PDF(Pubmed)
Abstract：
UNASSIGNED: Türkiye confirmed its first case of SARS-CoV-2 on March 11, 2020, coinciding with the declaration of the global COVID-19 pandemic. Subsequently, Türkiye swiftly increased testing capacity and implemented genomic sequencing in 2020. This paper describes Türkiye\'s journey of establishing genomic surveillance as a middle-income country with limited prior sequencing capacity and analyses sequencing data from the first two years of the pandemic. We highlight the achievements and challenges experienced and distill globally relevant lessons.
UNASSIGNED: We tracked the evolution of the COVID-19 pandemic in Türkiye from December 2020 to February 2022 through a timeline and analysed epidemiological, vaccination, and testing data. To investigate the phylodynamic and phylogeographic aspects of SARS-CoV-2, we used Nextstrain to analyze 31,629 high-quality genomes sampled from seven regions nationwide.
UNASSIGNED: Türkiye\'s epidemiological curve, mirroring global trends, featured four distinct waves, each coinciding with the emergence and spread of variants of concern (VOCs). Utilizing locally manufactured kits to expand testing capacity and introducing variant-specific quantitative reverse transcription polymerase chain reaction (RT-qPCR) tests developed in partnership with a private company was a strategic advantage in Türkiye, given the scarcity and fragmented global supply chain early in the pandemic. Türkiye contributed more than 86,000 genomic sequences to global databases by February 2022, ensuring that Turkish data was reflected globally. The synergy of variant-specific RT-qPCR kits and genomic sequencing enabled cost-effective monitoring of VOCs. However, data analysis was constrained by a weak sequencing sampling strategy and fragmented data management systems, limiting the application of sequencing data to guide the public health response. Phylodynamic analysis indicated that Türkiye\'s geographical position as an international travel hub influenced both national and global transmission of each VOC despite travel restrictions.
UNASSIGNED: This paper provides valuable insights into the testing and genomic surveillance systems adopted by Türkiye during the COVID-19 pandemic, proposing important lessons for countries developing national systems. The findings underscore the need for robust testing and sampling strategies, streamlined sample referral, and integrated data management with metadata linkage and data quality crucial for impactful epidemiological analysis. We recommend developing national genomic surveillance strategies to guide sustainable and integrated expansion of capacities built for COVID-19 and to optimize the effective utilization of sequencing data for public health action.
UNASSIGNED: We tracked the evolution of the COVID-19 pandemic in Türkiye from December 2020 to February 2022 through a timeline and analysed epidemiological, vaccination, and testing data. To investigate the phylodynamic and phylogeographic aspects of SARS-CoV-2, we used Nextstrain to analyze 31,629 high-quality genomes sampled from seven regions nationwide.
UNASSIGNED: Türkiye\'s epidemiological curve, mirroring global trends, featured four distinct waves, each coinciding with the emergence and spread of variants of concern (VOCs). Utilizing locally manufactured kits to expand testing capacity and introducing variant-specific quantitative reverse transcription polymerase chain reaction (RT-qPCR) tests developed in partnership with a private company was a strategic advantage in Türkiye, given the scarcity and fragmented global supply chain early in the pandemic. Türkiye contributed more than 86,000 genomic sequences to global databases by February 2022, ensuring that Turkish data was reflected globally. The synergy of variant-specific RT-qPCR kits and genomic sequencing enabled cost-effective monitoring of VOCs. However, data analysis was constrained by a weak sequencing sampling strategy and fragmented data management systems, limiting the application of sequencing data to guide the public health response. Phylodynamic analysis indicated that Türkiye\'s geographical position as an international travel hub influenced both national and global transmission of each VOC despite travel restrictions.
UNASSIGNED: This paper provides valuable insights into the testing and genomic surveillance systems adopted by Türkiye during the COVID-19 pandemic, proposing important lessons for countries developing national systems. The findings underscore the need for robust testing and sampling strategies, streamlined sample referral, and integrated data management with metadata linkage and data quality crucial for impactful epidemiological analysis. We recommend developing national genomic surveillance strategies to guide sustainable and integrated expansion of capacities built for COVID-19 and to optimize the effective utilization of sequencing data for public health action.
摘要：
■Türkiye于2020年3月11日确认了首例SARS-CoV-2病例，恰逢宣布全球COVID-19大流行。随后，Türkiye迅速提高了测试能力，并在2020年实施了基因组测序。本文描述了Türkiye作为一个中等收入国家建立基因组监测的旅程，其先前的测序能力有限，并分析了大流行前两年的测序数据。我们强调经历的成就和挑战，并总结全球相关的经验教训。
我们通过时间表跟踪了2020年12月至2022年2月TürkiyeCOVID-19大流行的演变，并分析了流行病学，疫苗接种,和测试数据。为了研究SARS-CoV-2的系统动力学和系统地理方面，我们使用Nextstrain分析了来自全国七个地区的31,629个高质量基因组。
■Türkiye的流行病学曲线，反映全球趋势，有四个不同的波浪，每个都与关注变体(VOC)的出现和传播相吻合。利用当地制造的试剂盒来扩大测试能力，并引入与一家私营公司合作开发的变体特异性定量逆转录聚合酶链反应（RT-qPCR）测试是Türkiye的战略优势，考虑到疫情早期的稀缺性和支离破碎的全球供应链。到2022年2月，Türkiye为全球数据库贡献了86,000多个基因组序列，确保了土耳其数据在全球范围内得到反映。变体特异性RT-qPCR试剂盒和基因组测序的协同作用使得能够经济有效地监测VOC。然而,数据分析受到弱测序采样策略和零散数据管理系统的限制，限制测序数据的应用，以指导公共卫生应对。系统动力学分析表明，尽管旅行受到限制，但Türkiye作为国际旅行中心的地理位置影响了每种VOC的国家和全球传播。
本文提供了有关Türkiye在COVID-19大流行期间采用的测试和基因组监测系统的宝贵见解，为发展国家体系的国家提供重要的经验教训。这些发现强调了对稳健测试和抽样策略的需求，简化的样本推荐，以及具有元数据链接和数据质量的集成数据管理对于有效的流行病学分析至关重要。我们建议制定国家基因组监测战略，以指导为COVID-19建立的能力的可持续和综合扩展，并优化测序数据的有效利用，以开展公共卫生行动。
我们通过时间表跟踪了2020年12月至2022年2月TürkiyeCOVID-19大流行的演变，并分析了流行病学，疫苗接种,和测试数据。为了研究SARS-CoV-2的系统动力学和系统地理方面，我们使用Nextstrain分析了来自全国七个地区的31,629个高质量基因组。
■Türkiye的流行病学曲线，反映全球趋势，有四个不同的波浪，每个都与关注变体(VOC)的出现和传播相吻合。利用当地制造的试剂盒来扩大测试能力，并引入与一家私营公司合作开发的变体特异性定量逆转录聚合酶链反应（RT-qPCR）测试是Türkiye的战略优势，考虑到疫情早期的稀缺性和支离破碎的全球供应链。到2022年2月，Türkiye为全球数据库贡献了86,000多个基因组序列，确保了土耳其数据在全球范围内得到反映。变体特异性RT-qPCR试剂盒和基因组测序的协同作用使得能够经济有效地监测VOC。然而,数据分析受到弱测序采样策略和零散数据管理系统的限制，限制测序数据的应用，以指导公共卫生应对。系统动力学分析表明，尽管旅行受到限制，但Türkiye作为国际旅行中心的地理位置影响了每种VOC的国家和全球传播。
本文提供了有关Türkiye在COVID-19大流行期间采用的测试和基因组监测系统的宝贵见解，为发展国家体系的国家提供重要的经验教训。这些发现强调了对稳健测试和抽样策略的需求，简化的样本推荐，以及具有元数据链接和数据质量的集成数据管理对于有效的流行病学分析至关重要。我们建议制定国家基因组监测战略，以指导为COVID-19建立的能力的可持续和综合扩展，并优化测序数据的有效利用，以开展公共卫生行动。
