SARS-CoV-2 (COVID-19 Virus) Variant of Concern (VoC) Screening and Genomic Sequencing for Surveillance

SARS-COV-2 VoC S-Gene Deletion Screen by Real-Time PCR

Since December 6, 2021 , S-gene target failure (SGTF) has been used in Ontario to identify the Omicron variant.

As of March 13, 2022, approximately 85% of global sequences of Omicron variant specimens sequenced to date possess a deletion at amino acid positions H69 and V70 (S69-70 deletion) within the spike protein. The Thermo Fisher TaqPathTM PCR assay has significantly reduced S-gene target sensitivity, and is negative in the presence of this mutation. Thus a distinct result pattern known as SGTF is observed on the TaqPath real-time PCR platform.

SARS-CoV-2 SGTF is a feature of the BA.1 and several other sublineages of the B.1.1.529 (Omicron) Variant of Concern (VOC) lineage, or more rarely B.1.1.7 (Alpha) VOC. Other lineages, including Variants of Interest (VOIs), may also possess this deletion. However, the sub-lineage BA.2 does not possess the S69-70 deletion in the spike (S) protein so is not detected for SGTF. Other lineages, currently circulating at very low levels, including B.1.617.2 (Delta) VOC and several Variants of Interest (VOI), are also not detected for this deletion.

Combined SGTF and whole genome sequencing (WGS) testing data from Ontario has confirmed that an SGTF positive result is a reliable proxy for B.1.1.529 (Omicron) BA.1 sublineage identification (98.9% sensitivity, 99.9% specificity, 99.5% positive predictive value, 99.7% negative predictive value). As such, since December 20, 2021, WGS has no longer be performed on all SGTF positive specimens, but will be performed on a subset of all eligible SARS-CoV-2 positive specimens regardless of SGTF result in line with the provincial representative sampling proportion.

Due to changes in the provincial testing strategy and to optimize the capacity of our laboratories and turnaround time, on December 30, 2021, PHO discontinued routine SGTF screening of all positive samples and performed SGTF screening on all specimens submitted (Ct ≤ 35) from hospitalized patients, and at least two specimens from each COVID-19 outbreak.
On January 26, 2022, PHO stopped routine SGTF testing of outbreak specimens after finding near universal SGTF presence in outbreak specimens (present in 98% of specimens). As of March 2, 2022, routine SGTF screening was discontinued for hospitalized patients.

SGTF screening is available for outbreaks, other investigations, and individual patients by request when required for clinical or public health management. See submission and instruction notes below for further test ordering information.

SARS-CoV-2 Whole Genome Sequencing for Surveillance

As of November 12, 2021 PHO Laboratory will be randomly selecting a proportion of all SARS-CoV-2 positive specimens, with Ct≤ 30* from the SARS-CoV-2 PCR diagnostic test, for whole genome sequencing (WGS).  This replaces the previous process implemented on May 26, 2021 for sequencing based on the VOC real-time PCR test.

The proportion of selected specimens will be adjusted periodically and determined according to positivity rates, the number of positive specimens, and testing capacity. When capacity allows, up to 100% of eligible specimens will be tested by WGS. This sampling method was first implemented on June 14, 2021, and aims to remove selection bias, provide better representation of known variants for surveillance, and allow improved detection of new emerging variants.

The following link provides the latest summary for SARS-CoV-2 Whole Genome Sequencing in Ontario.

SARS-CoV-2 Whole Genome Sequencing in Ontario

In addition to the selected proportion (if less than 100%), sequencing will be performed on specimens meeting the following criteria:

Routine sequencing:

  1. International travel – all specimens from travelers and contacts will be sequenced if travel is indicated on the COVID-19 diagnostic test requisition. If travel was not indicated on the requisition, testing can be added upon request.

For International travel, sequencing results will be sent as a standard report back to the ordering healthcare provider and to the public health unit for all specimens; however, only VOC lineages will be named on the report. Due to the dynamic nature of non-VOC lineage naming, lineages not currently designated as VOC will be reported back as “Variant of Concern not detected”. Similarly, Variants of Interest (VOIs) will not be identified as such on the laboratory report, nor will the lineage be reported. Descendent lineages of VOCs will be reported as the parent lineage only (e.g. AY.4 Delta descendent lineage reported as B.1.617.2).

As of December 23, 2021 all specimens indicating suspected vaccine breakthrough are no longer routinely sequenced for targeted surveillance. Vaccine breakthrough will continue to be monitored by sequencing through specimens identified as such in the proportional sampling described above.   

Sequencing by request:

  1. Suspected reinfection – sequencing can be requested to support the classification of a case as re-infection that does not meet criteria to be classified as a case of time-based reinfection as outlined in the Ontario COVID-19 Case Definition.
  2. Certain outbreak investigations – sequencing can be requested to support outbreak investigations.

For sequencing by request, the submitter may request a simple lineage-only report or in-depth genomic analysis. If WGS testing is agreed to by the Ontario COVID-19 Genomic Network, submitters should confirm the specimen’s eligibility and availability with the original testing lab and arrange for specimens to be sent to the WGS testing laboratory. Please refer to the SARS-CoV-2 Whole Genome Sequencing Request guidance document and contact IORT@oahpp.ca for support.

* The specimen’s SARS-CoV-2 PCR cycle threshold (Ct) value must be ≤ 30 for successful genome sequencing, although a subset of samples with a Ct ≤ 30 may not be successfully sequenced likely due to variability in determination of Ct values, RNA degradation, or sequencing technical issues.

Specimen Collection and Handling

Specimen Requirements

Test Requested Required Requisition(s) Specimen Type Minimum Volume Collection Kit

SARS-CoV-2 Genomic Surveillance

SARS-CoV-2 PCR-positive specimen

1.5 ml preferred (min 1.0 ml)

Samples should be submitted in screw cap tube (Simport or O-ring, etc) only. Do NOT submit samples in snap cap

Submission and Collection Notes

1

For SGTF requests, accompanying requisitions should indicate “VOC mutation PCR testing requested” and justification for such request in “Other (specify)” or “Outbreak / suspected super spreading event” for outbreak specimens to document the reason for requesting SGTF testing. In addition, enter the outbreak number under “Investigation or Outbreak No.”

2

For travel or suspected reinfection whole genome sequencing requests, if the specimen is at PHO laboratory call Customer Service Centre (416-235-6556 or 1-877-604-4567) or fax the SARS–CoV-2 Variant of Concern Testing/Whole Genome Sequencing Requisition to (416-235-6552) to request to add the test; if the specimen is at another laboratory use the form above to send the specimen to PHO laboratory.

3

For outbreak investigations email IORT@oahpp.ca to complete the request form and obtain approval/WGS-request ID before shipping any specimens. Submitters will receive information on signing up for a secure Incident and Outbreak Response Collaboration SharePoint Site account. This site has been authorized for the transfer of Personal Health Information and submitters will receive the in-depth genomic reports via this site.

Limitations

This laboratory-developed investigational assay is being used for surveillance purposes and public health management. It is not a clinical test.

Preparation Prior to Transport

For SARS-CoV-2-positive specimens being sent to PHO Laboratory for VOC mutation testing, 1.5 mL (minimum volume 1.0 mL) of specimen should be provided and maintained at 2-8°C during transportation (freeze if anticipated transport time to the laboratory is >72 hours).

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

SARS-CoV-2 PCR assay to detect SARS-CoV-2 SGTF) will be tested on specimens that meet acceptance criteria outlined above. Results will be available within 48 hours of receipt at PHO’s laboratory.

If performed, SARS-CoV-2 genome sequencing results will be available within 2-4 weeks.

Reporting

All VOC PCR and WGS results will be reported to the ordering healthcare provider and the local Public Health Unit.

Test Methods

This laboratory-developed investigational assay is being used for surveillance purposes and public health management.

SGTF VOC screening is done using the Thermo Fisher TaqPathTM Assay.

Sequencing involves PCR amplification, followed by sequencing of the majority of the approximately 30,000 base pair SARS-CoV-2 genome. Generated sequences are processed using bioinformatic tools and assigned a Pango lineage using the PANGOLINsoftware package, allowing for the identification of VOC and other lineages.

Algorithm

SGTF screening is available by request when required for clinical or public health management.

WGS Algorithm:

  1. A proportion of all SARS-CoV-2 positive specimens with Ct ≤ 30 will be selected for sequencing
  2. Specimens not already selected for sequencing that meet select conditions (e.g. international travel, outbreak) can be requested to be sequenced

Interpretation

Table 1. SGTF VOC PHO Laboratory result interpretation.

Orf 1a/b gene N gene S gene S Gene Deletion Screen Interpretation Additional Notes
Detected with Ct ≤ 30 Detected with Ct ≤ 30 Not Detected Detected Result consistent with SARS-CoV-2 S gene target failure (SGTF) due to a deletion at amino acid positions 69-70. *
Detected Ct > 30 Detected Ct > 30 Not Detected Inconclusive Inconclusive for SARS-CoV-2 S gene target failure (due to low viral load) * The S gene may not bear the deletion at amino acids 69-70 but be Not Detected due to low viral load in the specimen.
Detected or Not Detected Detected or Not Detected Detected Not Detected No evidence of SARS-CoV-2 S gene deletion at amino acid positions 69-70. *S gene detection is consistent with BA.2 sublineage of B.1.1.529 (Omicron) VOC, B.1.617.2 (Delta) VOC, or other lineages.
One of Orf1a/b or N gene may be detected Or Neither Orf1a/b nor N gene is detected And S gene is not detected. Unable to complete Unable to complete Unable to complete SARS-CoV-2 VOC S gene deletion screening due to failure to detect one of the two additional gene targets in the assay (N or orf1ab) or failure to detect any of the 3 gene targets in the assay (S, N, orf1ab). Detection of both N and orf1ab gene targets is required for documentation of S gene target failure due to a deletion of amino acid positions 69-70. *
Failed to detect internal control Invalid Invalid Test results are uninterpretable due to failed detection of internal control(s). Please resubmit another specimen for testing if clinically indicated.

* Based on current epidemiology, SARS-CoV-2 S gene target failure (SGTF) is consistent with BA.1 sublineage of B.1.1.529 (Omicron) Variant of Concern (VOC) lineage, or B.1.1.7 (Alpha), or other lineages, including Variants of Interest (VOIs), possessing this deletion.

As of March 13, 2022, 85% of global Omicron VOC genome sequences display the deletion at amino acids 69-70 that is responsible for SGTF. S gene detection is consistent with BA.2 sublineage of B.1.1.529 (Omicron) VOC, B.1.617.2 (Delta) VOC, or other lineages.

Data and Analysis

Updated 21 March 2022