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. 2021 Jun;1(1):100010.
doi: 10.1016/j.jcvp.2021.100010. Epub 2021 Mar 22.

Detection of the novel SARS-CoV-2 European lineage B.1.177 in Ontario, Canada

Jennifer L Guthrie  1 , Sarah Teatero  1 , Sandra Zittermann  1 , Yao Chen  1 , Ashleigh Sullivan  2 , Heather Rilkoff  1 , Esha Joshi  1 , Karthikeyan Sivaraman  1 , Richard de Borja  3 , Yogi Sundaravadanam  3 , Michael Laszloffy  3 , Lawrence Heisler  3 , Vanessa G Allen  1   4 , Jared T Simpson  3   5 , Nahuel Fittipaldi  1   4   6
Affiliations

Detection of the novel SARS-CoV-2 European lineage B.1.177 in Ontario, Canada

Jennifer L Guthrie et al. J Clin Virol Plus. 2021 Jun.

Abstract

Background: Travel-related dissemination of SARS-CoV-2 continues to contribute to the global pandemic. A novel SARS-CoV-2 lineage (B.1.177) reportedly arose in Spain in the summer of 2020, with subsequent spread across Europe linked to travel by infected individuals. Surveillance and monitoring through the use of whole genome sequencing (WGS) offers insights into the global and local movement of pathogens such as SARS-CoV-2 and can detect introductions of novel variants.

Methods: We analysed the genomes of SARS-CoV-2 sequenced for surveillance purposes from specimens received by Public Health Ontario (Sept 6 - Oct 10, 2020), collected from individuals in eastern Ontario, which comprised the study sample. Taxonomic lineages were identified using pangolin (v2.08) and phylogenetic analysis incorporated publicly available genomes covering the same time period as the study sample. Epidemiological data collected from laboratory requisitions and standard reportable disease case investigation was integrated into the analysis.

Results: Genomic surveillance identified a COVID-19 case with SARS-CoV-2 lineage B.1.177 from an individual in eastern Ontario in late September, 2020. The individual had recently returned from Europe. Genomic analysis with publicly available data indicate the most closely related genomes to this specimen were from Southern Europe. Genomic surveillance did not identify further cases with this lineage.

Conclusions: Genomic surveillance allowed for early detection of a novel SARS-CoV-2 lineage in Ontario which was deemed to be travel related. This type of genomic-based surveillance is a key tool to measure the effectiveness of public health measures such as mandatory self-isolation for returned travellers, aimed at preventing onward transmission of newly introduced lineages of SARS-CoV-2.

Keywords: COVID-19; Canada; Ontario; SARS-CoV-2; Whole-genome sequencing.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Fig 1
Fig. 1
Phylogenetic analysis of SARS-CoV-2 genomes from individuals residing in four health administrative units in eastern Ontario, Canada, diagnosed with COVID-19 and submitted to Public Health Ontario from September 6, 2020 through October 10, 2020 (n = 111). Tip points are coloured by lineage (https://github.com/cov-lineages/pangolin).
Fig 2
Fig. 2
Unrooted phylogenetic tree of SARS-CoV-2 genome sequences, randomly selected from the most common B.1 descendant lineages with specimen collection dates of September 6, 2020 through October 10, 2020 (n = 120) and deposited in GISAID (https://www.gisaid.org/) as of November 9, 2020. Included in the tree is the lineage B.1.177 SARS-CoV-2 genome from a specimen collected in Ontario, Canada. Tip points are coloured by location of specimen collection.
See this image and copyright information in PMC

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