Epidemiology has been part of infectious disease public health practice for decades. Epidemiologists address questions regarding the origins and transmission of communicable diseases, a pathogen's mutation rate, characterization of new strains, and how existing data can predict the emergence of novel viruses.
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In this podcast, Anjali Shah, senior director of product management at Thermo Fisher Scientific, discusses the benefits of using NGS to study and detect SARS-CoV-2 as well as lessons learned thus far from SARS-CoV-2 epidemiology.
Detection and analysis methods such as quantitative polymerase chain reaction (qPCR) and next-generation sequencing (NGS) play vital roles in molecular epidemiology, which focuses on the contribution of genetics and environmental risk factors in disease spread. These strategies have served public health through acute outbreaks of infectious diseases such as swine flu, Ebola, zika, and most recently, SARS-CoV-2.
Given that three of the top 10 global causes of death (acute lower respiratory infections, diarrheal diseases, and tuberculosis) involve bacterial or viral infection, public health agencies will continue to rely on molecular epidemiology to keep one step ahead of related pathogens.
qPCR has become the go-to method for studies requiring only pathogen detection. However, 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 allow even method-naïve researchers to conduct complex studies and obtain actionable results.
NGS provides insights into pathogen biology that enable retrospective studies on strain emergence and occurrence, contact tracing, outbreak surveillance (including through wastewater analysis), zoonotic transmission, and viral typing through phylogenic analysis.
A pathogen's biology holds the keys to understanding the processes of transmission and strain virulence. For retrospective studies, researchers use biobanked, formalin-fixed, paraffin-embedded (FFPE) samples. NGS facilitates complete genome sequencing of pathogen strains, including all variants and serotypes, by enabling parallel processing of many samples through rapid, automated workflows.
Surveillance is critical for measuring the effectiveness of infection-control strategies. Sequencing of viral samples allows officials to map infection spread and determines the overall rate of positivity in the population. To be effective these analyses must be fast, scalable, and accurate.
NGS also enables monitoring within an environment, including in wastewater, and tracking transmission across species. NGS provides unique advantages in variant analysis and strain identification over defined geographic areas. Zoonotic transmission is of particular interest since it often involves pathogen transmission from a source animal to humans via an intermediate species that does not get sick. NGS identifies these strains and tracks their mutations.
Epidemiologists use phylogenetic analysis to support identification of the initial source of an infection, track geographic spread, and to develop disease control strategies. Several analytic methods support the identification and differentiation of viral variants, although molecular techniques are used most frequently. Sequencing specific variable regions of the viral genome helps determine if certain pathogen variants are phylogenetically related.
NGS has transformed our understanding of SARS-CoV-2, but the method has a reputation for being time-, resource-, and expertise-intensive. Since time is a critical parameter in managing epidemics, NGS has been underutilized in epidemiology.
An ideal NGS workflow should therefore be accessible and easily integrated into a laboratory's existing operations. It should be designed for robustness, to provide consistent results across research groups and geographic locations. Since research objectives change frequently, the method must be adaptable to new challenges and novel approaches to tracking and characterizing infectious agents.
The main consideration in evaluating a new workflow is its value-add versus its direct and indirect costs. Automation has been a huge driver for delivering value through analytical methodologies, particularly for its ability to provide assay consistency and to allow laboratory workers to focus on higher-value activities.
Together, the Ion Torrent™ Genexus™ Integrated Sequencer with the Ion AmpliSeq™ SARS-CoV-2 Research Panel address all significant challenges for adapting NGS to epidemiologic workflows. This rapid, automated NGS solution enables nucleic acid to variant report in about one day, allowing labs to survey the complete SARS-CoV-2 genome at a speed never before possible.
Figure 1. A typical workflow for analyzing 16 samples using the Ion AmpliSeq SARS-CoV-2 Research Panel on the Genexus Integrated Sequencer, featuring rapid NGS automation.
The Genexus Integrated Sequencer, a revolutionary hardware platform for NGS, is accessible even to researchers who are new to sequencing, requiring only two user touch points for an entire experiment without compromising sequence coverage or accuracy.
Figure 2. Comparison of the targeted NGS workflows for SARS-CoV-2 on the Genexus Integrated Sequencer and Company I’s NGS system. The Genexus Integrated Sequencer enables labs to go from nucleic acid to variant report in a single day with minimal user intervention.
The Ion AmpliSeq SARS-CoV-2 Research Panel consists of two pools, with amplicons 125–275 bp in length, which cover more than 99% of the coronavirus genome, including variants and all serotypes.
The complete workflow solution provides rapid turnaround time (about 24 hours) for time-sensitive applications, around five minutes of hands-on time, highly accurate readouts with lower substitution errors for single-nucleotide variants, analysis of samples with viral loads as low as 1ng of RNA, and higher-resolution longer-read sequencing—factors of great relevance to epidemiologic viral typing.
Rapid, automated, accessible NGS helps epidemiologists answer questions regarding virus origins, evolution, and spread in real time.
Ion Torrent technology has already helped trace the virus in a real-world setting. When a patient, his mother, and four healthcare workers showed signs of SARS-CoV-2 infection simultaneously in the pediatric intensive care unit (PICU) at Children's Hospital Los Angeles, hospital officials were understandably concerned about possible transmission between patients and hospital staff.
After verifying infection in these patients, the hospital performed NGS on samples from all six individuals. Not unexpectedly, the mother and child carried nearly identical strains of the virus that originated in Utah, with links to Europe, while the four healthcare workers had strains only distantly related to each other and to the family. This confirmed that there was no transmission between the patient family and the healthcare workers. Most significantly, the hospital determined that the healthcare workers acquired the virus from community spread and not from treating patients.
"The NGS sequence data permitted Children's Hospital Los Angeles to draw definitive conclusions within 48 hours of sample procurement from the six individuals," said Timothy J. Triche, M.D., Ph.D., co-director, Center for Personalized Medicine at the hospital. "This information provided greater confidence in our ability to provide a safe environment for patients and team members."
Thermo Fisher Scientific introduced the Ion Torrent Genexus Integrated Sequencer in November 2019 as a versatile, easily adopted, turnkey platform that delivers the power of NGS to any lab, regardless of NGS expertise. Together with the Ion AmpliSeq SARS-CoV-2 Research Panel, the solution delivers, in about one day, results for surveillance use, mutation dynamics, characterization of new viral strains, the ability to analyze positive samples for common viral lineage, and many other studies supporting viral epidemiology. Through its almost entirely automated workflows, the Genexus Integrated Sequencer ensures lab-to-lab and over-time consistency, while freeing valuable scientific resources for more value-added activities.
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For research use only. Not for use in diagnostic procedures.