Understanding Covid-19 variants

Andy Felton on sequencing the SARS-CoV-2 genome to identify variants and inform community action

The Covid-19 public health crisis has continued to evolve since cases first began spreading. Although it was initially believed that mutations would have little impact on how the virus spreads, researchers quickly learned this was not the case. There are now thousands of different variants circulating around the world, some containing between 15-30 distinct mutations, with new strains becoming increasingly infectious due to selective pressures. The Delta variant, one of the latest prominent threats, is reportedly five times more infectious than the original strain and is now responsible for 93% of cases across the USA, according to the Centers for Disease Control and Prevention (CDC).

As new strains continue to emerge, there is an urgent need to understand not only if patients are Covid-19 positive or negative, but also what strain they are infected with to inform public health responses. While global surveillance efforts are underway, there is also a need at the community level for rapid, cost-effective SARS-CoV-2 surveillance to help local public health officials quickly identify any potential outbreaks and make real-time, data-driven decisions on guidelines such as business openings, access to recreational sites and in-person learning.

Monitoring for variants

Over the past year, we’ve seen rapid innovation and iteration in molecular technologies to try and gain a better understanding of Covid-19. In addition to the PCR tests used for diagnosis and population-scale screening, a dire need exists to ramp up viral genome sequencing to understand and track how SARS-CoV-2 is mutating. Next-generation sequencing (NGS) offers the full picture of the SARS-CoV-2 genome, capturing mutations across the virus to identify if a sample represents a new or known variant.

The CDC has announced that rapid genetic sequencing will be part of its overall strategy for managing this pandemic, and researchers globally are getting involved to provide more comprehensive sequencing coverage. To that end, Thermo Fisher Scientific has been working closely with many of these labs since the spring of 2020 to sequence millions of samples.

As one example, Thermo Fisher helped North Carolina-based reference lab Mako Medical quickly ramp up NGS testing capacity in partnership with the CDC to identify emerging SARS-CoV-2 variants. Equipped with Thermo Fisher’s high-capacity sequencing platforms, Mako is sequencing samples from 43 states and has the capacity to process 6,000 positive Covid samples a week. With new variants emerging, Mako is working with the CDC to increase awareness of what variants are circulating and monitoring new variants as they appear. The firm has observed 55 different lineages since May 2021, and is currently sequencing nearly all positive samples. In addition, with vaccinations increasing, the company is regularly asked by state health departments to sequence specific samples from “breakthrough” infections in people who have been fully vaccinated to gain a better understanding of vaccine efficacy against new and emerging variants of concern.

In the UK, Oncologica, a private precision oncology lab, worked with Thermo Fisher to pivot from cancer sequencing to SARS-CoV-2 sequencing. With this new capability, Oncologica is partnering with the International Travel Testing Programme to sequence positive samples from international travellers arriving in the country to better understand how variants are moving across borders.

To continue to support these programs and the need for real-time insights, Thermo Fisher introduced the Ion Ampliseq SARS-CoV-2 Insight Research Assay, a highly sensitive assay for sequencing SARS-CoV-2 samples, including those samples with lower viral loads.

New innovations support smarter tracking

The Ion AmpliSeq SARS-CoV-2 Insight Research Assay leverages a targeted sequencing approach that yields improved coverage and uniformity from samples previously inaccessible by NGS. Given SARS-CoV-2 is mutating so rapidly, it is hard to predict where the next mutation is going to occur; labs need a tool that doesn’t exclude regions of the SARS genome based on existing known mutations, but instead provides a complete picture of the virus’ genetic makeup. By sequencing more than 99% of the SARS-CoV-2 genome, including all known serotypes, the assay provides increased resilience against the impact of new and emerging mutations.

The company designed the assay knowing public health authorities and healthcare systems need rapid, real-time insights to understand the appearance and transmission of new variants within the population and take action within their communities to limit their spread. As part of a fast, automated NGS workflow, the new assay produces results in under a day. Optimised to run on the Ion GeneStudio S5 System* and the Ion Torrent Genexus System, the assay includes 237 amplicons specific to SARS-CoV-2, with the addition of variant-tolerant primers for emerging variants.

The new assay is ideally suited for sequencing samples of both symptomatic and asymptomatic individuals, including samples of those who have been vaccinated and may be experiencing a breakthrough infection. By offering a high level of sensitivity, researchers can better understand asymptomatic infections in which there’s a lower viral load and also identify strains with variants of concern that may impact vaccine performance.

In addition, the increased sensitivity of this assay will empower researchers to discover new variants from a variety of sample types, including nasopharyngeal and shallow nasal swabs and saliva, with cycle threshold (Ct) values higher than 28 and as low as 50 viral copies. In Mako’s lab, samples with Ct values between 29 and 35 represent 15-20% of their samples – without the sensitivity of this assay, these would have to be discarded.

As global researchers, public health organisations and reference laboratories prepare for what is potentially another wave of increasing cases, tools such as the Ion AmpliSeq SARS-CoV-2 Insight Research Assay are essential to quickly understand how variants of concern are spreading and when emerging mutations arise. Tracking known and new strains is not only important to public health policies, but will also inform development of vaccine boosters and use of treatments moving forward.

More widespread adoption of NGS is critical to ending the current Covid-19 global pandemic and has the potential to revolutionise public health. Coronavirus is not the only infectious disease capable of rapidly spreading around the globe, and ongoing surveillance is necessary for SARS-CoV-2 and other viruses that may emerge in the future.

Andy Felton is vice president of product mangement at Thermo Fisher Scientific.

* For Research Use Only. Not for use in diagnostic procedures.

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