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Comparison of DNA extraction methods for COVID-19 host genetics studies
Ronaldo Celerino da Silva1, Suelen Cristina de Lima1, Wendell Palôma Maria Dos Santos Reis1,2
1Department of Virology and Experimental Therapy (LAVITE), Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil.
Insights
The Chelex®100 resin method is the most cost-effective and efficient for extracting DNA from COVID-19 patient samples. This DNA extraction technique provides high yield and quality, crucial for genetic studies, especially in resource-limited settings.
Area of Science:
- Genetics
- Molecular Biology
- Infectious Diseases
Background:
- The COVID-19 pandemic highlighted global shortages in diagnostic supplies, particularly in developing nations.
- Host genetics are increasingly recognized as a factor influencing COVID-19 severity and outcomes.
- Accurate DNA extraction is fundamental for identifying genetic factors in SARS-CoV-2 infection.
Purpose of the Study:
- To compare the efficacy of three DNA extraction methods for COVID-19 host genetic studies.
- To evaluate methods based on cost, time, DNA yield, quality, and suitability for genetic analysis.
- To identify an optimal DNA extraction strategy for nasopharyngeal samples in COVID-19 research.
Main Methods:
- Comparison of Chelex®100 resin, phenol-chloroform, and QIAamp DNA extraction kit.
- Evaluation of DNA extraction from nasopharyngeal samples of COVID-19 patients.
- Assessment criteria included procedural steps, handling time, DNA quantity, DNA quality, and downstream application compatibility.
Main Results:
- Chelex®100 was the most economical, costing 33x less than the commercial kit and 13x less than phenol-chloroform.
- Chelex®100 yielded significantly more DNA (306x and 69x higher than the kit and phenol-chloroform, respectively).
- This method required fewer handling steps and provided sufficient DNA quality for genetic studies.
Conclusions:
- Chelex®100 resin is a superior method for DNA extraction from COVID-19 nasopharyngeal samples.
- It offers an inexpensive, safe, simple, and fast alternative for genetic research.
- This method is particularly advantageous for developing countries facing material processing constraints.
Abstract:
The coronavirus disease 2019 (COVID-19) pandemic has resulted in global shortages in supplies for diagnostic tests, especially in the developing world. Risk factors for COVID-19 severity include pre-existing comorbidities, older age and male sex, but other variables are likely play a role in disease outcome. There is indeed increasing evidence that supports the role of host genetics in the predisposition to COVID-19 outcomes. The identification of genetic factors associated with the course of SARS-CoV-2 infections relies on DNA extraction methods. This study compared three DNA extraction methods (Chelex®100 resin, phenol-chloroform and the QIAamp DNA extraction kit) for COVID-19 host genetic studies using nasopharyngeal samples from patients. The methods were compared regarding number of required steps for execution, sample handling time, quality and quantity of the extracted material and application in genetic studies. The Chelex®100 method was found to be cheapest (33 and 13 times cheaper than the commercial kit and phenol-chloroform, respectively), give the highest DNA yield (306 and 69 times higher than the commercial kit and phenol-chloroform, respectively), with the least handling steps while providing adequate DNA quality for downstream applications. Together, our results show that the Chelex®100 resin is an inexpensive, safe, simple, fast, and suitable method for DNA extraction of nasopharyngeal samples from COVID-19 patients for genetics studies. This is particularly relevant in developing countries where cost and handling are critical steps in material processing.
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