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, 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 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.