Next-Generation Sequencing: Tracking the Spread and Evolution of SARS-CoV-2

As scientists around the globe work to understand the novel coronavirus, how it spreads and how it evolves, genetic sequencing has provided enormous insight. Since the SARS-CoV-2 virus is an RNA virus, it naturally acquires mutations at a fairly consistent rate. Though many of these mutations do not affect the virus in meaningful ways, they’re extraordinarily important for understanding everything from how it moves through the population globally, to where a person might have been infected locally.

Next-generation sequencing (NGS) is an especially powerful tool for tracking these mutations, and even monitoring a patient’s infection progression and immune response. A key benefit of NGS is the ability to scale. For instance, a sequencing system can simultaneously sequence more than 100,000 samples, even when using identification that focuses on only one or two specific regions from the viral genome and one control region from the human genome.

The use of targeted NGS in COVID-19 research

Integrated DNA Technologies (IDT) has partnered with first-rate research institutions around the world, in an effort to support global efforts to address the COVID-19 pandemic. Researchers at New York University (NYU) Langone have used a targeted NGS method known as hybridization capture to map out regions of viral RNA from patient samples. Hybridization capture is effective as it isolates and thus enriches specific viral RNA from a background of host RNA and other potential pathogens.

The work, led by Dr Adriana Heguy, director of the Genome Technology Center at NYU Langone, used IDT’s xGen™ hybridization capture. Because nasal samples from patients contain not only the viral RNA, but also RNA and DNA from the patient along with other contaminants, it’s necessary to separate out the viral RNA. To do this, the viral RNA is first converted into cDNA and then an NGS library is constructed. Biotinylated oligonucleotide probes, or “baits”, are used, which are pieces of genetic material that hybridize to the cDNA sections of interest.  Probe-bound cDNA library fragments are then captured with streptavidin beads, purified, amplified, and sequenced on an NGS platform.  

Heguy and her team have reported that the first viral genome they sequenced was from a patient from an NYU hospital who had been diagnosed with COVID-19. They obtained a leftover or remnant sample and were not sure that this would be enough to work with. They sequenced hundreds of millions of parts of the sample and found that about 10,000 corresponded to viral genome.

Studying the viral mutations can pinpoint different lineages of the virus and show patterns of its movement both globally as well as locally. Heguy’s team was able to determine that the New York City outbreak likely began two months before testing even started, and that the lineages in the area likely originated in Europe rather than China.

Data sharing in COVID-19 times

The NYU group, along with researchers across the globe, have submitted their sequencing results to the database GISAID EpiFlu, the Global Initiative on Sharing All Influenza Data, which in addition to its regular influenza tracking, now also monitors the evolution of the novel coronavirus. As the database accrues more data, not only can the spread be traced in more detail, but hopefully different lineages can be correlated with clinical research data.

Another research group pioneering in the coronavirus mapping efforts is the ARTIC network, a consortium of researchers at universities and research institutes in the UK and US. The team have made use of the amplicon sequencing method, a type of targeted NGS used for analyzing genetic variation in the viral genome. Amplicon sequencing uses polymerase chain reaction (PCR) primers to amplify the sequences of interest.

After the first SARS-CoV-2 sequence was mapped out and published in December 2019, ARTIC researchers developed a detailed protocol to provide direction for researchers around the world who aimed to quickly and accurately sequence SARS-CoV-2. The protocol features a set of primers for amplicon sequencing, which IDT was able to provide (the ARTIC nCoV-2019 V3 Panel). The protocol and primers were sent to any researcher across the world requesting them, which amounted to 100 research groups in more than 40 countries. This partnership helped build coronavirus sequencing capacity globally, and importantly, ensured the reproducibility of findings, which is critical when making comparisons across regions.

Although NGS methods can save time and costs in the long run, securing all the components can be expensive. To help improve access and affordability, IDT recently launched a program, whose goal is to dissolve barriers to the latest NGS technologies by partnering with researchers who would otherwise not have access to facilities for large-scale genomics projects, including mapping the novel coronavirus as well as other areas of study.

Our inaugural partner was the McDonnell Genome Institute (MGI) at Washington University. The Institute has an impressive history of innovation—among its accomplishments, it was the first to sequence the complete genome of a cancer patient to observe her disease at its genetic roots. The Institute has recently been using a variety of NGS tools to map out the genes and lineages of the novel coronavirus since it emerged.

NGS represents a powerful array of strategies, not just regarding the current viral pandemic, but for numerous other infectious diseases, including Ebola, tuberculosis, and human papillomavirus. Collaboration among institutions is critical, as it hastens the breaking-down of research barriers, and accelerates progress. This is all the more important as we tackle serious existing and emerging diseases across the globe, and support the current and future generations of life scientists in their ground-breaking work.