In a few short months, the 2019 novel coronavirus has grown from a regional virus to a global pandemic, but its distribution is not the only thing that's changed. Viral genomes—particularly those of RNA viruses such as the novel coronavirus—can accumulate mutations extremely rapidly, meaning that the virus underlying each new infection can have subtle variations in its genome.
These mutations, while challenging, provide an opportunity. By identifying and linking viral mutations to observations in geographic origin, infectivity, and symptoms, we can better model how the virus has spread and how it may behave in a given infection. For example, it is believed that, based on genome evaluation, most cases of coronavirus in New York came from Europe. What's more, this offers the potential to guide treatment based on the specific viral strain(s) that are encountered.
However, many methods—such as the quantitative PCR (qPCR) technology underlying most of the viral testing strategies—don't give us this information. So how can we get it?
Molecular fingerprinting of pathogens with next-generation sequencing
Over the last decade, next-generation sequencing (NGS) technologies have gone from uncommon to ubiquitous. While qPCR amplifies a "chunk" of DNA with analysis based on size and/or quantity of amplified material, NGS methods allow DNA to be read directly, nucleotide by nucleotide (i.e., letter by letter).
When analyzing human samples, however, finding the little bit of viral genome among all the human DNA is like finding a needle in a haystack. The infectious disease research group led by Professor Judith Breuer, Director of Pathogen Genomics Unit at the University of College London, developed a virus sequencing approach using Agilent SureSelect target enrichment research technology. Using a SureSelect panel with probes targeting human coronavirus sequences, the researchers can capture the virus sequences from the human samples.
Researchers can then take their NGS sequence data, compare it to known sequences ("reference sequences"), and identify mutations, insertions, or deletions in the virus' genetic code. It's an extremely powerful approach, and Professor Breuer, as one of the researchers leading the charge, has pioneered its application to analyzing pathogens directly from clinical samples.
Giving researchers a new tool in the race to understand SARS-COV-2
Over the past 10 years, Professor Breuer has been an invaluable contributor not just to the field of pathogen research, but to the application of SureSelect technology in infectious disease research. Leveraging the flexible, high-performance SureSelect platform technology, we've worked with Dr. Breuer to release more than 20 pathogen NGS panels as part of the Agilent Community Design Program.
In response to the COVID-19 pandemic, Professor Breuer's group has designed a SureSelect panel to conduct coronavirus sequencing studies on breakout clusters in the UK hospitals. Professor Breuer, as one of the leading scientist in infectious disease research in the UK, became part of the COVID-19 Genomics UK Consortium last month.