Brief Description

SARS-CoV-2 Sequencing Submission Guidance
SARS-CoV-2 whole genome sequencing to detect variants
This testing is for epidemiological surveillance purposes only

Laboratory Unit



Whole Genome Sequencing (WGS)

Specimen Collection

2019-nCoV Collection Kits

Before sending specimens for SARS-CoV-2 Variant Surveillance, call the Missouri Department of Health and Senior Services (DHSS) Emergency Response Center at 1-800-392-0272, Monday through Friday, during the hours of 8:00 a.m. to 5:00 p.m. Note that before any specimen is sent for variant virus surveillance, DHSS staff must first be consulted. See Health Update from February 19, 2021

Requirements (Each of these is required for approval for specimen submission):

  • All persons must have been diagnosed with COVID-19 by a positive viral diagnostic test, such as RT-PCR, other nucleic acid amplification test, or an antigen test.
  • The RT-PCR Ct value is no more than 28. Not required if Ct value is not available, or can’t be obtained
  • Specimens must meet the required MSPHL submission criteria for COVID-19 testing available at, and must be received by the MSPHL within 72 hours of collection, or have been stored frozen and shipped frozen using dry ice.
  • Prior approval from DHSS is obtained prior to specimen submission.

Select Criteria (At least one of these is also required for approval for specimen submission):

  • RT-PCR test results demonstrate the “S-gene dropout”. This criteria may change based on the frequency and distribution of the emerging virus variants.
  • Person developed onset of symptoms or tested positive (asymptomatic) within 14 days of returning from international travel.
  • Person developed onset of symptoms or tested positive (asymptomatic) within 14 days of exposure to a person meeting criteria #2 above.
  • Person is suspected of COVID-19 reinfection, including persons previously treated with monoclonal antibody, convalescent plasma, or antiviral drug Remdesivir.
  • Person is fully immunized with an approved COVID-19 vaccine per CDC guidelines and developed onset of symptoms greater than 14 days after receiving the final dose of vaccine.

Submitting Specimens to the MSPHL: The submission of specimens to the MSPHL for testing and identification of variant SARS-CoV-2 viruses requires adhering to the following:

  • Complete a MSPHL Test Request Form (TRF) for each specimen. The TRF is available online at
  • Must include that the specimen is submitted for variant virus surveillance on the TRF. It is also important to note on the TRF if vaccine breakthrough infection is suspected.
  • Must include on the TRF what test was used to generate a positive result and the Ct values for each marker, as available.
  • Specimen must contain at least 500 μL of viral transport media (VTM) or saline
  • Store the specimens at -70°C pending shipment and ship on dry ice
Affix shipping label to the outside of box and write: SARS-CoV-2 Variant Surveillance on box


Specimens must be shipped to the MSPHL within 72 hours of collection. If this is not possible, the specimen must be frozen and shipped to the MSPHL on dry ice.

GIS map of courier drop off locations Monday-Friday

List of courier drop off locations by county Monday-Friday

Sunday Courier Locations

If you do not have access to the MSPHL Courier, please ship specimens by Fed Ex. Do not ship samples for arrival at the MSPHL on weekends or holidays. DO NOT use UPS to ship clinical specimens.

For questions about packaging and shipping an approved specimen for variant virus surveillance to the MSPHL, contact the MSPHL at 573-751-3334.

Acceptable Specimen Type(s)

Respiratory swab in Viral Transport Media (VTM) or Saline

Test Request Form(s)

Possible Results

Due to federal regulation, the MSPHL is unable to provide result reports for SARS-CoV-2 variant sequencing surveillance to the submitter or patient. SARS-CoV-2 variant surveillance whole genome sequencing is intended for public health surveillance purposes only and cannot be used for diagnostic or individual clinical patient management. This method is not FDA cleared or CLIA regulated.

Unacceptable Conditions

  • Specimen is not approved for testing.
  • The name on the specimen does not match the name on the requisition form.
  • The specimen container is not labeled with the patient’s name.
  • Improper storage/transport of specimen.
  • The sample collected with improper collection device—cotton-tipped or calcium-alginate swab, wooden-shaft swab, transport media not intended for viruses.
  • The specimen is not one of the listed acceptable specimens.
  • Quantity Not Sufficient for testing

Interfering Substances

Cotton-tipped or calcium-alginate swab, wooden-shaft swab, transport media not intended for viruses

Result Reported




CPT Codes




Additional Information