Guthrie Jennifer L, Teatero Sarah, Zittermann Sandra, Chen Yao, Sullivan Ashleigh, Rilkoff Heather, Joshi Esha, Sivaraman Karthikeyan, de Borja Richard, Sundaravadanam Yogi, Laszloffy Michael, Heisler Lawrence, Allen Vanessa G, Simpson Jared T, Fittipaldi Nahuel
Public Health Ontario, 661 University Ave, Toronto, Ontario, M5G 1M1, Canada.
Public Health Agency of Canada, Ottawa, Ontario, Canada.
J Clin Virol Plus. 2021 Jun;1(1):100010. doi: 10.1016/j.jcvp.2021.100010. Epub 2021 Mar 22.
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.
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.
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.
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.
与旅行相关的严重急性呼吸综合征冠状病毒2（SARS-CoV-2）传播仍在推动全球大流行。据报道，一种新的SARS-CoV-2谱系（B.1.177）于2020年夏天在西班牙出现，随后在欧洲的传播与受感染个体的旅行有关。通过全基因组测序（WGS）进行监测，有助于深入了解SARS-CoV-2等病原体在全球和本地的传播情况，并能检测到新变种的引入。
我们分析了安大略省公共卫生部门（2020年9月6日至10月10日）接收的、用于监测目的的SARS-CoV-2基因组，这些样本来自安大略省东部的个体，构成了研究样本。使用穿山甲软件（v2.08）确定分类谱系，并进行系统发育分析，纳入与研究样本同一时期的公开可用基因组。将从实验室申请单和标准法定报告疾病病例调查中收集的流行病学数据纳入分析。
基因组监测在2020年9月下旬发现安大略省东部一名个体感染了SARS-CoV-2谱系B.1.177的新冠肺炎病例。该个体最近从欧洲返回。与公开可用数据进行的基因组分析表明，与此样本最密切相关的基因组来自南欧。基因组监测未发现该谱系的其他病例。
基因组监测能够早期发现安大略省一种被认为与旅行相关的新型SARS-CoV-2谱系。这种基于基因组的监测是衡量公共卫生措施有效性的关键工具，例如针对归国旅行者的强制自我隔离措施，旨在防止新引入的SARS-CoV-2谱系进一步传播。
