While molecular methods like quantitative polymerase chain reaction (qPCR) are traditionally used for detection of SARS-CoV-2, targeted next-generation sequencing (NGS) provides complementary data down to the variant level, which is crucial when it comes to epidemiology investigations. Innovations in NGS and associated bioinformatics enable a growing number of applications that seek to answer the most critical questions regarding disease spread, origins, evolution, and virulence. Moreover accessible, streamlined, automated workflows now allow even method-naïve researchers to conduct complex studies and obtain actionable results.
In this podcast, Anjali Shah, Senior Director of Product Management at Thermo Fisher Scientific, discusses the benefits of using NGS to study SARS-CoV-2, as well as lessons learned thus far from SARS-CoV-2 epidemiology. This podcast was first available through Biocompare on December 14, 2020.
— Podcast transcript —
Tamlyn Oliver (TO): Hi everyone, welcome to Biocompare’s tech insights podcast where we speak to scientific experts about new technology that can help advance your research and optimize your workflows. I’m Tamlyn Oliver, managing editor of Biocompare. Today’s guest is Dr. Anjali Shah, Sr. Director of Product Management at Thermo Fisher Scientific. Dr. Shah led the development program that led to the culminated with the launch of the Ion AmpliSeq™ SARS-CoV-2 research panel. Thanks for joining us today, Dr. Shah.
Anjali Shah (AS): Happy to be here, thank you so much for the invitation.
TO: You’re welcome, I have quite a few questions for you, so let’s get started.
TO: Can you talk about the differences in use between qPCR and NGS when it comes to studying and detecting SARS-CoV-2?
AS: Absolutely. So qPCR and NGS are 2 primary technologies that are used for infectious disease.
AS: qPCR is a technology that allows you to do detection, to let you know if the virus is present or not in a sample.
AS: NGS complements qPCR. What it allows you to do is study the epidemiology of the virus which can inform the mutations and how they impact host response, the evolution of virus across regions and species, and the impact to future vaccines and therapeutic development. NGS complements qPCR by allowing you to study the epidemiology of the virus to better understand the cause and spread of the disease, to determine the factors underlying disease risk, and ultimately to develop method for their control
TO: Some people will argue that NGS is too expensive or too complex for routine epidemiology studies. How do you counter those arguments?
AS: As I mentioned before, epidemiology studies are critical for us to understand disease phenotypes and viral strain evolution for future therapy development. Especially in the case of coronavirus, cost is irrelevant compared to the almost 64M people infected with this virus and to major socioeconomic impact it has had on every country in the world. But for those who are still concerned in general about the “cost of NGS adoption”, whether it be related to complex sample processing workflow or bioinformatics expertise for data interpretation, the Ion Torrent™ portfolio has solved for those issues. Our platforms incorporate automation for fewer user touchpoints and innovative technological advancements for faster turnaround times. Such innovation allows you to rapidly go from specimen to results in as little as 24 hours.
TO: How can NGS address challenging sample types where there are low virus amounts present?
AS: yeah, that’s a great question. So, the answer lies within our flagship Ion AmpliSeq™ technology. This technology is a targeted resequencing approach, based on highly multiplexed amplification. You can imagine that when various sample types are collected for coronavirus testing, they all consist of mixture of human nucleic acid and viral nucleic acid. So, the facet of our technology allows us to amplify just the virus and analyze that without the complexity of the human material present in the sample. That feature allows us to work with challenging samples that have low amounts of viral copies, and in conjunction with the Ion Torrent sequencing workflow, to analyze and accurately identify critical variants. This higher resolution and limit of detection provides critical information for viral surveillance and contact tracing.
TO: What are the implications of knowing all viral variants?
Viral variants provide information on viral evolution rate, disease severity or risk, and inform the development of comprehensive therapies or vaccines to limit the spread of the virus across hosts. Many of the viral variants typically are single nucleotide polymorphisms, or SNPs, and hence high sensitivity and specificity of the technology in identifying those changes is paramount. This is where the Ion Torrent technology particular shines amongst the NGS technologies in the market.
TO: What are the “lessons learned” thus far from SARS-COV-2 epidemiology that will help us with future resurgence of the virus or other pathogens?
AS: We’ve learned quite a bit through these epidemiological studies.
AS: The first is zoonotic transmission events. When the virus spreads, what is its origin and exactly how does it spread across different species, as we’ve heard about suspected transmission events of coronavirus from bats, pangolins, and now most recently minks.
AS: The second is the criticality of contact tracing. Knowing for example that some of them may have a strain that originates from Asia and the others may have a strain that originated from Europe provides clues as to the transmission events and infection risk of the virus across multiple ethnic groups as well as regions.
AS: The third capability we gain from epidemiological studies viral surveillance. We’ve used our solution for SARS-CoV-2 sequencing to look at wastewater, and interestingly, the virus is present in stool samples. So by measuring wastewater, you can get an idea, not only of the prevalence of the virus in the population but also what strains are appearing or disappearing in those populations in a given period of time and what may be the causative events.
AS: Finally, to control or limit any future resurgence of any virus or pathogen, viral evolution studies are essential. How quickly does the virus change over time and how does that impact disease risk and host response. So this information really guides us on not only how frequently we need to monitor for the virus in the community but also about future therapies for individuals who do have symptoms of a more severe scale and comprehensive vaccine development that is required to protect us against any future resurgence.
TO: Thanks Dr. Shah for taking the time to talk to us and for your thorough and informative answers to our questions. For a more in depth review of the benefits of using NGS in epidemiological workflows, please read the related article, “Rapid, Automated Nucleic Acid-to-Variant Report Solution for SARS-CoV-2 Epidemiology Applications”. And thanks so much for listening. For more information on products, technologies and the latest scientific advancements, please visit biocompare.com. Have a great day.
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Learn about Ion AmpliSeq SARS-CoV-2 Research Panel, a rapid, automated NGS solution to survey the complete SARS-CoV-2 genome for epidemiological investigation