Assessment of Nucleic Acid Extraction Kits for SARS-CoV-2 Surveillance in Wastewater Samples

Year 2025, Volume: 15 Issue: 1, 241 - 251

Ahmet Sait , Serol Korkmaz , Ayşe Parmaksız , Bülent Bayraktar , İsmail Aslan

https://doi.org/10.31020/mutftd.1571019

Abstract

Objective: The aim of this study is to evaluate the effectiveness of three commercial nucleic acid extraction kits (kit A, B and C) in isolating SARS-CoV-2 viral RNA from wastewater samples.
Method: In this study, water samples were collected in March 2021 from three wastewater treatment plants located in different parts of Istanbul, and it was confirmed that they were negative for SARS-CoV-2. Different concentrations of the SARS-CoV-2 virus, previously inactivated at the BSL-3 laboratory of the Pendik Veterinary Control Institute, were added to the wastewater samples. RNA extraction and quantification were performed using commercial nucleic acid extraction kits and and RT-qPCR kit specific to SARS-CoV-2.
Results: At the end of the study, it was determined that kit C yielded the highest total RNA and produced more consistent results, significantly outperforming the other two kits in terms of RNA yield and purity. Statistical analysis revealed significant differences in RNA concentrations (p < 0.05) and gene copy numbers (p < 0.01) between the kits, and kit C demonstrated superior linearity and reproducibility.
Conclusion: According to the findings, although all three evaluated kits are suitable for detecting SARS-CoV-2 RNA in wastewater samples, kit C provides the most efficient and reliable performance, especially for high-throughput studies. Additionally, this study highlights the importance of selecting appropriate nucleic acid extraction methods for wastewater surveillance, which serves as an early warning system for outbreaks that threaten public health.

Keywords

Nucleic Acid Extraction, SARS-CoV-2, Surveillance, Wastewater

Atıksu Örneklerinde SARS-CoV-2 Sürveyansı için Nükleik Asit Ekstraksiyon Kitlerinin Değerlendirilmesi

Abstract

Amaç: Çalışmanın amacı, atık su numunelerinden SARS-CoV-2 virus RNA'sını izole etmek amacıyla üç ticari nükleik asit ekstraksiyon kitinin (kit A, B ve C) etkinliğini değerlendirmektir.
Yöntem: Çalışmada, 2021 yılı Mart ayında İstanbul ilinde farklı lokasyonlardaki üç atık su arıtma tesisinden su numuneleri toplandı ve SARS-CoV-2 virusu yönünden negatif olduğu teyit edildi. Pendik Veteriner Kontrol Enstitüsü'ndeki BSL-3 laboratuvarında daha önce inaktive edilmiş olan SARS-CoV-2 virusunun farklı konsantrasyonları atık su numunelerine eklendi. Ticari nükleik asit ekstraksiyon kitleri ve SARS-CoV-2 RT-qPCR kiti kullanılarak sırasıyla RNA ekstraksiyonu ve kantitasyonu gerçekleştirildi.
Bulgular: Çalışma sonunda, kit C’nin en yüksek toplam RNA'yı verdiği ve daha tutarlı sonuçlar ürettiği, RNA verimi ve saflığı açısından diğer iki kitten önemli ölçüde daha iyi performans gösterdiği belirlendi. İstatistiksel analiz, kitler arasında RNA konsantrasyonlarında (p < 0,05) ve gen kopya sayılarında (p < 0,01) önemli farklılıklar olduğunu ortaya koydu. Kit C’nin üstün doğrusallık ve tekrarlanabilirliğe sahip olduğunu gösterdi.
Sonuç: Elde edilen bulgular, değerlendirilen üç ticari kitin de atık su numunelerinde SARS-CoV-2 RNA'sını tespit etmek için uygun olduğunu göstermektedir. Ancak özellikle kit C, yüksek verimli çalışmalar için en etkili ve güvenilir performansı sunmaktadır. Ayrıca bu çalışma, halk sağlığını tehdit eden salgınlar için erken uyarı sistemi işlevi gören atık su gözetiminde, uygun nükleik asit ekstraksiyon yöntemlerinin seçilmesinin önemini vurgulamaktadır.

Keywords

Atıksu, Nükleik Asit Ekstraksiyonu, SARS-CoV-2, Sürveyans

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