Low-Cost Technology Developed for Finding New COVID Variants

Nicola Crosetto, senior researcher at the Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden. Credit: Stefan Zimmerman

Researchers at the Karolinska Institutet in Sweden have developed a technology for cost-effective monitoring of the global spread of novel SARS-CoV-2 variants. (SARS-CoV-2 is the virus that causes COVID-19.) The technique is presented in the scientific journal Nature Communications.

Since the onset of the COVID-19 pandemic, thousands of viral genomes have been sequenced to reconstruct the evolution and global spread of the coronavirus. This is important for the identification of variants of particular concern that are more infectious, pathogenic or resistant to the existing vaccines.

For global surveillance of the SARS-CoV-2 genome, it is critical to sequence and analyze many samples in a cost-effective manner. Therefore, researchers at the Bienko-Crosetto laboratory at Karolinska Institutet and Science for Life Laboratory (SciLifeLab) in Sweden have developed a new method, called COVseq, which can be used for large-scale surveillance of the viral genome at low cost.

First, many copies of the viral genome are made using so-called multiplex PCR (polymerase chain reaction). The samples are then labeled and pooled in the same sequencing library, using a previous method developed in the Bienko-Crosetto laboratory and now adapted for SARS-CoV-2 analysis.

“By running reactions in very small volumes and pooling hundreds of samples in the same sequence library, we could potentially sequence thousands of viral genomes per week for less than $15 per sample,” said Ning Zhang, postdoctoral researcher in the Department of Medical Biochemistry and Biophysics, Karolinska Institutet and co-first author together with PhD students Michele Simonetti and Luuk Harbers in the same department.

Comparative analyzes of 29 SARS-CoV-2 positive samples revealed that COVseq had a comparable ability to the standard method to identify small changes in the genome. Analyzes of 245 additional samples showed that COVseq also had a high ability to detect emerging coronavirus variants of potential concern. The main advantage of COVseq over existing methods is cost effectiveness.

“Our low-cost method could be immediately used for SARS-CoV-2 genomic surveillance by public health agencies and could also be easily adapted to other RNA viruses, such as influenza and dengue viruses,” said Nicola Crosetto, senior researcher at the University of Groningen. Department of Medical Biochemistry and Biophysics, Karolinska Institutet, and last author of the article.

Reference: “COVseq is a cost-effective workflow for massive SARS-CoV-2 genomic surveillance” by Michele Simonetti, Ning Zhang, Luuk Harbers, Maria Grazia Milia, Silvia Brossa, Thi Thu Huong Nguyen, Francesco Cerutti, Enrico Berrino, Anna Sapino, Magda Bienko, Antonino Sottile, Valeria Ghisetti and Nicola Crosetto, June 23, 2021, Nature Communications.
DOI: 10.1038/s41467-021-24078-9

The study was conducted in collaboration with researchers from the ‘Amedeo di Savoia’ Hospital and the Candiolo Cancer Institute in Turin, Italy. The research was supported by grants from the SciLifeLab National COVID-19 Research Program, funded by the Knut and Alice Wallenberg Foundation, and grants from the Swedish Foundation for Strategic Research, as well as private donations from Chiesi Pharma AB and Tetra Pak AB. The authors declare no competing interests.