Researchers at Karolinska Institutet in Sweden have developed a new method, named COVseq, that can be used for surveillance of the viral genome on a massive scale at a low cost.
For global surveillance of the SARS-CoV-2 genome, it is crucial to sequence and analyze many samples in a cost-effective way. Therefore, researchers in the Bienko-Crosetto laboratory at Karolinska Institutet and Science for Life Laboratory (SciLifeLab) in Sweden have developed the new method. First, many copies of the viral genome are created using so-called multiplex PCR (polymerase chain reaction). The samples are then labelled and pooled together in the same sequencing library, using a previous method developed in the Bienko-Crosetto laboratory and now adapted for SARS-CoV-2 analysis.
“By performing reactions in very small volumes and pooling together hundreds of samples into the same sequencing library, we can sequence potentially thousands of viral genomes per week at a cost of less than 15 dollars per sample,” says Ning Zhang, who previously worked as a postdoctoral researcher at the Department of Medical Biochemistry and Biophysics, Karolinska Institutet and is co-first author together with PhD students Michele Simonetti and Luuk Harbers active at the same department.
Comparative analyses of 29 SARS-CoV-2 positive samples revealed that COVseq had a similar ability as the standard method to identify small changes in the genome. Analyses of 245 additional samples showed that COVseq also had a high ability to detect emergent coronavirus variants of potential concern. The key advantage of COVseq over existing methods is cost-effectiveness.
“Our inexpensive method could immediately be 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,” says Nicola Crosetto, senior researcher at the Department of Medical Biochemistry and Biophysics, Karolinska Institutet, and last author of the paper.
Photo of Nicola Crosetto, senior researcher at the Department of Medical Biochemistry and Biophysics, Karolinska Institutet. Photographer: Stefan Zimmerman