SARS-COV-2 WHOLE GENOME SEQUENCING

Laboratory: Sequencing and Bioinformatics

Test Description: SARS-CoV-2 lineage determination through Whole Genome Sequencing

This test is intended for reporting lineages of the SARS-CoV-2 virus that are considered by the Centers for Disease Control and Prevention and international public health community to be of the greatest public health interest and concern. These classifications were developed by the CDC, in collaboration with the SARS-CoV-2 Interagency Group (SIG) established by US Department of Health and Human Services (HHS), to describe variants with potential or evidence-based increased transmissibility, disease severity, interference with diagnostic test targets, decreased susceptibility to one or more therapies, and/or decreased neutralization by antibodies generated during infection or post-vaccination.

Order Approval Required? No

Specimen Type: Nasopharyngeal or Nose (Anterior Nares) swab in Viral Transport Media

Collection Container: 15 mL conical polypropylene tube

Optimal Volume: >/= 1 mL

Collection Guidelines:

• Use the DCLS SARS-CoV-2 Sequencing and Category B Shipper Kits to collect and transport specimens
• Clearly write full patient name (last and first names), date of birth and “nose” for Anterior Nares, or “NP” for nasopharyngeal swab type on the label of the media tube
• Anterior Nares – use one polyester plastic shaft swab to sample both nares, do not use cotton
• Nasopharyngeal – Follow https://www.cdc.gov/covid/hcp/clinical-care/clinical-specimen-guidelines.html
• Place swab in media tube provided
• Tightly seal media tube to prevent leakage and place inside of the Biohazard Bag
• Accurately complete the DCLS SARS-CoV-2 Sequencing Submission Form with all relevant patient information
• Reason for Test Request: SARS-CoV-2 Sequencing, or other reasons indicated on the form
• Place paperwork in the outside pouch of the Biohazard Bag, do not place paperwork inside with the specimen

DCLS approved submitters can request collection kits at DCLS_SSSKits@dgs.virginia.gov, if a DCLS test kit is available.

Storage Container: 15 mL conical polypropylene tube

Storage Instructions: Store specimens refrigerated at 2-8˚C for transfer to DCLS within 72 hours, specimens that cannot be transferred within this timeframe should be frozen at -70˚C and shipped on dry ice

Transportation Instructions:

• Follow Saf-T-Pak Packaging Instructions included in the Category B Shipper Kit to prepare the container
• Two frozen ice packs must be included in the shipment
• If samples have been frozen, ship on dry ice
• Seal the box closed with packaging tape
• DCLS will coordinate a courier pick-up if the site is not routinely serviced by the DCLS courier
• Contact DCLS at (804)-648-4480 ext. 140 to request a courier pickup Monday – Friday from 9:00 AM – 5:00 PM

Test Methodology: ARTIC cDNA enrichment and Illumina DNA Prep Library generation. Sequencing performed on Illumina MiSeq or NextSeq 550

Additional Information: Sequencing data generated by DCLS is for public health purposes and should not be used to independently to make decisions regarding the management of patient care

Causes For Rejection:

• Quantity not sufficient for testing
• Improperly labeled specimen
• Out of holding time
• Specimen received out of the appropriate temperature range

Possible Results:

• Sequencing Not Successful
• Specific Lineage Characterized