---
title: "Applying RNA-seq to COVID19 clinical samples"
search_description: "Sequencing of the SARS-Cov2 genomes using standard RNA-Seq strategies has been so far mainly achieved using viral culture or BALF, providing adequate viral copies as input template. However, for large-scale surveys of genome mutations, their spread, along with the ability to assess potential co-infections, the analysis of common swab samples with an unbiased RNA-Seq approach is an ideal solution, potentially, for any respiratory infection. "
published: 2024-01-16 10:28:59.228873+00:00
locale: "it"
---

# Applying RNA-seq to COVID19 clinical samples

22 Apr 2020

Sequencing  of the SARS-Cov2 genomes using standard RNA-Seq strategies has been so  far mainly achieved using viral culture or BALF, providing adequate  viral copies as input template. However, for large-scale surveys of  genome mutations, their spread, along with the ability to assess  potential co-infections, the analysis of common swab samples with an  unbiased RNA-Seq approach is an ideal solution, potentially, for any  respiratory infection.

For this reason, we tested the [Tecan Genomics TRIO kit,](https://www.nugen.com/products/trio-rna-seq-library-preparation-kit)  which is capable of yielding sufficient quantities of cDNA from samples  with virtually non-detectable amounts of RNA by utilizing the SPIA  \(single primer isothermal amplification\).

We applied the [TRIO kit](https://www.nugen.com/products/trio-rna-seq-library-preparation-kit)  to total RNA samples extracted from naso-pharyngeal swabs from  SARS-CoV-2 positive patients. Despite the poor quality of the input RNA  extracted from the swabs, we were able to obtain from a large fraction  of them a nearly complete SARS-CoV2 sequence as well as additional  information on bacterial species present in the samples.