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

BackgroundTürkiye 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.MethodsWe 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.ResultsTürkiye’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.ConclusionThis 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

Nickel Sensitivity in Patients With Irritable Bowel Syndrome

Aim: Nickel (Ni) is the most common contact allergen in the population. We aimed to investigate whether there is a relationship between Ni sensitivity and irritable bowel syndrome (IBS) in our study.Materials and methods: This study was conducted in 50 patients with IBS who were followed up between March 2018 and July 2018, and 40 healthy people as a control group in a single center with a dermatology department. European standard contact allergen series Ni preparate and corticosteroid pomace were applied to the back region of the study subjects. The evaluation was performed at 48, 72, and 96 hours according to the scheme proposed by the International Contact Dermatitis Research Group (ICDRG). Those who reacted at 72 hours were considered to have Ni allergy.&nbsp;Results: The female/male ratio was 24/26 and 18/22 in the patient and control groups, respectively. The mean ages of the patient and control groups were 42.82 (±10.65) and 39.77 (±11.21) years, respectively. Ni sensitivity was present in 40% of the patient group and 17.5% of the control group (p=0.03).Conclusion: We believe that the presence of Ni sensitivity is important in the pathogenesis of IBS disease. In our study, Ni sensitivity was found to be quite high in IBS patients compared to the normal population.</p

Assessment of the Relationship Between Neutrophil-Lymphocyte Ratio and Dyspeptic Symptoms in Patients With Peptic Ulcer Diagnosed by Endoscopy and Patients Without Peptic Ulcer

Introduction: Neutrophil-lymphocyte ratio (NLR), a simple, inexpensive, and effective biomarker associated with various inflammatory and neoplastic diseases, has become the focus of attention in recent years. Nevertheless, it has not been adequately studied in dyspeptic patients with peptic ulcer (PU) and without PU, i.e., patients with non-ulcer dyspepsia (NUD).Materials and methods: The population of this retrospective study consisted of patients with dyspeptic complaints who underwent esophagogastroduodenoscopy between April 2023 and June 2023. A total of 180 patients included in the study sample were categorized into two groups based on the endoscopy results: patients without PU or NUD patients (Group 1) and those with PU (Group 2). Age, gender and pre-procedural NLR data, upper gastrointestinal endoscopy results, and the presence of&nbsp;Helicobacter pylori&nbsp;(Hp) in endoscopic biopsy information were recorded for all patients.Results: Of the 180 patients, 140 were diagnosed with NUD (Group 1), and 40 were diagnosed with PU (Group 2). There was a significant difference between Groups 1 and 2 in terms of NLR (Group 1: 2.5±1.8 vs. Group 2: 3.6±3.7, p=0.014). There was also a significant difference in NLR between Group 1 and Group Gastric Ulcer (p=0.030) but not between Group 1 and Group Duodenal Ulcer (p=0.064). Rates of patients with positive Hp&nbsp;test results were 25% and 32.5% in Groups 1 and 2, respectively, indicating a significant difference between the groups (p=0.026).Conclusion: The NLR measured in patients who presented with dyspeptic complaints was found to be significantly higher in PU patients than in NUD patients. The elevated NLR levels were even more evident in PU patients with GU compared to PU patients with DU.</p