Emerging coronavirus variants economically monitored with low-cost method

Whole genomic sequencing is used for rapidly tracking viruses in hospitals and communities, as well as to monitor outbreaks in mink farms and other potential hotspots. By sequencing thousands of viral genomes, scientists have traced new coronavirus variants as they emerged, spread, and mutated, including the UK (Alpha), South African (Beta), Brazilian (Gamma), and Indian (Delta) variants. This is vital for identifying threatening variants which may be more contagious, pathogenic, or vaccine resistant.

Reducing the availability of cost-effective and scalable methods for centralised sequencing of hundreds or thousands of samples on a weekly basis would be of great benefit as vaccinations programs proceed. This new technology (COVseq) described in Nature Communications, could be a candidate for cost-effective surveillance of new coronavirus variants.

The main bottleneck towards rapidly detecting emerging SARS-CoV-2 variants is that existing solutions for preparing sequencing libraries from thousands of samples are costly and time-consuming; this is mainly due to the high volumes of reagent necessary, and because a single library must be prepared from each individual sample and quantified pre-sequencing. This new method involves performing reactions in tiny volumes and pooling many samples into a single library for sequencing, using a method previously developed at the Swedish laboratory.

“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 per sample,” says Ning Zhang, a postdoctoral research at Karolinska Institutet and co-first author of the study.

“In contrast, the COVSeq method that we have described here allows constructing highly multiplexed sequencing libraries starting from small volumes of purified RNA samples and it only requires a nanodispensing device to drastically reduce reagent volumes and therefore the cost per sample.”

Comparative analyses of 29 positive coronavirus samples revealed that COVseq had a similar ability as the standard method (NEBNext) to identify small changes in the genome, reaching 95.4 per of concordance between single-nucleotide variants detected by the two methods. Further analyses of 245 samples showed it also performed well at detecting emergent coronavirus variants of potential concern, with just one of 32 single-nucleotide variants in the Alpha, Beta, and Gamma variants falling into a 'dark region' not covered by COVSeq.

The key advantage of COVseq over existing methods for coronavirus surveillance is cost efficiency – including in low-income countries – the researchers explained. It is also versatile, scalable, and immediately applicable in the coronavirus pandemic.

“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 Professor Nicola Crosetto, last author of the paper.