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Ben Ting

What is the difference between NAAT and PCR?

While the COVID-19 pandemic has brought phrases like “PCR test” and “antigen test” into wider use, one term that hasn’t been talked about as much is “NAAT,” which is short for nucleic acid amplification test (Figure 1).1 As the media has widely reported,2–7 most rapid COVID tests are antigen-based. Antigen tests are better at assessing if a person is infectious at the time of the testing rather than if they are carrying the SARS-CoV-2 virus, while lab-based PCR tests are better able to detect if a person has the virus.2,3,5–7

If you’re a healthcare professional or facility manager looking for a point-of-care testing system that can help support a COVID-free environment, you may be wondering where NAATs fit into all of this. There are some rapid tests that are not antigen tests and not PCR tests, but rather are described as NAATs. We’ve already covered the difference between antigen and molecular tests in another blog post . In this article, we’ll discuss the differences between NAAT and PCR, focusing on point-of-care testing for COVID-19 and other infectious diseases.

Figure 1. Google Trends shows the increased search volume for “antigen test” and “PCR test” in the months after the start of the COVID-19 pandemic.1

PCR is a type of NAAT8

The quick answer to “what is the difference between NAAT and PCR” is that PCR is a type of NAAT. Not every NAAT uses PCR methodology, but all PCR tests are a type of NAAT.8

The term “NAAT” applies to a range of different technologies where nucleic acid, i.e., RNA or DNA, from a pathogen is amplified and detected to determine if a pathogen is present.8 Typically, if the pathogen is a virus with an RNA genome like SARS-CoV-2 and influenza, the first step in the NAAT method will be to convert the RNA into DNA using a reverse transcriptase and then amplify the DNA.

Different NAATs approach nucleic acid amplification in different ways.8

PCR

The lab-based COVID-19 test that is considered the gold-standard uses real-time reverse transcriptase PCR (RT-PCR), which converts SARS-CoV-2 RNA into DNA and then amplifies the DNA by cycling it through different temperatures.9 By including a high temperature step in each cycle, the two DNA strands are separated, and each strand replicated, enabling the generation of many copies of the same DNA sequence from a single molecule.10

When PCR is used in lab tests, the process can take hours because of the need to extract the nucleic acid from the specimen11 and because the sample is typically run through thirty or more cycles of several minutes each (for a description of the COVID-19 testing process that is accessible to a general reader, see this article from NPR12).

Isothermal methods

Because PCR is a complex process that can take hours to perform,11 it is less suitable for a point-of-care test where results are needed in thirty minutes or less. To address this challenge, several diagnostics developers have focused on nucleic acid amplification methods that do not require multi-temperature cycles, such as RT-LAMP technology. This collection of techniques is referred to as “isothermal” because amplification is conducted at a single temperature.13, 14 Amplification can be achieved in minutes, instead of hours, using different enzymatic techniques to separate the two DNA strands prior to replication.13, 14

To learn more about the RT-LAMP technology used in Talis One, read the article “The Technology Behind the Talis One Molecular Point of Care Test”

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Not every NAAT delivers the same performance, especially point-of-care NAATs

From a practical point-of-view, you may be wondering if NAATs, especially point-of-care NAATs, can deliver the same quality results as lab-based PCR tests? When it comes to COVID-19, not every NAAT does,15 although more studies in real-world conditions are needed to confidently address this question.15

The Talis One COVID-19 Test System includes a nucleic acid extraction step to achieve central lab-level performance

One possible reason that some point-of-care NAATs don’t perform as well as lab-based PCR tests is that they don’t include a nucleic acid extraction step.11 While this saves time, compounds in the sample can potentially inhibit the amplification step.11 This is why the Talis team developed an instrument, the Talis One, that performs a solid-phase sample extraction step within the Talis One test cartridge; this enables the test system to achieve central lab-level performance.16

Learn more about our Talis One COVID-19 Test System

Meet the Talis One

The difference between NAAT and PCR: non-PCR NAAT’s hold great promise for fast and accurate testing at the point of care

Bringing the sensitivity and specificity of PCR to the point of care requires looking beyond PCR to isothermal NAAT methods.13, 14 Whether these tests are used for the ongoing COVID-19 pandemic or for other infectious diseases, non-PCR NAAT’s hold great promise for ensuring fast and accurate test results in a variety of care settings.13, 14

References

  1. Google Trends. Google Trends. Accessed November 6, 2021.
  2. How Accurate Are At-Home COVID Tests? Here’s What Experts Say. NBC Chicago. Accessed November 6, 2021.
  3. Rapid COVID-19 Tests: When to Use Them and How They Work. Healthline. Published October 13, 2021. Accessed November 6, 2021.
  4. Parker-Pope T. How to Use Rapid Home Tests (Once You Find Them). The New York Times. Published October 8, 2021. Accessed November 6, 2021.
  5. The differences to know between COVID tests as gatherings begin for the holidays. Masslive. Published November 5, 2021. Accessed November 6, 2021.
  6. Santora T. The Smartest Way to Use Rapid At-Home COVID Tests. Scientific American. Accessed November 6, 2021.
  7. Hartmann M. Where Are All the At-Home COVID Tests? Intelligencer. Published October 27, 2021. Accessed November 6, 2021.
  8. CDC – Nucleic acid amplification tests (NAATs). Centers for Disease Control and Prevention. Published February 11, 2020. Accessed November 6, 2021.
  9. How is the COVID-19 Virus Detected using Real Time RT-PCR? Published March 27, 2020. Accessed November 18, 2021.
  10. Polymerase Chain Reaction (PCR) Fact Sheet. Genome.gov. Accessed November 6, 2021.
  11. Walker FM, Hsieh K. Advances in Directly Amplifying Nucleic Acids from Complex Samples. Biosensors. 2019;9(4):117. doi:10.3390/bios9040117
  12. Appleby J. Why It Takes So Long To Get Most COVID-19 Test Results. NPR.  Published March 28, 2020. Accessed November 6, 2021.
  13. Pumford EA, Lu J, Spaczai I, et al. Developments in integrating nucleic acid isothermal amplification and detection systems for point-of-care diagnostics. Biosens Bioelectron. 2020;170:112674. doi:10.1016/j.bios.2020.112674
  14. James AS, Alwneh JI. COVID-19 Infection Diagnosis: Potential Impact of Isothermal Amplification Technology to Reduce Community Transmission of SARS-CoV-2. Diagnostics. 2020;10(6):399. doi:10.3390/diagnostics10060399
  15. Dinnes J, Deeks JJ, Berhane S, et al. Rapid, point?of?care antigen and molecular-based tests for diagnosis of SARS?CoV?2 infection. Cochrane Database Syst Rev. 2021;2021(3):CD013705. doi:10.1002/14651858.CD013705.pub2
  16. Talis Bio. Evaluation of the Talis OneTM Covid-19 Test System for the Rapid Detection of Sars-Cov-2 and Emerging Variants. Published online 2021. Accessed October 29, 2021.

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The Talis One™ COVID-19 Test System is expected to accurately detect the new coronavirus variant Omicron

Talis conducted a comprehensive in silico assessment comparing the Omicron (B1.1.529) variant published sequences from the GISAID database to its Talis One COVID-19 Test System. The bioinformatics analysis concluded that the Talis One COVID-19 molecular nucleic acid amplification test (NAAT) continues to be able to identify positive cases of COVID-19 caused by Omicron.

Like all viruses, SARS-CoV-2 continues to mutate. In anticipation of this fact, our scientists developed a test with a dual-gene target to ensure accurate results even in the case where one of the targets may become impacted by a mutation. The Omicron variant has been found to show multiple mutations, with a majority occurring on the spike (S) protein. Talis’ molecular NAAT does not rely on the S gene to detect the virus but rather focuses on two other targets: the N and Orf1a/b genes. Individually, >99% of the published Omicron sequences as of December 1, 2021 are a perfect match to both of the Talis primer regions, while across both targets 100% of the sequences match at least one primer set.

The robust multiple target test design helps to ensure that clinicians, researchers and public health officials have an effective tool for COVID-19 testing-even as the genetic makeup of the virus evolves.

Talis will continue surveillance of emerging SARS-CoV-2 variants of concern/interest (VOC/I) by assessing reactivity against genome sequence databases.

To date, Talis has performed assessments looking at the following variants

  • Alpha (B.1.1.7)
  • Beta (B.1.351)
  • Delta (B.1.617.2)
  • Epsilon (B.1.427 and B.1.429)
  • Eta (B.1.525)
  • Iota (B.1.525)
  • Gamma (P.1)
  • Zeta (P.2)
  • Omicron (B.1.1.529)
  • B.1.2
  • B.1.375

Talis One COVID-19 Test System

Central lab-quality SARS-CoV-2 molecular testing for a variety of care settings—less than 30 minutes from sample to results.

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References

  1. Data on file with Talis Biomedical. GISAID Database accessed December 1, 2021.

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Antigen vs Molecular Test: Which type of COVID-19 test is more reliable?

In the antigen vs molecular test debate, understanding which test is best is a matter of timing and application—the answer could change depending on how you’re using the test and how quickly you need the test results. In addition, the emergence of newer testing technologies may change the parameters of the debate, tipping the balance towards molecular testing for a number of situations.

To understand which test technology will work best for your application, let’s take a closer look at the pros and cons of each technology (note that for the sake of brevity, we are leaving the discussion of sample type for another article).

Molecular tests performed in a central lab are sensitive and specific, but take time to deliver results


What a molecular test detects

In general, molecular tests detect nucleic acid—either RNA or DNA.

Why this matters for diagnosing COVID-19

Molecular tests can detect the presence of SARS-CoV-2 even during the early stages of infection because they detect viral RNA, which can accumulate to high levels within a cell before virus particles are formed.

Benefits of molecular tests

Molecular tests are ideal for detecting emerging infectious diseases such as the SARS-CoV-2 virus because they are quick to develop and deploy.

Most molecular tests that are conducted in a central lab setting are very sensitive and specific, with commercially available SARS-CoV-2 molecular tests exhibiting >95% sensitivity and >99% specificity, with the potential to detect as little as a few dozen to a few hundred copies/mL of a nucleic acid sequence from the pathogen (i.e., they have low limits of detection (LOD)).1

Thus, molecular tests can detect disease in the very early stages of infection, when the viral load is fairly low.

Challenges of molecular tests

While the sensitivity and specificity of lab-conducted molecular tests is high and the LOD is low, the complexity of these tests typically restricts their use to the central lab setting. This adds time between when the sample is taken and when results are delivered. At best, the turnaround time can be as little as 24-48 hours, but at the height of the pandemic, some labs were experiencing turnaround times of as much as two weeks due to reagent shortages and insufficient testing throughput.

For highly infectious diseases like SARS-CoV-2, the delay in receiving test results can negatively impact both the patient—by potentially forcing them to quarantine while waiting for results—and public health, if an infectious patient does not quarantine while waiting for results.

Best applications for SARS-CoV-2 molecular tests

With their high sensitivity and specificity, SARS-CoV-2 molecular tests are often considered the gold standard for diagnosis. The Infectious Disease Society of America (ISDA) recommends molecular tests for symptomatic patients even if the suspicion of COVID-19 is low, and prefers that results be available within 48 hours.2

For asymptomatic patients, the ISDA recommends testing only in certain situations2, such as:

  • Upon known or suspected exposure to COVID-19
  • Upon admission to a hospital in an area with a high prevalence of COVID-19
  • Before certain medical procedures

Antigen tests can be performed at the point-of-care, but are not as sensitive as molecular tests leading to higher false negative rates


What an antigen test detects

In general, an antigen test detects a protein that’s unique to the pathogen. For SARS-CoV-2 detection, the antigen tests detect a protein of the virus particle.

Why this matters for diagnosing COVID-19

Because antigen tests rely on production of virus particles, they can miss newly-infected patients that have virus replicating within their cells but have not yet produced measurable amounts of virus particles.

Benefits of antigen tests

Antigen tests are easy to conduct, inexpensive, and deliver results in minutes. They are also highly specific and can be done at the point-of-care.3

Challenges of antigen tests

The benefits of antigen testing are balanced by a lower sensitivity than molecular tests, with sensitivity dependent on whether or not symptoms are present and how long after symptom onset the test is given. For tests given within seven days of symptom onset, pooled antigen test sensitivity is 84%, dropping to 49% in asymptomatic individuals.3

The lower sensitivity can lead to a higher false negative rate, i.e., more missed infections, which restricts their usefulness to certain situations when molecular tests are widely available.

Best applications for SARS-CoV-2 antigen tests

While the ISDA recommends molecular tests over antigen tests for symptomatic individuals unless test results will not be delivered within three days, their recommendations for asymptomatic individuals are neither for nor against antigen testing due to a lack of sufficient evidence either way.3

That said, a more recent simulation study based on real-world data suggests that although RT-PCR tests perform better than antigen tests in detecting infected individuals and preventing transmission, more frequent antigen testing, e.g., every day or every 3 days, is comparable to less frequent RT-PCR tests, at the expense of many more false-negative tests. This indicates that frequent antigen tests, potentially self-administered at home could be an important tool in combating spread of infection.4

The Talis One delivers all the benefits of molecular tests with similar speed and convenience of antigen tests

As can be seen from the above discussion, the antigen vs. molecular test debate has primarily been one of test quality versus speed, with the molecular test being used as the gold standard, although it can take days to get results, and the antigen test being used when speed is more important than sensitivity.

However, the Talis One is set to change the cost/benefit balance in this debate. It’s a molecular test that can be done quickly and easily at the point-of-care, delivering results in under 30 minutes. And unlike other point-of-care tests, the Talis One’s unique cartridge technology includes solid-phase nucleic acid extraction, which gives it a sensitivity and LOD that’s comparable to molecular tests performed in a lab, enabling excellence at the point of care.

Conclusion

In the antigen vs. molecular test debate, the best test is the one that gives you the highest sensitivity and specificity in the shortest amount of time. Molecular testing is the gold standard, although antigen testing can be effective when speed is necessary. Now, with the Talis One, you can get similar speed and point-of-care convenience as an antigen test with the quality you could previously only get from a central lab molecular test.

References

  1. Antigen and Molecular Tests for COVID-19. COVID-19 Testing Toolkit website. Accessed July 9, 2021. https://www.centerforhealthsecurity.org/covid-19TestingToolkit/molecular-based-tests/current-molecular-and-antigen-tests.html#Current-Molecular-Tests
  2. Hanson KE, et al. IDSA Guidelines on the Diagnosis of COVID-19: Molecular Diagnostic Testing. Clin Infect Dis. 2020 Jun 16;ciaa760. doi: 10.1093/cid/ciaa760.
  3. Hanson KE, et al. IDSA Guidelines on the Diagnosis of COVID-19: Antigen Testing. Clin Infect Dis. 2021 Jun 23;ciab557. doi: 10.1093/cid/ciab557.
  4. Ke R, et al. In vivo kinetics of SARS-CoV-2 infection and its relationship with a person’s infectiousness. medRxiv. Preprint. 2021 Jun 30. doi: 10.1101/2021.06.26.21259581. Accessed July 10, 2021.

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