MOLECULAR DIAGNOSTICS :: NEXT-GEN SEQUENCING
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The impact of next-gen sequencing on tracking SARS-CoV-2 variants
By Baha Abdalhamid and Ramin Khaksar T
he evolution of SARS-CoV-2 has been unpredictable. Factors such as inequitable global vaccine dis-
tribution, long-haul COVID-19 among immunocompromised patients, and possible transmission between humans and other mammals, have contributed to the rapid increase in the number of mutations. The continued emergence and spread of new variants reinforce the criti- cal role that genomic sequencing has in the enhanced surveillance of COVID-19. To keep pace with an ever-evolving
virus, efficient identification, and char- acterization in near real-time is critical. There are several ways to achieve this objective. PCR-based methods are ef- ficient and sensitive but are limited in their ability to detect novel disease agents or aggressive mutations of known patho- gens. Additionally, it only offers a binary, presence or absence result.
Next-generation sequencing (NGS) is a promising technology that overcomes these limitations. It is paramount to employ rapid and reliable genomic sur- veillance tools that track viral evolution. Through sequencing, specifically whole genome sequencing (WGS), researchers can determine the novel cause of infection and characterize the pathogen’s genetic material to better understand pathogenic virulence, transmission, susceptibility to antiviral agents, resistance to treatment,
16 MAY 2022
MLO-ONLINE.COM
or vaccine targets aimed at curbing the pandemic.
Unfortunately, NGS methods have traditionally been labor-intensive, expensive, and time-consuming, with sequencers taking several days to generate data along with a significant amount of bioinformatics analysis to interpret meaningful results. This is far too long to have any meaningful impact beyond academic utilization and does not achieve the goal of reducing the im- mediate spread of infection. While these barriers dissuade many laboratories from adopting sequencing technology, there are examples of laboratories incorporat- ing novel approaches to NGS-methods and adapting them for a rapidly changing landscape for infectious disease detec- tion and public health intervention. The Nebraska State Public Health Laboratory (NPHL) is located on the University of Nebraska Medical Campus (UNMC) and is supported by both UNMC as well as the Nebraska Department of Health and Human Services. As the Assistant Direc- tor at NPHL, we knew early-on in the pandemic that, even though sequencing would be time-consuming, it would be integral to monitoring the virus. At the start of the pandemic, NPHL
was approached by a California based start-up, Clear Labs, that developed an automated solution for sequencing.
NPHL piloted the system and was able to increase sequencing by three-fold to approximately 320 samples per week with minimal training, removing the requirement for staff to have expertise in sequencing. The Clear Dx WGS SARS- CoV-2 assay (RUO)* can process extracted RNA for up to 32 clinical samples in one run with a sample to result within 20 hours. The platform does this by automat- ing PCR, library preparation, sequencing, and bioinformatic consensus genome cre- ation (see Figure 1). The adoption of the Clear Labs Clear Dx SARS-CoV-2 WGS platform, and its turnkey approach, is helping NPHL better serve the residents of Nebraska and ensure that the Nebraska public health system has access to inno- vative technology that can help identify and manage future health events. Having an automated system builds laboratory capacity because staff and resources can be re-deployed to other testing needs to respond efficiently and effectively during the pandemic. The NPHL has been able to manage the sequencing workload of the entire State with 5 staff members due to the minimal hands-on time needed to set up a run (20-30 minutes) and the automated bioinformatics pipeline that allows staff to quickly analyze the data for a fast turn-around time for results In addition to sequencing being able to provide information about disease trans-
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