimen at 2-8^oC and ship with frozen cold packs
• If the specimen will Arrive at WSLH >72 hours after collection: Freeze (-70^oC ) the specimen and ship on plenty of dry ice
• Urgent Testing Requests – If WDPH determines that testing is urgent, WSLH will work with you to arrange transportation of the specimen. Do not contact Gold Cross courier on your own and order a STAT pick-up. STAT pick-ups can only be ordered by WSLH.
• Extended weekend hours are for COVID-19 specimens only
• Package as a UN3373 Biological Substance, Category B. Instructions for shipping and DOT Safety advisory

WSLH accepts specimens from many courier and delivery services.

Gold Cross Courier: 715-839-9989

Order by NOON for same-day pick-up for NEXT DAY delivery (Sun-Fri)

Please hold specimen at -20C to 4C on Saturday

 

Test Results:

Currently, test results will be available within 1 – 3 days of receipt of the specimen at WSLH. Results will not be called to the submitter. All results will be reported electronically, as soon as they are available, to the submitting lab, the health department, and HHS. Please call WSLH Customer Service at 800-862-1013 if you feel a result is missing. If there are urgent questions outside of business hours you may call the WSLH emergency pager at 608-263-3280.

• CDC Flu SC2 Multiplex Assay Fact Sheet for Healthcare Providers and Fact Sheet for Patients

NOTE: Patients with suspected or confirmed COVID-19 are reportable conditions in accordance with Wis. Stat. Ch. 252 and Wis. Admin. Code Ch. DHS 145. All suspect patients should be reported to WEDSS immediately. This is normally done by an Infection Preventionist or the Clinical Provider. WSLH will also report all of our COVID-19 test results to WEDSS, CDC, and HHS.

NOTE: If you are performing testing, please report all results in the weekly surveillance report to WSLH.

 

Testing in Your Clinical Lab:

To meet the growing need for COVID-19 testing the WSLH strongly encourages Clinical Labs to bring on NAAT testing in their labs.

 

Hundreds of FDA EUA COVID-19 Tests are available for use in Clinical Laboratories. Check the FDA Website for the most up to date list of approved tests: https://www.fda.gov/medical-devices/emergency-situations-medical-devices/emergency-use-authorizations

 

APHL Side-by-side comparison of test methods

FDA Reference panel comparison data

Test performance and population prevalence calculation tool

 

Biosafety Considerations:

CDC biosafety guidance can be found at https://www.cdc.gov/coronavirus/2019-nCoV/lab/lab-biosafety-guidelines.html. We strongly encourage each laboratory to perform a risk assessment for their facility and the procedures they will perform on a suspect COVID-19 patient. After performing this risk assessment you may choose to implement additional biosafety practices, such as enhanced PPE, when working with suspect COVID-19 patients/specimens.

Molecular testing assessment tool: https://www.aphl.org/programs/preparedness/Documents/APHL%20Potential%20Hazards%20and%20Recommended%20Mitigation%20Procedures%20for%20COVID-19.pdf

Antigen testing assessment tool: https://www.aphl.org/programs/preparedness/Documents/COVID-19%20Antigen%20Testing%20Biosafety%20Guidance.pdf

 

Reporting of COVID-19 Results

• All positive COVID-19 test results must be reported to public health. If you don’t currently have an account you can sign-up for WLR here.
• In addition, we request that all results generated in clinical labs are reported to the WSLH weekly surveillance report 

 

Frequently Asked Questions (FAQs)

Q: How much does the WSLH COVID-19 test cost?
A: All COVID-19 testing is fee exempt at the WSLH. We can also provide collection kits and transportation of specimens free of charge. Please contact our Customer Service department if you need help setting this up – (800) 862-1013.

 

Q: How long will it take to get my results?
A: Our current turnaround time is 1-2 days from receipt in the lab. This is subject to test volume and weekend delays. If we see a large volume of testing, then testing results may be delayed.

 

Q: To whom does the WSLH report results?
A: At WSLH positive results are sent electronically to the submitting facility. The submitter is responsible for reporting to the ordering clinician or patient. All positive and negative results are also reported electronically by ELR to WEDSS (state) and the CDC (a part of HHS).

 

Q: Can the WSLH perform COVID-19 testing on residual specimens after Flu testing is performed?
A: Yes, we will test residual primary specimen even if some volume has been used for other tests. Minimum volume is 1 mL. Please maintain PCR sterility.

 

Q: Will my specimens expire if testing is not performed within 72 hours of collection?
A: Specimens will not expire while at WSLH. As long as specimen are stored 2-8 C and we receive them within 72 hours after collection, we will either test immediately or store specimens at -70C to allow for later testing. You can also freeze your specimens and ship on dry ice to ensure specimen stability.

 

Other Resources:

Webinars:

Information in these webinars may be outdated due to the rapidly evolving situation. Please refer to information above for most recent guidance.

11/08/21 CLIA, Testing, and Reporting – Guidance for those looking to set up point-of-care testing Slides

03/17/21 WCLN COVID-19 Webinar – Impact of dropping prevalence and variants Slides

09/02/20 WCLN COVID-19 Webinar – Antigen testing and PPV Slides

06/24/20 WCLN COVID-19 Webinar – Reporting, Shipping, and testing at WSLH Slides

05/27/20 WCLN COVID-19 Webinar – Waves of cases, Pooling, reporting, and test of cure Slides

05/13/20 WCLN COVID-19 Webinar – Community testing and HHS reporting Slides

04/29/20 WCLN COVID-19 Webinar – Dr. Bateman, Serology and SEOC Webportal Slides

04/22/20 WCLN COVID-19 Webinar – Antibody testing Slides

04/15/20 WCLN COVID-19 Webinar – Reporting and update from DHS Slides

04/08/20 WCLN COVID-19 Webinar – PIF, SEOC Survey, and Serology Slides

04/01/20 WCLN COVID-19 Webinar – PIF, SEOC Survey, and WSLH testing Slides

03/25/20 WCLN COVID-19 Webinar – Triage, alternate collection kits, and validation panels Slides

03/18/20 WCLN COVID-19 Webinar – Triage, FDA tests, and CPT codes Slides

03/13/20 WCLN COVID-19 Webinar – Pandemic declared, where to test and how Slides

 

Wisconsin Department of Health Services (WDHS) COVID-19 and Outbreaks in Wisconsin

CDC COVID-19 information

Johns Hopkins visual website for tracking COVID-19 cases

World Health Organization COVID-19 situation reports

FDA Emergency Use Authorization for test to detect the virus that causes COVID-19