While next-generation sequencing (NGS) was critical in genomic surveillance during the height of the COVID-19 pandemic, its inability to provide rapid results limited its role in day-to-day diagnostics. A researcher at the Children’s Hospital of Los Angeles is hoping to change that.
By Chris Wolski
Next-generation sequencing (NGS) has become an important tool in genomic surveillance of SARS-CoV-2, which has been critical in identifying new variants and helping to develop a response to the COVID-19 pandemic. However, due to its inherent complexity and skills needed by laboratory personnel to process samples, NGS often has a long turnaround time, making it less effective for rapid diagnosis; a critical need during a pandemic.
CLP recently spoke with Jennifer Dien Bard, PhD, D(ABMM), F(CCM), whose research at the Children’s Hospital of Los Angeles aims to make next-generation sequencing a practical diagnostic tool, about the benefits of next-generation sequencing, how her research is a proof of concept for its practical use as a diagnostic tool, and what the future of NGS testing hold.
Dien Bard is a professor of pathology with clinical scholar designation in the Department of Pathology, Keck School of Medicine at the University of Southern California. She is the director of the Clinical Microbiology and Virology Laboratories and the chief of Academic and Research Development in the Department of Pathology and Laboratory Medicine at Children’s Hospital Los Angeles.
Her responses have been edited for length and clarity.
CLP: Next-generation sequencing is one of the buzzier types of testing—what does it bring to the table that older types of sequencing or other test types don’t?
Jennifer Dien Bard: Next-generation sequencing (NGS) allows for the massively parallel sequencing of DNA fragments and offers the ability to simultaneously detect multiple pathogens, either from culture or directly from a clinical specimen. Massively parallel sequencing is a clear advantage of NGS workflows over a traditional Sanger sequencing approach. You can simultaneously detect multiple pathogens in a clinical specimen at once with NGS rather than investigating potential targets one-by-one. This integrated approach can potentially save lab resources and can lead to quicker turnaround times.
Some major applications of NGS include targeted NGS (tNGS), whole genome sequencing (WGS) and metagenomic NGS (mNGS). In many cases, NGS bypasses the requirement for a priori knowledge of potential pathogens that may be causing the infection, which is another benefit over single-target or multi-target PCR assays. NGS offers discovery power to identify emerging pathogens or strains rather than only looking for what is known. We’ve seen this come into play with the identification of new SARS-CoV-2 variants, which are detected with genomic surveillance using WGS.
NGS can also contribute to outbreak investigation and infection prevention, emerging pathogen discovery, and the detection of resistance determinants to guide antimicrobial selection.
CLP: Your research focused on using NGS in identifying SARS-CoV-2 in children—is there any particular reason why?
Dien Bard: As a Medical Microbiologist that directs the clinical microbiology and virology laboratories in a major pediatric academic medical center, my clinical research focus is on the use of diagnostics for infectious diseases in children. We were early to recognize the important role that children play in the COVID pandemic, particularly as children under the age of 5 remain unvaccinated. We went live with SARS-CoV-2 PCR testing early in March 2020, and we recognized early on the role of NGS, specifically WGS, to identify key viral mutations and to investigate potential outbreak clusters. The bulk of the genomic data available was in the adult population, and we believe that there was a critical piece of the puzzle missing. Our genomic work led to the first report of prolonged COVID infection in immunocompromised children and young adults with a large accumulation of viral mutations.
CLP: You described your work as a “proof of concept”—what are the next steps of making it part of the regular diagnostic menu? How is your approach to NGS going to help increase access to NGS across the healthcare continuum?
Dien Bard: The work that we described in the published manuscript was considered proof of concept because it offered a scenario where NGS can be performed in a clinical microbiology laboratory setting where high-level molecular or NGS experience was not necessary. Automating the library preparation component allowed the test to be defined as moderate complexity rather than high complexity, opening the door for NGS to be performed in clinical laboratories that realistically would not be otherwise able to do it. The use of the automated approach for SARS-CoV-2 WGS was a proof-of-concept and the next steps would be to explore this for other infectious disease pathogens including possibly bacteria and fungi.
CLP: What do you see as the immediate and long-term future of next-generation sequencing?
Dien Bard: The COVID pandemic has highlighted the importance of NGS for infectious diseases in our laboratory. The immediate use of NGS is to continue to increase the generation of genotyping data for SARS-CoV-2 as the COVID pandemic continues and the detection of SARS-CoV-2 followed by WGS is essential for us to understand what variants are circulating in the community and what new variants may be emerging. I recently worked on an Infectious Diseases Society of America (IDSA) and American Society for Microbiology (ASM) consensus review document that discusses the potential clinical and infection prevention applications of SARS-CoV-2 genotyping. Knowing the variant that is causing the infection may allow clinicians to tailor the management and selection of monoclonal antibodies.
Although culture will never fully be replaced by molecular testing, there are studies that demonstrate an increase in pathogen detection and disease diagnosis using next-generation sequencing. To maximize the effect on patient care, NGS must be further integrated into the clinical space, specifically clinical microbiology laboratories, and not be reserved for a small percentage of academic medical centers. The outlook is promising for the use of NGS in the future, but it will require some of those key components that I previously mentioned, specifically automating wet lab protocols and bioinformatic analysis. This will also allow for more widespread implementation and significantly shortened time to report to ensure that the result can be actionable.
Chris Wolski is chief editor of CLP.