Nucleic-Acid Amplification Test for STIs

Nucleic-acid amplification tests, also known as NAATs, are used to identify small amounts of DNA or RNA in test samples. They can, therefore, be used to identify bacteria, viruses, and other pathogens even when the material of interest is present in very small amounts.

NAATs also can detect a variety of different sexually transmitted infections (STIs, formerly called sexually transmitted diseases, STDs). In fact, most urine tests for STIs are performed using NAATs.

A blood sample being held with a row of human samples for analytical testing including blood, urine, chemistry, proteins, anticoagulants and HIV in lab
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How Do Nucleic-Acid Amplification Tests Work?

Though there are several kinds of NAATs, all are based on the same principles. First, scientists have to figure out the sequence of the nucleic acids they want to identify and make probes that will attach to them. Then, the NAAT uses a series of repeated chemical reactions to make numerous copies of the DNA or RNA that doctors are trying to detect.

These reactions selectively amplify the signal of the interesting nucleic acids in the test sample so that they are easier to identify. For example, it's much simpler to find 10,000 copies of a gene than 10.

NAATs in STI Testing

The process of amplifying bacterial or viral nucleic acids is not in itself an STI test. Instead, once the amount of DNA or RNA has been increased in the sample using polymerase chain reaction (PCR) or ligase chain reaction (LCR), more conventional tests are used to detect it.

These tests usually involve some form of nucleic acid hybridization. In those tests, the sample is probed with an artificially produced complementary strand of DNA or RNA that has been labeled in some way that makes it easy to detect. It may help to picture it as a glow-in-the-dark tag that only sticks to one very specific piece of identifying information.

NAATs are incredibly useful for STI testing. They allow doctors to detect an STI pathogen even when only a very small number of organisms are present.

The nucleic acid test technology has made it possible to do urine testing for STIs that were previously only detectable by the swab.

Furthermore, since NAATs are incredibly sensitive to even small amounts of viral DNA, they are very important for screening the blood supply. These tests make it possible to detect tiny amounts of human immunodeficiency virus (HIV) and other blood-borne pathogens that might otherwise be missed.

Example of This Test in Action

NAATs are incredibly sensitive methods of detecting whether a bacterium or virus is present in a biological sample. When it comes to detecting genital herpes in a sore from a person who has symptoms, these tests serve as a viable alternative to viral cultures. Viral cultures can be difficult for some laboratories to perform.

Unlike herpes blood tests, a NAAT still involves the direct determination of whether a virus is present in the sample rather than looking for anti-herpes antibodies.

Nucleic-acid amplification has also allowed for easier and more widespread chlamydia and gonorrhea screening methods around the country. Now such screening can be done on urine samples instead of requiring a urethral (in the urethra, the tube through which urine passes out of the body) or cervicovaginal (in the uterine cervix and vagina) swab.

Therefore, it has become easy to test large numbers of young people for these STIs in a variety of both clinical and nonclinical settings. Collecting urine requires no medical expertise. People are also more likely to be willing to pee into a cup than undergo a genital swab.

Researchers have also used NAATs to get more information about the extent of the problem of asymptomatic (with no symptoms) STIs in the United States. Large-scale NAAT-based screening programs have been implemented in the military, in urban areas, and in men who have sex with men (MSM), for instance. These tests allow for the detection of STIs in the small urine or blood samples that are often taken as part of large research studies on population health. 

5 Sources
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  2. Fakruddin M, Mannan KSB, Chowdhury A, et al. Nucleic acid amplification: Alternative methods of polymerase chain reaction. J Pharm Bioallied Sci. 2013;5(4):245-252. doi:10.4103/0975-7406.120066

  3. Centers for Disease Control and Prevention. Recommendations for the laboratory-based detection of Chlamydia trachomatis and Neisseria gonorrhoeae--2014. MMWR Recomm Rep. 2014;63(RR-02):1-19.

  4. Rönn MM, Mc Grath-Lone L, Davies B, Wilson JD, Ward H. Evaluation of the performance of nucleic acid amplification tests (NAATs) in detection of chlamydia and gonorrhoea infection in vaginal specimens relative to patient infection status: a systematic review. BMJ Open. 2019;9(1):e022510. doi:10.1136/bmjopen-2018-022510

  5. Harbertson J, Scott P, Graf P, et al. 1583Randomized, Active-duty U.S. Military Population-based NAAT Screening for Asymptomatic Neisseria gonorrhoeae, Chlamydia trachomatis, and Trichomonas vaginalis Infection using De-identified Urine Samples Received by the Navy Drug Screening Laboratory, San Diego. Open Forum Infect Dis. 2014;1(suppl_1):S422-S422. doi:10.1093/ofid/ofu052.1129

Additional Reading

By Elizabeth Boskey, PhD
Elizabeth Boskey, PhD, MPH, CHES, is a social worker, adjunct lecturer, and expert writer in the field of sexually transmitted diseases.