New Technology Offers Cost-Effective Method for Finding New SARS-CoV-2 Variants

Researchers have developed a technology for cost-effective surveillance of the global spread of new SARS-CoV-2 variants.

The new method, named COVseq has been developed by researchers in the Bienko-Crosetto laboratory at Karolinska Institutet and Science for Life Laboratory (SciLifeLab; (Stockholm, Sweden) and can be used for surveillance of the viral genome on a massive scale at a low cost.


First, many copies of the viral genome are created using so-called multiplex PCR (polymerase chain reaction). The samples are then labeled 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. 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.

“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,” said Ning Zhang, co-first author of the paper.

“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,” added Nicola Crosetto, senior researcher at the Department of Medical Biochemistry and Biophysics, Karolinska Institutet, and last author of the paper.

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