Next Generation Sequencing (NGS)

Whole viral genome sequencing of SARS-CoV-2 (2019-nCoV)

• Respiratory tract infections
• COVID-19

a)    Respiratory specimens (nasopharyngeal swab or throat swab).  Volume required ≥ 0.5 mL. 

https://www.canada.ca/en/public-health/services/emerging-respiratory-pathogens/protocol-microbiological-investigations-severe-acute-respiratory-infections-sari.html

- OR – 

b)    Total RNA extracted from a clinical specimen. Volume required ≥ 40 μL

Use sterile swabs and swab the nasal cavity, throat, etc. Place swabs in 2-3 mL viral transport medium.

Keep clinical specimens refrigerated until shipped for testing. Ship on dry ice.  Keep total RNA extracts frozen at -25°C or -80°C. Ship on dry ice.

Shipping of specimens shall be done by a TDG certified individual in accordance with TDG regulations. For additional information regarding classification of specimens for the purposes of shipping, consult either Part 2 Appendix 3 of the TDG Regulations or section 3.6.2 of the IATA Dangerous Goods Regulations as applicable.

Positive for COVID-19

Completed Requisition for SARS-CoV-2 Next Generation Sequencing. The sender's lab name, address, and telephone number must be included for samples to be processed. Also, include identifier (sender lab number), patient date of birth, patient gender, type of specimen, and date collected. Under additional information, please include if possible/applicable: patient travel history and symptoms if known.

N/A

Whole genome sequence quality, variant, and lineage analyses.  Data will be forwarded to the NML Bioinformatics unit for analysis and interpretation.

Next Generation Sequencing of submitted SARS-CoV-2 samples is being carried out as part of a reference and surveillance program. Best efforts will be made to obtain whole genome sequence data for samples submitted however, due to sample complexities this may not be possible. Turnaround times for this service will evolve with the number of samples received and as protocols are formalized. Please contact Ruimin Gao (ruimin.gao@phac-aspc.gc.ca) for more information.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2): Infectious substances Pathogen Safety Data Sheet

National surveillance for Coronavirus disease (COVID-19)

Coronavirus disease (COVID-19): For health professionals

Interim national case definition: Coronavirus disease (COVID-19)

COVID-19 signs, symptoms and severity of disease: A clinician guide

Protocol for Microbiological Investigations of Severe Acute Respiratory Infections (SARI)

Severe Acute Respiratory Infection (SARI) Case Definition

Emerging Respiratory Pathogens

Coronavirus disease (COVID-19)