Countries across the world are doing their best to ensure that their populations are vaccinated against COVID-19. While this may help mitigate the chances of infection of the SARS-CoV-2 coronavirus, monitoring the spread of its variants—especially Variants of Concern (VOC)—is equally important. Now, scientists have reported the development of new technology for the cost-effective surveillance of the global spread of newer variants.
Researchers at the Karolinska Institutet have designed a platform called COVseq that can help generate complex sequencing libraries from hundreds of SARS-CoV-2 samples at a very low cost. The platform was developed by scientists from the Bienko-Crosetto laboratory at Karolinska Institutet and Science for Life Laboratory (SciLifeLab).
"We conclude that COVseq is a versatile and scalable method that is immediately applicable for SARS-CoV-2 genomic surveillance and easily adaptable to other pathogens such as influenza viruses," the authors wrote in the study.
Building A Sequencing Platform
Ever since the COVID-19 pandemic took hold of the world, thousands of viral genomes of the SARS-CoV-2 have been sequenced in order to reconstruct its evolution and global spread. This is crucial as it enables the identification of concerning variants that are highly transmissible and contagious, along with being able to exhibit resistance to existing vaccines. Therefore, an affordable method of bolstering sequencing libraries can help track the worrisome variants of the pathogen.
Sequencing refers to the technique that can evaluate the quantity and sequences of RNA (or DNA) in a sample utilizing a technology known as next generation sequencing (NGS). A sequencing library is a pool of RNA (or DNA) fragments with adapters (short RNA/DNA sequence that is attached to a fragment of interest) affixed.
As a part of the process for developing COVseq, several copies of the SARS-CoV-2's viral genome are produced using a multiplexed PCR (polymerase chain reaction) assay developed by the US Centers for Disease Control and Prevention (CDC). Next, the amplified genome samples are labeled and pooled together within the same sequencing library. This is done employing a method designed at the Bienko-Crosetto lab and has now been adapted for the analysis of SARS-CoV-2.
"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," stated Dr. Ning Zhang, co-first author of the study, in a statement.
High Efficiency and Compatibility
In order to evaluate the efficiency of the new technology, the authors conducted a comparative analysis of 29 COVID-19 positive samples. It was found that COVseq had a similar capacity of a standard library preparation method known as NEBNext. A 95.4 percent of concordance or agreement was achieved between the two methods.
Further analysis of 245 additional samples revealed that COVseq had a very high ability to detect emergent variants of concern (VOC) of the SARS-CoV-2 and compatibility with other sequencing uses for phylogenetic analyses (study of the evolutionary development of an organism).
The most prominent edge that COVseq has over other existing sequencing methods is its 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," noted Dr. Nicola Crosetto, last author of the study.
