Researchers at Karolinska Institutet in Sweden have developed a technology for cost-effective surveillance of the global spread of new SARS-CoV-2 variants. This could help low- and middle-income countries monitor variants in their own borders.
From the beginning of the pandemic, thousands of viral genomes have been sequenced in order to reconstruct the evolution and global spread of the coronavirus. Dependent on these is the identification of particularly concerning variants.
To achieve global surveillance of the SARS-CoV-2 genome, the sequencing and analysis of numerous samples cost-effectively is key. Therefore, researchers in the Bienko-Crosetto laboratory at Karolinska Institutet and Science for Life Laboratory (SciLifeLab) in Sweden have developed a new method, COVseq, that can be used for surveillance of the viral genome on a massive scale at a low cost.
Multiplex PCR (polymerase chain reaction) is used to make more copies of the virus. The samples are then labeled and pooled together in the same sequencing library, using a previous method developed in their 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,” said co-first author Ning Zhang, postdoctoral researcher at the Department of Medical Biochemistry and Biophysics, Karolinska Institutet.
Comparative analyses of 29 SARS-CoV-2 positive samples revealed that COVseq could detect small changes in the genome as well as standard methods. Analysing 245 additional samples, they showed that COVseq could also detect emerging variants of concern well. COVseq’s key advantage 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,” said last author Nicola Crosetto, senior researcher at the Department of Medical Biochemistry and Biophysics, Karolinska Institutet.
Source: Karolinska Institutet
Journal information: COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance. Nature Communications, 23 June 2021, DOI: 10.1038/s41467-021-24078-9