Infrastructure issues with NGS for COVID-19 variant testing

Published: 20-Apr-2022

Next Generation Sequencing is limited in its infrastructure for implementation, however there are new alternatives that only require a normal lab. These methods are not being used on a mass scale in the US, prolonging and exacerbating new COVID-19 variants, as PathogenDx CEO Milan Patel explains

As the battle against the global SARS-CoV-2 virus rages on, we need to make sure we're doing all we can to curb the spread and prevent mutations. Right now, we're falling short. In 2021, the SARS-CoV-2 virus mutated more than 30 times - with Omicron jumping the number of mutations to an unprecedented level. New variants can pop up at any time, and we do not have the proper infrastructure in place to detect and contain them in time.

Last April, the Biden Administration allocated $1.7 billion to help monitor, track and defeat emerging variants through genomic sequencing. While Next Generation Sequencing (NGS) is an excellent discovery tool, it does not provide the results or throughput that we need in time to keep up with the spread of this virus. It takes weeks to yield results, and by that time, the data loses much of its public health value and newer, not-yet-detected mutations pop up.

Detectx-Cv+ is essentially a perfect triage tool

For NGS to be effective, 5% of positive tests need to be sequenced. But since NGS is very costly to administer, requires high-end bioinformatics, and can only be performed at 88 highly advanced commercial and state lab sequencing sites in the US, reaching this 5% threshold has proved a major challenge.

Right now, as a country, the US is between 1 to 2%. And if you look at GISAID initiative data - the database where NGS information is tracked - you can see some states are at abysmally low percentages.

When talking about the 5% threshold for NGS to be effective, this really means we need 5% in each and every state - 10% in Colorado in no way offsets 0.5% in Alabama. If you're sequencing less than 5%, you can't legitimately tell if the preponderance of the samples are truly Omicron. Other samples in the backlog could show mutations but are missed.

To compound the throughput issue, timing is a huge problem with NGS.

The bare minimum time to get results for NGS is four days, but with backlogs and transportation to the high-tech labs where NGS can be performed, 10 to 15 days or longer is a much more common turnaround. Especially if samples come from rural areas - which unfortunately is where people are less vaxxed - the timing it takes to get results will be longer. And in these areas with lower vaccination numbers, people are more exposed to the contagions and the virus is more likely to incubate and mutate. It's easy to lose the window of opportunity to detect a new variant and contain it before it rapidly spreads.

I don't want to give the wrong impression: I am not knocking NGS. It's an incredibly valuable tool, but it has been applied incorrectly.

The federal government needs to seriously consider adopting other variant testing solutions to supplement NGS. At PathogenDX, we've created Detectx-CV+, a full-spectrum COVID-19 testing technology that has been designed to detect the SARS-CoV-2 virus and Variants of Concern (VoC), Variants of Interest (VoI), and has a built-in capability to detect new mutations and emerging variants - all in a single-well test. Rather than taking weeks, results are yielded in under six hours; it costs five to 15 times less than NGS while delivering equivalent accuracy; it only requires standard lab equipment and can be administered in any of the thousands of PCR labs in our country; and unlike NGS, it can be run by any PCR lab technician and doesn't require PhDs with high-end bioinformatics training.

NGS can only be performed at 88 sites in the US

The National Institutes of Health (NIH) has already supported this technology as part of its Rapid Acceleration of Diagnostics (RADx) programme for the identification of community-spread variants.

The purpose of NGS should be to discover new variants, not to confirm ones we know to exist. Yet because of the massive backlogs, NGS has been too slow at discovering new variants before they spread and in actuality has largely just been confirming variants we already know exist, which is a big waste of taxpayer money.

It would be great if instead of sending positive tests to NGS, we implemented Detectx-Cv+ tests in the thousands of PCR labs that already exist - because the infrastructure and lab equipment are already in place, this scaling is definitely feasible.

With this technology, PCR technicians can run through way more samples and deliver results way faster than NGS. Then, when technicians, using Detectx-Cv+, come across a sample that is not a known variant like Omicron but rather something unique and different, that's when they'd send it to NGS to confirm the new mutation. If NGS was resigned to these types of instances, there wouldn't be massive backlogs and the whole sequencing and detection process would be much quicker and more effective.

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Detectx-Cv+ is essentially a perfect triage tool. Right now, the way NGS is being used is not just wasteful but irresponsible. You shouldn't use a hacksaw when what you need is a scalpel. Throwing money at an issue isn't going to stop it; the government should be way more precise in allocating the right tools for the job.

As COVID variants continue to ravage the world, bringing incalculable damage in terms of lives lost and economic turmoil, establishing variant testing at scale is vital. NGS alone has proven ineffective, and the right technology to quickly and effectively identify variants and curb the spread already exists. Encouragingly, Detectx-Cv+ has already received CE-IVD certification, along with an approved CE Marking according to the Requirements of European Directive 98/79/EC of the European Parliament and the council on In Vitro Diagnostic Medical Devices (IVDD) Directive. With these certifications, we're able to set up our technology in everyday clinical and molecular labs across Europe, and we're in the process of working with distributors and labs to make this technology commercially available. Hopefully, the US will soon take up a similar approach.

The spread of Omicron and its mutations has been devastating, yet this will not be the last variant. In order to curb the emergence and spread of variants, we need to change course and aggressively adopt variant testing at scale. The quicker we do that, the quicker we can return to normalcy.

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