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Viral Next Generation Sequencing

Laboratory Fee Schedule
Procedure Number: N/A 

Synonym(s): Virus, Molecular, NGS, Viral Isolation, Variant of Concern (VOC), Surveillance, Diagnostic, Outbreak, Infectious disease, Genetic variation, Genetic mutation, Genome, Human Monkeypox Virus, hMpxV, Mpox, Epidemic/Pandemic, Amplicon, PCR, SARS-CoV-2
Requisition Form G-2V or DSHS Microbiology Laboratory line list
Test Description Viral RNA or DNA will be amplified through PCR, sequenced, and analyzed to identify characteristics of interest such as lineage, clade, variant calling, and genetic mutations for surveillance purposes. Sequencing files and de-identified data may be shared to public repositories (e.g., NCBI).
Pre-Approval Needed
  • Providers interested in submitting specimens for SARS-CoV-2 NGS surveillance testing must email the DSHS Austin Genetic Sequencing Branch at wgs.dshs@dshs.texas.gov before submitting specimens. 
  • Local/regional epidemiologists must be included in all SARS CoV-2 surveillance testing submission emails to the genetic sequencing branch. Email local/regional epis at eaidu-coronavirus@dshs.texas.gov. 
  • Providers interested in submitting specimens for Human Monkeypox Virus (HMpxV) surveillance testing must first email their local/regional epidemiologists and the genetic sequencing branch before submitting specimens.
  • Refer to the DSHS reporting contacts webpage for a list of public health region epis. 
Supplemental Information Required N/A
Supplemental Form(s) N/A
Performed on Specimens from (Success) 
  • Clinical, Human 
    • Specifically, tissue swabs (e.g., nasopharyngeal, nasal, oral, and genital)
Sample/Specimen Type for Testing 
  • Original clinical specimen (e.g., swab), or RNA or DNA extract. 
  • Original HMpxV specimens should be collected using dry, sterile rayon, Dacron, nylon, or polyester swabs.
  • Cotton swabs are not acceptable.
  • SARS-CoV-2 nasopharyngeal (NP), oropharyngeal (OP), and nasal swabs may be shipped in viral transport medium (VTM, preferred). 
  • SARS-CoV-2 swabs in universal transport medium (UTM), Amies, or 0.85% saline are acceptable.
Minimum Volume/Size Required
  • Single swab
  • 30 µl minimum for RNA and DNA extracts
  • All SARS-CoV-2 specimens must have a previous positive PCR result, with a cycle threshold (Ct) value ≤31.
  • Only vaccine breakthrough and reinfection cases with Ct >31 will be sequenced.
  • Previous PCR results with Ct ≤29 preferred for HMpxV.
  • Higher Ct value samples may be tested upon epidemiologist and DSHS Lab consultation.
  • SARS-CoV-2 NGS specimen collection and submission instructions are provided on request by emailing wgs.dshs@dshs.texas.gov.
Storage/Preservation Prior to Shipping
  • Store DNA extracts of HMpxV frozen at -20°C.
  • Store RNA extracts and clinical specimens of SARS-CoV2 frozen at -70°C. 
  • Refrigerate HMpxV clinical specimens at 2°C – 8 °C if they will be tested within 24 hours of collection. 
  • Freeze HMpxV clinical specimens at -20°C if testing will occur more than 24 hours after specimen collection. 
  • Lids of swab transport kits and viral nucleic acid extraction and transport kits must be threaded properly and tightened securely to minimize leaks.
  • Leaked or spilled specimens will not be tested.
Transport Medium

Transport media must sustain viral RNA and DNA.
Specimen Labeling
  • At least two patient identifiers required on specimen (e.g., patient full name, date of birth, medical record number) in addition to the date of collection. 
  • Three patient identifiers are preferred. 
  • Date of collection is required for all specimens. 
  • Identifiers on specimen label must exactly match identifiers on submission form/ line list. (e.g., abbreviated name on label and full name on form is not acceptable.)
  • Specimen labels, forms/line lists must be legible.
  • Additional DSHS Laboratory specimen labeling guidelines available online here.
Shipping and Specimen Handling 
Requirements
  • Overnight shipping for all specimens is preferred.
  • Ship SARS-CoV-2 specimens frozen on dry ice (preferred) for overnight delivery. 
  • SARS-CoV-2 clinical specimens can be shipped with multiple ice packs overnight to keep cold for up to 48 hrs. One ice pack is not enough. 
  • Ship according to Dangerous Goods Regulations, IATA, and/or CFR 49.
  • Category B Biological Substance, UN3373 shipping requirements apply.
  • Handle as infectious agent using universal precautions. Triple-contain in accordance with federal shipping regulations. Submitters are responsible for packaging and shipping specimens according to regulatory requirements. 
  • Specimen collection kits must be properly closed and secured to minimize leaks during shipping. Leaked specimens will not be tested.
  • Additional DSHS Laboratory specimen shipping guidelines online here.
Method

Next Generation Sequencing using Illumina and Clear Dx™ sequencing platforms
Turn-around Time  14 days from date of specimen receipt
Interferences/Limitations Specimens with a higher than accepted Ct value will be sequenced only upon consultation with an epidemiologist and the Laboratory
Common Causes for Rejection 
  • A specimen for viral NGS is considered unsatisfactory (UNSAT) and discarded if it does not meet specimen submission and/or shipping guidelines (e.g., arrives at the Laboratory at ambient temperature). 
  • Incorrect specimen collection or submission methods (e.g., missing required patient identifiers)
  • Insufficient specimen volume
  • Leaked in transit
  • Mixed specimen/contamination
  • Incorrect storage conditions 
  • Expired reagents/media/collection container
  • Discrepancies between submission form/line list and specimen label
  • Missing/incomplete/illegible submission form
Additional Information
  • ID-19/ SARS-CoV-2 NGS Specimen Collection and Submission Instructions and Microbiology Laboratory line list for Mpox/HMpxV specimens are available from the Sequencing Team.
  • Please request via email at wgs.dshs@dshs.texas.gov.