CanCOGeN Next Generation Sequencing (NGS)

Requisition Forms

Reference Details

Description:

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

Test Category:
Sequencing
Pathogen:
SARS-CoV-2
Illnesses and Diseases:
  • Respiratory tract infections
  • COVID-19
Specimen:

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 clinical specimen. Volume required ≥ 40 μL

Collection Method:

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

Specimen Processing, Storage and Shipping:

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.

Transportation of Dangerous Goods:

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.

For additional guidance on the transport of infectious substances in other languages, please click on the link below.

http://www.who.int/ihr/capacity-strengthening/infectious-substances/en/

Patient Criteria:

Positive for COVID-19

Accompanying Documentation:

Completed Requisition for CanCOGeN Next Generation Sequencing. Sender 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. 

Comments:

N/A

Methods and Interpretation of Results:

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

Turnaround Time:

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 Elsie Grudeski (elsie.grudeski@canada.ca) for more information.

Contact:
Phone: (204) 789-2022
Fax: (204) 789-2082
Additional Contacts
Elsie Grudeski
Phone: 204-789-6067
Fax: 204-789-2082
References:
Fact Sheets: