Coronavirus Disease 2019 (COVID-19) - Variant of Concern Screening and Whole Genome Sequencing Surveillance

Updates:

• As of February 6, 2023, SARS-COV-2 (COVID-19) Variant of Concern (VOC) PCR will no longer be performed at Public Health Ontario’s laboratory as this test no longer has any clinical, epidemiological or public health utility. Requests for COVID-19 VOC test will be rejected.
• Specimens for representative surveillance will continue to be sequenced, see section below.

As of November 12, 2021 PHO’s laboratory is 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. 

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.