As summer fades into the rearview mirror, we now find ourselves at a pivotal juncture in the year. Cold and flu season is among us, as is our ongoing battle against new variants of SARS-CoV-2.

In September 2023, the Centers for Disease Control and Prevention (CDC) announced $262 million in funding to support the detection, response to, and mitigation of public health emergencies.1 That same month, the Food and Drug Administration (FDA) approved and authorized an updated COVID-19 booster.2 This recent surge in activity from two leaders in public health heralds a new chapter in our collective commitment to understanding and combating infectious disease.

In this blog post, we’ll recap the evolution of COVID-19 research and shed light on the critical role of NGS library prep in shaping the future of how we detect and surveil this infectious disease.

Initial Phase of COVID Research

In the first few years of the pandemic, COVID-19 research primarily revolved around strain tracking. To this point, in April 2022, seqWell highlighted the work of Frank Middleton, PhD, professor and director of the Molecular Analysis Corps at SUNY Upstate Medical University.

Dr. Middleton utilized a sequencing platform to examine samples, which were collected on a statewide basis in a large fashion. By leveraging our transposase-based library prep technology, his team was able to monitor the divergence of the COVID virus and found more than 50 mutations of the Delta strain. 3 You can learn more about Dr. Middleton’s work in our webinar titled “Caught in the Act: Tracking the Emergence and Divergence of SARS-CoV-2 Through Statewide Testing and Sequencing”.4

Thanks to the work of Dr. Middleton and researchers like him, we progressed through the initial storm and established a new normal in a post-pandemic world. In March 2023, the World Health Organization updated its tracking system and working definitions for variants of concern, variants of interest, and variants under monitoring.5 The most up-to-date list can be found here.6 The previous working definitions can be found here.7

A Shift To Genomic Surveillance Methods

As the emphasis on strain tracking decreased significantly, SARS-CoV-2 research shifted towards comprehensive genomic surveillance methods and disease monitoring. seqWell library prep technology remained a powerful tool in this phase of research, as well.

For example, auto-normalization features, which are included in all our library prep kits, enable streamlined surveillance sequencing.8 Notably, researchers gain the ability to utilize short reads for rapid sequencing runs with high sensitivity and specificity at only 100,000 read pairs per sample. Additionally, our library prep tools are flexible enough that they’re compatible with multiple reverse transcription and multiplex PCR workflows. You can learn more about leveraging seqWell technologies for surveillance sequencing here.9

Empowering Researchers with Easy-To-Use Tools

Now in a state of relative stability, COVID researchers aren’t required to sequence as large of volumes as during prior iterations of the pandemic. In other words, high-throughput SARS-CoV-2 genomics is less of a concern.10

However, the current shift in focus created high demand for surveillance and monitoring. Now, when researchers are tasked with sequencing, they need solutions that are easy-to-use so they can focus less on troubleshooting and more on understanding and combating viral threats as they emerge.11

Our ExpressPlex Library Prep Kit builds on our plexWell technology, which was used in the initial stages of the pandemic. ExpressPlex provides researchers with a seamless solution for efficient viral sequencing. ExpressPlex mitigates errors in both the sample prep and library prep phases of NGS experiments. Plus, its ease-of-use ensures that viral sequencing can be reintroduced when necessary with minimal effort, thus bolstering our readiness for future variants.

“ExpressPlex makes everything so much easier for us. It combined three or four steps into one, which is unique to seqWell products. That made our library prep so much faster, and the quality control was significantly better compared to other kits. Now the risk of error has significantly decreased for our technicians.

My lab does a lot of COVID sequencing, but we also cover RSV, influenza, numerous bacteria and yeast, and the most recent monkeypox outbreak. We’ve used ExpressPlex for all these applications and never had a problem.”

– Lacy Simons, lab director of the Center for Pathogen Genomics and Microbial Evolution at Northwestern University


As we continue to coexist with SARS-CoV-2, it’s never been clearer that continuous surveillance of different variants and a deep knowledge of viral adaptation are both paramount. The benefits of this increased understanding extend far beyond COVID-19, encompassing the broader fields of viral sequencing and overall public health.

Maintaining a state of vigilance against the evolving changes in SARS-CoV-2 is also an important factor in the design and production of vaccine boosters. Here, it’s worth recognizing that the XBB.1.5 “Omicron” subvariant that began to emerge and dominate new COVID-19 cases less than a year ago has formed the basis for the Fall 2023 booster vaccine approved by the FDA last month.12

Innovative solutions, such as ExpressPlex, enable researchers to confidently monitor and track viral information and equip themselves with the foresight needed to prepare for emerging variants. By prioritizing ease of workflow, researchers can readily adapt to evolving circumstances and position themselves at the forefront of infectious disease research.


  1. CDC announces $262M funding to support National Network for Outbreak Response and Disease Modeling
  2. FDA Takes Action on Updated mRNA COVID-19 Vaccines to Better Protect Against Currently Circulating Variants
  3. seqWell | Transposase-based technology
  4. seqWell | Caught in the Act: Tracking the Emergence and Divergence of SARS-CoV-2 Through Statewide Testing and Sequencing
  5. WHO | COVID Tracker
  6. WHO | Updated working definitions and primary actions for SARS-CoV-2 variants
  7. WHO | Historical working definitions and primary actions for SARS-CoV-2 variants
  8. seqWell | SARS-CoV-2 surveillance sequencing with plexWell technology
  9. seqWell | SARS-CoV-2 Surveillance Sequencing with plexWell
  10. seqWell | High-Throughput SARS-CoV-2 Genomics Webinar
  11. seqWell | Avoid Costly Errors in NGS Sample Handling and Library Prep
  12. Pfizer and BioNTech Receive U.S. FDA Approval for 2023-2024 COVID-19 Vaccine