Skip Navigation LinksSARS-CoV-2-WGS

VIRAL AND RICKETTSIAL DISEASE LABORATORY

Test Order
SARS-CoV-2 Identification - Whole Genome Sequencing​​​​​

Information Category
​Information Detail
Pre-Approval
For Outbreak Investigations: Please email VRDL.submittal@cdph.ca.gov​ prior to sending any specimens. VRDL will accept up to 10 specimens per outbreak. 

For Routine Surveillance: VRDL will accept up to 25 specimens every two weeks.

Pre-approval is required for submissions that exceed these specimen limits above.​
​Supplemental Information Requested
  • ​Sample must be positive for SARS-CoV-2
  • Specimens must have a Ct value of ≤30 or an RLU value of ≥1100
  • Ct values or RLU values should be indicated on the submittal form when available
  • Outbreak location should be indicated on the submittal form if applicable
​Submittal Forms
Specimens must be accompanied with a hard copy of the completed VRDL General Purpose Specimen Submittal Form (PDF)​ or a form generated in the VRDL Lab Web Portal

Batch submittal forms are also available by request to VRDL.submittal@cdph.ca.gov.
Methodology 

Whole Genome Sequencing (LDT) (Surveillance use only)

Reflex Testing
Not applicable​
​Acceptable Specimen Type(s) and Collection Method
Human Specimens:
  • ​Upper Respiratory specimens :
    • ​A single nasopharyngeal (NP) swab is preferred. 
    • Acceptable alternatives include: 
      • ​A nasal mid-turbinate swab 
      • An anterior nares swab 
      • An oropharyngeal (OP) swab 
  • ​​SARS-CoV-2 positive nucleic acid extracts with original specimen if possible

Swabs must have a Dacron or synthetic tip with aluminum or plastic shaft (same type as the ones used for influenza testing).

If two sites are swabbed (e.g. nasopharyngeal and oropharyngeal combination swabs), place both swabs in the same sterile collection tube of Universal or Viral Transport Medium or sterile saline.

VRDL can accept swabs from some COVID-19 rapid antigen kits for whole genome sequencing; please contact VRDL.submittal@cdph.ca.gov for guidance and pre-approval if you are  if planning to submit this type of specimen.

Other specimen types, including lower respiratory tract specimens may be considered on a case-by-case basis. Please contact VRDL.submittal@cdph.ca.gov for more information.
​Minimum Volume Requested
  • ​Respiratory swabs: 2-3 mL of Universal or Viral Transport Medium or sterile saline.
  • Nucleic acid extracts: 25 µL-40 µL
​Transport Medium (if using)
Universal or Viral Transport Medium preferred. Molecular Transport Medium also acceptable: please indicated media on submittal form. ​
​Specimen Labeling
​Each specimen tube must be labeled with at least two unique patient identifiers; e.g., patient full name and date of birth.
​Storage & Preservation of Specimen / Shipping Conditions
  • Swabs and extracts: freeze or refrigerate specimens promptly after collection. Freezing is strongly recommended.​

Ship refrigerated specimens to VRDL on cold packs. Ship frozen specimens to VRDL on dry ice.

​Shipping Instructions
Work with your local public health department to ensure samples are packaged according to instructions for Biological Substance – Category B (UN 3373) shipment.  

Ship specimens and a hard copy of the completed submittal forms to:
     CDPH VRDL

     ATTN: Specimen Receiving

     850 Marina Bay Parkway
     Richmond, CA 94804
     Phone: 510-307-8585
Turnaround Time
  • 30 business days for in-house sequencing​
  • 90 business days for outsourced sequencing
Interferences & ​Limitations
This service is provided for public health investigational needs only. This is not a validated, diagnostic test, and results shall not be used for clinical management. Results will only be conveyed to local public health ​officials. 

Samples with low viral load (real-time PCR Cycle Threshold >30) or that have been improperly stored or subjected to conditions that negatively impact nucleic acid integrity may not provide interpretable results.

Results may not confirm or predict anti-viral resistance.​
​Additional Information
None​
​VRDL Points of Contact
Medical and Epidemiology​ Liaisons: (510) 307-8585 or VRDL.Submittal@cdph.ca.gov​ 
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