Genomic surveillance during the first two years of the COVID-19 pandemic - country experience and lessons learned from Türkiye

Genomic surveillance during the first two years of the COVID-19 pandemic - country experience and lessons learned from Türkiye

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...

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Published in:Frontiers in public health Vol. 12; p. 1332109
Main Authors: Yalçın, Süleyman, Coşgun, Yasemin, Dedeoğlu, Ege, Kopp, Katharina, Bayrakdar, Fatma, Ünal, Gültekin, Musul, Biran, Sağtaş, Ekrem, Korukluoğlu, Gülay, Raftery, Philomena, Kaygusuz, Sedat
Format: Journal Article
Language:English
Published: Switzerland Frontiers Media S.A 24-05-2024
Subjects:
COVID-19
COVID-19 - epidemiology
Genome, Viral
genomic surveillance
Genomics
Humans
Male
next generation sequencing (NGS)
Pandemics
Public Health
SARS-CoV-2 - genetics
severe acute respiratory syndrome coronavirus 2
COVID-19
next generation sequencing (NGS)
severe acute respiratory syndrome coronavirus 2
public health
genomic surveillance
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Summary: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. 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. 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. 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.
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These authors share senior authorship
Katharina Kopp, https://orcid.org/0000-0001-7261-7470
Gültekin Ünal, https://orcid.org/0000-0002-8996-7028
ORCID: Süleyman Yalçın, https://orcid.org/0000-0003-1434-2717
Edited by: Jin Wang, Fudan University, China
Ekrem Sağtaş, https://orcid.org/0009-0005-3002-6177
Philomena Raftery, https://orcid.org/0000-0002-2683-7154
Biran Musul, https://orcid.org/0000-0002-1241-4783
Gülay Korukluoğlu, https://orcid.org/0000-0001-7625-6350
Reviewed by: Abdul Ahad, National Institute of Health (Pakistan), Pakistan
Sedat Kaygusuz, https://orcid.org/0000-0003-3245-6582
ISSN:2296-2565
2296-2565
DOI:10.3389/fpubh.2024.1332109