Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties 'G. D'Alessandro', University of Palermo, Italy.
Clinical Epidemiology Unit and Regional Reference Laboratory of Western Sicily for the Emergence of COVID-19, University Hospital 'P. Giaccone', Palermo, Italy.
J Glob Health. 2024 Jul 5;14:05017. doi: 10.7189/jogh.14.05017.
The implementation genomic-based surveillance on emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in low-income countries, which have inadequate molecular and sequencing capabilities and limited vaccine storage, represents a challenge for public health. To date, there is little evidence on molecular investigations of SARS-CoV-2 variants in areas where they might emerge. We report the findings of an experimental SARS-CoV-2 molecular surveillance programme for migrants, refugees, and asylum seekers arriving to Europe via Italy through the Mediterranean Sea.
We descriptively analysed data on migrants collected at entry points in Sicily from February 2021 to May 2022. These entry points are integrated with a network of laboratories fully equipped for molecular analyses, which performed next-generation sequencing and used Nextclade and the Pangolin coronavirus disease 2019 (COVID-19) tools for clade/lineage assignment.
We obtained 472 full-length SARS-CoV-2 sequences and identified 12 unique clades belonging to 31 different lineages. The delta variant accounted for 43.6% of all genomes, followed by clades 21D (Eta) and 20A (25.4% and 11.4%, respectively). Notably, some of the identified lineages (A.23.1, A.27, and A.29) predicted their introduction into the migration area. The mutation analysis allowed us to identify 617 different amino acid substitutions, 156 amino acid deletions, 7 stop codons, and 6 amino acid insertions. Lastly, we highlighted the geographical distribution patterns of some mutational profiles occurring in the migrants' countries of origin.
Genome-based molecular surveillance dedicated to migrant populations from low-resource areas may be useful for forecasting new epidemiological scenarios related to SARS-CoV-2 variants or other emerging pathogens, as well as for informing the updating of vaccination strategies.
在分子和测序能力不足且疫苗储存有限的低收入国家,对新兴的严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 变体实施基于基因组的监测对公共卫生而言是一个挑战。迄今为止,关于这些地区可能出现的 SARS-CoV-2 变体的分子调查结果很少。我们报告了一项针对通过地中海抵达欧洲的移民、难民和寻求庇护者的 SARS-CoV-2 分子监测计划的结果。
我们对 2021 年 2 月至 2022 年 5 月西西里岛入境点收集的移民数据进行了描述性分析。这些入境点与一个完全具备分子分析能力的实验室网络相整合,该网络进行了下一代测序,并使用 Nextclade 和 Pangolin 冠状病毒病 2019 (COVID-19) 工具进行谱系/分支分配。
我们获得了 472 条全长 SARS-CoV-2 序列,并鉴定出 12 个独特的分支,属于 31 个不同的谱系。德尔塔变异株占所有基因组的 43.6%,其次是 21D 分支(Eta)和 20A 分支(分别为 25.4%和 11.4%)。值得注意的是,一些鉴定出的谱系(A.23.1、A.27 和 A.29)预计将被引入到移民地区。突变分析使我们能够识别出 617 种不同的氨基酸取代、156 种氨基酸缺失、7 个终止密码子和 6 种氨基酸插入。最后,我们强调了一些发生在移民原籍国的突变特征的地理分布模式。
针对低资源地区移民人群的基于基因组的分子监测对于预测与 SARS-CoV-2 变体或其他新出现的病原体相关的新的流行病学情况以及为更新疫苗接种策略提供信息可能是有用的。