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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples

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SARS-CoV-2: Comparative analysis of different RNA extraction methods.

Cecilia Ambrosi¹, Carla Prezioso², Paola Checconi¹

¹San Raffaele Roma Open University, 00166 Rome, Italy; IRCCS San Raffaele Pisana, 00166 Rome, Italy.

Journal of Virological Methods

|November 7, 2020

Summary

This study compared RNA extraction methods for SARS-CoV-2 detection. Several commercial kits and an in-house protocol showed efficiency for COVID-19 diagnosis via rRT-PCR.

Keywords:

Oro- nasopharyngeal swabs RNA extraction SARS-CoV-2 rRT-PCR

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Published on: February 11, 2022

Area of Science:

Virology
Molecular Diagnostics

Background:

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the COVID-19 pandemic.
Reverse-transcription real-time PCR (rRT-PCR) is the gold standard for detecting SARS-CoV-2 genetic material.
Efficient RNA extraction is crucial for accurate rRT-PCR results, and supply chain issues may necessitate alternative methods.

Purpose of the Study:

To compare the efficiency of three commercial RNA extraction kits and one in-house protocol.
To evaluate these methods for SARS-CoV-2 RNA extraction from clinical samples.
To identify suitable alternative RNA extraction protocols to address potential kit shortages.

Main Methods:

Comparison of RNA extraction efficiency using synthetic SARS-CoV-2 ssRNA standards.
Evaluation of extraction methods on oro- and nasopharyngeal swabs from COVID-19 positive patients.
Assessment of RNA yield and suitability for downstream rRT-PCR analysis.

Main Results:

Tested commercial kits demonstrated varying RNA yields but were suitable for SARS-CoV-2 genome detection with modifications.
The in-house protocol using EXTRAzol reagent showed lower efficiency due to its phase separation principle.
Differences in RNA yields were observed among the evaluated commercial kits.

Conclusions:

Commercial RNA extraction kits can be adapted for SARS-CoV-2 detection via rRT-PCR.
Alternative manual RNA extraction methods can be considered for SARS-CoV-2 diagnostics.
The choice of extraction method impacts RNA yield and diagnostic assay performance.