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.
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
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).
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
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
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
- Google Trends. Google Trends. Accessed November 6, 2021.
- How Accurate Are At-Home COVID Tests? Here’s What Experts Say. NBC Chicago. Accessed November 6, 2021.
- Rapid COVID-19 Tests: When to Use Them and How They Work. Healthline. Published October 13, 2021. Accessed November 6, 2021.
- 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.
- The differences to know between COVID tests as gatherings begin for the holidays. Masslive. Published November 5, 2021. Accessed November 6, 2021.
- Santora T. The Smartest Way to Use Rapid At-Home COVID Tests. Scientific American. Accessed November 6, 2021.
- Hartmann M. Where Are All the At-Home COVID Tests? Intelligencer. Published October 27, 2021. Accessed November 6, 2021.
- CDC – Nucleic acid amplification tests (NAATs). Centers for Disease Control and Prevention. Published February 11, 2020. Accessed November 6, 2021.
- How is the COVID-19 Virus Detected using Real Time RT-PCR? Published March 27, 2020. Accessed November 18, 2021.
- Polymerase Chain Reaction (PCR) Fact Sheet. Genome.gov. Accessed November 6, 2021.
- Walker FM, Hsieh K. Advances in Directly Amplifying Nucleic Acids from Complex Samples. Biosensors. 2019;9(4):117. doi:10.3390/bios9040117
- Appleby J. Why It Takes So Long To Get Most COVID-19 Test Results. NPR. Published March 28, 2020. Accessed November 6, 2021.
- 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
- 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
- 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
- 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.